Molecular evolution of poxviruses

Previous restriction fragment length polymorphism analysis divided variola virus (VARV) strains into two subtypes, one of which included West African and South American isolates. This allowed a dating to be introduced for the first time in estimation of the VARV evolution rate. The results were used to analyze the molecular evolution of the total family Poxviridae. Comparisons of the known nucleotide sequences were performed for the extended conserved central genome region in 42 orthopoxvirus strains and for the eight genes of multisubunit RNA polymerase in 65 viruses belonging to various genera of the family Poxviridae. Using the Bayesian dating method, the mutation accumulation rate of poxviruses was estimated at (1.7-8.8) x 10(-6) nucleotide substitutions per site per year. Computations showed that the modem poxvirus genera started diverging from an ancestral virus more than 200 thousand years ago and that an ancestor of the genus Orthopoxvirus emerged 131 +/- 45 thousand years ago. The other genera of mammalian poxviruses with a low GC content diverged approximately 110-90 thousand years ago. The independent evolution of VARV started 3.4 +/- 0.8 thousand years ago. It was shown with the example of VARV and the monkeypox virus (MPXV) that divergent evolution of these orthopoxviruses started and the West African subtypes of VARV and MPXV were formed as geographical conditions changed to allow isolation of West African animals from other African regions.     

Molecular evolution of enolase

Enolase (EC 4.2.1.11) is an enzyme of the glycolytic pathway catalyzing the dehydratation reaction of 2-phosphoglycerate. In vertebrates the enzyme exists in three isoforms: alpha, beta and gamma. The amino-acid and nucleotide sequences deposited in the GenBank and SwissProt databases were subjected to analysis using the following bioinformatic programs: ClustalX, GeneDoc, MEGA2 and S.I.F.T. (sort intolerant from tolerant). Phylogenetic trees of enolases created with the use of the MEGA2 program show evolutionary relationships and functional diversity of the three isoforms of enolase in vertebrates. On the basis of calculations and the phylogenetic trees it can be concluded that vertebrate enolase has evolved according to the "birth and death" model of evolution. An analysis of amino acid sequences of enolases: non-neuronal (NNE), neuron specific (NSE) and muscle specific (MSE) using the S.I.F.T. program indicated non-uniform number of possible substitutions. Tolerated substitutions occur most frequently in alpha-enolase, while the lowest number of substitutions has accumulated in gamma-enolase, which may suggest that it is the most recently evolved isoenzyme of enolase in vertebrates.     

Molecular evolution of poxviruses

Previous restriction fragment length polymorphism analysis divided variola virus (VARV) strains into two subtypes, one of which included West African and South American isolates. This allowed a dating to be introduced for the first time in estimation of the VARV evolution rate. The results were used to analyze the molecular evolution of the total family Poxviridae. Comparisons of the known nucleotide sequences were performed for the extended conserved central genome region in 42 orthopoxvirus strains and for the eight genes of multisubunit RNA polymerase in 65 viruses belonging to various genera of the family Poxviridae. Using the Bayesian dating method, the mutation accumulation rate of poxviruses was estimated at (1.7–8.8) × 10^?6 nucleotide substitutions per site per year. Computations showed that the modern poxvirus genera started diverging from an ancestral virus more than 200 thousand years ago and that an ancestor of the genus Orthopoxvirus emerged 131 ± 45 thousand years ago. The other genera of mammalian poxviruses with a low GC content diverged approximately 110–90 thousand years ago. The independent evolution of VARV started 3.4 ± 0.8 thousand years ago. It was shown with the example of VARV and the monkeypox virus (MPXV) that divergent evolution of these orthopoxviruses started and the West African subtypes of VARV and MPXV were formed as geographical conditions changed to allow isolation of West African animals from other African regions.     

Molecular bases of evolution

The general notions of the theory of evolution are listed. The unity of the "engineering principles" of the living nature is emphasized. The generalists and specialists species are discussed. The estimation of their evolution rates must be different if it is expressed by the number of species or by the morphological changes. The principles of "protein engineering" of the organisms and the role of metals in protein evolution are discussed. It is suggested that in the presence of ions of transition metals and zinc the Fox's proteinoids can possess more specific forms of enzymatic activity. In the evolution of language the horizontal transfer plays a much more important role than in the biological evolution. However in this case also the initial basis of the language remains. The random drift is considered and it is shown that in concordance with the neutralist theory there are no grounds to replace the calculation of the rates of mutational changes per time unity by the calculation per generation. The molecular drive is the main source of the evolutionary novelties. The drive is connected with drift. The synonymic mutations and the mutations in non-functional DNA are evolutionary important. The future mathematical theory of evolution must be based on the theory of Markov's chains with the stochastic matrix changing along the chain and containing the set of the non-diagonal members equal to zero. The results obtained in the theory of ontogeny are presented. The evolution of species is the evolution of ontogenies, the formation of the molecular theory of evolution can be possible only on the basis of the molecular theory of ontogeny. The internal causes of extinction of species reduce the accumulation of neutral and pseudo-neutral mutations.     

