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Evgeny Sagulenko - One of the best experts on this subject based on the ideXlab platform.
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towards understanding the molecular mechanism of the endocytosis like process in the bacterium gemmata obscuriglobus
Biochimica et Biophysica Acta, 2014Co-Authors: John A. Fuerst, Evgeny SagulenkoAbstract:An endocytosis-like process of protein uptake in the planctomycete Gemmata obscuriglobus is a recently discovered process unprecedented in the bacterial world. The molecular mechanisms underlying this process are not yet characterized. A homolog of the MC (membrane-coating) proteins of Eukaryotes has been proposed to be involved in the mechanism of this process, but its relationship to Eukaryote proteins is controversial. However, a number of other proteins of G. obscuriglobus with domains homologous to those involved in endocytosis in Eukaryotes can also be identified. Here we critically evaluate current bioinformatic knowledge, and suggest practical experimental steps to overcome the limits of bioinformatics in elucidating the molecular mechanism of endocytosis in bacteria. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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towards understanding the molecular mechanism of the endocytosis like process in the bacterium gemmata obscuriglobus
Biochimica et Biophysica Acta, 2014Co-Authors: John A. Fuerst, Evgeny SagulenkoAbstract:An endocytosis-like process of protein uptake in the planctomycete Gemmata obscuriglobus is a recently discovered process unprecedented in the bacterial world. The molecular mechanisms underlying this process are not yet characterized. A homolog of the MC (membrane-coating) proteins of Eukaryotes has been proposed to be involved in the mechanism of this process, but its relationship to Eukaryote proteins is controversial. However, a number of other proteins of G. obscuriglobus with domains homologous to those involved in endocytosis in Eukaryotes can also be identified. Here we critically evaluate current bioinformatic knowledge, and suggest practical experimental steps to overcome the limits of bioinformatics in elucidating the molecular mechanism of endocytosis in bacteria. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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planctomycetes their evolutionary implications for models for origins of Eukaryotes and the Eukaryote nucleus and endomembranes
2013Co-Authors: John A. Fuerst, Evgeny SagulenkoAbstract:Planctomycetes and their relatives in the PVC superphylum have significant implications for evolution of the diversity of bacterial and eukaryotic cell organisation. The compartmentalisation via internal membranes of an underlying plan shared by planctomycetes and by members of phyla Verrucomicrobia and Lentisphaerae within the PVC superphylum implies phylogenetic meaning to such structure. It is likely that the common ancestor of PVC superphylum members possessed such compartmentalisation. Compartmentalisation in PVC bacteria, especially within the Gemmata clade where the nucleoid is bounded by an envelope of two membranes, has implications for theories of the origin of the eukaryotic nucleus, suggesting autogenous theories should be considered seriously as major alternatives to those depending on early fusions between Archaea and Bacteria domains. Explanations for the origin of PVC compartmentalisation are considered here, as well as their implications for molecular correlates of such compartmentalisation, and their correlates with an integrated cell biology that may be an analogue or even a homologue of an ancient Eukaryote cell biology. PVC bacteria can form major experimental models for exploring what such a cell biology might have looked like.
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keys to eukaryality planctomycetes and ancestral evolution of cellular complexity
Frontiers in Microbiology, 2012Co-Authors: John A. Fuerst, Evgeny SagulenkoAbstract:Planctomycetes are known to display compartmentalization via internal membranes, thus resembling Eukaryotes. Significantly, the planctomycete Gemmata obscuriglobus has not only a nuclear region surrounded by a double-membrane, but is also capable of protein uptake via endocytosis. In order to clearly analyse implications for homology of their characters with Eukaryotes, a correct understanding of planctomycete structure is an essential starting point. Here we outline the major features of such structure necessary for assessing the case for or against homology with Eukaryote cell complexity. We consider an evolutionary model for cell organization involving reductive evolution of planctomycetes from a complex protoEukaryote-like LUCA ancestor, and evaluate alternative models for origins of the unique planctomycete cell plan. Overall, the structural and molecular evidence is not consistent with convergent evolution of Eukaryote-like features in a bacterium and favours a homologous relationship of planctomycetes and Eukaryotes
John A. Fuerst - One of the best experts on this subject based on the ideXlab platform.
