Full Text Available choanoflagellate Monosiga brevicollis Monosiga_brevicollis_L.png Monosiga_brevicollis..._NL.png Monosiga_brevicollis_S.png Monosiga_brevicollis_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Monosiga+brevicolli...s&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Monosiga+brevicollis&t=NL ht...tp://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Monosiga+brevicollis&t=S http://bi...osciencedbc.jp/taxonomy_icon/icon.cgi?i=Monosiga+brevicollis&t=NS http://togodb.biosciencedbc.jp/togodb/view/taxonomy_icon_comment_en?species_id=220 ...
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.
Thomsen, Helge Abildhauge; Østergaard, Jette Buch
Sex is found in all major eukaryotic groups of organisms. It has been known for some time that the choanoflagellates also possess the genes involved in meiosis and a full sexual cycle was also recently accounted for in Salpingoeca rosetta. With reference to the loricate choanoflagellates the curr......Sex is found in all major eukaryotic groups of organisms. It has been known for some time that the choanoflagellates also possess the genes involved in meiosis and a full sexual cycle was also recently accounted for in Salpingoeca rosetta. With reference to the loricate choanoflagellates...
Full Text Available hetical protein [Monosiga brevicollis MX1] gb|EDQ88566.1| predicted protein [Monosiga brevicollis MX1] 3e-57 65% MEGSLSLSLSLSLSLFLSLS...LSPSLPLSLSVSPSLSLSLSLFLSLSLCLSFSLSPSLSLSLSVSLSVSLSVSVSLSLSLSLCFSLSLCFSLSLSLPLCLSLCLCLSLSPSFSLCLSPSPSLPLSLS...PSLSLSVSVSLSVSLSLSLSLSLSLSLSVCLCLCLSLCLSVSVSVSVSVSVSLSLSLSLSLSLSLSLSLSLSLSLCVCVSLSLSLCLSPSPSLSRKRIRKGVEMRSYDDDDDKSLNLYSVYSVSRT ...
Full Text Available hetical protein [Monosiga brevicollis MX1] gb|EDQ88566.1| predicted protein [Monosiga brevicollis MX1] 2e-61 67% MRSAFSPPWSLS...SPKKGLIFRGLNQSSLWRMAEWSTVSLLPSLSFPLSLSLSLSLSLSPCQSLCLSDSLPHSFSVSVSITLSLCFSLLPSLSPSLSVSLSMSLSLCLCLSVSPSLSLSLSVSLSLS...VSLSLFLSLSLSLSPCQSLCLSPSLSLSVSLSPSLSLSVSLSPSLSLSVSLSLCLSLSLPHSLSLSLSLCLCLSLSLCLSLS...LSLSVSVSPSLYLSLSLSLTLSVSLFLSVSVSLCLSVSLCLSVSVSVCLSVSLSLSLSLSLSLSLSLSLSPLA ...
Full Text Available hetical protein [Monosiga brevicollis MX1] gb|EDQ88566.1| predicted protein [Monosiga brevicollis MX1] 2e-39 55% MALSLSLSLSLSVFLSLS...SLSLLSLLSLSSLSPLSLLSLCLSLSPXXXSPLSLSLSPSLSLSLSLSSLSPLSLSSLSLLSLSSLSSLSPLSPLSLSLSLSLSLSLSPSLSLSLSLSLPLSLSVSLSLS...LSLSLSLSLSLSLSSLSSLSSLSPLSPLSLSLSLSLSLALALALSLICFSAPLCVSLCLFLSLSLSVPVSISLS...VPLCLFLSVSLSVYFSLTLSLSVSFSLPPLSVSLSLSSPPAPTLPSFFLLSVLRTAIVWQRAEGHTENLTRLVVGSSQSQSGQLQLPPKQPFPRALEPFGIVLVLLSLGFDA ...
Suga, Hiroshi; Chen, Zehua; de Mendoza, Alex; Sebé-Pedrós, Arnau; Brown, Matthew W; Kramer, Eric; Carr, Martin; Kerner, Pierre; Vervoort, Michel; Sánchez-Pons, Núria; Torruella, Guifré; Derelle, Romain; Manning, Gerard; Lang, B Franz; Russ, Carsten; Haas, Brian J; Roger, Andrew J; Nusbaum, Chad; Ruiz-Trillo, Iñaki
To reconstruct the evolutionary origin of multicellular animals from their unicellular ancestors, the genome sequences of diverse unicellular relatives are essential. However, only the genome of the choanoflagellate Monosiga brevicollis has been reported to date. Here we completely sequence the genome of the filasterean Capsaspora owczarzaki, the closest known unicellular relative of metazoans besides choanoflagellates. Analyses of this genome alter our understanding of the molecular complexity of metazoans' unicellular ancestors showing that they had a richer repertoire of proteins involved in cell adhesion and transcriptional regulation than previously inferred only with the choanoflagellate genome. Some of these proteins were secondarily lost in choanoflagellates. In contrast, most intercellular signalling systems controlling development evolved later concomitant with the emergence of the first metazoans. We propose that the acquisition of these metazoan-specific developmental systems and the co-option of pre-existing genes drove the evolutionary transition from unicellular protists to metazoans.
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.
Busqué, Juan; Pedrosa, Mercedes Martin; Cabellos, Blanca; Muzquiz, Mercedes
Carex brevicollis (Cyperaceae) is a plant of mesic grasslands in calcareous mountains of southern Europe. It contains two different β-carboline alkaloids, brevicolline and brevicarine, the first of which is thought to produce abortions in mammals. In the rangeland of Aliva, within the Picos de Europa massif in northern Spain, the abundance of Carex brevicollis has been linked with the occurrence of teratogenesis in early gestating cows grazing in early summer. The concentration of alkaloids was measured in the summers of 2007 and 2008, at intervals of 2 weeks, at different altitudes within the rangeland (1,350, 1,600, and 1,850 m) and from different parts of the sedge (leaves, reproductive stems, and inflorescences). Estimated growing degree days were related to the flowering phenology of Carex brevicollis and were used to analyse its relation with the concentration of alkaloids. Brevicarine concentration was higher in inflorescences and brevicolline in leaves. Although it also depended on the zone and year, the concentrations of both alkaloids were related one to another in leaves and inflorescences but not in stems. Both alkaloids decreased with growing degree days in the inflorescences and showed no response in leaves. Our findings suggest that brevicarine, not brevicolline, could be the teratogen in pregnant cattle in this region. This hypothesis is supported by the observed frequent consumption of inflorescences and scarce consumption of leaves of Carex brevicollis by grazing livestock, and also by the coincidence of the toxicity in early pregnant cows with the flowering time of the sedge.
Distribution and morphology of choanoflagellates, collared heterotrophic flagellates bearing an extracellular siliceous lorica, were reviewed. Eleven species were reported from the Antarctic Ocean. Three of the eleven species were originally described from the Antarctic and are known to be endemic to the Antarctic. The other eight were found in various oceanic areas. Choanoflagellates had been found in both ice and water, which suggested their wide and abundant distribution in the Antarctic. ...
Labonte, James R
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 settings, based upon
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
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.
Kirkegaard, Julius B.; Goldstein, Raymond E.