Molecular evolution of olfactomedin

Olfactomedin is a secreted polymeric glycoprotein of unknown function, originally discovered at the mucociliary surface of the amphibian olfactory neuroepithelium and subsequently found throughout the mammalian brain. As a first step toward elucidating the function of olfactomedin, its phylogenetic history was examined to identify conserved structural motifs. Such conserved motifs may have functional significance and provide targets for future mutagenesis studies aimed at establishing the function of this protein. Previous studies revealed 33% amino acid sequence identity between rat and frog olfactomedins in their carboxyl terminal segments. Further analysis, however, reveals more extensive homologies throughout the molecule. Despite significant sequence divergence, cysteines essential for homopolymer formation such as the CXC motif near the amino terminus are conserved, as is the characteristic glycosylation pattern, suggesting that these posttranslational modifications are essential for function. Furthermore, evolutionary analysis of a region of 53 amino acids of fish, frog, rat, mouse, and human olfactomedins indicates that an ancestral olfactomedin gene arose before the evolution of terrestrial vertebrates and evolved independently in teleost, amphibian, and mammalian lineages. Indeed, a distant olfactomedin homolog was identified in Caenorhabditis elegans. Although the amino acid sequence of this invertebrate protein is longer and highly divergent compared with its vertebrate homologs, the protein from C. elegans shows remarkable similarities in terms of conserved motifs and posttranslational modification sites. Six universally conserved motifs were identified, and five of these are clustered in the carboxyl terminal half of the protein. Sequence comparisons indicate that evolution of the N-terminal half of the molecule involved extensive insertions and deletions; the C-terminal segment evolved mostly through point mutations, at least during vertebrate evolution. The widespread occurrence of olfactomedin among vertebrates and invertebrates underscores the notion that this protein has a function of universal importance. Furthermore, extensive modification of its N-terminal half and the acquisition of a C-terminal SDEL endoplasmic-reticulum- targeting sequence may have enabled olfactomedin to adopt new functions in the mammalian central nervous system.      

Ancient duplications of the human proglucagon gene

The human proglucagon gene (GCG) is encoded within a finished 576-kb DNA sequence generated by the Human Genome Project. GCG is flanked by 18 kb and 65 kb of DNA, 5' and 3', respectively, that do not encode genes. The genomic sequence that includes GCG was found to have a long history of gene duplication events. Some members of the glucagon-like family of genes, GCG on chromosome 2 and GIP on chromosome 17, may be products of ancient genome duplications on the early vertebrate lineage. A large genomic tandem duplication event that included DPP4-like and GCG genes occurred before the amphibian-mammal divergence, but one of the duplicated copies of GCG has been lost on the human lineage. Recently, a processed pseudogene of the X-chromosome-linked gene TIMM8A was inserted downstream of GCG. Some ancient duplicates of GCG may retain physiological functions in other vertebrates.     

Molecular evolution in bacteria

Recent advances in microbiology and molecular biology have a unifying influence on our understanding of genetic diversity/similarity and evolutionary relationships in microorganisms. This article attempts to unify information from diverse areas such as microbiology, molecular biology, microbial physiology, clay crystal genes, metals-microbe-clay interactions and bacterial DNA restriction-modification systems (R-M) as they may apply to molecular evolution of bacteria. The possibility is discussed that the first informational molecules may have been catalytic RNA (micro-assembler) not DNA (now the master copy) and these first micro-assemblers may have been precursors of ribosomes.     

Molecular evolution and optimization

Microbial populations (and life) not only evolve, they optimize. The transition from a random, unorganized, lifeless Earth to the present situation, where the Earth is virtually covered with nucleic acids and diverse and complex species, required numerous molecular changes and the integration of metabolic pathways over billions of years. Primitive prokaryotic life was dependent on and constrained by the physical-chemical conditions on the Earth, while slowly reshaping conditions present. In this review, molecular evolution and molecular optimization are examined with an emphasis on the order in which evolutionary events occurred.     

Molecular evolution of the gamma-Herpesvirinae

Genomic sequences available for members of the gamma-Herpesvirinae allow analysis of many aspects of the group's evolution. This paper examines four topics: (i) the phylogeny of the group; (ii) the histories of gamma-herpesvirus-specific genes; (iii) genomic variation of human herpesvirus 8 (HHV-8); and (iv) the relationship between Epstein-Barr virus types 1 and 2 (EBV-1 and EBV-2). A phylogenetic tree based on eight conserved genes has been constructed for eight gamma-herpesviruses and extended to 14 species with smaller gene sets. This gave a generally robust assignment of evolutionary relationships, with the exception of murine herpesvirus 4 (MHV-4), which could not be placed unambiguously on the tree and which has evidently experienced an unusually high rate of genomic change. The gamma-herpesviruses possess a variable complement of genes with cellular homologues. In the clearest cases these virus genes were shown to have originated from host genome lineages in the distant past. HHV-8 possesses at its left genomic terminus a highly diverse gene (K1) and at its right terminus a gene (K15) having two diverged alleles. It was proposed that the high diversity of K1 results from a positive selection on K1 and a hitchhiking effect that reduces diversity elsewhere in the genome. EBV-1 and EBV-2 differ in their alleles of the EBNA-2, EBNA-3A, EBNA-3B and EBNA-3C genes. It was suggested that EBV-1 and EBV-2 may recombine in mixed infections so that their sequences outside these genes remain homogeneous. Models for genesis of the types, by recombination between diverged parents or by local divergence from a single lineage, both present difficulties.     

