Conejo, Maria; Bertin, Matt; Pomponi, Shirley A; Ellington, W Ross
Arginine kinase (AK) is a member of a large family of phosphoryl transfer enzymes called phosphagen (guanidino) kinases. AKs are present in certain protozoans, sponges, cnidarians, and both lophotrochozoan and ecdysozoan protostomes. Another phosphagen kinase, creatine kinase (CK), is found in sponges, cnidarians, and both deuterostome and protostome groups but does not appear to be present in protozoans. To probe the early evolution of phosphagen kinases, we have amplified the cDNAs for AKs from three choanoflagellates and from the hexactinellid sponge Aphrocallistes beatrix and the demosponges Suberites fuscus and Microciona prolifera. Phylogenetic analysis using maximum likelihood of these choanoflagellate and sponge AKs with other AK sequences revealed that the AK from the choanoflagellate Monosiga brevicollis clusters with the AK from the glass sponge Aphrocallistes and is part of a larger cluster containing AKs from the demosponges Suberites and Microciona as well as basal and protostome invertebrates. In contrast, AKs from Codonosiga gracilis and Monosiga ovata form a distinct cluster apart from all other AK sequences. tBLASTn searches of the recently released M. brevicollis genome database showed that this species has three unique AK genes-one virtually identical to the M. brevicollis cDNA and the other two showing great similarity to C. gracilis and M. ovata AKs. Three distinct AK genes are likely present in choanoflagellates. Two of these AKs display extensive similarity to both CKs and an AK from sponges. Previous work has shown CK evolved from an AK-like ancestor prior to the divergence of sponges. The present results provide evidence suggesting that the initial gene duplication event(s) leading to the CK lineage may have occurred before the divergence of the choanoflagellate and animal lineages. PMID:18064398
Marconi, Veronica I.; Miño, Gaston L.; Sparacino, Javier; Banchio, Adolfo J.; Condat, Carlos A.; Koehl, Mimi A. R.; King, Nicole; Stocker, Roman
In freshwater environments, as well as in oceans, environmental conditions are in constant fluctuation. Some heterotrophic plankton must adapt their swimming behavior in order to survive under these conditions. In the case of the choanoflagellate, the closest animal ancestor, the ability to forage for food is given not only by its single flagellum, but also by its differentiation between fast and slow swimmers. The understanding of how these cells with different strategies to swim search for food can give us a better insight into how eukaryotes respond to different stimuli. In this work, we have designed a microfluidic device that sorts choanoflagellates by their speed. The optimal geometry was found by a numerical model using the experimentally determined motilities of each swimmer type.
Full Text Available Abstract Background Comparative genomics of the early diverging metazoan lineages and of their unicellular sister-groups opens new window to reconstructing the genetic changes which preceded or accompanied the evolution of multicellular body plans. A recent analysis found that the genome of the nerve-less sponges encodes the homologues of most vertebrate post-synaptic proteins. In vertebrate excitatory synapses, these proteins assemble to form the post-synaptic density, a complex molecular platform linking membrane receptors, components of their signalling pathways, and the cytoskeleton. Newly available genomes from Monosiga brevicollis (a member of Choanoflagellata, the closest unicellular relatives of animals and Trichoplax adhaerens (a member of Placozoa: besides sponges, the only nerve-less metazoans offer an opportunity to refine our understanding of post-synaptic protein evolution. Results Searches for orthologous proteins and reconstruction of gene gains/losses based on the taxon phylogeny indicate that post-synaptic proteins originated in two main steps. The backbone scaffold proteins (Shank, Homer, DLG and some of their partners were acquired in a unicellular ancestor of choanoflagellates and metazoans. A substantial additional set appeared in an exclusive ancestor of the Metazoa. The placozoan genome contains most post-synaptic genes but lacks some of them. Notably, the master-scaffold protein Shank might have been lost secondarily in the placozoan lineage. Conclusions The time of origination of most post-synaptic proteins was not concomitant with the acquisition of synapses or neural-like cells. The backbone of the scaffold emerged in a unicellular context and was probably not involved in cell-cell communication. Based on the reconstructed protein composition and potential interactions, its ancestral function could have been to link calcium signalling and cytoskeleton regulation. The complex later became integrated into the evolving
Orme, B. A. A.; Blake, J. R.; Otto, S. R.
The three-dimensional particle paths due to a helical beat pattern of the flagellum of a sessile choanoflagellate, Salpingoeca Amphoridium (SA), are modelled and compared to the experimental observations of Pettitt (2001). The organism’s main components are a flagellum and a cell body which are situated above a substrate such that the interaction between these entities is crucial in determining the fluid flow around the choanoflagellate. This flow of fluid can be characterized as Stokes flow and a flow field analogous to one created by the flagellum is generated by a distribution of stokeslets and dipoles along a helical curve.
Mark J Dayel
Full Text Available Choanoflagellates are unicellular and colonial aquatic microeukaryotes that capture bacteria using an apical flagellum surrounded by a feeding collar composed of actin-filled microvilli. Flow produced by the apical flagellum drives prey bacteria to the feeding collar for phagocytosis. We report here on the cell biology of prey capture in rosette-shaped colonies and unicellular "thecate" or substrate attached cells from the choanoflagellate S. rosetta. In thecate cells and rosette colonies, phagocytosis initially involves fusion of multiple microvilli, followed by remodeling of the collar membrane to engulf the prey, and transport of engulfed bacteria into the cell. Although both thecate cells and rosette colony cells produce ∼ 70 nm "collar links" that connect and potentially stabilize adjacent microvilli, only thecate cells were observed to produce a lamellipod-like "collar skirt" that encircles the base of the collar. This study offers insight into the process of prey ingestion by S. rosetta, and provides a context within which to consider potential ecological differences between solitary cells and colonies in choanoflagellates.
Nebria brevicollis (Fabricius) is one of the most frequently encountered and widely distributed carabid beetles in Europe. Until recently, the only North American records were based on two single specimens, both from the 1930’s in southeastern Canada. In 2008, this species was found at thirteen different sites in five counties in northwestern Oregon. As of the end of 2010, it has been found in thirty-four different sites in ten Oregon counties, with a north-south range of ~150 km and an...
LaBonte, James R.
Abstract Nebria brevicollis (Fabricius) is one of the most frequently encountered and widely distributed carabid beetles in Europe. Until recently, the only North American records were based on two single specimens, both from the 1930’s in southeastern Canada. In 2008, this species was found at thirteen different sites in five counties in northwestern Oregon. As of the end of 2010, it has been found in thirty-four different sites in ten Oregon counties, with a north-south range of ~150 km and an east-west range of ~90 km. It was also detected in 2010 in southwestern Washington (Vancouver), just north of Portland and the Columbia River. The ecological amplitude of Nebria brevicollis in Oregon rivals that of the most eurytopic native carabid species, e.g., Pterostichus algidus LeConte and Scaphinotus marginatus (Fischer von Waldheim). It has been found in highly degraded heavy industrial sites, agricultural fields, city parks, gardens, second growth woodlands, mature conifer forests, montane rock gardens, and otherwise pristine stands of old growth noble fir, with elevations ranging from essentially sea level to 1,249 meters. Climates at these locales vary from that of the Mediterranean Willamette Valley floor, where snow rarely occurs and summers are hot and dry, to the summit of the Oregon Coast Range, where deep snow may be present from November through April and summers are cool. The carabid communities in which Nebria brevicollis has been found range from those predominantly of fellow exotic species, e.g., at heavily perturbed sites, to those where it is the only exotic species, such as at the Coast Range summit. Nebria brevicollis is clearly an invasive species in that it is not restricted to anthropogenic habitats, is rapidly expanding its North American range, and can be abundant in essentially pristine settings. What is not yet clear is whether it is or will become a damaging species. Although it is already the most abundant carabid species in some
Full Text Available Nebria brevicollis (Fabricius is one of the most frequently encountered and widely distributed carabid beetles in Europe. Until recently, the only North American records were based on two single specimens, both from the 1930’s in southeastern Canada. In 2008, this species was found at thirteen different sites in five counties in northwestern Oregon. As of the end of 2010, it has been found in thirty-four different sites in ten Oregon counties, with a north-south range of ~150 km and an east-west range of ~90 km. It was also detected in 2010 in southwestern Washington (Vancouver, just north of Portland and the Columbia River.The ecological amplitude of N. brevicollis in Oregon rivals that of the most eurytopic native carabid species, e.g., Pterostichus algidus LeConte and Scaphinotus marginatus (Fischer von Waldheim. It has been found in highly degraded heavy industrial sites, agricultural fields, city parks, gardens, second growth woodlands, mature conifer forests, montane rock gardens, and otherwise pristine stands of old growth noble fir, with elevations ranging from essentially sea level to 1,249 meters. Climates at these locales vary from that of the Mediterranean Willamette Valley floor, where snow rarely occurs and summers are hot and dry, to the summit of the Oregon Coast Range, where deep snow may be present from November through April and summers are cool. The carabid communities in which N. brevicollis has been found range from those predominantly of fellow exotic species, e.g., at heavily perturbed sites, to those where it is the only exotic species, such as at the Coast Range summit.Nebria brevicollis is clearly an invasive species in that it is not restricted to anthropogenic habitats, is rapidly expanding its North American range, and can be abundant in essentially pristine settings. What is not yet clear is whether it is or will become a damaging species. Although it is already the most abundant carabid species in some settings
Rosa M. Canals; Leticia San-Emeterio; Salud Sanchez-Marquez; Igor Ruiz de los Mozos; Pablo Pujol; Iñigo Zabalgogeazcoa
The sedge Carex brevicollis is a common component of semi-natural grasslands and forests in temperate mountains of Central and Southern Europe. The consumption of this species causes a severe toxicity to livestock, associated to high plant concentrations of the β-carbolic alkaloid brevicolline. This research was started to ascertain the origin of this toxicity. An exploratory survey of alkaloid content in plants growing in contrasting habitats (grasslands/forests) did not contribute to find a...
Woznica, Arielle; Cantley, Alexandra M; Beemelmanns, Christine; Freinkman, Elizaveta; Clardy, Jon; King, Nicole
In choanoflagellates, the closest living relatives of animals, multicellular rosette development is regulated by environmental bacteria. The simplicity of this evolutionarily relevant interaction provides an opportunity to identify the molecules and regulatory logic underpinning bacterial regulation of development. We find that the rosette-inducing bacterium Algoriphagus machipongonensis produces three structurally divergent classes of bioactive lipids that, together, activate, enhance, and inhibit rosette development in the choanoflagellate Salpingoeca rosetta. One class of molecules, the lysophosphatidylethanolamines (LPEs), elicits no response on its own but synergizes with activating sulfonolipid rosette-inducing factors (RIFs) to recapitulate the full bioactivity of live Algoriphagus. LPEs, although ubiquitous in bacteria and eukaryotes, have not previously been implicated in the regulation of a host-microbe interaction. This study reveals that multiple bacterially produced lipids converge to activate, enhance, and inhibit multicellular development in a choanoflagellate. PMID:27354530
Spanggaard, Bettina; Skouboe, P.; Rossen, L.;
in the neighbor-joining tree, while in the parsimony tree the I. hoferi/rosette clade is equally distant to both the choanoflagellate and animal clades. Transmission electron microscopy showed that I. hoferi has a defined cell wall, an endoplasm that consists of a fine granulated matrix with numerous ribosomes...