Efficient uptake of prey and 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 choanoflagellate Salpingoeca rosetta, which can exist as a swimming cell, as a sessile thecate cell, and as colonies of cells in various shapes. In the absence of other requirements and in a homogeneously nutritious environment, we find that the optimal strategy to maximize filter-feeding by the collar of microvilli is to swim fast, which favors swimming unicells. In large external flows, the sessile thecate cell becomes advantageous. Effects of prey diffusion are discussed and also found to be to the advantage of the swimming unicell.
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
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
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 ...
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.
Ortutay, Csaba; Nore, Beston F; Vihinen, Mauno; Smith, C I Edvard
It is generally considered mammals and birds have five Tec family kinases (TFKs): Btk, Bmx (also known as Etk), Itk, Tec, and Txk (also known as Rlk). Here, we discuss the domains and their functions and regulation in TFKs. Over the last few years, a large number of genomes from various phyla have been sequenced making it possible to study evolutionary relationships at the molecular and sequence level. Using bioinformatics tools, we for the first time demonstrate that a TFK ancestor exists in the unicellular choanoflagellate Monosiga brevicollis, which is the closest known relative to metazoans with a sequenced genome. The analysis of the genomes for sponges, insects, hagfish, and frogs suggests that these species encode a single TFK. The insect form has a divergent and unique N-terminal region. Duplications generating the five members took place prior to the emergence of vertebrates. Fishes have two or three forms and the platypus, Ornithorhynchus anatinus, has four (lacks Txk). Thus, not all mammals have all five TFKs. The single identified TFK in frogs is an ortholog of Tec. Bmx seems to be unique to mammals and birds. SH3BP5 is a negative regulator of Btk. It is conserved in choanoflagellates and interestingly exists also in nematodes, which do not express TFKs, suggesting a broader function in addition to Btk regulation. The related SH3BP5-like protein is not found in Nematodes.
Evolving multicellularity is easy, especially in phototrophs and osmotrophs whose multicells feed like unicells. Evolving animals was much harder and unique; probably only one pathway via benthic 'zoophytes' with pelagic ciliated larvae allowed trophic continuity from phagocytic protozoa to gut-endowed animals. Choanoflagellate protozoa produced sponges. Converting sponge flask cells mediating larval settling to synaptically controlled nematocysts arguably made Cnidaria. I replace Haeckel's gastraea theory by a sponge/coelenterate/bilaterian pathway: Placozoa, hydrozoan diploblasty and ctenophores were secondary; stem anthozoan developmental mutations arguably independently generated coelomate bilateria and ctenophores. I emphasize animal origin's conceptual aspects (selective, developmental) related to feeding modes, cell structure, phylogeny of related protozoa, sequence evidence, ecology and palaeontology. Epithelia and connective tissue could evolve only by compensating for dramatically lower feeding efficiency that differentiation into non-choanocytes entails. Consequentially, larger bodies enabled filtering more water for bacterial food and harbouring photosynthetic bacteria, together adding more food than cell differentiation sacrificed. A hypothetical presponge of sessile triploblastic sheets (connective tissue sandwiched between two choanocyte epithelia) evolved oogamy through selection for larger dispersive ciliated larvae to accelerate benthic trophic competence and overgrowing protozoan competitors. Extinct Vendozoa might be elaborations of this organismal grade with choanocyte-bearing epithelia, before poriferan water channels and cnidarian gut/nematocysts/synapses evolved.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
Evolving multicellularity is easy, especially in phototrophs and osmotrophs whose multicells feed like unicells. Evolving animals was much harder and unique; probably only one pathway via benthic ‘zoophytes’ with pelagic ciliated larvae allowed trophic continuity from phagocytic protozoa to gut-endowed animals. Choanoflagellate protozoa produced sponges. Converting sponge flask cells mediating larval settling to synaptically controlled nematocysts arguably made Cnidaria. I replace Haeckel's gastraea theory by a sponge/coelenterate/bilaterian pathway: Placozoa, hydrozoan diploblasty and ctenophores were secondary; stem anthozoan developmental mutations arguably independently generated coelomate bilateria and ctenophores. I emphasize animal origin's conceptual aspects (selective, developmental) related to feeding modes, cell structure, phylogeny of related protozoa, sequence evidence, ecology and palaeontology. Epithelia and connective tissue could evolve only by compensating for dramatically lower feeding efficiency that differentiation into non-choanocytes entails. Consequentially, larger bodies enabled filtering more water for bacterial food and harbouring photosynthetic bacteria, together adding more food than cell differentiation sacrificed. A hypothetical presponge of sessile triploblastic sheets (connective tissue sandwiched between two choanocyte epithelia) evolved oogamy through selection for larger dispersive ciliated larvae to accelerate benthic trophic competence and overgrowing protozoan competitors. Extinct Vendozoa might be elaborations of this organismal grade with choanocyte-bearing epithelia, before poriferan water channels and cnidarian gut/nematocysts/synapses evolved. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’. PMID:27994119
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 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
Diekmann, Yoan; Seixas, Elsa; Gouw, Marc; Tavares-Cadete, Filipe; Seabra, Miguel C; Pereira-Leal, José B
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 at which we perform
Thomsen, Helge Abildhauge; Østergaard, Jette Buch
documenting possible morphotype changes that might similarly indicate the existence of complex life cycles. In this particular case, it revolves around the existence of so-called ‘combination loricas’ (i.e. two loricas that occur physically united), representing consistent species combinations from the genera...
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
Marron, Alan O.; Chappell, Helen; Ratcliffe, Sarah; Goldstein, Raymond E.
This is the final version of the article. It first appeared from Royal Society Publishing via http://dx.doi.org/10.1098/rsif.2016.0485 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 choanof...
Spanggaard, Bettina; Skouboe, P.; Rossen, L.
Ichthyophonus hoferi Plehn and Mulsow, 1911 is thought to be one of the few pathogenic fungal infections of marine fish. The result of an attack is severe epizootics in herring stocks with drastic reduction in the population as a consequence. The exact phylogenetic position of the genus Ichthyoph......Ichthyophonus hoferi Plehn and Mulsow, 1911 is thought to be one of the few pathogenic fungal infections of marine fish. The result of an attack is severe epizootics in herring stocks with drastic reduction in the population as a consequence. The exact phylogenetic position of the genus...... Ichthyophonus is not known. In the present study, a combination of molecular data, ultrastructure and biochemical characters were utilized to investigate the phylogeny of I. hoferi. The genomic DNA encoding the small subunit ribosomal RNA (18S rRNA) was amplified and sequenced. Comparisons with other eukaryotic...
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.
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
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.
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 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.
Jelínek, Josef; Mifsud, David
Information is given about four species of Monotomidae which occur in the Maltese Islands, namely Rhizophagus unicolor, Monotoma bicolor, M. brevicollis and M. spinicollis. A previous record of Rhizophagus bipustulatus was found to be incorrect and should refer to R. unicolor. A dichotomous key for the identification of the four species is also provided
Elek, Zoltán; Howe, Andrew Gordon; Enggaard, Mattias Kjartan
The seasonal activity of six carabid species (Nebria brevicollis, Carabus nemoralis, C. hortensis, C. coriaceus, Pterostichus melanarius and Abax parallelepipedus) was studied along an urbanisation series (rural forest - suburban forest - forest fragments in urban park) in Sorø, Denmark, during A...... of seasonality in order to distinguish whether the bioindicator's response is to habitat quality or stochastic seasonal events....
