Full Text Available The human cytomegalovirus (HCMV-encoded protein kinase, pUL97, is considered a cyclin-dependent kinase (CDK ortholog, due to shared structural and functional characteristics. The primary mechanism of CDK activation is binding to corresponding cyclins, including cyclin T1, which is the usual regulatory cofactor of CDK9. This study provides evidence of direct interaction between pUL97 and cyclin T1 using yeast two-hybrid and co-immunoprecipitation analyses. Confocal immunofluorescence revealed partial colocalization of pUL97 with cyclin T1 in subnuclear compartments, most pronounced in viral replication centres. The distribution patterns of pUL97 and cyclin T1 were independent of HCMV strain and host cell type. The sequence domain of pUL97 responsible for the interaction with cyclin T1 was between amino acids 231–280. Additional co-immunoprecipitation analyses showed cyclin B1 and cyclin A as further pUL97 interaction partners. Investigation of the pUL97-cyclin T1 interaction in an ATP consumption assay strongly suggested phosphorylation of pUL97 by the CDK9/cyclin T1 complex in a substrate concentration-dependent manner. This is the first demonstration of interaction between a herpesviral CDK ortholog and cellular cyclins.
Full Text Available Abstract Background It has repeatedly been shown that interacting protein families tend to have similar phylogenetic trees. These similarities can be used to predicting the mapping between two families of interacting proteins (i.e. which proteins from one family interact with which members of the other. The correct mapping will be that which maximizes the similarity between the trees. The two families may eventually comprise orthologs and paralogs, if members of the two families are present in more than one organism. This fact can be exploited to restrict the possible mappings, simply by impeding links between proteins of different organisms. We present here an algorithm to predict the mapping between families of interacting proteins which is able to incorporate information regarding orthologues, or any other assignment of proteins to "classes" that may restrict possible mappings. Results For the first time in methods for predicting mappings, we have tested this new approach on a large number of interacting protein domains in order to statistically assess its performance. The method accurately predicts around 80% in the most favourable cases. We also analysed in detail the results of the method for a well defined case of interacting families, the sensor and kinase components of the Ntr-type two-component system, for which up to 98% of the pairings predicted by the method were correct. Conclusion Based on the well established relationship between tree similarity and interactions we developed a method for predicting the mapping between two interacting families using genomic information alone. The program is available through a web interface.
Full Text Available One of the fundamental goals of genetics is to understand gene functions and their associated phenotypes. To achieve this goal, in this study we developed a computational algorithm that uses orthology and protein-protein interaction information to infer gene-phenotype associations for multiple species. Furthermore, we developed a web server that provides genome-wide phenotype inference for six species: fly, human, mouse, worm, yeast, and zebrafish. We evaluated our inference method by comparing the inferred results with known gene-phenotype associations. The high Area Under the Curve values suggest a significant performance of our method. By applying our method to two human representative diseases, Type 2 Diabetes and Breast Cancer, we demonstrated that our method is able to identify related Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways. The web server can be used to infer functions and putative phenotypes of a gene along with the candidate genes of a phenotype, and thus aids in disease candidate gene discovery. Our web server is available at http://jjwanglab.org/PhenoPPIOrth.
Full Text Available Abstract Background Large-scale identification of the interrelationships between different components of the cell, such as the interactions between proteins, has recently gained great interest. However, unraveling large-scale protein-protein interaction maps is laborious and expensive. Moreover, assessing the reliability of the interactions can be cumbersome. Results In this study, we have developed a computational method that exploits the existing knowledge on protein-protein interactions in diverse species through orthologous relations on the one hand, and functional association data on the other hand to predict and filter protein-protein interactions in Arabidopsis thaliana. A highly reliable set of protein-protein interactions is predicted through this integrative approach making use of existing protein-protein interaction data from yeast, human, C. elegans and D. melanogaster. Localization, biological process, and co-expression data are used as powerful indicators for protein-protein interactions. The functional repertoire of the identified interactome reveals interactions between proteins functioning in well-conserved as well as plant-specific biological processes. We observe that although common mechanisms (e.g. actin polymerization and components (e.g. ARPs, actin-related proteins exist between different lineages, they are active in specific processes such as growth, cancer metastasis and trichome development in yeast, human and Arabidopsis, respectively. Conclusion We conclude that the integration of orthology with functional association data is adequate to predict protein-protein interactions. Through this approach, a high number of novel protein-protein interactions with diverse biological roles is discovered. Overall, we have predicted a reliable set of protein-protein interactions suitable for further computational as well as experimental analyses.
Singh Rama S
Full Text Available Abstract Background Much of the morphological diversity in eukaryotes results from differential regulation of gene expression in which transcription factors (TFs play a central role. The nematode Caenorhabditis elegans is an established model organism for the study of the roles of TFs in controlling the spatiotemporal pattern of gene expression. Using the fully sequenced genomes of three Caenorhabditid nematode species as well as genome information from additional more distantly related organisms (fruit fly, mouse, and human we sought to identify orthologous TFs and characterized their patterns of evolution. Results We identified 988 TF genes in C. elegans, and inferred corresponding sets in C. briggsae and C. remanei, containing 995 and 1093 TF genes, respectively. Analysis of the three gene sets revealed 652 3-way reciprocal 'best hit' orthologs (nematode TF set, approximately half of which are zinc finger (ZF-C2H2 and ZF-C4/NHR types and HOX family members. Examination of the TF genes in C. elegans and C. briggsae identified the presence of significant tandem clustering on chromosome V, the majority of which belong to ZF-C4/NHR family. We also found evidence for lineage-specific duplications and rapid evolution of many of the TF genes in the two species. A search of the TFs conserved among nematodes in Drosophila melanogaster, Mus musculus and Homo sapiens revealed 150 reciprocal orthologs, many of which are associated with important biological processes and human diseases. Finally, a comparison of the sequence, gene interactions and function indicates that nematode TFs conserved across phyla exhibit significantly more interactions and are enriched in genes with annotated mutant phenotypes compared to those that lack orthologs in other species. Conclusion Our study represents the first comprehensive genome-wide analysis of TFs across three nematode species and other organisms. The findings indicate substantial conservation of transcription
Morselli, Eugenia; Shen, Shensi; Ruckenstuhl, Christoph; Bauer, Maria Anna; Mariño, Guillermo; Galluzzi, Lorenzo; Criollo, Alfredo; Michaud, Mickael; Maiuri, Maria Chiara; Chano, Tokuhiro; Madeo, Frank; Kroemer, Guido
The tumor suppressor protein p53 tonically suppresses autophagy when it is present in the cytoplasm. This effect is phylogenetically conserved from mammals to nematodes, and human p53 can inhibit autophagy in yeast, as we show here. Bioinformatic investigations of the p53 interactome in relationship to the autophagy-relevant protein network underscored the possible relevance of a direct molecular interaction between p53 and the mammalian ortholog of the essential yeast autophagy protein Atg17, namely RB1-inducible coiled-coil protein 1 (RB1CC1), also called FAK family kinase-interacting protein of 200 KDa (FIP200). Mutational analyses revealed that a single point mutation in p53 (K382R) abolished its capacity to inhibit autophagy upon transfection into p53-deficient human colon cancer or yeast cells. In conditions in which wild-type p53 co-immunoprecipitated with RB1CC1/FIP200, p53 (K382R) failed to do so, underscoring the importance of the physical interaction between these proteins for the control of autophagy. In conclusion, p53 regulates autophagy through a direct molecular interaction with RB1CC1/FIP200, a protein that is essential for the very apical step of autophagy initiation.
Batista, Marcelo Bueno; Chandra, Govind; Monteiro, Rose Adele; de Souza, Emanuel Maltempi; Dixon, Ray
Bacteria adjust the composition of their electron transport chain (ETC) to efficiently adapt to oxygen gradients. This involves differential expression of various ETC components to optimize energy generation. In Herbaspirillum seropedicae, reprogramming of gene expression in response to oxygen availability is controlled at the transcriptional level by three Fnr orthologs. Here, we characterised Fnr regulons using a combination of RNA-Seq and ChIP-Seq analysis. We found that Fnr1 and Fnr3 directly regulate discrete groups of promoters (Groups I and II, respectively), and that a third group (Group III) is co-regulated by both transcription factors. Comparison of DNA binding motifs between the three promoter groups suggests Group III promoters are potentially co-activated by Fnr3-Fnr1 heterodimers. Specific interaction between Fnr1 and Fnr3, detected in two-hybrid assays, was dependent on conserved residues in their dimerization interfaces, indicative of heterodimer formation in vivo. The requirements for co-activation of the fnr1 promoter, belonging to Group III, suggest either sequential activation by Fnr3 and Fnr1 homodimers or the involvement of Fnr3-Fnr1 heterodimers. Analysis of Fnr proteins with swapped activation domains provides evidence that co-activation by Fnr1 and Fnr3 at Group III promoters optimises interactions with RNA polymerase to fine-tune transcription in response to prevailing oxygen concentrations.
Bienkowski, Rick S.; Banerjee, Ayan; Rounds, J. Christopher; Rha, Jennifer; Omotade, Omotola F.; Gross, Christina; Morris, Kevin J.; Leung, Sara W.; Pak, ChangHui; Jones, Stephanie K.; Santoro, Michael R.; Warren, Stephen T.; Zheng, James Q.; Bassell, Gary J.; Corbett, Anita H.; Moberg, Kenneth H.
Summary The Drosophila dNab2 protein is an ortholog of human ZC3H14, a poly(A) RNA-binding protein required for intellectual function. dNab2 supports memory and axon projection, but its molecular role in neurons is undefined. Here we present a network of interactions that links dNab2 to cytoplasmic control of neuronal mRNAs in conjunction with and the Fragile-X protein ortholog dFMRP. dNab2 and dfmr1 interact genetically in control of neurodevelopment and olfactory memory and their encoded proteins co-localize in puncta within neuronal processes. dNab2 regulates CaMKII but not futsch mRNA, implying a selective role in control of dFMRP-bound transcripts. Reciprocally, dFMRP and vertebrate FMRP restrict mRNA poly(A)-tail length similar to dNab2/ZC3H14. Parallel studies of murine hippocampal neurons indicate that ZC3H14 is also a cytoplasmic regulator of neuronal mRNAs. In sum these findings suggest that dNab2 represses expression of a subset of dFMRP-target mRNAs, which could underlie brain-specific defects in patients lacking ZC3H14. PMID:28793261
Rick S. Bienkowski
Full Text Available The Drosophila dNab2 protein is an ortholog of human ZC3H14, a poly(A RNA binding protein required for intellectual function. dNab2 supports memory and axon projection, but its molecular role in neurons is undefined. Here, we present a network of interactions that links dNab2 to cytoplasmic control of neuronal mRNAs in conjunction with the fragile X protein ortholog dFMRP. dNab2 and dfmr1 interact genetically in control of neurodevelopment and olfactory memory, and their encoded proteins co-localize in puncta within neuronal processes. dNab2 regulates CaMKII, but not futsch, implying a selective role in control of dFMRP-bound transcripts. Reciprocally, dFMRP and vertebrate FMRP restrict mRNA poly(A tail length, similar to dNab2/ZC3H14. Parallel studies of murine hippocampal neurons indicate that ZC3H14 is also a cytoplasmic regulator of neuronal mRNAs. Altogether, these findings suggest that dNab2 represses expression of a subset of dFMRP-target mRNAs, which could underlie brain-specific defects in patients lacking ZC3H14.
Background As orthologous proteins are expected to retain function more often than other homologs, they are often used for functional annotation transfer between species. However, ortholog identification methods do not take into account changes in domain architecture, which are likely to modify a protein's function. By domain architecture we refer to the sequential arrangement of domains along a protein sequence. To assess the level of domain architecture conservation among orthologs, we carried out a large-scale study of such events between human and 40 other species spanning the entire evolutionary range. We designed a score to measure domain architecture similarity and used it to analyze differences in domain architecture conservation between orthologs and paralogs relative to the conservation of primary sequence. We also statistically characterized the extents of different types of domain swapping events across pairs of orthologs and paralogs. Results The analysis shows that orthologs exhibit greater domain architecture conservation than paralogous homologs, even when differences in average sequence divergence are compensated for, for homologs that have diverged beyond a certain threshold. We interpret this as an indication of a stronger selective pressure on orthologs than paralogs to retain the domain architecture required for the proteins to perform a specific function. In general, orthologs as well as the closest paralogous homologs have very similar domain architectures, even at large evolutionary separation. The most common domain architecture changes observed in both ortholog and paralog pairs involved insertion/deletion of new domains, while domain shuffling and segment duplication/deletion were very infrequent. Conclusions On the whole, our results support the hypothesis that function conservation between orthologs demands higher domain architecture conservation than other types of homologs, relative to primary sequence conservation. This supports the
George L Sutphin
Full Text Available The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs between 6 eukaryotic species-humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/.
Sutphin, George L.; Mahoney, J. Matthew; Sheppard, Keith; Walton, David O.; Korstanje, Ron
The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs) between 6 eukaryotic species—humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/. PMID:27812085
Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich
Background Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationa...
Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich
Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationally feasible in a reasonable amount of time. We propose to speed up the detection of orthologous proteins by using strings of domains to characterize the proteins. We present two new protein similarity measures, a cosine and a maximal weight matching score based on domain content similarity, and new software, named porthoDom. The qualities of the cosine and the maximal weight matching similarity measures are compared against curated datasets. The measures show that domain content similarities are able to correctly group proteins into their families. Accordingly, the cosine similarity measure is used inside porthoDom, the wrapper developed for proteinortho. porthoDom makes use of domain content similarity measures to group proteins together before searching for orthologs. By using domains instead of amino acid sequences, the reduction of the search space decreases the computational complexity of an all-against-all sequence comparison. We demonstrate that representing and comparing proteins as strings of discrete domains, i.e. as a concatenation of their unique identifiers, allows a drastic simplification of search space. porthoDom has the advantage of speeding up orthology detection while maintaining a degree of accuracy similar to proteinortho. The implementation of porthoDom is released using python and C++ languages and is available under the GNU GPL licence 3 at http://www.bornberglab.org/pages/porthoda .
Altenhoff, Adrian M; Boeckmann, Brigitte; Capella-Gutierrez, Salvador
Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision-recall...
Horner David S
Full Text Available Abstract Background Recent discoveries have highlighted the fact that alternative splicing and alternative transcripts are the rule, rather than the exception, in metazoan genes. Since multiple transcript and protein variants expressed by the same gene are, by definition, structurally distinct and need not to be functionally equivalent, the concept of gene orthology should be extended to the transcript level in order to describe evolutionary relationships between structurally similar transcript variants. In other words, the identification of true orthology relationships between gene products now should progress beyond primary sequence and "splicing orthology", consisting in ancestrally shared exon-intron structures, is required to define orthologous isoforms at transcript level. Results As a starting step in this direction, in this work we performed a large scale human- mouse gene comparison with a twofold goal: first, to assess if and to which extent traditional gene annotations such as RefSeq capture genuine splicing orthology; second, to provide a more detailed annotation and quantification of true human-mouse orthologous transcripts defined as transcripts of orthologous genes exhibiting the same splicing patterns. Conclusions We observed an identical exon/intron structure for 32% of human and mouse orthologous genes. This figure increases to 87% using less stringent criteria for gene structure similarity, thus implying that for about 13% of the human RefSeq annotated genes (and about 25% of the corresponding transcripts we could not identify any mouse transcript showing sufficient similarity to be confidently assigned as a splicing ortholog. Our data suggest that current gene and transcript data may still be rather incomplete - with several splicing variants still unknown. The observation that alternative splicing produces large numbers of alternative transcripts and proteins, some of them conserved across species and others truly species
Lafond, Manuel; El-Mabrouk, Nadia
A variety of methods based on sequence similarity, reconciliation, synteny or functional characteristics, can be used to infer orthology and paralogy relations between genes of a given gene family G. But is a given set C of orthology/paralogy constraints possible, i.e., can they simultaneously co-exist in an evolutionary history for G? While previous studies have focused on full sets of constraints, here we consider the general case where C does not necessarily involve a constraint for each pair of genes. The problem is subdivided in two parts: (1) Is C satisfiable, i.e. can we find an event-labeled gene tree G inducing C? (2) Is there such a G which is consistent, i.e., such that all displayed triplet phylogenies are included in a species tree? Previous results on the Graph sandwich problem can be used to answer to (1), and we provide polynomial-time algorithms for satisfiability and consistency with a given species tree. We also describe a new polynomial-time algorithm for the case of consistency with an unknown species tree and full knowledge of pairwise orthology/paralogy relationships, as well as a branch-and-bound algorithm in the case when unknown relations are present. We show that our algorithms can be used in combination with ProteinOrtho, a sequence similarity-based orthology detection tool, to extract a set of robust orthology/paralogy relationships.
Lafond, Manuel; El-Mabrouk, Nadia
Background A variety of methods based on sequence similarity, reconciliation, synteny or functional characteristics, can be used to infer orthology and paralogy relations between genes of a given gene family G . But is a given set C of orthology/paralogy constraints possible, i.e., can they simultaneously co-exist in an evolutionary history for G ? While previous studies have focused on full sets of constraints, here we consider the general case where C does not necessarily involve a ...
Huynen Martijn A
Full Text Available Abstract Background Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic relations results in inparalogs and outparalogs. For situations with more than two species we lack semantics to specifically describe the phylogenetic relations, let alone to exploit them. Published procedures to extract orthologous groups from phylogenetic trees do not allow identification of orthology at various levels of resolution, nor do they document the relations between the orthologous groups. Results We introduce "levels of orthology" to describe the multi-level nature of gene relations. This is implemented in a program LOFT (Levels of Orthology From Trees that assigns hierarchical orthology numbers to genes based on a phylogenetic tree. To decide upon speciation and gene duplication events in a tree LOFT can be instructed either to perform classical species-tree reconciliation or to use the species overlap between partitions in the tree. The hierarchical orthology numbers assigned by LOFT effectively summarize the phylogenetic relations between genes. The resulting high-resolution orthologous groups are depicted in colour, facilitating visual inspection of (large trees. A benchmark for orthology prediction, that takes into account the varying levels of orthology between genes, shows that the phylogeny-based high-resolution orthology assignments made by LOFT are reliable. Conclusion The "levels of orthology" concept offers high resolution, reliable orthology, while preserving the relations between orthologous groups. A Windows as well as a preliminary Java version of LOFT is available from the LOFT website http://www.cmbi.ru.nl/LOFT.
Lechner, Marcus; Hernandez-Rosales, Maribel; Doerr, Daniel; Wieseke, Nicolas; Thévenin, Annelyse; Stoye, Jens; Hartmann, Roland K.; Prohaska, Sonja J.; Stadler, Peter F.
The elucidation of orthology relationships is an important step both in gene function prediction as well as towards understanding patterns of sequence evolution. Orthology assignments are usually derived directly from sequence similarities for large data because more exact approaches exhibit too high computational costs. Here we present PoFF, an extension for the standalone tool Proteinortho, which enhances orthology detection by combining clustering, sequence similarity, and synteny. In the ...
Dessimoz, Christophe; Boeckmann, Brigitte; Roth, Alexander C J; Gonnet, Gaston H
Correct orthology assignment is a critical prerequisite of numerous comparative genomics procedures, such as function prediction, construction of phylogenetic species trees and genome rearrangement analysis. We present an algorithm for the detection of non-orthologs that arise by mistake in current orthology classification methods based on genome-specific best hits, such as the COGs database. The algorithm works with pairwise distance estimates, rather than computationally expensive and error-prone tree-building methods. The accuracy of the algorithm is evaluated through verification of the distribution of predicted cases, case-by-case phylogenetic analysis and comparisons with predictions from other projects using independent methods. Our results show that a very significant fraction of the COG groups include non-orthologs: using conservative parameters, the algorithm detects non-orthology in a third of all COG groups. Consequently, sequence analysis sensitive to correct orthology assignments will greatly benefit from these findings.
Heijden, R.T.J.M. van der; Snel, B.; Noort, V. van; Huynen, M.A.
BACKGROUND: Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic
Ruttink, Tom; Sterck, Lieven; Rohde, Antje
to outbreeding crop species hamper De Bruijn Graph-based de novo assembly algorithms, causing transcript fragmentation and the redundant assembly of allelic contigs. If multiple genotypes are sequenced to study genetic diversity, primary de novo assembly is best performed per genotype to limit the level......Despite current advances in next-generation sequencing data analysis procedures, de novo assembly of a reference sequence required for SNP discovery and expression analysis is still a major challenge in genetically uncharacterized, highly heterozygous species. High levels of polymorphism inherent...... of polymorphism and avoid transcript fragmentation. Here, we propose an Orthology Guided Assembly procedure that first uses sequence similarity (tBLASTn) to proteins of a model species to select allelic and fragmented contigs from all genotypes and then performs CAP3 clustering on a gene-by-gene basis. Thus, we...
Full Text Available BACKGROUND: Accurate identification of orthologs is crucial for evolutionary studies and for functional annotation. Several algorithms have been developed for ortholog delineation, but so far, manually curated genome-scale biological databases of orthologous genes for algorithm evaluation have been lacking. We evaluated four popular ortholog prediction algorithms (MultiParanoid; and OrthoMCL; RBH: Reciprocal Best Hit; RSD: Reciprocal Smallest Distance; the last two extended into clustering algorithms cRBH and cRSD, respectively, so that they can predict orthologs across multiple taxa against a set of 2,723 groups of high-quality curated orthologs from 6 Saccharomycete yeasts in the Yeast Gene Order Browser. RESULTS: Examination of sensitivity [TP/(TP+FN], specificity [TN/(TN+FP], and accuracy [(TP+TN/(TP+TN+FP+FN] across a broad parameter range showed that cRBH was the most accurate and specific algorithm, whereas OrthoMCL was the most sensitive. Evaluation of the algorithms across a varying number of species showed that cRBH had the highest accuracy and lowest false discovery rate [FP/(FP+TP], followed by cRSD. Of the six species in our set, three descended from an ancestor that underwent whole genome duplication. Subsequent differential duplicate loss events in the three descendants resulted in distinct classes of gene loss patterns, including cases where the genes retained in the three descendants are paralogs, constituting 'traps' for ortholog prediction algorithms. We found that the false discovery rate of all algorithms dramatically increased in these traps. CONCLUSIONS: These results suggest that simple algorithms, like cRBH, may be better ortholog predictors than more complex ones (e.g., OrthoMCL and MultiParanoid for evolutionary and functional genomics studies where the objective is the accurate inference of single-copy orthologs (e.g., molecular phylogenetics, but that all algorithms fail to accurately predict orthologs when paralogy
Full Text Available Abstract Background Signal peptide is one of the most important motifs involved in protein trafficking and it ultimately influences protein function. Considering the expected functional conservation among orthologs it was hypothesized that divergence in signal peptides within orthologous groups is mainly due to N-terminal protein sequence misannotation. Thus, discrepancies in signal peptide prediction of orthologous proteins were used to identify misannotated proteins in five Plasmodium species. Methods Signal peptide (SignalP and orthology (OrthoMCL were combined in an innovative strategy to identify orthologous groups showing discrepancies in signal peptide prediction among their protein members (Mixed groups. In a comparative analysis, multiple alignments for each of these groups and gene models were visually inspected in search of misannotated proteins and, whenever possible, alternative gene models were proposed. Thresholds for signal peptide prediction parameters were also modified to reduce their impact as a possible source of discrepancy among orthologs. Validation of new gene models was based on RT-PCR (few examples or on experimental evidence already published (ApiLoc. Results The rate of misannotated proteins was significantly higher in Mixed groups than in Positive or Negative groups, corroborating the proposed hypothesis. A total of 478 proteins were reannotated and change of signal peptide prediction from negative to positive was the most common. Reannotations triggered the conversion of almost 50% of all Mixed groups, which were further reduced by optimization of signal peptide prediction parameters. Conclusions The methodological novelty proposed here combining orthology and signal peptide prediction proved to be an effective strategy for the identification of proteins showing wrongly N-terminal annotated sequences, and it might have an important impact in the available data for genome-wide searching of potential vaccine and drug
Gains and losses shape the gene complement of animal lineages and are a fundamental aspect of genomic evolution. Acquiring a comprehensive view of the evolution of gene repertoires is limited by the intrinsic limitations of common sequence similarity searches and available databases. Thus, a subset of the gene complement of an organism consists of hidden orthologs, i.e., those with no apparent homology to sequenced animal lineages—mistakenly considered new genes—but actually representing rapidly evolving orthologs or undetected paralogs. Here, we describe Leapfrog, a simple automated BLAST pipeline that leverages increased taxon sampling to overcome long evolutionary distances and identify putative hidden orthologs in large transcriptomic databases by transitive homology. As a case study, we used 35 transcriptomes of 29 flatworm lineages to recover 3427 putative hidden orthologs, some unidentified by OrthoFinder and HaMStR, two common orthogroup inference algorithms. Unexpectedly, we do not observe a correlation between the number of putative hidden orthologs in a lineage and its “average” evolutionary rate. Hidden orthologs do not show unusual sequence composition biases that might account for systematic errors in sequence similarity searches. Instead, gene duplication with divergence of one paralog and weak positive selection appear to underlie hidden orthology in Platyhelminthes. By using Leapfrog, we identify key centrosome-related genes and homeodomain classes previously reported as absent in free-living flatworms, e.g., planarians. Altogether, our findings demonstrate that hidden orthologs comprise a significant proportion of the gene repertoire in flatworms, qualifying the impact of gene losses and gains in gene complement evolution. PMID:28400424
Full Text Available BACKGROUND: The Usher syndrome (USH is the most frequent deaf-blindness hereditary disease in humans. Deafness is attributed to the disorganization of stereocilia in the inner ear. USH1, the most severe subtype, is associated with mutations in genes encoding myosin VIIa, harmonin, cadherin 23, protocadherin 15, and sans. Myosin VIIa, harmonin, cadherin 23, and protocadherin 15 physically interact in vitro and localize to stereocilia tips in vivo, indicating that they form functional complexes. Sans, in contrast, localizes to vesicle-like structures beneath the apical membrane of stereocilia-displaying hair cells. How mutations in sans result in deafness and blindness is not well understood. Orthologs of myosin VIIa and protocadherin 15 have been identified in Drosophila melanogaster and their genetic analysis has identified essential roles in auditory perception and microvilli morphogenesis, respectively. PRINCIPAL FINDINGS: Here, we have identified and characterized the Drosophila ortholog of human sans. Drosophila Sans is expressed in tubular organs of the embryo, in lens-secreting cone cells of the adult eye, and in microvilli-displaying follicle cells during oogenesis. Sans mutants are viable, fertile, and mutant follicle cells appear to form microvilli, indicating that Sans is dispensable for fly development and microvilli morphogenesis in the follicle epithelium. In follicle cells, Sans protein localizes, similar to its vertebrate ortholog, to intracellular punctate structures, which we have identified as early endosomes associated with the syntaxin Avalanche. CONCLUSIONS: Our work is consistent with an evolutionary conserved function of Sans in vesicle trafficking. Furthermore it provides a significant basis for further understanding of the role of this Usher syndrome ortholog in development and disease.
Chaudhuri, Rima; Sadrieh, Arash; Hoffman, Nolan J; Parker, Benjamin L; Humphrey, Sean J; Stöckli, Jacqueline; Hill, Adam P; James, David E; Yang, Jean Yee Hwa
Most biological processes are influenced by protein post-translational modifications (PTMs). Identifying novel PTM sites in different organisms, including humans and model organisms, has expedited our understanding of key signal transduction mechanisms. However, with increasing availability of deep, quantitative datasets in diverse species, there is a growing need for tools to facilitate cross-species comparison of PTM data. This is particularly important because functionally important modification sites are more likely to be evolutionarily conserved; yet cross-species comparison of PTMs is difficult since they often lie in structurally disordered protein domains. Current tools that address this can only map known PTMs between species based on known orthologous phosphosites, and do not enable the cross-species mapping of newly identified modification sites. Here, we addressed this by developing a web-based software tool, PhosphOrtholog ( www.phosphortholog.com ) that accurately maps protein modification sites between different species. This facilitates the comparison of datasets derived from multiple species, and should be a valuable tool for the proteomics community. Here we describe PhosphOrtholog, a web-based application for mapping known and novel orthologous PTM sites from experimental data obtained from different species. PhosphOrtholog is the only generic and automated tool that enables cross-species comparison of large-scale PTM datasets without relying on existing PTM databases. This is achieved through pairwise sequence alignment of orthologous protein residues. To demonstrate its utility we apply it to two sets of human and rat muscle phosphoproteomes generated following insulin and exercise stimulation, respectively, and one publicly available mouse phosphoproteome following cellular stress revealing high mapping and coverage efficiency. Although coverage statistics are dataset dependent, PhosphOrtholog increased the number of cross-species mapped sites
Trachana, Kalliopi; Larsson, Tomas A; Powell, Sean; Chen, Wei-Hua; Doerks, Tobias; Muller, Jean; Bork, Peer
The increasing number of sequenced genomes has prompted the development of several automated orthology prediction methods. Tests to evaluate the accuracy of predictions and to explore biases caused by biological and technical factors are therefore required. We used 70 manually curated families to analyze the performance of five public methods in Metazoa. We analyzed the strengths and weaknesses of the methods and quantified the impact of biological and technical challenges. From the latter part of the analysis, genome annotation emerged as the largest single influencer, affecting up to 30% of the performance. Generally, most methods did well in assigning orthologous group but they failed to assign the exact number of genes for half of the groups. The publicly available benchmark set (http://eggnog.embl.de/orthobench/) should facilitate the improvement of current orthology assignment protocols, which is of utmost importance for many fields of biology and should be tackled by a broad scientific community. Copyright © 2011 WILEY Periodicals, Inc.
Lechner, Marcus; Hernandez-Rosales, Maribel; Doerr, Daniel; Wieseke, Nicolas; Thévenin, Annelyse; Stoye, Jens; Hartmann, Roland K; Prohaska, Sonja J; Stadler, Peter F
The elucidation of orthology relationships is an important step both in gene function prediction as well as towards understanding patterns of sequence evolution. Orthology assignments are usually derived directly from sequence similarities for large data because more exact approaches exhibit too high computational costs. Here we present PoFF, an extension for the standalone tool Proteinortho, which enhances orthology detection by combining clustering, sequence similarity, and synteny. In the course of this work, FFAdj-MCS, a heuristic that assesses pairwise gene order using adjacencies (a similarity measure related to the breakpoint distance) was adapted to support multiple linear chromosomes and extended to detect duplicated regions. PoFF largely reduces the number of false positives and enables more fine-grained predictions than purely similarity-based approaches. The extension maintains the low memory requirements and the efficient concurrency options of its basis Proteinortho, making the software applicable to very large datasets.
Full Text Available The elucidation of orthology relationships is an important step both in gene function prediction as well as towards understanding patterns of sequence evolution. Orthology assignments are usually derived directly from sequence similarities for large data because more exact approaches exhibit too high computational costs. Here we present PoFF, an extension for the standalone tool Proteinortho, which enhances orthology detection by combining clustering, sequence similarity, and synteny. In the course of this work, FFAdj-MCS, a heuristic that assesses pairwise gene order using adjacencies (a similarity measure related to the breakpoint distance was adapted to support multiple linear chromosomes and extended to detect duplicated regions. PoFF largely reduces the number of false positives and enables more fine-grained predictions than purely similarity-based approaches. The extension maintains the low memory requirements and the efficient concurrency options of its basis Proteinortho, making the software applicable to very large datasets.
Full Text Available List Contact us MicrobeDB.jp Ortholog Data detail Data name Ortholog DOI 10.18908/lsdba.nbdc01181-010.V002 V...814 triples - About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Ortholog - MicrobeDB.jp | LSDB Archive ...
Stone, Stacie; Sobeck, Alexandra; van Kogelenberg, Margriet; de Graaf, Bendert; Joenje, Hans; Christian, Jan; Hoatlin, Maureen E
Fanconi anemia (FA) is associated with variable developmental abnormalities, bone marrow failure and cancer susceptibility. FANCG/XRCC9 is member of the FA core complex, a group of proteins that control the monoubiquitylation of FANCD2, an event that plays a critical role in maintaining genomic stability. Here we report the identification of the Xenopus laevis ortholog of human FANCG (xFANCG), its expression during development, and its molecular interactions with a partner protein, xFANCA. The xFANCG protein sequence is 47% similar to its human ortholog, with highest conservation in the two putative N-terminal leucine zippers and the tetratricopeptide repeat (TPR) motifs. xFANCG is maternally and zygotically transcribed. Prior to the midblastula stage, a single xFANCG transcript is observed but two additional alternatively spliced mRNAs are detected after the midblastula transition. One of the variants is predicted to encode a novel isoform of xFANCG lacking exon 2. The mutual association between FANCG and FANCA required for their nuclear import is conserved in Xenopus egg extracts. Our data demonstrate that interactions between FANCA and FANCG occur at the earliest stage of vertebrate development and raise the possibility that functionally different isoforms of xFANCG may play a role in early development.
Rasmussen, Jane Lind Nybo; Vesth, Tammi Camilla; Theobald, Sebastian
of genotype-to-phenotype. To achieve this, we have developed orthologous protein prediction software that utilizes genus-wide genetic diversity. The approach is optimized for large data sets, based on BLASTp considering protein identity and alignment coverage, and clustering using single linkage of bi......The Aspergillus genus contains leading industrial microorganisms, excelling in producing bioactive compounds and enzymes. Using synthetic biology and bioinformatics, we aim to re-engineer these organisms for applications within human health, pharmaceuticals, environmental engineering, and food......-directional hits. The result is orthologous protein families describing the genomic and functional features of individual species, clades and the core/pan genome of Aspergillus; and applicable to genotype-to-phenotype analyses in other microbial genera....
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Marayati, Bahjat Fadi; Hoskins, Victoria; Boger, Robert W; Tucker, James F; Fishman, Emily S; Bray, Andrew S; Zhang, Ke
Meiosis is a highly regulated process by which genetic information is transmitted through sexual reproduction. It encompasses unique mechanisms that do not occur in vegetative cells, producing a distinct, well-regulated meiotic transcriptome. During vegetative growth, many meiotic genes are constitutively transcribed, but most of the resulting mRNAs are rapidly eliminated by the Mmi1-MTREC (Mtl1-Red1 core) complex. While Mmi1-MTREC targets premature meiotic RNAs for degradation by the nuclear 3'-5' exoribonuclease exosome during mitotic growth, its role in meiotic gene expression during meiosis is not known. Here, we report that Red5, an essential MTREC component, interacts with pFal1, an ortholog of eukaryotic translation initiation factor eIF4aIII in the fission yeast Schizosaccharomyces pombe In mammals, together with MAGO (Mnh1), Rnps1, and Y14, elF4AIII (pFal1) forms the core of the exon junction complex (EJC), which is essential for transcriptional surveillance and localization of mature mRNAs. In fission yeast, two EJC orthologs, pFal1 and Mnh1, are functionally connected with MTREC, specifically in the process of meiotic gene expression during meiosis. Although pFal1 interacts with Mnh1, Y14, and Rnps1, its association with Mnh1 is not disrupted upon loss of Y14 or Rnps1. Mutations of Red1, Red5, pFal1, or Mnh1 produce severe meiotic defects; the abundance of meiotic transcripts during meiosis decreases; and mRNA maturation processes such as splicing are impaired. Since studying meiosis in mammalian germline cells is difficult, our findings in fission yeast may help to define the general mechanisms involved in accurate meiotic gene expression in higher eukaryotes. © 2016 Marayati et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Full Text Available Junfeng Liu1,2, Liang Chen3, Hongyu Zhao4, Dirk F Moore1,2, Yong Lin1,2, Weichung Joe Shih1,21Biometrics Division, The Cancer, Institute of New Jersey, New Brunswick, NJ, USA; 2Department of Biostatistics, School of Public Health, University of Medicine and Dentistry of New Jersey, Piscataway, NJ, USA; 3Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA; 4Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USAAbstract: Probabilistic DNA sequence models have been intensively applied to genome research. Within the evolutionary biology framework, this article investigates the feasibility for rigorously estimating the probability of a set of orthologous DNA sequences which evolve from a common progenitor. We propose Monte Carlo integration algorithms to sample the unknown ancestral and/or root sequences a posteriori conditional on a reference sequence and apply pairwise Needleman–Wunsch alignment between the sampled and nonreference species sequences to estimate the probability. We test our algorithms on both simulated and real sequences and compare calculated probabilities from Monte Carlo integration to those induced by single multiple alignment.Keywords: evolution, Jukes–Cantor model, Monte Carlo integration, Needleman–Wunsch alignment, orthologous
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Wolf Yuri I; Novichkov Pavel S; Sorokin Alexander V; Makarova Kira S; Koonin Eugene V
Abstract Background An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs ...
Full Text Available Abstract Background Mapping of orthologous genes among species serves an important role in functional genomics by allowing researchers to develop hypotheses about gene function in one species based on what is known about the functions of orthologs in other species. Several tools for predicting orthologous gene relationships are available. However, these tools can give different results and identification of predicted orthologs is not always straightforward. Results We report a simple but effective tool, the Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool (DIOPT; http://www.flyrnai.org/diopt, for rapid identification of orthologs. DIOPT integrates existing approaches, facilitating rapid identification of orthologs among human, mouse, zebrafish, C. elegans, Drosophila, and S. cerevisiae. As compared to individual tools, DIOPT shows increased sensitivity with only a modest decrease in specificity. Moreover, the flexibility built into the DIOPT graphical user interface allows researchers with different goals to appropriately 'cast a wide net' or limit results to highest confidence predictions. DIOPT also displays protein and domain alignments, including percent amino acid identity, for predicted ortholog pairs. This helps users identify the most appropriate matches among multiple possible orthologs. To facilitate using model organisms for functional analysis of human disease-associated genes, we used DIOPT to predict high-confidence orthologs of disease genes in Online Mendelian Inheritance in Man (OMIM and genes in genome-wide association study (GWAS data sets. The results are accessible through the DIOPT diseases and traits query tool (DIOPT-DIST; http://www.flyrnai.org/diopt-dist. Conclusions DIOPT and DIOPT-DIST are useful resources for researchers working with model organisms, especially those who are interested in exploiting model organisms such as Drosophila to study the functions of human disease genes.
Hu, Yanhui; Flockhart, Ian; Vinayagam, Arunachalam; Bergwitz, Clemens; Berger, Bonnie; Perrimon, Norbert; Mohr, Stephanie E
Mapping of orthologous genes among species serves an important role in functional genomics by allowing researchers to develop hypotheses about gene function in one species based on what is known about the functions of orthologs in other species. Several tools for predicting orthologous gene relationships are available. However, these tools can give different results and identification of predicted orthologs is not always straightforward. We report a simple but effective tool, the Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool (DIOPT; http://www.flyrnai.org/diopt), for rapid identification of orthologs. DIOPT integrates existing approaches, facilitating rapid identification of orthologs among human, mouse, zebrafish, C. elegans, Drosophila, and S. cerevisiae. As compared to individual tools, DIOPT shows increased sensitivity with only a modest decrease in specificity. Moreover, the flexibility built into the DIOPT graphical user interface allows researchers with different goals to appropriately 'cast a wide net' or limit results to highest confidence predictions. DIOPT also displays protein and domain alignments, including percent amino acid identity, for predicted ortholog pairs. This helps users identify the most appropriate matches among multiple possible orthologs. To facilitate using model organisms for functional analysis of human disease-associated genes, we used DIOPT to predict high-confidence orthologs of disease genes in Online Mendelian Inheritance in Man (OMIM) and genes in genome-wide association study (GWAS) data sets. The results are accessible through the DIOPT diseases and traits query tool (DIOPT-DIST; http://www.flyrnai.org/diopt-dist). DIOPT and DIOPT-DIST are useful resources for researchers working with model organisms, especially those who are interested in exploiting model organisms such as Drosophila to study the functions of human disease genes.
Full Text Available Abstract Background The concept of orthology is key to decoding evolutionary relationships among genes across different species using comparative genomics. QuartetS is a recently reported algorithm for large-scale orthology detection. Based on the well-established evolutionary principle that gene duplication events discriminate paralogous from orthologous genes, QuartetS has been shown to improve orthology detection accuracy while maintaining computational efficiency. Description QuartetS-DB is a new orthology database constructed using the QuartetS algorithm. The database provides orthology predictions among 1621 complete genomes (1365 bacterial, 92 archaeal, and 164 eukaryotic, covering more than seven million proteins and four million pairwise orthologs. It is a major source of orthologous groups, containing more than 300,000 groups of orthologous proteins and 236,000 corresponding gene trees. The database also provides over 500,000 groups of inparalogs. In addition to its size, a distinguishing feature of QuartetS-DB is the ability to allow users to select a cutoff value that modulates the balance between prediction accuracy and coverage of the retrieved pairwise orthologs. The database is accessible at https://applications.bioanalysis.org/quartetsdb. Conclusions QuartetS-DB is one of the largest orthology resources available to date. Because its orthology predictions are underpinned by evolutionary evidence obtained from sequenced genomes, we expect its accuracy to continue to increase in future releases as the genomes of additional species are sequenced.
Kleinow, T.; Bhalerao, R.; Breuer, F.
Yeast Snf4 is a prototype of activating gamma-subunits of conserved Snf1/AMPK-related protein kinases (SnRKs) controlling glucose and stress signaling in eukaryotes. The catalytic subunits of Arabidopsis SnRKs, AKIN10 and AKIN11, interact with Snf4 and suppress the snf1 and snf4 mutations in yeast....... By expression of an Arabidopsis cDNA library in yeast, heterologous multicopy snf4 suppressors were isolated. In addition to AKIN10 and AKIN11, the deficiency of yeast snf4 mutant to grown on non-fermentable carbon source was suppressed by Arabidopsis Myb30, CAAT-binding factor Hap3b, casein kinase I, zinc......-finger factors AZF2 and ZAT10, as well as orthologs of hexose/UDP-hexose transporters, calmodulin, SMC1-cohesin and Snf4. Here we describe the characterization of AtSNF4, a functional Arabidopsis Snf4 ortholog, that interacts with yeast Snf1 and specifically binds to the C-terminal regulatory domain...
Mihail R Halachev
Full Text Available Among proteins, orthologs are defined as those that are derived by vertical descent from a single progenitor in the last common ancestor of their host organisms. Our goal is to compute a complete set of protein orthologs derived from all currently available complete bacterial and archaeal genomes. Traditional approaches typically rely on all-against-all BLAST searching which is prohibitively expensive in terms of hardware requirements or computational time (requiring an estimated 18 months or more on a typical server. Here, we present xBASE-Orth, a system for ongoing ortholog annotation, which applies a "divide and conquer" approach and adopts a pragmatic scheme that trades accuracy for speed. Starting at species level, xBASE-Orth carefully constructs and uses pan-genomes as proxies for the full collections of coding sequences at each level as it progressively climbs the taxonomic tree using the previously computed data. This leads to a significant decrease in the number of alignments that need to be performed, which translates into faster computation, making ortholog computation possible on a global scale. Using xBASE-Orth, we analyzed an NCBI collection of 1,288 bacterial and 94 archaeal complete genomes with more than 4 million coding sequences in 5 weeks and predicted more than 700 million ortholog pairs, clustered in 175,531 orthologous groups. We have also identified sets of highly conserved bacterial and archaeal orthologs and in so doing have highlighted anomalies in genome annotation and in the proposed composition of the minimal bacterial genome. In summary, our approach allows for scalable and efficient computation of the bacterial and archaeal ortholog annotations. In addition, due to its hierarchical nature, it is suitable for incorporating novel complete genomes and alternative genome annotations. The computed ortholog data and a continuously evolving set of applications based on it are integrated in the xBASE database, available
Chiba, Hirokazu; Nishide, Hiroyo; Uchiyama, Ikuo
Recently, various types of biological data, including genomic sequences, have been rapidly accumulating. To discover biological knowledge from such growing heterogeneous data, a flexible framework for data integration is necessary. Ortholog information is a central resource for interlinking corresponding genes among different organisms, and the Semantic Web provides a key technology for the flexible integration of heterogeneous data. We have constructed an ortholog database using the Semantic Web technology, aiming at the integration of numerous genomic data and various types of biological information. To formalize the structure of the ortholog information in the Semantic Web, we have constructed the Ortholog Ontology (OrthO). While the OrthO is a compact ontology for general use, it is designed to be extended to the description of database-specific concepts. On the basis of OrthO, we described the ortholog information from our Microbial Genome Database for Comparative Analysis (MBGD) in the form of Resource Description Framework (RDF) and made it available through the SPARQL endpoint, which accepts arbitrary queries specified by users. In this framework based on the OrthO, the biological data of different organisms can be integrated using the ortholog information as a hub. Besides, the ortholog information from different data sources can be compared with each other using the OrthO as a shared ontology. Here we show some examples demonstrating that the ortholog information described in RDF can be used to link various biological data such as taxonomy information and Gene Ontology. Thus, the ortholog database using the Semantic Web technology can contribute to biological knowledge discovery through integrative data analysis.
Curtis, Darren S.; Phillips, Aaron R.; Callister, Stephen J.; Conlan, Sean; McCue, Lee Ann
At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid. AVAILABILITY AND IMPLEMENTATION: A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required.
Sven Heinicke; Michael S Livstone; Charles Lu; Rose Oughtred; Fan Kang; Samuel V Angiuoli; Owen White; David Botstein; Kara Dolinski
Many biological databases that provide comparative genomics information and tools are now available on the internet. While certainly quite useful, to our knowledge none of the existing databases combine results from multiple comparative genomics methods with manually curated information from the literature. Here we describe the Princeton Protein Orthology Database (P-POD, http://ortholog.princeton.edu), a user-friendly database system that allows users to find and visualize the phylogenetic r...
J Peter Svensson
Full Text Available Studies in Saccharomyces cerevisiae show that many proteins influence cellular survival upon exposure to DNA damaging agents. We hypothesized that human orthologs of these S. cerevisiae proteins would also be required for cellular survival after treatment with DNA damaging agents. For this purpose, human homologs of S. cerevisiae proteins were identified and mapped onto the human protein-protein interaction network. The resulting human network was highly modular and a series of selection rules were implemented to identify 45 candidates for human toxicity-modulating proteins. The corresponding transcripts were targeted by RNA interference in human cells. The cell lines with depleted target expression were challenged with three DNA damaging agents: the alkylating agents MMS and 4-NQO, and the oxidizing agent t-BuOOH. A comparison of the survival revealed that the majority (74% of proteins conferred either sensitivity or resistance. The identified human toxicity-modulating proteins represent a variety of biological functions: autophagy, chromatin modifications, RNA and protein metabolism, and telomere maintenance. Further studies revealed that MMS-induced autophagy increase the survival of cells treated with DNA damaging agents. In summary, we show that damage recovery proteins in humans can be identified through homology to S. cerevisiae and that many of the same pathways are represented among the toxicity modulators.
Su, Fei; Ou, Hong-Yu; Tao, Fei; Tang, Hongzhi; Xu, Ping
With genomic sequences of many closely related bacterial strains made available by deep sequencing, it is now possible to investigate trends in prokaryotic microevolution. Positive selection is a sub-process of microevolution, in which a particular mutation is favored, causing the allele frequency to continuously shift in one direction. Wide scanning of prokaryotic genomes has shown that positive selection at the molecular level is much more frequent than expected. Genes with significant positive selection may play key roles in bacterial adaption to different environmental pressures. However, selection pressure analyses are computationally intensive and awkward to configure. Here we describe an open access web server, which is designated as PSP (Positive Selection analysis for Prokaryotic genomes) for performing evolutionary analysis on orthologous coding genes, specially designed for rapid comparison of dozens of closely related prokaryotic genomes. Remarkably, PSP facilitates functional exploration at the multiple levels by assignments and enrichments of KO, GO or COG terms. To illustrate this user-friendly tool, we analyzed Escherichia coli and Bacillus cereus genomes and found that several genes, which play key roles in human infection and antibiotic resistance, show significant evidence of positive selection. PSP is freely available to all users without any login requirement at: http://db-mml.sjtu.edu.cn/PSP/. PSP ultimately allows researchers to do genome-scale analysis for evolutionary selection across multiple prokaryotic genomes rapidly and easily, and identify the genes undergoing positive selection, which may play key roles in the interactions of host-pathogen and/or environmental adaptation.
Ampomah, Osei Yaw; Jensen, John Beck
Competitiveness for nodulation is a desirable trait in rhizobia strains used as inoculant. In Sinorhizobium meliloti 1021 mutation in either of the trehalose utilization genes thuA or thuB influences its competitiveness for root colonization and nodule occupancy depending on the interacting host. We have therefore investigated whether mutation in the thuA ortholog in Mesorhizobium loti MAFF303099 also leads to a similar competitive phenotype on its hosts. The results show that M. loti thuA mutant Ml7023 was symbiotically effective and was as competitive as the wild type in colonization and nodule occupancy on Lotus corniculatus and Lotus japonicus. The thuA gene in M. loti was not induced during root colonization or in the infection threads unlike in S. meliloti, despite its induction by trehalose and high osmolarity in in vitro assays.