Rosa M. Canals
Full Text Available The sedge Carex brevicollis is a common component of semi-natural grasslands and forests in temperate mountains of Central and Southern Europe. The consumption of this species causes a severe toxicity to livestock, associated to high plant concentrations of the β-carbolic alkaloid brevicolline. This research was started to ascertain the origin of this toxicity. An exploratory survey of alkaloid content in plants growing in contrasting habitats (grasslands/forests did not contribute to find a pattern of the variable contents of brevicolline in plants, and led us to address other possibilities, such as a potential role of fungal endophytism. Systemic, vertically-transmitted endophytes producers of herbivore-deterrent alkaloids are known to infect many known forage grasses. We did not detect systemic endophytes in C. brevicollis, but the sedge harboured a rich community of non-systemic fungi. To test experimentally whether non-systemic endophytes influenced the synthesis of the alkaloid, 24 plants were submitted to a fungicide treatment to remove the fungal assemblage, and the offspring ramets were analysed for alkaloid content. Brevicolline was the major β-carbolic alkaloid detected, and the contents were at least five times lower in the new ramets that developed from fungicide-treated plants than in the untreated plants. This result, although not conclusive about the primary source of the alkaloid (a plant or a fungal product indicates that fungal endophytes may affect the contents of the toxic brevicolline in this sedge.
Cantley, Alexandra M; Woznica, Arielle; Beemelmanns, Christine; King, Nicole; Clardy, Jon
The choanoflagellate Salpingoeca rosetta is a microbial marine eukaryote that can switch between unicellular and multicellular states. As one of the closest living relatives of animals, this organism has become a model for understanding how multicellularity evolved in the animal lineage. Previously our laboratories isolated and synthesized a bacterially produced sulfonolipid that induces S. rosetta to form multicellular "rosettes." In this study, we report the identification of a bacterially produced inhibitor of rosettes (IOR-1) as well as the total synthesis of this molecule and all of its stereoisomers. Our results confirm the previously noted specificity and potency of rosette-modulating molecules, expand our understanding of the complex chemical ecology between choanoflagellates and rosette-inducing bacteria, and provide a synthetic probe template for conducting further mechanistic studies on the emergence of multicellularity. PMID:26998963
Full Text Available Abstract Background Cell-to-cell communication is a key process in multicellular organisms. In multicellular animals, scaffolding proteins belonging to the family of membrane-associated guanylate kinases (MAGUK are involved in the regulation and formation of cell junctions. These MAGUK proteins were believed to be exclusive to Metazoa. However, a MAGUK gene was recently identified in an EST survey of Capsaspora owczarzaki, an unicellular organism that branches off near the metazoan clade. To further investigate the evolutionary history of MAGUK, we have undertook a broader search for this gene family using available genomic sequences of different opisthokont taxa. Results Our survey and phylogenetic analyses show that MAGUK proteins are present not only in Metazoa, but also in the choanoflagellate Monosiga brevicollis and in the protist Capsaspora owczarzaki. However, MAGUKs are absent from fungi, amoebozoans or any other eukaryote. The repertoire of MAGUKs in Placozoa and eumetazoan taxa (Cnidaria + Bilateria is quite similar, except for one class that is missing in Trichoplax, while Porifera have a simpler MAGUK repertoire. However, Vertebrata have undergone several independent duplications and exhibit two exclusive MAGUK classes. Three different MAGUK types are found in both M. brevicollis and C. owczarzaki: DLG, MPP and MAGI. Furthermore, M. brevicollis has suffered a lineage-specific diversification. Conclusions The diversification of the MAGUK protein gene family occurred, most probably, prior to the divergence between Metazoa+choanoflagellates and the Capsaspora+Ministeria clade. A MAGI-like, a DLG-like, and a MPP-like ancestral genes were already present in the unicellular ancestor of Metazoa, and new gene members have been incorporated through metazoan evolution within two major periods, one before the sponge-eumetazoan split and another within the vertebrate lineage. Moreover, choanoflagellates have suffered an independent MAGUK
Chappell, Helen; Ratcliffe, Sarah; Goldstein, Raymond E.
Silica biomineralization is a widespread phenomenon of major biotechnological interest. Modifying biosilica with substances like germanium (Ge) can confer useful new properties, although exposure to high levels of Ge disrupts normal biosilicification. No clear mechanism explains why this disruption occurs. Here, we study the effect of Ge on loricate choanoflagellates, a group of protists that construct a species-specific extracellular lorica from multiple siliceous costal strips. High Ge exposures were toxic, whereas lower Ge exposures produced cells with incomplete or absent loricae. These effects can be ameliorated by restoring the germanium : silicon ratio, as observed in other biosilicifying organisms. We developed simulations of how Ge interacts with polymerizing silica. In our models, Ge is readily incorporated at the ends of silica forming from silicic acid condensation, but this prevents further silica polymerization. Our ‘Ge-capping’ model is supported by observations from loricate choanoflagellates. Ge exposure terminates costal strip synthesis and lorica formation, resulting in disruption to cytokinesis and fatal build-up of silicic acid. Applying the Ge-capping model to other siliceous organisms explains the general toxicity of Ge and identifies potential protective responses in metalloid uptake and sensing. This can improve the design of new silica biomaterials, and further our understanding of silicon metabolism. PMID:27655668
Kirkegaard, Julius B
Efficient uptake of nutrients from the environment is an important component in the fitness of all microorganisms, and its dependence on size may reveal clues to the origins of evolutionary transitions to multicellularity. Because potential benefits in uptake rates must be viewed in the context of other costs and benefits of size, such as varying predation rates and the increased metabolic costs associated with larger and more complex body plans, the uptake rate itself is not necessarily that which is optimized by evolution. Uptake rates can be strongly dependent on local organism geometry and its swimming speed, providing selective pressure for particular arrangements. Here we examine these issues for choanoflagellates, filter-feeding microorganisms that are the closest relatives of the animals. We explore the different morphological variations of the choanoflagellete $Salpingoeca~rosetta$, which can exist as a swimming cell, a sessile thecate cell, and as colonies of cells in various shapes. In the absence ...
Schultheiss Kira P
Full Text Available Abstract Background Receptor tyrosine kinases (RTKs are crucial components of signal transduction systems in multicellular animals. Surprisingly, numerous RTKs have been identified in the genomes of unicellular choanoflagellates and other protists. Here, we report the first biochemical study of a unicellular RTK, namely RTKB2 from Monosiga brevicollis. Results We cloned, expressed, and purified the RTKB2 kinase, and showed that it is enzymatically active. The activity of RTKB2 is controlled by autophosphorylation, as in metazoan RTKs. RTKB2 possesses six copies of a unique domain (designated RM2 in its C-terminal tail. An isolated RM2 domain (or a synthetic peptide derived from the RM2 sequence served as a substrate for RTKB2 kinase. When phosphorylated, the RM2 domain bound to the Src homology 2 domain of MbSrc1 from M. brevicollis. NMR structural studies of the RM2 domain indicated that it is disordered in solution. Conclusions Our results are consistent with a model in which RTKB2 activation stimulates receptor autophosphorylation within the RM2 domains. This leads to recruitment of Src-like kinases (and potentially other M. brevicollis proteins and further phosphorylation, which may serve to increase or dampen downstream signals. Thus, crucial features of signal transduction circuitry were established prior to the evolution of metazoans from their unicellular ancestors.
Erwin, Douglas H.
Whole-genome sequences from the choanoflagellate Monosiga brevicollis, the placozoan Trichoplax adhaerens and the cnidarian Nematostella vectensis have confirmed results from comparative evolutionary developmental studies that much of the developmental toolkit once thought to be characteristic of bilaterians appeared much earlier in the evolution of animals. The diversity of transcription factors and signalling pathway genes in animals with a limited number of cell types and a restricted developmental repertoire is puzzling, particularly in light of claims that such highly conserved elements among bilaterians provide evidence of a morphologically complex protostome–deuterostome ancestor. Here, I explore the early origination of elements of what became the bilaterian toolkit, and suggest that placozoans and cnidarians represent a depauperate residue of a once more diverse assemblage of early animals, some of which may be represented in the Ediacaran fauna (c. 585–542 Myr ago). PMID:19571245
Orme, B. A. A.; Otto, S. R.; Blake, J. R.
The motion of particles and feeding currents created by micro-organisms due to a flagellum beating are considered. The calculations are pertinent to a range of sessile organisms, but we concentrate on a particular organism, namely Salpingoeca Amphoridium (SA) (a choanoflagellate); due to the availability of experimental data, Pettitt (2000). These flow fields are characterised as having very small Reynolds numbers, which implies that viscous forces dominate over inertial ones consistent with the Stokes flow limit. The flow generated by the flagella is modelled via consideration of a point force known as a stokeslet. The interaction between the boundary to which the organism is attached and its flagellum leads to toroidal eddies, which serve to transport particles towards the micro-organism; promoting filtering of nutrients by the microvilli which constitute the cell's collar (the filtering mechanism in SA). It is our conjecture that the interaction of multiple toroidal eddies will lead to chaotic advection and hence enhance the domain of feeding for these organisms. The degree of mixing in the region around SA is investigated using chaotic and statistical measures to study the influence the flagellum has on the surrounding fluid. Three-dimensional particle paths around such an organism are considered with the aim of showing the plane within which the stokeslets are situated is an attractor.
Full Text Available Abstract Background The patterns of emergence and diversification of the families of ubiquitin ligases provide insights about the evolution of the eukaryotic ubiquitination system. U-box ubiquitin ligases (UULs are proteins characterized by containing a peculiar protein domain known as U box. In this study, the origin of the animal UUL genes is described. Results Phylogenetic and structural data indicate that six of the seven main UUL-encoding genes found in humans (UBE4A, UBE4B, UIP5, PRP19, CHIP and CYC4 were already present in the ancestor of all current metazoans and the seventh (WDSUB1 is found in placozoans, cnidarians and bilaterians. The fact that only 4 - 5 genes orthologous to the human ones are present in the choanoflagellate Monosiga brevicollis suggests that several animal-specific cooptions of the U box to generate new genes occurred. Significantly, Monosiga contains five additional UUL genes that are not present in animals. One of them is also present in distantly-related protozoans. Along animal evolution, losses of UUL-encoding genes are rare, except in nematodes, which lack three of them. These general patterns are highly congruent with those found for other two families (RBR, HECT of ubiquitin ligases. Conclusions Finding that the patterns of emergence, diversification and loss of three unrelated families of ubiquitin ligases (RBR, HECT and U-box are parallel indicates that there are underlying, linage-specific evolutionary forces shaping the complexity of the animal ubiquitin system.