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towards understanding the molecular mechanism of the endocytosis like process in the bacterium gemmata obscuriglobus
Biochimica et Biophysica Acta, 2014Co-Authors: John A. Fuerst, Evgeny SagulenkoAbstract:An endocytosis-like process of protein uptake in the planctomycete Gemmata obscuriglobus is a recently discovered process unprecedented in the bacterial world. The molecular mechanisms underlying this process are not yet characterized. A homolog of the MC (membrane-coating) proteins of Eukaryotes has been proposed to be involved in the mechanism of this process, but its relationship to Eukaryote proteins is controversial. However, a number of other proteins of G. obscuriglobus with domains homologous to those involved in endocytosis in Eukaryotes can also be identified. Here we critically evaluate current bioinformatic knowledge, and suggest practical experimental steps to overcome the limits of bioinformatics in elucidating the molecular mechanism of endocytosis in bacteria. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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towards understanding the molecular mechanism of the endocytosis like process in the bacterium gemmata obscuriglobus
Biochimica et Biophysica Acta, 2014Co-Authors: John A. Fuerst, Evgeny SagulenkoAbstract:An endocytosis-like process of protein uptake in the planctomycete Gemmata obscuriglobus is a recently discovered process unprecedented in the bacterial world. The molecular mechanisms underlying this process are not yet characterized. A homolog of the MC (membrane-coating) proteins of Eukaryotes has been proposed to be involved in the mechanism of this process, but its relationship to Eukaryote proteins is controversial. However, a number of other proteins of G. obscuriglobus with domains homologous to those involved in endocytosis in Eukaryotes can also be identified. Here we critically evaluate current bioinformatic knowledge, and suggest practical experimental steps to overcome the limits of bioinformatics in elucidating the molecular mechanism of endocytosis in bacteria. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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planctomycetes their evolutionary implications for models for origins of Eukaryotes and the Eukaryote nucleus and endomembranes
2013Co-Authors: John A. Fuerst, Evgeny SagulenkoAbstract:Planctomycetes and their relatives in the PVC superphylum have significant implications for evolution of the diversity of bacterial and eukaryotic cell organisation. The compartmentalisation via internal membranes of an underlying plan shared by planctomycetes and by members of phyla Verrucomicrobia and Lentisphaerae within the PVC superphylum implies phylogenetic meaning to such structure. It is likely that the common ancestor of PVC superphylum members possessed such compartmentalisation. Compartmentalisation in PVC bacteria, especially within the Gemmata clade where the nucleoid is bounded by an envelope of two membranes, has implications for theories of the origin of the eukaryotic nucleus, suggesting autogenous theories should be considered seriously as major alternatives to those depending on early fusions between Archaea and Bacteria domains. Explanations for the origin of PVC compartmentalisation are considered here, as well as their implications for molecular correlates of such compartmentalisation, and their correlates with an integrated cell biology that may be an analogue or even a homologue of an ancient Eukaryote cell biology. PVC bacteria can form major experimental models for exploring what such a cell biology might have looked like.
