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Search Results: 1 - 10 of 302 matches for " Natalya Yutin "
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Archaeal origin of tubulin
Natalya Yutin, Eugene V Koonin
Biology Direct , 2012, DOI: 10.1186/1745-6150-7-10
Abstract: This article was reviewed by Gáspár Jékely and J. Peter Gogarten.Tubulins comprise a distinct family of GTPases that are highly conserved among eukaryotes and are the major components of microtubules, an essential part of the eukaryotic cytoskeleton [1,2]. All eukaryotes encode multiple, paralogous tubulins that evolved through a series of gene duplications at early stages of eukaryote evolution as well as many subsequent, lineage-specific duplications [3]. Among prokaryotes, the only bona fide tubulins have been identified in several bacteria of the genus Prosthecobacter [4] in which they form microtubule-like sturctures closely resembling eukaryotic microtubulues [5]. The tubulins of Prosthecobacteria show high sequence and structural similarity to eukaryotic homologs, and given their extremely narrow distribution among prokaryotes, are thought to have evolved via horizontal transfer of a eukaryotic tubulin gene to an ancestor of this group of bacteria [6,7]. The great majority of bacteria and many Archaea encode the FtsZ protein which plays a central role in cell division of most bacteria and many archaea and is a prokaryotic homolog of tubulin [8]. Both FtsZ and tubulin undergo GTP- hydrolysis-dependent cycles of polymerization and depolymerization, and are mechanistically analogous [9,10]. However, FtsZ and tubulin share extremely weak sequence similarity, so that the homology has become apparent only through comparison of crystal structures of these proteins [11]. Recent progress in genome sequencing and comparative genomics has revealed numerous previously unrecognized members of the FtsZ-tubulin protein superfamily [12,13]. These proteins considerably expand the range of sequence divergence adoptable by the FtsZ-tubulin fold but none of them are candidates for the role of direct prokaryotic ancestors of tubulins. In the absence of such candidates, it is generally assumed that tubulin evolved from FtsZ at the onset of eukaryote evolution, and this evolution e
Evolution of DNA ligases of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes: a case of hidden complexity
Natalya Yutin, Eugene V Koonin
Biology Direct , 2009, DOI: 10.1186/1745-6150-4-51
Abstract: Phylogenetic analysis of the ATP-dependent and NAD-dependent DNA ligases encoded by the NCLDV reveals an unexpectedly complex evolutionary history. The NAD-dependent ligases are encoded only by a minority of NCLDV (including mimiviruses, some iridoviruses and entomopoxviruses) but phylogenetic analysis clearly indicated that all viral NAD-dependent ligases are monophyletic. Combined with the topology of the NCLDV tree derived by consensus of trees for universally conserved genes suggests that this enzyme was represented in the ancestral NCLDV. Phylogenetic analysis of ATP-dependent ligases that are encoded by chordopoxviruses, most of the phycodnaviruses and Marseillevirus failed to demonstrate monophyly and instead revealed an unexpectedly complex evolutionary trajectory. The ligases of the majority of phycodnaviruses and Marseillevirus seem to have evolved from bacteriophage or bacterial homologs; the ligase of one phycodnavirus, Emiliana huxlei virus, belongs to the eukaryotic DNA ligase I branch; and ligases of chordopoxviruses unequivocally cluster with eukaryotic DNA ligase III.Examination of phyletic patterns and phylogenetic analysis of DNA ligases of the NCLDV suggest that the common ancestor of the extant NCLDV encoded an NAD-dependent ligase that most likely was acquired from a bacteriophage at the early stages of evolution of eukaryotes. By contrast, ATP-dependent ligases from different prokaryotic and eukaryotic sources displaced the ancestral NAD-dependent ligase at different stages of subsequent evolution. These findings emphasize complex routes of viral evolution that become apparent through detailed phylogenomic analysis but not necessarily in reconstructions based on phyletic patterns of genes.This article was reviewed by: Patrick Forterre, George V. Shpakovski, and Igor B. Zhulin.Viruses are ubiquitous parasites of all cellular life forms. In recent years, extensive genome sequencing and comparative analysis of both viral and host genomes yielded
Proteorhodopsin genes in giant viruses
Yutin Natalya,Koonin Eugene V
Biology Direct , 2012, DOI: 10.1186/1745-6150-7-34
Abstract: Viruses with large genomes encode numerous proteins that do not directly participate in virus biogenesis but rather modify key functional systems of infected cells. We report that a distinct group of giant viruses infecting unicellular eukaryotes that includes Organic Lake Phycodnaviruses and Phaeocystis globosa virus encode predicted proteorhodopsins that have not been previously detected in viruses. Search of metagenomic sequence data shows that putative viral proteorhodopsins are extremely abundant in marine environments. Phylogenetic analysis suggests that giant viruses acquired proteorhodopsins via horizontal gene transfer from proteorhodopsin-encoding protists although the actual donor(s) could not be presently identified. The pattern of conservation of the predicted functionally important amino acid residues suggests that viral proteorhodopsin homologs function as sensory rhodopsins. We hypothesize that viral rhodopsins modulate light-dependent signaling, in particular phototaxis, in infected protists. This article was reviewed by Igor B. Zhulin and Laksminarayan M. Iyer. For the full reviews, see the Reviewers’ reports section.
Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes
Yutin Natalya,Koonin Eugene V
Virology Journal , 2012, DOI: 10.1186/1743-422x-9-161
Abstract: Background The Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) constitute an apparently monophyletic group that consists of at least 6 families of viruses infecting a broad variety of eukaryotic hosts. A comprehensive genome comparison and maximum-likelihood reconstruction of the NCLDV evolution revealed a set of approximately 50 conserved, core genes that could be mapped to the genome of the common ancestor of this class of eukaryotic viruses. Results We performed a detailed phylogenetic analysis of these core NCLDV genes and applied the constrained tree approach to show that the majority of the core genes are unlikely to be monophyletic. Several of the core genes have been independently acquired from different sources by different NCLDV lineages whereas for the majority of these genes displacement by homologs from cellular organisms in one or more groups of the NCLDV was demonstrated. Conclusions A detailed study of the evolution of the genomic core of the NCLDV reveals substantial complexity and diversity of evolutionary scenarios that was largely unsuspected previously. The phylogenetic coherence between the core genes is sufficient to validate the hypothesis on the evolution of all NCLDV from a common ancestral virus although the set of ancestral genes might be smaller than previously inferred from patterns of gene presence-absence.
Phylogenomics of Prokaryotic Ribosomal Proteins
Natalya Yutin, Pere Puigbò, Eugene V. Koonin, Yuri I. Wolf
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0036972
Abstract: Archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). Despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of their short lengths and biased sequence composition. We developed an automated computational pipeline for identification of r-protein genes and applied it to 995 completely sequenced bacterial and 87 archaeal genomes available in the RefSeq database. The pipeline employs curated seed alignments of r-proteins to run position-specific scoring matrix (PSSM)-based BLAST searches against six-frame genome translations, mitigating possible gene annotation errors. As a result of this analysis, we performed a census of prokaryotic r-protein complements, enumerated missing and paralogous r-proteins, and analyzed the distributions of ribosomal protein genes among chromosomal partitions. Phyletic patterns of bacterial and archaeal r-protein genes were mapped to phylogenetic trees reconstructed from concatenated alignments of r-proteins to reveal the history of likely multiple independent gains and losses. These alignments, available for download, can be used as search profiles to improve genome annotation of r-proteins and for further comparative genomics studies.
Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution
Natalya Yutin, Yuri I Wolf, Didier Raoult, Eugene V Koonin
Virology Journal , 2009, DOI: 10.1186/1743-422x-6-223
Abstract: A comprehensive comparison of the protein sequences encoded in the genomes of 45 NCLDV belonging to 6 families was performed in order to delineate cluster of orthologous viral genes. Using previously developed computational methods for orthology identification, 1445 Nucleo-Cytoplasmic Virus Orthologous Groups (NCVOGs) were identified of which 177 are represented in more than one NCLDV family. The NCVOGs were manually curated and annotated and can be used as a computational platform for functional annotation and evolutionary analysis of new NCLDV genomes. A maximum-likelihood reconstruction of the NCLDV evolution yielded a set of 47 conserved genes that were probably present in the genome of the common ancestor of this class of eukaryotic viruses. This reconstructed ancestral gene set is robust to the parameters of the reconstruction procedure and so is likely to accurately reflect the gene core of the ancestral NCLDV, indicating that this virus encoded a complex machinery of replication, expression and morphogenesis that made it relatively independent from host cell functions.The NCVOGs are a flexible and expandable platform for genome analysis and functional annotation of newly characterized NCLDV. Evolutionary reconstructions employing NCVOGs point to complex ancestral viruses.Viruses span approximately 3 orders of magnitude (~103 to ~106 nucleotides) in genome size and show tremendous diversity of virion architecture, size and complexity [1-3]. Highly diverse viruses share homologous "hallmark genes" encoding some of the key proteins involved in genome replication and virion structure formation [4]. However, no gene is common to all viruses, so there is no evidence of a monophyletic origin of all viruses, at least, not within the traditional concept of monophyly. Nevertheless, large groups of viruses infecting diverse hosts do appear to be monophyletic as indicated by the conservation of sets of genes encoding proteins responsible for most of the functions essent
The origins of phagocytosis and eukaryogenesis
Natalya Yutin, Maxim Y Wolf, Yuri I Wolf, Eugene V Koonin
Biology Direct , 2009, DOI: 10.1186/1745-6150-4-9
