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

<p>Abstract</p> <p>Background</p> <p>Prokaryotic 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 <it>P. furiosus, P. horikoshii</it>, and <it>P. abyssi </it>to identify features of their molecular evolution related to adaptation strategy to diverse environmental conditions.</p> <p>Results</p> <p>Phylogenetic analysis of rRNA genes from 26 Pyrococcus strains suggested that the divergence of <it>P. furiosus, P. horikoshii </it>and <it>P. abyssi </it>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 <it>P. furiosus </it>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 <it>P. horikoshii </it>divergence, positive selection was found to operate mainly on the transcription machinery; divergence of <it>P. abyssi </it>was related with positive selection for the genes mainly involved in inorganic ion transport. Analysis of radical amino acid replacement rate in evolving <it>P. furiosus, P. horikoshii </it>and <it>P. abyssi </it>showed that the fixation rate was higher for radical substitutions relative to the volume of amino acid side-chain.</p> <p>Conclusions</p> <p>The current results give due credit to the important role of hydrostatic pressure as a cause of variability in the <it>P. furiosus, P. horikoshii </it>and <it>P. abyssi </it>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 <it>P. horikoshii </it>and <it>P. abyssi</it>, an essential evolutionary role may be assigned to changes in the trophic chain, namely, acquisition of a consumer status at a high (<it>P. horikoshii</it>) or low level (<it>P. abyssi</it>).</p

A compendium of human genes regulating feeding behavior and body weight, its functional characterization and identification of GWAS genes involved in brain-specific PPI network

BACKGROUND: Obesity is heritable. It predisposes to many diseases. The objectives of this study were to create a compendium of genes relevant to feeding behavior (FB) and/or body weight (BW) regulation; to construct and to analyze networks formed by associations between genes/proteins; and to identify the most significant genes, biological processes/pathways, and tissues/organs involved in BW regulation. RESULTS: The compendium of genes controlling FB or BW includes 578 human genes. Candidate genes were identified from various sources, including previously published original research and review articles, GWAS meta-analyses, and OMIM (Online Mendelian Inheritance in Man). All genes were ranked according to knowledge about their biological role in body weight regulation and classified according to expression patterns or functional characteristics. Substantial and overrepresented numbers of genes from the compendium encoded cell surface receptors, signaling molecules (hormones, neuropeptides, cytokines), transcription factors, signal transduction proteins, cilium and BBSome components, and lipid binding proteins or were present in the brain-specific list of tissue-enriched genes identified with TSEA tool. We identified 27 pathways from KEGG, REACTOME and BIOCARTA whose genes were overrepresented in the compendium. Networks formed by physical interactions or homological relationships between proteins or interactions between proteins involved in biochemical/signaling pathways were reconstructed and analyzed. Subnetworks and clusters identified by the MCODE tool included genes/proteins associated with cilium morphogenesis, signal transduction proteins (particularly, G protein-coupled receptors, kinases or proteins involved in response to insulin stimulus) and transcription regulation (particularly nuclear receptors). We ranked GWAS genes according to the number of neighbors in three networks and revealed 22 GWAS genes involved in the brain-specific PPI network. On the base of the most reliable PPIs functioning in the brain tissue, new regulatory schemes interpreting relevance to BW regulation are proposed for three GWAS genes (ETV5, LRP1B, and NDUFS3). CONCLUSIONS: A compendium comprising 578 human genes controlling FB or BW was designed, and the most significant functional groups of genes, biological processes/pathways, and tissues/organs involved in BW regulation were revealed. We ranked genes from the GWAS meta-analysis set according to the number and quality of associations in the networks and then according to their involvement in the brain-specific PPI network and proposed new regulatory schemes involving three GWAS genes (ETV5, LRP1B, and NDUFS3) in BW regulation. The compendium is expected to be useful for pathology risk estimation and for design of new pharmacological approaches in the treatment of human obesity

LEAF HAIRINESS IN POTATO Solanum tuberosum: MORPHOLOGY, FUNCTION AND METHODS OF ANALYSIS

