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Search Results: 1 - 10 of 132721 matches for " Eugene V Koonin "
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Are There Laws of Genome Evolution?
Eugene V. Koonin
PLOS Computational Biology , 2011, DOI: 10.1371/journal.pcbi.1002173
Abstract: Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the evolutionary rates of orthologous genes; the power law–like distributions of paralogous family size and node degree in various biological networks; the negative correlation between a gene's sequence evolution rate and expression level; and differential scaling of functional classes of genes with genome size. The universals of genome evolution can be accounted for by simple mathematical models similar to those used in statistical physics, such as the birth-death-innovation model. These models do not explicitly incorporate selection; therefore, the observed universal regularities do not appear to be shaped by selection but rather are emergent properties of gene ensembles. Although a complete physical theory of evolutionary biology is inconceivable, the universals of genome evolution might qualify as “laws of evolutionary genomics” in the same sense “law” is understood in modern physics.
The origin and early evolution of eukaryotes in the light of phylogenomics
Eugene V Koonin
Genome Biology , 2010, DOI: 10.1186/gb-2010-11-5-209
Abstract: The origin of eukaryotes is a huge enigma and a major challenge for evolutionary biology [1-3]. There is a sharp divide in the organizational complexity of the cell between eukaryotes, which have complex intracellular compartmentalization, and even the most sophisticated prokaryotes (archaea and bacteria), which do not [4-6]. A typical eukaryotic cell is about 1,000-fold bigger by volume than a typical bacterium or archaeon, and functions under different physical principles: free diffusion has little role in eukaryotic cells, but is crucial in prokaryotes [7,8]. The compartmentalization of eukaryotic cells is supported by an elaborate endomembrane system and by the actin-tubulin-based cytoskeleton [9,10]. There are no direct counterparts of these organelles in archaea or bacteria. The other hallmark of the eukaryotic cell is the presence of mitochondria, which have a central role in energy transformation and perform many additional roles in eukaryotic cells, such as in signaling and cell death.The conservation of the major features of cellular organization and the existence of a large set of genes that are conserved across eukaryotes leave no doubt that all extant eukaryotic forms evolved from a last eukaryote common ancestor (LECA; see below). All eukaryotes that have been studied in sufficient detail possess either mitochondria or organelles derived from mitochondria [11-13], so it is thought that LECA already possessed mitochondria (see below). Plants and many unicellular eukaryotes also have another type of organelle, plastids.The organizational complexity of the eukaryotic cells is complemented by extremely sophisticated, cross-talking signaling networks [14]. The main signaling systems in eukaryotes are the kinase-phosphatase machinery that regulates protein function through phosphorylation and dephosphorylation [15-18]; the ubiquitin network that governs protein turnover and localization through reversible protein ubiquitylation [19-21]; regulation of transla
An apology for orthologs - or brave new memes
Eugene V Koonin
Genome Biology , 2001, DOI: 10.1186/gb-2001-2-4-comment1005
Abstract: Let me put it bluntly: I am confident that orthologs and paralogs not only 'add something to the subject' but are critical for the development of evolutionary genomics (and as soon as two genomes were sequenced, all genomics became evolutionary). These are not fancy words (nor new, by the way: the notion of orthology versus paralogy was introduced by Walter Fitch in a seminal 1970 paper; SystZool 1970, 19:99-113), but are essential designations for two distinct types of evolutionary relationships. In a nutshell, orthologs are direct evolutionary counterparts derived from a common ancestor through vertical descent; whenever we speak of 'the same gene in different species', we actually mean orthologs. In contrast, paralogs are genes within the same genome that have evolved by duplication. Distinguishing between ortho and para is critical if we strive to describe evolution with any semblance of accuracy. It is equally important for inferring gene function. Conservation of function is not part of the definition of orthology but rather its consequence.The distinction is not only logical but also very practical, because it is quite common for the same function in different organisms to be performed by proteins that are not orthologs nor even homologs (defining homologs as any genes that have common ancestry, including both orthologs and paralogs). Hence another neologism of comparative genomics that might induce a cringe even in some stronger souls who put up with orthologs and paralogs: non-orthologous gene displacement, when unrelated - or at least not orthologous - genes perform analogous functions (see Koonin EV, Mushegian AR, Bork P: Trends Genet 1996, 12:334-336). I do maintain, however, that this one also helps us to speak more, rather than less, accurately and comprehensibly about what is really going on during genome evolution.There is, however, yet another wrinkle that becomes apparent when one tries to think this through. Look at the trivialized schematic in Fi
The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life
Eugene V Koonin
Biology Direct , 2007, DOI: 10.1186/1745-6150-2-15
Abstract: Origin of life is a chicken and egg problem: for biological evolution that is governed, primarily, by natural selection, to take off, efficient systems for replication and translation are required, but even barebones cores of these systems appear to be products of extensive selection. The currently favored (partial) solution is an RNA world without proteins in which replication is catalyzed by ribozymes and which serves as the cradle for the translation system. However, the RNA world faces its own hard problems as ribozyme-catalyzed RNA replication remains a hypothesis and the selective pressures behind the origin of translation remain mysterious. Eternal inflation offers a viable alternative that is untenable in a finite universe, i.e., that a coupled system of translation and replication emerged by chance, and became the breakthrough stage from which biological evolution, centered around Darwinian selection, took off. A corollary of this hypothesis is that an RNA world, as a diverse population of replicating RNA molecules, might have never existed. In this model, the stage for Darwinian selection is set by anthropic selection of complex systems that rarely but inevitably emerge by chance in the infinite universe (multiverse).The plausibility of different models for the origin of life on earth directly depends on the adopted cosmological scenario. In an infinite universe (multiverse), emergence of highly complex systems by chance is inevitable. Therefore, under this cosmology, an entity as complex as a coupled translation-replication system should be considered a viable breakthrough stage for the onset of biological evolution.This article was reviewed by Eric Bapteste, David Krakauer, Sergei Maslov, and Itai Yanai.This article was reviewed by Eric Bapteste, David Krakauer, Sergei Maslov, and Itai Yanai.The "many worlds in one" (hereinafter MWO) model makes the startling prediction that all macroscopic, "coarse-grain" histories of events that are not forbidden by co
The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?