Andersen, Anders; Nielsen, Lasse Tor; Dolger, Julia; Kiorboe, Thomas
Microbial filter-feeders form an important group of plankton with significance to the aquatic food webs. While the concept of filter-feeding is straightforward, our quantitative understanding of microbial filter-feeding leaves a lot to be desired. As a model organism, we focus on the filter-feeding choanoflagellate Diaphanoeca grandis. We quantify the feeding flow using particle tracking, and demonstrate that hydrodynamic theory underestimates the observed clearance rate by an order of magnitude. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. To resolve the paradox we argue that D. grandis and other choanoflagellates must have so far unbeknownst morphological features. Specifically, we suggest a flagellar vane that connects the flagellum to the filter, as known in choanocytes of sponges, creating a radically different, and order of magnitude more capable, pumping mechanism. The Centre for Ocean Life is a VKR Centre of Excellence supported by the Villum Foundation.
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...
Full Text Available Animals are evolutionarily related to fungi and to the predominantly unicellular protozoan phylum Choanozoa, together known as opisthokonts. To establish the sequence of events when animals evolved from unicellular ancestors, and understand those key evolutionary transitions, we need to establish which choanozoans are most closely related to animals and also the evolutionary position of each choanozoan group within the opisthokont phylogenetic tree. Here we focus on Ministeria vibrans, a minute bacteria-eating cell with slender radiating tentacles. Single-gene trees suggested that it is either the closest unicellular relative of animals or else sister to choanoflagellates, traditionally considered likely animal ancestors. Sequencing thousands of Ministeria protein genes now reveals about 14 with domains of key significance for animal cell biology, including several previously unknown from deeply diverging Choanozoa, e.g. domains involved in hedgehog, Notch and tyrosine kinase signaling or cell adhesion (cadherin. Phylogenetic trees using 78 proteins show that Ministeria is not sister to animals or choanoflagellates (themselves sisters to animals, but to Capsaspora, another protozoan with thread-like (filose tentacles. The Ministeria/Capsaspora clade (new class Filasterea is sister to animals and choanoflagellates, these three groups forming a novel clade (filozoa whose ancestor presumably evolved filose tentacles well before they aggregated as a periciliary collar in the choanoflagellate/sponge common ancestor. Our trees show ichthyosporean choanozoans as sisters to filozoa; a fusion between ubiquitin and ribosomal small subunit S30 protein genes unifies all holozoa (filozoa plus Ichthyosporea, being absent in earlier branching eukaryotes. Thus, several successive evolutionary innovations occurred among their unicellular closest relatives prior to the origin of the multicellular body-plan of animals.
Shalchian-Tabrizi, Kamran; Minge, Marianne A; Espelund, Mari; Orr, Russell; Ruden, Torgeir; Jakobsen, Kjetill S; Cavalier-Smith, Thomas
Animals are evolutionarily related to fungi and to the predominantly unicellular protozoan phylum Choanozoa, together known as opisthokonts. To establish the sequence of events when animals evolved from unicellular ancestors, and understand those key evolutionary transitions, we need to establish which choanozoans are most closely related to animals and also the evolutionary position of each choanozoan group within the opisthokont phylogenetic tree. Here we focus on Ministeria vibrans, a minute bacteria-eating cell with slender radiating tentacles. Single-gene trees suggested that it is either the closest unicellular relative of animals or else sister to choanoflagellates, traditionally considered likely animal ancestors. Sequencing thousands of Ministeria protein genes now reveals about 14 with domains of key significance for animal cell biology, including several previously unknown from deeply diverging Choanozoa, e.g. domains involved in hedgehog, Notch and tyrosine kinase signaling or cell adhesion (cadherin). Phylogenetic trees using 78 proteins show that Ministeria is not sister to animals or choanoflagellates (themselves sisters to animals), but to Capsaspora, another protozoan with thread-like (filose) tentacles. The Ministeria/Capsaspora clade (new class Filasterea) is sister to animals and choanoflagellates, these three groups forming a novel clade (filozoa) whose ancestor presumably evolved filose tentacles well before they aggregated as a periciliary collar in the choanoflagellate/sponge common ancestor. Our trees show ichthyosporean choanozoans as sisters to filozoa; a fusion between ubiquitin and ribosomal small subunit S30 protein genes unifies all holozoa (filozoa plus Ichthyosporea), being absent in earlier branching eukaryotes. Thus, several successive evolutionary innovations occurred among their unicellular closest relatives prior to the origin of the multicellular body-plan of animals.
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
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.
Serjoscha W. Evers
Full Text Available Sigilmassasaurus brevicollis is an enigmatic theropod dinosaur from the early Late Cretaceous (Cenomanian of Morocco, originally based on a few isolated cervical vertebrae. Ever since its original description, both its taxonomic validity and systematic affinities were contentious. Originally considered to represent its own family, Sigilmassasauridae, the genus has variously been suggested to represent a carcharodontosaurid, an ornithischian, and, more recently, a spinosaurid. Here we describe new remains referrable to this taxon and re-evaluate its taxonomic status and systematic affinities. Based on the new remains, a re-evaluation of the original materials, and comparisons with other spinosaurids, the holotype of Sigilmassasaurus brevicollis is identified as an anterior dorsal, rather than a cervical vertebra, and differences between elements referred to this taxon can be explained by different positions of the elements in question within the vertebral column. Many characters used previously to diagnose the genus and species are found to be more widespread among basal tetanurans, and specifically spinosaurids. However, the taxon shows several autapomorphies that support its validity, including the presence of a strongly rugose, ventrally offset triangular platform that is confluent with a ventral keel anteriorly in the mid-cervical vertebral centra and a strongly reduced lateral neural arch lamination, with no or an incomplete distinction between anterior and posterior centrodiapophyseal laminae in the posterior cervical and anterior dorsal vertebrae. We argue furthermore that Spinosaurus maroccanus, also described on the basis of isolated cervical vertebrae from the same stratigraphic unit and in the same paper as Sigilmassasaurus brevicollis, is a subjective synonym of the latter. Both a detailed comparison of this taxon with other theropods and a formal phylogenetic analysis support spinosaurid affintities for Sigilmassasaurus. However, we
Rauhut, Oliver W.M.; Milner, Angela C.; McFeeters, Bradley; Allain, Ronan
Sigilmassasaurus brevicollis is an enigmatic theropod dinosaur from the early Late Cretaceous (Cenomanian) of Morocco, originally based on a few isolated cervical vertebrae. Ever since its original description, both its taxonomic validity and systematic affinities were contentious. Originally considered to represent its own family, Sigilmassasauridae, the genus has variously been suggested to represent a carcharodontosaurid, an ornithischian, and, more recently, a spinosaurid. Here we describe new remains referrable to this taxon and re-evaluate its taxonomic status and systematic affinities. Based on the new remains, a re-evaluation of the original materials, and comparisons with other spinosaurids, the holotype of Sigilmassasaurus brevicollis is identified as an anterior dorsal, rather than a cervical vertebra, and differences between elements referred to this taxon can be explained by different positions of the elements in question within the vertebral column. Many characters used previously to diagnose the genus and species are found to be more widespread among basal tetanurans, and specifically spinosaurids. However, the taxon shows several autapomorphies that support its validity, including the presence of a strongly rugose, ventrally offset triangular platform that is confluent with a ventral keel anteriorly in the mid-cervical vertebral centra and a strongly reduced lateral neural arch lamination, with no or an incomplete distinction between anterior and posterior centrodiapophyseal laminae in the posterior cervical and anterior dorsal vertebrae. We argue furthermore that Spinosaurus maroccanus, also described on the basis of isolated cervical vertebrae from the same stratigraphic unit and in the same paper as Sigilmassasaurus brevicollis, is a subjective synonym of the latter. Both a detailed comparison of this taxon with other theropods and a formal phylogenetic analysis support spinosaurid affintities for Sigilmassasaurus. However, we reject the recently
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.