Pubescence is one of the important biotic factors in plants related to protection from stressful environmental factors. In potato, the interest in the study of pubescence is associated primarily with the fact that it plays a significant role in the protection of plants from insect pests. The review focuses on the functional role and genetic control of leaf pubescence in potato. The review describes morphological features of pubescence of potatoes, which consists of simple and glandular trichomes of several types. The ratio of trichomes of different types in potato species potato is diverse, especially for wild species. Therefore, the pubescence may serve as a classifying trait. The role of trichomes as “factories” of secondary metabolites of potatoes, among which are the esters of sucrose and terpene derivatives that serve as insect repellents. Trichomes also synthesize polyphenol oxidases, which lead to the biosynthesis of compounds which are harmful to the insects. The review presents information about the currently known genes responsible for pubescence. These are genes involved in the formation of a complex of MYB-bHLH-WD40, which controls the differentiation and development of trichomes in plants. The proteins of this complex in potatoes are primarily studied in connection with the regulation of the biosynthesis of anthocyanins. The fundamental basis for identification of genes controlling pubescence in potato is currently sequence data from complete genome sequencing. By analysis of homology with the genes of model organisms, it allows candidate genes that control important traits in potato to be identified. Work in this direction is already underway, but at the initial stage. In the final section, the review describes the methods ofphenotyping trichomes, based on the visual analysis of microscopic images (obtained both with optical and electron microscopes). The urgency of developing new high-performance approaches to the study of the morphology of the trait in potatoes has been demonstrated

INFORMATIONAL RESOURCES ON POTATO GERMPLASM COLLECTIONS

The potato (Solanum tuberosum L.) is one of the most important food crops, the advantage of which is the ability to give a high yield in a wide range of agroecosystems, high specific production of dry weight per unit of cultivated area. Nowadays potato is considered a source of vitamins, minerals, dietary fiber and other nutrients. Potato cultivars are characterized by low genetic diversity, which reduces their potential to produce varieties with improved properties. Wild potato relatives retain a high degree of genetic diversity, which can be used to find the superior alleles and for their further transfer to cultural genotypes. To this end, there is an intense development of potato gene banks, with the help of the information technology to access the data. The present review is devoted to global information resources in potato. It describes the most relevant information portals and databases of genetic resources for potatoes. Analysis of information in the Internet shows that the main information resources on potato collections are concentrated in the United States and Europe. Information portals provide a wide variety of information useful to producers, consumers and breeders. On such portals, there is an intensive information support of the latest technologies in the field of potato growing and breeding. An interesting direction is the provision of services to determine the DNA prints (markers) of potato varieties, involvement of potato growers in the process of operational monitoring of diseases and pests of potatoes. Integration of data on potato collections plays an important role at the present stage. In line with this, European collections and databases are being developed. However, despite the existence of pan-European potato collection, national collections are still given support. An important collection-related trend in recent years has been inclusion of samples with a large number (more than a hundred) characteristics, which are evaluated by constantly testing varieties within the framework of foreign state breeding programs. As a result of access to such information, the breeder can effectively plan an experiment with the purpose of directed selection for key features of plants. These trends confirm the effectiveness of the use of the latest technologies (including information) in the maintenance and dissemination of potato genetic resources

Analysis of color and texture characteristics of cereals on digital images

The color of the grain shell of cereals is an important feature that characterizes the pigments and metabolites contained in it. The grain shell is the main barrier between the grain and the environment, so its characteristics are associated with a number of important biological functions: moisture absorption, grain viability, resistance to pre-harvest germination. The presence of pigments in the shell affects various technological properties of the grain. Color characteristics, as well as the appearance of the grain shell are an important indicator of plant diseases. In addition, the color of the grains serves as a classifying feature of plants. Genetic control of the color formation of both grains and other plant organs is exerted by genes encoding enzymes involved in the biosynthesis of pigments, as well as regulatory genes. For a number of pigments, these genes are well understood, but for some pigments, such as melanin, which causes the black color of grains in barley, the molecular mechanisms of biosynthesis are still poorly understood. When studying the mechanisms of genetic control of grain color, breeders and geneticists are constantly faced with the need to assess the color characteristics of their shell. The technical means of addressing this problem include spectrophotometers, spectrometers, hyperspectral cameras. However, these cameras are expensive, especially with high resolution, both spatial and spectral. An alternative is to use digital cameras that allow you to get high-quality images with high spatial and color resolution. In this regard, recently, in the field of plant phenotyping, methods for evaluating the color and texture characteristics of cereals based on the analysis of two-dimensional images obtained by digital cameras have been intensively developed. This mini-review is devoted to the main tasks related to the analysis of color and texture characteristics of cereals, and to methods of their description based on digital images

A protocol for analysis of the quantitative characteristics of leaf pubescence in potato

Plant leaf pubescence is one of the important features, which is responsible for microclimate formation near the epidermis. It is involved in protection against adverse biotic and abiotic environmental factors. In Solanaceae, to which belongs the potato Solanum tuberosum L., leaf pubescence appears as multicellular unbranched trichomes of diverse size and morphology. Pubescence of this plants promotes resistance to insect pests, in particular, Colorado potato beetle and aphid, which is a carrier of viral diseases. During the process of breeding and genetic experiments, there is a need to assess the intensity of leaf pubescence of potato plants. For this task, micrographs taken under a microscope are commonly used. They are used to count different types of trichomes on the leaf surface to characterize the intensity of potato leaf pubescence. This approach requires visual counting of trichomes under a microscope and is fairly laborious. This protocol describes a rapid technology for quantitative assessment of the characteristics of potato pubescence (the number of trichomes on the leaf surface and the average length of trichomes) to solve the problems of genetics and breeding of this plant. It consists of a preparation technology, digital imaging of leaf folds with an optical microscope in transmitted light and subsequent automatic processing of images using the LHDetect2 software