Molecular evolution of rodent insulins

Several trees of amino acid sequences of rodent insulins were derived with the maximum-parsimony procedure. Possible orthologous and paralogous relationships were investigated. Except for a recent gene duplication in the ancestor of rat and mouse, there are no strong arguments for other paralogous relationships. Therefore, a tree in agreement with other biological data is the most reasonable one. According to this tree, the capacity to form zinc-binding hexamers was lost once in the ancestor of the hystricomorph rodents, followed by moderately increased evolutionary rates in the lineages to African porcupine and chinchilla but highly increased rates in at least three independent lines to other taxa of this suborder: guinea pig, cuis, and Octodontoidea (coypu and casiragua).      

Molecular evolution of ubiquitin genes

Ubiquitin is a singular protein with multiple functions. It is probably the most slowly evolving protein known, is encoded by genes with a unique structure, and provides an intriguing case study for various aspects of molecular evolution. In particular, the multiple ubiquitin-coding repeats which have been characterized in man, yeast and a slime mould graphically illustrate the dynamics of concerted evolution, but cast doubts on the effectiveness of this process for unlinked arrays in this repeat family.     

Molecular evolution of pancreatic-type ribonucleases

Amino acid sequences of 39 mammalian ribonucleases have been used to construct trees by the maximum parsimony procedure. These trees are in fairly good agreement with the biological classification of the species involved. In the branching order of the six investigated eutherian mammalian orders, the edentates diverge first, followed, probably, by the primates. No definite conclusions can be drawn about the order of divergence of the perissodactyls, the rodents, and the group consisting of artiodactyls plus cetaceans. Nucleic acid sequences of part of the messenger RNAs of rat pancreatic and bovine seminal ribonuclease were compared. Both messengers have a second stop codon at position 129, which is in agreement with the addition of four residues at the C-terminus in several other ribonucleases. Turtle pancreatic ribonuclease and human angiogenin differ from each other and from the mammalian ribonucleases at 55%-70% of the amino acid positions; they share a number of structural features. Mammalian nonsecretory ribonucleases are homologous to the pancreatic ribonucleases in sequence regions where the active-site histidine residues are located.     

Molecular mechanisms of colicin evolution

This review explores features of the origin and evolution of colicins in Escherichia coli. First, the evolutionary relationships of 16 colicin and colicin-related proteins are inferred from amino acid and DNA sequence comparisons. These comparisons are employed to detail the evolutionary mechanisms involved in the origin and diversification of colicin clusters. Such mechanisms include movement of colicin plasmids between strains of E. coli and subsequent plasmid cointegration, transposition- and recombination-mediated transfer of colicin and related sequences, and rapid diversification of colicin and immunity proteins through the action of positive selection. The wealth of information contained in colicin sequence comparisons makes this an ideal system with which to explore molecular mechanisms of evolutionary change.      

Molecular evolution of interleukin-3

Chimpanzee, tamarin, and marmoset interleukin-3 (IL-3) genes were cloned, sequenced, and expressed. Western blot analysis demonstrated that functional genes were isolated. IL-3 sequences were compared with those of mouse, rat, rhesus monkey, gibbon, and man. Multiple alignment of the IL-3 coding regions showed that only a few regions had been conserved during mammalian evolution, which are likely associated with functional domains of the IL-3 protein. Substitution rates for the various lineages were calculated and the numbers of synonymous and nonsynonymous substitutions were estimated separately. Distance matrices of the IL-3 coding regions were used to construct phylogenetic trees which revealed large differences in IL-3 evolution rate as well as a more rapid substitution rate for rodents and a rate slowdown during hominoid evolution. Extremes were rhesus monkey IL-3, which accumulated few synonymous substitutions, and gibbon IL-3, which had almost exclusively synonymous substitutions. In rhesus monkey IL-3, nonsynonymous substitutions outnumbered synonymous substitutions, which could not be readily explained by a random process of substitutions. We assume that during evolution of IL-3, the majority of the amino acid replacements and the impaired interspecies functional cross-reactivity originate from selection mechanisms with the most likely selective force being the structure of the heterodimeric IL-3 cell-surface receptor. Insight into IL-3 architecture and structural analysis of the IL-3 receptor are needed to analyze the unusually fast evolution of IL-3 in more detail.