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
Elek, Zoltán; Lövei, Gabor L; Batki, Marton
the usefulness of FA in morphological traits as an indicator of environmental quality, we studied the effect of urbanisation on FA in ground beetles (Carabidae) near a Danish city. First, we performed a critical examina- tion whether morphological character traits suggested in the literature displayed true...... fluctuating asymmetry in three common predatory ground beetles, Carabus nemoralis, Nebria brevicollis and Pterostichus melanarius. Eight metrical (length of the second and third antennal segments, elytral length, length of the first tarsus segment, length of the first and second tibiae, length of the proximal...... traits along an urbanisation gradient (forest - suburban forest - forest fragments in urban park) to test whether environmental stress created by urbanisation is reflected in FA. Ground beetles common along a Danish urbanisation gradient did not seem to indicate differences in habitat quality...
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.
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.
Sánchez-Pons, Núria; Fairclough, Stephen R.; Lang, B. Franz; King, Nicole; Ruiz-Trillo, Iñaki
Filopodia are fine actin-based cellular projections used for both environmental sensing and cell motility, and they are essential organelles for metazoan cells. In this study, we reconstruct the origin of metazoan filopodia and microvilli. We first report on the evolutionary assembly of the filopodial molecular toolkit and show that homologs of many metazoan filopodial components, including fascin and myosin X, were already present in the unicellular or colonial progenitors of metazoans. Furthermore, we find that the actin crosslinking protein fascin localizes to filopodia-like structures and microvilli in the choanoflagellate Salpingoeca rosetta. In addition, homologs of filopodial genes in the holozoan Capsaspora owczarzaki are upregulated in filopodia-bearing cells relative to those that lack them. Therefore, our findings suggest that proteins essential for metazoan filopodia and microvilli are functionally conserved in unicellular and colonial holozoans and that the last common ancestor of metazoans bore a complex and specific filopodial machinery. PMID:23770652
Kirkegaard, Julius; Bouillant, Ambre; Marron, Alan; Leptos, Kyriacos; Goldstein, Raymond
Animals are multicellular in nature, but evolved from unicellular organisms. In the closest relatives of animals, the choanoflagellates, the unicellular species Salpincgoeca rosetta has the ability to form colonies, resembling true multicellularity. In this work we use a combination of experiments, theory, and simulations to understand the physical differences that arise from feeding, swimming and navigating as colonies instead of as single cells. We show that the feeding efficiency decreases with colony size for distinct reasons in the small and large Péclet number limits, and we find that swimming as a colony changes the conventional active random walks of microorganism to stochastic helices, but that this does not hinder effective navigation towards chemoattractants.
Rosa, Paolo; Bernasconi, Marco Valerio; Wyniger, Denise
Historical notes on Walter Linsenmaier, his entomological career and his Chrysididae collection are given. The purpose of this article is to supply the main results obtained during the GBIF digitalization project and the subsequent reorganization of the Chrysididae collection housed in the Natur-Museum Luzern (Switzerland); we also provide the complete list of the 720 taxa described by the Swiss author (species-group and genus-group names). Observations on the type material is given. A new synonymy (valid name is first) is proposed for: C. consanguinea Mocsáry, 1889 = C. consanguinea iberica Linsenmaier, 1959, syn. nov.; C. pyrophana Dahlbom, 1854 = C. pyrophana var. orionea Linsenmaier, 1951, syn. nov.; Hedychridium elegantulum du Buysson, 1887 = H. hybridum Linsenmaier, 1959, syn. nov.; H. perpunctatum Balthasar, 1953 = H. insequosum Linsenmaier, 1959, syn. nov.; Euchroeus (Pseudospinolia) incrassatus (Spinola, 1838) = E. (P.) humboldti jerichoensis Linsenmaier, 1959, syn. nov. A new replacement name Chrysis vulcanica Rosa, nom. nov. is proposed for Chrysis brevicollis Linsenmaier, 1987, nom praeocc., nec Mocsáry, 1899. The lectotype of Chrysis auriceps Linsenmaier, 1959 is designated.
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.
Lopes-Andrade, Cristiano; Webster, Reginald P.; Webster, Vincent L.; Alderson, Chantelle A.; Hughes, Cory C.; Sweeney, Jon D.
Abstract The Ciidae of New Brunswick, Canada are reviewed. Seventeen species are recorded for New Brunswick, including the following 10 species that are newly recorded for the province: Ceracis singularis (Dury), Ceracis thoracicornis (Ziegler), Cis angustus Hatch, Cis fuscipes Mellié, Cis horridulus Casey, Cis striatulus Mellié, Dolichocis laricinus (Mellié), Malacocis brevicollis (Casey), Orthocis punctatus (Mellié), and Plesiocis cribrum Casey. Additional locality data are provided for the following species previously known from the province: Cis americanus Mannerheim, Cis creberrimus Mellié, Cis levettei (Casey), Cis submicans Abeille de Perrin, Dolichocis manitoba Dury, Hadreule elongatula (Gyllenhal), and Octotemnus glabriculus (Gyllenhal). Seven synonyms are proposed here; Cis pistoria Casey with Cis submicans Abeille de Perrin; Cis fraternus Casey, Cis macilentus Casey and Cis striolatus Casey with Cis striatulus Mellié; Dolichocis indistinctus Hatch with Dolichocis laricinus (Mellié); and Octotemnus denudatus Casey and Octotemnus laevis Casey with Octotemnus glabriculus (Gyllenhal). Lindgren funnel traps provided the majority of specimens for 15 of the 17 species reported from New Brunswick and were the sole source of specimens for seven of the 10 species newly reported here, suggesting they are a very useful tool for sampling Ciidae in the forests of New Brunswick. PMID:27110172
Fahey, Bryony; Degnan, Bernard M
Laminins are a family of multidomain glycoproteins that are important contributors to the structure of metazoan extracellular matrices. To investigate the origin and evolution of the laminin family, we characterized the full complement of laminin-related genes in the genome of the sponge, Amphimedon queenslandica. As a representative of the Demospongiae, a group consistently placed within the earliest diverging branch of animals by molecular phylogenies, Amphimedon is uniquely placed to provide insight into early steps in the evolution of metazoan gene families. Five Amphimedon laminin-related genes possess the conserved molecular features, and most of the domains found in bilaterian laminins, but all display domain architectures distinct from those of the canonical laminin chain types known from model bilaterians. This finding prompted us to perform a comparative genomic analysis of laminins and related genes from a choanoflagellate and diverse metazoans and to conduct phylogenetic analyses using the conserved Laminin N-terminal domain in order to explore the relationships between genes with distinct architectures. Laminin-like genes appear to have originated in the holozoan lineage (choanoflagellates + metazoans + several other unicellular opisthokont taxa), with several laminin domains originating later and appearing only in metazoan (animal) or eumetazoan (placozoans + ctenophores + cnidarians + bilaterians) laminins. Typical bilaterian α, β, and γ laminin chain forms arose in the eumetazoan stem and another chain type that is conserved in Amphimedon, the cnidarian, Nematostella vectensis, and the echinoderm, Strongylocentrotus purpuratus, appears to have been lost independently from the placozoan, Trichoplax adhaerens, and from multiple bilaterians. Phylogenetic analysis did not clearly reconstruct relationships between the distinct laminin chain types (with the exception of the α chains) but did reveal how several members of the netrin family were