Abstract: Comparisons of the sets of proteins implicated in phagocytosis in different eukaryotes reveal extreme diversity, with very few highly conserved components that typically do not possess readily identifiable prokaryotic homologs. Nevertheless, phylogenetic analysis of those proteins for which such homologs do exist yields clues to the possible origin of phagocytosis. The central finding is that a subset of archaea encode actins that are not only monophyletic with eukaryotic actins but also share unique structural features with actin-related proteins (Arp) 2 and 3. All phagocytic processes are strictly dependent on remodeling of the actin cytoskeleton and the formation of branched filaments for which Arp2/3 are responsible. The presence of common structural features in Arp2/3 and the archaeal actins suggests that the common ancestors of the archaeal and eukaryotic actins were capable of forming branched filaments, like modern Arp2/3. The Rho family GTPases that are ubiquitous regulators of phagocytosis in eukaryotes appear to be of bacterial origin, so assuming that the host of the mitochondrial endosymbiont was an archaeon, the genes for these GTPases come via horizontal gene transfer from the endosymbiont or in an earlier event.The present findings suggest a hypothetical scenario of eukaryogenesis under which the archaeal ancestor of eukaryotes had no cell wall (like modern Thermoplasma) but had an actin-based cytoskeleton including branched actin filaments that allowed this organism to produce actin-supported membrane protrusions. These protrusions would facilitate accidental, occasional engulfment of bacteria, one of which eventually became the mitochondrion. The acquisition of the endosymbiont triggered eukaryogenesis, in particular, the emergence of the endomembrane system that eventually led to the evolution of modern-type phagocytosis, independently in several eukaryotic lineages.This article was reviewed by Simonetta Gribaldo, Gaspar Jekely, and Pierre Pontaro
Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer
Wolf Yuri I,Makarova Kira S,Yutin Natalya,Koonin Eugene V
Biology Direct , 2012, DOI: 10.1186/1745-6150-7-46
Abstract: Background Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. Results The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major ‘highways’ of horizontal gene transfer. Conclusions The updated collection of arCOGs is expected to become a key resource for comparative genomics, evolutionary reconstruction and functional annotation of new archaeal genomes. Given that, in spite of the major increase in the number of genomes, the conserved core of archaeal genes appears to be stabilizing, the major evolutionary trends revealed here have a chance to stand the test of time. Reviewers This article was reviewed by (for complete reviews see the Reviewers’ Reports section): Dr. PLG, Prof. PF, Dr. PL (nominated by Prof. JPG).
Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia
Shaobin Hou, Kira S Makarova, Jimmy HW Saw, Pavel Senin, Benjamin V Ly, Zhemin Zhou, Yan Ren, Jianmei Wang, Michael Y Galperin, Marina V Omelchenko, Yuri I Wolf, Natalya Yutin, Eugene V Koonin, Matthew B Stott, Bruce W Mountain, Michelle A Crowe, Angela V Smirnova, Peter F Dunfield, Lu Feng, Lei Wang, Maqsudul Alam
Biology Direct , 2008, DOI: 10.1186/1745-6150-3-26
Abstract: We report the complete genome sequence of strain V4, the first one from a representative of the Verrucomicrobia. Isolate V4, initially named "Methylokorus infernorum" (and recently renamed Methylacidiphilum infernorum) is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of M. infernorum was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C1-utilization pathways compared to other known methylotrophs. The M. infernorum genome does not encode tubulin, which was previously discovered in bacteria of the genus Prosthecobacter, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of M. infernorum shows apparent adaptations for existence under extremely acidic conditions including a major upward shift in the isoelectric points of proteins.The results of genome analysis of M. infernorum support the monophyly of the PVC superphylum. M. infernorum possesses a streamlined genome but seems to have acquired numerous genes including those for enzymes of methylotrophic pathways via horizontal gene transfer, in particular, from Proteobacteria.This article was reviewed by John A. Fuerst, Ludmila Chistoserdova, and Radhey S. Gupta.The phylum Verrucomicrobia is an intriguing but poorly characterized group of bacteria. Representatives of this phylum have been found in a wide range of habitats including soils, aquatic systems,
Adrenocortical system activity in alloxan-resistant and alloxan-susceptible Wistar rats  [PDF]
Vera G. Selyatitskaya, Natalya A. Palchikova, Natalya V. Kuznetsova
Journal of Diabetes Mellitus (JDM) , 2012, DOI: 10.4236/jdm.2012.22026
Abstract: In the dynamics of the disease development, diuresis and glycosuria increase in alloxan-susceptible rats, while in alloxan-resistant rats the increase in the values of these indices is expressed to a lesser extent, and they begin to decrease by day 8 of the disease. In alloxan-susceptible rats, the mass index of adrenal gland is increased, and that of thymus is decreased and corticosterone concentration in blood, adrenal gland and urine as well as alanine and aspartate aminotransferase activities in liver are increased; in alloxan-resistant rats the values of these indices do not differ from those of rats of the control group.
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