Alan O Marron
Full Text Available BACKGROUND: Nitrile hydratases are enzymes involved in the conversion of nitrile-containing compounds into ammonia and organic acids. Although they are widespread in prokaryotes, nitrile hydratases have only been reported in two eukaryotes: the choanoflagellate Monosiga brevicollis and the stramenopile Aureococcus anophagefferens. The nitrile hydratase gene in M. brevicollis was believed to have arisen by lateral gene transfer from a prokaryote, and is a fusion of beta and alpha nitrile hydratase subunits. Only the alpha subunit has been reported in A. anophagefferens. METHODOLOGY/PRINCIPAL FINDINGS: Here we report the detection of nitrile hydratase genes in five eukaryotic supergroups: opisthokonts, amoebozoa, archaeplastids, CCTH and SAR. Beta-alpha subunit fusion genes are found in the choanoflagellates, ichthyosporeans, apusozoans, haptophytes, rhizarians and stramenopiles, and potentially also in the amoebozoans. An individual alpha subunit is found in a dinoflagellate and an individual beta subunit is found in a haptophyte. Phylogenetic analyses recover a clade of eukaryotic-type nitrile hydratases in the Opisthokonta, Amoebozoa, SAR and CCTH; this is supported by analyses of introns and gene architecture. Two nitrile hydratase sequences from an animal and a plant resolve in the prokaryotic nitrile hydratase clade. CONCLUSIONS/SIGNIFICANCE: The evidence presented here demonstrates that nitrile hydratase genes are present in multiple eukaryotic supergroups, suggesting that a subunit fusion gene was present in the last common ancestor of all eukaryotes. The absence of nitrile hydratase from several sequenced species indicates that subunits were lost in multiple eukaryotic taxa. The presence of nitrile hydratases in many other eukaryotic groups is unresolved due to insufficient data and taxon sampling. The retention and expression of the gene in distantly related eukaryotic species suggests that it plays an important metabolic role. The novel
Full Text Available Abstract Background Two categories of introns are known, a common U2 type and a rare U12 type. These two types of introns are removed by distinct spliceosomes. The phylogenetic distribution of spliceosomal RNAs that are characteristic of the U12 spliceosome, i.e. the U11, U12, U4atac and U6atac RNAs, suggest that U12 spliceosomes were lost in many phylogenetic groups. We have now examined the distribution of U2 and U12 introns in many of these groups. Results U2 and U12 introns were predicted by making use of available EST and genomic sequences. The results show that in species or branches where U12 spliceosomal components are missing, also U12 type of introns are lacking. Examples are the choanoflagellate Monosiga brevicollis, Entamoeba histolytica, green algae, diatoms, and the fungal lineage Basidiomycota. Furthermore, whereas U12 splicing does not occur in Caenorhabditis elegans, U12 introns as well as U12 snRNAs are present in Trichinella spiralis, which is deeply branching in the nematode tree. A comparison of homologous genes in T. spiralis and C. elegans revealed different mechanisms whereby U12 introns were lost. Conclusions The phylogenetic distribution of U12 introns and spliceosomal RNAs give further support to an early origin of U12 dependent splicing. In addition, this distribution identifies a large number of instances during eukaryotic evolution where such splicing was lost.
Full Text Available Mammalian Myc proteins are important determinants of cell proliferation as well as the undifferentiated state of stem cells and their activity is frequently deregulated in cancer. Based mainly on conservation in the C-terminal DNA-binding and dimerization domain, Myc-like proteins have been reported in many simpler organisms within and outside the Metazoa but they have not been found in fungi or plants. Several important signature motifs defining mammalian Myc proteins are found in the N-terminal domain but the extent to which these are found in the Myc-like proteins from simpler organisms is not well established. The extent of N-terminal signature sequence conservation would give important insights about the evolution of Myc proteins and their current function in mammalian physiology and disease. In a systematic study of Myc-like proteins we show that N-terminal signature motifs are not readily detectable in individual Myc-like proteins from invertebrates but that weak similarities to Myc boxes 1 and 2 can be found in the N-termini of the simplest Metazoa as well as the unicellular choanoflagellate, Monosiga brevicollis, using multiple protein alignments. Phylogenetic support for the connections of these proteins to established Myc proteins is however poor. We show that the pattern of predicted protein disorder along the length of Myc proteins can be used as a complementary approach to making dendrograms of Myc proteins that aids the classification of Myc proteins. This suggests that the pattern of disorder within Myc proteins is more conserved through evolution than their amino acid sequence. In the disorder-based dendrograms the Myc-like proteins from simpler organisms, including M. brevicollis, are connected to established Myc proteins with a higher degree of certainty. Our results suggest that protein disorder based dendrograms may be of general significance for studying distant relationships between proteins, such as transcription factors
Päri, Mailis; Kuusksalu, Anne; Lopp, Annika; Kjaer, Karina Hansen; Justesen, Just; Kelve, Merike
2',5'-Oligoadenylate synthetases (OASs) belong to the nucleotidyl transferase family together with poly(A) polymerases, CCA-adding enzymes and the recently discovered cyclic-GMP-AMP synthase (cGAS). Mammalian OASs have been thoroughly characterized as components of the interferon-induced antiviral system. The OAS activity and the respective genes were also discovered in marine sponges where the interferon system is absent. In this study the recombinant OASs from several multicellular animals and their closest unicellular relative, a choanoflagellate, were expressed in a bacterial expression system and their enzymatic activities were examined. We demonstrated 2-5A synthesizing activities of OASs from the marine sponge Tedania ignis, a representative of the phylogenetically oldest metazoan phylum (Porifera), from an invertebrate of the protostome lineage, the mollusk Mytilus californianus (Mollusca), and from a vertebrate species, a cartilaginous fish Leucoraja erinacea (Chordata). However, the expressed proteins from an amphibian, the salamander Ambystoma mexicanum (Chordata), and from a protozoan, the marine choanoflagellate Monosiga brevicollis (Choanozoa), did not show 2-5A synthesizing activity. Differently from other studied OASs, OAS from the marine sponge T. ignis was able to catalyze the formation of oligomers having both 2',5'- and 3',5'-phosphodiester linkages. Our data suggest that OASs from sponges and evolutionarily higher animals have similar activation mechanisms which still include different affinities and possibly different structural requirements for the activating RNAs. Considering their 2'- and 3'-specificities, sponge OASs could represent a link between evolutionarily earlier nucleotidyl transferases and 2'-specific OASs from higher animals. PMID:24184688
Full Text Available Abstract Background The transcription factors of the LSF/Grainyhead (GRH family are characterized by the possession of a distinctive DNA-binding domain that bears no clear relationship to other known DNA-binding domains, with the possible exception of the p53 core domain. In triploblastic animals, the LSF and GRH subfamilies have diverged extensively with respect to their biological roles, general expression patterns, and mechanism of DNA binding. For example, Grainyhead (GRH homologs are expressed primarily in the epidermis, and they appear to play an ancient role in maintaining the epidermal barrier. By contrast, LSF homologs are more widely expressed, and they regulate general cellular functions such as cell cycle progression and survival in addition to cell-lineage specific gene expression. Results To illuminate the early evolution of this family and reconstruct the functional divergence of LSF and GRH, we compared homologs from 18 phylogenetically diverse taxa, including four basal animals (Nematostella vectensis, Vallicula multiformis, Trichoplax adhaerens, and Amphimedon queenslandica, a choanoflagellate (Monosiga brevicollis and several fungi. Phylogenetic and bioinformatic analyses of these sequences indicate that (1 the LSF/GRH gene family originated prior to the animal-fungal divergence, and (2 the functional diversification of the LSF and GRH subfamilies occurred prior to the divergence between sponges and eumetazoans. Aspects of the domain architecture of LSF/GRH proteins are well conserved between fungi, choanoflagellates, and metazoans, though within the Metazoa, the LSF and GRH families are clearly distinct. We failed to identify a convincing LSF/GRH homolog in the sequenced genomes of the algae Volvox carteri and Chlamydomonas reinhardtii or the amoebozoan Dictyostelium purpureum. Interestingly, the ancestral GRH locus has become split into two separate loci in the sea anemone Nematostella, with one locus encoding a DNA binding
Full Text Available Rab proteins are small GTPases that act as essential regulators of vesicular trafficking. 44 subfamilies are known in humans, performing specific sets of functions at distinct subcellular localisations and tissues. Rab function is conserved even amongst distant orthologs. Hence, the annotation of Rabs yields functional predictions about the cell biology of trafficking. So far, annotating Rabs has been a laborious manual task not feasible for current and future genomic output of deep sequencing technologies. We developed, validated and benchmarked the Rabifier, an automated bioinformatic pipeline for the identification and classification of Rabs, which achieves up to 90% classification accuracy. We cataloged roughly 8.000 Rabs from 247 genomes covering the entire eukaryotic tree. The full Rab database and a web tool implementing the pipeline are publicly available at www.RabDB.org. For the first time, we describe and analyse the evolution of Rabs in a dataset covering the whole eukaryotic phylogeny. We found a highly dynamic family undergoing frequent taxon-specific expansions and losses. We dated the origin of human subfamilies using phylogenetic profiling, which enlarged the Rab repertoire of the Last Eukaryotic Common Ancestor with Rab14, 32 and RabL4. Furthermore, a detailed analysis of the Choanoflagellate Monosiga brevicollis Rab family pinpointed the changes that accompanied the emergence of Metazoan multicellularity, mainly an important expansion and specialisation of the secretory pathway. Lastly, we experimentally establish tissue specificity in expression of mouse Rabs and show that neo-functionalisation best explains the emergence of new human Rab subfamilies. With the Rabifier and RabDB, we provide tools that easily allows non-bioinformaticians to integrate thousands of Rabs in their analyses. RabDB is designed to enable the cell biology community to keep pace with the increasing number of fully-sequenced genomes and change the scale
