The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Jack A M Leunissen - One of the best experts on this subject based on the ideXlab platform.
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genealogy of the α crystallin small heat shock protein superfamily
International Journal of Biological Macromolecules, 1998Co-Authors: Wilfried W De Jong, Gertjan Caspers, Jack A M LeunissenAbstract:Sequences of 40 very diverse representatives of the alpha-crystallin-small heat-shock protein (alpha-Hsp) superfamily are compared. Their characteristic C-terminal 'alpha-crystallin domain' of 80-100 residues contains short consensus sequences that are highly conserved from prokaryotes to Eukaryotes. There are, in addition, some positions that clearly distinguish animal from non-animal alpha-Hsps. The alpha-crystallin domain is predicted to consist of two hydrophobic beta-sheet motifs, separated by a hydrophilic region which is variable in length. Combination of a conserved alpha-crystallin domain with a variable N-terminal domain and C-terminal extension probably modulates the properties of the various alpha-Hsps as stress-protective and structural oligomeric proteins. Phylogeny reconstruction indicates that multiple alpha-Hsps were already present in the last common ancestor of pro- and Eukaryotes. It is suggested that during eukaryote evolution, animal and non-animal alpha-Hsps originated from different ancestral gene copies. Repeated gene duplications gave rise to the multiple alpha-Hsps present in most organisms.
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genealogy of the α crystallin small heat shock protein superfamily
International Journal of Biological Macromolecules, 1998Co-Authors: Wilfried W De Jong, Gertjan Caspers, Jack A M LeunissenAbstract:Sequences of 40 very diverse representatives of the α-crystallin–small heat-shock protein (α-Hsp) superfamily are compared. Their characteristic C-terminal `α-crystallin domain' of 80–100 residues contains short consensus sequences that are highly conserved from prokaryotes to Eukaryotes. There are, in addition, some positions that clearly distinguish animal from non-animal α-Hsps. The α-crystallin domain is predicted to consist of two hydrophobic β-sheet motifs, separated by a hydrophilic region which is variable in length. Combination of a conserved α-crystallin domain with a variable N-terminal domain and C-terminal extension probably modulates the properties of the various α-Hsps as stress-protective and structural oligomeric proteins. Phylogeny reconstruction indicates that multiple α-Hsps were already present in the last common ancestor of pro- and Eukaryotes. It is suggested that during eukaryote evolution, animal and non-animal α-Hsps originated from different ancestral gene copies. Repeated gene duplications gave rise to the multiple α-Hsps present in most organisms.
Wilfried W De Jong - One of the best experts on this subject based on the ideXlab platform.
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genealogy of the α crystallin small heat shock protein superfamily
International Journal of Biological Macromolecules, 1998Co-Authors: Wilfried W De Jong, Gertjan Caspers, Jack A M LeunissenAbstract:Sequences of 40 very diverse representatives of the alpha-crystallin-small heat-shock protein (alpha-Hsp) superfamily are compared. Their characteristic C-terminal 'alpha-crystallin domain' of 80-100 residues contains short consensus sequences that are highly conserved from prokaryotes to Eukaryotes. There are, in addition, some positions that clearly distinguish animal from non-animal alpha-Hsps. The alpha-crystallin domain is predicted to consist of two hydrophobic beta-sheet motifs, separated by a hydrophilic region which is variable in length. Combination of a conserved alpha-crystallin domain with a variable N-terminal domain and C-terminal extension probably modulates the properties of the various alpha-Hsps as stress-protective and structural oligomeric proteins. Phylogeny reconstruction indicates that multiple alpha-Hsps were already present in the last common ancestor of pro- and Eukaryotes. It is suggested that during eukaryote evolution, animal and non-animal alpha-Hsps originated from different ancestral gene copies. Repeated gene duplications gave rise to the multiple alpha-Hsps present in most organisms.
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genealogy of the α crystallin small heat shock protein superfamily
International Journal of Biological Macromolecules, 1998Co-Authors: Wilfried W De Jong, Gertjan Caspers, Jack A M LeunissenAbstract:Sequences of 40 very diverse representatives of the α-crystallin–small heat-shock protein (α-Hsp) superfamily are compared. Their characteristic C-terminal `α-crystallin domain' of 80–100 residues contains short consensus sequences that are highly conserved from prokaryotes to Eukaryotes. There are, in addition, some positions that clearly distinguish animal from non-animal α-Hsps. The α-crystallin domain is predicted to consist of two hydrophobic β-sheet motifs, separated by a hydrophilic region which is variable in length. Combination of a conserved α-crystallin domain with a variable N-terminal domain and C-terminal extension probably modulates the properties of the various α-Hsps as stress-protective and structural oligomeric proteins. Phylogeny reconstruction indicates that multiple α-Hsps were already present in the last common ancestor of pro- and Eukaryotes. It is suggested that during eukaryote evolution, animal and non-animal α-Hsps originated from different ancestral gene copies. Repeated gene duplications gave rise to the multiple α-Hsps present in most organisms.
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.
Peter Tompa - One of the best experts on this subject based on the ideXlab platform.
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structural disorder in Eukaryotes
PLOS ONE, 2012Co-Authors: Rita Pancsa, Peter TompaAbstract:Based on early bioinformatic studies on a handful of species, the frequency of structural disorder of proteins is generally thought to be much higher in Eukaryotes than in prokaryotes. To refine this view, we present here a comparative prediction study and analysis of 194 fully described eukaryotic proteomes and 87 reference prokaryotes for structural disorder. We found that structural disorder does distinguish Eukaryotes from prokaryotes, but its frequency spans a very wide range in the two superkingdoms that largely overlap. The number of disordered binding regions and different Pfam domain types also contribute to distinguish Eukaryotes from prokaryotes. Unexpectedly, the highest levels – and highest variability – of predicted disorder is found in protists, i.e. single-celled Eukaryotes, often surpassing more complex eukaryote organisms, plants and animals. This trend contrasts with that of the number of domain types, which increases rather monotonously toward more complex organisms. The level of structural disorder appears to be strongly correlated with lifestyle, because some obligate intracellular parasites and endosymbionts have the lowest levels, whereas host-changing parasites have the highest level of predicted disorder. We conclude that protists have been the evolutionary hot-bed of experimentation with structural disorder, in a period when structural disorder was actively invented and the major functional classes of disordered proteins established.
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: Clement 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: Clement 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: Clement 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).