Eugene V Koonin
Biology Direct , 2006, DOI: 10.1186/1745-6150-1-22
Abstract: I argue that several lines of evidence now suggest a coherent solution to the introns-early versus introns-late debate, and the emerging picture of intron evolution integrates aspects of both views although, formally, there seems to be no support for the original version of introns-early. Firstly, there is growing evidence that spliceosomal introns evolved from group II self-splicing introns which are present, usually, in small numbers, in many bacteria, and probably, moved into the evolving eukaryotic genome from the α-proteobacterial progenitor of the mitochondria. Secondly, the concept of a primordial pool of 'virus-like' genetic elements implies that self-splicing introns are among the most ancient genetic entities. Thirdly, reconstructions of the ancestral state of eukaryotic genes suggest that the last common ancestor of extant eukaryotes had an intron-rich genome. Thus, it appears that ancestors of spliceosomal introns, indeed, have existed since the earliest stages of life's evolution, in a formal agreement with the introns-early scenario. However, there is no evidence that these ancient introns ever became widespread before the emergence of eukaryotes, hence, the central tenet of introns-early, the role of introns in early evolution of proteins, has no support. However, the demonstration that numerous introns invaded eukaryotic genes at the outset of eukaryotic evolution and that subsequent intron gain has been limited in many eukaryotic lineages implicates introns as an ancestral feature of eukaryotic genomes and refutes radical versions of introns-late. Perhaps, most importantly, I argue that the intron invasion triggered other pivotal events of eukaryogenesis, including the emergence of the spliceosome, the nucleus, the linear chromosomes, the telomerase, and the ubiquitin signaling system. This concept of eukaryogenesis, in a sense, revives some tenets of the exon hypothesis, by assigning to introns crucial roles in eukaryotic evolutionary innovation.Th
The Biological Big Bang model for the major transitions in evolution
Eugene V Koonin
Biology Direct , 2007, DOI: 10.1186/1745-6150-2-21
Abstract: I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. This biphasic model of evolution incorporates the previously developed concepts of the emergence of protein folds by recombination of small structural units and origin of viruses and cells from a pre-cellular compartmentalized pool of recombining genetic elements. The model is extended to encompass other major transitions. It is proposed that bacterial and archaeal phyla emerged independently from two distinct populations of primordial cells that, originally, possessed leaky membranes, which made the cells prone to rampant gene exchange; and that the eukaryotic supergroups emerged through distinct, secondary endosymbiotic events (as opposed to the primary, mitochondrial endosymbiosis). This biphasic model of evolution is substantially analogous to the scenario of the origin of universes in the eternal inflation version of modern cosmology. Under this model, universes like ours emerge in the infinite multiverse when the eternal process of exponential expansion, known as inflation, ceases in a particular region as a result of false vacuum decay, a first order phase transition process. The result is the nucl
Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases
Eugene V Koonin
Biology Direct , 2006, DOI: 10.1186/1745-6150-1-39
Abstract: I propose a specific succession for the emergence of different DNA replication systems, drawing argument from the differences in their representation among viruses and other selfish replicating elements. In a striking pattern, the DNA replication systems of viruses infecting bacteria and eukaryotes are dominated by the archaeal-type B-family DNA polymerase (PolB) whereas the bacterial replicative DNA polymerase (PolC) is present only in a handful of bacteriophage genomes. There is no apparent mechanistic impediment to the involvement of the bacterial-type replication machinery in viral DNA replication. Therefore, I hypothesize that the observed, markedly unequal distribution of the replicative DNA polymerases among the known cellular and viral replication systems has a historical explanation. I propose that, among the two types of DNA replication machineries that are found in extant life forms, the archaeal-type, PolB-based system evolved first and had already given rise to a variety of diverse viruses and other selfish elements before the advent of the bacterial, PolC-based machinery. Conceivably, at that stage of evolution, the niches for DNA-viral reproduction have been already filled with viruses replicating with the help of the archaeal system, and viruses with the bacterial system never took off. I further suggest that the two other systems of DNA replication, the rolling circle mechanism and the protein-primed mechanism, which are represented in diverse selfish elements, also evolved prior to the emergence of the bacterial replication system. This hypothesis is compatible with the distinct structural affinities of PolB, which has the palm-domain fold shared with reverse transcriptases and RNA-dependent RNA polymerases, and PolC that has a distinct, unrelated nucleotidyltransferase fold. I propose that PolB is a descendant of polymerases that were involved in the replication of genetic elements in the RNA-protein world, prior to the emergence of DNA replicatio
