K. V. Gunbin

Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions.

BackgroundProkaryotic microorganisms are able to survive and proliferate in severe environmental conditions. The increasing number of complete sequences of prokaryotic genomes has provided the basis for studying the molecular mechanisms of their adaptation at the genomic level. We apply here a computer-based approach to compare the genomes and proteomes from P. furiosus, P. horikoshii, and P. abyssi to identify features of their molecular evolution related to adaptation strategy to diverse environmental conditions.ResultsPhylogenetic analysis of rRNA genes from 26 Pyrococcus strains suggested that the divergence of P. furiosus, P. horikoshii and P. abyssi might have occurred from ancestral deep-sea organisms. It was demonstrated that the function of genes that have been subject to positive Darwinian selection is closely related to abiotic and biotic conditions to which archaea managed to become adapted. Divergence of the P. furiosus archaea might have been due to loss of some genes involved in cell motility or signal transduction, and/or to evolution under positive selection of the genes for translation machinery. In the course of P. horikoshii divergence, positive selection was found to operate mainly on the transcription machinery; divergence of P. abyssi was related with positive selection for the genes mainly involved in inorganic ion transport. Analysis of radical amino acid replacement rate in evolving P. furiosus, P. horikoshii and P. abyssi showed that the fixation rate was higher for radical substitutions relative to the volume of amino acid side-chain.ConclusionsThe current results give due credit to the important role of hydrostatic pressure as a cause of variability in the P. furiosus, P. horikoshii and P. abyssi genomes evolving in different habitats. Nevertheless, adaptation to pressure does not appear to be the sole factor ensuring adaptation to environment. For example, at the stage of the divergence of P. horikoshii and P. abyssi, an essential evolutionary role may be assigned to changes in the trophic chain, namely, acquisition of a consumer status at a high (P. horikoshii) or low level (P. abyssi).

vasa-related genes and their expression in stem cells of colonial parasitic rhizocephalan barnacle Polyascus polygenea (Arthropoda: Crustacea: Cirripedia: Rhizocephala)

vasa (vas)‐related genes are members of the DEAD‐box protein family and are expressed in the germ cells of many Metazoa. We cloned vasa‐related genes (PpVLG, CpVLG) and other DEAD‐box family related genes (PpDRH1, PpDRH2, CpDRH, AtDRHr) from the colonial parasitic rhizocephalan barnacle Polyascus polygenea, the non‐colonial Clistosaccus paguri (Crustacea: Cirripedia: Rhizocephala), and the parasitic isopodan Athelgis takanoshimensis (Crustacea: Isopoda). The colonial Polyascus polygenea, a parasite of the coastal crabs Hemigrapsus sanguineus and Hemigrapsus longitarsis was used as a model object for further detailed investigations. Phylogenetic analysis suggested that PpVLG and CpVLG are closely related to vasa‐like genes of other Arthropoda. The rest of the studied genes form their own separate branch on the phylogenetic tree and have a common ancestry with the p68 and PL10 subfamilies. We suppose this group may be a new subfamily of the DEAD‐box RNA helicases that is specific for parasitic Crustacea. We found PpVLG and PpDRH1 expression products in stem cells from stolons and buds of internae, during asexual reproduction of colonial P. polygenea, and in germ cells from sexually reproducing externae, including male spermatogenic cells and female oogenic cells.

Molecular evolution of cyclin proteins in animals and fungi

BackgroundThe passage through the cell cycle is controlled by complexes of cyclins, the regulatory units, with cyclin-dependent kinases, the catalytic units. It is also known that cyclins form several families, which differ considerably in primary structure from one eukaryotic organism to another. Despite these lines of evidence, the relationship between the evolution of cyclins and their function is an open issue. Here we present the results of our study on the molecular evolution of A-, B-, D-, E-type cyclin proteins in animals and fungi.ResultsWe constructed phylogenetic trees for these proteins, their ancestral sequences and analyzed patterns of amino acid replacements. The analysis of infrequently fixed atypical amino acid replacements in cyclins evidenced that accelerated evolution proceeded predominantly during paralog duplication or after it in animals and fungi and that it was related to aromorphic changes in animals. It was shown also that evolutionary flexibility of cyclin function may be provided by consequential reorganization of regions on protein surface remote from CDK binding sites in animal and fungal cyclins and by functional differentiation of paralogous cyclins formed in animal evolution.ConclusionsThe results suggested that changes in the number and/or nature of cyclin-binding proteins may underlie the evolutionary role of the alterations in the molecular structure of cyclins and their involvement in diverse molecular-genetic events.

Plant auxin biosynthesis did not originate in charophytes.

The major pathway of auxin biosynthesis in plants requires tryptophan aminotransferase (TAA) and flavin-containing monooxygenase (YUCCA) enzymes [1,2]. Their evolution appears to be tightly connected, with a pathway origin that is currently unclear. Recently, Yue et al. [3] analyzed homologs of the TAA and YUCCA enzymes and suggested that they originated in land plants through horizontal gene transfer from bacteria. Wang et al. [4] revisited this question while considering the entire genome of Klebsormidium flaccidum [5] and transcriptome data from four other charophytes and three chlorophytes.