Full Text Available Abstract Background Early evolution of animals led to profound changes in body plan organization, symmetry and the rise of tissue complexity including formation of muscular and nervous systems. This process was associated with massive restructuring of animal genomes as well as deletion, acquisition and rapid differentiation of genes from a common metazoan ancestor. Here, we present a simple but efficient workflow for elucidation of gene gain and gene loss within major branches of the animal kingdom. Methods We have designed a pipeline of sequence comparison, clustering and functional annotation using 12 major phyla as illustrative examples. Specifically, for the input we used sets of ab initio predicted gene models from the genomes of six bilaterians, three basal metazoans (Cnidaria, Placozoa, Porifera, two unicellular eukaryotes (Monosiga and Capsospora and the green plant Arabidopsis as an out-group. Due to the large amounts of data the software required a high-performance Linux cluster. The final results can be imported into standard spreadsheet analysis software and queried for the numbers and specific sets of genes absent in specific genomes, uniquely present or shared among different taxons. Results and conclusions The developed software is open source and available free of charge on Open Source principles. It allows the user to address a number of specific questions regarding gene gain and gene loss in particular genomes, and user-defined groups of genomes can be formulated in a type of logical expression. For example, our analysis of 12 sequenced genomes indicated that these genomes possess at least 90,000 unique genes and gene families, suggesting enormous diversity of the genome repertoire in the animal kingdom. Approximately 9% of these gene families are shared universally (homologous among all genomes, 53% are unique to specific taxa, and the rest are shared between two or more distantly related genomes.
Graham, J M; Kent, A D; Lauster, G H; Yannarell, A C; Graham, L E; Triplett, E W
Species diversity and richness, and seasonal population dynamics of phytoplankton, planktonic protozoa, and bacterioplankton sampled from the epilimnion of Crystal Bog in 2000, were examined in order to test the hypothesis that these groups' diversity and abundance patterns might be linked. Crystal Bog, a humic lake in Vilas County, Wisconsin, is part of the North Temperate Lakes Long-Term Ecological Research Site. Phytoplankton and planktonic protozoa were identified and enumerated in a settling chamber with an inverted microscope. Bacterial cells were enumerated with the use of fluorescence 4', 6'-diamidino-2-phenylindole (DAPI)-staining procedures, and automated ribosomal intergenic spacer analysis (ARISA) was used to assess bacterioplankton diversity. Bacterial cell counts showed little seasonal variation and averaged 2.6 x 10(6) cells/mL over the ice-free season. Phytoplankton and planktonic protozoan numbers varied by up to two orders of magnitude and were most numerous in late spring and summer. Dinoflagellates largely dominated Crystal Bog throughout the ice-free period, specifically Peridiniopsis quadridens in the spring, Peridinium limbatum in summer, and Gymnodinium fuscum and P. quadridens in fall. Brief blooms of Cryptomonas, Dinobryon, and Synura occurred between periods of dinoflagellate domination. The dominant dinoflagellate, Peridinium limbatum, was calculated to have a growth rate of 0.065 day(-1) and a doubling time of 10.7 days. Heterotrophic nanoflagellates (HNFs) were a consistent component of the planktonic protozoa; seasonal patterns were determined for three genera of HNFs (Monosiga, Bicosoeca, and Desmarella moniliformis). Three genera of ciliates (Coleps, Strobilidium, and Strombidium) comprised the greater part of the planktonic protozoa in Crystal Bog. The number of species of planktonic protozoa was too low to calculate a diversity index. Shannon-Weaver diversity indices for phytoplankton and bacterioplankton in the epilimnion
Babonis, Leslie S; Martindale, Mark Q
Communication among cells was paramount to the evolutionary increase in cell type diversity and, ultimately, the origin of large body size. Across the diversity of Metazoa, there are only few conserved cell signalling pathways known to orchestrate the complex cell and tissue interactions regulating development; thus, modification to these few pathways has been responsible for generating diversity during the evolution of animals. Here, we summarize evidence for the origin and putative function of the intracellular, membrane-bound and secreted components of seven metazoan cell signalling pathways with a special focus on early branching metazoans (ctenophores, poriferans, placozoans and cnidarians) and basal unikonts (amoebozoans, fungi, filastereans and choanoflagellates). We highlight the modular incorporation of intra- and extracellular components in each signalling pathway and suggest that increases in the complexity of the extracellular matrix may have further promoted the modulation of cell signalling during metazoan evolution. Most importantly, this updated view of metazoan signalling pathways highlights the need for explicit study of canonical signalling pathway components in taxa that do not operate a complete signalling pathway. Studies like these are critical for developing a deeper understanding of the evolution of cell signalling.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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.
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.
Thaler, Mary; Lovejoy, Connie
Heterotrophic marine flagellates (HF) are ubiquitous in the world's oceans and represented in nearly all branches of the domain Eukaryota. However, the factors determining distributions of major taxonomic groups are poorly known. The Arctic Ocean is a good model environment for examining the distribution of functionally similar but phylogenetically diverse HF because the physical oceanography and annual ice cycles result in distinct environments that could select for microbial communities or favor specific taxa. We reanalyzed new and previously published high-throughput sequencing data from multiple studies in the Arctic Ocean to identify broad patterns in the distribution of individual taxa. HF accounted for fewer than 2% to over one-half of the reads from the water column and for up to 60% of reads from ice, which was dominated by Cryothecomonas. In the water column, many HF phylotypes belonging to Telonemia and Picozoa, uncultured marine stramenopiles (MAST), and choanoflagellates were geographically widely distributed. However, for two groups in particular, Telonemia and Cryothecomonas, some species level taxa showed more restricted distributions. For example, several phylotypes of Telonemia favored open waters with lower nutrients such as the Canada Basin and offshore of the Mackenzie Shelf. In summary, we found that while some Arctic HF were successful over a range of conditions, others could be specialists that occur under particular conditions. We conclude that tracking species level diversity in HF not only is feasible but also provides a potential tool for understanding the responses of marine microbial ecosystems to rapidly changing ice regimes.
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.
McDonald, Kent L
A variety of specimens including bacteria, ciliates, choanoflagellates (Salpingoeca rosetta), zebrafish (Danio rerio) embryos, nematode worms (Caenorhabditis elegans), and leaves of white clover (Trifolium repens) plants were high pressure frozen, freeze-substituted, infiltrated with either Epon, Epon-Araldite, or LR White resins, and polymerized. Total processing time from freezing to blocks ready to section was about 6 h. For epoxy embedding the specimens were freeze-substituted in 1% osmium tetroxide plus 0.1% uranyl acetate in acetone. For embedding in LR White the freeze-substitution medium was 0.2% uranyl acetate in acetone. Rapid infiltration was achieved by centrifugation through increasing concentrations of resin followed by polymerization at 100°C for 1.5-2 h. The preservation of ultrastructure was comparable to standard freeze substitution and resin embedding methods that take days to complete. On-section immunolabeling results for actin and tubulin molecules were positive with very low background labeling. The LR White methods offer a safer, quicker, and less-expensive alternative to Lowicryl embedding of specimens processed for on-section immunolabeling without traditional aldehyde fixatives.