Full Text Available Abstract Background Ortholog assignment is a critical and fundamental problem in comparative genomics, since orthologs are considered to be functional counterparts in different species and can be used to infer molecular functions of one species from those of other species. MSOAR is a recently developed high-throughput system for assigning one-to-one orthologs between closely related species on a genome scale. It attempts to reconstruct the evolutionary history of input genomes in terms of genome rearrangement and gene duplication events. It assumes that a gene duplication event inserts a duplicated gene into the genome of interest at a random location (i.e., the random duplication model. However, in practice, biologists believe that genes are often duplicated by tandem duplications, where a duplicated gene is located next to the original copy (i.e., the tandem duplication model. Results In this paper, we develop MSOAR 2.0, an improved system for one-to-one ortholog assignment. For a pair of input genomes, the system first focuses on the tandemly duplicated genes of each genome and tries to identify among them those that were duplicated after the speciation (i.e., the so-called inparalogs, using a simple phylogenetic tree reconciliation method. For each such set of tandemly duplicated inparalogs, all but one gene will be deleted from the concerned genome (because they cannot possibly appear in any one-to-one ortholog pairs, and MSOAR is invoked. Using both simulated and real data experiments, we show that MSOAR 2.0 is able to achieve a better sensitivity and specificity than MSOAR. In comparison with the well-known genome-scale ortholog assignment tool InParanoid, Ensembl ortholog database, and the orthology information extracted from the well-known whole-genome multiple alignment program MultiZ, MSOAR 2.0 shows the highest sensitivity. Although the specificity of MSOAR 2.0 is slightly worse than that of InParanoid in the real data experiments
Full Text Available Orthology detection requires more effective scaling algorithms. In this paper, a set of gene pair features based on similarity measures (alignment scores, sequence length, gene membership to conserved regions, and physicochemical profiles are combined in a supervised pairwise ortholog detection approach to improve effectiveness considering low ortholog ratios in relation to the possible pairwise comparison between two genomes. In this scenario, big data supervised classifiers managing imbalance between ortholog and nonortholog pair classes allow for an effective scaling solution built from two genomes and extended to other genome pairs. The supervised approach was compared with RBH, RSD, and OMA algorithms by using the following yeast genome pairs: Saccharomyces cerevisiae-Kluyveromyces lactis, Saccharomyces cerevisiae-Candida glabrata, and Saccharomyces cerevisiae-Schizosaccharomyces pombe as benchmark datasets. Because of the large amount of imbalanced data, the building and testing of the supervised model were only possible by using big data supervised classifiers managing imbalance. Evaluation metrics taking low ortholog ratios into account were applied. From the effectiveness perspective, MapReduce Random Oversampling combined with Spark SVM outperformed RBH, RSD, and OMA, probably because of the consideration of gene pair features beyond alignment similarities combined with the advances in big data supervised classification.
Balaji, Jayashree; Crouch, Jonathan H; Petite, Prasad V N S; Hoisington, David A
A minimal requirement to initiate a comparative genomics study on plant responses to abiotic stresses is a dataset of orthologous sequences. The availability of a large amount of sequence information, including those derived from stress cDNA libraries allow for the identification of stress related genes and orthologs associated with the stress response. Orthologous sequences serve as tools to explore genes and their relationships across species. For this purpose, ESTs from stress cDNA libraries across 16 crop species including 6 important cereal crops and 10 dicots were systematically collated and subjected to bioinformatics analysis such as clustering, grouping of tentative orthologous sets, identification of protein motifs/patterns in the predicted protein sequence, and annotation with stress conditions, tissue/library source and putative function. All data are available to the scientific community at http://intranet.icrisat.org/gt1/tog/homepage.htm. We believe that the availability of annotated plant abiotic stress ortholog sets will be a valuable resource for researchers studying the biology of environmental stresses in plant systems, molecular evolution and genomics.
IONS: Identification of Orthologs by Neighborhood and Similarity-an Automated Method to Identify Orthologs in Chromosomal Regions of Common Evolutionary Ancestry and its Application to Hemiascomycetous Yeasts.
Seret, Marie-Line; Baret, Philippe V
Comparative sequence analysis is widely used to infer gene function and study genome evolution and requires proper ortholog identification across different genomes. We have developed a program for the Identification of Orthologs in one-to-one relationship by Neighborhood and Similarity (IONS) between closely related species. The algorithm combines two levels of evidence to determine co-ancestrality at the genome scale: sequence similarity and shared neighborhood. The method was initially designed to provide anchor points for syntenic blocks within the Génolevures project concerning nine hemiascomycetous yeasts (about 50,000 genes) and is applicable to different input databases. Comparison based on use of a Rand index shows that the results are highly consistent with the pillars of the Yeast Gene Order Browser, a manually curated database. Compared with SYNERGY, another algorithm reporting homology relationships, our method's main advantages are its automation and the absence of dataset-dependent parameters, facilitating consistent integration of newly released genomes.
Full Text Available Abstract Background With the rapid growth in the availability of genome sequence data, the automated identification of orthologous genes between species (orthologs is of fundamental importance to facilitate functional annotation and studies on comparative and evolutionary genomics. Genes with no apparent orthologs between the bovine and human genome may be responsible for major differences between the species, however, such genes are often neglected in functional genomics studies. Results A BLAST-based method was exploited to explore the current annotation and orthology predictions in Ensembl. Genes with no orthologs between the two genomes were classified into groups based on alignments, ontology, manual curation and publicly available information. Starting from a high quality and specific set of orthology predictions, as provided by Ensembl, hidden relationship between genes and genomes of different mammalian species were unveiled using a highly sensitive approach, based on sequence similarity and genomic comparison. Conclusions The analysis identified 3,801 bovine genes with no orthologs in human and 1010 human genes with no orthologs in cow, among which 411 and 43 genes, respectively, had no match at all in the other species. Most of the apparently non-orthologous genes may potentially have orthologs which were missed in the annotation process, despite having a high percentage of identity, because of differences in gene length and structure. The comparative analysis reported here identified gene variants, new genes and species-specific features and gave an overview of the other side of orthology which may help to improve the annotation of the bovine genome and the knowledge of structural differences between species.
Haberer, Georg; Panda, Arup; Das Laha, Shayani; Ghosh, Tapas Chandra; Schäffner, Anton R.
The identification of functionally equivalent, orthologous genes (functional orthologs) across genomes is necessary for accurate transfer of experimental knowledge from well-characterized organisms to others. This frequently relies on automated, coding sequence-based approaches such as OrthoMCL, Inparanoid, and KOG, which usually work well for one-to-one homologous states. However, this strategy does not reliably work for plants due to the occurrence of extensive gene/genome duplication. Frequently, for one query gene, multiple orthologous genes are predicted in the other genome, and it is not clear a priori from sequence comparison and similarity which one preserves the ancestral function. We have studied 11 organ-dependent and stress-induced gene expression patterns of 286 Arabidopsis lyrata duplicated gene groups and compared them with the respective Arabidopsis (Arabidopsis thaliana) genes to predict putative expressologs and nonexpressologs based on gene expression similarity. Promoter sequence divergence as an additional tool to substantiate functional orthology only partially overlapped with expressolog classification. By cloning eight A. lyrata homologs and complementing them in the respective four Arabidopsis loss-of-function mutants, we experimentally proved that predicted expressologs are indeed functional orthologs, while nonexpressologs or nonfunctionalized orthologs are not. Our study demonstrates that even a small set of gene expression data in addition to sequence homologies are instrumental in the assignment of functional orthologs in the presence of multiple orthologs. PMID:27303025
Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that i...
Skipper, Martin; Johansen, Louise Buchholt; Pedersen, Kim B.
Studies have shown that several plant species posses AGAMOUS (AG) and SEEDSTICK (STK) orthologs. These genes are part of the so-called C- and D MADS-box gene lineages and play key roles in ovule development in Arabidopsis thaliana. We have cloned an AG- and STK ortholog in the orchid Dendrobium...
Poietti, S.; Bertini, L.; Ent, S. van der; Leon Reyes, H.A.; Pieterse, C.M.J.; Tucci, M.; Caporale, C.; Caruso, C.
WRKY proteins are transcription factors involved in many plant processes including plant responses to pathogens. Here, the cross activity of TaWRKY78 from the monocot wheat and AtWRKY20 from the dicot Arabidopsis on the cognate promoters of the orthologous PR4-type genes wPR4e and AtHEL of wheat and
Trachtulec, Zdeněk; Forejt, Jiří
Roč. 12, č. 3 (2001), s. 227-231 ISSN 0938-8990 Institutional research plan: CEZ:AV0Z5052915 Keywords : synteny of orthologous genes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.318, year: 2001
Full Text Available e relevant data in the databases. By submitting queries to the PGDBj Ortholog DB with keywords or amino acid sequences, users... taxa including both model plants and crop plants. Following the links obtained, users can retrieve the actu
Lechner, Marcus; Findeiss, Sven; Steiner, Lydia; Marz, Manja; Stadler, Peter F; Prohaska, Sonja J
Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases. The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes. Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware.
Full Text Available Abstract Background Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases. Results The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes. Conclusions Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware.
Full Text Available Abstract Background Comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. Detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. This is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving. Results We have developed a suite of programs that automate three essential steps to study conservation of gene order, and validated them with a set of 107 bacteria and archaea that cover the majority of the prokaryotic taxonomic space. We identified the whole set of shared homologs between two or more species and computed the evolutionary distance separating each pair of homologs. We applied two strategies to extract from the set of homologs a collection of valid orthologs shared by at least two genomes. The first computes the Reciprocal Smallest Distance (RSD using the PAM distances separating pairs of homologs. The second method groups homologs in families and reconstructs each family's evolutionary tree, distinguishing bona fide orthologs as well as paralogs created after the last speciation event. Although the phylogenetic tree method often succeeds where RSD fails, the reverse could occasionally be true. Accordingly, we used the data obtained with either methods or their intersection to number the orthologs that are adjacent in for each pair of genomes, the Positional Orthologous Genes (POGs, and to further study their properties. Once all these synteny blocks have been detected, we showed that POGs are subject to more evolutionary constraints than orthologs outside synteny groups, whichever the taxonomic distance separating the compared organisms. Conclusion The suite of programs described in this paper allows a reliable detection of orthologs and is useful for evaluating gene
Nichio, Bruno T L; Marchaukoski, Jeroniza Nunes; Raittz, Roberto Tadeu
Nowadays defying homology relationships among sequences is essential for biological research. Within homology the analysis of orthologs sequences is of great importance for computational biology, annotation of genomes and for phylogenetic inference. Since 2007, with the increase in the number of new sequences being deposited in large biological databases, researchers have begun to analyse computerized methodologies and tools aimed at selecting the most promising ones in the prediction of orthologous groups. Literature in this field of research describes the problems that the majority of available tools show, such as those encountered in accuracy, time required for analysis (especially in light of the increasing volume of data being submitted, which require faster techniques) and the automatization of the process without requiring manual intervention. Conducting our search through BMC, Google Scholar, NCBI PubMed, and Expasy, we examined more than 600 articles pursuing the most recent techniques and tools developed to solve most the problems still existing in orthology detection. We listed the main computational tools created and developed between 2011 and 2017, taking into consideration the differences in the type of orthology analysis, outlining the main features of each tool and pointing to the problems that each one tries to address. We also observed that several tools still use as their main algorithm the BLAST "all-against-all" methodology, which entails some limitations, such as limited number of queries, computational cost, and high processing time to complete the analysis. However, new promising tools are being developed, like OrthoVenn (which uses the Venn diagram to show the relationship of ortholog groups generated by its algorithm); or proteinOrtho (which improves the accuracy of ortholog groups); or ReMark (tackling the integration of the pipeline to turn the entry process automatic); or OrthAgogue (using algorithms developed to minimize processing
Bruno T. L. Nichio
Full Text Available Nowadays defying homology relationships among sequences is essential for biological research. Within homology the analysis of orthologs sequences is of great importance for computational biology, annotation of genomes and for phylogenetic inference. Since 2007, with the increase in the number of new sequences being deposited in large biological databases, researchers have begun to analyse computerized methodologies and tools aimed at selecting the most promising ones in the prediction of orthologous groups. Literature in this field of research describes the problems that the majority of available tools show, such as those encountered in accuracy, time required for analysis (especially in light of the increasing volume of data being submitted, which require faster techniques and the automatization of the process without requiring manual intervention. Conducting our search through BMC, Google Scholar, NCBI PubMed, and Expasy, we examined more than 600 articles pursuing the most recent techniques and tools developed to solve most the problems still existing in orthology detection. We listed the main computational tools created and developed between 2011 and 2017, taking into consideration the differences in the type of orthology analysis, outlining the main features of each tool and pointing to the problems that each one tries to address. We also observed that several tools still use as their main algorithm the BLAST “all-against-all” methodology, which entails some limitations, such as limited number of queries, computational cost, and high processing time to complete the analysis. However, new promising tools are being developed, like OrthoVenn (which uses the Venn diagram to show the relationship of ortholog groups generated by its algorithm; or proteinOrtho (which improves the accuracy of ortholog groups; or ReMark (tackling the integration of the pipeline to turn the entry process automatic; or OrthAgogue (using algorithms developed to
Full Text Available Secreted papain-like Cys proteases are important players in plant immunity. We previously reported that the C14 protease of tomato is targeted by cystatin-like EPIC proteins that are secreted by the oomycete pathogen Phytophthora infestans (Pinf during infection. C14 has been under diversifying selection in wild potato species coevolving with Pinf and reduced C14 levels result in enhanced susceptibility for Pinf. Here, we investigated the role C14-EPIC-like interactions in the natural pathosystem of Arabidopsis with the oomycete pathogen Hyaloperonospora arabidopsidis (Hpa. In contrast to the Pinf-solanaceae pathosystem, the C14 orthologous protease of Arabidopsis, RD21, does not evolve under diversifying selection in Arabidopsis, and rd21 null mutants do not show phenotypes upon compatible and incompatible Hpa interactions, despite the evident lack of a major leaf protease. Hpa isolates express highly conserved EPIC-like proteins during infections, but it is unknown if these HpaEPICs can inhibit RD21 and one of these HpaEPICs even lacks the canonical cystatin motifs. The rd21 mutants are unaffected in compatible and incompatible interactions with Pseudomonas syringae pv. tomato, but are significantly more susceptible for the necrotrophic fungal pathogen Botrytis cinerea, demonstrating that RD21 provides immunity to a necrotrophic pathogen.
Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu
The microbial genome database for comparative analysis (MBGD) (available at http://mbgd.genome.ad.jp/) is a comprehensive ortholog database for flexible comparative analysis of microbial genomes, where the users are allowed to create an ortholog table among any specified set of organisms. Because of the rapid increase in microbial genome data owing to the next-generation sequencing technology, it becomes increasingly challenging to maintain high-quality orthology relationships while allowing the users to incorporate the latest genomic data available into an analysis. Because many of the recently accumulating genomic data are draft genome sequences for which some complete genome sequences of the same or closely related species are available, MBGD now stores draft genome data and allows the users to incorporate them into a user-specific ortholog database using the MyMBGD functionality. In this function, draft genome data are incorporated into an existing ortholog table created only from the complete genome data in an incremental manner to prevent low-quality draft data from affecting clustering results. In addition, to provide high-quality orthology relationships, the standard ortholog table containing all the representative genomes, which is first created by the rapid classification program DomClust, is now refined using DomRefine, a recently developed program for improving domain-level clustering using multiple sequence alignment information. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
Full Text Available Abstract Background In mammals, pheromones play an important role in social and innate reproductive behavior within species. In rodents, vomeronasal receptor type 1 (V1R, which is specifically expressed in the vomeronasal organ, is thought to detect pheromones. The V1R gene repertoire differs dramatically between mammalian species, and the presence of species-specific V1R subfamilies in mouse and rat suggests that V1R plays a profound role in species-specific recognition of pheromones. In ruminants, however, the molecular mechanism(s for pheromone perception is not well understood. Interestingly, goat male pheromone, which can induce out-of-season ovulation in anestrous females, causes the same pheromone response in sheep, and vice versa, suggesting that there may be mechanisms for detecting "inter-species" pheromones among ruminant species. Results We isolated 23 goat and 21 sheep intact V1R genes based on sequence similarity with 32 cow V1R genes in the cow genome database. We found that all of the goat and sheep V1R genes have orthologs in their cross-species counterparts among these three ruminant species and that the sequence identity of V1R orthologous pairs among these ruminants is much higher than that of mouse-rat V1R orthologous pairs. Furthermore, all goat V1Rs examined thus far are expressed not only in the vomeronasal organ but also in the main olfactory epithelium. Conclusion Our results suggest that, compared with rodents, the repertoire of orthologous V1R genes is remarkably conserved among the ruminants cow, sheep and goat. We predict that these orthologous V1Rs can detect the same or closely related chemical compound(s within each orthologous set/pair. Furthermore, all identified goat V1Rs are expressed in the vomeronasal organ and the main olfactory epithelium, suggesting that V1R-mediated ligand information can be detected and processed by both the main and accessory olfactory systems. The fact that ruminant and rodent V1Rs
Wolf Yuri I
Full Text Available Abstract Background An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs. Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes. Results New Archaeal Clusters of Orthologous Genes (arCOGs were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for identification of remote orthologs. The annotation of arCOGs is a consensus between three assignments based on the COGs, the CDD database, and the annotations of homologs in the NR database. The 7538 arCOGs, on average, cover ~88% of the genes in a genome compared to a ~76% coverage in COGs. The finer granularity of ortholog identification in the arCOGs is apparent from the fact that 4538 arCOGs correspond to 2362 COGs; ~40% of the arCOGs are new. The archaeal gene core (protein-coding genes found in all 41 genome consists of 166 arCOGs. The arCOGs were used to reconstruct gene loss and gene gain events during archaeal evolution and gene sets of ancestral forms. The Last Archaeal Common Ancestor (LACA is conservatively estimated to possess 996 genes compared to 1245 and 1335 genes for the last common ancestors of Crenarchaeota and Euryarchaeota, respectively. It is inferred that LACA was a chemoautotrophic hyperthermophile
IONS: Identification of Orthologs by Neighborhood and Similarity—an Automated Method to Identify Orthologs in Chromosomal Regions of Common Evolutionary Ancestry and its Application to Hemiascomycetous Yeasts
Seret, Marie-Line; Baret, Philippe V.
Comparative sequence analysis is widely used to infer gene function and study genome evolution and requires proper ortholog identification across different genomes. We have developed a program for the Identification of Orthologs in one-to-one relationship by Neighborhood and Similarity (IONS) between closely related species. The algorithm combines two levels of evidence to determine co-ancestrality at the genome scale: sequence similarity and shared neighborhood. The method was initially designed to provide anchor points for syntenic blocks within the Génolevures project concerning nine hemiascomycetous yeasts (about 50,000 genes) and is applicable to different input databases. Comparison based on use of a Rand index shows that the results are highly consistent with the pillars of the Yeast Gene Order Browser, a manually curated database. Compared with SYNERGY, another algorithm reporting homology relationships, our method’s main advantages are its automation and the absence of dataset-dependent parameters, facilitating consistent integration of newly released genomes. PMID:21918595
Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD
This paper considers the impact of visual art and performance on robotics and human-computer interaction and outlines a research project that combines puppetry and live performance with robotics. Kinesics—communication through movement—is the foundation of many theatre and performance traditions ...
Brandon W. Carr
Full Text Available Zipper-interacting protein kinase (ZIPK is a conserved vertebrate-specific regulator of actomyosin contractility in smooth muscle and non-muscle cells. Murine ZIPK has undergone an unusual divergence in sequence and regulation compared to other ZIPK orthologs. In humans, subcellular localization is controlled by phosphorylation of threonines 299 and 300. In contrast, ZIPK subcellular localization in mouse and rat is controlled by interaction with PAR-4. We carried out a comparative biochemical characterization of the regulation of the zebrafish ortholog of ZIPK. Like the human orthologs zebrafish ZIPK undergoes nucleocytoplasmic-shuttling and is abundant in the cytoplasm, unlike the primarily nuclear rat ZIPK. Rat ZIPK, but not human or zebrafish ZIPK, interacts with zebrafish PAR-4. Mutation of the conserved residues required for activation of the mammalian orthologs abrogated activity of the zebrafish ZIPK. In contrast to the human ortholog, mutation of threonine 299 and 300 in the zebrafish ZIPK has no effect on the activity or subcellular localization. Thus, we found that zebrafish ZIPK functions in a manner most similar to the human ZIPK and quite distinct from murine orthologs, yet the regulation of subcellular localization is not conserved.
Full Text Available BOG (Bacterium and virus analysis of Orthologous Groups is a package for identifying groups of differentially regulated genes in the light of gene functions for various virus and bacteria genomes. It is designed to identify Clusters of Orthologous Groups (COGs that are enriched among genes that have gone through significant changes under different conditions. This would contribute to the detection of pathogens, an important scientific research area of relevance in uncovering bioterrorism, among others. Particular statistical analyses include hypergeometric, Mann–Whitney rank sum, and gene set enrichment. Results from the analyses are organized and presented in tabular and graphical forms for ease of understanding and dissemination of results. BOG is implemented as an R-package, which is available from CRAN or can be downloaded from http://www.stat.osu.edu/~statgen/SOFTWARE/BOG/.
Nicholas J Marini
Full Text Available Computational predictions of the functional impact of genetic variation play a critical role in human genetics research. For nonsynonymous coding variants, most prediction algorithms make use of patterns of amino acid substitutions observed among homologous proteins at a given site. In particular, substitutions observed in orthologous proteins from other species are often assumed to be tolerated in the human protein as well. We examined this assumption by evaluating a panel of nonsynonymous mutants of a prototypical human enzyme, methylenetetrahydrofolate reductase (MTHFR, in a yeast cell-based functional assay. As expected, substitutions in human MTHFR at sites that are well-conserved across distant orthologs result in an impaired enzyme, while substitutions present in recently diverged sequences (including a 9-site mutant that "resurrects" the human-macaque ancestor result in a functional enzyme. We also interrogated 30 sites with varying degrees of conservation by creating substitutions in the human enzyme that are accepted in at least one ortholog of MTHFR. Quite surprisingly, most of these substitutions were deleterious to the human enzyme. The results suggest that selective constraints vary between phylogenetic lineages such that inclusion of distant orthologs to infer selective pressures on the human enzyme may be misleading. We propose that homologous proteins are best used to reconstruct ancestral sequences and infer amino acid conservation among only direct lineal ancestors of a particular protein. We show that such an "ancestral site preservation" measure outperforms other prediction methods, not only in our selected set for MTHFR, but also in an exhaustive set of E. coli LacI mutants.
Moreira, Maria-Céu; Klur, Sandra; Watanabe, Mitsunori; Németh, Andrea H; Le Ber, Isabelle; Moniz, José-Carlos; Tranchant, Christine; Aubourg, Patrick; Tazir, Meriem; Schöls, Lüdger; Pandolfo, Massimo; Schulz, Jörg B; Pouget, Jean; Calvas, Patrick; Shizuka-Ikeda, Masami; Shoji, Mikio; Tanaka, Makoto; Izatt, Louise; Shaw, Christopher E; M'Zahem, Abderrahim; Dunne, Eimear; Bomont, Pascale; Benhassine, Traki; Bouslam, Naïma; Stevanin, Giovanni; Brice, Alexis; Guimarães, João; Mendonça, Pedro; Barbot, Clara; Coutinho, Paula; Sequeiros, Jorge; Dürr, Alexandra; Warter, Jean-Marie; Koenig, Michel
Ataxia-ocular apraxia 2 (AOA2) was recently identified as a new autosomal recessive ataxia. We have now identified causative mutations in 15 families, which allows us to clinically define this entity by onset between 10 and 22 years, cerebellar atrophy, axonal sensorimotor neuropathy, oculomotor apraxia and elevated alpha-fetoprotein (AFP). Ten of the fifteen mutations cause premature termination of a large DEAxQ-box helicase, the human ortholog of yeast Sen1p, involved in RNA maturation and termination.
Bruno T. L. Nichio; Jeroniza Nunes Marchaukoski; Roberto Tadeu Raittz
Nowadays defying homology relationships among sequences is essential for biological research. Within homology the analysis of orthologs sequences is of great importance for computational biology, annotation of genomes and for phylogenetic inference. Since 2007, with the increase in the number of new sequences being deposited in large biological databases, researchers have begun to analyse computerized methodologies and tools aimed at selecting the most promising ones in the prediction of orth...
Lechner, Marcus; Findeiß, Sven; Steiner, Lydia; Marz, Manja; Stadler, Peter F; Prohaska, Sonja J
Abstract Background Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes i...
Fujiwara, Shoko; Takatsuka, Yukiko; Hirokawa, Yasutaka; Tsuzuki, Mikio; Takano, Tomoyuki; Kobayashi, Masaaki; Suda, Kunihiro; Asamizu, Erika; Yokoyama, Koji; Shibata, Daisuke; Tabata, Satoshi; Yano, Kentaro
Pleurochrysis is a coccolithophorid genus, which belongs to the Coccolithales in the Haptophyta. The genus has been used extensively for biological research, together with Emiliania in the Isochrysidales, to understand distinctive features between the two coccolithophorid-including orders. However, molecular biological research on Pleurochrysis such as elucidation of the molecular mechanism behind coccolith formation has not made great progress at least in part because of lack of comprehensive gene information. To provide such information to the research community, we built an open web database, the Pleurochrysome (http://bioinf.mind.meiji.ac.jp/phapt/), which currently stores 9,023 unique gene sequences (designated as UNIGENEs) assembled from expressed sequence tag sequences of P. haptonemofera as core information. The UNIGENEs were annotated with gene sequences sharing significant homology, conserved domains, Gene Ontology, KEGG Orthology, predicted subcellular localization, open reading frames and orthologous relationship with genes of 10 other algal species, a cyanobacterium and the yeast Saccharomyces cerevisiae. This sequence and annotation information can be easily accessed via several search functions. Besides fundamental functions such as BLAST and keyword searches, this database also offers search functions to explore orthologous genes in the 12 organisms and to seek novel genes. The Pleurochrysome will promote molecular biological and phylogenetic research on coccolithophorids and other haptophytes by helping scientists mine data from the primary transcriptome of P. haptonemofera. PMID:26746174
Medvedeva, Irina V; Demenkov, Pavel S; Ivanisenko, Vladimir A
Functional sites define the diversity of protein functions and are the central object of research of the structural and functional organization of proteins. The mechanisms underlying protein functional sites emergence and their variability during evolution are distinguished by duplication, shuffling, insertion and deletion of the exons in genes. The study of the correlation between a site structure and exon structure serves as the basis for the in-depth understanding of sites organization. In this regard, the development of programming resources that allow the realization of the mutual projection of exon structure of genes and primary and tertiary structures of encoded proteins is still the actual problem. Previously, we developed the SitEx system that provides information about protein and gene sequences with mapped exon borders and protein functional sites amino acid positions. The database included information on proteins with known 3D structure. However, data with respect to orthologs was not available. Therefore, we added the projection of sites positions to the exon structures of orthologs in SitEx 2.0. We implemented a search through database using site conservation variability and site discontinuity through exon structure. Inclusion of the information on orthologs allowed to expand the possibilities of SitEx usage for solving problems regarding the analysis of the structural and functional organization of proteins. Database URL: http://www-bionet.sscc.ru/sitex/ .
Lentz, Christian S; Halls, Victoria S; Hannam, Jeffrey S; Strassel, Silke; Lawrence, Sarah H; Jaffe, Eileen K; Famulok, Michael; Hoerauf, Achim; Pfarr, Kenneth M
The heme biosynthesis enzyme porphobilinogen synthase (PBGS) is a potential drug target in several human pathogens. wALADin1 benzimidazoles have emerged as species-selective PBGS inhibitors against Wolbachia endobacteria of filarial worms. In the present study, we have systematically tested wALADins against PBGS orthologs from bacteria, protozoa, metazoa, and plants to elucidate the inhibitory spectrum. However, the effect of wALADin1 on different PBGS orthologs was not limited to inhibition: several orthologs were stimulated by wALADin1; others remained unaffected. We demonstrate that wALADins allosterically modulate the PBGS homooligomeric equilibrium with inhibition mediated by favoring low-activity oligomers, while 5-aminolevulinic acid, Mg(2+), or K(+) stabilized high-activity oligomers. Pseudomonas aeruginosa PBGS could be inhibited or stimulated by wALADin1 depending on these factors and pH. We have defined the wALADin chemotypes responsible for either inhibition or stimulation, facilitating the design of tailored PBGS modulators for potential application as antimicrobial agents, herbicides, or drugs for porphyric disorders.
Goodstadt, Leo; Ponting, Chris P
Accurate predictions of orthology and paralogy relationships are necessary to infer human molecular function from experiments in model organisms. Previous genome-scale approaches to predicting these relationships have been limited by their use of protein similarity and their failure to take into account multiple splicing events and gene prediction errors. We have developed PhyOP, a new phylogenetic orthology prediction pipeline based on synonymous rate estimates, which accurately predicts orthology and paralogy relationships for transcripts, genes, exons, or genomic segments between closely related genomes. We were able to identify orthologue relationships to human genes for 93% of all dog genes from Ensembl. Among 1:1 orthologues, the alignments covered a median of 97.4% of protein sequences, and 92% of orthologues shared essentially identical gene structures. PhyOP accurately recapitulated genomic maps of conserved synteny. Benchmarking against predictions from Ensembl and Inparanoid showed that PhyOP is more accurate, especially in its predictions of paralogy. Nearly half (46%) of PhyOP paralogy predictions are unique. Using PhyOP to investigate orthologues and paralogues in the human and dog genomes, we found that the human assembly contains 3-fold more gene duplications than the dog. Species-specific duplicate genes, or "in-paralogues," are generally shorter and have fewer exons than 1:1 orthologues, which is consistent with selective constraints and mutation biases based on the sizes of duplicated genes. In-paralogues have experienced elevated amino acid and synonymous nucleotide substitution rates. Duplicates possess similar biological functions for either the dog or human lineages. Having accounted for 2,954 likely pseudogenes and gene fragments, and after separating 346 erroneously merged genes, we estimated that the human genome encodes a minimum of 19,700 protein-coding genes, similar to the gene count of nematode worms. PhyOP is a fast and robust
Full Text Available Accurate predictions of orthology and paralogy relationships are necessary to infer human molecular function from experiments in model organisms. Previous genome-scale approaches to predicting these relationships have been limited by their use of protein similarity and their failure to take into account multiple splicing events and gene prediction errors. We have developed PhyOP, a new phylogenetic orthology prediction pipeline based on synonymous rate estimates, which accurately predicts orthology and paralogy relationships for transcripts, genes, exons, or genomic segments between closely related genomes. We were able to identify orthologue relationships to human genes for 93% of all dog genes from Ensembl. Among 1:1 orthologues, the alignments covered a median of 97.4% of protein sequences, and 92% of orthologues shared essentially identical gene structures. PhyOP accurately recapitulated genomic maps of conserved synteny. Benchmarking against predictions from Ensembl and Inparanoid showed that PhyOP is more accurate, especially in its predictions of paralogy. Nearly half (46% of PhyOP paralogy predictions are unique. Using PhyOP to investigate orthologues and paralogues in the human and dog genomes, we found that the human assembly contains 3-fold more gene duplications than the dog. Species-specific duplicate genes, or "in-paralogues," are generally shorter and have fewer exons than 1:1 orthologues, which is consistent with selective constraints and mutation biases based on the sizes of duplicated genes. In-paralogues have experienced elevated amino acid and synonymous nucleotide substitution rates. Duplicates possess similar biological functions for either the dog or human lineages. Having accounted for 2,954 likely pseudogenes and gene fragments, and after separating 346 erroneously merged genes, we estimated that the human genome encodes a minimum of 19,700 protein-coding genes, similar to the gene count of nematode worms. PhyOP is a
Kriventseva, Evgenia V; Tegenfeldt, Fredrik; Petty, Tom J; Waterhouse, Robert M; Simão, Felipe A; Pozdnyakov, Igor A; Ioannidis, Panagiotis; Zdobnov, Evgeny M
Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the OrthoDB hierarchical catalog of orthologs (http://www.orthodb.org) covers 3027 complete genomes, including the most comprehensive set of 87 arthropods, 61 vertebrates, 227 fungi and 2627 bacteria (sampling the most complete and representative genomes from over 11,000 available). In addition to the most extensive integration of functional annotations from UniProt, InterPro, GO, OMIM, model organism phenotypes and COG functional categories, OrthoDB uniquely provides evolutionary annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups and gene architectures. We re-designed the entirety of the OrthoDB website from the underlying technology to the user interface, enabling the user to specify species of interest and to select the relevant orthology level by the NCBI taxonomy. The text searches allow use of complex logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases. Gene copy-number profiles can also be queried. This release comes with the freely available underlying ortholog clustering pipeline (http://www.orthodb.org/software). © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
OhEigeartaigh, Sean S
Abstract Background In standard BLAST searches, no information other than the sequences of the query and the database entries is considered. However, in situations where two genes from different species have only borderline similarity in a BLAST search, the discovery that the genes are located within a region of conserved gene order (synteny) can provide additional evidence that they are orthologs. Thus, for interpreting borderline search results, it would be useful to know whether the syntenic context of a database hit is similar to that of the query. This principle has often been used in investigations of particular genes or genomic regions, but to our knowledge it has never been implemented systematically. Results We made use of the synteny information contained in the Yeast Gene Order Browser database for 11 yeast species to carry out a systematic search for protein-coding genes that were overlooked in the original annotations of one or more yeast genomes but which are syntenic with their orthologs. Such genes tend to have been overlooked because they are short, highly divergent, or contain introns. The key features of our software - called SearchDOGS - are that the database entries are classified into sets of genomic segments that are already known to be orthologous, and that very weak BLAST hits are retained for further analysis if their genomic location is similar to that of the query. Using SearchDOGS we identified 595 additional protein-coding genes among the 11 yeast species, including two new genes in Saccharomyces cerevisiae. We found additional genes for the mating pheromone a-factor in six species including Kluyveromyces lactis. Conclusions SearchDOGS has proven highly successful for identifying overlooked genes in the yeast genomes. We anticipate that our approach can be adapted for study of further groups of species, such as bacterial genomes. More generally, the concept of doing sequence similarity searches against databases to which external
Cabrera, Antonio; Kozik, Alex; Howad, Werner; Arus, Pere; Iezzoni, Amy F; van der Knaap, Esther
Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple), Fragaria (strawberry), and Prunus (peach, cherry, apricot and almond)]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies. We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS), 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae. Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. Moreover, these markers will also function as useful anchor points for the genome sequencing efforts currently ongoing in this family as well as for comparative QTL
Atambayeva, Shara; Niyazova, Raigul; Ivashchenko, Anatoliy; Pyrkova, Anna; Pinsky, Ilya; Akimniyazova, Aigul; Labeit, Siegfried
Normally, one miRNA interacts with the mRNA of one gene. However, there are miRNAs that can bind to many mRNAs, and one mRNA can be the target of many miRNAs. This significantly complicates the study of the properties of miRNAs and their diagnostic and medical applications. The search of 2,750 human microRNAs (miRNAs) binding sites in 12,175 mRNAs of human genes using the MirTarget program has been completed. For the binding sites of the miR-619-5p the hybridization free energy of the bonds was equal to 100% of the maximum potential free energy. The mRNAs of 201 human genes have complete complementary binding sites of miR-619-5p in the 3'UTR (214 sites), CDS (3 sites), and 5'UTR (4 sites). The mRNAs of CATAD1, ICA1L, GK5, POLH, and PRR11 genes have six miR-619-5p binding sites, and the mRNAs of OPA3 and CYP20A1 genes have eight and ten binding sites, respectively. All of these miR-619-5p binding sites are located in the 3'UTRs. The miR-619-5p binding site in the 5'UTR of mRNA of human USP29 gene is found in the mRNAs of orthologous genes of primates. Binding sites of miR-619-5p in the coding regions of mRNAs of C8H8orf44, C8orf44, and ISY1 genes encode the WLMPVIP oligopeptide, which is present in the orthologous proteins. Binding sites of miR-619-5p in the mRNAs of transcription factor genes ZNF429 and ZNF429 encode the AHACNP oligopeptide in another reading frame. Binding sites of miR-619-5p in the 3'UTRs of all human target genes are also present in the 3'UTRs of orthologous genes of mammals. The completely complementary binding sites for miR-619-5p are conservative in the orthologous mammalian genes. The majority of miR-619-5p binding sites are located in the 3'UTRs but some genes have miRNA binding sites in the 5'UTRs of mRNAs. Several genes have binding sites for miRNAs in the CDSs that are read in different open reading frames. Identical nucleotide sequences of binding sites encode different amino acids in different proteins. The binding sites of miR-619-5p
Miñarro-Gimenez, Jose Antonio; Egaña Aranguren, Mikel; Martínez Béjar, Rodrigo; Fernández-Breis, Jesualdo Tomás; Madrid, Marisa
Semantic Web technologies like RDF and OWL are currently applied in life sciences to improve knowledge management by integrating disparate information. Many of the systems that perform such task, however, only offer a SPARQL query interface, which is difficult to use for life scientists. We present the OGO system, which consists of a knowledge base that integrates information of orthologous sequences and genetic diseases, providing an easy to use ontology-constrain driven query interface. Such interface allows the users to define SPARQL queries through a graphical process, therefore not requiring SPARQL expertise. Copyright © 2011 Elsevier Inc. All rights reserved.
Full Text Available Eggplant, pepper and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage.Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits.The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp.Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation.In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10% affecting key agronomic traits. Most were confirmed to cluster in
of these two genes with all other genes of the other one species. In addition, to be considered orthologs, the BBH pairs had to satisfy two conditions ...BBH pair computations employed as part of the outgroup and QuartetS methods, we used the same two conditions as the ones described above. In our...versus proteins. Genetica , 118, 209–216. 4. Serres,M.H., Kerr,A.R., McCormack,T.J. and Riley,M. (2009) Evolution by leaps: gene duplication in bacteria
Full Text Available List Contact us PGDBj - Ortholog DB License License to Use This Database Last updated : 2017/03/07 You may use this database...cifies the license terms regarding the use of this database and the requirements you must follow in using this database.... The license for this database is specified in the Creative Commons A...ttribution-Share Alike 4.0 International . If you use data from this database, please be sure attribute this database...hare Alike 4.0 International is found here . With regard to this database, you are licensed to: freely acces
Makarova, Kira; Wolf, Yuri; Koonin, Eugene
With the continuously accelerating genome sequencing from diverse groups of archaea and bacteria, accurate identification of gene orthology and availability of readily expandable clusters of orthologous genes are essential for the functional annotation of new genomes. We report an update of the collection of archaeal Clusters of Orthologous Genes (arCOGs) to cover, on average, 91% of the protein-coding genes in 168 archaeal genomes. The new arCOGs were constructed using refined algorithms for...
Chitta, Mohan S; Duhé, Roy J; Kermode, John C
Interaction of von Willebrand factor (VWF) with circulating platelets promotes hemostasis when a blood vessel is injured. The A1 domain of VWF is responsible for the initial interaction with platelets and is well conserved among species. Knowledge of the cDNA and genomic DNA sequences for human VWF allowed us to predict the cDNA sequence for murine VWF in silico and amplify its entire coding region by RT-PCR. The murine VWF cDNA has an open reading frame of 8,442 bp, encoding a protein of 2,813 amino acid residues with 83% identity to human pre-pro-VWF. The same strategy was used to predict in silico the cDNA sequence for the ortholog of VWF in a further six species. Many of these predictions diverged substantially from the putative Reference Sequences derived by ab initio methods. Our predicted sequences indicated that the VWF gene has a conserved structure of 52 exons in all seven mammalian species examined, as well as in the chicken. There is a minor structural variation in the pufferfish Takifugu rubripes insofar as the VWF gene in this species has 53 exons. Comparison of the translated amino acid sequences also revealed a high degree of conservation. In particular, the cysteine residues are conserved precisely throughout both the pro-peptide and the mature VWF sequence in all species, with a minor exception in the pufferfish VWF ortholog where two adjacent cysteine residues are omitted. The marked conservation of cysteine residues emphasizes the importance of the intricate pattern of disulfide bonds in governing the structure of pro-VWF and regulating the function of the mature VWF protein. It should also be emphasized that many of the conserved features of the VWF gene and protein were obscured when the comparison among species was based on the putative Reference Sequences instead of our predicted cDNA sequences.
Zielezinski, Andrzej; Dziubek, Michal; Sliski, Jan; Karlowski, Wojciech M
ORCAN (ORtholog sCANner) is a web-based meta-server for one-click evolutionary and functional annotation of protein sequences. The server combines information from the most popular orthology-prediction resources, including four tools and four online databases. Functional annotation utilizes five additional comparisons between the query and identified homologs, including: sequence similarity, protein domain architectures, functional motifs, Gene Ontology term assignments and a list of associated articles. Furthermore, the server uses a plurality-based rating system to evaluate the orthology relationships and to rank the reference proteins by their evolutionary and functional relevance to the query. Using a dataset of ∼1 million true yeast orthologs as a sample reference set, we show that combining multiple orthology-prediction tools in ORCAN increases the sensitivity and precision by 1-2 percent points. The service is available for free at http://www.combio.pl/orcan/ . email@example.com. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: firstname.lastname@example.org
Cenci, Albero; Guignon, Valentin; Roux, Nicolas; Rouard, Mathieu
Identifying the molecular mechanisms underlying tolerance to abiotic stresses is important in crop breeding. A comprehensive understanding of the gene families associated with drought tolerance is therefore highly relevant. NAC transcription factors form a large plant-specific gene family involved in the regulation of tissue development and responses to biotic and abiotic stresses. The main goal of this study was to set up a framework of orthologous groups determined by an expert sequence comparison of NAC genes from both monocots and dicots. In order to clarify the orthologous relationships among NAC genes of different species, we performed an in-depth comparative study of four divergent taxa, in dicots and monocots, whose genomes have already been completely sequenced: Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa. Due to independent evolution, NAC copy number is highly variable in these plant genomes. Based on an expert NAC sequence comparison, we propose forty orthologous groups of NAC sequences that were probably derived from an ancestor gene present in the most recent common ancestor of dicots and monocots. These orthologous groups provide a curated resource for large-scale protein sequence annotation of NAC transcription factors. The established orthology relationships also provide a useful reference for NAC function studies in newly sequenced genomes such as M. acuminata and other plant species.
Huson, Daniel H; Tappu, Rewati; Bazinet, Adam L; Xie, Chao; Cummings, Michael P; Nieselt, Kay; Williams, Rohan
Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. However, for some questions, only specific genes of interest need to be assembled. This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes. We present a new method for performing gene-centric assembly, called protein-alignment-guided assembly, and provide an implementation in our metagenome analysis tool MEGAN. Genes are assembled on the fly, based on the alignment of all reads against a protein reference database such as NCBI-nr. Specifically, the user selects a gene family based on a classification such as KEGG and all reads binned to that gene family are assembled. Using published synthetic community metagenome sequencing reads and a set of 41 gene families, we show that the performance of this approach compares favorably with that of full-featured assemblers and that of a recently published HMM-based gene-centric assembler, both in terms of the number of reference genes detected and of the percentage of reference sequence covered. Protein-alignment-guided assembly of orthologous gene families complements whole-metagenome assembly in a new and very useful way.
Yang, Xiaowen; Wang, Jiawei; Bing, Guoxia; Bie, Pengfei; De, Yanyan; Lyu, Yanli; Wu, Qingmin
Bioinformatics and comparative genomics analysis methods were used to predict unknown pathogen genes based on homology with identified or functionally clustered genes. In this study, the genes of common pathogens were analyzed to screen and identify genes associated with intracellular survival through sequence similarity, phylogenetic tree analysis and the λ-Red recombination system test method. The total 38,952 protein-coding genes of common pathogens were divided into 19,775 clusters. As demonstrated through a COG analysis, information storage and processing genes might play an important role intracellular survival. Only 19 clusters were present in facultative intracellular pathogens, and not all were present in extracellular pathogens. Construction of a phylogenetic tree selected 18 of these 19 clusters. Comparisons with the DEG database and previous research revealed that seven other clusters are considered essential gene clusters and that seven other clusters are associated with intracellular survival. Moreover, this study confirmed that clusters screened by orthologs with similar function could be replaced with an approved uvrY gene and its orthologs, and the results revealed that the usg gene is associated with intracellular survival. The study improves the current understanding of intracellular pathogens characteristics and allows further exploration of the intracellular survival-related gene modules in these pathogens. Copyright © 2018. Published by Elsevier B.V.
Costafreda, Maria Isabel; Kaplan, Gerardo
The hepatitis A virus (HAV) cellular receptor 1 (HAVCR1), classified as CD365, was initially discovered as an HAV cellular receptor using an expression cloning strategy. Due to the lack of HAV receptor-negative replication-competent cells, it was not possible to fully prove that HAVCR1 was a functional HAV receptor. However, biochemistry, classical virology, and epidemiology studies further supported the functional role of HAVCR1 as an HAV receptor. Here, we show that an anti-HAVCR1 monoclonal antibody that protected African green monkey kidney (AGMK) cells against HAV infection only partially protected monkey Vero E6 cells and human hepatoma Huh7 cells, indicating that these two cell lines express alternative yet unidentified HAV receptors. Therefore, we focused our work on AGMK cells to further characterize the function of HAVCR1 as an HAV receptor. Advances in clustered regularly interspaced short palindromic repeat/Cas9 technology allowed us to knock out the monkey ortholog of HAVCR1 in AGMK cells. The resulting AGMK HAVCR1 knockout (KO) cells lost susceptibility to HAV infection, including HAV-free viral particles (vpHAV) and exosomes purified from HAV-infected cells (exo-HAV). Transfection of HAVCR1 cDNA into AGMK HAVCR1 KO cells restored susceptibility to vpHAV and exo-HAV infection. Furthermore, transfection of the mouse ortholog of HAVCR1, mHavcr1, also restored the susceptibility of AGMK HAVCR1 KO cells to HAV infection. Taken together, our data clearly show that HAVCR1 and mHavcr1 are functional HAV receptors that mediate HAV infection. This work paves the way for the identification of alternative HAV receptors to gain a complete understanding of their interplay with HAVCR1 in the cell entry and pathogenic processes of HAV. IMPORTANCE HAVCR1, an HAV receptor, is expressed in different cell types, including regulatory immune cells and antigen-presenting cells. How HAV evades the immune response during a long incubation period of up to 4 weeks and the
Paul D Thomas
Full Text Available A recent paper (Nehrt et al., PLoS Comput. Biol. 7:e1002073, 2011 has proposed a metric for the "functional similarity" between two genes that uses only the Gene Ontology (GO annotations directly derived from published experimental results. Applying this metric, the authors concluded that paralogous genes within the mouse genome or the human genome are more functionally similar on average than orthologous genes between these genomes, an unexpected result with broad implications if true. We suggest, based on both theoretical and empirical considerations, that this proposed metric should not be interpreted as a functional similarity, and therefore cannot be used to support any conclusions about the "ortholog conjecture" (or, more properly, the "ortholog functional conservation hypothesis". First, we reexamine the case studies presented by Nehrt et al. as examples of orthologs with divergent functions, and come to a very different conclusion: they actually exemplify how GO annotations for orthologous genes provide complementary information about conserved biological functions. We then show that there is a global ascertainment bias in the experiment-based GO annotations for human and mouse genes: particular types of experiments tend to be performed in different model organisms. We conclude that the reported statistical differences in annotations between pairs of orthologous genes do not reflect differences in biological function, but rather complementarity in experimental approaches. Our results underscore two general considerations for researchers proposing novel types of analysis based on the GO: 1 that GO annotations are often incomplete, potentially in a biased manner, and subject to an "open world assumption" (absence of an annotation does not imply absence of a function, and 2 that conclusions drawn from a novel, large-scale GO analysis should whenever possible be supported by careful, in-depth examination of examples, to help ensure the
Schaub, Christoph; Nagaso, Hideyuki; Jin, Hong; Frasch, Manfred
Members of the T-Box gene family of transcription factors are important players in regulatory circuits that generate myogenic and cardiogenic lineage diversities in vertebrates. We show that during somatic myogenesis in Drosophila, the single ortholog of vertebrate Tbx1, optomotor-blind-related-gene-1 (org-1), is expressed in a small subset of muscle progenitors, founder cells and adult muscle precursors, where it overlaps with the products of the muscle identity genes ladybird (lb) and slouch (slou). In addition, org-1 is expressed in the lineage of the heart-associated alary muscles. org-1 null mutant embryos lack Lb and Slou expression within the muscle lineages that normally co-express org-1. As a consequence, the respective muscle fibers and adult muscle precursors are either severely malformed or missing, as are the alary muscles. To address the mechanisms that mediate these regulatory interactions between Org-1, Lb and Slou, we characterized distinct enhancers associated with somatic muscle expression of lb and slou. We demonstrate that these lineage- and stage-specific cis-regulatory modules (CRMs) bind Org-1 in vivo, respond to org-1 genetically and require T-box domain binding sites for their activation. In summary, we propose that org-1 is a common and direct upstream regulator of slou and lb in the developmental pathway of these two neighboring muscle lineages. Cross-repression between slou and lb and combinatorial activation of lineage-specific targets by Org-1-Slou and Org-1-Lb, respectively, then leads to the distinction between the two lineages. These findings provide new insights into the regulatory circuits that control the proper pattering of the larval somatic musculature in Drosophila.