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keys to eukaryality planctomycetes and ancestral evolution of cellular complexity
Frontiers in Microbiology, 2012Co-Authors: John A. Fuerst, Evgeny SagulenkoAbstract:Planctomycetes are known to display compartmentalization via internal membranes, thus resembling Eukaryotes. Significantly, the planctomycete Gemmata obscuriglobus has not only a nuclear region surrounded by a double-membrane, but is also capable of protein uptake via endocytosis. In order to clearly analyse implications for homology of their characters with Eukaryotes, a correct understanding of planctomycete structure is an essential starting point. Here we outline the major features of such structure necessary for assessing the case for or against homology with Eukaryote cell complexity. We consider an evolutionary model for cell organization involving reductive evolution of planctomycetes from a complex protoEukaryote-like LUCA ancestor, and evaluate alternative models for origins of the unique planctomycete cell plan. Overall, the structural and molecular evidence is not consistent with convergent evolution of Eukaryote-like features in a bacterium and favours a homologous relationship of planctomycetes and Eukaryotes
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a canonical ftsz protein in verrucomicrobium spinosum a member of the bacterial phylum verrucomicrobia that also includes tubulin producing prosthecobacter species
BMC Evolutionary Biology, 2007Co-Authors: Benjamin Yee, James T. Staley, Feras F Lafi, Brian B Oakley, John A. FuerstAbstract:Background The origin and evolution of the homologous GTP-binding cytoskeletal proteins FtsZ typical of Bacteria and tubulin characteristic of Eukaryotes is a major question in molecular evolutionary biology. Both FtsZ and tubulin are central to key cell biology processes – bacterial septation and cell division in the case of FtsZ and in the case of tubulins the function of microtubules necessary for mitosis and other key cytoskeleton-dependent processes in Eukaryotes. The origin of tubulin in particular is of significance to models for Eukaryote origins. Most members of domain Bacteria possess FtsZ, but bacteria in genus Prosthecobacter of the phylum Verrucomicrobia form a key exception, possessing tubulin homologs BtubA and BtubB. It is therefore of interest to know whether other members of phylum Verrucomicrobia possess FtsZ or tubulin as their FtsZ-tubulin gene family representative.
Didier Debroas - One of the best experts on this subject based on the ideXlab platform.
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Succession and regulation factors of small Eukaryote community composition in a lacustrine ecosystem (Lake Pavin)
Applied and Environmental Microbiology, 2006Co-Authors: Cecile Lepere, Delphine Boucher, Ludwig Jardillier, Isabelle Domaizon, Didier DebroasAbstract:The structure and dynamics of small Eukaryotes (cells with a diameter less than 5 microm) were studied over two consecutive years in an oligomesotrophic lake (Lake Pavin in France). Water samples were collected at 5 and 30 m below the surface; when the lake was stratified, these depths corresponded to the epilimnion and hypolimnion. Changes in small-Eukaryote structure were analyzed using terminal restriction fragment length polymorphism (T-RFLP) and cloning and sequencing of the 18S rRNA genes. Terminal restriction fragments from clones were used to reveal the dominant taxa in T-RFLP profiles of the environmental samples. Spumella-like cells (Chrysophyceae) did not dominate the small Eukaryote community identified by molecular techniques in lacustrine ecosystems. Small Eukaryotes appeared to be dominated by heterotrophic cells, particularly Cercozoa, which represented nearly half of the identified phylotypes, followed by the Fungi-LKM11 group (25%), choanoflagellates (10.3%) and Chrysophyceae (8.9%). Bicosoecida, Cryptophyta, and ciliates represented less than 9% of the community studied. No seasonal reproducibility in temporal evolution of the small-Eukaryote community was observed from 1 year to the next. The T-RFLP patterns were related to bottom-up (resources) and top-down (grazing) variables using canonical correspondence analysis. The results showed a strong top-down regulation of small Eukaryotes by zooplankton, more exactly, by cladocerans at 5 m and copepods at 30 m. Among bottom-up factors, temperature had a significant effect at both depths. The concentrations of nitrogenous nutrients and total phosphorus also had an effect on small-Eukaryote dynamics at 5 m, whereas bacterial abundance and dissolved oxygen played a more important structuring role in the deeper zone.