Lambeth J David
Full Text Available Abstract Background The reactive oxygen-generating NADPH oxidases (Noxes function in a variety of biological roles, and can be broadly classified into those that are regulated by subunit interactions and those that are regulated by calcium. The prototypical subunit-regulated Nox, Nox2, is the membrane-associated catalytic subunit of the phagocyte NADPH-oxidase. Nox2 forms a heterodimer with the integral membrane protein, p22phox, and this heterodimer binds to the regulatory subunits p47phox, p67phox, p40phox and the small GTPase Rac, triggering superoxide generation. Nox-organizer protein 1 (NOXO1 and Nox-activator 1 (NOXA1, respective homologs of p47phox and p67phox, together with p22phox and Rac, activate Nox1, a non-phagocytic homolog of Nox2. NOXO1 and p22phox also regulate Nox3, whereas Nox4 requires only p22phox. In this study, we have assembled and analyzed amino acid sequences of Nox regulatory subunit orthologs from vertebrates, a urochordate, an echinoderm, a mollusc, a cnidarian, a choanoflagellate, fungi and a slime mold amoeba to investigate the evolutionary history of these subunits. Results Ancestral p47phox, p67phox, and p22phox genes are broadly seen in the metazoa, except for the ecdysozoans. The choanoflagellate Monosiga brevicollis, the unicellular organism that is the closest relatives of multicellular animals, encodes early prototypes of p22phox, p47phox as well as the earliest known Nox2-like ancestor of the Nox1-3 subfamily. p67phox- and p47phox-like genes are seen in the sea urchin Strongylocentrotus purpuratus and the limpet Lottia gigantea that also possess Nox2-like co-orthologs of vertebrate Nox1-3. Duplication of primordial p47phox and p67phox genes occurred in vertebrates, with the duplicated branches evolving into NOXO1 and NOXA1. Analysis of characteristic domains of regulatory subunits suggests a novel view of the evolution of Nox: in fish, p40phox participated in regulating both Nox1 and Nox2, but after the
Full Text Available OS=Homo ... 33 0.91 sp|P03315|POLS_SFV Structural polyprotein OS=Semliki forest viru... 32 1.5 sp|P25386|USO...ATK 206 Query: 8 PL 3 L Sbjct: 207 KL 208 >sp|P03315|POLS_SFV Structural polyprotein OS=Semliki forest...r|Q8JMP5|Q8JMP5_SFV Structural polyprotein OS=Semliki forest vi... 34 4.4 tr|A9BD99|A9BD99_PROM4 Trigger fac... Predicted protein OS=Monosiga brevicollis... 34 4.4 tr|Q87049|Q87049_SFV Virion protein OS=Semliki forest... virus GN=C... 34 5.8 tr|Q809B6|Q809B6_SFV Structural polyprotein OS=Semliki forest
Full Text Available n 2 OS=Homo ... 33 0.91 sp|P03315|POLS_SFV Structural polyprotein OS=Semliki forest viru... 32 1.5 sp|P25386...ESSAATK 206 Query: 8 PL 3 L Sbjct: 207 KL 208 >sp|P03315|POLS_SFV Structural polyprotein OS=Semliki forest....6 tr|Q8JMP5|Q8JMP5_SFV Structural polyprotein OS=Semliki forest vi... 34 4.4 tr|A9BD99|A9BD99_PROM4 Trigger...ion protein OS=Semliki forest virus GN=C... 34 5.8 tr|Q809B6|Q809B6_SFV Structural polyprotein OS=Semliki forest...ONBE Predicted protein OS=Monosiga brevicollis... 34 4.4 tr|Q87049|Q87049_SFV Vir
Full Text Available Abstract Background Intraflagellar transport (IFT genes, which are critical for the development and function of cilia and flagella in metazoans, are tightly regulated by the Regulatory Factor X (RFX transcription factors (TFs. However, how and when their evolutionary relationship was established remains unknown. Results We have identified evidence suggesting that RFX TFs and IFT genes evolved independently and their evolution converged before the first appearance of metazoans. Both ciliary genes and RFX TFs exist in all metazoans as well as some unicellular eukaryotes. However, while RFX TFs and IFT genes are found simultaneously in all sequenced metazoan genomes, RFX TFs do not co-exist with IFT genes in most pre-metazoans and thus do not regulate them in these organisms. For example, neither the budding yeast nor the fission yeast possesses cilia although both have well-defined RFX TFs. Conversely, most unicellular eukaryotes, including the green alga Chlamydomonas reinhardtii, have typical cilia and well conserved IFT genes but lack RFX TFs. Outside of metazoans, RFX TFs and IFT genes co-exist only in choanoflagellates including M. brevicollis, and only one fungus Allomyces macrogynus of the 51 sequenced fungus genomes. M. brevicollis has two putative RFX genes and a full complement of ciliary genes. Conclusions The evolution of RFX TFs and IFT genes were independent in pre-metazoans. We propose that their convergence in evolution, or the acquired transcriptional regulation of IFT genes by RFX TFs, played a pivotal role in the establishment of metazoan.
Watari, A; Iwabe, N; Masuda, H; Okada, M
Proto-oncogenes encode signaling molecular switches regulating cellular homeostasis in metazoans, and can be converted to oncogenes by gain-of-function mutations. To address the molecular basis for development of the regulatory system of proto-oncogenes during evolution, we screened for ancestral proto-oncogenes from the unicellular choanoflagellate Monosiga ovata by monitoring their transforming activities, and isolated a Pak gene ortholog encoding a serine/threonine kinase as a 'primitive oncogene'. We also cloned Pak orthologs from fungi and the multicellular sponge Ephydatia fluviatilis, and compared their regulatory features with that of M. ovata Pak (MoPak). MoPak is constitutively active and induces cell transformation in mammalian fibroblasts, although the Pak orthologs from multicellular animals are strictly regulated. Analyses of Pak mutants revealed that structural alteration of the auto-inhibitory domain (AID) of MoPak confers higher constitutive kinase activity, as well as greater binding ability to Rho family GTPases than the multicellular Paks, and this structural alteration is responsible for cell transformation and disruption of multicellular tissue organization. These results show that maturation of AID function was required for the development of the strict regulatory system of the Pak proto-oncogene, and suggest a potential link between the establishment of the regulatory system of proto-oncogenes and metazoan evolution.
Holden, Todd; Dehipawala, S.; Cheung, E.; Bienaime, R.; Ye, J.; Tremberger, G., Jr.; Schneider, P.; Lieberman, D.; Cheung, T.
The Rubisco protein-enzyme is arguably the most abundance protein on Earth. The biology dogma of transcription and translation necessitates the study of the Rubisco genes and Rubisco-like genes in various species. Stronger correlation of fractal dimension of the atomic number fluctuation along a DNA sequence with Shannon entropy has been observed in the studied Rubisco-like gene sequences, suggesting a more diverse evolutionary pressure and constraints in the Rubisco sequences. The strategy of using metal for structural stabilization appears to be an ancient mechanism, with data from the porphobilinogen deaminase gene in Capsaspora owczarzaki and Monosiga brevicollis. Using the chi-square distance probability, our analysis supports the conjecture that the more ancient Rubisco-like sequence in Microcystis aeruginosa would have experienced very different evolutionary pressure and bio-chemical constraint as compared to Bordetella bronchiseptica, the two microbes occupying either end of the correlation graph. Our exploratory study would indicate that high fractal dimension Rubisco sequence would support high carbon dioxide rate via the Michaelis- Menten coefficient; with implication for the control of the whooping cough pathogen Bordetella bronchiseptica, a microbe containing a high fractal dimension Rubisco-like sequence (2.07). Using the internal comparison of chi-square distance probability for 16S rRNA (~ E-22) versus radiation repair Rec-A gene (~ E-05) in high GC content Deinococcus radiodurans, our analysis supports the conjecture that high GC content microbes containing Rubisco-like sequence are likely to include an extra-terrestrial origin, relative to Deinococcus radiodurans. Similar photosynthesis process that could utilize host star radiation would not compete with radiation resistant process from the biology dogma perspective in environments such as Mars and exoplanets.
França, Gustavo S; Cancherini, Douglas V; de Souza, Sandro J
Exon shuffling has been characterized as one of the major evolutionary forces shaping both the genome and the proteome of eukaryotes. This mechanism was particularly important in the creation of multidomain proteins during animal evolution, bringing a number of functional genetic novelties. Here, genome information from a variety of eukaryotic species was used to address several issues related to the evolutionary history of exon shuffling. By comparing all protein sequences within each species, we were able to characterize exon shuffling signatures throughout metazoans. Intron phase (the position of the intron regarding the codon) and exon symmetry (the pattern of flanking introns for a given exon or block of adjacent exons) were features used to evaluate exon shuffling. We confirmed previous observations that exon shuffling mediated by phase 1 introns (1-1 exon shuffling) is the predominant kind in multicellular animals. Evidence is provided that such pattern was achieved since the early steps of animal evolution, supported by a detectable presence of 1-1 shuffling units in Trichoplax adhaerens and a considerable prevalence of them in Nematostella vectensis. In contrast, Monosiga brevicollis, one of the closest relatives of metazoans, and Arabidopsis thaliana, showed no evidence of 1-1 exon or domain shuffling above what it would be expected by chance. Instead, exon shuffling events are less abundant and predominantly mediated by phase 0 introns (0-0 exon shuffling) in those non-metazoan species. Moreover, an intermediate pattern of 1-1 and 0-0 exon shuffling was observed for the placozoan T. adhaerens, a primitive animal. Finally, characterization of flanking intron phases around domain borders allowed us to identify a common set of symmetric 1-1 domains that have been shuffled throughout the metazoan lineage.