Computational structural and functional proteomics 235 IDENTIFICATION AND STRUCTURE-FUNCTIONAL ANALYSIS OF THE SPECIFICITY DETERMINING RESIDUES OF THE ALPHA SUBUNITS OF THE PROTEOSOMAL COMPLEX

SUMMARY Motivation: Proteosomes are polyenzymatic proteolytic structures that provide the degradation of the bulk of cytoplasmic proteins to oligopeptides. The proteosomal genes in the eukaryotes all arose by duplication of a single ancestral gene encoding the proteosomal subunits in the bacteria. The analysis of evolutionary events after duplication may be useful for discovering new information about proteosomal structural and functional properties. Results: We confine our study here to the detection of the positions of the α-subunits whose amino acid substitutions are specific to particular subunits of the proteosomal alpha-rings. We detected a set of the α-subunit positions whose substitutions are specific to the genes that encode the various proteosomal subunits. It was demonstrated that these specific amino acid substitutions are the features of residues that form the subunit contacts in the α-ring of the proteosomes. Availability: The proteosomal sequences, multiple sequence alignments and phylogenetic tree used in analysis are available upon request

Online resources on gene networks containing human and animal data

Gene networks are molecular genetic systems that ensure the formation of phenotypic characteristics of organisms (molecular, biochemical, structural, morphological, behavioral, etc.) based on  information encoded in their genomes. Reconstruction of gene networks provides a methodological basis for modern systems biology. In this regard, the information on the structural and functional organization of gene networks accumulated in modern databases is extremely valuable. This review characterizes a number of Internetaccessible information resources oriented to humans and animals and containing data on gene networks and their functional modules. Without pretending to fully cover all information resources containing data related to humans and animals on the subject, the current review was created to report the current status of the problem and to present the criteria according to which we propose to evaluate the utility of webresources for specific research tasks. On this basis, we compiled and characterized a collection of databases containing information on metabolic and signaling pathways, as well as pathways of regulation of biological processes at the cellular and organismal levels. In addition, we observed the characteristics of several well­known databases containing data on interactions between biomolecules of various types. The following characteristics of databases were considered: (1) the types of information accumulated in the databases; (2) methods of data presentation; (3) methods of data collection; (4) data sources; (5) special search tools and options for data analysis. A comparison of the above characteristics showed that the databases are very heterogeneous according to their scopes, sources and types of data, interfaces, as well as according to their search options and data analysis tools. It was concluded that at the first step of the gene network reconstruction it is important to form a full set of information resources from which the data can be obtained. The web portals accumulating information about the databases that may be useful for the reconstruction and analysis of gene networks are specified

Haplotype analysis of APOE intragenic SNPs

BACKGROUND: APOE epsilon4 allele is most common genetic risk factor for Alzheimer\u27s disease (AD) and cognitive decline. However, it remains poorly understood why only some carriers of APOE epsilon4 develop AD and how ethnic variabilities in APOE locus contribute to AD risk. Here, to address the role of APOE haplotypes, we reassessed the diversity of APOE locus in major ethnic groups and in Alzheimer\u27s Disease Neuroimaging Initiative (ADNI) dataset on patients with AD, and subjects with mild cognitive impairment (MCI), and control non-demented individuals. RESULTS: We performed APOE gene haplotype analysis for a short block of five SNPs across the gene using the ADNI whole genome sequencing dataset. The compilation of ADNI data with 1000 Genomes identified the APOE epsilon4 linked haplotypes, which appeared to be distant for the Asian, African and European populations. The common European epsilon4-bearing haplotype is associated with AD but not with MCI, and the Africans lack this haplotype. Haplotypic inference revealed alleles that may confer protection against AD. By assessing the DNA methylation profile of the APOE haplotypes, we found that the AD-associated haplotype features elevated APOE CpG content, implying that this locus can also be regulated by genetic-epigenetic interactions. CONCLUSIONS: We showed that SNP frequency profiles within APOE locus are highly skewed to population-specific haplotypes, suggesting that the ancestral background within different sites at APOE gene may shape the disease phenotype. We propose that our results can be utilized for more specific risk assessment based on population descent of the individuals and on higher specificity of five site haplotypes associated with AD