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genetic diversity of small Eukaryotes in lakes differing by their trophic status
Applied and Environmental Microbiology, 2005Co-Authors: Marie Lefranc, Cecile Lepere, Aurelie Thenot, Didier DebroasAbstract:Small Eukaryotes, cells with a diameter of less than 5 μm, are fundamental components of lacustrine planktonic systems. In this study, small-Eukaryote diversity was determined by sequencing cloned 18S rRNA genes in three libraries from lakes of differing trophic status in the Massif Central, France: the oligotrophic Lake Godivelle, the oligomesotrophic Lake Pavin, and the eutrophic Lake Aydat. This analysis shows that the least diversified library was in the eutrophic lake (12 operational taxonomic units [OTUs]) and the most diversified was in the oligomesotrophic lake (26 OTUs). Certain groups were present in at least two ecosystems, while the others were specific to one lake on the sampling date. Cryptophyta, Chrysophyceae, and the strictly heterotrophic Eukaryotes, Ciliophora and fungi, were identified in the three libraries. Among the small Eukaryotes found only in two lakes, Choanoflagellida and environmental sequences (LKM11) were not detected in the eutrophic system whereas Cercozoa were confined to the oligomesotrophic and eutrophic lakes. Three OTUs, linked to the Perkinsozoa, were detected only in the Aydat library, where they represented 60% of the clones of the library. Chlorophyta and Haptophyta lineages were represented by a single clone and were present only in Godivelle and Pavin, respectively. Of the 127 clones studied, classical pigmented organisms (autotrophs and mixotrophs) represented only a low proportion regardless of the library's origin. This study shows that the small-Eukaryote community composition may differ as a function of trophic status; certain lineages could be detected only in a single ecosystem.
Richard Cordaux - One of the best experts on this subject based on the ideXlab platform.
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Viruses as vectors of horizontal transfer of genetic material in Eukaryotes.
Current Opinion in Virology, 2017Co-Authors: Clément Gilbert, Richard CordauxAbstract:Horizontal transfer (HT) of genetic material, mainly transposable elements, is increasingly recognized as an important factor shaping Eukaryote genomes. Yet our understanding of the mechanisms and vectors underpinning these transfers is still limited. It has been proposed that such transfers may be facilitated by viruses, because they typically inject their genomes into host cells to replicate and they can be horizontally transmitted between their hosts. Recent evidence from high throughput sequencing of viral populations and paleovirology shows that both virus-to-host and host-to-virus gene flow can be common in a variety of Eukaryote lineages. We argue that such studies reinforce the hypothesis of viruses as major vectors of HT in Eukaryotes.
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population genomics supports baculoviruses as vectors of horizontal transfer of insect transposons
Nature Communications, 2014Co-Authors: Clément Gilbert, Aurélien Chateigner, Lise Ernenwein, Valérie Barbe, Annie Bézier, Elisabeth A Herniou, Richard CordauxAbstract:Horizontal transfer (HT) of DNA is an important factor shaping Eukaryote evolution. Although several hundreds of Eukaryote-to-Eukaryote HTs of transposable elements (TEs) have been reported, the vectors underlying these transfers remain elusive. Here, we show that multiple copies of two TEs from the cabbage looper (Trichoplusia ni) transposed in vivo into genomes of the baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) during caterpillar infection. We further demonstrate that both TEs underwent recent HT between several sympatric moth species (T. ni, Manduca sexta, Helicoverpa spp.) showing different degrees of susceptibility to AcMNPV. Based on two independent population genomics data sets (reaching a total coverage >330,000X), we report a frequency of one moth TE in ~8,500 AcMNPV genomes. Together, our results provide strong support for the role of viruses as vectors of TE HT between animals, and they call for a systematic evaluation of the frequency and impact of virus-mediated HT on the evolution of host genomes. Horizontal transfer of DNA is common among Eukaryotes but the vectors involved remain elusive. Here, Gilbert et al. show high frequency of in vivotransposition from the cabbage looper moth into genomes of a baculovirus, suggesting that viruses can act as vectors of horizontal transfer between animals.