Full Text Available Abstract Background The nutrient-sensing Tor pathway governs cell growth and is conserved in nearly all eukaryotic organisms from unicellular yeasts to multicellular organisms, including humans. Tor is the target of the immunosuppressive drug rapamycin, which in complex with the prolyl isomerase FKBP12 inhibits Tor functions. Rapamycin is a gold standard drug for organ transplant recipients that was approved by the FDA in 1999 and is finding additional clinical indications as a chemotherapeutic and antiproliferative agent. Capitalizing on the plethora of recently sequenced genomes we have conducted comparative genomic studies to annotate the Tor pathway throughout the fungal kingdom and related unicellular opisthokonts, including Monosiga brevicollis, Salpingoeca rosetta, and Capsaspora owczarzaki. Results Interestingly, the Tor signaling cascade is absent in three microsporidian species with available genome sequences, the only known instance of a eukaryotic group lacking this conserved pathway. The microsporidia are obligate intracellular pathogens with highly reduced genomes, and we hypothesize that they lost the Tor pathway as they adapted and streamlined their genomes for intracellular growth in a nutrient-rich environment. Two TOR paralogs are present in several fungal species as a result of either a whole genome duplication or independent gene/segmental duplication events. One such event was identified in the amphibian pathogen Batrachochytrium dendrobatidis, a chytrid responsible for worldwide global amphibian declines and extinctions. Conclusions The repeated independent duplications of the TOR gene in the fungal kingdom might reflect selective pressure acting upon this kinase that populates two proteinaceous complexes with different cellular roles. These comparative genomic analyses illustrate the evolutionary trajectory of a central nutrient-sensing cascade that enables diverse eukaryotic organisms to respond to their natural
Full Text Available Sialidases are glycohydrolytic enzymes present from virus to mammals that remove sialic acid from oligosaccharide chains. Four different sialidase forms are known in vertebrates: the lysosomal NEU1, the cytosolic NEU2 and the membrane-associated NEU3 and NEU4. These enzymes modulate the cell sialic acid content and are involved in several cellular processes and pathological conditions. Molecular defects in NEU1 are responsible for sialidosis, an inherited disease characterized by lysosomal storage disorder and neurodegeneration. The studies on the biology of sialic acids and sialyltransferases, the anabolic counterparts of sialidases, have revealed a complex picture with more than 50 sialic acid variants selectively present in the different branches of the tree of life. The gain/loss of specific sialoconjugates have been proposed as key events in the evolution of deuterostomes and Homo sapiens, as well as in the host-pathogen interactions. To date, less attention has been paid to the evolution of sialidases. Thus we have conducted a survey on the state of the sialidase family in metazoan. Using an in silico approach, we identified and characterized sialidase orthologs from 21 different organisms distributed among the evolutionary tree: Metazoa relative (Monosiga brevicollis, early Deuterostomia, precursor of Chordata and Vertebrata (teleost fishes, amphibians, reptiles, avians and early and recent mammals. We were able to reconstruct the evolution of the sialidase protein family from the ancestral sialidase NEU1 and identify a new form of the enzyme, NEU5, representing an intermediate step in the evolution leading to the modern NEU3, NEU4 and NEU2. Our study provides new insights on the mechanisms that shaped the substrate specificity and other peculiar properties of the modern mammalian sialidases. Moreover, we further confirm findings on the catalytic residues and identified enzyme loop portions that behave as rapidly diverging regions and may
Full Text Available The beta amyloid (APP cleaving enzyme (BACE1 has been a drug target for Alzheimer's Disease (AD since 1999 with lead inhibitors now entering clinical trials. In 2011, the paralogue, BACE2, became a new target for type II diabetes (T2DM having been identified as a TMEM27 secretase regulating pancreatic β cell function. However, the normal roles of both enzymes are unclear. This study outlines their evolutionary history and new opportunities for functional genomics. We identified 30 homologues (UrBACEs in basal phyla including Placozoans, Cnidarians, Choanoflagellates, Porifera, Echinoderms, Annelids, Mollusks and Ascidians (but not Ecdysozoans. UrBACEs are predominantly single copy, show 35% to 45% protein sequence identity with mammalian BACE1, are approximately 100 residues longer than cathepsin paralogues with an aspartyl protease domain flanked by a signal peptide and a C-terminal transmembrane domain. While multiple paralogues in Trichoplax and Monosiga pre-date the nervous system, duplication of the UrBACE in fish gave rise to BACE1 and BACE2 in the vertebrate lineage. The latter evolved more rapidly as the former maintained the emergent neuronal role. In mammals, Ka/Ks for BACE2 is higher than BACE1 but low ratios for both suggest purifying selection. The 5’ exons show higher Ka/Ks than the catalytic section. Model organism genomes show the absence of certain BACE human substrates when the UrBACE is present. Experiments could thus reveal undiscovered substrates and roles. The human protease double-target status means that evolutionary trajectories and functional shifts associated with different substrates will have implications for the development of clinical candidates for both AD and T2DM. A rational basis for inhibition specificity ratios and assessing target-related side effects will be facilitated by a more complete picture of BACE1 and BACE2 functions informed by their evolutionary context.
The products of proto-oncogene play critical roles in the development or maintenance of multicellular societies in animals via strict regulatory systems. When these regulatory systems are disrupted, proto-oncogenes can become oncogenes, and thereby induce cell transformation and carcinogenesis. To understand the molecular basis for development of the regulatory system of proto-oncogenes during evolution, we screened for ancestral proto-oncogenes from the unicellular choanoflagellate Monosiga ovata (M. ovata) by monitoring their transforming ability in mammalian cells; consequently, we isolated a Pak gene ortholog, which encodes a serine/threonine kinase as a 'primitive oncogene'. We also cloned Pak orthologs from fungi and the multicellular sponge Ephydatia fluviatilis, and compared their regulatory features with that of M. ovata Pak (MoPak). MoPak is constitutively active and induces cell transformation in mammalian cells. In contrast, Pak orthologs from multicellular animals are strictly regulated. Analyses of Pak mutants revealed that structural alterations in the auto-inhibitory domain (AID) are responsible for the enhanced kinase activity and the oncogenic activity of MoPak. Furthermore, we show that Rho family GTPases-mediated regulatory system of Pak kinase is conserved throughout the evolution from unicellular to multicellular animals, but the MoPak is more sensitive to the Rho family GTPases-mediated activation than multicellular Pak. These results show that maturation of AID function was required for the development of the strict regulatory system of the Pak proto-oncogene, and support the potential link between the development of the regulatory system of proto-oncogenes and the evolution of multicellularity. Further analysis of oncogenic functions of proto-oncogene orthologs in the unicellular genes would provide some insights into the mechanisms of the destruction of multicellular society in cancer.
Full Text Available Notes, descriptions, synonymies and reinstatement in Hesperandra Arigony, 1977 (Coleoptera, Cerambycidae, Parandrinae. The genus Hesperandra Arigony, 1977, is divided in three subgenera: Hesperandra s. str., Zikandra subgen. nov. and Tavandra subgen. nov. Keys to the subgenera and species are added. H. glaberrima (Zikán, 1948 is revalidated and redescribed. H. humboldti sp. nov., from Colombia and Ecuador is described. New synonymies established: Hesperandra galapagoensis (Van Dyke, 1953 = H. brevicollis (Lameere, 1902; H. scrobriculata (Zikán, 1948 = Acutandra murrayi (Lameere, 1912. The lectotype of Parandra brevicollis Lameere, 1902 is designated.
Kirkegaard, Julius B; Marron, Alan O; Leptos, Kyriacos C; Goldstein, Raymond E
As the closest unicellular relatives of animals, choanoflagellates serve as useful model organisms for understanding the evolution of animal multicellularity. An important factor in animal evolution was the increasing ocean oxygen levels in the Precambrian, which are thought to have influenced the emergence of complex multicellular life. As a first step in addressing these conditions, we study here the response of the colony-forming choanoflagellate $Salpingoeca~rosetta$ to oxygen gradients. Using a microfluidic device that allows spatio-temporal variations in oxygen concentrations, we report the discovery that $S.~rosetta$ display positive aerotaxis. Analysis of the spatial population distributions provides evidence for logarithmic sensing of oxygen, which enhances sensing in low oxygen neighborhoods. Analysis of search strategy models on the experimental colony trajectories finds that choanoflagellate aerotaxis is consistent with stochastic navigation, the statistics of which are captured using an effective...
Kjær, Karina Hansen; Poulsen, Jesper Buchhave; Reitamm, Tonu;
in bacteria that contains the five OAS-specific motifs. This indicates a specific relationship to OAS. The wide distribution of the OAS genes has made it possible to suggest how the OAS1 gene could have evolved from a common ancestor to choanoflagellates and metazoans. Furthermore, we suggest that the OASL...
Schütze, J; Krasko, A.; Custodio, M R; Efremova, S M; Müller, I M; Müller, W E
Recent molecular data provide strong support for the view that all metazoan phyla, including Porifera, are of monophyletic origin. The relationship of Metazoa, including the Porifera, to Plantae, Fungi and unicellular eukaryotes has only rarely been studied by using cDNAs coding for proteins. Sequence data from rDNA suggested a relationship of Porifera to unicellular eukaryotes (choanoflagellates). However, ultrastructural studies of choanocytes did not support these findings. In the present ...
Zakon, Harold H.
Voltage-gated Na+-permeable (Nav) channels form the basis for electrical excitability in animals. Nav channels evolved from Ca2+ channels and were present in the common ancestor of choanoflagellates and animals, although this channel was likely permeable to both Na+ and Ca2+. Thus, like many other neuronal channels and receptors, Nav channels predated neurons. Invertebrates possess two Nav channels (Nav1 and Nav2), whereas vertebrate Nav channels are of the Nav1 family. Approximately 500 Mya ...
Alan O Marron
Full Text Available BACKGROUND: Cultures of heterotrophic protists often require co-culturing with bacteria to act as a source of nutrition. Such cultures will contain varying levels of intrinsic bacterial contamination that can interfere with molecular research and cause problems with the collection of sufficient material for sequencing. Measuring the levels of bacterial contamination for the purposes of molecular biology research is non-trivial, and can be complicated by the presence of a diverse bacterial flora, or by differences in the relative nucleic acid yield per bacterial or eukaryotic cell. PRINCIPAL FINDINGS: Here we describe a duplex PCR-based assay that can be used to measure the levels of contamination from marine bacteria in a culture of loricate choanoflagellates. By comparison to a standard culture of known target sequence content, the assay can be used to quantify the relative proportions of bacterial and choanoflagellate material in DNA or RNA samples extracted from a culture. We apply the assay to compare methods of purifying choanoflagellate cultures prior to DNA extraction, to determine their effectiveness in reducing bacterial contamination. Together with measurements of the total nucleic acid concentration, the assay can then be used as the basis for determining the absolute amounts of choanoflagellate DNA or RNA present in a sample. CONCLUSIONS: The assay protocol we describe here is a simple and relatively inexpensive method of measuring contamination levels in nucleic acid samples. This provides a new way to establish quantification and purification protocols for molecular biology and genomics in novel heterotrophic protist species. Guidelines are provided to develop a similar protocol for use with any protistan culture. This assay method is recommended where qPCR equipment is unavailable, where qPCR is not viable because of the nature of the bacterial contamination or starting material, or where prior sequence information is insufficient
Nedelcu, A M; Miles, I H; Fagir, A M; Karol, K
In addition to mutation, gene duplication and recombination, the transfer of genetic material between unrelated species is now regarded as a potentially significant player in the shaping of extant genomes and the evolution and diversification of life. Although this is probably true for prokaryotes, the extent of such genetic exchanges in eukaryotes (especially eukaryote-to-eukaryote transfers) is more controversial and the selective advantage and evolutionary impact of such events are less documented. A laterally transferred gene could either be added to the gene complement of the recipient or replace the recipient's homologue; whereas gene replacements can be either adaptive or stochastic, gene additions are most likely adaptive. Here, we report the finding of four stress-related genes (two ascorbate peroxidase and two metacaspase genes) of algal origin in the closest unicellular relatives of animals, the choanoflagellates. At least three of these sequences represent additions to the choanoflagellate gene complement, which is consistent with these transfers being adaptive. We suggest that these laterally acquired sequences could have provided the primitive choanoflagellates with additional or more efficient means to cope with stress, especially in relation to adapting to freshwater environments and/or sessile or colonial lifestyles. PMID:18717747
Full Text Available Abstract Background Eukaryotic genes with cyanobacterial ancestry in plastid-lacking protists have been regarded as important evolutionary markers implicating the presence of plastids in the early evolution of eukaryotes. Although recent genomic surveys demonstrated the presence of cyanobacterial and algal ancestry genes in the genomes of plastid-lacking protists, comparative analyses on the origin and distribution of those genes are still limited. Results We identified 12 gene families with cyanobacterial ancestry in the genomes of a taxonomically wide range of plastid-lacking eukaryotes (Phytophthora [Chromalveolata], Naegleria [Excavata], Dictyostelium [Amoebozoa], Saccharomyces and Monosiga [Opisthokonta] using a novel phylogenetic pipeline. The eukaryotic gene clades with cyanobacterial ancestry were mostly composed of genes from bikonts (Archaeplastida, Chromalveolata, Rhizaria and Excavata. We failed to find genes with cyanobacterial ancestry in Saccharomyces and Dictyostelium, except for a photorespiratory enzyme conserved among fungi. Meanwhile, we found several Monosiga genes with cyanobacterial ancestry, which were unrelated to other Opisthokonta genes. Conclusion Our data demonstrate that a considerable number of genes with cyanobacterial ancestry have contributed to the genome composition of the plastid-lacking protists, especially bikonts. The origins of those genes might be due to lateral gene transfer events, or an ancient primary or secondary endosymbiosis before the diversification of bikonts. Our data also show that all genes identified in this study constitute multi-gene families with punctate distribution among eukaryotes, suggesting that the transferred genes could have survived through rounds of gene family expansion and differential reduction.