Hurni, Severine; Brunner, Susanne; Stirnweis, Daniel; Herren, Gerhard; Peditto, David; McIntosh, Robert A; Keller, Beat
The powdery mildew resistance gene Pm8 derived from rye is located on a 1BL.1RS chromosome translocation in wheat. However, some wheat lines with this translocation do not show resistance to isolates of the wheat powdery mildew pathogen avirulent to Pm8 due to an unknown genetically dominant suppression mechanism. Here we show that lines with suppressed Pm8 activity contain an intact and expressed Pm8 gene. Therefore, the absence of Pm8 function in certain 1BL.1RS-containing wheat lines is not the result of gene loss or mutation but is based on suppression. The wheat gene Pm3, an ortholog of rye Pm8, suppressed Pm8-mediated powdery mildew resistance in lines containing Pm8 in a transient single-cell expression assay. This result was further confirmed in transgenic lines with combined Pm8 and Pm3 transgenes. Expression analysis revealed that suppression is not the result of gene silencing, either in wheat 1BL.1RS translocation lines carrying Pm8 or in transgenic genotypes with both Pm8 and Pm3 alleles. In addition, a similar abundance of the PM8 and PM3 proteins in single or double homozygous transgenic lines suggested that a post-translational mechanism is involved in suppression of Pm8. Co-expression of Pm8 and Pm3 genes in Nicotiana benthamiana leaves followed by co-immunoprecipitation analysis showed that the two proteins interact. Therefore, the formation of a heteromeric protein complex might result in inefficient or absent signal transmission for the defense reaction. These data provide a molecular explanation for the suppression of resistance genes in certain genetic backgrounds and suggest ways to circumvent it in future plant breeding. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.
Full Text Available The phytophagous mirid bugs of Apolygus lucorum, Lygus pratensis as well as three Adelphocoris spp., including Adelphocoris lineolatus, A. suturalis, and A. fasciaticollis are major pests of multiple agricultural crops in China, which have distinct geographical distribution and occurrence ranges. Like many insect species, these bugs heavily rely on olfactory cues to search preferred host plants, thereby investigation on functional co-evolution and divergence of olfactory genes seems to be necessary and is of great interest. In the odorant detection pathway, olfactory receptor co-receptor (Orco plays critical role in the perception of odors. In this study, we identified the full-length cDNA sequences encoding three putative Orcos (AsutOrco, AfasOrco, and LpraOrco in bug species of A. suturalis, A. fasciaticollis, and L. pratensis based on homology cloning method. Next, sequence alignment, membrane topology and gene structure analysis showed that these three Orco orthologs together with previously reported AlinOrco and AlucOrco shared high amino acid identities and similar topology structure, but had different gene structure especially at the length and insertion sites of introns. Furthermore, the evolutional estimation on the ratios of non-synonymous to synonymous (Ka/Ks revealed that Orco genes were under strong purifying selection, but the degrees of variation were significant different between genera. The results of quantitative real-time PCR experiments showed that these five Orco genes had a similar antennae-biased tissue expression pattern. Taking these data together, it is thought that Orco genes in the mirid species could share conserved olfaction roles but had different evolution rates. These findings would lay a foundation to further investigate the molecular mechanisms of evolutionary interactions between mirid bugs and their host plants, which might in turn contribute to the development of pest management strategy for mirid bugs.
Full Text Available Abstract Background Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple, Fragaria (strawberry, and Prunus (peach, cherry, apricot and almond]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies. Results We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS, 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae. Conclusion Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. Moreover, these markers will also function as useful anchor points for the genome sequencing efforts currently
Full Text Available AtDIR1 (Defective in Induced Resistance1 is an acidic lipid transfer protein essential for systemic acquired resistance (SAR in Arabidopsis thaliana. Upon SAR induction, DIR1 moves from locally infected to distant uninfected leaves to activate defense priming; however, a molecular function for DIR1 has not been elucidated. Bioinformatic analysis and in silico homology modeling identified putative AtDIR1 orthologs in crop species, revealing conserved protein motifs within and outside of DIR1’s central hydrophobic cavity. In vitro assays to compare the capacity of recombinant AtDIR1 and targeted AtDIR1-variant proteins to bind the lipophilic probe TNS (6,P-toluidinylnaphthalene-2-sulfonate provided evidence that conserved leucine 43 and aspartic acid 39 contribute to the size of the DIR1 hydrophobic cavity and possibly hydrophobic ligand binding. An Arabidopsis–cucumber SAR model was developed to investigate the conservation of DIR1 function in cucumber (Cucumis sativus, and we demonstrated that phloem exudates from SAR-induced cucumber rescued the SAR defect in the Arabidopsis dir1-1 mutant. Additionally, an AtDIR1 antibody detected a protein of the same size as AtDIR1 in SAR-induced cucumber phloem exudates, providing evidence that DIR1 function during SAR is conserved in Arabidopsis and cucumber. In vitro TNS displacement assays demonstrated that recombinant AtDIR1 did not bind the SAR signals azelaic acid (AzA, glycerol-3-phosphate or pipecolic acid. However, recombinant CsDIR1 and CsDIR2 interacted weakly with AzA and pipecolic acid. Bioinformatic and functional analyses using the Arabidopsis–cucumber SAR model provide evidence that DIR1 orthologs exist in tobacco, tomato, cucumber, and soybean, and that DIR1-mediated SAR signaling is conserved in Arabidopsis and cucumber.
Ondracek, Caitlin R; Frappier, Vincent; Ringel, Alison E; Wolberger, Cynthia; Guarente, Leonard
Sirtuin enzymes depend on NAD + to catalyze protein deacetylation. Therefore, the lowering of NAD + during aging leads to decreased sirtuin activity and may speed up aging processes in laboratory animals and humans. In this study, we used a genetic screen to identify two mutations in the catalytic domain of yeast Sir2 that allow the enzyme to function in an NAD + -depleted environment. These mutant enzymes give rise to a significant increase of yeast replicative lifespan and increase deacetylation by the Sir2 ortholog, SIRT1, in mammalian cells. Our data suggest that these mutations increase the stability of the conserved catalytic sirtuin domain, thereby increasing the catalytic efficiency of the mutant enzymes. Our approach to identifying sirtuin mutants that permit function in NAD + -limited environments may inform the design of small molecules that can maintain sirtuin activity in aging organisms. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
Flor-Parra, Ignacio; Iglesias-Romero, Ana Belén; Chang, Fred
The organization and number of microtubules (MTs) in a cell depend on the proper regulation of MT nucleation. Currently, the mechanism of nucleation is the most poorly understood aspect of MT dynamics. XMAP215/chTOG/Alp14/Stu2 proteins are MT polymerases that stimulate MT polymerization at MT plus ends by binding and releasing tubulin dimers. Although these proteins also localize to MT organizing centers and have nucleating activity in vitro, it is not yet clear whether these proteins participate in MT nucleation in vivo. Here, we demonstrate that in the fission yeast Schizosaccharomyces pombe, the XMAP215 ortholog Alp14 is critical for efficient MT nucleation in vivo. In multiple assays, loss of Alp14 function led to reduced nucleation rate and numbers of interphase MT bundles. Conversely, activation of Alp14 led to increased nucleation frequency. Alp14 associated with Mto1 and γ-tubulin complex components, and artificially targeting Alp14 to the γ-tubulin ring complexes (γ-TuRCs) stimulated nucleation. In imaging individual nucleation events, we found that Alp14 transiently associated with a γ-tubulin particle shortly before the appearance of a new MT. The transforming acidic coiled-coil (TACC) ortholog Alp7 mediated the localization of Alp14 at nucleation sites but not plus ends, and was required for efficient nucleation but not for MT polymerization. Our findings provide the strongest evidence to date that Alp14 serves as a critical MT nucleation factor in vivo. We suggest a model in which Alp14 associates with the γ-tubulin complex in an Alp7-dependent manner to facilitate the assembly or stabilization of the nascent MT. Copyright © 2018 Elsevier Ltd. All rights reserved.
Hall Ross S
Full Text Available Abstract Background New drug targets are urgently needed for parasites of socio-economic importance. Genes that are essential for parasite survival are highly desirable targets, but information on these genes is lacking, as gene knockouts or knockdowns are difficult to perform in many species of parasites. We examined the applicability of large-scale essentiality information from four model eukaryotes, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Saccharomyces cerevisiae, to discover essential genes in each of their genomes. Parasite genes that lack orthologues in their host are desirable as selective targets, so we also examined prediction of essential genes within this subset. Results Cross-species analyses showed that the evolutionary conservation of genes and the presence of essential orthologues are each strong predictors of essentiality in eukaryotes. Absence of paralogues was also found to be a general predictor of increased relative essentiality. By combining several orthology and essentiality criteria one can select gene sets with up to a five-fold enrichment in essential genes compared with a random selection. We show how quantitative application of such criteria can be used to predict a ranked list of potential drug targets from Ancylostoma caninum and Haemonchus contortus - two blood-feeding strongylid nematodes, for which there are presently limited sequence data but no functional genomic tools. Conclusions The present study demonstrates the utility of using orthology information from multiple, diverse eukaryotes to predict essential genes. The data also emphasize the challenge of identifying essential genes among those in a parasite that are absent from its host.
Background Conserved ortholog set (COS) markers are an important functional genomics resource that has greatly improved orthology detection in Asterid species. A comprehensive list of these markers is available at Sol Genomics Network (http://solgenomics.net/) and many of these have been placed on the genetic maps of a number of solanaceous species. Results We amplified over 300 COS markers from eight potato accessions involving two diploid landraces of Solanum tuberosum Andigenum group (formerly classified as S. goniocalyx, S. phureja), and a dihaploid clone derived from a modern tetraploid cultivar of S. tuberosum and the wild species S. berthaultii, S. chomatophilum, and S. paucissectum. By BLASTn (Basic Local Alignment Search Tool of the NCBI, National Center for Biotechnology Information) algorithm we mapped the DNA sequences of these markers into the potato genome sequence. Additionally, we mapped a subset of these markers genetically in potato and present a comparison between the physical and genetic locations of these markers in potato and in comparison with the genetic location in tomato. We found that most of the COS markers are single-copy in the reference genome of potato and that the genetic location in tomato and physical location in potato sequence are mostly in agreement. However, we did find some COS markers that are present in multiple copies and those that map in unexpected locations. Sequence comparisons between species show that some of these markers may be paralogs. Conclusions The sequence-based physical map becomes helpful in identification of markers for traits of interest thereby reducing the number of markers to be tested for applications like marker assisted selection, diversity, and phylogenetic studies. PMID:23758607
Kong, Jin Sun; Kang, Ji-Youn; Kim, Hye Lim; Kwon, O-Seob; Lee, Kon Ho; Park, Young Shik
6-Pyruvoyltetrahydropterin synthase (PTPS) catalyzes the second step of tetrahydrobiopterin (BH4) synthesis. We previously identified PTPS orthologs (bPTPS-Is) in bacteria which do not produce BH4. In this study we disrupted the gene encoding bPTPS-I in Synechococcus sp. PCC 7942, which produces BH4-glucoside. The mutant was normal in BH4-glucoside production, demonstrating that bPTPS-I does not participate in BH4 synthesis in vivo and bringing us a new PTPS ortholog (bPTPS-II) of a bimodular polypeptide. The recombinant Synechococcus bPTPS-II was assayed in vitro to show PTPS activity higher than human enzyme. Further computational analysis revealed the presence of mono and bimodular bPTPS-II orthologs mostly in green sulfur bacteria and cyanobacteria, respectively, which are well known for BH4-glycoside production. In summary we found new bacterial PTPS orthologs, having either a single or dual domain structure and being responsible for BH4 synthesis in vivo, thereby disclosing all the bacterial PTPS homologs.
Leal, Fernanda Munhoz Dos Anjos; Virginio, Veridiana Gomes; Martello, Carolina Lumertz; Paes, Jéssica Andrade; Borges, Thiago J; Jaeger, Natália; Bonorino, Cristina; Ferreira, Henrique Bunselmeyer
Mycoplasma hyopneumoniae and Mycoplasma flocculare are two genetically close species found in the swine respiratory tract. Despite their similarities, while M. hyopneumoniae is the causative agent of porcine enzootic pneumonia, M. flocculare is a commensal bacterium. Genomic and transcriptional comparative analyses so far failed to explain the difference in pathogenicity between these two species. We then hypothesized that such difference might be, at least in part, explained by amino acid sequence and immunological or functional differences between ortholog surface proteins. In line with that, it was verified that approximately 85% of the ortholog surface proteins from M. hyopneumoniae 7448 and M. flocculare present one or more differential domains. To experimentally assess possible immunological implications of this kind of difference, the extracellular differential domains from one pair of orthologous surface proteins (MHP7448_0612, from M. hyopneumoniae, and MF_00357, from M. flocculare) were expressed in E. coli and used to immunize mice. The recombinant polypeptides (rMHP61267-169 and rMF35767-196, respectively) induced distinct cellular immune responses. While, rMHP61267-169 induced both Th1 and Th2 responses, rMF35767-196 induced just an early pro-inflammatory response. These results indicate that immunological properties determined by differential domains in orthologous surface protein might play a role in pathogenicity, contributing to elicit specific and differential immune responses against each species. Copyright © 2016 Elsevier B.V. All rights reserved.
Galpert, Deborah; Fernández, Alberto; Herrera, Francisco; Antunes, Agostinho; Molina-Ruiz, Reinaldo; Agüero-Chapin, Guillermin
The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog classification approach implemented in a big data platform that considered several pairwise protein features and the low ortholog pair ratios found between two annotated proteomes (Galpert, D et al., BioMed Research International, 2015). The supervised models were built and tested using a Saccharomycete yeast benchmark dataset proposed by Salichos and Rokas (2011). Despite several pairwise protein features being combined in a supervised big data approach; they all, to some extent were alignment-based features and the proposed algorithms were evaluated on a unique test set. Here, we aim to evaluate the impact of alignment-free features on the performance of supervised models implemented in the Spark big data platform for pairwise ortholog detection in several related yeast proteomes. The Spark Random Forest and Decision Trees with oversampling and undersampling techniques, and built with only alignment-based similarity measures or combined with several alignment-free pairwise protein features showed the highest classification performance for ortholog detection in three yeast proteome pairs. Although such supervised approaches outperformed traditional methods, there were no significant differences between the exclusive use of alignment-based similarity measures and their combination with alignment-free features, even within the twilight zone of the studied proteomes. Just when alignment-based and alignment-free features were combined in Spark Decision Trees with imbalance management, a higher success rate (98.71%) within the twilight zone could be achieved for a yeast proteome pair that underwent a whole genome duplication. The feature selection study showed that alignment-based features were top-ranked for the best classifiers while the runners-up were
Jolene S Fernandes
Full Text Available Regulation of spatio-temporal gene expression in diverse cell and tissue types is a critical aspect of development. Progression through Caenorhabditis elegans vulval development leads to the generation of seven distinct vulval cell types (vulA, vulB1, vulB2, vulC, vulD, vulE, and vulF, each with its own unique gene expression profile. The mechanisms that establish the precise spatial patterning of these mature cell types are largely unknown. Dissection of the gene regulatory networks involved in vulval patterning and differentiation would help us understand how cells generate a spatially defined pattern of cell fates during organogenesis. We disrupted the activity of 508 transcription factors via RNAi and assayed the expression of ceh-2, a marker for vulB fate during the L4 stage. From this screen, we identified the tailless ortholog nhr-67 as a novel regulator of gene expression in multiple vulval cell types. We find that one way in which nhr-67 maintains cell identity is by restricting inappropriate cell fusion events in specific vulval cells, namely vulE and vulF. nhr-67 exhibits a dynamic expression pattern in the vulval cells and interacts with three other transcriptional regulators cog-1 (Nkx6.1/6.2, lin-11 (LIM, and egl-38 (Pax2/5/8 to generate the composite expression patterns of their downstream targets. We provide evidence that egl-38 regulates gene expression in vulB1, vulC, vulD, vulE, as well as vulF cells. We demonstrate that the pairwise interactions between these regulatory genes are complex and vary among the seven cell types. We also discovered a striking regulatory circuit that affects a subset of the vulval lineages: cog-1 and nhr-67 inhibit both one another and themselves. We postulate that the differential levels and combinatorial patterns of lin-11, cog-1, and nhr-67 expression are a part of a regulatory code for the mature vulval cell types.
Tang, Mingyong; Tao, Yan-Bin; Fu, Qiantang; Song, Yaling; Niu, Longjian; Xu, Zeng-Fu
Jatropha curcas seeds are an excellent biofuel feedstock, but seed yields of Jatropha are limited by its poor flowering and fruiting ability. Thus, identifying genes controlling flowering is critical for genetic improvement of seed yield. We isolated the JcLFY, a Jatropha ortholog of Arabidopsis thaliana LEAFY (LFY), and identified JcLFY function by overexpressing it in Arabidopsis and Jatropha. JcLFY is expressed in Jatropha inflorescence buds, flower buds, and carpels, with highest expression in the early developmental stage of flower buds. JcLFY overexpression induced early flowering, solitary flowers, and terminal flowers in Arabidopsis, and also rescued the delayed flowering phenotype of lfy-15, a LFY loss-of-function Arabidopsis mutant. Microarray and qPCR analysis revealed several flower identity and flower organ development genes were upregulated in JcLFY-overexpressing Arabidopsis. JcLFY overexpression in Jatropha also induced early flowering. Significant changes in inflorescence structure, floral organs, and fruit shape occurred in JcLFY co-suppressed plants in which expression of several flower identity and floral organ development genes were changed. This suggests JcLFY is involved in regulating flower identity, floral organ patterns, and fruit shape, although JcLFY function in Jatropha floral meristem determination is not as strong as that of Arabidopsis.
Michelle L Castelletto
Full Text Available Based on metabolic and morphological similarities between infective third-stage larvae of parasitic nematodes and dauer larvae of Caenorhabditis elegans, it is hypothesized that similar genetic mechanisms control the development of these forms. In the parasite Strongyloides stercoralis, FKTF-1 is an ortholog of DAF-16, a forkhead transcription factor that regulates dauer larval development in C. elegans. Using transgenesis, we investigated the role of FKTF-1 in S. stercoralis' infective larval development. In first-stage larvae, GFP-tagged recombinant FKTF-1b localizes to the pharynx and hypodermis, tissues remodeled in infective larvae. Activating and inactivating mutations at predicted AKT phosphorylation sites on FKTF-1b give constitutive cytoplasmic and nuclear localization of the protein, respectively, indicating that its post-translational regulation is similar to other FOXO-class transcription factors. Mutant constructs designed to interfere with endogenous FKTF-1b function altered the intestinal and pharyngeal development of the larvae and resulted in some transgenic larvae failing to arrest in the infective stage. Our findings indicate that FKTF-1b is required for proper morphogenesis of S. stercoralis infective larvae and support the overall hypothesis of similar regulation of dauer development in C. elegans and the formation of infective larvae in parasitic nematodes.
Alagarasan, Ganesh; Dubey, Mahima; Aswathy, Kumar S; Chandel, Girish
Genes in the ZIP family encode transcripts to store and transport bivalent metal micronutrient, particularly iron (Fe) and or zinc (Zn). These transcripts are important for a variety of functions involved in the developmental and physiological processes in many plant species, including most, if not all, Poaceae plant species and the model species Arabidopsis. Here, we present the report of a genome wide investigation of orthologous ZIP genes in Setaria italica and the identification of 7 single copy genes. RT-PCR shows 4 of them could be used to increase the bio-availability of zinc and iron content in grains. Of 36 ZIP members, 25 genes have traces of signal peptide based sub-cellular localization, as compared to those of plant species studied previously, yet translocation of ions remains unclear. In silico analysis of gene structure and protein nature suggests that these two were preeminent in shaping the functional diversity of the ZIP gene family in S. italica . NAC, bZIP and bHLH are the predominant Fe and Zn responsive transcription factors present in SiZIP genes. Together, our results provide new insights into the signal peptide based/independent iron and zinc translocation in the plant system and allowed identification of ZIP genes that may be involved in the zinc and iron absorption from the soil, and thus transporting it to the cereal grain underlying high micronutrient accumulation.
Full Text Available Genes in the ZIP family encode transcripts to store and transport bivalent metal micronutrient, particularly iron (Fe and or zinc (Zn. These transcripts are important for a variety of functions involved in the developmental and physiological processes in many plant species, including most, if not all, Poaceae plant species and the model species Arabidopsis. Here, we present the report of a genome wide investigation of orthologous ZIP genes in Setaria italica and the identification of 7 single copy genes. RT-PCR shows 4 of them could be used to increase the bio-availability of zinc and iron content in grains. Of 36 ZIP members, 25 genes have traces of signal peptide based sub-cellular localization, as compared to those of plant species studied previously, yet translocation of ions remains unclear. In silico analysis of gene structure and protein nature suggests that these two were preeminent in shaping the functional diversity of the ZIP gene family in S. italica. NAC, bZIP and bHLH are the predominant Fe and Zn responsive transcription factors present in SiZIP genes. Together, our results provide new insights into the signal peptide based/independent iron and zinc translocation in the plant system and allowed identification of ZIP genes that may be involved in the zinc and iron absorption from the soil, and thus transporting it to the cereal grain underlying high micronutrient accumulation.
Zhang, Li-Na; Zhang, Xian-Zhi; Zhang, Yu-Xiao; Zeng, Chun-Xia; Ma, Peng-Fei; Zhao, Lei; Guo, Zhen-Hua; Li, De-Zhu
The temperate woody bamboos (Arundinarieae) are highly diverse in morphology but lack a substantial amount of genetic variation. The taxonomy of this lineage is intractable, and the relationships within the tribe have not been well resolved. Recent studies indicated that this tribe could have a complex evolutionary history. Although phylogenetic studies of the tribe have been carried out, most of these phylogenetic reconstructions were based on plastid data, which provide lower phylogenetic resolution compared with nuclear data. In this study, we intended to identify a set of desirable nuclear genes for resolving the phylogeny of the temperate woody bamboos. Using two different methodologies, we identified 209 and 916 genes, respectively, as putative single copy orthologous genes. A total of 112 genes was successfully amplified and sequenced by next-generation sequencing technologies in five species sampled from the tribe. As most of the genes exhibited intra-individual allele heterozygotes, we investigated phylogenetic utility by reconstructing the phylogeny based on individual genes. Discordance among gene trees was observed and, to resolve the conflict, we performed a range of analyses using BUCKy and HybTree. While caution should be taken when inferring a phylogeny from multiple conflicting genes, our analysis indicated that 74 of the 112 investigated genes are potential markers for resolving the phylogeny of the temperate woody bamboos. © 2014 John Wiley & Sons Ltd.
Grabowski, Melissa M; Svrzikapa, Nenad; Tissenbaum, Heidi A
Bloom syndrome is caused by mutation of the Bloom helicase (BLM), a member of the RecQ helicase family. Loss of BLM function results in genomic instability that causes a high incidence of cancer. It has been demonstrated that BLM is important for maintaining genomic stability by playing a role in DNA recombination and repair; however, the exact function of BLM is not clearly understood. To determine the mechanism by which BLM controls genomic stability in vivo, we examined the phenotypes caused by mutation of the C. elegans BLM helicase ortholog, HIM-6. We find that the loss of HIM-6 leads to genomic instability as evidenced by an increased number of genomic insertions and deletions, which results in visible random mutant phenotypes. In addition to the mutator phenotype, him-6 mutants have a low brood size, a high incidence of males, a shortened life span, and an increased amount of germ line apoptosis. Upon exposure to high temperature, him-6 mutants that are serially passed become sterile demonstrating a mortal germ line phenotype. Our data suggest a model in which loss of HIM-6 results in genomic instability due to an increased number of DNA lesions, which either cannot be repaired and/or are introduced by low fidelity recombination events. The increased level of genomic instability that leads to him-6(ok412) mutants having a shortened life span.
Michael D Stubenvoll
Full Text Available Centrosomes are critical sites for orchestrating microtubule dynamics, and exhibit dynamic changes in size during the cell cycle. As cells progress to mitosis, centrosomes recruit more microtubules (MT to form mitotic bipolar spindles that ensure proper chromosome segregation. We report a new role for ATX-2, a C. elegans ortholog of Human Ataxin-2, in regulating centrosome size and MT dynamics. ATX-2, an RNA-binding protein, forms a complex with SZY-20 in an RNA-independent fashion. Depleting ATX-2 results in embryonic lethality and cytokinesis failure, and restores centrosome duplication to zyg-1 mutants. In this pathway, SZY-20 promotes ATX-2 abundance, which inversely correlates with centrosome size. Centrosomes depleted of ATX-2 exhibit elevated levels of centrosome factors (ZYG-1, SPD-5, γ-Tubulin, increasing MT nucleating activity but impeding MT growth. We show that ATX-2 influences MT behavior through γ-Tubulin at the centrosome. Our data suggest that RNA-binding proteins play an active role in controlling MT dynamics and provide insight into the control of proper centrosome size and MT dynamics.
Jonavičienė, Kristina; Studer, Bruno; Asp, Torben
In order to characterize the response of selected grasses to water stress, relative water content (RWC) in leaves and quantum efficiency of photosystem 2 (Fv/Fm) were measured in Phleum pratense L., P. bertolonii DC. and P. phleoides H. Karst. during 6 d of water stress. The results indicated...... differential responses to water stress among the three Phleum species with higher water deficit sensitivity of P. pratense and P. bertolonii than that of P. phleoides. The cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique was applied to identify differentially expressed genes responding...... to water stress in P. pratense. Cloned and sequenced differentially expressed fragments (DEFs) were used for primer design in order to identify orthologous genes in Lolium perenne L. Twelve genes orthologous to P. pratense DEFs were mapped in the L. perenne mapping population VrnA based on a high...
Rovenská, Miroslava; Hlouchová, Klára; Šácha, Pavel; Mlčochová, Petra; Horák, Vratislav; Zámečník, J.; Bařinka, C.; Konvalinka, Jan
Roč. 68, č. 2 (2008), s. 171-182 ISSN 0270-4137 R&D Projects: GA MŠk 1M0508; GA ČR GA524/04/0102 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50450515 Keywords : prostate specific membrane antigen * glutamate carboxypeptidase II * animal orthologs * prostate cancer * animal model Subject RIV: CE - Biochemistry Impact factor: 3.069, year: 2008
Huerta-Cepas, J.; Szklarczyk, D.; Forslund, K.; Cook, H.; Heller, D.; Walter, M.C.; Rattei, T.; Mende, D.R.; Sunagawa, S.; Kuhn, M.; Jensen, L.J.; von Mering, C.; Bork, P.
eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes to the algorithm for creating OGs across taxonomic levels, making nested groups hierarchically consistent. This allows for a better propagation of functional terms across nested OGs and led to the novel annotation of 95 890 previously uncharacterized OGs, increasing...
Enciso-Rodríguez, Felix; Martínez, Rodrigo; Lobo, Mario; Barrero, Luz Stella
The Lulo or naranjilla (Solanum quitoense Lam.) and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt.) are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32) and tree tomatoes (n = 30) through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII) in other Solanaceae...
Full Text Available The human cytochrome P450 (CYP superfamily consisting of 57 functional genes is the most important group of Phase I drug metabolizing enzymes that oxidize a large number of xenobiotics and endogenous compounds, including therapeutic drugs and environmental toxicants. The CYP superfamily has been shown to expand itself through gene duplication, and some of them become pseudogenes due to gene mutations. Orthologs and paralogs are homologous genes resulting from speciation or duplication, respectively. To explore the evolutionary and functional relationships of human CYPs, we conducted this bioinformatic study to identify their corresponding paralogs, homologs, and orthologs. The functional implications and implications in drug discovery and evolutionary biology were then discussed. GeneCards and Ensembl were used to identify the paralogs of human CYPs. We have used a panel of online databases to identify the orthologs of human CYP genes: NCBI, Ensembl Compara, GeneCards, OMA (“Orthologous MAtrix” Browser, PATHER, TreeFam, EggNOG, and Roundup. The results show that each human CYP has various numbers of paralogs and orthologs using GeneCards and Ensembl. For example, the paralogs of CYP2A6 include CYP2A7, 2A13, 2B6, 2C8, 2C9, 2C18, 2C19, 2D6, 2E1, 2F1, 2J2, 2R1, 2S1, 2U1, and 2W1; CYP11A1 has 6 paralogs including CYP11B1, 11B2, 24A1, 27A1, 27B1, and 27C1; CYP51A1 has only three paralogs: CYP26A1, 26B1, and 26C1; while CYP20A1 has no paralog. The majority of human CYPs are well conserved from plants, amphibians, fishes, or mammals to humans due to their important functions in physiology and xenobiotic disposition. The data from different approaches are also cross-validated and validated when experimental data are available. These findings facilitate our understanding of the evolutionary relationships and functional implications of the human CYP superfamily in drug discovery.
Keller, Lani C; Romijn, Edwin P; Zamora, Ivan; Yates, John R; Marshall, Wallace F
The centriole is one of the most enigmatic organelles in the cell. Centrioles are cylindrical, microtubule-based barrels found in the core of the centrosome. Centrioles also act as basal bodies during interphase to nucleate the assembly of cilia and flagella. There are currently only a handful of known centriole proteins. We used mass-spectrometry-based MudPIT (multidimensional protein identification technology) to identify the protein composition of basal bodies (centrioles) isolated from the green alga Chlamydomonas reinhardtii. This analysis detected the majority of known centriole proteins, including centrin, epsilon tubulin, and the cartwheel protein BLD10p. By combining proteomic data with information about gene expression and comparative genomics, we identified 45 cross-validated centriole candidate proteins in two classes. Members of the first class of proteins (BUG1-BUG27) are encoded by genes whose expression correlates with flagellar assembly and which therefore may play a role in ciliogenesis-related functions of basal bodies. Members of the second class (POC1-POC18) are implicated by comparative-genomics and -proteomics studies to be conserved components of the centriole. We confirmed centriolar localization for the human homologs of four candidate proteins. Three of the cross-validated centriole candidate proteins are encoded by orthologs of genes (OFD1, NPHP-4, and PACRG) implicated in mammalian ciliary function and disease, suggesting that oral-facial-digital syndrome and nephronophthisis may involve a dysfunction of centrioles and/or basal bodies. By analyzing isolated Chlamydomonas basal bodies, we have been able to obtain the first reported proteomic analysis of the centriole.
Gottwein, Eva; Mukherjee, Neelanjan; Sachse, Christoph; Frenzel, Corina; Majoros, William H.; Chi, Jen-Tsan A.; Braich, Ravi; Manoharan, Muthiah; Soutschek, Jürgen; Ohler, Uwe; Cullen, Bryan R.
All metazoan eukaryotes express microRNAs (miRNAs), ∼22 nt regulatory RNAs that can repress the expression of mRNAs bearing complementary sequences1. Several DNA viruses also express miRNAs in infected cells, suggesting a role in viral replication and pathogenesis2. While specific viral miRNAs have been shown to autoregulate viral mRNAs3,4 or downregulate cellular mRNAs5,6, the function of the majority of viral miRNAs remains unknown. Here, we report that the miR-K12−11 miRNA encoded by Kaposi's Sarcoma Associated Herpesvirus (KSHV) shows significant homology to cellular miR-155, including the entire miRNA “seed” region7. Using a range of assays, we demonstrate that expression of physiological levels of miR-K12−11 or miR-155 results in the downregulation of an extensive set of common mRNA targets, including genes with known roles in cell growth regulation. Our findings indicate that viral miR-K12−11 functions as an ortholog of cellular miR-155 and has likely evolved to exploit a pre-existing gene regulatory pathway in B-cells. Moreover, the known etiological role of miR-155 in B-cell transformation8-10 suggests that miR-K12−11 may contribute to the induction of KSHV-positive B-cell tumors in infected patients. PMID:18075594
Li, Airong; Hooli, Basavaraj; Mullin, Kristina; Tate, Rebecca E; Bubnys, Adele; Kirchner, Rory; Chapman, Brad; Hofmann, Oliver; Hide, Winston; Tanzi, Rudolph E
SOX5 encodes a transcription factor that is expressed in multiple tissues including heart, lung and brain. Mutations in SOX5 have been previously found in patients with amyotrophic lateral sclerosis (ALS) and developmental delay, intellectual disability and dysmorphic features. To characterize the neuronal role of SOX5, we silenced the Drosophila ortholog of SOX5, Sox102F, by RNAi in various neuronal subtypes in Drosophila. Silencing of Sox102F led to misorientated and disorganized michrochaetes, neurons with shorter dendritic arborization (DA) and reduced complexity, diminished larval peristaltic contractions, loss of neuromuscular junction bouton structures, impaired olfactory perception, and severe neurodegeneration in brain. Silencing of SOX5 in human SH-SY5Y neuroblastoma cells resulted in a significant repression of WNT signaling activity and altered expression of WNT-related genes. Genetic association and meta-analyses of the results in several large family-based and case-control late-onset familial Alzheimer's disease (LOAD) samples of SOX5 variants revealed several variants that show significant association with AD disease status. In addition, analysis for rare and highly penetrate functional variants revealed four novel variants/mutations in SOX5, which taken together with functional prediction analysis, suggests a strong role of SOX5 causing AD in the carrier families. Collectively, these findings indicate that SOX5 is a novel candidate gene for LOAD with an important role in neuronal function. The genetic findings warrant further studies to identify and characterize SOX5 variants that confer risk for AD, ALS and intellectual disability. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: email@example.com.
Camarata, Troy; Vasilyev, Aleksandr; Hadjiargyrou, Michael
Mustn1 is a small nuclear protein that is involved in the development and regeneration of the musculoskeletal system. Previous work established a role for Mustn1 in myogenic and chondrogenic differentiation. In addition, recent evidence suggests a potential role for Mustn1 in cilia function in zebrafish. A detailed study of Mustn1 expression has yet to be conducted in zebrafish. As such, we report herein the cloning of the zebrafish Mustn1 orthologs, mustn1a and mustn1b, and their expression during zebrafish embryonic and larval development. Results indicate a 44% nucleotide identity between the two paralogs. Phylogenetic analysis further confirmed that the Mustn1a and 1b predicted proteins were highly related to other vertebrate members of the Mustn1 protein family. Whole mount in situ hybridization revealed expression of both mustn1a and 1b at the 7-somite stage through 72hpf in structures such as Kupffer's vesicle, segmental mesoderm, head structures, and otic vesicle. Additionally, in 5day old larva, mustn1a and 1b expression is detected in the neurocranium, otic capsule, and the gut. Although both were expressed in the neurocranium, mustn1a was localized in the hypophyseal fenestra whereas mustn1b was found near the posterior basicapsular commissure. mustn1b also displayed expression in the ceratohyal and ceratobranchial elements of the pharyngeal skeleton. These expression patterns were verified temporally by q-PCR analysis. Taken together, we conclude that Mustn1 expression is conserved in vertebrates and that the variations in expression of the two zebrafish paralogs suggest different modes of molecular regulation. Copyright © 2016 Elsevier B.V. All rights reserved.
Full Text Available Abstract Background Systemic acquired resistance (SAR is induced in non-inoculated leaves following infection with certain pathogenic strains. SAR is effective against many pathogens. Salicylic acid (SA is a signaling molecule of the SAR pathway. The development of SAR is associated with the induction of pathogenesis related (PR genes. Arabidopsis non-expressor of PR1 (NPR1 is a regulatory gene of the SA signal pathway 123. SAR in soybean was first reported following infection with Colletotrichum trancatum that causes anthracnose disease. We investigated if SAR in soybean is regulated by a pathway, similar to the one characterized in Arabidopsis. Results Pathogenesis-related gene GmPR1 is induced following treatment of soybean plants with the SAR inducer, 2,6-dichloroisonicotinic acid (INA or infection with the oomycete pathogen, Phytophthora sojae. In P. sojae-infected plants, SAR was induced against the bacterial pathogen, Pseudomonas syringae pv. glycinea. Soybean GmNPR1-1 and GmNPR1-2 genes showed high identities to Arabidopsis NPR1. They showed similar expression patterns among the organs, studied in this investigation. GmNPR1-1 and GmNPR1-2 are the only soybean homologues of NPR1and are located in homoeologous regions. In GmNPR1-1 and GmNPR1-2 transformed Arabidopsis npr1-1 mutant plants, SAR markers: (i PR-1 was induced following INA treatment and (ii BGL2 following infection with Pseudomonas syringae pv. tomato (Pst, and SAR was induced following Pst infection. Of the five cysteine residues, Cys82, Cys150, Cys155, Cys160, and Cys216 involved in oligomer-monomer transition in NPR1, Cys216 in GmNPR1-1 and GmNPR1-2 proteins was substituted to Ser and Leu, respectively. Conclusion Complementation analyses in Arabidopsis npr1-1 mutants revealed that homoeologous GmNPR1-1 and GmNPR1-2 genes are orthologous to Arabidopsis NPR1. Therefore, SAR pathway in soybean is most likely regulated by GmNPR1 genes. Substitution of Cys216 residue, essential
Sandhu, Devinder; Tasma, I Made; Frasch, Ryan; Bhattacharyya, Madan K
Systemic acquired resistance (SAR) is induced in non-inoculated leaves following infection with certain pathogenic strains. SAR is effective against many pathogens. Salicylic acid (SA) is a signaling molecule of the SAR pathway. The development of SAR is associated with the induction of pathogenesis related (PR) genes. Arabidopsis non-expressor of PR1 (NPR1) is a regulatory gene of the SA signal pathway 123. SAR in soybean was first reported following infection with Colletotrichum trancatum that causes anthracnose disease. We investigated if SAR in soybean is regulated by a pathway, similar to the one characterized in Arabidopsis. Pathogenesis-related gene GmPR1 is induced following treatment of soybean plants with the SAR inducer, 2,6-dichloroisonicotinic acid (INA) or infection with the oomycete pathogen, Phytophthora sojae. In P. sojae-infected plants, SAR was induced against the bacterial pathogen, Pseudomonas syringae pv. glycinea. Soybean GmNPR1-1 and GmNPR1-2 genes showed high identities to Arabidopsis NPR1. They showed similar expression patterns among the organs, studied in this investigation. GmNPR1-1 and GmNPR1-2 are the only soybean homologues of NPR1and are located in homoeologous regions. In GmNPR1-1 and GmNPR1-2 transformed Arabidopsis npr1-1 mutant plants, SAR markers: (i) PR-1 was induced following INA treatment and (ii) BGL2 following infection with Pseudomonas syringae pv. tomato (Pst), and SAR was induced following Pst infection. Of the five cysteine residues, Cys82, Cys150, Cys155, Cys160, and Cys216 involved in oligomer-monomer transition in NPR1, Cys216 in GmNPR1-1 and GmNPR1-2 proteins was substituted to Ser and Leu, respectively. Complementation analyses in Arabidopsis npr1-1 mutants revealed that homoeologous GmNPR1-1 and GmNPR1-2 genes are orthologous to Arabidopsis NPR1. Therefore, SAR pathway in soybean is most likely regulated by GmNPR1 genes. Substitution of Cys216 residue, essential for oligomer-monomer transition of Arabidopsis NPR1
Full Text Available The detection and amplification of extracellular signals requires the involvement of multiple protein components. In mammalian cells the receptor of activated C kinase (RACK1 is an important scaffolding protein for signal transduction networks. Further, it also performs a critical function in regulating the cell cycle by modulating the G1/S transition. Many eukaryotic cells express RACK1 orthologs, with one example being Cpc2p in the fission yeast Schizosaccharomyces pombe. In contrast to RACK1, Cpc2p has been described to positively regulate, at the ribosomal level, cells entry into M phase. In addition, Cpc2p controls the stress response pathways through an interaction with Msa2p, and sexual development by modulating Ran1p/Pat1p. Here we describe investigations into the role, which Cpc2p performs in controlling the G protein-mediated mating response pathway. Despite structural similarity to Gβ-like subunits, Cpc2p appears not to function at the G protein level. However, upon pheromone stimulation, cells overexpressing Cpc2p display substantial cell morphology defects, disorientation of septum formation and a significantly protracted G1 arrest. Cpc2p has the potential to function at multiple positions within the pheromone response pathway. We provide a mechanistic interpretation of this novel data by linking Cpc2p function, during the mating response, with its previous described interactions with Ran1p/Pat1p. We suggest that overexpressing Cpc2p prolongs the stimulated state of pheromone-induced cells by increasing ste11 gene expression. These data indicate that Cpc2p regulates the pheromone-induced cell cycle arrest in fission yeast by delaying cells entry into S phase.
Hudson, Brian D; Christiansen, Elisabeth; Tikhonova, Irina G
When it is difficult to develop selective ligands within a family of related G-protein-coupled receptors (GPCRs), chemically engineered receptors activated solely by synthetic ligands (RASSLs) are useful alternatives for probing receptor function. In the present work, we explored whether a RASSL...... on this receptor and demonstrates that exploitation of pharmacological variation between species orthologs is a powerful method to generate novel chemically engineered GPCRs.-Hudson, B. D., Christiansen, E., Tikhonova, I. G., Grundmann, M., Kostenis, E., Adams, D. R., Ulven, T., Milligan, G. Chemically engineering...
Xu, Yuli; Gristwood, Tamzin; Hodgson, Ben; Trinidad, Jonathan C; Albers, Sonja-Verena; Bell, Stephen D
The regulated recruitment of Cdc45 and GINS is key to activating the eukaryotic MCM(2-7) replicative helicase. We demonstrate that the homohexameric archaeal MCM helicase associates with orthologs of GINS and Cdc45 in vivo and in vitro. Association of these factors with MCM robustly stimulates the MCM helicase activity. In contrast to the situation in eukaryotes, archaeal Cdc45 and GINS form an extremely stable complex before binding MCM. Further, the archaeal GINS•Cdc45 complex contains two copies of Cdc45. Our analyses give insight into the function and evolution of the conserved core of the archaeal/eukaryotic replisome.
Rodríguez-Cruz, Maricela; Coral-Vázquez, Ramón M.; Hernández-Stengele, Gabriel; Sánchez, Raúl; Salazar, Emmanuel; Sanchez-Muñoz, Fausto; Encarnación-Guevara, Sergio; Ramírez-Salcedo, Jorge
The mammary gland (MG) undergoes functional and metabolic changes during the transition from pregnancy to lactation, possibly by regulation of conserved genes. The objective was to elucidate orthologous genes, chromosome clusters and putative conserved transcriptional modules during MG development. We analyzed expression of 22,000 transcripts using murine microarrays and RNA samples of MG from virgin, pregnant, and lactating rats by cross-species hybridization. We identified 521 transcripts differentially expressed; upregulated in early (78%) and midpregnancy (89%) and early lactation (64%), but downregulated in mid-lactation (61%). Putative orthologous genes were identified. We mapped the altered genes to orthologous chromosomal locations in human and mouse. Eighteen sets of conserved genes associated with key cellular functions were revealed and conserved transcription factor binding site search entailed possible coregulation among all eight block sets of genes. This study demonstrates that the use of heterologous array hybridization for screening of orthologous gene expression from rat revealed sets of conserved genes arranged in chromosomal order implicated in signaling pathways and functional ontology. Results demonstrate the utilization power of comparative genomics and prove the feasibility of using rodent microarrays to identification of putative coexpressed orthologous genes involved in the control of human mammary gland development. PMID:24288657
Full Text Available WRKY transcription factors have been extensively characterized in the past 20 years, but in wheat, studies onWRKY genes and their function are lagging behind many other species. To explore the function of wheat WRKY genes, we identified a TaWRKY68 gene from a common wheat cultivar. It encodes a protein comprising 313 amino acids which harbors 19 conserved motifs or active sites. Gene expression patterns were determined by analyzing microarray data of TaWRKY68 in wheat and of orthologous genes from maize, rice and barley using Genevestigator. TaWRKY68 orthologs were identified and clustered using DELTA-BLAST and COBALT programs available at NCBI. The results showed that these genes, which are expressed in all tissues tested, had relatively higher levels in the roots and were up-regulated in response to biotic stresses. Bioinformatics results were confirmed by RT-PCR experiments using wheat plants infected by Agrobacterium tumefaciens and Blumeria graminis, or treated with Deoxynivalenol, a Fusarium graminearum-induced mycotoxin in wheat or barley. In summary,TaWRKY68 functions differ during plant developmental stages and might be representing a hub gene function in wheat responses to various biotic stresses. It was also found that including data from major cereal genes in the bioinformatics analysis gave more accurate and comprehensive predictions of wheat gene functions.
Novichkov, Pavel S.; Ratnere, Igor; Wolf, Yuri I.; Koonin, Eugene V.; Dubchak, Inna
The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.gov.
Full Text Available Precise genome editing in livestock is of great value for the fundamental investigation of disease modeling. However, genetically modified pigs carrying subtle point mutations were still seldom reported despite the rapid development of programmable endonucleases. Here, we attempt to investigate single-stranded oligonucleotides (ssODN mediated knockin by introducing two orthologous pathogenic mutations, p.E693G for Alzheimer's disease and p.G2019S for Parkinson's disease, into porcine APP and LRRK2 loci, respectively. Desirable homology-directed repair (HDR efficiency was achieved in porcine fetal fibroblasts (PFFs by optimizing the dosage and length of ssODN templates. Interestingly, incomplete HDR alleles harboring partial point mutations were observed in single-cell colonies, which indicate the complex mechanism of ssODN-mediated HDR. The effect of mutation-to-cut distance on incorporation rate was further analyzed by deep sequencing. We demonstrated that a mutation-to-cut distance of 11 bp resulted in a remarkable difference in HDR efficiency between two point mutations. Finally, we successfully obtained one cloned piglet harboring the orthologous p.C313Y mutation at the MSTN locus via somatic cell nuclear transfer (SCNT. Our proof-of-concept study demonstrated efficient ssODN-mediated incorporation of pathogenic point mutations in porcine somatic cells, thus facilitating further development of disease modeling and genetic breeding in pigs.
Meiler, Arno; Klinger, Claudia; Kaufmann, Michael
The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC's NUCOCOG dataset as the largest one available for that purpose thus far. Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills.
Full Text Available Abstract Background The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Results Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC’s NUCOCOG dataset as the largest one available for that purpose thus far. Conclusions Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills.
Background The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Results Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC’s NUCOCOG dataset as the largest one available for that purpose thus far. Conclusions Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills. PMID:22958836
de Villena Fernando
Full Text Available Abstract Background The central metabolic pathway of glycolysis converts glucose to pyruvate, with the net production of 2 ATP and 2 NADH per glucose molecule. Each of the ten reactions in this pathway is typically catalyzed by multiple isozymes encoded by a multigene family. Several isozymes in this pathway are expressed only during spermatogenesis, and gene targeting studies indicate that they are essential for sperm function and male fertility in mouse. At least three of the novel glycolytic isozymes are encoded by retrogenes (Pgk2, Aldoart1, and Aldoart2. Their restricted expression profile suggests that retrotransposition may play a significant role in the evolution of sperm glycolytic enzymes. Results We conducted a comprehensive genomic analysis of glycolytic enzymes in the human and mouse genomes and identified several intronless copies for all enzymes in the pathway, except Pfk. Within each gene family, a single orthologous gene was typically retrotransposed frequently and independently in both species. Several retroposed sequences maintained open reading frames (ORFs and/or provided evidence of alternatively spliced exons. We analyzed expression of sequences with ORFs and Gpi1 transcript in mouse spermatogenic cells. Conclusions Our analysis detected frequent, recent, and lineage-specific retrotransposition of orthologous glycolytic enzymes in the human and mouse genomes. Retrotransposition events are associated with LINE/LTR and genomic integration is random. We found evidence for the alternative splicing of parent genes. Many retroposed sequences have maintained ORFs, suggesting a functional role for these genes.