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horizontal transfer and evolution of prokaryote transposable elements in Eukaryotes
Genome Biology and Evolution, 2013Co-Authors: Clément Gilbert, Richard CordauxAbstract:Horizontal transfer (HT) of transposable elements (TEs) plays a key role in prokaryotic evolution, and mounting evidence suggests that it has also had an important impact on eukaryotic evolution. Although many prokaryote-to-prokaryote and Eukaryote-to-Eukaryote HTs of TEs have been characterized, only few cases have been reported between prokaryotes and Eukaryotes. Here, we carried out a comprehensive search for all major groups of prokaryotic insertion sequences (ISs) in 430 Eukaryote genomes. We uncovered a total of 80 sequences, all deriving from the IS607 family, integrated in the genomes of 14 Eukaryote species belonging to four distinct phyla (Amoebozoa, Ascomycetes, Basidiomycetes, and Stramenopiles). Given that Eukaryote IS607-like sequences are most closely related to cyanobacterial IS607 and that their phylogeny is incongruent with that of their hosts, we conclude that the presence of IS607-like sequences in eukaryotic genomes is the result of several HT events. Selection analyses further suggest that our ability to detect these prokaryote TEs today in Eukaryotes is because HT of these sequences occurred recently and/or some IS607 elements were domesticated after HT, giving rise to new Eukaryote genes. Supporting the recent age of some of these HTs, we uncovered intact full-length, potentially active IS607 copies in the amoeba Acanthamoeba castellani. Overall, our study shows that prokaryote-to-Eukaryote HT of TEs occurred at relatively low frequency during recent Eukaryote evolution and it sets IS607 as the most widespread TE (being present in prokaryotes, Eukaryotes, and viruses).
Patricia J. Johnson - One of the best experts on this subject based on the ideXlab platform.
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a metazoan plant like capping enzyme and cap modified nucleotides in the unicellular Eukaryote trichomonas vaginalis
PLOS Pathogens, 2010Co-Authors: Augusto Simoesbarbosa, Robert P. Hirt, Patricia J. JohnsonAbstract:The cap structure of eukaryotic messenger RNAs is initially elaborated through three enzymatic reactions: hydrolysis of the 5′-triphosphate, transfer of guanosine through a 5′-5′ triphosphate linkage and N7-methylation of the guanine cap. Three distinctive enzymes catalyze each reaction in various microbial Eukaryotes, whereas the first two enzymes are fused into a single polypeptide in metazoans and plants. In addition to the guanosine cap, adjacent nucleotides are 2′-O-ribose methylated in metazoa and plants, but not in yeast. Analyses of various cap structures have suggested a linear phylogenetic trend of complexity. These findings have led to a model in which plants and metazoa evolved a two-component capping apparatus and modification of adjacent nucleotides while many microbial Eukaryotes maintained the three-component system and did not develop modification of adjacent nucleotides. Here, we have characterized a bifunctional capping enzyme in the divergent microbial Eukaryote Trichomonas vaginalis using biochemical and phylogenetic analyses. This unicellular parasite was found to harbor a metazoan/plant-like capping apparatus that is represented by a two-domain polypeptide containing a C-terminus guanylyltransferase and a cysteinyl phosphatase triphosphatase, distinct from its counterpart in other microbial Eukaryotes. In addition, T. vaginalis mRNAs contain a cap 1 structure represented by m7GpppAmpUp or m7GpppCmpUp; a feature typical of metazoan and plant mRNAs but absent in yeast mRNAs. Phylogenetic and biochemical analyses of the origin of the T. vaginalis capping enzyme suggests a complex evolutionary model where differential gene loss and/or acquisition occurred in the development of the RNA capping apparatus and cap modified nucleotides during Eukaryote diversification.
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Genetic evidence for a mitochondriate ancestry in the 'amitochondriate' flagellate Trimastix pyriformis.