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.
Kiss, Aron Keve; Acs, Eva; Kiss, Keve Tihamér; Török, Júlia Katalin
Seasonal dynamics of all major protozoan groups were investigated in the plankton of the River Danube, upstream of Budapest (Hungary), by bi-weekly sampling over a 1-year long period. Sixty-one heterotrophic flagellate, 14 naked amoeba, 50 testate amoeba, 4 heliozoan and 83 ciliate morphospecies were identified. The estimated abundance ranges of major groups throughout the year were as follows: heterotrophic flagellates, 0.27-7.8 x 10(6)ind.l(-1); naked amoebae, max. 3300ind.l(-1); testaceans, max. 1600ind.l(-1); heliozoans, max. 8500ind.l(-1); ciliates, 132-34,000ind.l(-1). In terms of biovolume, heterotrophic flagellates dominated throughout the year (max. 0.58mm(3)l(-1)), and ciliates only exceeded their biovolume in summer (max. 0.76mm(3)l(-1)). Naked amoeba and heliozoan biovolume was about one, and testacean biovolume 1-3, orders of magnitude lower than that of ciliates. In winter, flagellates, mainly chrysomonads, had the highest biomass, whilst ciliates were dominated by peritrichs. In 2005 from April to July a long spring/summer peak occurred for all protozoan groups. Beside chrysomonads typical flagellates were choanoflagellates, bicosoecids and abundant microflagellates (large chrysomonads and Collodictyon). Most abundant ciliates were oligotrichs, while Phascolodon, Urotricha, Vorticella, haptorids, Suctoria, Climacostomum and Stokesia also contributed significantly to biovolume during rapid succession processes. In October and November a second high protozoan peak occurred, with flagellate dominance, and slightly different taxonomic composition.
Lang, B F; Seif, E; Gray, M W; O'Kelly, C J; Burger, G
The Organelle Genome Megasequencing Program (OGMP) investigates mitochondrial genome diversity and evolution by systematically determining the complete mitochondrial DNA (mtDNA) sequences of a phylogenetically broad selection of protists. The mtDNAs of lower fungi and choanoflagellates are being analyzed by the Fungal Mitochondrial Genome Project (FMGP), a sister project to the OGMP. Some of the most interesting protists include the jakobid flagellates Reclinomonas americana, Malawimonas jakobiformis, and Jakoba libera, which share ultrastructural similarities with amitochondriate retortamonads, and harbor mitochondrial genes not seen before in mtDNAs of other organisms. In R. americana and J. libera, gene clusters are found that resemble, to an unprecedented degree, the contiguous ribosomal protein operons str, S10, spc, and alpha of eubacteria. In addition, their mtDNAs code for an RNase P RNA that displays all the elements of a bacterial minimum consensus structure. This structure has been instrumental in detecting the rnpB gene in additional protists. Gene repertoire and gene order comparisons as well as multiple-gene phylogenies support the view of a single endosymbiotic origin of mitochondria, whose closest extant relatives are Rickettsia-type alpha-Proteobacteria.
Full Text Available Abstract Background Coronins belong to the superfamily of the eukaryotic-specific WD40-repeat proteins and play a role in several actin-dependent processes like cytokinesis, cell motility, phagocytosis, and vesicular trafficking. Two major types of coronins are known: First, the short coronins consisting of an N-terminal coronin domain, a unique region and a short coiled-coil region, and secondly the tandem coronins comprising two coronin domains. Results 723 coronin proteins from 358 species have been identified by analyzing the whole-genome assemblies of all available sequenced eukaryotes (March 2011. The organisms analyzed represent most eukaryotic kingdoms but also cover every taxon several times to provide a better statistical sampling. The phylogenetic tree of the coronin domains based on the Bayesian method is in accordance with the most recent grouping of the major kingdoms of the eukaryotes and also with the grouping of more recently separated branches. Based on this "holistic" approach the coronins group into four classes: class-1 (Type I and class-2 (Type II are metazoan/choanoflagellate specific classes, class-3 contains the tandem-coronins (Type III, and the new class-4 represents the coronins fused to villin (Type IV. Short coronins from non-metazoans are equally related to class-1 and class-2 coronins and thus remain unclassified. Conclusions The coronin class distribution suggests that the last common eukaryotic ancestor possessed a single and a tandem-coronin, and most probably a class-4 coronin of which homologs have been identified in Excavata and Opisthokonts although most of these species subsequently lost the class-4 homolog. The most ancient short coronin already contained the trimerization motif in the coiled-coil domain.
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 The C2H2 zinc finger (ZF domain is widely conserved among eukaryotic proteins. In Zic/Gli/Zap1 C2H2 ZF proteins, the two N-terminal ZFs form a single structural unit by sharing a hydrophobic core. This structural unit defines a new motif comprised of two tryptophan side chains at the center of the hydrophobic core. Because each tryptophan residue is located between the two cysteine residues of the C2H2 motif, we have named this structure the tandem CWCH2 (tCWCH2 motif. Results Here, we characterized 587 tCWCH2-containing genes using data derived from public databases. We categorized genes into 11 classes including Zic/Gli/Glis, Arid2/Rsc9, PacC, Mizf, Aebp2, Zap1/ZafA, Fungl, Zfp106, Twincl, Clr1, and Fungl-4ZF, based on sequence similarity, domain organization, and functional similarities. tCWCH2 motifs are mostly found in organisms belonging to the Opisthokonta (metazoa, fungi, and choanoflagellates and Amoebozoa (amoeba, Dictyostelium discoideum. By comparison, the C2H2 ZF motif is distributed widely among the eukaryotes. The structure and organization of the tCWCH2 motif, its phylogenetic distribution, and molecular phylogenetic analysis suggest that prototypical tCWCH2 genes existed in the Opisthokonta ancestor. Within-group or between-group comparisons of the tCWCH2 amino acid sequence identified three additional sequence features (site-specific amino acid frequencies, longer linker sequence between two C2H2 ZFs, and frequent extra-sequences within C2H2 ZF motifs. Conclusion These features suggest that the tCWCH2 motif is a specialized motif involved in inter-zinc finger interactions.