Full Text Available Cell division cycle 25 (cdc25 is an evolutionarily conserved phosphatase that promotes cell cycle progression. Among the four cdc25 orthologs in Caenorhabditis elegans, we found that cdc-25.4 mutant males failed to produce outcrossed progeny. This was not caused by defects in sperm development, but by defects in male mating behavior. The cdc-25.4 mutant males showed various defects during male mating, including contact response, backing, turning, and vulva location. Aberrant turning behavior was the most prominent defect in the cdc-25.4 mutant males. We also found that cdc-25.4 is expressed in many neuronal cells throughout development. The turning defect in cdc-25.4 mutant males was recovered by cdc-25.4 transgenic expression in neuronal cells, suggesting that cdc-25.4 functions in neurons for male mating. However, the neuronal morphology of cdc-25.4 mutant males appeared to be normal, as examined with several neuronal markers. Also, RNAi depletion of wee-1.3, a C. elegans ortholog of Wee1/Myt1 kinase, failed to suppress the mating defects of cdc-25.4 mutant males. These findings suggest that, for successful male mating, cdc-25.4 does not target cell cycles that are required for neuronal differentiation and development. Rather, cdc-25.4 likely regulates noncanonical substrates in neuronal cells.
Muller, J; Szklarczyk, D; Julien, P
The identification of orthologous relationships forms the basis for most comparative genomics studies. Here, we present the second version of the eggNOG database, which contains orthologous groups (OGs) constructed through identification of reciprocal best BLAST matches and triangular linkage...... of the tree of life; in addition to the species groups included in our first release (i.e. fungi, metazoa, insects, vertebrates and mammals), we have now constructed OGs for archaea, fishes, rodents and primates. We automatically annotate the non-supervised orthologous groups (NOGs) with functional...... descriptions, protein domains, and functional categories as defined initially for the COG/KOG database. In-depth analysis is facilitated by precomputed high-quality multiple sequence alignments and maximum-likelihood trees for each of the available OGs. Altogether, eggNOG covers 2,242 035 proteins (built from...
Full Text Available Lepidopteran pheromone receptors (PRs, for which orthologies are evident among closely related species, provide an intriguing example of gene family evolution in terms of how new functions may arise. However, only a limited number of PRs have been functionally characterized so far and thus evolutionary scenarios suffer from elements of speculation. In this study we investigated the turnip moth Agrotis segetum, in which female moths produce a mixture of chemically related pheromone components that elicit specific responses from receptor cells on male antennae. We cloned nine A. segetum PR genes and the Orco gene by degenerate primer based RT-PCR. The nine PR genes, named as AsegOR1 and AsegOR3-10, fall into four distinct orthologous clusters of known lepidopteran PRs, of which one contains six paralogues. The paralogues are under relaxed selective pressure, contrasting with the purifying selection on other clusters. We identified the receptors AsegOR9, AsegOR4 and AsegOR5, specific for the respective homologous pheromone components (Z-5-decenyl, (Z-7-dodecenyl and (Z-9-tetradecenyl acetates, by two-electrode voltage clamp recording from Xenopus laevis oocytes co-expressing Orco and each PR candidate. These receptors occur in three different orthologous clusters. We also found that the six paralogues with high sequence similarity vary dramatically in ligand selectivity and sensitivity. Different from AsegOR9, AsegOR6 showed a relatively large response to the behavioural antagonist (Z-5-decenol, and a small response to (Z-5-decenyl acetate. AsegOR1 was broadly tuned, but most responsive to (Z-5-decenyl acetate, (Z-7-dodecenyl acetate and the behavioural antagonist (Z-8-dodecenyl acetate. AsegOR8 and AsegOR7, which differ from AsegOR6 and AsegOR1 by 7 and 10 aa respectively, showed much lower sensitivities. AsegOR10 showed only small responses to all the tested compounds. These results suggest that new receptors arise through gene duplication, and
Heimbucher, Thomas; Hunter, Tony
FOXO family transcription factors are downstream effectors of Insulin/IGF-1 signaling (IIS) and are regulated by posttranslational modification and coregulators, including components of the ubiquitin-proteasome system (UPS). Cofactors promoting DAF-16/FOXO protein stability and function in IIS have not been described yet. In a recent study, we have identified the deubiquitylating enzyme MATH-33, the ortholog of mammalian USP7/HAUSP, as an essential DAF-16 coregulator. We found that MATH-33 actively stabilizes DAF-16 protein levels when IIS is downregulated. Here we discuss how DAF-16/FOXO transcription factors are regulated by the UPS, in particular by the interplay of E3-ubiquitin ligases and deubiquitylating enzymes, which is critical for balancing DAF-16/FOXO activity and degradation. Recent findings raise the intriguing possibility that regulated oscillations in DAF-16/FOXO steady state levels play an integral role in mechanisms controlling healthspan and lifespan extension.
Jain, Sourabh; Panda, Arup; Colson, Philippe; Raoult, Didier; Pontarotti, Pierre
With the inclusion of new members, understanding about evolutionary mechanisms and processes by which members of the proposed order, Megavirales, have evolved has become a key area of interest. The central role of gene acquisition has been shown in previous studies. However, the major drawback in gene acquisition studies is the focus on few MV families or putative families with large variation in their genetic structure. Thus, here we have tried to develop a methodology by which we can detect horizontal gene transfers (HGTs), taking into consideration orthologous groups of distantly related Megavirale families. Here, we report an automated workflow MimiLook, prepared as a Perl command line program, that deduces orthologous groups (OGs) from ORFomes of Megavirales and constructs phylogenetic trees by performing alignment generation, alignment editing and protein-protein BLAST (BLASTP) searching across the National Center for Biotechnology Information (NCBI) non-redundant (nr) protein sequence database. Finally, this tool detects statistically validated events of gene acquisitions with the help of the T-REX algorithm by comparing individual gene tree with NCBI species tree. In between the steps, the workflow decides about handling paralogs, filtering outputs, identifying Megavirale specific OGs, detection of HGTs, along with retrieval of information about those OGs that are monophyletic with organisms from cellular domains of life. By implementing MimiLook, we noticed that nine percent of Megavirale gene families (i.e., OGs) have been acquired by HGT, 80% OGs were Megaviralespecific and eight percent were found to be sharing common ancestry with members of cellular domains (Eukaryote, Bacteria, Archaea, Phages or other viruses) and three percent were ambivalent. The results are briefly discussed to emphasize methodology. Also, MimiLook is relevant for detecting evolutionary scenarios in other targeted phyla with user defined modifications. It can be accessed at
Full Text Available Notwithstanding the well-characterised roles of a number of oncogenes in neoplastic transformation, microRNAs (miRNAs are increasingly implicated in several human cancers. Discovery of miRNAs in several oncogenic herpesviruses such as KSHV has further highlighted the potential of virus-encoded miRNAs to contribute to their oncogenic capabilities. Nevertheless, despite the identification of several possible cancer-related genes as their targets, the direct in vivo role of virus-encoded miRNAs in neoplastic diseases such as those induced by KSHV is difficult to demonstrate in the absence of suitable models. However, excellent natural disease models of rapid-onset Marek's disease (MD lymphomas in chickens allow examination of the oncogenic potential of virus-encoded miRNAs. Using viruses modified by reverse genetics of the infectious BAC clone of the oncogenic RB-1B strain of MDV, we show that the deletion of the six-miRNA cluster 1 from the viral genome abolished the oncogenicity of the virus. This loss of oncogenicity appeared to be primarily due to the single miRNA within the cluster, miR-M4, the ortholog of cellular miR-155, since its deletion or a 2-nucleotide mutation within its seed region was sufficient to inhibit the induction of lymphomas. The definitive role of this miR-155 ortholog in oncogenicity was further confirmed by the rescue of oncogenic phenotype by revertant viruses that expressed either the miR-M4 or the cellular homolog gga-miR-155. This is the first demonstration of the direct in vivo role of a virus-encoded miRNA in inducing tumors in a natural infection model. Furthermore, the use of viruses deleted in miRNAs as effective vaccines against virulent MDV challenge, enables the prospects of generating genetically defined attenuated vaccines.
Full Text Available Chitin synthases (CHSs are key enzymes in the biosynthesis of chitin, an important structural component of fungal cell walls that can trigger innate immune responses in host plants and animals. Members of CHS gene family perform various functions in fungal cellular processes. Previous studies focused primarily on classifying diverse CHSs into different classes, regardless of their functional diversification, or on characterizing their functions in individual fungal species. A complete and systematic comparative analysis of CHS genes based on their orthologous relationships will be valuable for elucidating the evolution and functions of different CHS genes in fungi. Here, we identified and compared members of the CHS gene family across the fungal tree of life, including 18 divergent fungal lineages. Phylogenetic analysis revealed that the fungal CHS gene family is comprised of at least 10 ancestral orthologous clades, which have undergone multiple independent duplications and losses in different fungal lineages during evolution. Interestingly, one of these CHS clades (class III was expanded in plant or animal pathogenic fungi belonging to different fungal lineages. Two clades (classes VIb and VIc identified for the first time in this study occurred mainly in plant pathogenic fungi from Sordariomycetes and Dothideomycetes. Moreover, members of classes III and VIb were specifically up-regulated during plant infection, suggesting important roles in pathogenesis. In addition, CHS-associated networks conserved among plant pathogenic fungi are involved in various biological processes, including sexual reproduction and plant infection. We also identified specificity-determining sites, many of which are located at or adjacent to important structural and functional sites that are potentially responsible for functional divergence of different CHS classes. Overall, our results provide new insights into the evolution and function of members of CHS gene
Finan Christopher L
Full Text Available Abstract Background In Micrococcus luteus growth and resuscitation from starvation-induced dormancy is controlled by the production of a secreted growth factor. This autocrine resuscitation-promoting factor (Rpf is the founder member of a family of proteins found throughout and confined to the actinobacteria (high G + C Gram-positive bacteria. The aim of this work was to search for and characterise a cognate gene family in the firmicutes (low G + C Gram-positive bacteria and obtain information about how they may control bacterial growth and resuscitation. Results In silico analysis of the accessory domains of the Rpf proteins permitted their classification into several subfamilies. The RpfB subfamily is related to a group of firmicute proteins of unknown function, represented by YabE of Bacillus subtilis. The actinobacterial RpfB and firmicute YabE proteins have very similar domain structures and genomic contexts, except that in YabE, the actinobacterial Rpf domain is replaced by another domain, which we have called Sps. Although totally unrelated in both sequence and secondary structure, the Rpf and Sps domains fulfil the same function. We propose that these proteins have undergone "non-orthologous domain displacement", a phenomenon akin to "non-orthologous gene displacement" that has been described previously. Proteins containing the Sps domain are widely distributed throughout the firmicutes and they too fall into a number of distinct subfamilies. Comparative analysis of the accessory domains in the Rpf and Sps proteins, together with their weak similarity to lytic transglycosylases, provide clear evidence that they are muralytic enzymes. Conclusions The results indicate that the firmicute Sps proteins and the actinobacterial Rpf proteins are cognate and that they control bacterial culturability via enzymatic modification of the bacterial cell envelope.
Pallesen, Lone Tjener; Pedersen, Lise Refstrup Linnebjerg; Petersen, Torben Ellebæk
expression in placenta, salivary gland, thyroid gland, trachea, esophagus, kidney, testis, and the leukemia K-562 cell line. Furthermore, moderate expression was seen in the pancreas, adult and fetal lung, fetal kidney, lymph node, adult and fetal thymus, and parietal lobe. Structural motifs for interactions...
Jessica J R Hudson
Full Text Available The SMC5-6 protein complex is involved in the cellular response to DNA damage. It is composed of 6-8 polypeptides, of which Nse1, Nse3 and Nse4 form a tight sub-complex. MAGEG1, the mammalian ortholog of Nse3, is the founding member of the MAGE (melanoma-associated antigen protein family and Nse4 is related to the EID (E1A-like inhibitor of differentiation family of transcriptional repressors.Using site-directed mutagenesis, protein-protein interaction analyses and molecular modelling, we have identified a conserved hydrophobic surface on the C-terminal domain of Nse3 that interacts with Nse4 and identified residues in its N-terminal domain that are essential for interaction with Nse1. We show that these interactions are conserved in the human orthologs. Furthermore, interaction of MAGEG1, the mammalian ortholog of Nse3, with NSE4b, one of the mammalian orthologs of Nse4, results in transcriptional co-activation of the nuclear receptor, steroidogenic factor 1 (SF1. In an examination of the evolutionary conservation of the Nse3-Nse4 interactions, we find that several MAGE proteins can interact with at least one of the NSE4/EID proteins.We have found that, despite the evolutionary diversification of the MAGE family, the characteristic hydrophobic surface shared by all MAGE proteins from yeast to humans mediates its binding to NSE4/EID proteins. Our work provides new insights into the interactions, evolution and functions of the enigmatic MAGE proteins.
Identification of four families of yCCR4- and Mg2+-dependent endonuclease-related proteins in higher eukaryotes, and characterization of orthologs of yCCR4 with a conserved leucine-rich repeat essential for hCAF1/hPOP2 binding
Full Text Available Abstract Background The yeast yCCR4 factor belongs to the CCR4-NOT transcriptional regulatory complex, in which it interacts, through its leucine-rich repeat (LRR motif with yPOP2. Recently, yCCR4 was shown to be a component of the major cytoplasmic mRNA deadenylase complex, and to contain a fold related to the Mg2+-dependent endonuclease core. Results Here, we report the identification of nineteen yCCR4-related proteins in eukaryotes (including yeast, plants and animals, which all contain the yCCR4 endonuclease-like fold, with highly conserved CCR4-specific residues. Phylogenetic and genomic analyses show that they form four distinct families, one of which contains the yCCR4 orthologs. The orthologs in animals possess a leucine-rich repeat domain. We show, using two-hybrid and far-Western assays, that the human member binds to the human yPOP2 homologs, i.e. hCAF1 and hPOP2, in a LRR-dependent manner. Conclusions We have identified the mammalian orthologs of yCCR4 and have shown that the human member binds to the human yPOP2 homologs, thus strongly suggesting conservation of the CCR4-NOT complex from yeast to human. All members of the four identified yCCR4-related protein families show stricking conservation of the endonuclease-like catalytic motifs of the yCCR4 C-terminal domain and therefore constitute a new family of potential deadenylases in mammals.
Gasparis, Sebastian; Orczyk, Waclaw; Nadolska-Orczyk, Anna
Secaloindoline a (Sina) and secaloindoline b (Sinb) genes of hexaploid triticale (x Triticosecale Wittmack) are orthologs of puroindoline a (Pina) and puroindoline b (Pinb) in hexaploid wheat (Triticum aestivum L.). It has already been proven that RNA interference (RNAi)-based silencing of Pina and Pinb genes significantly decreased the puroindoline a and puroindoline b proteins in wheat and essentially increased grain hardness (J Exp Bot 62:4025-4036, 2011). The function of Sina and Sinb in triticale was tested by means of RNAi silencing and compared to wheat. Novel Sina and Sinb alleles in wild-type plants of cv. Wanad were identified and their expression profiles characterized. Alignment with wheat Pina-D1a and Pinb-D1a alleles showed 95% and 93.3% homology with Sina and Sinb coding sequences. Twenty transgenic lines transformed with two hpRNA silencing cassettes directed to silence Sina or Sinb were obtained by the Agrobacterium-mediated method. A significant decrease of expression of both Sin genes in segregating progeny of tested T1 lines was observed independent of the silencing cassette used. The silencing was transmitted to the T4 kernel generation. The relative transcript level was reduced by up to 99% in T3 progeny with the mean for the sublines being around 90%. Silencing of the Sin genes resulted in a substantial decrease of secaloindoline a and secaloindoline b content. The identity of SIN peptides was confirmed by mass spectrometry. The hardness index, measured by the SKCS (Single Kernel Characterization System) method, ranged from 22 to 56 in silent lines and from 37 to 49 in the control, and the mean values were insignificantly lower in the silent ones, proving increased softness. Additionally, the mean total seed protein content of silenced lines was about 6% lower compared with control lines. Correlation coefficients between hardness and transcript level were weakly positive. We documented that RNAi-based silencing of Sin genes resulted in
Full Text Available Abstract Background The potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. A core subset of stress-associated bZIP transcription factors from rice (Oryza sativa formed ten clusters of orthologous groups (COG with genes from the monocot sorghum (Sorghum bicolor and dicot Arabidopsis (Arabidopsis thaliana. The total cis-regulatory information content of each stress-associated COG was examined by phylogenetic footprinting to reveal ortholog-specific, lineage-specific and species-specific conservation patterns. Results The most apparent pattern observed was the occurrence of spatially conserved ‘core modules’ among the COGs but not among paralogs. These core modules are comprised of various combinations of two to four putative transcription factor binding site (TFBS classes associated with either developmental or stress-related functions. Outside the core modules are specific stress (ABA, oxidative, abiotic, biotic or organ-associated signals, which may be functioning as ‘regulatory fine-tuners’ and further define lineage-specific and species-specific cis-regulatory signatures. Orthologous monocot and dicot promoters have distinct TFBS classes involved in disease and oxidative-regulated expression, while the orthologous rice and sorghum promoters have distinct combinations of root-specific signals, a pattern that is not particularly conserved in Arabidopsis. Conclusions Patterns of cis-regulatory conservation imply that each ortholog has distinct signatures, further suggesting that they are potentially unique in a regulatory context despite the presumed conservation of broad biological function during speciation. Based on the observed patterns of conservation, we postulate that core modules are likely primary determinants of basal developmental programming, which may be integrated with and further elaborated by additional intrinsic or extrinsic signals in
The Lulo or naranjilla (Solanum quitoense Lam.) and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt.) are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32) and tree tomatoes (n = 30) through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII) in other Solanaceae (Asterid) species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested) and tree tomatoes (26 out of 41) for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with FST > 0.90), which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species. PMID:21637482
Mittasch, Juliane; Böttcher, Christoph; Frolov, Andrej; Strack, Dieter; Milkowski, Carsten
As a result of the phenylpropanoid pathway, many Brassicaceae produce considerable amounts of soluble hydroxycinnamate conjugates, mainly sinapate esters. From oilseed rape (Brassica napus), we cloned two orthologs of the Arabidopsis (Arabidopsis thaliana) gene REDUCED EPIDERMAL FLUORESCENCE1 (REF1) encoding a coniferaldehyde/sinapaldehyde dehydrogenase. The enzyme is involved in the formation of ferulate and sinapate from the corresponding aldehydes, thereby linking lignin and hydroxycinnamate biosynthesis as a potential branch-point enzyme. We used RNA interference to silence REF1 genes in seeds of oilseed rape. Nontargeted metabolite profiling showed that BnREF1-suppressing seeds produced a novel chemotype characterized by reduced levels of sinapate esters, the appearance of conjugated monolignols, dilignols, and trilignols, altered accumulation patterns of kaempferol glycosides, and changes in minor conjugates of caffeate, ferulate, and 5-hydroxyferulate. BnREF1 suppression affected the level of minor sinapate conjugates more severely than that of the major component sinapine. Mapping of the changed metabolites onto the phenylpropanoid metabolic network revealed partial redirection of metabolic sequences as a major impact of BnREF1 suppression. PMID:23424250
Mittasch, Juliane; Böttcher, Christoph; Frolov, Andrej; Strack, Dieter; Milkowski, Carsten
As a result of the phenylpropanoid pathway, many Brassicaceae produce considerable amounts of soluble hydroxycinnamate conjugates, mainly sinapate esters. From oilseed rape (Brassica napus), we cloned two orthologs of the Arabidopsis (Arabidopsis thaliana) gene reduced epidermal fluorescence1 (REF1) encoding a coniferaldehyde/sinapaldehyde dehydrogenase. The enzyme is involved in the formation of ferulate and sinapate from the corresponding aldehydes, thereby linking lignin and hydroxycinnamate biosynthesis as a potential branch-point enzyme. We used RNA interference to silence REF1 genes in seeds of oilseed rape. Nontargeted metabolite profiling showed that BnREF1-suppressing seeds produced a novel chemotype characterized by reduced levels of sinapate esters, the appearance of conjugated monolignols, dilignols, and trilignols, altered accumulation patterns of kaempferol glycosides, and changes in minor conjugates of caffeate, ferulate, and 5-hydroxyferulate. BnREF1 suppression affected the level of minor sinapate conjugates more severely than that of the major component sinapine. Mapping of the changed metabolites onto the phenylpropanoid metabolic network revealed partial redirection of metabolic sequences as a major impact of BnREF1 suppression.
Jensen, Jacob Kruger [Michigan State Univ., East Lansing, MI (United States). Dept. of Plant Biology; Michigan State Univ., East Lansing, MI (United States). DOE Great Lakes Bioenergy Research Center; Busse-Wicher, Marta [Univ. of Cambridge (United Kingdom). Dept. of Biochemistry; Poulsen, Christian Peter [Carlsberg Research Lab., Copenhagen (Denmark); Fangel, Jonatan Ulrik [Carlsberg Research Lab., Copenhagen (Denmark); Smith, Peter James [Univ. of Georgia, Athens, GA (United States). Complex Carbohydrate Research Center; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC); Yang, Jeong-Yeh [Univ. of Georgia, Athens, GA (United States). Complex Carbohydrate Research Center; Peña, Maria-Jesus [Univ. of Georgia, Athens, GA (United States). Complex Carbohydrate Research Center; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC); Dinesen, Malene Hessellund [Carlsberg Research Lab., Copenhagen (Denmark); Martens, Helle Juel [Univ. of Copenhagen (Denmark). Dept. of Plant and Environmental Sciences; Melkonian, Michael [Univ. zu Koln (Germany). Botanical Inst., Dept. of Biological Sciences; Wong, Gane Ka-Shu [BGI-Shenzhen, Shenzhen, Guangdong (China); Moremen, Kelley W. [Univ. of Georgia, Athens, GA (United States). Complex Carbohydrate Research Center; Wilkerson, Curtis Gene [Michigan State Univ., East Lansing, MI (United States). Dept. of Plant Biology; Michigan State Univ., East Lansing, MI (United States). DOE Great Lakes Bioenergy Research Center; Michigan State Univ., East Lansing, MI (United States). Dept. of Biochemistry and Molecular Biology; Scheller, Henrik Vibe [Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division; Dupree, Paul [Univ. of Cambridge (United Kingdom). Dept. of Biochemistry; Ulvskov, Peter [Univ. of Georgia, Athens, GA (United States). Complex Carbohydrate Research Center; Urbanowicz, Breeanna Rae [Univ. of Georgia, Athens, GA (United States). Complex Carbohydrate Research Center; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC); Harholt, Jesper [Carlsberg Research Lab., Copenhagen (Denmark)
Insights into the evolution of plant cell walls have important implications for comprehending these diverse and abundant biological structures. In order to understand the evolving structure-function relationships of the plant cell wall, it is imperative to trace the origin of its different components. The present study is focused on plant 1,4-β-xylan, tracing its evolutionary origin by genome and transcriptome mining followed by phylogenetic analysis, utilizing a large selection of plants and algae. It substantiates the findings by heterologous expression and biochemical characterization of a charophyte alga xylan synthase. Of the 12 known gene classes involved in 1,4-β-xylan formation, XYS1/IRX10 in plants, IRX7, IRX8, IRX9, IRX14 and GUX occurred for the first time in charophyte algae. An XYS1/IRX10 ortholog from Klebsormidium flaccidum, designated K. flaccidumXYLAN SYNTHASE-1 (KfXYS1), possesses 1,4-β-xylan synthase activity, and 1,4-β-xylan occurs in the K. flaccidum cell wall. Finally, these data suggest that plant 1,4-β-xylan originated in charophytes and shed light on the origin of one of the key cell wall innovations to occur in charophyte algae, facilitating terrestrialization and emergence of polysaccharide-based plant cell walls.
McEwan, Deborah L; Feinbaum, Rhonda L; Stroustrup, Nicholas; Haas, Wilhelm; Conery, Annie L; Anselmo, Anthony; Sadreyev, Ruslan; Ausubel, Frederick M
Many pathogens secrete toxins that target key host processes resulting in the activation of immune pathways. The secreted Pseudomonas aeruginosa toxin Exotoxin A (ToxA) disrupts intestinal protein synthesis, which triggers the induction of a subset of P. aeruginosa-response genes in the nematode Caenorhabditis elegans. We show here that one ToxA-induced C. elegans gene, the Tribbles pseudokinase ortholog nipi-3, is essential for host survival following exposure to P. aeruginosa or ToxA. We find that NIPI-3 mediates the post-developmental expression of intestinal immune genes and proteins and primarily functions in parallel to known immune pathways, including p38 MAPK signaling. Through mutagenesis screening, we identify mutants of the bZIP C/EBP transcription factor cebp-1 that suppress the hypersusceptibility defects of nipi-3 mutants. NIPI-3 is a negative regulator of CEBP-1, which in turn negatively regulates protective immune mechanisms. This pathway represents a previously unknown innate immune signaling pathway in intestinal epithelial cells that is involved in the surveillance of cellular homeostasis. Because NIPI-3 and CEBP-1 are also essential for C. elegans development, NIPI-3 is analogous to other key innate immune signaling molecules such as the Toll receptors in Drosophila that have an independent role during development.
Enciso-Rodríguez, Felix; Martínez, Rodrigo; Lobo, Mario; Barrero, Luz Stella
The Lulo or naranjilla (Solanum quitoense Lam.) and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt.) are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32) and tree tomatoes (n = 30) through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII) in other Solanaceae (Asterid) species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested) and tree tomatoes (26 out of 41) for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with F(ST) > 0.90), which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species.
Full Text Available The Lulo or naranjilla (Solanum quitoense Lam. and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt. are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32 and tree tomatoes (n = 30 through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII in other Solanaceae (Asterid species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested and tree tomatoes (26 out of 41 for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with F ST > 0.90, which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species.
Jackson, Daniel J; Reim, Laurin; Randow, Clemens; Cerveau, Nicolas; Degnan, Bernard M; Fleck, Claudia
Despite the evolutionary success and ancient heritage of the molluscan shell, little is known about the molecular details of its formation, evolutionary origins, or the interactions between the material properties of the shell and its organic constituents. In contrast to this dearth of information, a growing collection of molluscan shell-forming proteomes and transcriptomes suggest they are comprised of both deeply conserved, and lineage specific elements. Analyses of these sequence data sets have suggested that mechanisms such as exon shuffling, gene co-option, and gene family expansion facilitated the rapid evolution of shell-forming proteomes and supported the diversification of this phylum specific structure. In order to further investigate and test these ideas we have examined the molecular features and spatial expression patterns of two shell-forming genes (Lustrin and ML1A2) and coupled these observations with materials properties measurements of shells from a group of closely related gastropods (abalone). We find that the prominent "GS" domain of Lustrin, a domain believed to confer elastomeric properties to the shell, varies significantly in length between the species we investigated. Furthermore, the spatial expression patterns of Lustrin and ML1A2 also vary significantly between species, suggesting that both protein architecture, and the regulation of spatial gene expression patterns, are important drivers of molluscan shell evolution. Variation in these molecular features might relate to certain materials properties of the shells of these species. These insights reveal an important and underappreciated source of variation within shell-forming proteomes that must contribute to the diversity of molluscan shell phenotypes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Han, Sungwon; Bahmanyar, Shirin; Zhang, Peixiang; Grishin, Nick; Oegema, Karen; Crooke, Roseann; Graham, Mark; Reue, Karen; Dixon, Jack E.; Goodman, Joel M.
Lipin-1 catalyzes the formation of diacylglycerol from phosphatidic acid. Lipin-1 mutations cause lipodystrophy in mice and acute myopathy in humans. It is heavily phosphorylated, and the yeast ortholog Pah1p becomes membrane-associated and active upon dephosphorylation by the Nem1p-Spo7p membrane complex. A mammalian ortholog of Nem1p is the C-terminal domain nuclear envelope phosphatase 1 (CTDNEP1, formerly “dullard”), but its Spo7p-like partner is unknown, and the need for its existence is debated. Here, we identify the metazoan ortholog of Spo7p, TMEM188, renamed nuclear envelope phosphatase 1-regulatory subunit 1 (NEP1-R1). CTDNEP1 and NEP1-R1 together complement a nem1Δspo7Δ strain to block endoplasmic reticulum proliferation and restore triacylglycerol levels and lipid droplet number. The two human orthologs are in a complex in cells, and the amount of CTDNEP1 is increased in the presence of NEP1-R1. In the Caenorhabditis elegans embryo, expression of nematode CTDNEP1 and NEP1-R1, as well as lipin-1, is required for normal nuclear membrane breakdown after zygote formation. The expression pattern of NEP1-R1 and CTDNEP1 in human and mouse tissues closely mirrors that of lipin-1. CTDNEP1 can dephosphorylate lipins-1a, -1b, and -2 in human cells only in the presence of NEP1-R1. The nuclear fraction of lipin-1b is increased when CTDNEP1 and NEP1-R1 are co-expressed. Therefore, NEP1-R1 is functionally conserved from yeast to humans and functions in the lipin activation pathway. PMID:22134922
Anita M Quintana
Full Text Available There are 8 different human syndromes caused by mutations in the cholesterol synthesis pathway. A subset of these disorders such as Smith-Lemli-Opitz disorder, are associated with facial dysmorphia. However, the molecular and cellular mechanisms underlying such facial deficits are not fully understood, primarily because of the diverse functions associated with the cholesterol synthesis pathway. Recent evidence has demonstrated that mutation of the zebrafish ortholog of HMGCR results in orofacial clefts. Here we sought to expand upon these data, by deciphering the cholesterol dependent functions of the cholesterol synthesis pathway from the cholesterol independent functions. Moreover, we utilized loss of function analysis and pharmacological inhibition to determine the extent of sonic hedgehog (Shh signaling in animals with aberrant cholesterol and/or isoprenoid synthesis. Our analysis confirmed that mutation of hmgcs1, which encodes the first enzyme in the cholesterol synthesis pathway, results in craniofacial abnormalities via defects in cranial neural crest cell differentiation. Furthermore targeted pharmacological inhibition of the cholesterol synthesis pathway revealed a novel function for isoprenoid synthesis during vertebrate craniofacial development. Mutation of hmgcs1 had no effect on Shh signaling at 2 and 3 days post fertilization (dpf, but did result in a decrease in the expression of gli1, a known Shh target gene, at 4 dpf, after morphological deficits in craniofacial development and chondrocyte differentiation were observed in hmgcs1 mutants. These data raise the possibility that deficiencies in cholesterol modulate chondrocyte differentiation by a combination of Shh independent and Shh dependent mechanisms. Moreover, our results describe a novel function for isoprenoids in facial development and collectively suggest that cholesterol regulates craniofacial development through versatile mechanisms.
Li, Airong; Ahsen, Osman O; Liu, Jonathan J; Du, Chuang; McKee, Mary L; Yang, Yan; Wasco, Wilma; Newton-Cheh, Christopher H; O'Donnell, Christopher J; Fujimoto, James G; Zhou, Chao; Tanzi, Rudolph E
The SRY-related HMG-box 5 (SOX5) gene encodes a member of the SOX family of transcription factors. Recently, genome-wide association studies have implicated SOX5 as a candidate gene for susceptibility to four cardiac-related endophenotypes: higher resting heart rate (HR), the electrocardiographic PR interval, atrial fibrillation and left ventricular mass. We have determined that human SOX5 has a highly conserved Drosophila ortholog, Sox102F, and have employed transgenic Drosophila models to quantitatively measure cardiac function in adult flies. For this purpose, we have developed a high-speed and ultrahigh-resolution optical coherence tomography imaging system, which enables rapid cross-sectional imaging of the heart tube over various cardiac cycles for the measurement of cardiac structural and dynamical parameters such as HR, dimensions and areas of heart chambers, cardiac wall thickness and wall velocities. We have found that the silencing of Sox102F resulted in a significant decrease in HR, heart chamber size and cardiac wall velocities, and a significant increase in cardiac wall thickness that was accompanied by disrupted myofibril structure in adult flies. In addition, the silencing of Sox102F in the wing led to increased L2, L3 and wing marginal veins and increased and disorganized expression of wingless, the central component of the Wnt signaling pathway. Collectively, the silencing of Sox102F resulted in severe cardiac dysfunction and structural defects with disrupted Wnt signaling transduction in flies. This implicates an important functional role for SOX5 in heart and suggests that the alterations in SOX5 levels may contribute to the pathogenesis of multiple cardiac diseases or traits.
Dominic J. Bennett
Full Text Available The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data available can pose considerable barriers to their usefulness. A key issue in this domain is the high frequency of sequence mislabeling encountered when searching for suitable sequences for phylogenetic analysis. These issues include, among others, the incorrect identification of sequenced species, non-standardized and ambiguous sequence annotation, and the inadvertent addition of paralogous sequences by users. Taken together, these issues likely add considerable noise, error or bias to phylogenetic inference, a risk that is likely to increase with the size of phylogenies or the molecular datasets used to generate them. Here we present a software package, phylotaR that bypasses the above issues by using instead an alignment search tool to identify orthologous sequences. Our package builds on the framework of its predecessor, PhyLoTa, by providing a modular pipeline for identifying overlapping sequence clusters using up-to-date GenBank data and providing new features, improvements and tools. We demonstrate and test our pipeline’s effectiveness by presenting trees generated from phylotaR clusters for two large taxonomic clades: Palms and primates. Given the versatility of this package, we hope that it will become a standard tool for any research aiming to use GenBank data for phylogenetic analysis.
Full Text Available BACKGROUND: Gene duplication is a key evolutionary mechanism providing material for the generation of genes with new or modified functions. The fate of duplicated gene copies has been amply discussed and several models have been put forward to account for duplicate conservation. The specialization model considers that duplication of a bifunctional ancestral gene could result in the preservation of both copies through subfunctionalization, resulting in the distribution of the two ancestral functions between the gene duplicates. Here we investigate whether the presumed bifunctional character displayed by the single branched chain amino acid aminotransferase present in K. lactis has been distributed in the two paralogous genes present in S. cerevisiae, and whether this conservation has impacted S. cerevisiae metabolism. PRINCIPAL FINDINGS: Our results show that the KlBat1 orthologous BCAT is a bifunctional enzyme, which participates in the biosynthesis and catabolism of branched chain aminoacids (BCAAs. This dual role has been distributed in S. cerevisiae Bat1 and Bat2 paralogous proteins, supporting the specialization model posed to explain the evolution of gene duplications. BAT1 is highly expressed under biosynthetic conditions, while BAT2 expression is highest under catabolic conditions. Bat1 and Bat2 differential relocalization has favored their physiological function, since biosynthetic precursors are generated in the mitochondria (Bat1, while catabolic substrates are accumulated in the cytosol (Bat2. Under respiratory conditions, in the presence of ammonium and BCAAs the bat1Δ bat2Δ double mutant shows impaired growth, indicating that Bat1 and Bat2 could play redundant roles. In K. lactis wild type growth is independent of BCAA degradation, since a Klbat1Δ mutant grows under this condition. CONCLUSIONS: Our study shows that BAT1 and BAT2 differential expression and subcellular relocalization has resulted in the distribution of the
Hong-Jing Li; Xiang-Hua Li; Jing-Hua Xiao; Rod A. Wing; Shi-Ping Wang
The rice disease resistance (R) gene Xa3/Xa26 (having also been named Xa3 and Xa26) against Xanthomonas oryzae pv.oryzae (Xoo),which causes bacterial blight disease,belongs to a multiple gene family clustered in chromosome 11 and is from an AA genome rice cultivar (Oryza sativa L.).This family encodes leucine-rich repeat (LRR) receptor kinasetype proteins.Here,we show that the orthologs (alleles) of Xa3/Xa26,Xa3/Xa26-2,and Xa3/Xa26-3,from wild Oryza species O.officinalis (CC genome) and O.minuta (BBCC genome),respectively,were also R genes against Xoo.Xa3/Xa26-2 and Xa3/Xa26-3 conferred resistance to 16 of the 18 Xoo strains examined.Comparative sequence analysis of the Xa3/Xa26 families in the two wild Oryza species showed that Xa3/Xa26-3 appeared to have originated from the CC genome of O.minuta.The predicted proteins encoded by Xa3/Xa26,Xa3/Xa26-2,and Xa3/Xa26-3 share 91-99％ sequence identity and 94-99％ sequence similarity.Transgenic plants carrying a single copy of Xa3/Xa26,Xa3/Xa26-2,or Xa3/Xa26-3,in the same genetic background,showed a similar resistance spectrum to a set of Xoo strains,although plants carrying Xa3/Xa26-2 or Xa3/Xa26-3 showed lower resistance levels than the plants carrying Xa3/Xa26.These results suggest that the Xa3/Xa26 locus predates the speciation of A and C genome,which is approximately 7.5 million years ago.Thus,the resistance specificity of this locus has been conserved for a long time.
James H Catterson
Full Text Available The vertebrate Kindlins are an evolutionarily conserved family of proteins critical for integrin signalling and cell adhesion. Kindlin-2 (KIND2 is associated with intercalated discs in mice, suggesting a role in cardiac syncytium development; however, deficiency of Kind2 leads to embryonic lethality. Morpholino knock-down of Kind2 in zebrafish has a pleiotropic effect on development that includes the heart. It therefore remains unclear whether cardiomyocyte Kind2 expression is required for cardiomyocyte junction formation and the development of normal cardiac function. To address this question, the expression of Fermitin 1 and Fermitin 2 (Fit1, Fit2, the two Drosophila orthologs of Kind2, was silenced in Drosophila cardiomyocytes. Heart development was assessed in adult flies by immunological methods and videomicroscopy. Silencing both Fit1 and Fit2 led to a severe cardiomyopathy characterised by the failure of cardiomyocytes to develop as a functional syncytium and loss of synchrony between cardiomyocytes. A null allele of Fit1 was generated but this had no impact on the heart. Similarly, the silencing of Fit2 failed to affect heart function. In contrast, the silencing of Fit2 in the cardiomyocytes of Fit1 null flies disrupted syncytium development, leading to severe cardiomyopathy. The data definitively demonstrate a role for Fermitins in the development of a functional cardiac syncytium in Drosophila. The findings also show that the Fermitins can functionally compensate for each other in order to control syncytium development. These findings support the concept that abnormalities in cardiomyocyte KIND2 expression or function may contribute to cardiomyopathies in humans.
Ding, Lihua; Wang, Yanwen; Yu, Hao
SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) encodes a MADS-box protein that plays an essential role in integrating multiple flowering signals to regulate the transition from vegetative to reproductive development in the model plant Arabidopsis. Although SOC1-like genes have been isolated in various angiosperms, its orthologs in Orchidaceae, one of the largest families of flowering plants, are so far unknown. To investigate the regulatory mechanisms of flowering time control in orchids, we isolated a SOC1-like gene, DOSOC1, from Dendrobium Chao Praya Smile. DOSOC1 was highly expressed in reproductive organs, including inflorescence apices, pedicels, floral buds and open flowers. Its expression significantly increased in whole plantlets during the transition from vegetative to reproductive development, which usually occurred after 8 weeks of culture in Dendrobium Chao Praya Smile. In the shoot apex at the floral transitional stage, DOSOC1 was particularly expressed in emerging floral meristems. Overexpression of DOSOC1 in wild-type Arabidopsis plants resulted in early flowering, which was coupled with the up-regulation of two other flowering promoters, AGAMOUS-LIKE 24 and LEAFY. In addition, overexpression of DOSOC1 was able partially to complement the late-flowering phenotype of Arabidopsis soc1-2 loss-of-function mutants. Furthermore, we successfully created seven 35S:DOSOC1 transgenic Dendrobium orchid lines, which consistently exhibited earlier flowering than wild-type orchids. Our results suggest that SOC1-like genes play an evolutionarily conserved role in promoting flowering in the Orchidaceae family, and that DOSOC1 isolated from Dendrobium Chao Praya Smile could serve as an important target for genetic manipulation of flowering time in orchids.
Full Text Available Physical interactions between proteins mediate a variety of biological functions, including signal transduction, physical structuring of the cell and regulation. While extensive catalogs of such interactions are known from model organisms, their evolutionary histories are difficult to study given the lack of interaction data from phylogenetic outgroups. Using phylogenomic approaches, we infer a upper bound on the time of origin for a large set of human protein-protein interactions, showing that most such interactions appear relatively ancient, dating no later than the radiation of placental mammals. By analyzing paired alignments of orthologous and putatively interacting protein-coding genes from eight mammals, we find evidence for weak but significant co-evolution, as measured by relative selective constraint, between pairs of genes with interacting proteins. However, we find no strong evidence for shared instances of directional selection within an interacting pair. Finally, we use a network approach to show that the distribution of selective constraint across the protein interaction network is non-random, with a clear tendency for interacting proteins to share similar selective constraints. Collectively, the results suggest that, on the whole, protein interactions in mammals are under selective constraint, presumably due to their functional roles.
Wolf Yuri I
Full Text Available Abstract Background Collections of Clusters of Orthologous Genes (COGs provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs. Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. Results The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major ‘highways’ of horizontal gene transfer. Conclusions The updated collection
Natale, D A; Shankavaram, U T; Galperin, M Y; Wolf, Y I; Aravind, L; Koonin, E V
Standard archival sequence databases have not been designed as tools for genome annotation and are far from being optimal for this purpose. We used the database of Clusters of Orthologous Groups of proteins (COGs) to reannotate the genomes of two archaea, Aeropyrum pernix, the first member of the Crenarchaea to be sequenced, and Pyrococcus abyssi. A. pernix and P. abyssi proteins were assigned to COGs using the COGNITOR program; the results were verified on a case-by-case basis and augmented by additional database searches using the PSI-BLAST and TBLASTN programs. Functions were predicted for over 300 proteins from A. pernix, which could not be assigned a function using conventional methods with a conservative sequence similarity threshold, an approximately 50% increase compared to the original annotation. A. pernix shares most of the conserved core of proteins that were previously identified in the Euryarchaeota. Cluster analysis or distance matrix tree construction based on the co-occurrence of genomes in COGs showed that A. pernix forms a distinct group within the archaea, although grouping with the two species of Pyrococci, indicative of similar repertoires of conserved genes, was observed. No indication of a specific relationship between Crenarchaeota and eukaryotes was obtained in these analyses. Several proteins that are conserved in Euryarchaeota and most bacteria are unexpectedly missing in A. pernix, including the entire set of de novo purine biosynthesis enzymes, the GTPase FtsZ (a key component of the bacterial and euryarchaeal cell-division machinery), and the tRNA-specific pseudouridine synthase, previously considered universal. A. pernix is represented in 48 COGs that do not contain any euryarchaeal members. Many of these proteins are TCA cycle and electron transport chain enzymes, reflecting the aerobic lifestyle of A. pernix. Special-purpose databases organized on the basis of phylogenetic analysis and carefully curated with respect to known and
Ng, Chee-Hoe; Basil, Adeline H; Hang, Liting; Tan, Royston; Goh, Kian-Leong; O'Neill, Sharon; Zhang, Xiaodong; Yu, Fengwei; Lim, Kah-Leong
Despite intensive research, the etiology of Parkinson's disease (PD) remains poorly understood and the disease remains incurable. However, compelling evidence gathered over decades of research strongly support a role for mitochondrial dysfunction in PD pathogenesis. Related to this, PGC-1α, a key regulator of mitochondrial biogenesis, has recently been proposed to be an attractive target for intervention in PD. Here, we showed that silencing of expression of the Drosophila PGC-1α ortholog spargel results in PD-related phenotypes in flies and also seem to negate the effects of AMPK activation, which we have previously demonstrated to be neuroprotective, that is, AMPK-mediated neuroprotection appears to require PGC-1α. Importantly, we further showed that genetic or pharmacological activation of the Drosophila PGC-1α ortholog spargel is sufficient to rescue the disease phenotypes of Parkin and LRRK2 genetic fly models of PD, thus supporting the proposed use of PGC-1α-related strategies for neuroprotection in PD. Copyright © 2017 National Neuroscience Institute. Published by Elsevier Inc. All rights reserved.
Ukena, Kazuyoshi; Iwakoshi-Ukena, Eiko; Osugi, Tomohiro; Tsutsui, Kazuyoshi
Gonadotropin-inhibitory hormone (GnIH) was discovered in 2000 as a novel hypothalamic neuropeptide that inhibited gonadotropin release in the Japanese quail. GnIH and its orthologs have a common C-terminal LPXRFamide (X=L or Q) motif, and have been identified in vertebrates from agnathans to humans, apart from reptiles. In the present study, we characterized a cDNA encoding GnIH orthologs in the brain of the red-eared slider turtle. The deduced precursor protein consisted of 205 amino-acid residues, encoding three putative peptide sequences that included the LPXRFamide motif at their C-termini. In addition, the precursor sequence was most similar to those of avian species. Immunoaffinity purification combined with mass spectrometry confirmed that three mature peptides were produced in the brain. In situ hybridization and immunohistochemistry showed that turtle GnIH-containing cells were restricted to the periventricular hypothalamic nucleus. Immunoreactive fibers were densely distributed in the median eminence. Thus, GnIH and related peptides may act on the pituitary to regulate pituitary hormone release in turtles as well as other vertebrates. Copyright © 2015 Elsevier Inc. All rights reserved.
Poopanitpan, Napapol; Kobayashi, Satoshi; Fukuda, Ryouichi; Horiuchi, Hiroyuki; Ohta, Akinori
Research highlights: → POR1 is a Yarrowia lipolytica ortholog of farA involved in fatty acid response in A. nidulans. → Deletion of POR1 caused growth defects on fatty acids. → Δpor1 strain exhibited defects in the induction of genes involved in fatty acid utilization. -- Abstract: The yeast Yarrowia lipolytica effectively utilizes hydrophobic substrates such as fatty acids and n-alkanes. To identify a gene(s) regulating fatty acid utilization in Y. lipolytica, we first studied homologous genes to OAF1 and PIP2 of Saccharomyces cerevisiae, but their disruption did not change growth on oleic acid at all. We next characterized a Y. lipolytica gene, POR1 (primary oleate regulator 1), an ortholog of farA encoding a transcriptional activator that regulates fatty acid utilization in Aspergillus nidulans. The deletion mutant of POR1 was defective in the growth on various fatty acids, but not on glucose, glycerol, or n-hexadecane. It exhibited slight defect on n-decane. The transcriptional induction of genes involved in β-oxidation and peroxisome proliferation by oleate was distinctly diminished in the Δpor1 strains. These data suggest that POR1 encodes a transcriptional activator widely regulating fatty acid metabolism in Y. lipolytica.
Campoli, Chiara; Shtaya, Munqez; Davis, Seth J; von Korff, Maria
The circadian clock is an endogenous mechanism that coordinates biological processes with daily changes in the environment. In plants, circadian rhythms contribute to both agricultural productivity and evolutionary fitness. In barley, the photoperiod response regulator and flowering-time gene Ppd-H1 is orthologous to the Arabidopsis core-clock gene PRR7. However, relatively little is known about the role of Ppd-H1 and other components of the circadian clock in temperate crop species. In this study, we identified barley clock orthologs and tested the effects of natural genetic variation at Ppd-H1 on diurnal and circadian expression of clock and output genes from the photoperiod-response pathway. Barley clock orthologs HvCCA1, HvGI, HvPRR1, HvPRR37 (Ppd-H1), HvPRR73, HvPRR59 and HvPRR95 showed a high level of sequence similarity and conservation of diurnal and circadian expression patterns, when compared to Arabidopsis. The natural mutation at Ppd-H1 did not affect diurnal or circadian cycling of barley clock genes. However, the Ppd-H1 mutant was found to be arrhythmic under free-running conditions for the photoperiod-response genes HvCO1, HvCO2, and the MADS-box transcription factor and vernalization responsive gene Vrn-H1. We suggest that the described eudicot clock is largely conserved in the monocot barley. However, genetic differentiation within gene families and differences in the function of Ppd-H1 suggest evolutionary modification in the angiosperm clock. Our data indicates that natural variation at Ppd-H1 does not affect the expression level of clock genes, but controls photoperiodic output genes. Circadian control of Vrn-H1 in barley suggests that this vernalization responsive gene is also controlled by the photoperiod-response pathway. Structural and functional characterization of the barley circadian clock will set the basis for future studies of the adaptive significance of the circadian clock in Triticeae species.