Bahillo de la Puebla, P.
Full Text Available Vesperus jertensis sp. nov. from the Jerte river valley (Cáceres prov., Spain is described and compared with the closest allies in the genus. It differs from the closest species, V. serranoi, by the longer antennae and the brighter head, pronotum and elytral surface because of the lesser density of punctures. From the remainder of the species of Vesperus, it differs, among other characters, by the interocular distance being wider than the interantennal one. Moreover, two groups of species are defined based upon characters of head morphology and male genitalia, the V. brevicollis group and the V. conicicollis group.Se describe Vesperus jertensis sp. nov. del valle del Jerte (provincia de Cáceres, España y se compara con las especies afines del género. De V. serranoi, la especie más próxima, se separa por la mayor longitud antenal y la superficie cefálica, pronotal y elitral que es brillante en la nueva especie debido a una menor densidad de su puntuación. Del resto de las especies de Vesperus se separa, entre otros caracteres, porque la distancia interocular es mayor que la distancia entre las inserciones antenales. Además se definen dos grupos de especies, el grupo de V. brevicollis y el grupo de V. conicicollis, atendiendo a caracteres de la morfología cefálica y de la armadura genital masculina.
Seawater samples were collected from the 0 and 50m layers along the transect of 75°E in the Indian sector of the Southern Ocean in the austral summer of 1983-84 during the BIOMASS SIBEX I cruise of the R. V. KAIYO MARU of Japan Fisheries Agency. Distribution and taxonomy of heterotrophic protists were investigated. Naked amoebae and choanoflagellates were the dominant heterotrophic protists in the Indian sector of the Southern Ocean. The total cell volume of heterotrophic protists was larger ...
Full Text Available 3D03.y1 1119 - RescueMu Grid AA Zea mays genomic, genomicsurvey sequence. 34 0.029 2 L32141 |L32141.1 Mitoch...escueMu Grid AA Zea mays genomic, genomic survey sequence. 32 0.10 2 CG804004 |CG...804004.1 1118047C06.y1 1118 - RescueMu Grid S Zea mays genomic, genomic survey sequence. 34 0.12 2 X75544 |X... - RescueMu Grid AA Zea mays genomic, genomic survey sequence. 32 0.31 2 AF538053 |AF538053.1 Monosiga brevi...tis elegans YAC Y56A3A. 44 0.52 1 CG726928 |CG726928.1 1119092C08.y1 1119 - RescueMu Grid AA Zea mays genomic, genomic survey
Gadallah, Neveen S; Ghahari, Hassan; Achterberg, Kees Van
The Iranian species diversity of five braconid subfamilies, Euphorinae (54 species in 16 genera and 8 tribes), Gnamptodontinae (4 species in 1 genus and 1 tribe), Helconinae (9 species in 5 genera and 2 tribes), Hormiinae (8 species in 4 genera and 2 tribe) and Rhysipolinae (3 species in 2 genera) are summarized in this catalogue. A faunistic list is given comprising both local and global distribution of each species under study as well as host records. In the present study ten new records are added to the Iranian fauna: Centistes (Ancylocentrus) ater (Nees), Centistes cuspidatus (Haliday), Meteorus affinis (Wesmael), Meteorus rufus (DeGeer), Microctonus brevicollis (Haliday), Microctonus falciger Ruthe, Peristenus nitidus (Curtis) (Euphorinae), Aspicolpus carinator (Nees), Diospilus capito (Nees) and Diospilus productus Marshall (Helconinae s.l.). Euphorus pseudomitis Hedwig, 1957 is transferred to the subfamily Hormiinae and Hormisca pseudomitis (Hedwig, 1957) is a new combination. PMID:27395908
Vandekerckhove, T T; Willems, A; Gillis, M; Coomans, A
Numerous micro-organisms have been described as cytoplasmic symbionts of eukaryotes. Many so-called obligate endosymbionts rely exclusively on maternal (vertical or transovarial) transmission to maintain themselves, rendering them dependent on the host sex ratio, which they would tend to manipulate to their own advantage. The latter phenomenon is often associated with the presence of Wolbachia pipientis (alpha-Proteobacteria) in arthropods and nematodes. A potentially similar situation was discovered involving members of a new clade of Verrucomicrobia, another main line of descent in the Bacteria. Nematode species of the Xiphinema americanum group (Nematoda, Longidoridae), viz. Xiphinema americanum, Xiphinema rivesi and Xiphinema brevicollum, each harbour their own specific verrucomicrobial endosymbionts. They are exclusively maternally inherited and their hosts reproduce by thelytokous (mother-to-daughter) parthenogenesis, males being extremely rare. A new genus, 'Candidatus Xiphinematobacter' gen. nov., along with three new candidate verrucomicrobial species, 'Candidatus Xiphinematobacter americani' sp. nov., 'Candidatus Xiphinematobacter rivesi' sp. nov. and 'Candidatus Xiphinematobacter brevicolli' sp. nov., are described on the basis of transmission electron microscopy, scanning electron microscopy, DAPI (4',6-diamidino-2-phenylindole) epifluorescence microscopy and 16S rDNA sequence analysis. These are the first endosymbiotic species described among the Verrucomicrobia. They share a mean 16S rDNA similarity of about 93%, whereas similarity to their closest relative, clone WCHD3-88, is less than 87%. Thus, the endosymbionts form a homogeneous clade for which the new candidate genus 'Candidatus Xiphinematobacter' gen. nov. is proposed. The type species is 'Candidatus Xiphinematobacter brevicolli' sp. nov.
Partho Sarothi Ray
Full Text Available Repeated domains in proteins that have undergone duplication or loss, and sequence divergence, are especially informative about phylogenetic relationships. We have exploited divergent repeats of the highly structured, 50-amino acid WHEP domains that join the catalytic subunits of bifunctional glutamyl-prolyl tRNA synthetase (EPRS as a sequence-informed repeat (SIR to trace the origin and evolution of EPRS in holozoa. EPRS is the only fused tRNA synthetase, with two distinct aminoacylation activities, and a non-canonical translation regulatory function mediated by the WHEP domains in the linker. Investigating the duplications, deletions and divergence of WHEP domains, we traced the bifunctional EPRS to choanozoans and identified the fusion event leading to its origin at the divergence of ichthyosporea and emergence of filozoa nearly a billion years ago. Distribution of WHEP domains from a single species in two or more distinct clades suggested common descent, allowing the identification of linking organisms. The discrete assortment of choanoflagellate WHEP domains with choanozoan domains as well as with those in metazoans supported the phylogenetic position of choanoflagellates as the closest sister group to metazoans. Analysis of clustering and assortment of WHEP domains provided unexpected insights into phylogenetic relationships amongst holozoan taxa. Furthermore, observed gaps in the transition between WHEP domain groupings in distant taxa allowed the prediction of undiscovered or extinct evolutionary intermediates. Analysis based on SIR domains can provide a phylogenetic counterpart to palaentological approaches of discovering "missing links" in the tree of life.
Full Text Available The emergence of multicellularity and epithelia in relation to the appearance of cellular junctions, in order to illustrate the first steps of animal evolution, is discussed. We analyzed the structure and roles of adherens and occludins, considered to be the oldest. Also treated are some aspects of the main proteins that constitute them, the cadherins and claudins, as well as the related structures observed in sponges and choanoflagellates, the most ancient animals and the ancestors of these, respectively. It was concluded that the animal ancestor probably possessed some kind of adherens and possibly occludins, appearing as the first of major importance. These junctions increased in complexity through until the complexity observed in modern times.
Eswarappa, Sandeepa M; Fox, Paul L
The vertebrate multiaminoacyl tRNA synthetase complex (MARS) is an assemblage of nine aminoacyl tRNA synthetases (ARSs) and three non-synthetase scaffold proteins, aminoacyl tRNA synthetase complex-interacting multifunctional protein (AIMP)1, AIMP2, and AIMP3. The evolutionary origin of the MARS is unclear, as is the significance of the inclusion of only nine of 20 tRNA synthetases. Eight of the nine amino acids corresponding to ARSs of the MARS are derived from two citric acid cycle intermediates, α-ketoglutatrate and oxaloacetate. We propose that the metabolic link with the citric acid cycle, the appearance of scaffolding proteins AIMP2 and AIMP3, and the subsequent disappearance of the glyoxylate cycle, together facilitated the origin of the MARS in a common ancestor of metazoans and choanoflagellates.
Karolewski, Piotr; Giertych, Marian J.; Żmuda, Michał; Jagodziński, Andrzej M.; Oleksyn, Jacek
Understory shrubs contribute to overall species diversity, providing habitat and forage for animals, influence soil chemistry and forest microclimate. However, very little is known about the chemical defense of various shrub species against folivorous insects. Using six shrub species, we tested how seasonal changes and light conditions affect their constitutive defense to insect damage. We monitored leaf perforation, concentrations of total phenols, condensed tannins, nitrogen (N), and total nonstructural carbohydrates (TNC). Leaf damage caused by insects was low in Sambucus nigra, Cornus sanguinea, and Frangula alnus, intermediate in Corylus avellana and Prunus serotina, and high in Prunus padus. Leaves of all the species, when growing in high light conditions, had high concentrations of defense metabolites. Except for C. avellana, leaves of the other shrub species growing in full sun were less injured than those in shade. This may be due to higher concentrations of defense metabolites and lower concentrations of nitrogen. Similar patterns of the effects of light on metabolites studied and N were observed for leaves with varying location within the crown of individual shrubs (from the top of the south direction to the bottom of the north), as for leaves from shrubs growing in full sun and shrubs in the shade of canopy trees. A probable cause of the greater damage of more sunlit leaves of C. avellana was the fact that they were herbivorized mostly by Altica brevicollis, a specialist insect that prefers plant tissues with a high TNC level and is not very sensitive to a high level of phenolic compounds.