Josephine C. Adams
Full Text Available Basement membrane (BM extracellular matrices are crucial for the coordination of different tissue layers. A matrix adhesion receptor that is important for BM function and stability in many mammalian tissues is the dystroglycan (DG complex. This comprises the non-covalently-associated extracellular α-DG, that interacts with laminin in the BM, and the transmembrane β-DG, that interacts principally with dystrophin to connect to the actin cytoskeleton. Mutations in dystrophin, DG, or several enzymes that glycosylate α-DG underlie severe forms of human muscular dystrophy. Nonwithstanding the pathophysiological importance of the DG complex and its fundamental interest as a non-integrin system of cell-ECM adhesion, the evolution of DG and its interacting proteins is not understood. We analysed the phylogenetic distribution of DG, its proximal binding partners and key processing enzymes in extant metazoan and relevant outgroups. We identify that DG originated after the divergence of ctenophores from porifera and eumetazoa. The C-terminal half of the DG core protein is highly-conserved, yet the N-terminal region, that includes the laminin-binding region, has undergone major lineage-specific divergences. Phylogenetic analysis based on the C-terminal IG2_MAT_NU region identified three distinct clades corresponding to deuterostomes, arthropods, and mollusks/early-diverging metazoans. Whereas the glycosyltransferases that modify α-DG are also present in choanoflagellates, the DG-binding proteins dystrophin and laminin originated at the base of the metazoa, and DG-associated sarcoglycan is restricted to cnidarians and bilaterians. These findings implicate extensive functional diversification of DG within invertebrate lineages and identify the laminin-DG-dystrophin axis as a conserved adhesion system that evolved subsequent to integrin-ECM adhesion, likely to enhance the functional complexity of cell-BM interactions in early metazoans.
Adams, Josephine C; Brancaccio, Andrea
Basement membrane (BM) extracellular matrices are crucial for the coordination of different tissue layers. A matrix adhesion receptor that is important for BM function and stability in many mammalian tissues is the dystroglycan (DG) complex. This comprises the non-covalently-associated extracellular α-DG, that interacts with laminin in the BM, and the transmembrane β-DG, that interacts principally with dystrophin to connect to the actin cytoskeleton. Mutations in dystrophin, DG, or several enzymes that glycosylate α-DG underlie severe forms of human muscular dystrophy. Nonwithstanding the pathophysiological importance of the DG complex and its fundamental interest as a non-integrin system of cell-ECM adhesion, the evolution of DG and its interacting proteins is not understood. We analysed the phylogenetic distribution of DG, its proximal binding partners and key processing enzymes in extant metazoan and relevant outgroups. We identify that DG originated after the divergence of ctenophores from porifera and eumetazoa. The C-terminal half of the DG core protein is highly-conserved, yet the N-terminal region, that includes the laminin-binding region, has undergone major lineage-specific divergences. Phylogenetic analysis based on the C-terminal IG2_MAT_NU region identified three distinct clades corresponding to deuterostomes, arthropods, and mollusks/early-diverging metazoans. Whereas the glycosyltransferases that modify α-DG are also present in choanoflagellates, the DG-binding proteins dystrophin and laminin originated at the base of the metazoa, and DG-associated sarcoglycan is restricted to cnidarians and bilaterians. These findings implicate extensive functional diversification of DG within invertebrate lineages and identify the laminin-DG-dystrophin axis as a conserved adhesion system that evolved subsequent to integrin-ECM adhesion, likely to enhance the functional complexity of cell-BM interactions in early metazoans.
Suga, Hiroshi; Torruella, Guifré; Burger, Gertraud; Brown, Matthew W.; Ruiz-Trillo, Iñaki
Phosphotyrosine (pTyr) signaling is involved in development and maintenance of metazoans’ multicellular body through cell-to-cell communication. Tyrosine kinases (TKs), tyrosine phosphatases, and other proteins relaying the signal compose the cascade. Domain architectures of the pTyr signaling proteins are diverse in metazoans, reflecting their complex intercellular communication. Previous studies had shown that the metazoan-type TKs, as well as other pTyr signaling proteins, were already diversified in the common ancestor of metazoans, choanoflagellates, and filastereans (which are together included in the clade Holozoa) whereas they are absent in fungi and other nonholozoan lineages. However, the earliest-branching holozoans Ichthyosporea and Corallochytrea, as well as the two fungi-related amoebae Fonticula and Nuclearia, have not been studied. Here, we analyze the complete genome sequences of two ichthyosporeans and Fonticula, and RNAseq data of three additional ichthyosporeans, one corallochytrean, and Nuclearia. Both the ichthyosporean and corallochytrean genomes encode a large variety of receptor TKs (RTKs) and cytoplasmic TKs (CTKs), as well as other pTyr signaling components showing highly complex domain architectures. However, Nuclearia and Fonticula have no TK, and show much less diversity in other pTyr signaling components. The CTK repertoires of both Ichthyosporea and Corallochytrea are similar to those of Metazoa, Choanoflagellida, and Filasterea, but the RTK sets are totally different from each other. The complex pTyr signaling equipped with positive/negative feedback mechanism likely emerged already at an early stage of holozoan evolution, yet keeping a high evolutionary plasticity in extracellular signal reception until the co-option of the system for cell-to-cell communication in metazoans. PMID:24307687
Arendt, Detlev; Benito-Gutierrez, Elia; Brunet, Thibaut; Marlow, Heather
Prerequisite for tracing nervous system evolution is understanding of the body plan, feeding behaviour and locomotion of the first animals in which neurons evolved. Here, a comprehensive scenario is presented for the diversification of cell types in early metazoans, which enhanced feeding efficiency and led to the emergence of larger animals that were able to move. Starting from cup-shaped, gastraea-like animals with outer and inner choanoflagellate-like cells, two major innovations are discussed that set the stage for nervous system evolution. First, the invention of a mucociliary sole entailed a switch from intra- to extracellular digestion and increased the concentration of nutrients flowing into the gastric cavity. In these animals, an initial nerve net may have evolved via division of labour from mechanosensory-contractile cells in the lateral body wall, enabling coordinated movement of the growing body that involved both mucociliary creeping and changes of body shape. Second, the inner surface of the animals folded into metameric series of gastric pouches, which optimized nutrient resorption and allowed larger body sizes. The concomitant acquisition of bilateral symmetry may have allowed more directed locomotion and, with more demanding coordinative tasks, triggered the evolution of specialized nervous subsystems. Animals of this organizational state would have resembled Ediacarian fossils such as Dickinsonia and may have been close to the cnidarian-bilaterian ancestor. In the bilaterian lineage, the mucociliary sole was used mostly for creeping, or frequently lost. One possible remnant is the enigmatic Reissner's fibre in the ventral neural tube of cephalochordates and vertebrates.
Piasecki, Brian P; Burghoorn, Jan; Swoboda, Peter
Cilia were present in the last eukaryotic common ancestor (LECA) and were retained by most organisms spanning all extant eukaryotic lineages, including organisms in the Unikonta (Amoebozoa, fungi, choanoflagellates, and animals), Archaeplastida, Excavata, Chromalveolata, and Rhizaria. In certain animals, including humans, ciliary gene regulation is mediated by Regulatory Factor X (RFX) transcription factors (TFs). RFX TFs bind X-box promoter motifs and thereby positively regulate >50 ciliary genes. Though RFX-mediated ciliary gene regulation has been studied in several bilaterian animals, little is known about the evolutionary conservation of ciliary gene regulation. Here, we explore the evolutionary relationships between RFX TFs and cilia. By sampling the genome sequences of >120 eukaryotic organisms, we show that RFX TFs are exclusively found in unikont organisms (whether ciliated or not), but are completely absent from the genome sequences of all nonunikont organisms (again, whether ciliated or not). Sampling the promoter sequences of 12 highly conserved ciliary genes from 23 diverse unikont and nonunikont organisms further revealed that phylogenetic footprints of X-box promoter motif sequences are found exclusively in ciliary genes of certain animals. Thus, there is no correlation between cilia/ciliary genes and the presence or absence of RFX TFs and X-box promoter motifs in nonanimal unikont and in nonunikont organisms. These data suggest that RFX TFs originated early in the unikont lineage, distinctly after cilia evolved. The evolutionary model that best explains these observations indicates that the transcriptional rewiring of many ciliary genes by RFX TFs occurred early in the animal lineage.