PLOS ONE, 2008Co-Authors: Vladimír Hampl, Patricia J. Johnson, Jeffrey D. Silberman, Alexandra Stechmann, Sara Diaz-trivino, Andrew J. RogerAbstract:Most modern Eukaryotes diverged from a common ancestor that contained the α-proteobacterial endosymbiont that gave rise to mitochondria. The ‘amitochondriate’ anaerobic protist parasites that have been studied to date, such as Giardia and Trichomonas harbor mitochondrion-related organelles, such as mitosomes or hydrogenosomes. Yet there is one remaining group of mitochondrion-lacking flagellates known as the Preaxostyla that could represent a primitive ‘pre-mitochondrial’ lineage of Eukaryotes. To test this hypothesis, we conducted an expressed sequence tag (EST) survey on the preaxostylid flagellate Trimastix pyriformis, a poorly-studied free-living anaerobe. Among the ESTs we detected 19 proteins that, in other Eukaryotes, typically function in mitochondria, hydrogenosomes or mitosomes, 12 of which are found exclusively within these organelles. Interestingly, one of the proteins, aconitase, functions in the tricarboxylic acid cycle typical of aerobic mitochondria, whereas others, such as pyruvate:ferredoxin oxidoreductase and [FeFe] hydrogenase, are characteristic of anaerobic hydrogenosomes. Since Trimastix retains genetic evidence of a mitochondriate ancestry, we can now say definitively that all known living Eukaryote lineages descend from a common ancestor that had mitochondria.
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spliceosomal introns in the deep branching Eukaryote trichomonas vaginalis
Proceedings of the National Academy of Sciences of the United States of America, 2005Co-Authors: Stěpanka Vaňacova, Weihong Yan, Jane M Carlton, Patricia J. JohnsonAbstract:Eukaryotes have evolved elaborate splicing mechanisms to remove introns that would otherwise destroy the protein-coding capacity of genes. Nuclear premRNA splicing requires sequence motifs in the intron and is mediated by a ribonucleoprotein complex, the spliceosome. Here we demonstrate the presence of a splicing apparatus in the protist Trichomonas vaginalis and show that RNA motifs found in yeast and metazoan introns are required for splicing. We also describe the first introns in this deep-branching lineage. The positions of these introns are often conserved in orthologous genes, indicating they were present in a common ancestor of trichomonads, yeast, and metazoa. All examined T. vaginalis introns have a highly conserved 12-nt 3′ splice-site motif that encompasses the branch point and is necessary for splicing. This motif is also found in the only described intron in a gene from another deep-branching Eukaryote, Giardia intestinalis. These studies demonstrate the conservation of intron splicing signals across large evolutionary distances, reveal unexpected motif conservation in deep-branching lineages that suggest a simplified mechanism of splicing in primitive unicellular Eukaryotes, and support the presence of introns in the earliest Eukaryote.
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analysis of a ubiquitous promoter element in a primitive Eukaryote early evolution of the initiator element
Molecular and Cellular Biology, 1999Co-Authors: David R Liston, Patricia J. JohnsonAbstract:Typical metazoan core promoter elements, such as TATA boxes and Inr motifs, have yet to be identified in early-evolving Eukaryotes, underscoring the extensive divergence of these organisms. Towards the identification of core promoters in protists, we have studied transcription of protein-encoding genes in one of the earliest-diverging lineages of Eukaryota, that represented by the parasitic protist Trichomonas vaginalis. A highly conserved element, comprised of a motif similar to a metazoan initiator (Inr) element, surrounds the start site of transcription in all examined T. vaginalis genes. In contrast, a metazoan-like TATA element appears to be absent in trichomonad promoters. We demonstrate that the conserved motif found in T. vaginalis protein-encoding genes is an Inr promoter element. This trichomonad Inr is essential for transcription, responsible for accurate start site selection, and interchangeable between genes, demonstrating its role as a core promoter element. The sequence requirements of the trichomonad Inr are similar to metazoan Inrs and can be replaced by a mammalian Inr. These studies show that the Inr is a ubiquitous, core promoter element for protein-encoding genes in an early-evolving Eukaryote. Functional and structural similarities between this protist Inr and the metazoan Inr strongly indicate that the Inr promoter element evolved early in eukaryotic evolution.