Taming of the shrewd: novel eukaryotic genes from RNA viruses
Eugene V Koonin
BMC Biology , 2010, DOI: 10.1186/1741-7007-8-2
Abstract: In a recent BMC Biology article Taylor and Bruenn [1] for the first time report a detailed molecular and evolutionary study of non-retroviral RNA virus genes integrated into eukaryotic genomes (hereinafter NIRV, non-retroviral integrated Rna viruses). The conclusions are no less than stunning: not only are NIRV widespread in fungi but they have become bona fide, functional genes. For retroid viruses, integration into the host genomic DNA is a regular stage of the reproduction cycle and sequences derived from retroelements comprise almost half of mammalian genomic DNA [2] and, strikingly, >75% of the genomic DNA in some plants such as maize [3]; in the more compact fungal genomes, retroelement-derived sequences are less abundant but also common [4].So far, NIRV have been a completely different story: reliable reports of integration of DNA copies of non-retroviral RNA virus genes into host genomes can be counted on the fingers of one hand. The idea that reverse transcriptase (RT) present in eukaryotic cells could produce NIRV was first championed by Zhdanov soon after RT was discovered [5], followed by reports on integrated copies of several, diverse single-stranded RNA viruses [6,7]. However, these reports were not independently confirmed [8], with one notable exception where integrated virus-specific sequences were discovered in mice infected with lymphocytic choriomeningitis virus (LCMV), leading to the intriguing hypothesis that the integrated copies might contributed to the lifelong immunity of the survivor animals [9]. More recently, long integrated sequences, apparently derived from a novel flavivirus, were detected in the genomes of Aedes albopictus and Aedes aegypti mosquitoes [10,11]. The change of tide for NIRV seems to come from the recent work of Frank and Wolfe who surveyed the available genomes of Hemiascomycete fungi (Saccharomycotina) for sequences homologous to those of viruses and plasmids, and detected over 10 inserts derived from double-stranded (
Does the central dogma still stand?
Koonin Eugene V
Biology Direct , 2012, DOI: 10.1186/1745-6150-7-27
Abstract: Prions are agents of analog, protein conformation-based inheritance that can confer beneficial phenotypes to cells, especially under stress. Combined with genetic variation, prion-mediated inheritance can be channeled into prion-independent genomic inheritance. Latest screening shows that prions are common, at least in fungi. Thus, there is non-negligible flow of information from proteins to the genome in modern cells, in a direct violation of the Central Dogma of molecular biology. The prion-mediated heredity that violates the Central Dogma appears to be a specific, most radical manifestation of the widespread assimilation of protein (epigenetic) variation into genetic variation. The epigenetic variation precedes and facilitates genetic adaptation through a general ‘look-ahead effect’ of phenotypic mutations. This direction of the information flow is likely to be one of the important routes of environment-genome interaction and could substantially contribute to the evolution of complex adaptive traits. Reviewers This article was reviewed by Jerzy Jurka, Pierre Pontarotti and Juergen Brosius. For the complete reviews, see the Reviewers’ Reports section.
The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life: The possibility of chance emergence of the replication and translation systems, and the protein superfolds
Eugene V. Koonin
Quantitative Biology , 2007,
Abstract: Evolution of life on earth was governed, primarily, by natural selection, with major contribution of other evolutionary processes, such as neutral variation, exaptation, and gene duplication. However, for biological evolution to take off, a certain minimal degree of complexity is required such that a replicating genome encodes means for its own replication with sufficient rate and fidelity. In all existing life forms, this is achieved by dedicated proteins, polymerases (replicases), that are produced by the elaborate translation system. However, evolution of the coupled system of replication and translation does not appear possible without pre-existing efficient replication; hence a chicken-egg type paradox. I argue that the many-worlds-in-one version of the cosmological model of eternal inflation implies that emergence of replication and translation, as well as the major protein folds, by chance alone, as opposed to biological evolution, is a realistic possibility and could provide for the onset of biological evolution. Hence an RNA world, as it is currently conceived, might have never existed although catalytic activities of RNA were, probably, critical for the onset of biological evolution and its early stages.
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