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
Cavalier-Smith, Thomas; Chao, Ema E-Y
The primary diversification of eukaryotes involved protozoa, especially zooflagellates-flagellate protozoa without plastids. Understanding the origins of the higher eukaryotic kingdoms (two purely heterotrophic, Animalia and Fungi, and two primarily photosynthetic, Plantae and Chromista) depends on clarifying evolutionary relationships among the phyla of the ancestral kingdom Protozoa. We therefore sequenced 18S rRNA genes from 10 strains from the protozoan phyla Choanozoa and Apusozoa. Eukaryote diversity is encompassed by three early-radiating, arguably monophyletic groups: Amoebozoa, opisthokonts, and bikonts. Our taxon-rich rRNA phylogeny for eukaryotes allowing for intersite rate variation strongly supports the opisthokont clade (animals, Choanozoa, Fungi). It agrees with the view that Choanozoa are sisters of or ancestral to animals and reveals a novel nonflagellate choanozoan lineage, Ministeriida, sister either to choanoflagellates, traditionally considered animal ancestors, or to animals. Maximum likelihood trees suggest that within animals Placozoa are derived from medusozoan Cnidaria (we therefore place Placozoa as a class within subphylum Medusozoa of the Cnidaria) and hexactinellid sponges evolved from demosponges. The bikont and amoebozoan radiations are both very ill resolved. Bikonts comprise the kingdoms Plantae and Chromista and three major protozoan groups: alveolates, excavates, and Rhizaria. Our analysis weakly suggests that Apusozoa, represented by Ancyromonas and the apusomonads ( Apusomonas and the highly diverse and much more ancient genus Amastigomonas, from which it evolved), are not closely related to other Rhizaria and may be the most divergent bikont lineages. Although Ancyromonas and apusomonads appear deeply divergent in 18S rRNA trees, the trees neither refute nor support the monophyly of Apusozoa. The bikont phylum Cercozoa weakly but consistently appears as sister to Retaria (Foraminifera; Radiolaria), together forming a hitherto
Full Text Available Abstract Background The aquiferous body plan of poriferans revolves around internal chambers comprised of choanocytes, a cell type structurally similar to choanoflagellates. These choanocyte chambers perform a range of physiological and developmental functions, including the capture of food and the generation of stem cells. Despite the increasing interest for choanocytes as sponge stem cells, there is limited knowledge on the development of choanocyte chambers. Using a combination of cell lineage tracing, antibody staining and EdU labeling, here we examine the development of choanocytes and the chambers they comprise during metamorphosis in the marine demosponge Amphimedon queenslandica. Results Lineage-tracing experiments show that larval epithelial cells transform into mesenchymal pluripotent stem cells, resembling archeocytes, within 24 h of initiating metamorphosis. By 36 h, some of these labeled archeocyte-like cells have differentiated into choanocytes that will form the first postlarval choanocyte chambers. Non-labeled cells also contribute to these primary choanocyte chambers, consistent with these chambers being a chimera of multiple transdifferentiated larval cell types and not the proliferation of a single choanocyte precursor. Moreover, cell proliferation assays demonstrate that, following the initial formation of choanocyte chambers, chambers grow at least partially by the proliferation of choanocytes within the chamber, although recruitment of individual cells into established chambers also appears to occur. EdU labeling of postlarvae and juveniles reveals that choanocyte chambers are the primary location of cell proliferation during metamorphosis. Conclusion Our results show that multiple larval cell lineages typically contribute to formation of individual choanocyte chambers at metamorphosis, contrary to previous reports in other species that show sponge choanocyte chambers form clonally. Choanocytes in postlarval and juvenile
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
张晓妍; 安利国; 杨桂文
The innate immune system is the first defense against the microorganisms in all metazoans. Akirin, as a new nuclear factor which discovered in the innate immune response of Drosophila melanogaster, plays a critical role in the immune deficiency (Imd) pathway. Akirin proto-orthologue gene exists in a wide range of metazoans from Choanoflagellates, Drosophila to mammals and its sequences are highly conserved. In the Imd pathway of Drosophila and the Toll pathway of vertebrates, Akirin combining with the transcription factor NF-κB can modulate the transcription of target genes. Besides, Akirin's overexpression and knockout influence animals' defense ability against bacteria. Recently, some progress has been made in the immune-related signaling pathway of Akirin.This article will summarize its structure, function, regulatory mechanisms and evolution.%天然免疫系统是多细胞动物抵御细菌感染的第一道防线.Akirin是新近发现于果蝇中的天然免疫系统新成员,它在果蝇免疫缺陷(Imd)通路中发挥重要作用.Akirin同源基因广泛存在于从低等多细胞生物到高等脊椎动物中,进化上高度保守.已有的研究表明:Akirin在果蝇Imd通路和脊椎动物TLR通路下游,与NF-κB家族转录因子形成复合物,参与调控免疫相关靶基因的转录,是天然免疫调控机制中不可或缺的转录因子,其过表达或缺失直接影响动物对细菌的防御能力.近年来,Akirin在相关信号通路中的功能研究取得重大进展.该文对Akirin的结构、参与天然免疫的分子调控机制以及基因进化等方面进行综述.
靳春艳; 盛自章; 黄京飞
DNA连接酶Ⅲ被认为只存在于脊椎动物,并在细胞核DNA的修复和线粒体DNA的复制和修复过程中发挥功能.虽然近来有关于无脊椎动物中存在着DNA连接酶Ⅲ的报道,但其功能演化及在无脊椎动物中的分布仍不清楚.为进一步探讨DNA连接酶Ⅲ的功能演化,进行了数据库搜索、线粒体定位信号(MLS)预测和功能位点保守性分析等.研究结果显示:DNA连接酶Ⅲ在变形虫、动物界和领鞭毛虫中广泛存在,但其在真菌界等发生整个蛋白或部分结构域的丢失；很多物种的DNA连接酶Ⅲ不含线粒体定位信号,因此,它们不太可能在线粒体中发挥作用,而参与细胞核DNA的修复是DNA连接酶Ⅲ较为古老和保守的功能.%Previous studies revealed that DNA ligase III was restricted to vertebrates and functioned in nucleus DNA repair and mitochondria DNA replication and repair. Although recent researches have reported that DNA ligase m is also found in non-vertebrates, little attention has been devoted to the distribution and functional evolution of DNA ligase III. To probe the functional evolution of DNA ligase III , database searches, mitochondrial localization signal prediction (MLS) and functional conservation analysis were performed. The results show that, DNA ligase III can be observed in amoebozoa, metazoa and choanoflagellates, but the whole protein or some domains are lost in some species including fungi. The MLS prediction analysis suggests that, the DNA ligase III in many species can not function in mitochondria, and is consequently less likely to play a role for DNA ligase III in mitochondria. The conservation analyses of functional site demonstrate that nucleus DNA repair is an ancient and conserved function of DNA ligase III.
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
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
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