Full Text Available Abstract Background Human α-galactosidase A (α-GAL and α-N-acetylgalactosaminidase (α-NAGA are presumed to share a common ancestor. Deficiencies of these enzymes cause two well-characterized human lysosomal storage disorders (LSD – Fabry (α-GAL deficiency and Schindler (α-NAGA deficiency diseases. Caenorhabditis elegans was previously shown to be a relevant model organism for several late endosomal/lysosomal membrane proteins associated with LSDs. The aim of this study was to identify and characterize C. elegans orthologs to both human lysosomal luminal proteins α-GAL and α-NAGA. Results BlastP searches for orthologs of human α-GAL and α-NAGA revealed a single C. elegans gene (R07B7.11 with homology to both human genes (α-galactosidase and α-N-acetylgalactosaminidase – gana-1. We cloned and sequenced the complete gana-1 cDNA and elucidated the gene organization. Phylogenetic analyses and homology modeling of GANA-1 based on the 3D structure of chicken α-NAGA, rice α-GAL and human α-GAL suggest a close evolutionary relationship of GANA-1 to both human α-GAL and α-NAGA. Both α-GAL and α-NAGA enzymatic activities were detected in C. elegans mixed culture homogenates. However, α-GAL activity on an artificial substrate was completely inhibited by the α-NAGA inhibitor, N-acetyl-D-galactosamine. A GANA-1::GFP fusion protein expressed from a transgene, containing the complete gana-1 coding region and 3 kb of its hypothetical promoter, was not detectable under the standard laboratory conditions. The GFP signal was observed solely in a vesicular compartment of coelomocytes of the animals treated with Concanamycin A (CON A or NH4Cl, agents that increase the pH of the cellular acidic compartment. Immunofluorescence detection of the fusion protein using polyclonal anti-GFP antibody showed a broader and coarsely granular cytoplasmic expression pattern in body wall muscle cells, intestinal cells, and a vesicular compartment of
Ariyarathna, H A Chandima K; Oldach, Klaus H; Francki, Michael G
Although the HKT transporter genes ascertain some of the key determinants of crop salt tolerance mechanisms, the diversity and functional role of group II HKT genes are not clearly understood in bread wheat. The advanced knowledge on rice HKT and whole genome sequence was, therefore, used in comparative gene analysis to identify orthologous wheat group II HKT genes and their role in trait variation under different saline environments. The four group II HKTs in rice identified two orthologous gene families from bread wheat, including the known TaHKT2;1 gene family and a new distinctly different gene family designated as TaHKT2;2. A single copy of TaHKT2;2 was found on each homeologous chromosome arm 7AL, 7BL and 7DL and each gene was expressed in leaf blade, sheath and root tissues under non-stressed and at 200 mM salt stressed conditions. The proteins encoded by genes of the TaHKT2;2 family revealed more than 93% amino acid sequence identity but ≤52% amino acid identity compared to the proteins encoded by TaHKT2;1 family. Specifically, variations in known critical domains predicted functional differences between the two protein families. Similar to orthologous rice genes on chromosome 6L, TaHKT2;1 and TaHKT2;2 genes were located approximately 3 kb apart on wheat chromosomes 7AL, 7BL and 7DL, forming a static syntenic block in the two species. The chromosomal region on 7AL containing TaHKT2;1 7AL-1 co-located with QTL for shoot Na(+) concentration and yield in some saline environments. The differences in copy number, genes sequences and encoded proteins between TaHKT2;2 homeologous genes and other group II HKT gene families within and across species likely reflect functional diversity for ion selectivity and transport in plants. Evidence indicated that neither TaHKT2;2 nor TaHKT2;1 were associated with primary root Na(+) uptake but TaHKT2;1 may be associated with trait variation for Na(+) exclusion and yield in some but not all saline environments.
Yeats, Trevor H.; Huang, Wenlin; Chatterjee, Subhasish
synthases within the large GDSL superfamily. We demonstrate that members of this ancient and conserved family of cutin synthase‐like (CUS) proteins act as polyester synthases with negligible hydrolytic activity. Moreover, solution‐state NMR analysis indicates that CD1 catalyzes the formation of primarily...... of hydroxyacylglycerol precursors, catalyzed by the GDSL‐motif lipase/hydrolase family protein (GDSL) Cutin Deficient 1 (CD1). Here, we present additional biochemical characterization of CD1 and putative orthologs from Arabidopsis thaliana and the moss Physcomitrella patens, which represent a distinct clade of cutin...... linear cutin oligomeric products in vitro. These results reveal a conserved mechanism of cutin polyester synthesis in land plants, and suggest that elaborations of the linear polymer, such as branching or cross‐linking, may require additional, as yet unknown, factors....
Zhao, Meixia; Du, Jianchang; Lin, Feng; Tong, Chaobo; Yu, Jingyin; Huang, Shunmou; Wang, Xiaowu; Liu, Shengyi; Ma, Jianxin
Recent sequencing of the Brassica rapa and Brassica oleracea genomes revealed extremely contrasting genomic features such as the abundance and distribution of transposable elements between the two genomes. However, whether and how these structural differentiations may have influenced the evolutionary rates of the two genomes since their split from a common ancestor are unknown. Here, we investigated and compared the rates of nucleotide substitution between two long terminal repeats (LTRs) of individual orthologous LTR-retrotransposons, the rates of synonymous and non-synonymous substitution among triplicated genes retained in both genomes from a shared whole genome triplication event, and the rates of genetic recombination estimated/deduced by the comparison of physical and genetic distances along chromosomes and ratios of solo LTRs to intact elements. Overall, LTR sequences and genic sequences showed more rapid nucleotide substitution in B. rapa than in B. oleracea. Synonymous substitution of triplicated genes retained from a shared whole genome triplication was detected at higher rates in B. rapa than in B. oleracea. Interestingly, non-synonymous substitution was observed at lower rates in the former than in the latter, indicating shifted densities of purifying selection between the two genomes. In addition to evolutionary asymmetry, orthologous genes differentially regulated and/or disrupted by transposable elements between the two genomes were also characterized. Our analyses suggest that local genomic and epigenomic features, such as recombination rates and chromatin dynamics reshaped by independent proliferation of transposable elements and elimination between the two genomes, are perhaps partially the causes and partially the outcomes of the observed inter-specific asymmetric evolution. © 2013 Purdue University The Plant Journal © 2013 John Wiley & Sons Ltd.
Full Text Available Volvox is a very interesting oogamous organism that exhibits various types of sexuality and/or sexual spheroids depending upon species or strains. However, molecular bases of such sexual reproduction characteristics have not been studied in this genus. In the model species V. carteri, an ortholog of the minus mating type-determining or minus dominance gene (MID of isogamous Chlamydomonas reinhardtii is male-specific and determines the sperm formation. Male and female genders are genetically determined (heterothallism in V. carteri, whereas in several other species of Volvox both male and female gametes (sperm and eggs are formed within the same clonal culture (homothallism. To resolve the molecular basis of the evolution of Volvox species with monoecious spheroids, we here describe a MID ortholog in the homothallic species V. africanus that produces both monoecious and male spheroids within a single clonal culture. Comparison of synonymous and nonsynonymous nucleotide substitutions in MID genes between V. africanus and heterothallic volvocacean species suggests that the MID gene of V. africanus evolved under the same degree of functional constraint as those of the heterothallic species. Based on semi quantitative reverse transcription polymerase chain reaction analyses using the asexual, male and monoecious spheroids isolated from a sexually induced V. africanus culture, the MID mRNA level was significantly upregulated in the male spheroids, but suppressed in the monoecious spheroids. These results suggest that the monoecious spheroid-specific down regulation of gene expression of the MID homolog correlates with the formation of both eggs and sperm in the same spheroid in V. africanus.
Grandi, Nicole; Cadeddu, Marta; Blomberg, Jonas; Mayer, Jens; Tramontano, Enzo
The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after their exogenous counterparts went extinct. Among human ERVs (HERVs), the HERV-W group is of particular interest for our physiology and pathology. A HERV-W provirus in locus 7q21.2 has been coopted during evolution to exert an essential role in placenta, and the group expression has been tentatively linked to Multiple Sclerosis and other diseases. Following up on a detailed analysis of 213 HERV-W insertions in the human genome, we now investigated the ERV-W group genomic spread within primate lineages. We analyzed HERV-W orthologous loci in the genome sequences of 12 non-human primate species belonging to Simiiformes (parvorders Catarrhini and Platyrrhini), Tarsiiformes and to the most primitive Prosimians. Analysis of HERV-W orthologous loci in non-human Catarrhini primates revealed species-specific insertions in the genomes of Chimpanzee (3), Gorilla (4), Orangutan (6), Gibbon (2) and especially Rhesus Macaque (66). Such sequences were acquired in a retroviral fashion and, in the majority of cases, by L1-mediated formation of processed pseudogenes. There were also a number of LTR-LTR homologous recombination events that occurred subsequent to separation of Catarrhini sub-lineages. Moreover, we retrieved 130 sequences in Marmoset and Squirrel Monkeys (family Cebidae, Platyrrhini parvorder), identified as ERV1-1_CJa based on RepBase annotations, which appear closely related to the ERV-W group. Such sequences were also identified in Atelidae and Pitheciidae, representative of the other Platyrrhini families. In contrast, no ERV-W-related sequences were found in genome sequence assemblies of Tarsiiformes and Prosimians. Overall, our
Hamidou Soumana, Illiassou; Tchicaya, Bernadette; Rialle, Stéphanie; Parrinello, Hugues; Geiger, Anne
Blood-feeding Glossina palpalis gambiense (Gpg) fly transmits the single-celled eukaryotic parasite Trypanosoma brucei gambiense (Tbg), the second Glossina fly African trypanosome pair being Glossina morsitans / T .brucei rhodesiense. Whatever the T. brucei subspecies, whereas the onset of their developmental program in the zoo-anthropophilic blood feeding flies does unfold in the fly midgut, its completion is taking place in the fly salivary gland where does emerge a low size metacyclic trypomastigote population displaying features that account for its establishment in mammals-human individuals included. Considering that the two Glossina - T. brucei pairs introduced above share similarity with respect to the developmental program of this African parasite, we were curious to map on the Glossina morsitans morsitans (Gmm), the Differentially Expressed Genes (DEGs) we listed in a previous study. Briefly, using the gut samples collected at days 3, 10, and 20 from Gpg that were fed or not at day 0 on Tbg-hosting mice, these DGE lists were obtained from RNA seq-based approaches. Here, post the mapping on the quality controlled DEGs on the Gmm genome, the identified ortholog genes were further annotated, the resulting datasets being compared. Around 50% of the Gpg DEGs were shown to have orthologs in the Gmm genome. Under one of the three Glossina midgut sampling conditions, the number of DEGs was even higher when mapping on the Gmm genome than initially recorded. Many Gmm genes annotated as "Hypothetical" were mapped and annotated on many distinct databases allowing some of them to be properly identified. We identify Glossina fly candidate genes encoding (a) a broad panel of proteases as well as (b) chitin-binding proteins, (c) antimicrobial peptide production-Pro3 protein, transferrin, mucin, atttacin, cecropin, etc-to further select in functional studies, the objectives being to probe and validated fly genome manipulation that prevents the onset of the developmental
Full Text Available Aldehyde deformylating oxygenase (ADO is a unique enzyme found exclusively in photosynthetic cyanobacteria, which natively converts acyl aldehyde precursors into hydrocarbon products embedded in cellular lipid bilayers. This capacity has opened doors for potential biotechnological applications aiming at biological production of diesel-range alkanes and alkenes, which are compatible with the nonrenewable petroleum-derived end-products in current use. The development of production platforms, however, has been limited by the relative inefficiency of ADO enzyme, promoting research towards finding new strategies and information to be used for rational design of enhanced pathways for hydrocarbon over-expression. In this work we present an optimized approach to study different ADO orthologs derived from different cyanobacterial species in an in vivo set-up in Escherichia coli. The system enabled comparison of alternative ADOs for the production efficiency of short-chain volatile C3-C7 alkanes, propane, pentane and heptane, and provided insight on the differences in substrate preference, catalytic efficiency and limitations associated with the enzymes. The work concentrated on five ADO orthologs which represent the most extensively studied cyanobacterial species in the field, and revealed distinct differences between the enzymes. In most cases the ADO from Nostoc punctiforme PCC 73102 performed the best in respect to yields and initial rates for the production of the volatile hydrocarbons. At the other extreme, the system harboring the ADO form Synechococcus sp. RS9917 produced very low amounts of the short-chain alkanes, primarily due to poor accumulation of the enzyme in E. coli. The ADOs from Synechocystis sp. PCC 6803 and Prochlorococcus marinus MIT9313, and the corresponding variant A134F displayed less divergence, although variation between chain-length preferences could be observed. The results confirmed the general trend of ADOs having
Full Text Available A decisive element in the human cation channel TRPM2 is a region in its cytosolic C-terminus named NUDT9H because of its homology to the NUDT9 enzyme, a pyrophosphatase degrading ADP-ribose (ADPR. In hTRPM2, however, the NUDT9H domain has lost its enzymatic activity but serves as a binding domain for ADPR. As consequence of binding, gating of the channel is initiated. Since ADPR is produced after oxidative DNA damage, hTRPM2 mediates Ca2+ influx in response to oxidative stress which may lead to cell death. In the genome of the sea anemone Nematostella vectensis (nv, a preferred model organism for the evolution of key bilaterian features, a TRPM2 ortholog has been identified that contains a NUDT9H domain as well. Heterologous expression of nvTRPM2 in HEK-293 cells reveals a cation channel with many close similarities to the human counterpart. Most notably, nvTRPM2 is activated by ADPR, and Ca2+ is a co-agonist. However, the intramolecular mechanisms of ADPR gating as well as the role of NUDT9H are strikingly different in the two species. Whereas already subtle changes of NUDT9H abolish ADPR gating in hTRPM2, the region can be completely removed from nvTRPM2 without loss of responses to ADPR. An alternative ADPR binding site seems to be present but has not yet been characterized. The ADP-ribose pyrophosphatase (ADPRase function of nvNUDT9H has been preserved but can be abolished by numerous genetic manipulations. All these manipulations create channels that are sensitive to hydrogen peroxide which fails to induce channel activity in wild-type nvTRPM2. Therefore, the function of NUDT9H in nvTRPM2 is the degradation of ADPR, thereby reducing agonist concentration in the presence of oxidative stress. Thus, the two TRPM2 orthologs have evolved divergently but nevertheless gained analogous functional properties, i.e., gating by ADPR with Ca2+ as co-factor. Opposite roles are played by the respective NUDT9H domains, either binding of ADPR and mediating
Stewart, Lucy R; Hwang, Min Sook; Falk, Bryce W
Interactions of Lettuce infectious yellows virus (LIYV)-encoded proteins were tested by yeast-two-hybrid (Y2H) assays. LIYV-encoded P34, Hsp70h, P59, CP, CPm, and P26 were tested in all possible pairwise combinations. Interaction was detected only for the P26-P26 combination. P26 self-interaction domains were mapped using a series of N- and C-terminal truncations. Orthologous P26 proteins from the criniviruses Beet pseudoyellows virus (BPYV), Cucurbit yellow stunting disorder virus (CYSDV), and Lettuce chlorosis virus (LCV) were also tested, and each exhibited strong self-interaction but no interaction with orthologous proteins. Two small putative proteins encoded by LIYV RNA2, P5 and P9, were also tested for interactions with the six aforementioned LIYV proteins and each other. No interactions were detected for P5, but P9-P9 self-interaction was detected. P26- and P9-encoding genes are present in all described members of the genus Crinivirus, but are not present in other members of the family Closteroviridae. LIYV P26 has previously been demonstrated to induce a unique LIYV cytopathology, plasmalemma deposits (PLDs), but no role is yet known for P9.
Breitkopf, Susanne B.; Yang, Xuemei; Begley, Michael J.; Kulkarni, Meghana; Chiu, Yu-Hsin; Turke, Alexa B.; Lauriol, Jessica; Yuan, Min; Qi, Jie; Engelman, Jeffrey A.; Hong, Pengyu; Kontaridis, Maria I.; Cantley, Lewis C.; Perrimon, Norbert; Asara, John M.
Using a series of immunoprecipitation (IP) - tandem mass spectrometry (LC-MS/MS) experiments and reciprocal BLAST, we conducted a fly-human cross-species comparison of the phosphoinositide-3-kinase (PI3K) interactome in a drosophila S2R+ cell line and several NSCLC and human multiple myeloma cell lines to identify conserved interacting proteins to PI3K, a critical signaling regulator of the AKT pathway. Using H929 human cancer cells and drosophila S2R+ cells, our data revealed an unexpected direct binding of Corkscrew, the drosophila ortholog of the non-receptor protein tyrosine phosphatase type II (SHP2) to the Pi3k21B (p60) regulatory subunit of PI3K (p50/p85 human ortholog) but no association with Pi3k92e, the human ortholog of the p110 catalytic subunit. The p85-SHP2 association was validated in human cell lines, and formed a ternary regulatory complex with GRB2-associated-binding protein 2 (GAB2). Validation experiments with knockdown of GAB2 and Far-Western blots proved the direct interaction of SHP2 with p85, independent of adaptor proteins and transfected FLAG-p85 provided evidence that SHP2 binding on p85 occurred on the SH2 domains. A disruption of the SHP2-p85 complex took place after insulin/IGF1 stimulation or imatinib treatment, suggesting that the direct SHP2-p85 interaction was both independent of AKT activation and positively regulates the ERK signaling pathway.
Knoll, Alexander; Higgins, James D; Seeliger, Katharina; Reha, Sarah J; Dangel, Natalie J; Bauknecht, Markus; Schröpfer, Susan; Franklin, F Christopher H; Puchta, Holger
The human hereditary disease Fanconi anemia leads to severe symptoms, including developmental defects and breakdown of the hematopoietic system. It is caused by single mutations in the FANC genes, one of which encodes the DNA translocase FANCM (for Fanconi anemia complementation group M), which is required for the repair of DNA interstrand cross-links to ensure replication progression. We identified a homolog of FANCM in Arabidopsis thaliana that is not directly involved in the repair of DNA lesions but suppresses spontaneous somatic homologous recombination via a RecQ helicase (At-RECQ4A)-independent pathway. In addition, it is required for double-strand break-induced homologous recombination. The fertility of At-fancm mutant plants is compromised. Evidence suggests that during meiosis At-FANCM acts as antirecombinase to suppress ectopic recombination-dependent chromosome interactions, but this activity is antagonized by the ZMM pathway to enable the formation of interference-sensitive crossovers and chromosome synapsis. Surprisingly, mutation of At-FANCM overcomes the sterility phenotype of an At-MutS homolog4 mutant by apparently rescuing a proportion of crossover-designated recombination intermediates via a route that is likely At-MMS and UV sensitive81 dependent. However, this is insufficient to ensure the formation of an obligate crossover. Thus, At-FANCM is not only a safeguard for genome stability in somatic cells but is an important factor in the control of meiotic crossover formation.
Taylor, S; Hofer, J; Murfet, I
Isolation and characterization of two severe alleles at the Stamina pistilloida (Stp) locus reveals that Stp is involved in a wide range of developmental processes in the garden pea. The most severe allele, stp-4, results in flowers consisting almost entirely of sepals and carpels. Production of ectopic secondary flowers in stp-4 plants suggests that Stp is involved in specifying floral meristem identity in pea. The stp mutations also reduce the complexity of the compound pea leaf, and primary inflorescences often terminate prematurely in an aberrant sepaloid flower. In addition, stp mutants were shorter than their wild-type siblings due to a reduction in cell number in their internodes. Fewer cells were also found in the epidermis of the leaf rachis of stp mutants. Examination of the effects of stp-4 in double mutant combinations with af, tl, det, and veg2-2-mutations known to influence leaf, inflorescence, and flower development in pea-suggests that Stp function is independent of these genes. A synergistic interaction between weak mutant alleles at Stp and Uni indicated that these two genes act together, possibly to regulate primordial growth. Molecular analysis revealed that Stp is the pea homolog of the Antirrhinum gene Fimbriata (Fim) and of UNUSUAL FLORAL ORGANS (UFO) from Arabidopsis. Differences between Fim/UFO and Stp mutant phenotypes and expression patterns suggest that expansion of Stp activity into the leaf was an important step during evolution of the compound leaf in the garden pea.
Li, Zhijie; Chakraborty, Sayan; Xu, Guozhou (NCSU)
Does not respond to nucleotides 1 (DORN1) has recently been identified as the first membrane-integral plant ATP receptor, which is required for ATP-induced calcium response, mitogen-activated protein kinase activation and defense responses in
Full Text Available The pentaspan membrane glycoprotein prominin-1 (CD133 is widely used in medicine as a cell surface marker of stem and cancer stem cells. It has opened new avenues in stem cell-based regenerative therapy and oncology. This molecule is largely used with human samples or the mouse model, and consequently most biological tools including antibodies are directed against human and murine prominin-1. Although the general structure of prominin-1 including its membrane topology is conserved throughout the animal kingdom, its primary sequence is poorly conserved. Thus, it is unclear if anti-human and -mouse prominin-1 antibodies cross-react with their orthologs in other species, especially dog. Answering this issue is imperative in light of the growing number of studies using canine prominin-1 as an antigenic marker. Here, we address this issue by cloning the canine prominin-1 and use its overexpression as a green fluorescent protein fusion protein in Madin-Darby canine kidney cells to determine its immunoreactivity with antibodies against human or mouse prominin-1. We used immunocytochemistry, flow cytometry and immunoblotting techniques and surprisingly found no cross-species immunoreactivity. These results raise some caution in data interpretation when anti-prominin-1 antibodies are used in interspecies studies.
Ignacio Perez de la Cruz
Full Text Available Loss-of-function mutations in the Caenorhabditis elegans gene sup-18 suppress the defects in muscle contraction conferred by a gain-of-function mutation in SUP-10, a presumptive regulatory subunit of the SUP-9 two-pore domain K(+ channel associated with muscle membranes. We cloned sup-18 and found that it encodes the C. elegans ortholog of mammalian iodotyrosine deiodinase (IYD, an NADH oxidase/flavin reductase that functions in iodine recycling and is important for the biosynthesis of thyroid hormones that regulate metabolism. The FMN-binding site of mammalian IYD is conserved in SUP-18, which appears to require catalytic activity to function. Genetic analyses suggest that SUP-10 can function with SUP-18 to activate SUP-9 through a pathway that is independent of the presumptive SUP-9 regulatory subunit UNC-93. We identified a novel evolutionarily conserved serine-cysteine-rich region in the C-terminal cytoplasmic domain of SUP-9 required for its specific activation by SUP-10 and SUP-18 but not by UNC-93. Since two-pore domain K(+ channels regulate the resting membrane potentials of numerous cell types, we suggest that the SUP-18 IYD regulates the activity of the SUP-9 channel using NADH as a coenzyme and thus couples the metabolic state of muscle cells to muscle membrane excitability.
Wei, Jingli; Hu, Xiaorong; Yang, Jingjing; Yang, Wencai
The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG) Release2.3 Predicted CDS (SL2.40) discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2%) of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei's genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis.
Full Text Available The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG Release2.3 Predicted CDS (SL2.40 discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2% of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei's genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis.
Full Text Available Abstract Interactomes of proteins under positive selection from ionizing-radiation-resistant bacteria (IRRB might be a part of the answer to the question as to how IRRB, particularly Deinococcus radiodurans R1 (Deira, resist ionizing radiation. Here, using the Database of Interacting Proteins (DIP and the Protein Structural Interactome (PSI-base server for PSI map, we have predicted novel interactions of orthologs of the 58 proteins under positive selection in Deira and other IRRB, but which are absent in IRSB. Among these, 18 domains and their interactomes have been identified in DNA checkpoint and repair; kinases pathways; energy and nucleotide metabolisms were the important biological processes that were found to be involved. This finding provides new clues to the cellular pathways that can to be important for ionizing-radiation resistance in Deira.
Luciani , Annie
International audience; The expression instrumental interaction as been introduced by Claude Cadoz to identify a human-object interaction during which a human manipulates a physical object - an instrument - in order to perform a manual task. Classical examples of instrumental interaction are all the professional manual tasks: playing violin, cutting fabrics by hand, moulding a paste, etc.... Instrumental interaction differs from other types of interaction (called symbolic or iconic interactio...
Lin, Lin; Gårdsvoll, Henrik; Huai, Qing
this difference by solving the crystal structure for the murine uPA.uPAR complex and demonstrate by extensive surface plasmon resonance studies that the kinetic rate constants for this interaction can be swapped completely between these orthologs by exchanging only two residues. This study not only discloses......The high affinity interaction between the urokinase-type plasminogen activator (uPA) and its glycolipid-anchored receptor (uPAR) is decisive for cell surface-associated plasminogen activation. Because plasmin activity controls fibrinolysis in a variety of pathological conditions, including cancer...
Reinick, Christina L; Liang, Liang; Angleson, Josepha K; Dores, Robert M
The melanocortin-5 receptor (MC(5)) of the dogfish Squalus acanthias (SacMC(5) receptor) can be functionally expressed in CHO cells in the absence of the co-expression of an exogenous MRAP cDNA. Both human ACTH(1-24) and dogfish ACTH(1-25) were much better stimulators of the SacMC(5) receptor than any of the mammalian or dogfish MSH ligands that were tested. The order of ligand selectivity for the dogfish melanocortins was ACTH(1-25)>αMSH>γ-MSH=δ-MSH>β-MSH. Unlike mammalian MC(5) receptors, the functional expression of the SacMC(5) receptor was not negatively impacted when the receptor was co-expressed with a cartilaginous fish (Callorhinchus milii) MRAP2 cDNA. However, co-expression with either mouse mMRAP1 or zebrafish zfMRAP1 increased the sensitivity of SacMC(5) receptor for hACTH(1-24) by at least one order of magnitude. Hence, SacMC(5) receptor has the potential to interact with MRAP1 orthologs and in this regard behaved more like a melanocortin MC(2) receptor ortholog than a melanocortin MC(5) receptor ortholog. These observations are discussed in light of the evolution of the melanocortin receptor gene family in cartilaginous fish, and the physiological implications of these observations are considered. Copyright © 2012 Elsevier B.V. All rights reserved.
Balan, Andrea; Santacruz-Pérez, Carolina; Moutran, Alexandre; Ferreira, Luís Carlos Souza; Neshich, Goran; Gonçalves Barbosa, João Alexandre Ribeiro
In Xanthomonas axonopodis pv. citri (Xac or X. citri), the modA gene codes for a periplasmic protein (ModA) that is capable of binding molybdate and tungstate as part of the ABC-type transporter required for the uptake of micronutrients. In this study, we report the crystallographic structure of the Xac ModA protein with bound molybdate. The Xac ModA structure is similar to orthologs with known three-dimensional structures and consists of two nearly symmetrical domains separated by a hinge region where the oxyanion-binding site lies. Phylogenetic analysis of different ModA orthologs based on sequence alignments revealed three groups of molybdate-binding proteins: bacterial phytopathogens, enterobacteria and soil bacteria. Even though the ModA orthologs are segregated into different groups, the ligand-binding hydrogen bonds are mostly conserved, except for Archaeglobus fulgidus ModA. A detailed discussion of hydrophobic interactions in the active site is presented and two new residues, Ala38 and Ser151, are shown to be part of the ligand-binding pocket.
Zhang, Haokun; Kiuchi, Takashi; Wang, Lingyan; Kawamoto, Munetaka; Suzuki, Yutaka; Sugano, Sumio; Banno, Yutaka; Katsuma, Susumu; Shimada, Toru
"Tanaka's mottled translucent" (otm) is a mutation of the silkworm Bombyx mori that exhibits translucent skin during larval stages. We performed positional cloning of the gene responsible for otm and mapped it to a 364-kb region on chromosome 5 that contains 22 hypothetical protein-coding genes. We performed RNA-seq analysis of the epidermis and fat body of otm larvae and determined that the gene BGIBMGA002619 may be responsible for the otm mutation. BGIBMGA002619 encodes the biosynthesis of lysosome-related organelles complex 1 (BLOC-1) subunit 5, whose ortholog is responsible for the Muted mutant in mouse. Accordingly, we named this gene Bm-muted. We discovered that the expression of Bm-muted in the epidermis and fat body of otm mutants was dramatically suppressed compared with the wild type. We determined the nucleotide sequences of the full-length cDNA and genomic region corresponding to Bm-muted and found that a 538-bp long DNA sequence similar to B. mori transposon Organdy was inserted into the 3' end of the first intron of Bm-muted in two otm strains. The Bm-muted cDNA of otm mutants lacked exon 2, and accordingly generated a premature stop codon in exon 3. In addition, short interfering RNA (siRNA)-mediated knockdown of this gene caused localized partial translucency of larval skin. These data indicate that the mutation in Bm-muted caused the otm-mutant phenotype. We propose that the insertion of Organdy caused a splicing disorder in Bm-muted in the otm mutant, resulting in a null mutation of Bm-muted. This mutation is likely to cause deficiencies in urate granule formation in epidermal cells that result in translucent larval skin. Copyright © 2017 Elsevier B.V. All rights reserved.
Full Text Available MicroRNAs (miRNAs are small non-coding RNAs that have been identified in animals, plants, and viruses. These small RNAs play important roles in post-transcriptional regulation of various cellular processes, including development, differentiation, and all aspects of cancer biology. Rapid-onset T-cell lymphoma of chickens, namely Marek’s disease (MD, induced by Gallid alphaherpesvirus 2 (GaHV2, could provide an ideal natural animal model for herpesvirus-related cancer research. GaHV2 encodes 26 mature miRNAs derived from 14 precursors assembled in three distinct gene clusters in the viral genome. One of the most highly expressed GaHV2 miRNAs, miR-M4-5p, shows high sequence similarity to the cellular miR-155 and the miR-K12-11 encoded by Kaposi’s sarcoma-associated herpesvirus, particularly in the miRNA “seed region.” As with miR-K12-11, miR-M4-5p shares a common set of host and viral target genes with miR-155, suggesting that they may target the same regulatory cellular networks; however, differences in regulatory function between miR-155 and miR-M4-5p may distinguish non-viral and viral mediated tumorigenesis. In this review, we focus on the functions of miR-M4-5p as the viral ortholog of miR-155 to explore how the virus mimics a host pathway to benefit the viral life cycle and trigger virus-induced tumorigenesis.
Full Text Available Abstract Background Tremendous progress has been made in the field of evo-devo through comparisons of related genes from diverse taxa. While the vast number of species in nature precludes a complete analysis of the molecular evolution of even one single gene family, this would not be necessary to understand fundamental mechanisms underlying gene evolution if experiments could be designed to systematically sample representative points along the path of established phylogenies to trace changes in regulatory and coding gene sequence. This isolation of homologous genes from phylogenetically diverse, representative species can be challenging, especially if the gene is under weak selective pressure and evolving rapidly. Results Here we present an approach - Rapid Isolation of Gene Homologs across Taxa (RIGHT - to efficiently isolate specific members of gene families. RIGHT is based upon modification and a combination of degenerate polymerase chain reaction (PCR and gene-specific amplified fragment length polymorphism (AFLP. It allows targeted isolation of specific gene family members from any organism, only requiring genomic DNA. We describe this approach and how we used it to isolate members of several different gene families from diverse arthropods spanning millions of years of evolution. Conclusions RIGHT facilitates systematic isolation of one gene from large gene families. It allows for efficient gene isolation without whole genome sequencing, RNA extraction, or culturing of non-model organisms. RIGHT will be a generally useful method for isolation of orthologs from both distant and closely related species, increasing sample size and facilitating the tracking of molecular evolution of gene families and regulatory networks across the tree of life.
Lee, Youngdeuk; Elvitigala, Don Anushka Sandaruwan; Whang, Ilson; Lee, Sukkyoung; Kim, Hyowon; Zoysa, Mahanama De; Oh, Chulhong; Kang, Do-Hyung; Lee, Jehee
Immune signaling cascades have an indispensable role in the host defense of almost all the organisms. Tumor necrosis factor (TNF) signaling is considered as a prominent signaling pathway in vertebrate as well as invertebrate species. Within the signaling cascade, TNF receptor-associated factor (TRAF) and TNF receptor-associated protein (TTRAP) has been shown to have a crucial role in the modulation of immune signaling in animals. Here, we attempted to characterize a novel molluskan ortholog of TTRAP (AbTTRAP) from disk abalone (Haliotis discus discus) and analyzed its expression levels under pathogenic stress. The complete coding sequence of AbTTRAP consisted of 1071 nucleotides, coding for a 357 amino acid peptide, with a predicted molecular mass of 40 kDa. According to our in-silico analysis, AbTTRAP resembled the typical TTRAP domain architecture, including a 5'-tyrosyl DNA phosphodiesterase domain. Moreover, phylogenetic analysis revealed its common ancestral invertebrate origin, where AbTTRAP was clustered with molluskan counterparts. Quantitative real time PCR showed universally distributed expression of AbTTRAP in selected tissues of abalone, from which more prominent expression was detected in hemocytes. Upon stimulation with two pathogen-derived mitogens, lipopolysaccharide (LPS) and polyinosinic:polycytidylic acid (poly I:C), transcript levels of AbTTRAP in hemocytes and gill tissues were differentially modulated with time. In addition, the recombinant protein of AbTTRAP exhibited prominent endonuclease activity against abalone genomic DNA, which was enhanced by the presence of Mg(2+) in the medium. Collectively, these results reinforce the existence of the TNF signaling cascade in mollusks like disk abalone, further implicating the putative regulatory behavior of TTRAP in invertebrate host pathology. Copyright © 2014 Elsevier Ltd. All rights reserved.
The theoretical and experimental evidences to form a basis for Lagrangian Quantum field theory for Weak Interactions are discussed. In this context, gauge invariance aspects of such interactions are showed. (L.C.) [pt
Kaplan, I.G.; Rodimova, O.B.; AN SSSR, Tomsk. Inst. Optiki Atmosfery)
The present state of the intermolecular interaction theory is described. The general physical picture of the molecular interactions is given, the relative contributions of interactions of different types are analyzed (electrostatic, resonance, induction, dispersion, relativistic, magnetostatic and exchange), and the main ones in each range of separations are picked out. The methods of the potential curve calculations are considered, specific for definite separations between the interacting systems. The special attention is paid to the analysis of approximations used in different theoretical calculation methods
Christina M Taylor
Full Text Available Finding new drug targets for pathogenic infections would be of great utility for humanity, as there is a large need to develop new drugs to fight infections due to the developing resistance and side effects of current treatments. Current drug targets for pathogen infections involve only a single protein. However, proteins rarely act in isolation, and the majority of biological processes occur via interactions with other proteins, so protein-protein interactions (PPIs offer a realm of unexplored potential drug targets and are thought to be the next-generation of drug targets. Parasitic worms were chosen for this study because they have deleterious effects on human health, livestock, and plants, costing society billions of dollars annually and many sequenced genomes are available. In this study, we present a computational approach that utilizes whole genomes of 6 parasitic and 1 free-living worm species and 2 hosts. The species were placed in orthologous groups, then binned in species-specific orthologous groups. Proteins that are essential and conserved among species that span a phyla are of greatest value, as they provide foundations for developing broad-control strategies. Two PPI databases were used to find PPIs within the species specific bins. PPIs with unique helminth proteins and helminth proteins with unique features relative to the host, such as indels, were prioritized as drug targets. The PPIs were scored based on RNAi phenotype and homology to the PDB (Protein DataBank. EST data for the various life stages, GO annotation, and druggability were also taken into consideration. Several PPIs emerged from this study as potential drug targets. A few interactions were supported by co-localization of expression in M. incognita (plant parasite and B. malayi (H. sapiens parasite, which have extremely different modes of parasitism. As more genomes of pathogens are sequenced and PPI databases expanded, this methodology will become increasingly
Full Text Available BACKGROUND: In the genesis of many tissues, a phase of cell proliferation is followed by cell cycle exit and terminal differentiation. The latter two processes overlap: genes involved in the cessation of growth may also be important in triggering differentiation. Though conceptually distinct, they are often causally related and functional interactions between the cell cycle machinery and cell fate control networks are fundamental to coordinate growth and differentiation. A switch from proliferation to differentiation may also be important in the life cycle of single-celled organisms, and genes which arose as regulators of microbial differentiation may be conserved in higher organisms. Studies in microorganisms may thus contribute to understanding the molecular links between cell cycle machinery and the determination of cell fate choice networks. METHODOLOGY/PRINCIPAL FINDINGS: Here we show that in the amoebozoan D. discoideum, an ortholog of the metazoan antiproliferative gene btg controls cell fate, and that this function is dependent on the presence of a second tumor suppressor ortholog, the retinoblastoma-like gene product. Specifically, we find that btg-overexpressing cells preferentially adopt a stalk cell (and, more particularly, an Anterior-Like Cell fate. No btg-dependent preference for ALC fate is observed in cells in which the retinoblastoma-like gene has been genetically inactivated. Dictyostelium btg is the only example of non-metazoan member of the BTG family characterized so far, suggesting that a genetic interaction between btg and Rb predated the divergence between dictyostelids and metazoa. CONCLUSIONS/SIGNIFICANCE: While the requirement for retinoblastoma function for BTG antiproliferative activity in metazoans is known, an interaction of these genes in the control of cell fate has not been previously documented. Involvement of a single pathway in the control of mutually exclusive processes may have relevant implication in the
This chapter attempts to describe and compare some of the more important nucleon-nucleon interactions that have been used in nuclear structure calculations, and to relate them where possible to the real nucleon-nucleon interaction. Explains that different interactions have been used depending on whether one is fitting to total binding energies and densities with a Hartree Fock (HF) calculation or fitting to spectra and spectroscopic data in a shell model calculation. Examines both types of calculation after two preliminary sections concerned with notation and with the philosophy underlying the use of model spaces and effective interactions. Discusses Skyrme interactions, finite range interactions, small model space, large model space, and the Sussex potential matrix elements. Focuses on the more empirical approaches in which a simple form is chosen for the effective interaction in a given model space and the parameters are deduced from fitting many-body data
Hlouchová, Klára; Navrátil, Václav; Tykvart, Jan; Šácha, Pavel; Konvalinka, Jan
Roč. 19, č. 9 (2012), s. 1316-1322 ISSN 0929-8673 R&D Projects: GA ČR GAP304/12/0847 Institutional research plan: CEZ:AV0Z40550506 Keywords : PSMA * GCPIII * NAALADase L * splice variants * homologs * PSMAL Subject RIV: CE - Biochemistry Impact factor: 4.070, year: 2012
Bathige, S D N K; Umasuthan, Navaneethaiyer; Priyathilaka, Thanthrige Thiunuwan; Thulasitha, William Shanthakumar; Jayasinghe, J D H E; Wan, Qiang; Nam, Bo-Hye; Lee, Jehee
Signal transducer and activator of transcription 2 (STAT2) is a key element that transduces signals from the cell membrane to the nucleus via the type I interferon-signaling pathway. Although the structural and functional aspects of STAT proteins are well studied in mammals, information on teleostean STATs is very limited. In this study, a STAT paralog, which is highly homologous to the STAT2 members, was identified from a commercially important fish species called rock bream and designated as RbSTAT2. The RbSTAT2 gene was characterized at complementary DNA (cDNA) and genomic sequence levels, and was found to possess structural features common with its mammalian counterparts. The complete cDNA sequence was distributed into 24 exons in the genomic sequence. The promoter proximal region was analyzed and found to contain potential transcription factor binding sites to regulate the transcription of RbSTAT2. Phylogenetic studies and comparative genomic structure organization revealed the distinguishable evolution for fish and other vertebrate STAT2 orthologs. Transcriptional quantification was performed by SYBR Green quantitative real-time PCR (qPCR) and the ubiquitous expression of RbSTAT2 transcripts was observed in all tissues analyzed from healthy fish, with a remarkably high expression in blood cells. Significantly (Prock bream irido virus; RBIV), bacterial (Edwardsiella tarda and Streptococcus iniae), and immune stimulants (poly I:C and LPS). Antiviral potential was further confirmed by WST-1 assay, by measuring the viability of rock bream heart cells treated with RBIV. In addition, results of an in vitro challenge experiment signified the influence of rock bream interleukin-10 (RbIL-10) on transcription of RbSTAT2. Subcellular localization studies by transfection of pEGFP-N1/RbSTAT2 into rock bream heart cells revealed that the RbSTAT2 was usually located in the cytoplasm and translocated near to the nucleus upon poly I:C administration. Altogether, these
Sajjad, Muhammad; Ma, Xiaoling; Habibullah Khan, Sultan; Shoaib, Muhammad; Song, Yanhong; Yang, Wenlong; Zhang, Aimin; Liu, Dongcheng
The Flo2 gene is a member of a conserved gene family in plants. This gene has been found to be related to thousand grain weight (TGW) in rice. Its orthologs in hexaploid wheat were cloned, and the haplotype variation in TaFlo2-A1 was tested for association with TGW. The cloned sequences of TaFlo2-A1, TaFlo2-B1 and TaFlo2-D1 contained 23, 23 and 24 exons, respectively. The deduced proteins of TaFlo2-A1 (1734 aa), TaFlo2-B1 (1698 aa) and TaFlo2-D1 (1682 aa) were highly similar (>94%) and exhibited >77% similarity with the rice FLO2 protein. Like the rice FLO2 protein, four tetratricopeptide repeat (TPR) motifs were observed in the deduced TaFLO2 protein. An 8-bp InDel (-10 to -17 bp) in the promoter region and five SNPs in first intron of TaFlo2-A1 together formed two haplotypes, TaFlo2-A1a and TaFlo2-A1b, in bread wheat. TaFlo2 was located on homeologous group 2 chromosomes. TaFlo2-A1 was inferred to be located on deletion bin '2AL1-0.85-1.00'. The TaFlo2-A1 haplotypes were characterized in the Chinese Micro Core Collection (MCC) and Pakistani wheat collection using the molecular marker TaFlo2-Indel8. TaFlo2-A1 was found to be associated with TGW but not with grain number per spike (GpS) in both the MCC and Pakistani wheat collections. The frequency of TaFlo2-A1b (positive haplotype) was low in commercial wheat cultivars; thus this haplotype can be selected to improve grain weight without negatively affecting GpS. The expression level of TaFlo2-A1 in developing grains at 5 DAF (days after flowering) was positively correlated with TGW in cultivars carrying the positive haplotype. This study will likely lead to additional investigations to understand the regulatory mechanism of the Flo2 gene in hexaploid wheat. Furthermore, the newly developed molecular marker 'TaFlo2-InDel8' could be incorporated into the kit of wheat breeders for use in marker-assisted selection.
Full Text Available In mammalian organisms liquid tumors such as acute myeloid leukemia (AML are related to spontaneous chromosomal translocations ensuing in gene fusions. We previously developed a system named bridge-induced translocation (BIT that allows linking together two different chromosomes exploiting the strong endogenous homologous recombination system of the yeast Saccharomyces cerevisiae. The BIT system generates a heterogeneous population of cells with different aneuploidies and severe aberrant phenotypes reminiscent of a cancerogenic transformation. In this work, thanks to a complex pop-out methodology of the marker used for the selection of translocants, we succeeded by BIT technology to precisely reproduce in yeast the peculiar chromosome translocation that has been associated with AML, characterized by the fusion between the human genes NUP98 and TOP2B. To shed light on the origin of the DNA fragility within NUP98, an extensive analysis of the curvature, bending, thermostability, and B-Z transition aptitude of the breakpoint region of NUP98 and of its yeast ortholog NUP145 has been performed. On this basis, a DNA cassette carrying homologous tails to the two genes was amplified by PCR and allowed the targeted fusion between NUP145 and TOP2, leading to reproduce the chimeric transcript in a diploid strain of S. cerevisiae. The resulting translocated yeast obtained through BIT appears characterized by abnormal spherical bodies of nearly 500 nm of diameter, absence of external membrane and defined cytoplasmic localization. Since Nup98 is a well-known regulator of the post-transcriptional modification of P53 target genes, and P53 mutations are occasionally reported in AML, this translocant yeast strain can be used as a model to test the constitutive expression of human P53. Although the abnormal phenotype of the translocant yeast was never rescued by its expression, an exogenous P53 was recognized to confer increased vitality to the translocants, in
Full Text Available BACKGROUND: Hyphal growth and multidrug resistance of C. albicans are important features for virulence and antifungal therapy of this pathogenic fungus. METHODOLOGY/PRINCIPAL FINDINGS: Here we show by phenotypic complementation analysis that the C. albicans gene AGE3 is the functional ortholog of the yeast ARF-GAP-encoding gene GCS1. The finding that the gene is required for efficient endocytosis points to an important functional role of Age3p in endosomal compartments. Most C. albicans age3Delta mutant cells which grew as cell clusters under yeast growth conditions showed defects in filamentation under different hyphal growth conditions and were almost completely disabled for invasive filamentous growth. Under hyphal growth conditions only a fraction of age3Delta cells shows a wild-type-like polarization pattern of the actin cytoskeleton and lipid rafts. Moreover, age3Delta cells were highly susceptible to several unrelated toxic compounds including antifungal azole drugs. Irrespective of the AGE3 genotype, C-terminal fusions of GFP to the drug efflux pumps Cdr1p and Mdr1p were predominantly localized in the plasma membrane. Moreover, the plasma membranes of wild-type and age3Delta mutant cells contained similar amounts of Cdr1p, Cdr2p and Mdr1p. CONCLUSIONS/SIGNIFICANCE: The results indicate that the defect in sustaining filament elongation is probably caused by the failure of age3Delta cells to polarize the actin cytoskeleton and possibly of inefficient endocytosis. The high susceptibility of age3Delta cells to azoles is not caused by inefficient transport of efflux pumps to the cell membrane. A possible role of a vacuolar defect of age3Delta cells in drug susceptibility is proposed and discussed. In conclusion, our study shows that the ARF-GAP Age3p is required for hyphal growth which is an important virulence factor of C. albicans and essential for detoxification of azole drugs which are routinely used for antifungal therapy. Thus, it
Full Text Available Flowering in the appropriate season is critical for successful reproduction in angiosperms. The orchid species, Dendrobium nobile, requires vernalization to achieve flowering in the spring, but the underlying regulatory network has not been identified to date. The MADS-box transcription factor DnAGL19 was previously identified in a study of low-temperature treated D. nobile buds and was suggested to regulate vernalization-induced flowering. In this study, phylogenetic analysis of DnAGL9 and the MADS-box containing proteins showed that DnAGL19 is phylogenetically closely related to the SOC1-like protein from orchid Dendrobium Chao Parya Smile, DOSOC1. The orchid clade closed to but is not included into the SOC1-1/TM3 clades associated with either eudicots or monocots, suggesting that DnAGL19 is an SOC1-1/TM3-like ortholog. DnAGL19 was found to be highly expressed in pseudobulbs, leaves, roots and axillary buds but rarely in flowers, and to be substantially upregulated in axillary buds by prolonged low-temperature treatments. Overexpression of DnAGL19 in Arabidopsis thaliana resulted in a small but significantly reduced time to bolting, suggesting that flowering time was slightly accelerated under normal growth conditions. Consistent with this, the A. thaliana APETELA1 (AP1 gene was expressed at an earlier stage in transgenic lines than in wild type plants, while the FLOWERING LOCUS T (FT gene was suppressed, suggesting that altered regulations on these transcription factors caused the weak promotion of flowering. HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 1 (HOS1 was slightly activated under the same conditions, suggesting that the HOS1-FT module may be involved in the DnAGL19-related network. Under vernalization conditions, FT expression was significantly upregulated, whereas HOS1 expression in the transgenic A. thaliana has a level similar to that in wild type. Taken together, these results suggest that DnAGL19 controls the action of the
Ogava, S.; Savada, S.; Nakagava, M.
The problem of the use of weak interaction laws to study models of elementary particles is discussed. The most typical examples of weak interaction is beta-decay of nucleons and muons. Beta-interaction is presented by quark currents in the form of universal interaction of the V-A type. Universality of weak interactions is well confirmed using as examples e- and μ-channels of pion decay. Hypothesis on partial preservation of axial current is applicable to the analysis of processes with pion participation. In the framework of the model with four flavours lepton decays of hadrons are considered. Weak interaction without lepton participation are also considered. Properties of neutral currents are described briefly
Cross-species prophylactic efficacy of Sm-p80-based vaccine and intracellular localization of Sm-p80/Sm-p80 ortholog proteins during development in Schistosoma mansoni, Schistosoma japonicum, and Schistosoma haematobium.