Full Text Available Hupehsuchia is a group of enigmatic Triassic marine reptiles that is known exclusively from two counties in Hubei Province, China. One of the common features of the group was a modestly long neck with nine to ten cervical vertebrae. We report a new species of Hupehsuchia, Eohupehsuchus brevicollis gen. et sp. nov., which for the first time shows a short neck in this group, with six cervicals. The configuration of the skull roof in Eohupehsuchus is also unique among Hupehsuchia, with narrow frontals and posteriorly shifted parietals, warranting recognition of a new species. The taxon superficially resembles Nanchangosaurus in retaining hupehsuchian plesiomorphies, such as low neural spines and small body size. However, its limbs are well-developed, unlike in Nanchangosaurus, although the latter genus is marginally larger in body length. Thus, the individual is unlikely to be immature. Also, Eohupehsuchus shares a suite of synapomorphies with Hupehsuchus, including the second and third layers of dermal ossicles above the dorsal neural spines. A phylogenetic analysis suggests that the new species is not the most basal hupehsuchian despite its short neck, and instead forms the sister taxon of Hupehsuchidae. Until recently, Hupehsuchia contained only two monotypic genera. Now there are at least four genera among Hupehsuchia, and the undescribed diversity is even higher. The left forelimb of the only specimen is incomplete, ending with broken phalanges distally. The breakage could only have occurred pre-burial. The individual may have been attacked by a predator and escaped, given that scavenging is unlikely.
Pasha, Shaik Naseer; Meenakshi, Iyer; Sowdhamini, Ramanathan
Myosins are actin-based motor proteins involved in many cellular movements. It is interesting to study the evolutionary patterns and the functional attributes of various types of myosins. Computational search algorithms were performed to identify putative myosin members by phylogenetic analysis, sequence motifs, and coexisting domains. This study is aimed at understanding the distribution and the likely biological functions of myosins encoded in various taxa and available eukaryotic genomes. We report here a phylogenetic analysis of around 4,064 myosin motor domains, built entirely from complete or near-complete myosin repertoires incorporating many unclassified, uncharacterized sequences and new myosin classes, with emphasis on myosins from Fungi, Haptophyta, and other Stramenopiles, Alveolates, and Rhizaria (SAR). The identification of large classes of myosins in Oomycetes, Cellular slime molds, Choanoflagellates, Pelagophytes, Eustigmatophyceae, Fonticula, Eucoccidiorida, and Apicomplexans with novel myosin motif variants that are conserved and thus presumably functional extends our knowledge of this important family of motor proteins. This work provides insights into the distribution and probable function of myosins including newly identified myosin classes. PMID:27597808
Moon-van der Staay, Seung Yeo; De WachterRDanielVaulot, RupertDe WachterR.Daniel
Picoplankton-cells with a diameter of less than 3µm-are the dominant contributors to both primary production and biomass in open oceanic regions. However, compared with the prokaryotes, the eukaryotic component of picoplankton is still poorly known. Recent discoveries of new eukaryotic algal taxa based on picoplankton cultures suggest the existence of many undiscovered taxa. Conventional approaches based on phenotypic criteria have limitations in depicting picoplankton composition due to their tiny size and lack of distinctive taxonomic characters. Here we analyse, using an approach that has been very successful for prokaryotes but has so far seldom been applied to eukaryotes, 35 full sequences of the small-subunit (18S) ribosomal RNA gene derived from a picoplanktonic assemblage collected at a depth of 75m in the equatorial Pacific Ocean, and show that there is a high diversity of picoeukaryotes. Most of the sequences were previously unknown but could still be assigned to important marine phyla including prasinophytes, haptophytes, dinoflagellates, stramenopiles, choanoflagellates and acantharians. We also found a novel lineage, closely related to dinoflagellates and not previously described.
Albert J Erives
Full Text Available The evolution of animals involved acquisition of an emergent gene repertoire for gastrulation. Whether loss of genes also co-evolved with this developmental reprogramming has not yet been addressed. Here, we identify twenty-four genetic functions that are retained in fungi and choanoflagellates but undetectable in animals. These lost genes encode: (i sixteen distinct biosynthetic functions; (ii the two ancestral eukaryotic ClpB disaggregases, Hsp78 and Hsp104, which function in the mitochondria and cytosol, respectively; and (iii six other assorted functions. We present computational and experimental data that are consistent with a joint function for the differentially localized ClpB disaggregases, and with the possibility of a shared client/chaperone relationship between the mitochondrial Fe/S homoaconitase encoded by the lost LYS4 gene and the two ClpBs. Our analyses lead to the hypothesis that the evolution of gastrulation-based multicellularity in animals led to efficient extraction of nutrients from dietary sources, loss of natural selection for maintenance of energetically expensive biosynthetic pathways, and subsequent loss of their attendant ClpB chaperones.
Nicholas A Stover
Full Text Available Fusions of the first two enzymes in the pentose phosphate pathway, glucose-6-phosphate dehydrogenase (G6PD and 6-phosphogluconolactonase (6PGL, have been previously described in two distant clades, chordates and species of the malarial parasite Plasmodium. We have analyzed genome and expressed sequence data from a variety of organisms to identify the origins of these gene fusion events. Based on the orientation of the domains and range of species in which homologs can be found, the fusions appear to have occurred independently, near the base of the metazoan and apicomplexan lineages. Only one of the two metazoan paralogs of G6PD is fused, showing that the fusion occurred after a duplication event, which we have traced back to an ancestor of choanoflagellates and metazoans. The Plasmodium genes are known to contain a functionally important insertion that is not seen in the other apicomplexan fusions, highlighting this as a unique characteristic of this group. Surprisingly, our search revealed two additional fusion events, one that combined 6PGL and G6PD in an ancestor of the protozoan parasites Trichomonas and Giardia, and another fusing G6PD with phosphogluconate dehydrogenase (6PGD in a species of diatoms. This study extends the range of species known to contain fusions in the pentose phosphate pathway to many new medically and economically important organisms.
Sebé-Pedrós, Arnau; Roger, Andrew J; Lang, Franz B; King, Nicole; Ruiz-Trillo, Iñaki
The evolution of animals (metazoans) from their unicellular ancestors required the emergence of novel mechanisms for cell adhesion and cell-cell communication. One of the most important cell adhesion mechanisms for metazoan development is integrin-mediated adhesion and signaling. The integrin adhesion complex mediates critical interactions between cells and the extracellular matrix, modulating several aspects of cell physiology. To date this machinery has been considered strictly metazoan specific. Here we report the results of a comparative genomic analysis of the integrin adhesion machinery, using genomic data from several unicellular relatives of Metazoa and Fungi. Unexpectedly, we found that core components of the integrin adhesion complex are encoded in the genome of the apusozoan protist Amastigomonas sp., and therefore their origins predate the divergence of Opisthokonta, the clade that includes metazoans and fungi. Furthermore, our analyses suggest that key components of this apparatus have been lost independently in fungi and choanoflagellates. Our data highlight the fact that many of the key genes that had formerly been cited as crucial for metazoan origins have a much earlier origin. This underscores the importance of gene cooption in the unicellular-to-multicellular transition that led to the emergence of the Metazoa.
Emma C Baker
Full Text Available HCN channels play a unique role in bilaterian physiology as the only hyperpolarization-gated cation channels. Their voltage-gating is regulated by cyclic nucleotides and phosphatidylinositol 4,5-bisphosphate (PIP2. Activation of HCN channels provides the depolarizing current in response to hyperpolarization that is critical for intrinsic rhythmicity in neurons and the sinoatrial node. Additionally, HCN channels regulate dendritic excitability in a wide variety of neurons. Little is known about the early functional evolution of HCN channels, but the presence of HCN sequences in basal metazoan phyla and choanoflagellates, a protozoan sister group to the metazoans, indicate that the gene family predates metazoan emergence. We functionally characterized two HCN channel orthologs from Nematostella vectensis (Cnidaria, Anthozoa to determine which properties of HCN channels were established prior to the emergence of bilaterians. We find Nematostella HCN channels share all the major functional features of bilaterian HCNs, including reversed voltage-dependence, activation by cAMP and PIP2, and block by extracellular Cs+. Thus bilaterian-like HCN channels were already present in the common parahoxozoan ancestor of bilaterians and cnidarians, at a time when the functional diversity of voltage-gated K+ channels was rapidly expanding. NvHCN1 and NvHCN2 are expressed broadly in planulae and in both the endoderm and ectoderm of juvenile polyps.