The evolution of Homo sapiens denisova and Homo sapiens neanderthalensis miRNA targeting genes in the prenatal and postnatal brain

BackgroundAs the evolution of miRNA genes has been found to be one of the important factors in formation of the modern type of man, we performed a comparative analysis of the evolution of miRNA genes in two archaic hominines, Homo sapiens neanderthalensis and Homo sapiens denisova, and elucidated the expression of their target mRNAs in bain.ResultsA comparative analysis of the genomes of primates, including species in the genus Homo, identified a group of miRNA genes having fixed substitutions with important implications for the evolution of Homo sapiens neanderthalensis and Homo sapiens denisova. The mRNAs targeted by miRNAs with mutations specific for Homo sapiens denisova exhibited enhanced expression during postnatal brain development in modern humans. By contrast, the expression of mRNAs targeted by miRNAs bearing variations specific for Homo sapiens neanderthalensis was shown to be enhanced in prenatal brain development.ConclusionsOur results highlight the importance of changes in miRNA gene sequences in the course of Homo sapiens denisova and Homo sapiens neanderthalensis evolution. The genetic alterations of miRNAs regulating the spatiotemporal expression of multiple genes in the prenatal and postnatal brain may contribute to the progressive evolution of brain function, which is consistent with the observations of fine technical and typological properties of tools and decorative items reported from archaeological Denisovan sites. The data also suggest that differential spatial-temporal regulation of gene products promoted by the subspecies-specific mutations in the miRNA genes might have occurred in the brains of Homo sapiens denisova and Homo sapiens neanderthalensis, potentially contributing to the cultural differences between these two archaic hominines.

Computer and statistical analysis of transcription factor binding and chromatin modifications by ChIP-seq data in embryonic stem cell.

Advances in high throughput sequencing technology have enabled the identification of transcription factor (TF) binding sites in genome scale. TF binding studies are important for medical applications and stem cell research. Somatic cells can be reprogrammed to a pluripotent state by the combined introduction of factors such as Oct4, Sox2, c-Myc, Klf4. These reprogrammed cells share many characteristics with embryonic stem cells (ESCs) and are known as induced pluripotent stem cells (iPSCs). The signaling requirements for maintenance of human and murine embryonic stem cells (ESCs) differ considerably. Genome wide ChIP-seq TF binding maps in mouse stem cells include Oct4, Sox2, Nanog, Tbx3, Smad2 as well as group of other factors. ChIP-seq allows study of new candidate transcription factors for reprogramming. It was shown that Nr5a2 could replace Oct4 for reprogramming. Epigenetic modifications play important role in regulation of gene expression adding additional complexity to transcription network functioning. We have studied associations between different histone modification using published data together with RNA Pol II sites. We found strong associations between activation marks and TF binding sites and present it qualitatively. To meet issues of statistical analysis of genome ChIP-sequencing maps we developed computer program to filter out noise signals and find significant association between binding site affinity and number of sequence reads. The data provide new insights into the function of chromatin organization and regulation in stem cells.

Molecular-genetic systems of development: Functional dynamics and molecular evolution

This work for the first time compares results obtained with studies of parametric robustness of the Hh-and Dpp/BMP signal cascades responsible for morphogenesis and molecular evolution of the Hh-and Dpp/BMP cascade genes. There is a link between adaptive evolution of genes and those changes in kinetic parameters of the signal cascade models, which are critical for normal functioning of these cascades. Special attention is paid to events of the molecular evolution of the Hh-and Dpp/BMP cascade genes that matched with the emergence of the major taxonomic types and classes of Bilateria.

Complete Genome Sequences of Two Newcastle Disease Virus Strains Isolated from a Wild Duck and a Pigeon in Russia

ABSTRACT Here, we report the complete genome sequences of two Newcastle disease virus (NDV) isolates, Adygea/duck/12/2008, from a wild duck in Russia, and Altai/pigeon/777/2010, from a pigeon in Russia. Based on comparative sequence analysis of the F gene, these strains were classified as NDV class II, genotypes VIId and VIb/2, respectively.

Analysis of the Conservative Motifs in Promoters of miRNA Genes, Expressed in Different Tissues of Mammalians

Numerous miRNAs play an important role in translation regulation, modulating embryo development, stem cells proliferation, and tissue differentiation. Aberrant miRNA expression has been associated with diseases like cancer, microcephaly, and schizophrenia. It is too little known about regulation of miRNA expression. A computer approach was developed in order to reveal the significant oligonucleotide motifs in the regulatory regions of eukaryotic genes. The regulatory signals that are specific to the promoter regions of miRNA containing genes, which are expressed in different tissues of mammalians, were obtained and classified.

Important role of hydrophobic interactions in high-pressure adaptation of proteins

113 High pressure is a damaging factor for living organ� isms [1]. It leads to denaturation of proteins as result of penetration of water molecules through pores into the hydrophobic core [2]. However, there are piezotoler� ant and piezophilic organisms that live at pressures reaching several hundreds of atmospheres (tens of MPa; 1 atm ~ 0.1 MPa). In this paper, to study the molecular mechanisms of their adaptation to pressure, we compared the models of structures of Nip7 proteins