Molehin, Adebayo J; Sennoune, Souad R; Zhang, Weidong; Rojo, Juan U; Siddiqui, Arif J; Herrera, Karlie A; Johnson, Laura; Sudduth, Justin; May, Jordan; Siddiqui, Afzal A
Schistosomiasis remains a major global health problem. Despite large-scale schistosomiasis control efforts, clear limitations such as possible emergence of drug resistance and reinfection rates highlight the need for an effective schistosomiasis vaccine. Schistosoma mansoni large subunit of calpain (Sm-p80)-based vaccine formulations have shown remarkable efficacy in protecting against S. mansoni challenge infections in mice and baboons. In this study, we evaluated the cross-species protective efficacy of Sm-p80 vaccine against S. japonicum and S. haematobium challenge infections in rodent models. We also elucidated the expression of Sm-p80 and Sm-p80 ortholog proteins in different developmental stages of S. mansoni, S. haematobium, and S. japonicum. Immunization with Sm-p80 vaccine reduced worm burden by 46.75% against S. japonicum challenge infection in mice. DNA prime/protein boost (1 + 1 dose administered on a single day) resulted in 26.95% reduction in worm burden in S. haematobium-hamster infection/challenge model. A balanced Th1 (IFN-γ, TNF-α, IL-2, and IL-12) and Th2 (IL-4, IgG1) type of responses were observed following vaccination in both S. japonicum and S. haematobium challenge trials and these are associated with the prophylactic efficacy of Sm-p80 vaccine. Immunohistochemistry demonstrated that Sm-p80/Sm-p80 ortholog proteins are expressed in different life cycle stages of the three major human species of schistosomes studied. The data presented in this study reinforce the potential of Sm-p80-based vaccine for both hepatic/intestinal and urogenital schistosomiasis occurring in different geographical areas of the world. Differential expression of Sm-p80/Sm-p80 protein orthologs in different life cycle makes this vaccine potentially useful in targeting different levels of infection, disease, and transmission.
Petersen, Marianne Graves; Krogh, Peter; Ludvigsen, Martin
Within architecture, there is a long tradition of careful design of floors. The design has been concerned with both decorating floors and designing floors to carry information. Ubiquitous computing technology offers new opportunities for designing interactive floors. This paper presents three...... different interactive floor concepts. Through an urban perspective it draws upon the experiences of floors in architecture, and provides a set of design issues for designing interactive floors....
The video Playful Interaction describes a future architectural office, and envisions ideas and concepts for playful interactions between people, materials and appliances in a pervasive and augmented working environment. The video both describes existing developments, technologies and designs...... as well as ideas not yet implemented such as playful modes of interaction with an augmented ball. Playful Interaction has been used as a hybrid of a vision video and a video prototype (1). Externally the video has been used to visualising our new ideas, and internally the video has also worked to inspire...
Petersen, Marianne Graves; Iversen, Ole Sejer; Krogh, Peter
, as it promotes aesthetics of use, rather than aesthetics of appearance. We coin this approach in the perspective of aesthetic interaction. Finally we make the point that aesthetics is not re-defining everything known about interactive systems. We provide a framework placing this perspective among other...
Lawson, Lartey; Nielsen, Kurt
We discuss individual learning by interactive benchmarking using stochastic frontier models. The interactions allow the user to tailor the performance evaluation to preferences and explore alternative improvement strategies by selecting and searching the different frontiers using directional...... in the suggested benchmarking tool. The study investigates how different characteristics on dairy farms influences the technical efficiency....
Löwgren, Jonas; Eriksen, Mette Agger; Linde, Per
We report an ongoing study of palpable computing to support surgical rehabilitation, in the general field of interaction design for ubiquitous computing. Through explorative design, fieldwork and participatory design techniques, we explore the design principle of explicit interaction as an interp...
Fogtmann, Maiken Hillerup; Fritsch, Jonas; Kortbek, Karen Johanne
Within the Human-Computer Interaction community there is a growing interest in designing for the whole body in interaction design. The attempts aimed at addressing the body have very different outcomes spanning from theoretical arguments for understanding the body in the design process, to more...... practical examples of designing for bodily potential. This paper presents Kinesthetic Interaction as a unifying concept for describing the body in motion as a foundation for designing interactive systems. Based on the theoretical foundation for Kinesthetic Interaction, a conceptual framework is introduced...... to reveal bodily potential in relation to three design themes – kinesthetic development, kinesthetic means and kinesthetic disorder; and seven design parameters – engagement, sociality, movability, explicit motivation, implicit motivation, expressive meaning and kinesthetic empathy. The framework is a tool...
Ready to create rich interactive experiences with your artwork, designs, or prototypes? This is the ideal place to start. With this hands-on guide, you'll explore several themes in interactive art and design-including 3D graphics, sound, physical interaction, computer vision, and geolocation-and learn the basic programming and electronics concepts you need to implement them. No previous experience is necessary. You'll get a complete introduction to three free tools created specifically for artists and designers: the Processing programming language, the Arduino microcontroller, and the openFr
Li, Weiqiang; Yoshida, Akiko; Takahashi, Megumu; Maekawa, Masahiko; Kojima, Mikiko; Sakakibara, Hitoshi; Kyozuka, Junko
The DWARF14 (D14) gene of rice functions within the signaling pathway of strigolactones, a group of plant hormones that inhibits shoot branching. We isolated a recessive mutant named super apical dormant (sad1-1) from a suppressor screen of d14-1. The growth of tillers (vegetative shoot branches) is suppressed in both the d14-1 sad1-1 double mutant and the sad1-1 single mutant. In addition, the sad1-1 mutant shows pleiotropic defects throughout development. SAD1 encodes an ortholog of RPA34.5, a subunit of RNA polymerase I (Pol I). Consequently, the level of ribosomal RNA (rRNA) is severely reduced in the sad1-1 mutant. These results indicate that proper ribosome function is a prerequisite for normal development in plants. The Arabidopsis ortholog of SAD1 was previously isolated as a Mediator-interacting protein. Here we show that SAD1 interacts physically with the Mediator complex through direct binding with OsMED4, a component of the middle module of the Mediator complex in rice. It is known that Mediator interacts with Pol II, which transcribes mRNAs and functions as a central regulator of transcription. This study indicates a novel aspect of Mediator function in Pol I-controlled rRNA transcription. TFIIF2 and RPC53 are the counterparts of RPA34.5 in Pol II and Pol III, respectively. We demonstrate that the rice orthologs of these proteins also interact with OsMED4. Our results suggest that interaction with MED4 in the Mediator complex is a common feature of the three types of RNA polymerases. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.
Interaction graphs were introduced as a general, uniform, construction of dynamic models of linear logic, encompassing all Geometry of Interaction (GoI) constructions introduced so far. This series of work was inspired from Girard's hyperfinite GoI, and develops a quantitative approach that should...... be understood as a dynamic version of weighted relational models. Until now, the interaction graphs framework has been shown to deal with exponentials for the constrained system ELL (Elementary Linear Logic) while keeping its quantitative aspect. Adapting older constructions by Girard, one can clearly define...... "full" exponentials, but at the cost of these quantitative features. We show here that allowing interpretations of proofs to use continuous (yet finite in a measure-theoretic sense) sets of states, as opposed to earlier Interaction Graphs constructions were these sets of states were discrete (and finite...
Deterding, Sebastian; Lucero, Andrés; Holopainen, Jussi
Wherever the rapid evolution of interactive technologies disrupts standing situational norms, creates new, often unclear situational audiences, or crosses cultural boundaries, embarrassment is likely. This makes embarrassment a fundamental adoption and engagement hurdle, but also a creative design...
Del Duca, V.; Marage, P.
The general framework of diffractive deep inelastic scattering is introduced and reports given in the session on diffractive interactions at the international workshop on deep-inelastic scattering and related phenomena, Rome, April 1996, are presented. (orig.)
This pattern describes the idea of making a user interface of discrete, reusable entities---here called interaction widgets. The idea behind widgets is described using two perspectives, that of the user and that of the developer. It is the forces from these two perspectives that are balanced...... in the pattern. The intended audience of the pattern is developers and researchers within the field of human computer interaction....
Cani , Marie-Paule; Bertails , Florence
International audience; Processing interactions is one of the main challenges in hair animation. Indeed, in addition to the collisions with the body, an extremely large number of contacts with high friction rates are permanently taking place between individual hair strands. Simulating the latter is essential: without hair self-interactions, strands would cross each other during motion or come to rest at the same location, yielding unrealistic behavior and a visible lack of hair volume. This c...
Davis, Darren; Yaveroğlu, Ömer Nebil; Malod-Dognin, Noël; Stojmirovic, Aleksandar; Pržulj, Nataša
Proteins underlay the functioning of a cell and the wiring of proteins in protein-protein interaction network (PIN) relates to their biological functions. Proteins with similar wiring in the PIN (topology around them) have been shown to have similar functions. This property has been successfully exploited for predicting protein functions. Topological similarity is also used to guide network alignment algorithms that find similarly wired proteins between PINs of different species; these similarities are used to transfer annotation across PINs, e.g. from model organisms to human. To refine these functional predictions and annotation transfers, we need to gain insight into the variability of the topology-function relationships. For example, a function may be significantly associated with specific topologies, while another function may be weakly associated with several different topologies. Also, the topology-function relationships may differ between different species. To improve our understanding of topology-function relationships and of their conservation among species, we develop a statistical framework that is built upon canonical correlation analysis. Using the graphlet degrees to represent the wiring around proteins in PINs and gene ontology (GO) annotations to describe their functions, our framework: (i) characterizes statistically significant topology-function relationships in a given species, and (ii) uncovers the functions that have conserved topology in PINs of different species, which we term topologically orthologous functions. We apply our framework to PINs of yeast and human, identifying seven biological process and two cellular component GO terms to be topologically orthologous for the two organisms. © The Author 2015. Published by Oxford University Press.
Sørensen, Eva; Torfing, Jacob; Peters, B. Guy
Governance has become one of the most commonly used concepts in contemporary political science. It is, however, often used to mean a variety of different things. This book helps to clarify this conceptual muddle by concentrating on one variety of governance-interactive governance. The authors argue...... that although the state may remain important for many aspects of governing, interactions between state and society represent an important, and perhaps increasingly important, dimension of governance. These interactions may be with social actors such as networks, with market actors or with other governments......, but all these forms represent means of governing involving mixtures of state action with the actions of other entities.This book explores thoroughly this meaning of governance, and links it to broader questions of governance. In the process of explicating this dimension of governance the authors also...
To study multiquark interactions (MQI) the data of experiments confirming the presence of 3q, 6q, 12q states in interacting nuclear nucleons, in hadron- and lepton-nuclear processes at high energies and high momentum transfers are considered. Experimental data on cumulative processes pointing to the existence of MQI are analyzed. Two-channel model of a nucleus (the model of interacting nucleons) in the theory of coupled channels is discussed. The behaviour of form factor of deuteron and NQI (6q) contributions to ed scattering as well as deep inelastic scattering on nuclei are studied. The data known as EMC effect are discussed. It is pointed out that introduction of the notion MQI and consideration of a nucleus as a system of nucleons with a low MQI addition will help to explain such processes as cumulative reactions, form factors of a deuteron and light nuclei, deep inelastic scattering on nuclei
The Interaction Region Group addressed the basic questions of how to collide the SLC beams, how to maximize and monitor the luminosity, and how to minimize the detector backgrounds at the interaction region. In practice, five subgroups evolved to study these questions. The final focus group provided three alternative designs to acheive the 1 to 2 micron beam spot size required by the SLC, as well as studying other problems including: eta, eta' matching from the collider arcs, the implementation of soft bends near the interaction region, beam emittance growth, and magnet tolerances in the final focus. The beam position monitor group proposed two devices, a strip line monitor, and a beamstrahlung monitor, to bring the beams into collision. The luminosity monitor group reviewed the possible QED processes that would be insensitive to weak interaction (Z 0 ) effects. The beam dumping group proposed locations for kicker and septum magnets in the final focus that would achieve a high dumping efficiency and would meet the desired beam tolerances at the Moller scattering target in the beam dump line. Working with the Polarization Group, the Moller experiment was designed into the beam dump beam line. A beam dump was proposed that would maintain radiation backgrounds (penetrating muons) at acceptible levels. The detector backgrounds group proposed soft-bend and masking configurations to shield the detector from synchrotron radiation from the hard/soft bends and from the final focus quadrupoles and evaluated the effectiveness of these designs for the three final focus optics designs. Backgrounds were also estimated from: large angle synchrotron radiation, local and distant beam-gas interactions, 2-photon interactions, and from neutrons and backscattered photons from the beamstrahlung dump
Make cool stuff. If you're a designer or artist without a lot of programming experience, this book will teach you to work with 2D and 3D graphics, sound, physical interaction, and electronic circuitry to create all sorts of interesting and compelling experiences -- online and off. Programming Interactivity explains programming and electrical engineering basics, and introduces three freely available tools created specifically for artists and designers: Processing, a Java-based programming language and environment for building projects on the desktop, Web, or mobile phonesArduino, a system t
Eggleton, P.P.; Pringle, J.E.
This volume contains 15 review articles in the field of binary stars. The subjects reviewed span considerably, from the shortest period of interacting binaries to the longest, symbiotic stars. Also included are articles on Algols, X-ray binaries and Wolf-Rayet stars (single and binary). Contents: Preface. List of Participants. Activity of Contact Binary Systems. Wolf-Rayet Stars and Binarity. Symbiotic Stars. Massive X-ray Binaries. Stars that go Hump in the Night: The SU UMa Stars. Interacting Binaries - Summing Up
Fischer, J.; Kolar, P.; Kundrat, V.
The proceedings contain invited lectures and papers presente at the symposium. Attention was devoted to hadron interactions a high energy in QCD, to the structure and decay of hadrons, the production of hadrons and supersymmetric particles in e + e - and ep collisions, to perturbation theory in quantum field theory, and new supersymmetric extensions of relativistic algebra. (Z.J
Schoenau-Fog, Henrik; Reng, Lars
This book constitutes the refereed proceedings of the 8th International Conference on Interactive Digital Storytelling, ICIDS 2015, held in Copenhagen, Denmark, in November/December 2015. The 18 revised full papers and 13 short papers presented together with 9 posters, 9 workshop descriptions, an...
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Full Text Available Vertebrate evolution is accompanied by a substantial conservation of transcriptional programs with more than a third of unique orthologous genes showing constrained levels of expression. Moreover, there are genes and exons exhibiting excellent expression stability according to RNA-seq data across a panel of eighteen tissues including the ovary (Human Body Map 2.0.We hypothesized that orthologs of these exons would also be highly uniformly expressed across neonatal ovaries of the horse, which would render them appropriate reference genes (RGs for normalization of reverse transcription quantitative PCR (RT-qPCR data in this context. The expression stability of eleven novel RGs (C1orf43, CHMP2A, EMC7, GPI, PSMB2, PSMB4, RAB7A, REEP5, SNRPD3, VCP and VPS29 was assessed by RT-qPCR in ovaries of seven neonatal fillies and compared to that of the expressed repetitive element ERE-B, two universal (OAZ1 and RPS29 and four traditional RGs (ACTB, GAPDH, UBB and B2M. Expression stability analyzed with the software tool RefFinder top ranked the normalization factor constituted of the genes SNRPD3 and VCP, a gene pair that is not co-expressed according to COEXPRESdb and GeneMANIA. The traditional RGs GAPDH, B2M, ACTB and UBB were only ranked 3rd and 12th to 14th, respectively.The functional diversity of the novel RGs likely facilitates expression studies over a wide range of physiological and pathological contexts related to the neonatal equine ovary. In addition, this study augments the potential for RT-qPCR-based profiling of human samples by introducing seven new human RG assays (C1orf43, CHMP2A, EMC7, GPI, RAB7A, VPS29 and UBB.
Vosmeer, M.; Schouten, B.; Mitchell, A.
Technologies that were initially developed to be applied within the domain of video games are currently being used in experiments to explore their meaning and possibilities for cinema and cinema audiences. In this position paper we examine how narrativity, interactivity and engagement are mutually
Di Guilmi, Corrado; Gallegati, Mauro; Landini, Simone
Preface; List of tables; List of figures, 1. Introduction; Part I. Methodological Notes and Tools: 2. The state space notion; 3. The master equation; Part II. Applications to HIA Based Models: 4. Financial fragility and macroeconomic dynamics I: heterogeneity and interaction; 5. Financial fragility and macroeconomic Dynamics II: learning; Part III. Conclusions: 6. Conclusive remarks; Part IV. Appendices and Complements: Appendix A: Complements to Chapter 3; Appendix B: Solving the ME to solve the ABM; Appendix C: Specifying transition rates; Index.
Kang, Ming-Hsi; Roy, Bibhuti B; Finnen, Renée L; Le Sage, Valerie; Johnston, Susan M; Zhang, Hui; Banfield, Bruce W
The Us2 gene encodes a tegument protein that is conserved in most members of the Alphaherpesvirinae. Previous studies on the pseudorabies virus (PRV) Us2 ortholog indicated that it is prenylated, associates with membranes, and spatially regulates the enzymatic activity of the MAP (mitogen-activated protein) kinase ERK (extracellular signal-related kinase) through direct binding and sequestration of ERK at the cytoplasmic face of the plasma membrane. Here we present an analysis of the herpes simplex virus 2 (HSV-2) Us2 ortholog and demonstrate that, like PRV Us2, HSV-2 Us2 is a virion component and that, unlike PRV Us2, it does not interact with ERK in yeast two-hybrid assays. HSV-2 Us2 lacks prenylation signals and other canonical membrane-targeting motifs yet is tightly associated with detergent-insoluble membranes and localizes predominantly to recycling endosomes. Experiments to identify cellular proteins that facilitate HSV-2 Us2 membrane association were inconclusive; however, these studies led to the identification of HSV-2 Us2 as a ubiquitin-interacting protein, providing new insight into the functions of HSV-2 Us2.
Full Text Available Elongation factor, RNA polymerase II, 2 (ELL2 is expressed and regulated by androgens in the prostate. ELL2 and ELL-associated factor 2 (EAF2 form a stable complex, and their orthologs in Caenorhabditis elegans appear to be functionally similar. In C. elegans, the EAF2 ortholog eaf-1 was reported to interact with the retinoblastoma (RB pathway to control development and fertility in worms. Because RB loss is frequent in prostate cancer, ELL2 interaction with RB might be important for prostate homeostasis. The present study explored physical and functional interaction of ELL2 with RB in prostate cancer. ELL2 expression in human prostate cancer specimens was detected using quantitative polymerase chain reaction coupled with laser capture microdissection. Co-immunoprecipitation coupled with deletion mutagenesis was used to determine ELL2 association with RB. Functional interaction between ELL2 and RB was tested using siRNA knockdown, BrdU incorporation, Transwell, and/or invasion assays in LNCaP, C4-2, and 22Rv1 prostate cancer cells. ELL2 expression was downregulated in high–Gleason score prostate cancer specimens. ELL2 could be bound and stabilized by RB, and this interaction was mediated through the N-terminus of ELL2 and the C-terminus of RB. Concurrent siRNA knockdown of ELL2 and RB enhanced cell proliferation, migration, and invasion as compared to knockdown of ELL2 or RB alone in prostate cancer cells. ELL2 and RB can interact physically and functionally to suppress prostate cancer progression.
Governance analysis has exploded in recent years, and it has become nearly impossible to tell what difference the concept and practice of governance makes from those of government and state. In addition governance analysis has been placed more and more in the shadow of the new institutionalisms and...... and growth. However, interactive governance is not a property or effect of institutions; nor does it apply solely to those individuals who seek success above everything else. It is connective more than individualistic or collectivistic in nature; and it manifests a governability capacity which...
E. Fischer, Joel; Porcheron, Martin; Lucero, Andrés
interactions. Yet, new challenges abound as people wear and carry more devices than ever, creating fragmented device ecologies at work, and changing the ways we socialise with each other. In this workshop we seek to start a dialogue to look back as well as forward, review best practices, discuss and design......In the 25 years since Ellis, Gibbs, and Rein proposed the time-space taxonomy, research in the ‘same time, same place’ quadrant has diversified, perhaps even fragmented. This one-day workshop will bring together researchers with diverse, yet convergent interests in tabletop, surface, mobile...
Weak interactions are studied from a phenomenological point of view, by using a minimal number of theoretical hypotheses. Charged-current phenomenology, and then neutral-current phenomenology are discussed. This all is described in terms of a global SU(2) symmetry plus an electromagnetic correction. The intermediate-boson hypothesis is introduced and lower bounds on the range of the weak force are inferred. This phenomenology does not yet reconstruct all the predictions of the conventional SU(2)xU(1) gauge theory. To do that requires an additional assumption of restoration of SU(2) symmetry at asymptotic energies
Strong interactions are introduced by their more obvious aspect: nuclear forces. In hadron family, the nucleon octet, OMEGA - decuplet, and quark triply are successively considered. Pion wave having been put at the origin of nuclear forces, low energy phenomena are described, the force being explained as an exchange of structure corresponding to a Regge trajectory in a variable rotating state instead of the exchange of a well defined particle. At high energies the concepts of pomeron, parton and stratons are introduced, pionization and fragmentation are briefly differentiated [fr
Mogensen, Preben Holst
augmented reality, interactive building elements, and mobile devices to support new ways of working in a diversity of application domains with work situations ranging from individual work, through local collaboration, to distributed collaboration. The work situations may take place in offices/project rooms......Many application domains such as architecture, engineering, industrial design, city planning, environmental supervision, health care etc. share the properties of users working collaboratively with complex mixtures of physical and digital materials. Studies in such domains show that it is hard...... to maintain and integrate these heterogeneous materials in traditional desktop computing environments. Our thesis is that pervasive computing technologies can be developed to support a more natural user collaboration in a rich variety of application. This may be achieved by going beyond the traditional...
Bosanac, Slobodan Danko
This book is devoted to theoretical methods used in the extreme circumstances of very strong electromagnetic fields. The development of high power lasers, ultrafast processes, manipulation of electromagnetic fields and the use of very fast charged particles interacting with other charges requires an adequate theoretical description. Because of the very strong electromagnetic field, traditional theoretical approaches, which have primarily a perturbative character, have to be replaced by descriptions going beyond them. In the book an extension of the semi-classical radiation theory and classical dynamics for particles is performed to analyze single charged atoms and dipoles submitted to electromagnetic pulses. Special attention is given to the important problem of field reaction and controlling dynamics of charges by an electromagnetic field.
A point of view of the electroweak interaction is presented. It begins phenomenologically and moves in stages toward the conventional gauge theory formalism containing elementary scalar Higgs-fields and then beyond. The purpose in so doing is that the success of the standard SU(2) x U(1) theory in accounting for low energy phenomena need not automatically imply success at high energies. It is deemed unlikely by most theorists that the predicted W +- or Z 0 does not exist or does not have the mass and/or couplings anticipated in the standard model. However, the odds that the standard predictions will work are not 100%. Therefore there is some reason to look at the subject as one would were he forced by a wrong experimental outcome - to go back to fundamentals and ascertain what is the minimal amount of theory necessary to account for the data
Jeong, Hyundoo; Qian, Xiaoning; Yoon, Byung-Jun
Comparative analysis of protein-protein interaction (PPI) networks provides an effective means of detecting conserved functional network modules across different species. Such modules typically consist of orthologous proteins with conserved interactions, which can be exploited to computationally predict the modules through network comparison. In this work, we propose a novel probabilistic framework for comparing PPI networks and effectively predicting the correspondence between proteins, represented as network nodes, that belong to conserved functional modules across the given PPI networks. The basic idea is to estimate the steady-state network flow between nodes that belong to different PPI networks based on a Markov random walk model. The random walker is designed to make random moves to adjacent nodes within a PPI network as well as cross-network moves between potential orthologous nodes with high sequence similarity. Based on this Markov random walk model, we estimate the steady-state network flow - or the long-term relative frequency of the transitions that the random walker makes - between nodes in different PPI networks, which can be used as a probabilistic score measuring their potential correspondence. Subsequently, the estimated scores can be used for detecting orthologous proteins in conserved functional modules through network alignment. Through evaluations based on multiple real PPI networks, we demonstrate that the proposed scheme leads to improved alignment results that are biologically more meaningful at reduced computational cost, outperforming the current state-of-the-art algorithms. The source code and datasets can be downloaded from http://www.ece.tamu.edu/~bjyoon/CUFID .
Karlgren, Klas; Ramberg, Robert; Artman, Henrik
Interaction design is usually described as being concerned with interactions with and through artifacts but independent of a specific implementation. Design work has been characterized as a conversation between the designer and the situation and this conversation poses a particular challenge for interaction design as interactions can be elusive…
Tanaka, Takumi; Nakayama, Mayumi; Takahashi, Toru; Nanatani, Kei; Yamagata, Youhei; Abe, Keietsu
Hydrophobins are amphipathic secretory proteins with eight conserved cysteine residues and are ubiquitous among filamentous fungi. In the fungus Aspergillus oryzae, the hydrophobin RolA and the polyesterase CutL1 are co-expressed when the sole available carbon source is the biodegradable polyester polybutylene succinate-co-adipate (PBSA). RolA promotes the degradation of PBSA by attaching to the particle surface, changing its structure and interacting with CutL1 to concentrate CutL1 on the PBSA surface. We previously reported that positively charged residues in RolA and negatively charged residues in CutL1 are cooperatively involved in the ionic interaction between RolA and CutL1. We also reported that hydrophobin RodA of the model fungus Aspergillus nidulans, which was obtained via an A. oryzae expression system, interacted via ionic interactions with CutL1. In the present study, phylogenetic and alignment analyses revealed that the N-terminal regions of several RolA orthologs contained positively charged residues and that the corresponding negatively charged residues on the surface of CutL1 that were essential for the RolA-CutL1 interaction were highly conserved in several CutL1 orthologs. A PBSA microparticle degradation assay, a pull-down assay using a dispersion of Teflon particles, and a kinetic analysis using a quartz crystal microbalance revealed that recombinant A. nidulans RodA interacted via ionic interactions with two recombinant A. nidulans cutinases. Together, these results imply that ionic interactions between hydrophobins and cutinases may be common among aspergilli and other filamentous fungi.
Vandamme, Julien; Völkel, Pamela; Rosnoblet, Claire
Polycomb group (PcG) proteins maintain transcriptional repression of hundreds of genes involved in development, signaling or cancer using chromatin-based epigenetic mechanisms. Biochemical studies in Drosophila have revealed that PcG proteins associate in at least two classes of protein complexes...... known as Polycomb repressive complexes 1 and 2 (PRC1 and PRC2). Drosophila core PRC1 is composed of four subunits, Polycomb (Pc), Sex combs extra (Sce), Polyhomeotic (Ph), and Posterior sex combs (Psc). Each of these proteins has multiple orthologs in vertebrates classified respectively as the CBX, RING...... in order to identify interacting partners of CBX family proteins under the same experimental conditions. Our analysis identified with high confidence about 20 proteins co-eluted with CBX2 and CBX7 tagged proteins, about 40 with CBX4, and around 60 with CBX6 and CBX8. We provide evidences that the CBX...
Zhou, Qingwen; Kojic, Milorad; Cao, Zhimin
Brh2, the BRCA2 ortholog in Ustilago maydis, enables recombinational repair of DNA by controlling Rad51 and is in turn regulated by Dss1. Interplay with Rad51 is conducted via the BRC element located in the N-terminal region of the protein and through an unrelated domain, CRE, at the C terminus....... Mutation in either BRC or CRE severely reduces functional activity, but repair deficiency of the brh2 mutant can be complemented by expressing BRC and CRE on different molecules. This intermolecular complementation is dependent upon the presence of Dss1. Brh2 molecules associate through the region...... overlapping with the Dss1-interacting domain to form at least dimer-sized complexes, which in turn, can be dissociated by Dss1 to monomer. We propose that cooperation between BRC and CRE domains and the Dss1-provoked dissociation of Brh2 complexes are requisite features of Brh2's molecular mechanism...
Garcia-Garcia, Javier; Schleker, Sylvia; Klein-Seetharaman, Judith; Oliva, Baldo
Protein-protein interactions (PPIs) play a crucial role in biology, and high-throughput experiments have greatly increased the coverage of known interactions. Still, identification of complete inter- and intraspecies interactomes is far from being complete. Experimental data can be complemented by the prediction of PPIs within an organism or between two organisms based on the known interactions of the orthologous genes of other organisms (interologs). Here, we present the BIANA (Biologic Interactions and Network Analysis) Interolog Prediction Server (BIPS), which offers a web-based interface to facilitate PPI predictions based on interolog information. BIPS benefits from the capabilities of the framework BIANA to integrate the several PPI-related databases. Additional metadata can be used to improve the reliability of the predicted interactions. Sensitivity and specificity of the server have been calculated using known PPIs from different interactomes using a leave-one-out approach. The specificity is between 72 and 98%, whereas sensitivity varies between 1 and 59%, depending on the sequence identity cut-off used to calculate similarities between sequences. BIPS is freely accessible at http://sbi.imim.es/BIPS.php.
Phillips, Jennifer B; Västinsalo, Hanna; Wegner, Jeremy; Clément, Aurélie; Sankila, Eeva-Marja; Westerfield, Monte
Clarin-1 (CLRN1) is the causative gene in Usher syndrome type 3A, an autosomal recessive disorder characterized by progressive vision and hearing loss. CLRN1 encodes Clarin-1, a glycoprotein with homology to the tetraspanin family of proteins. Previous cell culture studies suggest that Clarin-1 localizes to the plasma membrane and interacts with the cytoskeleton. Mouse models demonstrate a role for the protein in mechanosensory hair bundle integrity, but the function of Clarin-1 in hearing remains unclear. Even less is known of its role in vision, because the Clrn1 knockout mouse does not exhibit a retinal phenotype and expression studies in murine retinas have provided conflicting results. Here, we describe cloning and expression analysis of the zebrafish clrn1 gene, and report protein localization of Clarin-1 in auditory and visual cells from embryonic through adult stages. We detect clrn1 transcripts as early as 24h post-fertilization, and expression is maintained through adulthood. In situ hybridization experiments show clrn1 transcripts enriched in mechanosensory hair cells and supporting cells of the inner ear and lateral line organ, photoreceptors, and cells of the inner retina. In mechanosensory hair cells, Clarin-1 is polarized to the apical cell body and the synapses. In the retina, Clarin-1 localizes to lateral cell contacts between photoreceptors and is associated with the outer limiting membrane and subapical processes emanating from Müller glial cells. We also find Clarin-1 protein in the outer plexiform, inner nuclear and ganglion cell layers of the retina. Given the importance of Clarin-1 function in the human retina, it is imperative to find an animal model with a comparable requirement. Our data provide a foundation for exploring the role of Clarin-1 in retinal cell function and survival in a diurnal, cone-dominant species. Copyright © 2013 Elsevier B.V. All rights reserved.
Full Text Available The human ATRX gene encodes hATRX, a chromatin-remodeling protein harboring an helicase/ATPase and ADD domains. The ADD domain has two zinc fingers that bind to histone tails and mediate hATRX binding to chromatin. dAtrx, the putative ATRX homolog in Drosophila melanogaster, has a conserved helicase/ATPase domain but lacks the ADD domain. A bioinformatic search of the Drosophila genome using the human ADD sequence allowed us to identify the CG8290 annotated gene, which encodes three ADD harboring- isoforms generated by alternative splicing. This Drosophila ADD domain is highly similar in structure and in the amino acids which mediate the histone tail contacts to the ADD domain of hATRX as shown by 3D modeling. Very recently the CG8290 annotated gene has been named dadd1. We show through pull-down and CoIP assays that the products of the dadd1 gene interact physically with dAtrxL and HP1a and all of them mainly co-localize in the chromocenter, although euchromatic localization can also be observed through the chromosome arms. We confirm through ChIP analyses that these proteins are present in vivo in the same heterochromatic regions. The three isoforms are expressed throughout development. Flies carrying transheterozygous combinations of the dadd1 and atrx alleles are semi-viable and have different phenotypes including the appearance of melanotic masses. Interestingly, the dAdd1-b and c isoforms have extra domains, such as MADF, which suggest newly acquired functions of these proteins. These results strongly support that, in Drosophila, the atrx gene diverged and that the dadd1-encoded proteins participate with dAtrx in some cellular functions such as heterochromatin maintenance.
Aalt D J van Dijk
Full Text Available Protein sequences encompass tertiary structures and contain information about specific molecular interactions, which in turn determine biological functions of proteins. Knowledge about how protein sequences define interaction specificity is largely missing, in particular for paralogous protein families with high sequence similarity, such as the plant MADS domain transcription factor family. In comparison to the situation in mammalian species, this important family of transcription regulators has expanded enormously in plant species and contains over 100 members in the model plant species Arabidopsis thaliana. Here, we provide insight into the mechanisms that determine protein-protein interaction specificity for the Arabidopsis MADS domain transcription factor family, using an integrated computational and experimental approach. Plant MADS proteins have highly similar amino acid sequences, but their dimerization patterns vary substantially. Our computational analysis uncovered small sequence regions that explain observed differences in dimerization patterns with reasonable accuracy. Furthermore, we show the usefulness of the method for prediction of MADS domain transcription factor interaction networks in other plant species. Introduction of mutations in the predicted interaction motifs demonstrated that single amino acid mutations can have a large effect and lead to loss or gain of specific interactions. In addition, various performed bioinformatics analyses shed light on the way evolution has shaped MADS domain transcription factor interaction specificity. Identified protein-protein interaction motifs appeared to be strongly conserved among orthologs, indicating their evolutionary importance. We also provide evidence that mutations in these motifs can be a source for sub- or neo-functionalization. The analyses presented here take us a step forward in understanding protein-protein interactions and the interplay between protein sequences and
Analysis of genomic DNA of DcACS1, a 1-aminocyclopropane-1-carboxylate synthase gene, expressed in senescing petals of carnation (Dianthus caryophyllus) and its orthologous genes in D. superbus var. longicalycinus.
Harada, Taro; Murakoshi, Yuino; Torii, Yuka; Tanase, Koji; Onozaki, Takashi; Morita, Shigeto; Masumura, Takehiro; Satoh, Shigeru
Carnation (Dianthus caryophyllus) flowers exhibit climacteric ethylene production followed by petal wilting, a senescence symptom. DcACS1, which encodes 1-aminocyclopropane-1-carboxylate synthase (ACS), is a gene involved in this phenomenon. We determined the genomic DNA structure of DcACS1 by genomic PCR. In the genome of 'Light Pink Barbara', we found two distinct nucleotide sequences: one corresponding to the gene previously shown as DcACS1, designated here as DcACS1a, and the other novel one designated as DcACS1b. It was revealed that both DcACS1a and DcACS1b have five exons and four introns. These two genes had almost identical nucleotide sequences in exons, but not in some introns and 3'-UTR. Analysis of transcript accumulation revealed that DcACS1b is expressed in senescing petals as well as DcACS1a. Genomic PCR analysis of 32 carnation cultivars showed that most cultivars have only DcACS1a and some have both DcACS1a and DcACS1b. Moreover, we found two DcACS1 orthologous genes with different nucleotide sequences from D. superbus var. longicalycinus, and designated them as DsuACS1a and DsuACS1b. Petals of D. superbus var. longicalycinus produced ethylene in response to exogenous ethylene, accompanying accumulation of DsuACS1 transcripts. These data suggest that climacteric ethylene production in flowers was genetically established before the cultivation of carnation.
Nicoludis, John M; Lau, Sze-Yi; Schärfe, Charlotta P I; Marks, Debora S; Weihofen, Wilhelm A; Gaudet, Rachelle
Clustered protocadherin (Pcdh) proteins mediate dendritic self-avoidance in neurons via specific homophilic interactions in their extracellular cadherin (EC) domains. We determined crystal structures of EC1-EC3, containing the homophilic specificity-determining region, of two mouse clustered Pcdh isoforms (PcdhγA1 and PcdhγC3) to investigate the nature of the homophilic interaction. Within the crystal lattices, we observe antiparallel interfaces consistent with a role in trans cell-cell contact. Antiparallel dimerization is supported by evolutionary correlations. Two interfaces, located primarily on EC2-EC3, involve distinctive clustered Pcdh structure and sequence motifs, lack predicted glycosylation sites, and contain residues highly conserved in orthologs but not paralogs, pointing toward their biological significance as homophilic interaction interfaces. These two interfaces are similar yet distinct, reflecting a possible difference in interaction architecture between clustered Pcdh subfamilies. These structures initiate a molecular understanding of clustered Pcdh assemblies that are required to produce functional neuronal networks. Copyright © 2015 Elsevier Ltd. All rights reserved.
Full Text Available Specialized trafficking systems in eukaryotic cells serve a critical role in partitioning intracellular proteins between the nucleus and cytoplasm. Cytoplasmic proteins (including chromatin remodeling enzymes and transcription factors must gain access to the nucleus to exert their functions to properly program fundamental cellular events ranging from cell cycle progression to gene transcription. Knowing that nuclear import mediated by members of the karyopherin α family of transport receptors plays a critical role in regulating development and differentiation, we wanted to determine the identity of proteins that are trafficked by this karyopherin α pathway. To this end, we performed a GST pull-down assay using porcine orthologs of karyopherin α1 (KPNA1 and karyopherin α7 (KPNA7 and prey protein derived from porcine fibroblast cells and used a liquid chromatography and tandem mass spectrometry (LC-MS/MS approach to determine the identity of KPNA1 and KPNA7 interacting proteins. Our screen revealed that the proteins that interact with KPNA1 and KPNA7 are generally nuclear proteins that possess nuclear localization signals. We further validated two candidate proteins from this screen and showed that they are able to be imported into the nucleus in vivo and also interact with members of the karyopherin α family of proteins in vitro. Our results also reveal the utility of using a GST pull-down approach coupled with LC-MS/MS to screen for protein interaction partners in a non-traditional model system.
Cai, Liquan; Wang, Dan [Department of Urology, The University of Pittsburgh, 5200 Centre Avenue, Pittsburgh, PA 15216 (United States); Fisher, Alfred L., E-mail: firstname.lastname@example.org [Division of Geriatrics, Gerontology, and Palliative Medicine, Department of Medicine, UTHSCSA, San Antonio, TX 78229 (United States); Center for Healthy Aging, UTHSCSA, San Antonio, TX 78229 (United States); GRECC, STVAHCS, San Antonio, TX 78229 (United States); Wang, Zhou, E-mail: email@example.com [Department of Urology, The University of Pittsburgh, 5200 Centre Avenue, Pittsburgh, PA 15216 (United States); GRECC, STVAHCS, San Antonio, TX 78229 (United States)
Highlights: • RNAi screen identified genetic enhancers for the C. elegans homolog of EAF2. • EAF2 and RBBP4 proteins physically bind to each other and alter transcription. • Overexpression of EAF2 and RBBP4 induces the cell death in prostate cancer cells. - Abstract: The tumor suppressor EAF2 is regulated by androgen signaling and associated with prostate cancer. While EAF2 and its partner ELL have been shown to be members of protein complexes involved in RNA polymerase II transcriptional elongation, the biologic roles for EAF2 especially with regards to the development of cancer remains poorly understood. We have previously identified the eaf-1 gene in Caenorhabditiselegans as the ortholog of EAF2, and shown that eaf-1 interacts with the ELL ortholog ell-1 to control development and fertility in worms. To identify genetic pathways that interact with eaf-1, we screened RNAi libraries consisting of transcription factors, phosphatases, and chromatin-modifying factors to identify genes which enhance the effects of eaf-1(tm3976) on fertility. From this screen, we identified lin-53, hmg-1.2, pha-4, ruvb-2 and set-6 as hits. LIN-53 is the C. elegans ortholog of human retinoblastoma binding protein 4/7 (RBBP 4/7), which binds to the retinoblastoma protein and inhibits the Ras signaling pathway. We find that lin-53 showed a synthetic interaction with eaf-1(tm3976) where knockdown of lin-53 in an eaf-1(tm3976) mutant resulted in sterile worms. This phenotype may be due to cell death as the treated worms contain degenerated embryos with increased expression of the ced-1:GFP cell death marker. Further we find that the interaction between eaf-1 and lin-53/RBBP4/7 also exists in vertebrates, which is reflected by the formation of a protein complex between EAF2 and RBBP4/7. Finally, overexpression of either human EAF2 or RBBP4 in LNCaP cells induced the cell death while knockdown of EAF2 in LNCaP enhanced cell proliferation, indicating an important role of EAF2 in
U.S. Department of Health & Human Services — The Interaction API is a web service for accessing drug-drug interactions. No license is needed to use the Interaction API. Currently, the API uses DrugBank for its...
Hammond, Thomas M.; Xiao, Hua; Boone, Erin C.; Perdue, Tony D.; Pukkila, Patricia J.; Shiu, Patrick K. T.
In Neurospora crassa, genes lacking a pairing partner during meiosis are suppressed by a process known as meiotic silencing by unpaired DNA (MSUD). To identify novel MSUD components, we have developed a high-throughput reverse-genetic screen for use with the N. crassa knockout library. Here we describe the screening method and the characterization of a gene (sad-3) subsequently discovered. SAD-3 is a putative helicase required for MSUD and sexual spore production. It exists in a complex with other known MSUD proteins in the perinuclear region, a center for meiotic silencing activity. Orthologs of SAD-3 include Schizosaccharomyces pombe Hrr1, a helicase required for RNAi-induced heterochromatin formation. Both SAD-3 and Hrr1 interact with an RNA-directed RNA polymerase and an Argonaute, suggesting that certain aspects of silencing complex formation may be conserved between the two fungal species. PMID:22384347
Airik, Rannar; Schueler, Markus; Airik, Merlin
Recessive mutations in the SDCCAG8 gene cause a nephronophthisis-related ciliopathy with Bardet-Biedl syndrome-like features in humans. Our previous characterization of the orthologous Sdccag8gt/gt mouse model recapitulated the retinal-renal disease phenotypes and identified impaired DNA damage...... response signaling as an underlying disease mechanism in the kidney. However, several other phenotypic and mechanistic features of Sdccag8gt/gt mice remained unexplored. Here we show that Sdccag8gt/gt mice exhibit developmental and structural abnormalities of the skeleton and limbs, suggesting impaired...... Hedgehog (Hh) signaling. Indeed, cell culture studies demonstrate the requirement of SDCCAG8 for ciliogenesis and Hh signaling. Using an affinity proteomics approach, we demonstrate that SDCCAG8 interacts with proteins of the centriolar satellites (OFD1, AZI1), of the endosomal sorting complex (RABEP2, ERC...
Full Text Available 017 ... 38832:3226 ... 38833:3539 ... 564608:3539 predicted protein Micromonas pusilla CCMP1545 MHPPLTLENHPLCKDVVIALKRCHRDNPWARAWGACNEQKWALDDCLKKQKLFKFRANHAKAKAQQDRLRRRVEKYGHATTNGQFKG
Full Text Available n all1672 Nostoc sp. PCC 7120 MFKILFDSDLILDAVMNRTELAEDVRTLLENLHPSIRLYLTDVGLQKVSTYTYCLKNSQIPEIIVDWLQEQIQICPIDQGLLQKARYSPLRDFESAVELACINHYQLNAIVTNKPEDFIVTAHPLCVWSFADLWLRVNLESQLQATIHS ...
Full Text Available thetical protein Synechococcus sp. WH 7803 MSRQRFRGLYLQNTGHPLCFSFVTYTPQTREQMVACGDLRADEEYFSPVLFDFLLFVSEGILGASPGVAFPFGYDDLAIVASRIRGTGVQHEYLIAINASAWNESKQAVLQQLRDILSRDLWDGARLRRGNDHPSPSE
Full Text Available ica MASRSITYPGLLLLVVALVLVPSSQAKRSPPRSAPTPAPRIAPSPAPRSAPTPAPRSAPTPAPRAPQALSPTPAPTPAPRTAPTPAPRSAPTPAPRA...PQAPSPTPAPTPAPTPAPRTAPTPAPRSAPTPAPRAPQAPSPTPAPMPAPRTAPTLAPRSAPTPAPRAPQAPSPTPAPRTAPISAPTPAPRSAPTPAPRA...PQAPSPTPAPTPAPRTAPTPAPRSAPTPAQRAPQAPSPTPAPTPPPRTAPTPAPAPAPKSAPTPAPMAPQAPSPTPAPTASPMTAPTPAPTSAPTPAPRAPQAPSPTPAPTPAPMDGSNTCS
Full Text Available ynechocystis sp. PCC 6803 MYFLLVTLVILVFPLLSIALEWTTSGNSQALVDVLARWFVFWGVGVRLFLAGVVQITKPSFTAEKILGVQSQDSLILVKELGIGNLAIASVALGSIFVNAWVLGAALAGGIFYLLAGINHILQPERNAKENYAMATDLFLGLLLGGILFFAWQP ...
Full Text Available ycine max MRKASSTMHCALLRFWVPLLLLASFSYAPSVSATTEISGNEVNTDGKVINEELAKPSLKGHDEEAKFKGFFPKPIPIVKPIPKPIPIIKPI...PIPVYKPIPKPIPIVKPIPKSIPVAKPIPNEEEKFKGFIPKPIPIIKPIPKIIPIVKPIPKIIPIVKPIPIPVYKPKPKLIPVVKPIPVIKPVPKIIPVVKPIPIIKPVPKPI...PIIKPIPKPFIVKKPIPTVESEEFLKPKPFFKKPIIPKLPLHPKFKKPLLPPLPIHKPIPTP
Full Text Available ycine max MRKPSSLQSALLRFGVPLLLVITFCYATSTAAATTQVSGNEELPKTNLNGHDEEAKFGFFHHKPIFKKHIPIPVYKPVPKPFPVYKPI...PKPVPVPVYKPIPKPVYKPIPKPVPVYKPIPKPVPVPVYKPIPKPVYKPIPKPVYKPIPKPVPVYKPIPKPVPVPVYKPIPKPVYKPIPKPVYKPIPKPVPVYKPIPKPVPVYKPI...PKPVYKPIPKPVPVYKPIPKPVPIYKPIPIFKPIPKPVPIYKPIPIFKPVPKPVPIYKPIPIFKPVPTPIPFFKPIPKPVPIVKPIPIPVFKPIPKPFPIVKPIP
Full Text Available SGAIIPALMHRIPSELRSSAAGGGEGSCALLAQDMSGAIIPALMHRIPSELRSSAAGGGEGSCALLAQDMSGSAAGGGEGSCALLAQGMSGAIIPALMHRIPSELRSSAAGGAGGVLCIVGAGHVGCDHTST...NAPDPIRTPQLGGGGRGGVLCIVGAGHVGCDHTSTNAPDPIRTPQLGGGGRGGVLCIVGAGHVGCDHTST...NAPDPIRTPQLGGGGRGGVLCIVGAGHVGCDHTSTNAPDLIRTPQLGGGGRGGVFCIVGAGHVGCDHTSTNAPDLIRTLQLGGGGRGGVFRIVGAGHVGCDHTST
Full Text Available 30 696747:230 ... WD-40 repeat protein Arthrospira platensis NIES-39 MVIASGGASLFNLATGEAVWEIDCPALGGAVSADGRLLALRSNKDIYLWDLSTGQLLRQLTGHTST...VNSVRFSRRGQTLASGSGDNTVRLWDVATGRELRQLTGHTSTVNSVRFSRRGQTLASGSGDNTVRLWDVATGRELRQLTGHTSTVYSVSFSRRGQTLASGSDDGVVRLWRVGF
Full Text Available KIYTIPDHVKKILRNLPARFRSKVTTIQEAKDLNNLLEINLLRSPDPLLWNLKDNMLKLFKMLNPKKRILMENQTVVQMRKRWCDHTITNAPDPIRTPQLIVLGCDHTSTNAPDPIRTPQLIVLGCDHTST...NAPDSIRTQQLTVLGCDHISTNAPDPIRTQQLSVLGCDHTSTNAPEPIRTQQLSVLGCDHTSTNAPDPIRTQQLSVLGCDHTSTN...APDSIRTQQLTVLGCDHISTNAPDPIRTQQLSVLGCDHTSTNAPDPIRTQQLSVLGCDHTSTNAPDPIRTQQLSVLGCDHISTNAPDPIRTPQLRVLGRE
Full Text Available MAFKKMSMIPCRLRNRWINCRKLLCRMNFVITHIYREDNRCADKLASKGLDIEGVTIWLNMPDFINNFVIHDRLGMCDHTSTNAPDPIRTPQLSVLGCDHTST...NAPDPIRTPQLSVLGCDHTSTNAPDPIKTPQLSVLGCDHTSTNAPDPIRTPQLSVLGSKSVADFNRTRAQKVPNRWPIFHDAKAQNCSKNRWCVHTST...DAPDPIRTPQLSVLGCVHTSTDAPDPIRTPQLRVLGCVHTSTDAPDPIRTLQLSVLGFVYTSTDAPDPIRTPQLSVLGFHQNSVVKRAWARVVLGWVTFWEVLVLCDHTST
Full Text Available 436017:4420 predicted protein Ostreococcus lucimarinus CCE9901 MSTRRPTTRARADDGFARDDDEDDGAHDDVAANTIVVYTKPGCCLCDGLKDKLDAAVDAAARAPPGASL...ECLRDFALCVRDVSTNAAWAESYAGSVPRVFVRVAVDAASTERSSVVSREFARPPPKRAAARVAEDLASLVRRACAPARAGWTVVTTTAWDAPSSSF ...