Soo Chan Lee
Full Text Available BACKGROUND: Microsporidia are obligate intracellular, eukaryotic pathogens that infect a wide range of animals from nematodes to humans, and in some cases, protists. The preponderance of evidence as to the origin of the microsporidia reveals a close relationship with the fungi, either within the kingdom or as a sister group to it. Recent phylogenetic studies and gene order analysis suggest that microsporidia share a particularly close evolutionary relationship with the zygomycetes. METHODOLOGY/PRINCIPAL FINDINGS: Here we expanded this analysis and also examined a putative sex-locus for variability between microsporidian populations. Whole genome inspection reveals a unique syntenic gene pair (RPS9-RPL21 present in the vast majority of fungi and the microsporidians but not in other eukaryotic lineages. Two other unique gene fusions (glutamyl-prolyl tRNA synthetase and ubiquitin-ribosomal subunit S30 that are present in metazoans, choanoflagellates, and filasterean opisthokonts are unfused in the fungi and microsporidians. One locus previously found to be conserved in many microsporidian genomes is similar to the sex locus of zygomycetes in gene order and architecture. Both sex-related and sex loci harbor TPT, HMG, and RNA helicase genes forming a syntenic gene cluster. We sequenced and analyzed the sex-related locus in 11 different Encephalitozoon cuniculi isolates and the sibling species E. intestinalis (3 isolates and E. hellem (1 isolate. There was no evidence for an idiomorphic sex-related locus in this Encephalitozoon species sample. According to sequence-based phylogenetic analyses, the TPT and RNA helicase genes flanking the HMG genes are paralogous rather than orthologous between zygomycetes and microsporidians. CONCLUSION/SIGNIFICANCE: The unique genomic hallmarks between microsporidia and fungi are independent of sequence based phylogenetic comparisons and further contribute to define the borders of the fungal kingdom and support the
Full Text Available BACKGROUND: The Nme gene family is involved in multiple physiological and pathological processes such as cellular differentiation, development, metastatic dissemination, and cilia functions. Despite the known importance of Nme genes and their use as clinical markers of tumor aggressiveness, the associated cellular mechanisms remain poorly understood. Over the last 20 years, several non-vertebrate model species have been used to investigate Nme functions. However, the evolutionary history of the family remains poorly understood outside the vertebrate lineage. The aim of the study was thus to elucidate the evolutionary history of the Nme gene family in Metazoans. METHODOLOGY/PRINCIPAL FINDINGS: Using a total of 21 eukaryote species including 14 metazoans, the evolutionary history of Nme genes was reconstructed in the metazoan lineage. We demonstrated that the complexity of the Nme gene family, initially thought to be restricted to chordates, was also shared by the metazoan ancestor. We also provide evidence suggesting that the complexity of the family is mainly a eukaryotic innovation, with the exception of Nme8 that is likely to be a choanoflagellate/metazoan innovation. Highly conserved gene structure, genomic linkage, and protein domains were identified among metazoans, some features being also conserved in eukaryotes. When considering the entire Nme family, the starlet sea anemone is the studied metazoan species exhibiting the most conserved gene and protein sequence features with humans. In addition, we were able to show that most of the proteins known to interact with human NME proteins were also found in starlet sea anemone. CONCLUSION/SIGNIFICANCE: Together, our observations further support the association of Nme genes with key cellular functions that have been conserved throughout metazoan evolution. Future investigations of evolutionarily conserved Nme gene functions using the starlet sea anemone could shed new light on a wide variety of
I discuss eukaryote megaphylogeny and the timing of major innovations in the light of multigene trees and the rarity of marine/freshwater evolutionary transitions. The first eukaryotes were aerobic phagotrophs, probably substratum-associated heterotrophic amoeboflagellates. The primary eukaryote bifurcation generated unikonts (ancestrally probably unicentriolar, with a conical microtubular [MT] cytoskeleton) and bikonts (ciliary transformation from anterior cilium to ancestrally gliding posterior cilium; cytoskeleton of ventral MT bands). Unikonts diverged into Amoebozoa with anterior cilia, lost when lobosan broad pseudopods evolved for locomotion, and Choanozoa with posterior cilium and filose pseudopods that became unbranched tentacles/microvilli in holozoa and eventually the choanoflagellate/choanocyte collar. Of choanozoan ancestry, animals evolved epithelia, fibroblasts, eggs, and sperm. Fungi and Ichthyosporea evolved walls. Bikonts, ancestrally with ventral grooves, include three adaptively divergent megagroups: Rhizaria (Retaria and Cercozoa, ancestrally reticulofilose soft-surfaced gliding amoeboflagellates), and the originally planktonic Excavata, and the corticates (Plantae and chromalveolates) that suppressed pseudopodia. Excavata evolved cilia-generated feeding currents for grooval ingestion; corticates evolved cortical alveoli and ciliary hairs. Symbiogenetic origin and transfers of chloroplasts stimulated an explosive radiation of corticates--hard to resolve on multigene trees--and opisthokonts, and ensuing Cambrian explosions of animals and protists. Plantae lost phagotrophy and multiply evolved walls and macroalgae. Apusozoa, with dorsal pellicle and ventral pseudopods, are probably the most divergent bikonts or related to opisthokonts. Eukaryotes probably originated 800-850 My ago. Amoebozoa, Apusozoa, Loukozoa, and Metamonada may be the only extant eukaryote phyla pre-dating Neoproterozoic snowball earth. New subphyla are established for
Full Text Available Abstract Background An important role in the evolution of intracellular trafficking machinery in eukaryotes played small GTPases belonging to the Rab family known as pivotal regulators of vesicle docking, fusion and transport. The Rab family is very diversified and divided into several specialized subfamilies. We focused on the VII functional group comprising Rab7 and Rab9, two related subfamilies, and analysed 210 sequences of these proteins. Rab7 regulates traffic from early to late endosomes and from late endosome to vacuole/lysosome, whereas Rab9 participates in transport from late endosomes to the trans-Golgi network. Results Although Rab7 and Rab9 proteins are quite small and show heterogeneous rates of substitution in different lineages, we found a phylogenetic signal and inferred evolutionary relationships between them. Rab7 proteins evolved before radiation of main eukaryotic supergroups while Rab9 GTPases diverged from Rab7 before split of choanoflagellates and metazoans. Additional duplication of Rab9 and Rab7 proteins resulting in several isoforms occurred in the early evolution of vertebrates and next in teleost fishes and tetrapods. Three Rab7 lineages emerged before divergence of monocots and eudicots and subsequent duplications of Rab7 genes occurred in particular angiosperm clades. Interestingly, several Rab7 copies were identified in some representatives of excavates, ciliates and amoebozoans. The presence of many Rab copies is correlated with significant differences in their expression level. The diversification of analysed Rab subfamilies is also manifested by non-conserved sequences and structural features, many of which are involved in the interaction with regulators and effectors. Individual sites discriminating different subgroups of Rab7 and Rab9 GTPases have been identified. Conclusion Phylogenetic reconstructions of Rab7 and Rab9 proteins were performed by a variety of methods. These Rab GTPases show diversification
Hedges, S. Blair; Blair, Jaime E.; Venturi, Maria L.; Shoe, Jason L.
BACKGROUND: The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. RESULTS: Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20-188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to
Venturi Maria L
Full Text Available Abstract Background The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. Results Our phylogenetic analyses revealed that (i animals are more closely related to fungi than to plants, (ii red algae are closer to plants than to animals or fungi, (iii choanoflagellates are closer to animals than to fungi or plants, (iv diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v diplomonads are basal to other eukaryotes (including alveolates and euglenozoans. Divergence times were estimated from global and local clock methods using 20–188 proteins per node, with data treated separately (multigene and concatenated (supergene. Different time estimation methods yielded similar results (within 5%: vertebrate-arthropod (964 million years ago, Ma, Cnidaria-Bilateria (1,298 Ma, Porifera-Eumetozoa (1,351 Ma, Pyrenomycetes-Plectomycetes (551 Ma, Candida-Saccharomyces (723 Ma, Hemiascomycetes-filamentous Ascomycota (982 Ma, Basidiomycota-Ascomycota (968 Ma, Mucorales-Basidiomycota (947 Ma, Fungi-Animalia (1,513 Ma, mosses-vascular plants (707 Ma, Chlorophyta-Tracheophyta (968 Ma, Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma, Plantae-Animalia (1,609 Ma, Alveolata-plants+animals+fungi (1,973 Ma, Euglenozoa-plants+animals+fungi (1,961 Ma, and Giardia-plants+animals+fungi (2,309 Ma. By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to ~10
Horacio M. Canelas
Full Text Available The authors outline the development of the spine and skull, particularly of axis, atlas and occipital bone. As neuro-skeletal dysmorphisms, the occipito-cervical malformations belong to the neurodysplastic group. They are classified as skeletal anomalies, associated nervous malformations and meningeal reactions. Vertebralization of the occipital bone and occipitalization of atlas, subluxation of odontoid process, dysplasia of the occipital bone, dystrophia brevicollis and other anomalies are discussed. Special care is given to the study of basilar impression; its concept, history, incidence, clinical and neurological symptoms, radiological characterization (craniographic, perimyelographic and iodoventriculographic aspects and surgical treatment are reviewed. The authors report five cases of occipito-cervical malformations, which are the first references in Brazilian literature. In case 1 the anomalies (manifestation of occipital vertebra and Arnold-Chiari deformity were disclosed at an operation for cisticercosis of the posterior fossa. In the following four cases invagination of the basilar portion of the occipital bone (basilar impression could be radiologically demonstrated; in case 2 a suboccipital craniectomy and a laminectomy of atlas and axis were performed but the patient died a week later and the necroscopic examination confirmed the neuro-skeletal anomalies. In all cases there were several associated malformations. In case 2 there were occipitalization of the atlas, fusion of the first and second cervical vertebrae, supernumerary rib of the seventh cervical vertebra, supernumerary lumbar vertebra, and Arnold-Chiari deformity; at necropsy it was found a syringomyelic cyst on the cervical cord and a fibrous dural ring over the foramen magnum. Case 3 showed the syndrome of Klippel-Feil, besides supernumerary ribs of the seventh cervical and first dorsal vertebrae, Arnold-Chiari malfotmation and probable aplasia of cell groups in the
The divergence times and evolutionary relationships of some major protoctist clades were resolved by equation for molecular absolute evolutionary rates and several protein molecules:EF-1α,EF-2,NADH1 and CytB.The results showed that protoctists evolved from the route as:algae→fungi→protozoan.Their respective evolutionary routes are:(1) After the seperation of red algae at 1.331 Ga ago,the green algae separated from it around 1.1744 Ga ago, Mosses seperated at 0.4527 Ga ago,ferns seperated at 0.437 Ga ago.The divergence times of club-mosses,liverworts, Chlamydomonadales and Chlorellales are 0.4185,0.4457,0.5202 and 0.5239 Ga ago,respectively;(2) both Slime molds and oomycetes belonge to Fungi evolutionary branch,which separated about 1.0456 and 0.9032 Ga ago;(3) In protozoan branch,Apicomplexa and Choanoflagellates separated about 1.045 and 0.8122 Ga ago,respectively.Our results agreed well with the references work based on fossil records,and provided a new way to precisely resolve the evolutionary relationships of all protoctists.%使用本文作者提出的分子绝对进化速率的计算公式和EF-1α,EF-2,NADH1和CytB等蛋白质分子,对原生生物的一些主要类群:藻类、真菌和原生动物的物种分歧时间和演化关系进行了定量计算.结果显示,原核生物沿着藻类→真菌→原生动物的方向演化.它们的演化关系为:(1)红藻自13.31亿年前分化出后,于11.74亿年前分化出绿藻,绿藻于4.527亿年前分化出藓类,4.37亿年前分化出蕨类;其他物种如石松类、肝苔类、团藻和小球藻分别于4.185亿年前、4.457亿年前、5.202亿年前和5.239亿年前分化出;(2)黏菌和卵菌均属于真菌进化分枝,分别于10.456亿年前和9.032亿年前分化出;(3)原生动物进化分枝中于10.45亿年前分化出孢子虫等,8.122亿年前领鞭毛虫与多细胞动物分化.这些结果均与基于化石记录的文献报道相符.
Full Text Available Data gathered from publications, entomological collections and field observations along the last eight years, provide information about the presence of 40 especies of the family Meloidae in Comunidad de Madrid. Seven species are only known from collections made more than 25 years ago, while two species have been found only during recent field surveys (Meloe rugosus and Nemognatha chrysomelina. Two out of the seven species without recent records (Stenoria apicalis and Meloe baudueri are represented in Madrid by one or two specimens, so that their current presence in the region may have been overlooked. This is not the case of the other five (Meloe variegatus, M. cavensis, M. violaceus, Mylabris uhagonii and M. amorii, which are represented by numerous specimens in the historical collections. Meloe variegatus, M. cavensis and Mylabris uhagonii, must be considered at risk of extinction, but if new specimens are not found in the near future they should be treated as definitively extinct. Mylabris amorii has been found in only one locality at the northernmost edge of its known distribution range, and the evaluation of its status depends on new information. Meloe violaceus has suffered and evident decline and therefore should be treated as Vulnerable. Five additional species suffered evident reductions of their distribution ranges in Madrid (Meloe brevicollis, M. autumnalis, M. proscarabaeus, Hycleus dufourii and Mylabris dejeani. Most of the recent records for those species are restricted to mountain areas, while the lowland populations seem to have been disappeared and consequently, these species should be listed as Vulnerable. If the current tendency continues they will be transferred to the Extinction Risk level. Meloe tuccius, a frequently found species 10 to 15 years ago in the urban area of Madrid can be considerered today as nearly extinct in the area, and therefore should be