Full Text Available PAVLGINFGKSKLTPLEQAPDDYAASLECLAPWADYAVINVSSPNTPGLRDLQDSTQLRRLVERLRRLPACPPLLVKIAPD...LEGVATELQRQDLRLEQVLFGCRFSNPVGLAAGFDKNGVAAGVWDCFGFGFAEVGTVTWHGQPGNPRPRLFRLAAERAALNRMGFNNNGAEAMQRTLERQALPAPGHR
Full Text Available hetical protein Rivularia sp. PCC 7116 MAEDNNLTNNSATNISSESQTLNKDIEELVTRQAKAWENADSEAIIADFAENGAFIAPGTSLKGKADIKKAAEDYFKEFTDTKVKITRIFSDGKEGGVEWTWSDKNKKTGEKSLIDDAIIFEIKDGKIIYWREYFDKQTVSS
Full Text Available ckel incorporation protein HypA Oscillatoria acuminata PCC 6304 MHEVSLMENTLNIALDCASAQNASKIHRLKMRVGDLSGVVPDALEFAFDVVTRGTIAEGAKFEIERVPVVCHCSTCDRNFEPIDLFYECPHCHQLTYQIQSGQEIELTSLEVS ...
Full Text Available protein Mastigocoleus testarum MLEQIELKPNWERNQVAFLDFIVNGTSLHDQFDHPQVRDLCTVFTSDQYEFDGKSSAAIHASWFLGYGETPFPDDRIPVYICSSGDFDCGTVTAYLTVNDGTIKWSEFRIERLTEELQDQPIELTSVKQCVFERNAYEKLFQPFLRKVID
Full Text Available protein of unknown function DUF1818 Gloeocapsa sp. PCC 7428 MERVVKSGTGWRVGWNPHAAKYQALIGTDDWAIELTSAEFYDFCRLAVQLTEAIAQISQELMDEEKISCEAESDLVWMEVTGYPHAYSLHFILHTGRGVEGTWTPQAVPHLIQAVQMIQVF
Full Text Available 107:2633 ... hypothetical protein Cylst_3595 Cylindrospermum stagnale PCC 7417 MNKNNIQNYRFVCTLTFGDIYGQIIVWLITITISLASALALMGARRPVYALVTVGLVVLLTLPFLLFAFVTTLINHIELTSIEPGTKMEPIPGNVSQQQPIQASS
Full Text Available predicted protein Chlamydomonas reinhardtii MSSRPKRAASANMANVIAAEKANKAAALHAWPKMWATKLEAQLQLMFMPTRLHRRPLHQGTCRNYSTAPGITGVIELTSAFYRMYPNATFVFNKETAAKGTYRGEEETAASWWLKHVGSKLEIYLSPLRCRPEVSR ...
Full Text Available INWSLSGPMLRASGVSWDLRKVDSYECYDDFDWQIASEKEGDCYARYRVRVEEMRQSLSIIRQACKMIPGGPTENLEAQRMATEDKKSEIFGIDYQYVAKKVAPTFKIPNGELYTRLESGKGEIGVFIQGNNEVTPWRFKIRAADLNNLQILPHILKGAKIADIMAILGSIDVIMGSVDR
Full Text Available otein SPLC1_S051210 Arthrospira platensis C1 MKVAINKLPLPTIIDDCTLSSFVPAIMAILELVSVAALGVLVGLFLFNINSKREEQRQLDHAFYQLIESQDGEISLIQLAALARVSADVAQEYLDRQAGVFAAIPEFDQDGNTFYRFPRLRLPKQFPERSPNQDW ...
Full Text Available rotein AmaxDRAFT_3596 Arthrospira maxima CS-328 MAINKLPLPTIIDDCTLSSFVPAIMAILELVSVAALGVLVGLFLFNINSKREEQRQLDHAFYQLIESQDGEISLIQLAALARVSADVAQEYLDRQAGVFAAIPEFDQDGNTFYRFPRLRLPKQFPERSPNQDW ...
Full Text Available 79506 Solanum tuberosum MEETSTSSNNAKAKARVRVCITRKKTLKDKRAKLYIIRRCLYMLLCWKERAEFCNVGNRESTA ...3993 4070:3993 ... 424551:3993 ... 424574:3993 ... 4107:3993 ... 4113:2476 ... PREDICTED: uncharacterized protein LOC1025
Full Text Available OC100796589 Glycine max MEETSWEQRVQALTHILTSPTTTPSLHSQFFIATQIPCYLNWDYPPFLCSSNPQLLK...803:12853 ... 3814:12853 ... 163735:5410 ... 3846:8024 1462606:8024 3847:8024 ... PREDICTED: uncharacterized protein L
Full Text Available 09 ... 214909:3609 ... 3640:3609 ... 3641:3609 ... Uncharacterized protein TCM_008191 Theobroma cacao MEETSLGLSFTKDENFREWYSEIYFVAVNSEMIECNDISSYYILRSRAISIGRLTCTFPAAVCTPEIKASFNILLRVNDVQ
Full Text Available 02412 Synechococcus sp. PCC 7502 MKLTPYLFLTITVTAIIGTSVWQSSAQMNKMMNHNMDEMSMELGAADANLDLRFIDAMIPHHQGAVQMAKEALKK...SKRPEIQKLATAIIKAQQEEIAQLQKWRKLWYPNMSSTPMAWHGEMGHMMTMSASQQKAMMMSMDLGAGDAKFDLRFIDAMIPHHEGALTMAQEALSKSKRPEIQKLAKAIITSQKAEIIEMQKWRKAWY ...
Full Text Available GGWIGITDKYWMTALVPDQSANSRMSFSDTPLRGQDVYQADYLRDPITVPANGTASITDRLFAGAKVVRIIDAYEGALGIDNFELAIDWGWFYFITKPLFLALLYIQGIVGNFGVAIIVLTILIKLAFFPLAN...TSYVAMSKMKKVQPEMMKLRDRYKDDKQRQQQELMELYRREKVNPLAGCLPILIQIPVFFALYKVLFVTIEMRHAPFFGWIED
Full Text Available VIIHAYSGNIEIESGATIGSGVLLVGKSKIGANVCIGSLATILEQNLESEKVVLPASIIGNSGRQFSDNSTISLPDQDSNQSYLFSNETQESSYSLNLANTASSTEETSTETEKANTQLPLANTS...LPAEETPTETEKANTQLPLANTSLPAEETPTETEKANTQLPLANTSLPVEETPTETEKANTQLPLANTSLPVEETPTETEKANTQLQEESPPNIDAQIYGKEYVNKIMQTLFPYKNSLSSHPDDED ...
Full Text Available 551115:2260 ... 50S ribosomal protein L20 'Nostoc azollae' 0708 MTRVKRGNVARKRRNKILKLAKGFRGSHSTLFRTAHQQVMKALRSAYRDRKKKKRDFRRLWITRINAASRQNGLSYSQLIGNLKKANVELNRKMLAQLAVLDPASFAKVAELANSVKA
Full Text Available se with PAS/PAC and GAF sensors Oscillatoria nigro-viridis PCC 7112 MIEESKSIKEKFGVLDSVPVGACLLQDDFVVLFWNTCLEE...YP_007117793.1 1117:4890 1150:2464 1158:318 482564:246 179408:246 diguanylate cycla
Full Text Available se with PAS/PAC and GAF sensors Arthrospira maxima CS-328 MMDKYLCPCCSEPLLIHIIAHKKIGFCMNCHQEMPLIEQSRQMATVTEPV...ZP_03273626.1 1117:4884 1150:2505 35823:234 129910:158 513049:158 diguanylate cycla
Full Text Available ZP_09781866.1 1117:4884 1150:2505 35823:234 376219:95 putative Diguanylate cyclase with PAS/PAC and GAF sens...ors Arthrospira sp. PCC 8005 MNQLMEDRSKILWIAGNVGNDNHSLPQSILQNNGYEVHLVIGLKPAYNAIQSWP
Full Text Available se with PAS/PAC and GAF sensors Oscillatoria nigro-viridis PCC 7112 MYLILPDLYANMTYQIDERLNTSPCGFLSFADDGTIVMVN...YP_007118829.1 1117:4890 1150:2464 1158:318 482564:246 179408:246 diguanylate cycla
Full Text Available ith PAS/PAC and Chase2 sensors Nostoc sp. PCC 7107 MSKQLGKSFVSSNLNLNLKQLLDRKYRQLVVAFSVAVCIILLRSVGMFQSLELAGLD...YP_007048593.1 1117:4890 1161:684 1162:948 1177:381 317936:58 diguanylate cyclase w
Full Text Available ZP_09782276.1 1117:4884 1150:2505 35823:234 376219:114 putative Diguanylate cyclase with PAS/PAC and GAF sen...sors Arthrospira sp. PCC 8005 MMDKYLCPCCSEPLLIHIIAHKKIGFCMNCHQEMPLIEQSRQMATVTEPVDVS
Full Text Available ZP_08491810.1 1117:4890 1150:2448 44471:122 119532:63 756067:63 diguanylate cyclase with PAS/PAC and GAF sen...sors Microcoleus vaginatus FGP-2 MANMTYQIDELLNTSPCGFLSFADDGTILMVNATLLQLLGYETDELRERK
Full Text Available se with PAS/PAC and GAF sensors Oscillatoria nigro-viridis PCC 7112 MLYNNEILPTLTVESSPRSMNILLYKLLSLRRIEYIAVDR...YP_007115817.1 1117:4890 1150:2464 1158:318 482564:246 179408:246 diguanylate cycla
Full Text Available YP_007068440.1 1117:4890 1161:684 1185:224 1186:169 99598:92 diguanylate cyclase with PAS/PAC and Chase2 sen...sors Calothrix sp. PCC 7507 MSKQLGKCLVKFIFGLKQSLGRGHRELITASSVVICILFLRSIGLLQFLELAALD
Full Text Available se with PAS/PAC and GAF sensors Crinalium epipsammum PCC 9333 MIEQDKTKDQLLAELATMRQLNNFLLFSGMGVQQHLEKLLIEEREF...YP_007141850.1 1117:4890 1150:2445 241421:53 241425:53 1173022:53 diguanylate cycla
Full Text Available YP_007168782.1 1117:4879 1118:3357 92682:39 76023:39 65093:39 diguanylate cyclase with PAS/PAC and GAF senso...rs Halothece sp. PCC 7418 MDKYLARRTQDLRQQAQARLEQRERETDLNEMTPAELAHELEIHQTELEIQYEELQR
Full Text Available ZP_08493855.1 1117:4890 1150:2448 44471:122 119532:63 756067:63 diguanylate cyclase with PAS/PAC and GAF sen...sors Microcoleus vaginatus FGP-2 MIEESKSIKEKFGVLDSVPVGACLLQDDFVVLFWNTCLEEWTKIPRSQIL
Full Text Available YP_003890085.1 NC_014501 1117:8352 ... 1118:3762 1301283:19569 ... 43988:641 497965:226 ... PAS/PAC and GAF sens...ors-containing diguanylate cyclase Cyanothece sp. PCC 7822 MWEFISNFLAPKSYIPHGHCYLWQ
Full Text Available 05 696747:1505 ... hypothetical protein Arthrospira platensis NIES-39 MGGGNGTQQHHLSVMLGFTLVSPNLPRAIAYLSRLGGGNGTQQHHLSVMLGFTLVSPKLPRAIA...YLSRLGGGNGTQQHHLSVMLGFTLVSPNLPRAIAYLSRLGGGNGTQQHHLSVMLGFTLVSPNLQMLGETRATKSDRLFK
Full Text Available ical protein Prochlorothrix hollandica MYENERDNERENEYDLISPVEILPVIVARAIAPPSPPATTPDDPERVYESENEREDESISPVEILPVIVARAIA...PPSPPSTAPDDPEDEYERGDEREDEYEDEAISPVEILPVIVARAIAPPSPPATAPDEDAAAPDENEDEYEEI
Full Text Available 05 696747:1505 ... hypothetical protein Arthrospira platensis NIES-39 MGGGNGTQQHHLSVMLGFTLVSPNLPRAIAYLSRLGGGNGTQQHHLSVMLGFTLVSPKLPRAIA...YLSRLGGGNGTQQHHLSVMLGFTLVSPNLPRAIAYLSRLGGGNGTQQHHLSVMLGFTLVSPNLQMLGETRATKSDRLFK
Full Text Available othetical protein Fischerella sp. PCC 9605 MLTSYNIKDYEKAIFDFSKAIALEPNNPINHYERGNAYFLLKDYQRAIADYSKAIELKPNDSNAYELRGFAYFYLKGYQRAIA...DYTKVLELKTNDANAYELRGFAYFYLKGYQRAIADYSKAIELKPNNTNAYVLRGLAYYKLLDYQKAITDVQQASRLYYQQNNREGFQKAEDLLQELQSLINN
Full Text Available 05 696747:1505 ... hypothetical protein Arthrospira platensis NIES-39 MEVRNPTTPSLNDVGFHGVSPNLQRAIAYLSRLGGGNGTQHHHLSVMFGFTLVSPNLPRAIA...YLSRLGGGNGTQQHHLSVMLGFTLVSPKLPRAIAYLSRLGGGNGTQHHHLSVILGFTLVSPNLQMLGETQATKSDRLFK
Full Text Available WP_026796581.1 ... 1117:7580 ... 1150:51181 1301283:72257 ... 54304:1131 54307:211 ... hypothetical protein Plankt...NDVINTIEHLLETEFQQSCIHKRLKLPGLASEIALVVDGTLQTIGFYHQKIHVLSEMNKTIACSIAKAQRELGYNPTIALEEGMRRSLKWIFENYGGLD
Full Text Available WP_027254540.1 ... 1117:3646 ... 1150:52865 1301283:74127 ... 54304:528 1160:1354 ... hypothetical protein Plankt...FCQRYKPKEKKTPTRCHWGSKLLAGVHLSNKTLTTNPKKSKSRLVQTPCQVSKSPELTRVVSQFIEANRAPWQAEKDF
Full Text Available WP_026798282.1 ... 1117:5648 ... 1150:51942 1301283:73102 ... 54304:1817 54307:1346 ... hypothetical protein Plankt...othrix prolifica MNKTKLKFSTELRKLTTVQNPEALRAYCQSLKSQLVADPSNYAKGRYRLWLFHEVDFRDGTLSKGY
Full Text Available WP_026797240.1 ... 1117:7814 ... 1150:52263 1301283:73459 ... 54304:2105 54307:820 ... rRN...LSQDTPRCEWVSPEVLEAMATTVHPDGVIALAPRIPSKPQTLEGLGIALETLQDPGNLGTIIRTAAATGVEGLWLSADSVDLDHPKVLRASAGAWFGLNKTVSPNLAR
Full Text Available agellar biosynthesis anti-sigma factor FlgM Planktothrix prolifica MDFNFFLQSFLNGLSIGSVYAIFALGYTLVFSILGVINFAH...AINFGTATKPIMIRSVQVIIFTVCMVIVALLTYLVNKTKIGKALQAVAEDEITASLLGINPEQFIILTFFVSGFLAGLAGT
Full Text Available WP_026796754.1 ... 1117:7970 ... 1150:52478 1301283:73697 ... 54304:23 54307:536 ... hypothetical protein Plankt...LAKLKQDIAQTEALNPMEKAMVEVPIKMIESELQKPEANKTLINQAVVALKKGLEGVETLAEPVIKVAAILAKVWI
Full Text Available WP_027248983.1 ... 1117:6845 ... 1150:53031 1301283:74313 ... 54304:678 1160:388 ... modification methylase Plankt...LSEKPDDRGYFPNLKTLRNYVEKTGESIDKFRFDVQVGERATERSKAKIYPEEYHLQELEDRLLYEESAFAADIRGKDRPVDRKLNGNGNKTNNSPQQIAEYIQPELWS
Full Text Available WP_026785726.1 ... 1117:3298 ... 1150:52043 1301283:73215 ... 54304:1908 59512:262 ... hypothetical protein Plankt...othrix rubescens MPTFFPEGKTININGEVELLAFQCQDTVVQLAAIAPGAIFPLHQHTESQIGMIFNGNLEMNLNGNKT
Full Text Available WP_027249473.1 ... 1117:5662 ... 1150:51230 1301283:72312 ... 54304:1176 1160:459 ... hypothetical protein Plankt...RQISFRDQNNTVQWVIHRPDETPTESQWTILDQGVQIDTEETTLYQNKTTKIWRMQFDHKGRANGQLGRMTVSLRNGSPAKRCTFVSTLLGTLRTSQNNPKPKDGKYCY
Full Text Available thetical protein, partial Planktothrix agardhii MKFINPKTDYAFKKIFGSDQSQDILISFLNAIVYQGETFITYLEIIDPYAPGRISGLKTT...YFDVKAQLNNGENVLIEMQAFNVPAFGKRILYNTAKMYVNQLKLGEVYPELRAAIGVAVTDFIMFNEHNKVISQFTLKEDELQVNYQHSPLKLVFVELPKFNKTLEELTTITDKWLYFLRKAPDLEVVPESMLIVPEIEKAFTIADRVNLSLEEVDDLEKREQFERERIGAIELG
Full Text Available WP_027255124.1 ... 1117:6845 ... 1150:53031 1301283:74313 ... 54304:678 1160:388 ... modification methylase Plankt...LSGKPDDRGYFPNLKTLRNYVEKTGESIDKFRFDVQVGERATERSKAKIYPEEYHLQELEDRLLYEESAFAADIRGKDRPVDRKLNGNGNKTNNSPQQIAEYIQPELWS
Full Text Available WP_027249761.1 ... 1117:7024 ... 1150:51478 1301283:72586 ... 54304:14 1160:19 ... alpha/beta hydrolase Plankt...othrix agardhii MTVATNPNKTVISVNGVDHYCEWVTTANSTPGSKPVMVFIHGWGGSGRYWESTAQALSQEFDCLIYDLRGFG
Full Text Available WP_026787603.1 ... 1117:6086 ... 1150:52096 1301283:73273 ... 54304:1956 59512:755 ... hypothetical protein Plankt...othrix rubescens MKNAMLEAADIKILEAAAAEDLARDRQFILEEDSNKTLAQQSYKAQQRDQRLVKAALIPRTGEAASP
Full Text Available WP_026796485.1 ... 1117:7766 ... 1150:53377 1301283:74696 ... 54304:99 54307:105 ... hypothetical protein Plankt...GNYADSEAIFRQLVENQPKEAKYHFYLGNSLFYQRKIEEATQVYQEAISLNPQYGLAYNALGFLHASQGQWDEAIAQYQKALEINPDYAEALKNLGESLWKKGNTAEANNAWKKALELYTQQGNNKAVLQLQEMLNKTSQ
Full Text Available WP_026788149.1 ... 1117:1255 ... 1150:52201 1301283:73391 ... 54304:205 59512:888 ... hypothetical protein Plankt...ARTEQLPEPVYTQGLIRTYADALGLNGVELANFFLPEPQKVGMKSKLNFLTLPQLRPTHLYLTYILLIICAINGVSYLNKTANFASVSGEPVATTNPPEVNPQLRQAV
Full Text Available gellar biosynthesis anti-sigma factor FlgM Planktothrix rubescens MDFNFFLQSFLNGLSIGSVYAIFALGYTLVFSILGVINFAHG...INFGTATKPIMIRSVQVIIFTVCMVIVALLTYLVNKTKIGKALQAVAEDEITASLLGINPEQFIILTFFVSGFLAGLAGTL
Full Text Available WP_026786633.1 ... 1117:7276 ... 1150:53339 1301283:74654 ... 54304:955 59512:541 ... hypothetical protein Plankt...HEAQPDKFPHIPASMWWAVITLTTVGYGDVYPITPLGRLLGGILALLGIGLIALPAGIIASGFTEVIALNQRKNKTIYPKICPHCGKNIDQPLEDSTDLDH
Full Text Available WP_026785525.1 ... 1117:5888 ... 1150:52976 1301283:74250 ... 54304:628 59512:189 ... hypothetical protein Plankt...GVALLGMAYPIFSKMLSNDTLTKEPFRVFFALAIFLLSIASFTLLFKARVKLWKGIFATFTGMGLIILGSQPEIYRRDNEWFVSHYYYGITAALLMIFSVAIVQDIYQDKQNRWRTAHIILNCFALLLFIGQGMTGARDLLEIPLHWQEHYIYQCDFTNKTCSQPK
Full Text Available WP_027255564.1 ... 1117:4943 ... 1150:53097 1301283:74385 ... 54304:737 1160:1650 ... hypothetical protein Plankt...TSGRKQAKSGKGFSPVMVGQKWMLSQLEKLVPVVKIEGYRTASTRKYLGLKKNKTDKSKPEFNTHAVDGVAIAATAFVEYR
Full Text Available WP_027248974.1 ... 1117:6200 ... 1150:51081 1301283:72146 ... 54304:1041 1160:304 ... hypothetical protein Plankt...NGENVLIEMQAFNVPAFGKRILYNTAKMYVNQLKLGEVYPELRAAIGVAVTDFIMFNEHNKVISQFTLKEDELQVNYQHSPLKLVFVELPKFNKTLEELTTITDKWLY
Full Text Available WP_026798303.1 ... 1117:6692 ... 1150:51953 1301283:73114 ... 54304:1827 54307:1360 ... hypothetical protein Plankt...othrix prolifica MKRWKILSFQIILAALESCFLPAYSDLITNPAYINKMCQRQQDLPQIERFTVFYQQEFSSQNKTYW
Full Text Available WP_027255213.1 ... 1117:7881 ... 1150:51355 1301283:72450 ... 54304:1289 1160:584 ... hypothetical protein Plankt...SPPDGVSPLSETPTPAITTPISPTPQVKQPESAILGLVFVTPAQKPIQPALKPQIIPGTQSQNKTSTKTACSVQPTTGNICTTPLPSAVVPSSTTTESYWATPFILYF
Full Text Available rug ABC transporter ATP-binding protein Planktothrix prolifica MNWAIEVKDSASMSSLNPVVATQNLGKFYRTGFWMNQKIESLKSC...QMRQYSKGMLQRVGMAQALINNPEVVFLDEPMSGLDPMGRYQIREIILSLKAQNKTVFFNSHVLSDVEKICDRIAILAEGE
Full Text Available WP_026798031.1 ... 1117:6249 ... 1150:53365 1301283:74683 ... 54304:979 54307:314 ... hypothetical protein Plankt...LCEEISSQLLLPVETDYVDSDFNYSSLWQNKTVETSWFSKILYTAQKPNSQPIFSPSLVSFLVGCTDSEATAKKSKKIRIYLNPEQKKLLKQWFGVSRFVYNETIKYLQQPDTKANWMAIKTGILNGLPEWAKPWVD
Full Text Available family transcriptional regulator Planktothrix agardhii MALYTTVSFKSELNDKGWRLTPQRETILQVFQNLPKGNHLSAEDLYTLLKSRG...EAISLSTIYRTLKLMARMGILRELELAEGHKHYEINQPYPHHHHHLVCVQCNKTLEFKNDSISKTSMKQAEKSGFHLLDCQLTIHTICHEALRMGWPSLISTNWSCSKVIADGLSEIDEIECQ
Full Text Available WP_026796565.1 ... 1117:6622 ... 1150:52114 1301283:73294 ... 54304:1972 54307:411 ... hypothetical protein Plankt...othrix prolifica MFPLKSYLISKRISSQAFLISVLAVFTVILTVTLDSVSLAMTHPDAARNQTVYGQELIAQSRIPTSDQPSPSSLSDIPTADTASLFQNNRYAVRVFRQENKAYVNIYDKENKTLTLNNE
Full Text Available WP_027254883.1 ... 1117:2965 ... 1150:52982 1301283:74257 ... 54304:633 1160:1456 ... hypothetical protein Plankt...othrix agardhii MKTSLLILCQNRLKQKSLLQHQKTSGFTMIELLIGMIMAAVIITPILAFVVDVLQSDRKEGVKAATDQELEAATDFIKRDLSQAIYIYNKT
Full Text Available WP_027248948.1 ... 1117:44906 ... 1150:51132 1301283:72203 ... 54304:1088 1160:350 ... hypothetical protein Plankt...IFVEEGSVLNEKIEKAYSELKIEVKKKESTSDQQEKARNWMIENFYDIRMFGAVLSTGLNAGQVWGPLQISWGRSYDPVLPISATITRCAATEAKEKKDNKTMGRKEL
Full Text Available WP_026786488.1 ... 1117:44775 ... 1150:52433 1301283:73648 ... 54304:2259 59512:501 ... hypothetical protein Plankt...othrix rubescens MKIIQGYNPSKTISPMKIRKVKGVTIVEKYGDNLYVLPDENNNKTVPEFNKTDSFDINNWAEQATDLDGFYFINAITMTGNYLGSEWNDIILGLKFRGLATYISNH
Full Text Available alamin biosynthesis protein CobW Planktothrix prolifica MANLDVETPDFVLNIPKRGMPVTIITGFLGSGKTTLLNQILKNKQDLKIAVL...VNEFGDINIDSQLLISTDDDMVELSNGCICCTINDGLLDAVYRVLEREDRIDYMVIETTGVADPLPIILTFVGTELRELTNLDSVLTVIDAEAFTPEHFDSEAAFKQIVFGDIILLNKT
Full Text Available WP_026788598.1 ... 1117:7257 ... 1150:51123 1301283:72193 ... 54304:108 59512:73 ... hypothetical protein Plankt...othrix rubescens MNSVEELARLQKRFQEAAKVIDDLSRIKQELDQLSKSYKDKLSNNSFELSQTKQEIESLSINHKEYKKYWHETFNAIHNKT
Full Text Available WP_027249156.1 ... 1117:7027 ... 1150:51287 1301283:72374 ... 54304:1227 1160:523 ... carbonate dehydratase Plankt...othrix agardhii MNKTQQNLTISRRNLLKFGAGVAGTAVLTVGLGTKVSLFKAQPAVAQNNITPEEALKQLLEGNQRFIE
Full Text Available WP_026787645.1 ... 1117:7766 ... 1150:53377 1301283:74696 ... 54304:99 59512:39 ... hypothetical protein Plankt...NYAASEAIFRQLVENQPKEAKYHFYLGNSLFYQRKIEEATQVYQEAISLNPQYGLAYNALGFLHASQGQWDEAIAQYQKALEINPDYAEALKNLGESLWKKGNTAEANNAWKKALELYTQQGNNKAVLQLQEMLNKTSQ
Full Text Available phosphoribosyl)-5-amino-4-imidazole-carboxylate carboxylase Planktothrix agardhii MNPEALQQLLESVASGQITPTDALDK...IKYFDFEPVGDFARIDHHRKLRTGFPEVIWGLNKTPEQIIKIIEVMRQRNPVVMATRIEPHVYQQLQAQIPDLRYYEIAKICAIHPDEIPRSNSTGIITILTAGTADL
Full Text Available WP_027255690.1 ... 1117:21960 ... 1150:53273 1301283:74581 ... 54304:896 1160:1705 ... hypothetical protein Plankt...othrix agardhii MIPNKTQFLSELQVDSELDLELSTDPNQSIRKFVEHKQVIKFLSEQLSEIEPDAIVEALAIHQDNMNN
Full Text Available family transcriptional regulator Planktothrix rubescens MLTQDQPLTETVFLAKLNEIIESNHLLKHPFYQMWTEGKLTLTMLQEYAQE...YYLHVHNFPTYVSATHAACDDINIRKMLLENLIEEERGSAHHPELWLRFAEGLGVERSAVLDRQRLNKTQESVQILKKLSRSEEAEKGLAALYAYESQFPEVSTTKISGLEEFYGINEESALSFFKVHEKADEIHSQMTRKALLQLCQTTEQQRAALDSVQTAVDAFNLLLDGVYEEYCQN
Full Text Available WP_026796708.1 ... 1117:53359 ... 1150:52148 1301283:73331 ... 54304:2001 54307:507 ... hypothetical protein Plankt...othrix prolifica MKTTFSWLSSYFLLTGLAISGITFLGEVRPASACTGFWGRMDPTCDHGGITNPVHMTTQDFKICNKTENSISFTLNGSLEAPLRVGYCRTYTNVILPGNVAFDASYADGYQESSYGLDDEKNYSFKLNNQGSGIDLFAD
Full Text Available WP_026796694.1 ... 1117:5991 ... 1150:52142 1301283:73325 ... 54304:1998 54307:498 ... hypothetical protein Plankt...othrix prolifica MLKITLTPEQEQFLQAQLKTGKYNNPQEVISKAFKLLEKENKTELLANIPASASAKKILTEKIKEFRDNLENTQNQPLNPEREKLSREVKELFDKTQSIPGIGDITEEEIAAEIEA
Full Text Available WP_026798653.1 ... 1117:6200 ... 1150:51081 1301283:72146 ... 54304:1041 54307:1121 ... hypothetical protein Plankt...QLNNGENVLIEMQAFNVPAFGKKILYNTAKMYVNQLKLGEVYPELRAAIGVAVTDFIMFNEHNKVISQFTLKEDELQVNYQHSPLKLVFVELPKFNKTLEELTTITDK
Full Text Available WP_026796900.1 ... 1117:3511 ... 1150:51681 1301283:72812 ... 54304:1582 54307:631 ... exosortase Plankt...othrix prolifica MATSLKKLLIGTSVAVGMSAVGITPALAGSLTNATIGGTASTDYLIYGKEGNKTVVIPNSVANLQSVLDGNAVSPTG
Full Text Available WP_027254510.1 ... 1117:7257 ... 1150:51123 1301283:72193 ... 54304:108 1160:168 ... hypothetical protein Plankt...othrix agardhii MNSVEELARLQKRFQEAAKVIDDLSRIKQELDQLSKSYKDKLSNNSFELSQTKQEIDSLSINHKEYKKYWHETFNAIHNKTENILTQISQIENKT
Full Text Available family transcriptional regulator Planktothrix agardhii MLTQDQPLTETVFLAKLNEIIESNHLLKHPFYQMWTEGKLTLTMLQEYAQEY...YLHVHNFPTYVSATHAACDDINIRKMLLENLIEEERGSAHHPELWLRFAEGLGVERSAVLDRQRLNKTQESVQILKKLSRSEEAEKGLAALYAYESQFPEVSTTKISGLEEFYGINEESALSFFKVHEKADEIHSQMTRKALLQLCQTTEQQQAALDSVQTAVDAFNLLLDGVYEEYCQN
Full Text Available WP_027249886.1 ... 1117:7580 ... 1150:51181 1301283:72257 ... 54304:1131 1160:409 ... hypothetical protein Plankt...VINTIEHLLETEFQQSCIHKRLKLPGLASEIALVVDGTLQTLGFYHQKIHVLSEMNKTIACSIAKAQRELGYNPTIALEEGMRRSLKWIFENYGGLD
Full Text Available WP_027250437.1 ... 1117:53495 ... 1150:52763 1301283:74014 ... 54304:436 1160:1265 ... hypothetical protein Plankt...othrix agardhii MIVMPPPPPAIVSQVPHQAIFRDDFSRGCPGYSQAENQQIGNTAANHLAGITKNKTDSLVIFFTREFT
Full Text Available family transcriptional regulator Planktothrix agardhii MALYTTVSFKSELNDKGWRLTPQRETILQVFQNLPKGNHLSAEDLYTLLKSRG...EVISLSTIYRTLKLMARMGILRELELAEGHKHYEINQPYPHHHHHLVCVQCNKTLEFKNDSISKTSMKQAEKSGFHLLDCQLTIHTICHEALRMGWPSLISTNWSCSKVIADGPSEIDEIECR
Full Text Available WP_027254794.1 ... 1117:7880 ... 1150:53167 1301283:74463 ... 54304:80 1160:53 ... hypothetical protein Plankt...othrix agardhii MEFEQALEVVNNAIAPKIARTLTEVEVALLFGAWNNLTYDRIAERSGYSINYLQRDIGPKFWKFLSEALGRKVNKT
Full Text Available WP_026786359.1 ... 1117:2598 ... 1150:51863 1301283:73014 ... 54304:1746 59512:466 ... hypothetical protein Plankt...INCYRVIKDNVEELIEVLKVHKAKNSKEYFDYLRERDRLKQYNKFSDIQKAARIIYLNKTCYNGLFRVNSKGQFNVPFGSYKNPNILDEAVLRGVNDYLNQKSVTFLN
Full Text Available WP_026786388.1 ... 1117:7027 ... 1150:51287 1301283:72374 ... 54304:1227 59512:475 ... carbonate dehydratase Plankt...othrix rubescens MNKTQQNLTISRRNLLKFGAGVAGTAVLTVGLGTKVSLFKAQPAVAQNGITPDEALNQLLEGNKRF
Full Text Available WP_026796248.1 ... 1117:5667 ... 1150:53378 1301283:74697 ... 54304:990 54307:186 ... alcohol dehydrogenase Plankt...RLRNLRISLELMLTPMLQARIHDQLDQTKILQQCARLIDEGKLKILVNKTFPLASASEAHQLLEAGGMKGKLVLTIE
Full Text Available WP_027250244.1 ... 1117:4728 ... 1150:51209 1301283:72288 ... 54304:1157 1160:435 ... hypothetical protein Plankt...DKVMTIVESLSGYKLYKTASENFGLIFETAQKIINLPEPARKDIAKWLKLSNPCSVNKIGDIQENLYFLGDFSEAIIQAGLSQNKTFFSRN
Full Text Available WP_027249441.1 ... 1117:5593 ... 1150:51293 1301283:72381 ... 54304:1232 1160:703 ... hypothetical protein Plankt...KWIREDRMSSGMWRTIIHIGEIFLSSEGSVILIDEFENSLGINCIDILTEDLIHENKTLQFIATSHHPYIINNIPYEYWKIVTRQGGHISIGNASDYHLGKSKQDAFIQLTKILEKQS
Full Text Available mine monophosphate kinase Planktothrix agardhii MLIKDIGEQGLLEIVKGFCPSEIVGDDAAILAVSGDESLVITTDMLVDEVHFSDRTTSPF...DVGWRGAAVNLSDLAAMGAFPIGITVALGITDNKTVSWVEQLYQGLTTCLNQYQTPIVGGDICRSAVTCISITAFGRVNPKLAIRRSVARPGDKIIVTGDHGDSRAGL
Full Text Available WP_026796884.1 ... 1117:41752 ... 1150:52182 1301283:73369 ... 54304:2032 54307:622 ... hypothetical protein Plankt...othrix prolifica MNTNDEDQSISNIKRKLLEQINTLKCEDERMYNILAIDVWALAKTMDEFQPGFWGAFMKNREKALKRFLAESAKNKTDTDSKRPPFLR
Full Text Available WP_026787834.1 ... 1117:7580 ... 1150:51181 1301283:72257 ... 54304:1131 59512:170 ... hypothetical protein Plankt...NDIINTIEHLLETEFQQSCTHKRLKLPGLASEIALVVDGTLQTLGFYHQKIHVLSEMNKTIACSIAKSQRELGYNPTITLEEGMRRSLKWIFENYGGLD
Full Text Available thetical protein, partial Planktothrix agardhii STPQGSTEDGPVAVPTQVQVQTEDGDVWQDVASPTSDNTDEKGRYYTTLSEYLERNKERH...ENRVFYCTDETTQATYIQLHTSQGLEVLFFDSFIDSHFISFLEREHTDVKFARVDAELDDNLIAKDNSPEIVDPKTNKTRSEIIKDLFTAALNKPKLTIRTESLKSEN
Full Text Available WP_026796432.1 ... 1117:6249 ... 1150:53365 1301283:74683 ... 54304:979 54307:314 ... hypothetical protein Plankt...LCEEISSQLLLPVETDYVDSDFNYSSLWQNKTVETSWFSKILYTAQKPNSQPIFSPSLVSFLVGCTDSEATAKKSKKIRIYLNPEQKKLLKQWFGVSRFVYNETIKYLQQPDTKANWMAIKTGILNGLPEWAKPGID
Full Text Available WP_026798668.1 ... 1117:7321 ... 1150:52735 1301283:73983 ... 54304:410 54307:1082 ... hypothetical protein Plankt...othrix prolifica MHGGFYCTDETTQATYIQLHTSQGLEVLFFDSFIDSHFISFLEREHTDVKFARVDAELDDNLIAKDNSPEIVDPKTNKT
Full Text Available RLSQDTPRCEWVSPEVLEAMATTVHPDGVIALAPRIPSKPQTLEGLGIALETLQDPGNLGTIIRTAAATGVEGLWLSADSVDLDHPKVLRASAGAWFGLNKTVSPNLA... WP_026789106.1 ... 1117:7814 ... 1150:52263 1301283:73459 ... 54304:2105 59512:1069 ... rR...NA methyltransferase Planktothrix rubescens MLTSLQNPLVKQIRKLHQAKGRKEQQLFLLEGTHLVEAACEVGYPLTTVCYTSSWQGRHQPLLE
Full Text Available WP_026786027.1 ... 1117:3646 ... 1150:52865 1301283:74127 ... 54304:528 59512:364 ... hypothetical protein Plankt...GFCQRYKPKEKKTPTRCHWGSKLLAGVHLSNKTLTTNPKKSKSRLVQTPCQVSKRPELTRIVSQFIEANRAPWQAEKDF
Full Text Available WP_027249996.1 ... 1117:1255 ... 1150:52201 1301283:73391 ... 54304:205 1160:1045 ... hypothetical protein Plankt...RTEQLPEPVYTQGLIRTYADALGLNGVELANFFLPEPQKVGMKSKLNFLTLPQLRPTHLYLTYILLIICAINGVSYLNKTANFASVSGEPVATTNPPEVNAQLRQAVV
Full Text Available WP_026797935.1 ... 1117:2598 ... 1150:51863 1301283:73014 ... 54304:1746 54307:1182 ... hypothetical protein Plankt...LINCYRVIKDNVEELIEVLKVHKAKNSKEYFDYLRERDRLKQYNKFSDIQKAARIIYLNKTCYNGLFRVNSKGQFNVPFGSYKNPNILDEAVLRGVNDYLNQKSVTFL
Full Text Available WP_026787843.1 ... 1117:7208 ... 1150:51556 1301283:72673 ... 54304:147 59512:85 ... histidine kinase Plankt...ALNLSSVVIILTANDTVIDCRNAFKFGAWDYISKNMRGNVFDAVHDSIEEAITYFNRWGNVHNEQWITENLESLEKDYWGKYIAVINKTVIETADKEDSLNALLEQRK
Full Text Available WP_026797957.1 ... 1117:53289 ... 1150:51871 1301283:73023 ... 54304:1753 54307:1193 ... h...QILKDASKVSGDQLKYGQQLVQDFGNNLQAIDYADISNKTNSFLANINIPVNQLVLDSISFAGEQVLGKNKQLRKDMKVFLQSTPETMCQSYLDKVQGGDSSSWTAIE
Full Text Available WP_027254413.1 ... 1117:3316 ... 1150:51705 1301283:72839 ... 54304:1603 1160:934 ... hypothetical protein Plankt...NLNSDWFCYHDRNFGRFRWGEDIGWEWFVIFAQTETKIPLTLILDWRTNKTHSQGGLPYIFIYQNHQLRKIFLGETLRLNW
Full Text Available WP_026787847.1 ... 1117:3748 ... 1150:52103 1301283:73282 ... 54304:1962 59512:816 ... NUDIX hydrolase Plankt...othrix rubescens MNKTLILEDFKVGVDNVIFSVDTEQNRLLVLLVKRKEEPFINTWSLPGTLVQKGESLENAAYRILAEKILVE
Full Text Available WP_026797408.1 ... 1117:6743 ... 1150:53326 1301283:74640 ... 54304:943 54307:169 ... hypothetical protein Plankt...WLWNRQNQLGIAFDSSTGFHLPNGADRSPDASWIRQERWDLLTQEEREIFAPICPDFVLELRSKNDAIEKLQAKMIEYIENGASLGWLIDRKNKTVEIYRQNQDIELLNHPLILSGEDILPGFMLNLTEVWN
Full Text Available WP_027249824.1 ... 1117:3316 ... 1150:51705 1301283:72839 ... 54304:1603 1160:934 ... hypothetical protein Plankt...NLNSDWFCYHDRNFGRFRWGEDIGWEWFVIFAQTETKIPLTLILDWRTNKTHSQGGLPYIFIYQNHQLRKIFLGETLRLNW
Full Text Available WP_027255601.1 ... 1117:6743 ... 1150:53326 1301283:74640 ... 54304:943 1160:195 ... hypothetical protein Plankt...othrix agardhii MVQILNKTLSLEDFLNLPETKPANEYINGQIIQKPMPQGKHSKLQGKLVTVINNMAEEQAIALALPELRC
Full Text Available WP_027254369.1 ... 1117:7580 ... 1150:51181 1301283:72257 ... 54304:1131 1160:409 ... hypothetical protein Plankt...VINTIEHLLETEFQQSCIHKRLKLPGLASEIALVVDGTLQTIGFYHQKIHVLSEMNKTIACSIAKAQRELGYNPTIALEAGMRKSLKWIFENYGGLD
Full Text Available WP_026796217.1 ... 1117:3298 ... 1150:52043 1301283:73215 ... 54304:1908 54307:20 ... hypothetical protein Plankt...othrix prolifica MPTFFPEGKTININGEVELLAFQCQDTVVQLAAIAPGAIFPLHQHTESQIGMIFNGNLEMNLNGNKTV
Full Text Available WP_027255308.1 ... 1117:42 ... 1150:53120 1301283:74412 ... 54304:758 1160:1574 ... molecu...GLLLQVLPKAATDEELITKLESRVASLSGFTPLLRANKTLPDILQELLGDIGLVILPESQLVRFDCSCSFERVLGALKMFGTEELQDMIEKDNGAEAKCEFCGEMYQANSDHLHQLIEDLRIKPEPEEVRKNSILF
Full Text Available WP_026796771.1 ... 1117:6176 ... 1150:52159 1301283:73343 ... 54304:2011 54307:550 ... cytochrome C6 Plankt...othrix prolifica MKKLLSVLILSFLLLTVLLPKSALAEGVLSGSTIFSNSCAACHINGNNVIVANKTLKKKALTKYLKGYEENPLAAIINQVTNGKNAMPNFKSRLTAREITTVAAYVAEQAEKAWSPLQ
Full Text Available WP_027254586.1 ... 1117:6743 ... 1150:53326 1301283:74640 ... 54304:943 1160:197 ... hypothetical protein Plankt...WNRQNQLGIAFDSSTGFHLPNGADRSPDASWIRQERWDLLTQEEREIFAPICPDFVLELRSKNDALEKLQAKMIEYIENGASLGWLIDRKNKTVEIYRQNQDIELLNHPLILSGEDILPGFMLDLTEVWN
Full Text Available ltransferase type 11 Planktothrix agardhii MAPVSYWDAQLYDSHHSFVSNLAVDLLELLDPRIGEHILDLGCGTGNLSYKITNTGAEVIGIDKASTMIKKANKT...YPGLNFLVIDGANLVWKEQFDAVFSNAVLHWIKQPEKVISGVCQALKPGGRFVAEFGGKGNIDTIITAIDQALDAAGYPKNKTLNPWYFPSISEYGML... WP_027255198.1 ... 1117:7185 ... 1150:53327 1301283:74641 ... 54304:944 1160:203 ... methy
Full Text Available 5-phosphoribosyl)-5-amino-4-imidazole-carboxylate carboxylase Planktothrix prolifica MNPEALQQLLESVASGQITPTDA...LDKIKYFDFEPVGDFARIDHHRKLRTGFPEVIWGLNKTPEQIIKIIEVMRQRNPVVMATRIEPHVYQQLQAQIPDLRYYEIAKICAIHPDEIPRSNSTGIITILTAGT
Full Text Available WP_027249778.1 ... 1117:3511 ... 1150:51681 1301283:72812 ... 54304:1582 1160:909 ... hypothetical protein Plankt...othrix agardhii MATSLKKLLIGTSVAVGISAVGITPALAGSLTNATIGGTASTDYLIYGKEGNKTVVIPNSVANLQSVLD...ATKWFGETLSKYGMTSSQTLFSNFLLAGGFQRFSDPNISYVNQDNKTGKITIGLAGHYDAASLLGLPSNPNNPIPNPNNPI
Full Text Available WP_027250041.1 ... 1117:7881 ... 1150:51355 1301283:72450 ... 54304:1289 1160:584 ... hypothetical protein Plankt...SPPDGVSPLWETPTPAITTPISPTPQVKQPQSAILGLVFVTPAQKPIQPALKPQIIPGTQSQNKTSTKTACSVQPTTGNICTTPLPSAVVPSSTTTESYWATPFILYF
Full Text Available WP_027254850.1 ... 1117:5593 ... 1150:51293 1301283:72381 ... 54304:1232 1160:703 ... hypothetical protein Plankt...WIREDRMSSGMWRTIIHIGEIFLSSEGSVILIDEFENSLGINCIDILTEDLIHENKTLQFIATSHHPYIINNIPYEYWKIVTRQGGHISIGNASDYHLGKSKQDAFIQLTKILEKQS
Full Text Available WP_026796473.1 ... 1117:3549 ... 1150:52595 1301283:73827 ... 54304:285 54307:343 ... haloacid dehalogenase Plankt...LRDVVQKFGERLGFSPTPTELESLANSIQDWQPFPDTIAALKALKQKYKLVIISNIDDNLFAQTNQHLQIEFDHIITAQQAQSYKPSAHNFQFALNKTGLSSDKLLHVAQSIFHDIATANSLGLTTVWVNRRQGQPGGGATKAAIAQPDLEVPDLKSLVDLIFEV
Full Text Available WP_026796606.1 ... 1117:6743 ... 1150:53326 1301283:74640 ... 54304:943 54307:170 ... hypothetical protein Plankt...othrix prolifica MVQILNKTLSLEDFLNLPETKPANEYINGQIIQKPMPQGKHSKLQGKLVTVINNMAEEQAIALALPEL
Full Text Available WP_026787573.1 ... 1117:6169 ... 1150:52274 1301283:73471 ... 54304:2115 59512:749 ... hypothetical protein Plankt...othrix rubescens MGNVSFASENKTLAQSSNISGWVDSFGFASTKQGAGQAGIDQGEKLGILFDGNFDNVINSLKANQLK
Full Text Available WP_026786329.1 ... 1117:7618 ... 1150:52216 1301283:73407 ... 54304:2063 59512:458 ... hypothetical protein Plankt...othrix rubescens MIPFQDSRLLLRALTYRSYMFENPNKTQGDNEQLEFLGDSVLQFLAGDYVYEKYFGEQEGQLTQKRE
Full Text Available WP_027249923.1 ... 1117:7063 ... 1150:51701 1301283:72835 ... 54304:160 1160:1002 ... chem...otaxis protein MotB Planktothrix agardhii MSDLSELELETELQEEQDSGVYLSIGDLMSGLLMFFALLFITVMVQLNKTQDIIKRIPDEMFTTMQ
Full Text Available phosphoribosyl)-5-amino-4-imidazole-carboxylate carboxylase Planktothrix agardhii MNPEALQQLLESVASGQITPTDALDK...IKYFDFEPVGDFARIDHHRKLRTGFPEVIWGLNKTPEQIIKIIEVMRQRNPVVMATRIEPHVYQQLQAQIPDLRYYEIAKICAIHPDEIPRSNSTGIITILTAGTADL
Full Text Available WP_027254871.1 ... 1117:17730 ... 1150:52975 1301283:74249 ... 54304:627 1160:1450 ... hypothetical protein Plankt...DCCAWSMQTVYSELQKHGAEFRFVPWDTFRDGARERNKTVPSELGGFSRSNDAAFLQEAADFINNQLDPNRPLVLIGHSFGGDSLLSLVPRINRRIQFLGVIDPTAAG
Full Text Available WP_027254483.1 ... 1117:7024 ... 1150:51478 1301283:72586 ... 54304:14 1160:19 ... alpha/beta hydrolase Plankt...othrix agardhii MTVATNPNKTVISVNGVDHYCEWVTTANSTPGTKPVMVFIHGWGGSGRYWESTAQALSQEFDCLIYDLRGFG
Full Text Available conserved hypothetical protein, ribA/ribD-fused Moorea producens MTIYFYDISEKPYGCFSNFSPHGFELDGLWWPTSEHYFQAQK...FAGTSHVEEIRSCKTPAEAASMGRERTRPLRRDWEEIKEDVMGRGLLCKFQTHADIREILLGTGDELIVEDAPQDYYWGCGKDRSGKNRLGEILMEIRAILRES
Full Text Available pothetical protein Fischerella sp. JSC-11 MHYYVHPFQLELHKLENMIVHVQHVNNQEVKQIADSRLFTSQAIGEEGGDTVTTKAIGEEGGDTVTTQAIGEEGGDTVTTKAIGEEGGDTVTTQAIGEEGGDTVTTQAIGEEGGDTVTTKAIGEEGGDTVTTLAFGEEGGF
Full Text Available ... hypothetical protein Calothrix sp. PCC 7103 MDYVHPFQMELHKLESMIVHVQYADIKEVDKTLASNDAVSTQAVGEEGGTKVSTRALGEEGGNILTTYAVGEEGGNILTTYAVGEEGGDKVTTQAVGEEGGTRVTTYAVGEEGGGRVTTKAVGEEGGSIIRR
Full Text Available SSAPNLEVIPSSLEEVSEIESALNIANMANLSNEELEELEQQEKLIRDKKGQISLARKEGIEIGREEGIGIGREEGIGIGREEGIGIGKEEGIGIGREEG...IGIGREEGIGIGKEEGIGIGREEGIGIGREEGIGIGREEGIGIGREEGMRILVKRQIRRKFGEVPPEVQTQIEQLSLEKLDILGDEIFDLAIIADLENWLANNG ...
Full Text Available SSAPNLEVIPSSLEEVSEIESALNIANMANLSNEELEELEQQEKLIRDKKGQISLARKEGIEIGREEGIGIGREEGIGIGREEGIGIGREEGIGIGREEG...IGIGREEGIGIGREEGIGIGREEGIGIGREEGIGIGREEGIGIGREEGMRILVKRQIRRKFGEVPPEVQTQIEQLSLEKLDILGDEIFDLAIIADLENWLANNG ...
Full Text Available oxin T-superfamily Coleofasciculus chthonoplastes MGGDNSKKPVLGLMNKGGFCCSVIGEEGGFCCSVIGEEGGFCCSVIGEEGGFCCSVIGEEGGFCCSVIGEEGGFCCSVIGEEGGFCCSVIGEEGGFCCSVIGEEGGFCCSVIGEEGGFCCSVISAIADFSP
Full Text Available 3436 hypothetical protein CHLREDRAFT_180911 Chlamydomonas reinhardtii MTTEEPLSCSKIRSWNITVYSFTLKGLPGCLEPSHSFWVKEREGEWGLKCLSETFSHELVENVPGREEVSNLLKKGGSSNKSQKGGWICCERNCFLCQHKKCQVLI ...
Full Text Available 5297 3694:5297 predicted protein Populus trichocarpa MMMNAVFAADAEIGSDAVFAADSGLGSDAVFAADFGLGSDAVFAADAEIGSDAVFAA...DSGLGSDTAFTTDTEIGSNTVFAAHFLIGSDAVFAADAEIGSDAVFAADFSMNSDAELGGRVFAADAEIGSDAVFAADSGLGSEAVFAADSGLGSDAVFAA...DAEIGSDAVFAADSGLGSDAVFAADSGLGSDAVFAADAEIGSDKVFAADSGLGSDAVFAADSGLGSHAVFAADAEIGSDAVFAADSGLGSDAVFAA...DSGLGSDAAFTTDTEIGSDTVFAAHFLIGSDAVFAADAEIGSDAVFAADFSMNSDAELGGRGKNWF ...
Full Text Available 5297 3694:5297 predicted protein Populus trichocarpa MMINVVFAADSGLGSDAVFAADAEIGSDAVFAADSGLGSDAVFAADAEIGSDAVFAADSGLGSDAVFAADSGLVFAA...DSGLGNDAVFAADSGLGSDAVFAADAEIDSDAVFAADSGMGSDAAFAADSGLGSDAVFAADAEISSDAVFAADSGLGSDAVFAA...HFLIGSDAVFAADAEIGSDAVFAADAEIGSDAVFAADFSMNSDAELGGRGKTDFR ...
Full Text Available xylamine reductase Arthrospira platensis NIES-39 MFCEQCEQTASGQGCHQWGACGKGPDVNAVQDLL... YP_005071100.1 NC_016640 1117:23174 ... 1150:27534 1301283:45982 ... 35823:1467 118562:2804 696747:2804 ... hydro
Full Text Available YP_007084156.1 NC_019694 1117:23174 ... 1150:9233 1301283:90386 ... 1158:1065 118323:857 56110:857 ... hydroxylam...ine reductase Oscillatoria acuminata PCC 6304 MYCSQCEQTAGGEACYQWGACGKSPEVDALQDLLTHL
Full Text Available 58024:13655 3398:13655 71240:8416 91827:8416 71275:10680 91836:5614 3699:5614 3700:5614 980083:5614 3701:5614 3702:5735 post-illumin...ation chlorophyll fluorescence increase protein Arabidopsis thaliana MAAAANTSAVFASP
Full Text Available pothetical protein ANA_C11310 Anabaena sp. 90 MSVGAKHLEDELSVIAKNSSPNASPVQLLVGGKHLEDKLSVIAKNSSPNASPVQLSVGAKHLEDKLSVIAKNSSPNASPVQLSVVICPENNPKEQIICAVICGVEEKSNEITAIPELIKVLDMTGCLYSTHLNYLI
Full Text Available 0:477 ... hypothetical protein, partial Prochlorococcus sp. scB243_498P3 MSTKSDSLKEKLIENFSDFSKLSDYSFMNYLRADPQ...STKDGNDHKPRSVYSGHYVPVLPTAIPEPEYISHSKKLFKELRLSSDLTKDKNFCLFFSGDISVANYPMSPVGWATGYALSIYGTEYTQQCPFGTGNGYGDGIAISVFEGLFNGKRMEMQLKGGGPTPYCRGA
Full Text Available :1418 ... nitrogen fixation protein Microcoleus sp. PCC 7113 MTATNTTTETTTEEILAKPLMQELVKQIRGQDSYGTYRTWSDELLLKPFIVSKERKRKISVDGDVDLVTKARI...MAFYRAIAARIEQETGLLGQVIIDLSHEGFGWALVFCGRLLVVAKTLRDAQRFGFDSFEKLDAEGEKLLQKGIDLAKRYPEVGNI
Full Text Available NRQRDPFDFDLILEDQAVELAREIANRCQAGFVVLDAERDMARIVFAEGTVDFARIEGESLEQDLHRRDFTINAIAHHLQSQTLIDPLQGKQDLEARVIKMVSPQNLRDDPLRLLRAYRQAGQLTFTIDESTR...ESIREIAPCLQAVAAERIQTELSYLLATSQGSFYLQQAWEDGVLSPWFPNLTQESV
Full Text Available PEDINPSRRKLAETVSKQIAISLANLKLRETLQNQSFRDVLTGLYNRRYLEASIVRELHRVSRSNSTLGVILFDIDHFKRFNDTWGHDAGDAVLKAVGNLLQESTR...ESDIACRYGGEEFLIIMPDASLEDTQRRAHQLQIEIKHLQVSTRSQQLESITVSMGVASFPEHGLNYELLLRTADEALYRAKQQGRDRIVCAV ...
Full Text Available :36 ... hypothetical protein, partial Prochlorococcus sp. scB241_526B22 VYSSHLNNQRELIVTSESTRESINLAKYLTDNGVVKYSAYWCPNCLNQSELFGKQAYRELNVVECARDGINSQTQLCIDKKIKGFPTGEINGALILGVLSLKELSKLTGFKN
Full Text Available ASASYICHPKAPKRIAKVLPHVKLIALLRDPVDRAYSHYHHTKRIGRENLSFEEAIAQEETRVRQIESGGRRPGNNQPQAYNYTYLSSGLYAEQLQNWLEQFSKQQLLVLNSEDFFRNPPSSFKQVINFLKLPSWSLKNYRKHNFNQYPEPLKESTRESLTEYFRPHNHKLFELLGTDFGWSH
Full Text Available HNHEVLDAYEPNDLCAVLERHSGFESTRESWDTDRGIDISFMEAQRSPNVESGDQIEKKLPSNSDKTAIKKNGIIGRKVPEVRSKIVQGYLGKSKTEMTSKGKKSSLA...DWFVINHSGKPESQDAANCMLSLEGDSSNAKPSRKDVLVDDSFMVHARSTADDPYDSQWKTDIRTAADLTLSSQPENGTAD
Full Text Available tical protein Calothrix sp. PCC 7507 MYSQQLRTAIYGFFKRSHHLQLNCIDLQLNCIDLQLSCIDLQLSCIDLQLSCIDLQLNCIDLQLSCIDLQLSCIDLQLSCIDLQLSCIDLQLSCI...DLQLSCIDLQLSCIDLQLSCIDLQLSCIDLQSLNYPFLHFTDSFFVVMGTLKI
Full Text Available ... hypothetical protein Cal7507_4468 Calothrix sp. PCC 7507 MYSQQLRTAIYGFFKRSHHLQLNCIDLQLNCIDLQLSCIDLQLSCIDLQLSCIDLQLNCIDLQLSCIDLQLSCI...DLQLSCIDLQLSCIDLQLSCIDLQLSCIDLQLSCIDLQLSCIDLQLSCIDLQSLNYPFLHFTDSFFVVMGTLKI
Full Text Available in Cal7507_4468 Calothrix sp. PCC 7507 MYSQQLRTAIYGFFKRSHHLQLNCIDLQLNCIDLQLSCIDLQLSCIDLQLSCIDLQLNCIDLQLSCIDLQLSCIDLQLSCIDLQLSCI...DLQLSCIDLQLSCIDLQLSCIDLQLSCIDLQLSCIDLQSLNYPFLHFTDSFFVVMGTLKI ...
Full Text Available hetical protein Microcystis aeruginosa PCC 9806 MMEDIVWKMQQRSRTLQDYRKDIRGLWQDEAAKTLNRRYLDPHEDDDQKMIEFLQKQVQGLEKTNEELVKAKDYALEAERYSQQVEHFLEREKQEVKQAYYSYDRSIEYYGLTQAELPNIHRLIQQANRSCN ...
Full Text Available VPEQWWEKQNRCYLLWQFDKPPDVVIEIVSNREGDELEGKLSRYEQMRVSYYAVFDPNHELGPEELRIFELRGRHYAEMTETWLEQVGLGLTVWEGVFEGKQARWLRWCDAQGQLLLTGDERAELERERAEQERQRAEQERQRAEQERQRAEQERQRAERLAARLRALGEDPDLES ...
Full Text Available ANVGIYTTPSRPPIVSDVFLSLDVTVPEQWWEKQNRCYLLWQFDKPPDVVIEIVSNREGDELGGKFSRYEQMRVSYYVVFDPNHELGSEELRLFELRGRHYAEMTETWLEQVELGLRLWDGVFEGKQARWLRWCDAKGQLLLTGDERAELERQRAEQERQRAERLAARLRALGEDPDLER
Full Text Available AQEILNIYASDGEHIFPNFSLSKEIYKRLTLILNAFLLGKLIEVDSRTRFLASQPIFDGTELEKSTRKVFGEETFGVFKKKNKRVIVIAYDCWNSIPVIFDSEDPIYHNLKIVDILMASSAYPGGFPSRDISE...PSFLEQWIKQSDSRCSHPPNNLLPVVDGGLAANNPALIALSEYLKQDHQKSSVILA
Full Text Available n of unknown function DUF1830 Calothrix sp. PCC 6303 MAQILDSLPPEQSGKILCCYVNATSKIQVARITNIPNWYFERVVFPGQRLAFEAPRAAHLEIHTGMMASAILSDNIPCDRLVISEPSDPEPETNSTTEDENTCKNTIAPSIDNSTGDTPKNFKIAGLV ...
Full Text Available rotein Sta7437_0097 Stanieria cyanosphaera PCC 7437 MNYQFLNIPNPQSKQEAVISEPSNINRNTGENLAVPPAALIVIPGGLLVLAAILGFYRKINLTKIKDRSLFETDEQTTCKNCRFFSHNPYLKCALHPSRVSTTESIECADYWSNKSDRFQQKSK ...
Full Text Available tein Nos7524_5075 Nostoc sp. PCC 7524 MSLSYDISSILNLLRSLPSTELRTVKEEIDSILKERGTTIRIPDPFKIVPAQVVLKDSNLEESTSEVKLEEEYQQINEDISEPSGVLNLSSIKDATDNKAEKKEAIQEIPRPLGIWKGKVEISEDFYETTNDILSEFGIEE ...
Full Text Available YQGLHLGEVQLKGENIRINIGQVLRGKPLQLLETIRVSGAVAISNQNLQASISSALLGEGFKGLLETLLEHQGISEPSQLLDNYDIDWLGAYLDNNYFILQGKLTHDGVTQPLKIKAKLTLIPPQTLHLSEVEINGIPDLNNHNIKDFSVDLGSDVSINSFELDTDKLICEGELLIRP ...
Full Text Available hypothetical protein Anabaena sp. PCC 7108 MTVRFLLDSNIISEPSRPIPNIQVLDQLNRYRSEVAIASVVVHEILYGCWRLPPSKRKDSLWKYIQDSVLNLPVFDYNLNAAKWHAQERARLSKIGKTPAFIDGQIASIAFCNDLILVTNNVADFQDFQDLVIENWFI
Full Text Available TTKKKQSIFPAGKAAAILMEIDRRRRQLSLIPIDERFTSQRNKLPRILTEKHSHEPIHPDASSSIQTPLHPPRRLFIHPDASSSIQTPRHPFRRLVIHPDASS...SIQTPRHPFRRLVIHSDASSSIQTPRHPFRRLVIHSDASSSIQTPRHPFRRLVIHSDASSSIQTPRHPSLNSSAWMLFRRTVRIVISSNGCVSSLV
Full Text Available 745:703 ... 171637:1864 ... 721813:1696 ... 3749:1696 ... 3750:1696 ... PREDICTED: cytochrome P450 87A3-like Malus domest...ica MWSLVGLSFLVSLVVIFITPWIXKWRYPKCNGALPPGSMGLPFIGETLSLIIPSYSHDLLPFIKKRVRRYGPIFRTS
Full Text Available ATKDDNIKSALAELFPRSSSANLHHLKPLYVTAHIEGYPVSKVFVDYGATVNIMPMNIMKALRRSNDELIPSGIIMSSFIGDKSQTKGVLPLTVNIAGRTHMTAFFVVDSKTEYNALLGRDWIXQTSCIPSSLYQVLVFWDGFNDEGRPTRISVQKAIEVGAETVHQDSARLGLANFLPEADV
Full Text Available 745:703 ... 171637:1864 ... 721813:1696 ... 3749:1696 ... 3750:1696 ... PREDICTED: cytochrome P450 87A3-like Malus domest...ica MWSLVGLSFLVSLVVIFITPWIXKWRYPKCNGALPPGSMGLPFIGETLSLIIPSYSHDLLPFIKKRVRRYGPIFRTS
Full Text Available hypodium distachyon MMLSMPTDCWPDPVDCYEHLFCHMMQIYSLKLAYTSADADTSGNPILLYGFMAVRDCLNPR...RNYVFRRTRDDPFVVVQDSNGSSFIRMSGPKRGIEMQSLVLVEFDMRIKIGENEEDDLQLIDGAIYFDSLVLPPDMIINRRIVGDCGAVDMSLAFLHCAAEATIQVGI
Full Text Available rotein MicvaDRAFT_0707 Microcoleus vaginatus FGP-2 MIDFNTVTEFSHTYCIAICAFLVPANLLTTLVTVILTALNRPRIQIWASVVVASLWATAMIFHVFCWFAIGVVMPPTYILLVMGITCLTINVWAIAHPASMMQLIRVAVSVVRGSLQRKKDLVILERRM ...
Full Text Available achyantha MEQEGTGKEENDGSRWTEKLSPMEQEGTGKEENDGSRWTEKLSPMEQEGTGKEENDGSRWTEKLSPMEQEGTGKEENDGSRWTEKLSPME...QEGTGKEENDGSRWTEKLSPMEQEGTGKEENDGSRWTEKLSPMEQEGTGKEENDGSRWTEKLSPMEQEGTGKEENDGSRWTEKLSPMEQEGTGKEENDGSRWTEKLSPME...QEGTGKEENDGSRWTEKLSPMEQEEPLLEGLLQNGRLKFGQLMEQTISKVPEALSDAGGFSEIPCIMEDASNANDSPHSSVTGAKTV
Full Text Available IEEVGERYFDELLSRSLFQRPRLDRPSFTMHDLINDLAMFVSRKFCFRLDQKNSHEVPERVRHLSYMSEEFDISSKFEPLKGVKCLRIFFPVSLAPFGSEYPGYVSNK...HPDSVEIGKQIARKCNGLPLAAKTLGGLLSCNLDYKEWNHILNSNLWDLHANSVLPSLRLSYHYLPTYLKRCFAYCSIFPKDYEFEKENVILLWMAEGLIPHAKNEKA
Full Text Available LVAAAEEELSPDAMEILCQRFPLNSRCQGANAATPSSDETTEESTPAEDSISPENSIEETTPGAPLPDSSPEGITPAPEEPLPGTTPEGLTPLPGSVPGDEVTPSEDDAPTNITPMPGTTPEGEVTPSEDDA...PTNITPMPGTTPEGEVTPSEDDAPTNITPMPGTTPEGEVTPSEDDAPTNITPMPGTTPEGEVTPSEDDA...PTNITPMPGTTPEGEVTPSEDDAPTNITPMPGTTPEGEATPSEDDAPTNITPMPGTTPEGEATPSEDDAPTNITPMPGTTPSEDDAPTNITPNEDSVTPEGEATPSEEDDAPTNITPTPDGVTPDSDSPSNMDNPGGTSLPDADIPANTEEQTNPSEGGAKILAPQ
Full Text Available lus vulgaris MKVMKKKKSDAESQHDDYNEFKSDEDKDDTQYKKEKKERRKKKMSEEGKSKEYNEFESNEGEDDAQSK...KRKKKKLSTESKSKEYKVLERNEGEGDVEGKKGKLKKLSEEGKSKKYNEFESNEGEDDALGKKRKKKNLSTESKSKEFKVLERNEGEGEGEGDVEGKKRKLEKLSEEGKSKECNEFENNDGEDDA...QGRKRKKKKFKESKSEEYNVFERNEGEGDVKGKKTKKKKLSEEGKSKEYNEFENNEVEDDAQGKKKKLSKESTSEEYNVFERNGGEDYIEG...KKRKKKKPSEEGKSMEYNEFQNNEGEDDAKGKKTKKKKPGEEGKSKEYNEFEKNEVEDDAQGKKKKLSKESTSEKYNVFER
Full Text Available vulgaris MKVMKKKKSDAESQHDDYNEFKSDEDKDDTQYKKEKKERRKKKMSEEGKSKEYNEFESNEGEDDAQSKKRKK...KKLSTESKSKEYKVLERNEGEGDVEGKKGKLKKLSEEGKSKKYNEFESNEGEDDALGKKRKKKNLSTESKSKEFKVLERNEGEGEGEGDVEGKKRKLEKLSEEGKSKECNEFENNDGEDDA...QGRKRKKKKFKESKSEEYNVFERNEGEGDVKGKKTKKKKLSEEGKSKEYNEFENNEVEDDAQGKKKKLSKESTSEEYNVFERNGGEDYIEGKKRKKKKPSEEGKSMEYNEFQNNEGEDDA...KGKKTKKKKPGEEGKSKEYNEFEKNEVEDDAQGKKKKLSKESTSEKYNVFERNEGE
Full Text Available KEEKKEKRKHKRHRHHKSKSKRRHTTENSDSDESDDKDEGRKRVHSAVEHKREVKRSRQVKKDSREDSSDTDDNEPRKRRQERPEDDAPRRRRQDTPEDDAPRRRRQDTPEDDAPRRRRQDTPEDDA...LRRRQGTPEDDAPRKRRQDTPEDDAPRRRQQDRPEDDAPRRRQQNTPEDGEPRRREQEMALD
Full Text Available LNSRCQGANAATPSSDETTEESTPAEDSISPENSIEETTPGAPLPDSSPEGITPAPEEPLPGTTPEGLTPLPGSVPGDEVTPSEDDAPTNITPMPGTTPEGEVTPSEDDAPTNITPMPGTTPEGEVTPSEDDA...PTNITPMPGTTPEGEVTPSEDDAPTNITPMPGTTPEGEVTPSEDDAPTNITPMPGTTPEGEVTPSEDDA...PTNITPMPGTTPEGEATPSEDDAPTNITPMPGTTPEGEATPSEDDAPTNITPMPGTTPSEDDAPTNITPNEDSVTPEGEATPSEEDDAPTNITPTPDGVTPDSDSPSNMDNPGGTSLPDADIPANTEEQTNPSEGGAKILAPQ
Full Text Available VREENSQLQSQLSEVQTLLGQAHHHNEQLQSQLDRTEQQKAELQSQLDRVSSALQNVELQLADRSQQLSDTQSQLSSVQGERDQLQSELETANQTVAQLQSQLGDTQSQLSSVQGERD...QLQSELETANQTVAQLESQLGDTQSQLSSVQGERDQLQSELETANQTVAQLESQLGDTQSQLSSVQGERDQ...LQSELETANQTVAQLESQLGDTQSQLSSVQGERDQLQSELETANQTVAQLESQLGDTQSQLSSVQGERDQLQSELETANQTVAQLESQLGDTQSQLSSVQGERDQLQS...ELETANQTVAQLESQLGDTQSQLSSVQGERDQLQSELETANQTVAQLESQLSSVQGERDQLQSELETANQTVAQLESQLGDTQSQLSSVQGERDQLQSELETANQTVAQLESQLGDTQSQLSSVQGERD
Full Text Available 3065:1239 ... 3066:1239 ... 3067:1239 ... 3068:1239 ... hypothetical protein VOLCADRAFT_66785 Volvox carteri f. nagariensis MRVGERDCPRVGERD...CPGVGERDCPGVGERDCPRVGERDCPGVGERDCPGVGERDCPRVGERDCPGVGERDCPRVGERDCPGVGERDCPGVGERDCPGVGERDCWPNVDSWTNLSNGRLMRVGER...DCPRVGERDCPGVGERDCPGVGERDCPRVGERDCPGVGERDCPGVGERDCPRVGERDCPGVGERDCPRVGERDCPGVGERDCPGVGERDCPGVGERDCWPNVDSWTNVCVVFRFLNLGPN
Full Text Available 8:1201 ... hypothetical protein Oscillatoria sp. PCC 10802 MGHIPSSSFPDNRRAFSLWLWWGGLIEHRHVVAKIWALEIPGMNPTPQPPPRVRGGGERD...GFGGGGLIEHRHVVAKISALEIPGMNPAPQPPPRVRGGGERDGFGGGGFIDIRHVVAKIAGEPAPTNHRHPVSGEAADATHYIYADFEG
Full Text Available GYMPSLLLDPNVKNPSQIQQLKDFGTGIHSQVSQEPSPYTEFYVQQRTSNPRKCKFMGCVKGARGASGLCISHGGGQRCQKPGCNKGAESKTTFCKTHGGGKRCEHLGCTKSAEGKTDFCISH...GGGRRCEFLEGCDKAARGRSGLCIKHGGGKRCNIEDCTRSAEGQAGLCISHGGGKRCQYFSGCEKGAQGSTNYCKAHGGGKRCIFSGCSKGAE
Full Text Available 065:363 ... 3066:363 ... 3067:363 ... 3068:363 ... hypothetical protein VOLCADRAFT_35996, partial Volvox carteri f. nagariensis HIAYCISH...IAYCISHIAYCISHIAYCILHIAYCISHIAYCVSHIAYRILHIAYRILHIAYRILHIAYCILHIAYCILHIAYRISHIAYCISHPYRCIWHIAY
Full Text Available 065:363 ... 3066:363 ... 3067:363 ... 3068:363 ... hypothetical protein VOLCADRAFT_99209 Volvox carteri f. nagariensis MQMHAHTYNISHIVYCISH...IAYCISHIAYRISHIAYRISHIVYRVSHIAYRILHIAYCILHIAYCILHIAYCILHIAYCILHIAYCILHIAYRISHIAAYMAYRISHTAYRISQIAYRCISHIAAYRCILHITYMHIIYAHI
Full Text Available 065:363 ... 3066:363 ... 3067:363 ... 3068:363 ... hypothetical protein VOLCADRAFT_100737 Volvox carteri f. nagariensis MYNISHIVYCISHIAYCISH...IAYRISHIAYRILHIAYCISHIAYCISHIAYCISHIAYRISHIPYRCTISLHMAYRISHTARISHIANCISLHIAYCILHIAYCISHIAYPISLHHIAAYGISHITYRTHIAYRKLHIAAYRISLHIAAYCISHIHICIYAHI
Full Text Available KRSGGYMPSLLLDPNVKNPSQIQQLKDFGTGIHSQVSQEPSPYTEFYVQQRTSNPRKCKFMGCVKGARGASGLCISHGGGQRCQKPGCNKGAESKTTFCKTHGGGKRCEHLGCTKSAEGKTDFCISH...GGGRRCEFLEGCDKAARGRSGLCIKHGGGKRCNIEDCTRSAEGQAGLCISHGGGKRCQYFSGCEKGAQGSTNYCKAHGGGKRCIFSGCS
Full Text Available ... hypothetical protein PCC8801_3595 Cyanothece sp. PCC 8801 MSIQYLLDENLPHLYREQLLRLKSDLTVWIIGDPGVPPKSTLDPEILIWCEQNKFILVTNNRASMPVHLADHLSQNRHIPGIFVLRPKASIGEIIDDLILIDELGNPQDYQDCISHIPFI
Full Text Available 065:363 ... 3066:363 ... 3067:363 ... 3068:363 ... hypothetical protein VOLCADRAFT_90903 Volvox carteri f. nagariensis MQMHIVYCISH...IAYCILHIAYRILHIAYCISHIAYRILHIAYCILHIAYCISHVAYCISHIPYRCIWHIARISHTAYRIPQITYRCISHIAAYRCILHITYTYMYIYAHI
Full Text Available KRSGGYMPSLLLDPTVRNPSQMQQLKDFGTGIHSQVSLEPSPYTALSVQQRTSNPRKCKFMGCLKGARGSSGLCISHGGGQRCQKPGCNKGAESRTTFCKTHGGGKRCEHLGCTKSAEGKTDFCISH...GGGRRCEFLEGCDKAARGKSGLCIKHGGGKRCNIENCTRSAEGQAGLCISHGGGKRCQFSSGCEKGAQGSTNYCKAHGGGKRCIFSGCS
Full Text Available 065:363 ... 3066:363 ... 3067:363 ... 3068:363 ... hypothetical protein VOLCADRAFT_71945 Volvox carteri f. nagariensis MRICLHIAYVCISH...IAYRICACLHIAISHIIHIAYRILPIAYCISHIAYCISHIAYCILHIAYCISHIAYRISHIAYCISHIAYCISHIAYCILHIAYCILHIAYCILHIAYCILHIAYCILHIAYCILHIAYCILHIAAYGILHIAYAYRSQHSIA
Full Text Available 2419 hypothetical protein CHLREDRAFT_123820, partial Chlamydomonas reinhardtii RVQCRLVDMPAPCLPPFLPTCPHKPRRIPMPCTDAH...ELVDMPAPCLPPFLPDNLPARAPQAPHAVTDAHECMQCRLVDMPAPCLPPFLPKCPHKPRRLPMPCTDAHECNMPAPCLPPFLPKCPHKPRRLPMPCTDAHECMQCRLVDMPAPCLPAFLPNCPHKPRRLPMPCTDAHECSAGW ...
Full Text Available ... 70447:1749 ... 70448:2455 ... TRAPP 20 K subunit (ISS) Ostreococcus tauri MSASAALTVVNANGRSVYERELGSSADSVDTDAH...VRELIGRAALDFADARSWESSATYLRLVDRFNDADAHGYRTSGGGRFVLTLRGRLRGNAGDETIRQFFTDAHEAYAIAKMNPMRDEDEDLGEAFDRAVRESFRRRLAPLFPFARTDE
Full Text Available 3051:329 ... 3052:329 ... 3055:329 ... predicted protein Chlamydomonas reinhardtii MAPAALPGRSVKSKQAHLLRTDAHRVKSKQAHLLRTDAHRVKSKQAHLLRTDA...HRVKSKQAHLLRTDAHRVKSKQAHLLRTDAHRVALTTLTGALSLFGGACTATSFVLQVSASAASYAASLRLSCPAVPSLTDVA
Full Text Available 436017:4609 distinct from photosynthetic electron transfer catalyst, CYC6, partial Ostreococcus lucimarinus CCE9901 RDLERNGVATKEDISNLIERGKGKMPGYGESCAPKGACTFGARLDAEEIDALATYVLDRAAVDW ...
Full Text Available 18 3068:3318 hypothetical protein VOLCADRAFT_120454 Volvox carteri f. nagariensis MLVTTRSHRQVSLDGGVLPPEEIKQLASLRRQQQADLAKDSNIVQGALEEAQLITWPTREKALLDTVLVLFIVAGSGAMIFGMNVLLAELSEWWYHLA ...
Full Text Available CELACDAGCDLGESPIWDAATSTLYFVDINSKRIHSYSPASGAHRTIQLEQPIGTVVPTSNPNILLAALEASCLPSLADCLDAWLARDIVEVDVAAGTTGRVLATTPE...EHGVDGMRFNDGKVSPQGTLLVGRMHCKWRDGQRGRLYRLDPGSSQLVEVLRPEEVHLPNGMAWDEAKGVVFYVDSGAETI
Full Text Available 832:429 ... 296587:152 ... predicted protein Micromonas sp. RCC299 MRARGKVEVELQGVQRLSARCKECGGSQICEHGRQRFHCRECGGSGICEHGRGRHRCKECG...GSQICEHGRVRSQCKECGGSGICEHGRRRSLCKECGGSGICEHGRQRYSCKECGGAGICEHGRERYSCKECRAAKAGTFPDVDVEVGVTEDA...SSKGAKRKRAPYTKGPCEHGVKYRSQCKVCSACPHGRQRNKCKECGGASICVHGRERNKCKECGGASICEHGRQRSHCKECGGASICVHARERNKCKECG...GASFCEHGRQRRYCKECGGSQICEHGRVRRLCKECGGSGICEHGRQRPQCKECGGSQICEHGRQRYSCKECRAAKAKQR
Full Text Available CEHGVKPRSRCKVCGACPHGKQRSRCKECGGSGICEHGRVRSLCKECGGSRICEHGRRRYECKACGGSQICEHGRERCRCKECGGGSICEHGRQRYRCKECGGSSICEHGRQRYRCKECG...GSQICKHGRERSKCKECGGSQICEHGRERCRCKECGGGSICEHGRQRSQCKECGGSAICEHGRHRSYCKECGGSAFCEHGRQRSQCKECG...GSQICEHGRIRSKCKECGGGSICEHGRMRSQCRECGGGSICEHGRRRSRCKECGGPRISTPP
Full Text Available 8832:429 ... 296587:152 ... predicted protein Micromonas sp. RCC299 MLPDVDVEVGVTEDASSKGTKRKRAPKTKGPCEHGVKRRSNCKVCSACPHGKWRYWCKECG...GAGICEHGRERRRCKECGGASICEHGRQRRYCKECGGGSICEHGRVRYYCKECGGSGICEHGRDRSRCKECGGGSICEHGRERYYCKECGGSQICEHGRRRSECKECG...GSQICEHGRRRSECKECGGSAICEHGRQRYYCKECGGSGICEHGRDRSRCKECGGGSICEHGRERYYCKECG...GAGICEHGRIRSTCKECGGSRICEHDRQRHTCKDCGGSQICEHGRVRSKCKECGGSGICEHGRHRQYCKECGGGSFCEHGRQRRKCKECGGSQI
Full Text Available GPCEHGVKPRSQCKVCSACPHGKRRRHCKECGGSQICEHGRVRSQCKECGGASICEHGRQRHRCKECGGAGICEHGRQRSVCKECGGSSICEHGRIRSTCKECGGSQICEHGRQRHRCKECG...GGGICEHGRQRSVCKECGGSQICEHGRVRSTCKECGGAGICEHGRQRHRCKECGGASICEHGRQRRYCKECGGSGICVHGRQRHSCKECG...GGGICEHDRQRHRCKECGGSQICEHGRVRSTCKECGGGSICEHGRRRSGCKECGGGGICEHGRQRSRCKECGGGSICEHGRRRCECKECGGSQICEHGRRRSQCKECGGASICEHGRHRHQCKECRAAKAKQSR
Full Text Available 8832:429 ... 296587:152 ... predicted protein Micromonas sp. RCC299 MPAIWNVSGPLPDVDVEVGVTEDASSKGTKRKRAPPTKGPCEHG...VKPRSKCKVCSACPHGKRRSECKECGGSQICEHGRRRTQCKECGGSQICEHGRVRSTCKECGGSGLCEHGRERSRCKECGGPGICEHGRVRSRCKECGGSQICEHGRQRSKCKECG...GGSICEHGRIRSTCKECGGSQICEHGRERSKCKECGGGAICEHGRIRSTCKECGGGAICEHGRERHRCKECGGSGICEHGRRRSQCKECG...GSAICEHGRHRQYCKECGGGSICEHGRIRSTCKECGGGAICEHGRQRHRCKECGGASFCEHGRQRSRCKECGGSGICEHGRRRSTCKECRAAN
Full Text Available EEEEDASNKGTKRKRAPYTKGPCEHGVKYRSKCKVCSACPHGRERRYCKDCGGSKICEHGRQRDYCKECGGGAICEHGRERHRCKECGGSGICEHGRRRSRCKECGGSGICEHGRVRSRCKECG...GGSICEHGRERSRCKECSGSGVCEHGRERSKCKECGGASICEHGRQRSHCKECGGGSTCEHGRERRYCKECGGSGICEHGRIRSQCKECG...GSGICEHGRRRSDCKECGGSQICEHGRIRSTCKECGGSQICEHGRQRSYCKECGGGSICEHGRRRSRCKECGGSQICEHGRERSKCKECGGASICEHGRQRSQCKECG...GSGVCEHGRQRTRCKECGGASICEHGRVRSQCKECGGGGICEHGRQRSKCKECRAAKAGTHS
Full Text Available KGPCEHGVKYRSQCKVCSACPHGKWRYTCKECDGASICEHGRMRSTCKECGGSQICEHGRIRSQCKECGGASICEHGRQRSSCKECGGASICEHGRERRRCKECGGSEICEHSRRRTECKECG...GSGICEHGRVRSQCRECGGSAICEHGRVRSRCKECGGSAICEHGRVRSRCKECGGGAICEHGRVRSRCKECGGGAICEHGRIRSECKECG...GGSICEHGRRRSRCKECGGSQICEHGRRRNQCKECGGSQICEHGRRRTRCKECGGSEICEHSRQRYQCKDCLS
Full Text Available GTKRKRAPYTKGPCEHGVKPRSQCKVCSACPHGKRRRYCKECGGSQICEHGRIRTLCKECGGSRICEHGRERRRCKECGGGSICEHGRQRSYCKECGGSGICEHGRQRHYCKECGGGSICEHGRRRSECKECG...GGSICEHSRVRYTCKECGGSQICAHGRQRSTCKECGGSQICEHGRIRSTCKECGGSQICEHDCIRSTCKECG...GGSICEHGRQRDYCKECGGSRICAHGRERRYCKECGGSGICEHGRQRKQCKECGGSAICEHGRQRHQCKECRGSSVPVGRWVL
Full Text Available KGPCEHGVKPRSRCKVCSACPHGKWRKQCKECGGASICEHGRIRSVCKECGGASICEHGRQRSQCKECGGSEICEHGRHRSKCKECGGSQICEHGRQRHRCKECGGSSICEHGRHRPQCKECG...GASICEHGRHRYSCKECGGASICEHGRHRSKCKECGGSQICEHGRQRSRCKECGGGSICEHGRERSLCKECGGSQICEHGRRRSRCKECG...GGSICEHGRIRSQCKECGGASICEHGRQRSQCKECGGSQICEHGRRRSQCKECGGGSICEHGRIRSQCKDCRCERL
Full Text Available DKRLFSQAVVQFQKALKAKDLEGDENTALIYNGLGYAHAAQEQYDIAIRQYKEALKLKPDYVVAFNNLGFAYEKKQLSAQALEAYESALALDPNNPTAKRRVEPLRKLYAPSAS ...pothetical protein Geitlerinema sp. PCC 7407 MDNSLTLSYLSLLLLLLAVASFFILRQVIRTRRTESTLSRLQNALKGGQGSAKDHYELGGIYL
Full Text Available NREKASPATAVKATFFLITGHLQPNSTLIESLIAQGHEIANHGTQDLRTSQLAADAFASQFREANDILSRLAGQELRWYRPGQAFYNQSMRSFLGTFPGYESRFALASMIPLDTGKATNHPQFTTWYISQFIFPGAILVLHGGSPERDENTALVLKNLLGKLHDQGYQVVTLSQLVDHKR
Full Text Available DTPSSNTLNENPSVNSLVETGQVVSDTERQTSQNNNDNNNVNSQDKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPET...KPPETKPPETKPPETKPPGHKPPETKPPETKPPETKPPGHRPPGHKPPETKPPGHKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETRPPETKPPDTKPPETKPPETRPPETKPPETKPPETKPPETKAPGN
Full Text Available HFEVLKWARANGALWDENTCSSAAWSGDLQILQWARANGCPWDGETCSEAAIHGHLELLQWARANGCPWDESTCSRAAEGEELEVLKWARANGCPWDTKTCAEAACGGQLEMLQWARANGAPWDEETCS...KAAEGEDLEVLKWARENGCPWDTKTCAEAATGGQLEMLQWARANGAPWDEETCSKAAEGNELEVLQWARANGCPWDKETCKKAEEGGHLEVLRWAGENGAP
Full Text Available 218 ... 38832:274 ... 38833:414 ... 564608:414 predicted protein Micromonas pusilla CCMP1545 MAQLPSYEVDDGEDSMPGAPGEGPMTDSMQGPPVEVPTSDSM...PGAPGEVPTMDSMHGPPVEVPTMDSMHGAPVEVPMMDSMPGAPVEVPTMDSMQGPPVEVPTMDSMQGAPGEGPMTDSMHGAPGEGPTMDSMNSGNPTKCVVPDWCSTYPPEMQKSKPECQCPDDSHP
Full Text Available 401 ... 38832:1362 ... 38833:877 ... 564608:877 predicted protein Micromonas pusilla CCMP1545 MQDSMHDTMHDSIQDSMHDSIQDSMQDSM...AKEEEEPAEPPAKEEEAHAEPPAKEEEAHAEPPAKEEDYAEPPAKEEDYAEPPAKEEAHSMDSMDSMDSMDSMDSMDSMHSMDSMDSMDSMDSMHSMDSMDSMDSM...DSMHSMDSMDSMDSMDSMDSMDSMHSMDTSIDAVDAAANVTDAADTAGAAANVTDAADTAGAAAEEKPPENASVDSLDSLLDG
Full Text Available 3051:4703 ... 3052:4703 ... 3055:4703 ... hypothetical protein CHLREDRAFT_120274, partial Chlamydomonas reinhardtii PPGCRCSSAPPGCRC...SSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCS
Full Text Available 058 3068:3058 hypothetical protein VOLCADRAFT_87241 Volvox carteri f. nagariensis MPNPLAEMELLGFWGLKLVATVTDCHMSDSGRVMTAFVFKVVSYRNEAAST...LAEMELLGFWGLKLVATVTDCHMSDSGRVMTAFVFKVVSYRNEAASTMLTPEPLPESLEYLQAQVERALDERRELERVMWA...AREGRGGPSMLSCKQLETIELSTMGEAAELEVKRALEAITVVQYSMPNPLAEMELLGFWGLKLVATVTDCHMSDSGRVMTAFVFKVVSYRNEAASTMLTPEPLPESLEYLQAQVERALDERRELERVMWAAREGRGGPSMLSCKQLETIELSTMGEAAELEVKRALEEMFH ...
Full Text Available transferase Halothece sp. PCC 7418 MKIVIARDFNDFARCIMIRTQVFVMEQGISAEIETDEWENHSTHYLAGDGEKALATARSRLINNQTAKIERVAVLKEARSQGVGTELMRYILQEIHSYSNIQTIKLGSQNSAIPFYEKLGFQVIGEEYLDAGIPHHLMMQRINT ...
Full Text Available CEAGDVQGAIEDCNQALRINPKLAEAYCNRSNARCESGDVEGAIEDCNQALRINPKLAEAYLNRGNARRESGDIKRAIEDYNQGLRINPNLAQAYRNRGFARCESGDF...KGAIEDFNQAIRINPNLAQAYQNRGFARCESGDFKGAIEDFNQALRINPNYAEAYYNRGLAHNYSGDRQAEIEDFNQALRINPNLAEAYLNRGVTRRESGDVKGAIEDYNQALHINPNLAEAYQNRGFARC
Full Text Available sp. CC9605 MIAPLPMPAEPLLEQYGQGARLCPCANDQITLVFSQEYPFDLVELEQLLEAVGWSRRPIRRVRKALSHSLLKVGLWRHDPRVPRLVGFARCTGDGVFEATVWDVAVHPLYQGNGLGKQLMAYILEALDQMGTERVSLFADPGVVSFYQGQGWDLEPQGHRCAFWYAN ...
Full Text Available DIISSFIDDSIAIIDSVISGDKGDDVIGLEAGLFNSSVIGGDGNDIISTENAFVTGGSIEGNNGEDSLSLGLLDSVAVNGNADNDVIDLRGNIESSSIRGGQGNDTIS...SFIDDSITITDSVIAGDKGDDVFGLEADLFNSSVIGGDGNDSISTVNAFLTGGSIEGNDGEDTLSLGLLDGVAVNGNADNDVI...DFRSDIESSSIRGGQGNDTISPAFFINITDSVIAGDKGDDAIILGELNIETPLYNSTFNNASSADVDTVIDGGAGNDVIAFDGTQVEDATILGGEGADTFQLWNGG
Full Text Available ursor Glycine max MKKASAMHCALLRFWVPLLLLASFSFAPSVLAKAEISGNEVNTHGKVVSEELTKSSLKEQNEEEKFKGFFPKPIPIIKPISKPI...PIIKPIPKSIPIVKPIPIPVYKPISKPIPIVKPIPKPFLIVKPIPNDEEKFKGVFPKPIPIVKPIPKPIPIVKPIPIPIYKPIPKSVPIVKPIPIIKPILKPNPIVKPI...PKLIPIVKPIPNPLRVKKSIPAFGSEEFLKPKPFFEKPIPKLPLDPKFKKPLLPPLPIHKPIPTP
Full Text Available e Solanum tuberosum MIDEVKEEWPETPSFLNPETPNSQNPETPTFSNPESPTFSKSETPTFSMPETPTFSKPETPSFSKPETPSFSKPET...PSSQKLEASTFSKTETPTFSKLETPSFSKLETPISPNPETPTFSKPKTPSFSKPEIPSFSKPKTPSFSKSETPTLSKPETPSSPKPETPNSPKIEAPSFSKPETPSFSKPET...PTFSNPETLSSPKSETLTFQKPEIPSSPKLETQSSSKPETPSFSKPETPTFSKSKTPSSSKPEMPSSPKPETPSFSKPEILTFSKPKTPSFSKPETPSFSKPETPSFSRPET...PSFSNPETPSSSKPEPETLSSPKPKTPSSAKLETPSFSKLETPSFSKPETPSSLKPETPSFSKPET...PSSPNPKTPSSPKSETPSFSKPKTPSFSKPETPSSSKLETPNFLKPETPSSLKLEAPPTFLKPETSSSTKPKTPSFSTPETPTFSKPETPTFSKSETPSFSKSETPSSFKPETPSFSKPETPSSPKFETPSSPKPETPSSPKT
Full Text Available NASKDTPSSNTLNENPSVNSLVETGQVVSDTERQTSQNNNDNNNVNSQDKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPET...KPPETKPPETKPPETKPPETKPPGHKPPETKPPETKPPETKPPGHRPPGHKPPETKPPGHKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETRPPETKPPDTKPPETKPPETRPPETKPPETKPPETKPPETKAPGN ...
Full Text Available 0:266 ... 424551:266 ... 424574:266 ... 4107:266 ... 4113:1088 ... PREDICTED: proteoglycan 4-like Solanum tuberosum MPTLSKLEIPNSPNPET...PGSPKSVTPSISKPKTPSFSKPETPSFSTPETPSFSRPETPSFSKPETPSSSKPEAPSSLTPETPSFSKPETLSFSKPET...PSSPKLEIRNSAKPETPSFSKPETPSFSKPKTPSSPKPETPSFSKPKTPSSPNLKTPTPSSPNSQTPSFSNSRKPEAPTFLKPETPSSPKPKTPSFSTPETPTFSKPET...PNFSKSETPSFSKPETPSSFKPETHSFLKSETPSSPKPETPSSPKFEPPSSPKPETPSSPKTENPSSPNTETPNFSKPETPSSPKPNTPSFPKLDTPSFSNPKTPSYETPSFPKFETTSSQKPETPNSPKFGTPSLPKSKIPSDPIFETISFSKPETSNSSKPKIPTTP
Full Text Available VVDNPSFLQLSNSSSSSSNASKDTPSSNTLNENPSVNSLVETGQVVSDTERQTSQNNNDNNNVNSQDKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPET...KPPETKPPETKPPETKPPETKPPETKPPETKPPETKPPGHKPPETKPPETKPPETKPPGHRPPGHKPPETKPPGHKPPETKPPETKPPETKPPETKPPETKPPET...KPPETKPPETKPPETRPPETKPPDTKPPETKPPETRPPETKPPETKPPETKPPETKAPGN
Full Text Available e Solanum tuberosum MAQHYKLSSILLLAFIYFIHDHMITTITARRILQTPSFSTPTTPSFSMPTTPSFSKSPGVSKPASPSFSNSPSLSKPET...PSFSKSETLSFSKPETPSFSTSETPSFSKPETPSFSKPETPSFSKPEIPSFSKPETPSSPRLETPIFIKPETPTFSKPETPTFSKPKTPSLLKPETPSSQKPETPTFSKPET...PIFSKSETHSFSKPETPTSPNPETPTFSKPETPSSPKPETPSFSKPETSSFSKPETPTFSKPETPSSPKSETPSFSKPETPTFSKPET...PSSPKSETPTFPKPKIPSSLKPETPSSPNLETPSFLKPETPIFSKPETPSFSKPEMPSSTKPETPIPQSPRPLLSQSLKSQILQTPRPQLETSSFSKPET...PSFSKPETPSSSKPEAPSSPTPEMQSFTKPETPSFSKPETPNSPKPETPSFPKPETSTFSKPQTSNSPKSETSSSPKPETSSFSKSETPSFSKPEMPSSPTPETPNFSKPET
Full Text Available LLIFVFVISMSLVLIITSGKPPSFPASIPDQILGLLGISSTSYVLGKALQGIKPSSAEEPSSVATAASPPPSPEPQSYDGQDLPPS ...etical protein Calothrix sp. PCC 7507 MPNINDLFTILALVIGCIITIFVAVLEIFILIFIWDGTWNVNTRKGKRRGINLEKLISESSGDASLARFQ
Full Text Available -repair coupling factor Arthrospira platensis C1 MCDRKFWAAKERGFRAIALVSYSLFRNHIITSPSPSPSVGARFRAIALVSYSLFRNHIIT...SPSPSPSVGARFRAIALVSYSLFRNHIITSPSPSPSVGARFRAIALVSYSLFRNHIITSPSPSPFVGARFRAIALVSYSLFRNHIITSPSPSPFVGARFRAIALVSYSLFRNHIIT...SPSPSPFVGARFRAIALVSYSLFRNHIITSPSPSPFVGARFRAIALVSYSLFRNHIITSPSPSPFVGEGFRVRGNVLSDW ...
Full Text Available ibiotic biosynthesis monooxygenase Chamaesiphon minutus PCC 6605 MPYVLIIHEVADYDAWKQ... YP_007097338.1 NC_019698 1117:24722 ... 1118:14027 1301283:4479 ... 217161:1887 1173032:1887 1173020:1887 ... Ant
Full Text Available YP_007118146.1 NC_019730 1117:843 ... 1150:13380 1301283:30256 ... 1158:4799 482564:3448 179408:3448 ... Antibiot...ic biosynthesis monooxygenase Oscillatoria nigro-viridis PCC 7112 MILEAVVLNVKSGCEGD
Full Text Available NYNSMNASIEIKQQESCQTNINHESCMFSKCMGGMQRFAIPPLPSFEVEQLNVVQGSRHCLSPHFQNSLVTFISYQKEKES... ... 1003877:124 ... 3655:124 ... 3656:1142 ... PREDICTED: transcription factor bHLH143-like Cucumis melo MVGTDTWQLH