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Author Mikhail S Gelfand

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Translation at first sight: the influence of leading codons.

Ilya A Osterman, Zoe S Chervontseva, Sergey A Evfratov, Alena V Sorokina, Vladimir A Rodin, Maria P Rubtsova, Ekaterina S Komarova, Timofei S Zatsepin, Marsel R Kabilov, Alexey A Bogdanov, Mikhail S Gelfand, Olga A Dontsova, Petr V Sergiev,

First triplets of mRNA coding region affect the yield of translation. We have applied the flowseq method to analyze >30 000 variants of the codons 2-11 of the fluorescent protein reporter to identify factors affecting the protein synthesis. While the negative influence of mRNA secondary structure on translation has been ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2020, :]

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Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches.

Vladislav V Babenko, Oleg V Podgorny, Valentin A Manuvera, Artem S Kasianov, Alexander I Manolov, Ekaterina N Grafskaia, Dmitriy A Shirokov, Alexey S Kurdyumov, Dmitriy V Vinogradov, Anastasia S Nikitina, Sergey I Kovalchuk, Nickolay A Anikanov, Ivan O Butenko, Olga V Pobeguts, Daria S Matyushkina, Daria V Rakitina, Elena S Kostryukova, Victor G Zgoda, Isolda P Baskova, Vladimir M Trukhan, Mikhail S Gelfand, Vadim M Govorun, Helgi B Schiöth, Vassili N Lazarev,

BACKGROUND:Salivary cell secretion (SCS) plays a critical role in blood feeding by medicinal leeches, making them of use for certain medical purposes even today. RESULTS:We annotated the Hirudo medicinalis genome and performed RNA-seq on salivary cells isolated from three closely related leech species, H. medicinalis, Hirudo orientalis, and Hirudo verbana. ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):331]

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Influence of the spacer region between the Shine-Dalgarno box and the start codon for fine-tuning of the translation efficiency in Escherichia coli.

Ekaterina S Komarova, Zoya S Chervontseva, Ilya A Osterman, Sergey A Evfratov, Maria P Rubtsova, Timofei S Zatsepin, Tatiana A Semashko, Elena S Kostryukova, Alexey A Bogdanov, Mikhail S Gelfand, Olga A Dontsova, Petr V Sergiev,

Translation efficiency contributes several orders of magnitude difference in the overall yield of exogenous gene expression in bacteria. In diverse bacteria, the translation initiation site, whose sequence is the primary determinant of the translation performance, is comprised of the start codon and the Shine-Dalgarno box located upstream. Here, we have ... Read more >>

Microb Biotechnol (Microbial biotechnology)
[2020, :]

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Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.

Olga M Sigalova, Andrei V Chaplin, Olga O Bochkareva, Pavel V Shelyakin, Vsevolod A Filaretov, Evgeny E Akkuratov, Valentina Burskaia, Mikhail S Gelfand,

BACKGROUND:Chlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria. RESULTS:We report pan-genomic analysis of sixteen species from genus Chlamydia including identification ... Read more >>

BMC Genomics (BMC genomics)
[2019, 20(1):710]

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Predictive models of protease specificity based on quantitative protease-activity profiling data.

Gennady G Fedonin, Alexey Eroshkin, Piotr Cieplak, Evgenii V Matveev, Gennady V Ponomarev, Mikhail S Gelfand, Boris I Ratnikov, Marat D Kazanov,

Bioinformatics-based prediction of protease substrates can help to elucidate regulatory proteolytic pathways that control a broad range of biological processes such as apoptosis and blood coagulation. The majority of published predictive models are position weight matrices (PWM) reflecting specificity of proteases toward target sequence. These models are typically derived from ... Read more >>

Biochim Biophys Acta Proteins Proteom (Biochimica et biophysica acta. Proteins and proteomics)
[2019, 1867(11):140253]

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Comparative Genomic Analysis of the Regulation of Aromatic Metabolism in Betaproteobacteria.

Inna A Suvorova, Mikhail S Gelfand,

Aromatic compounds are a common carbon and energy source for many microorganisms, some of which can even degrade toxic chloroaromatic xenobiotics. This comparative study of aromatic metabolism in 32 Betaproteobacteria species describes the links between several transcription factors (TFs) that control benzoate (BenR, BenM, BoxR, BzdR), catechol (CatR, CatM, BenM), ... Read more >>

Front Microbiol (Frontiers in microbiology)
[2019, 10:642]

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Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow.

Pavel V Shelyakin, Olga O Bochkareva, Anna A Karan, Mikhail S Gelfand,

BACKGROUND:The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we ... Read more >>

BMC Evol. Biol. (BMC evolutionary biology)
[2019, 19(1):83]

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Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.

Olga O Bochkareva, Elena V Moroz, Iakov I Davydov, Mikhail S Gelfand,

BACKGROUND:The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes. RESULTS:We performed integrated genomic analysis of ... Read more >>

BMC Genomics (BMC genomics)
[2018, 19(1):965]

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Microbiomes of gall-inducing copepod crustaceans from the corals Stylophora pistillata (Scleractinia) and Gorgonia ventalina (Alcyonacea).

Pavel V Shelyakin, Sofya K Garushyants, Mikhail A Nikitin, Sofya V Mudrova, Michael Berumen, Arjen G C L Speksnijder, Bert W Hoeksema, Diego Fontaneto, Mikhail S Gelfand, Viatcheslav N Ivanenko,

Corals harbor complex and diverse microbial communities that strongly impact host fitness and resistance to diseases, but these microbes themselves can be influenced by stresses, like those caused by the presence of macroscopic symbionts. In addition to directly influencing the host, symbionts may transmit pathogenic microbial communities. We analyzed two ... Read more >>

Sci Rep (Scientific reports)
[2018, 8(1):11563]

Cited: 1 time

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Comparative Genomic Analysis of Holospora spp., Intranuclear Symbionts of Paramecia.

Sofya K Garushyants, Alexandra Y Beliavskaia, Dmitry B Malko, Maria D Logacheva, Maria S Rautian, Mikhail S Gelfand,

While most endosymbiotic bacteria are transmitted only vertically, Holospora spp., an alphaproteobacterium from the Rickettsiales order, can desert its host and invade a new one. All bacteria from the genus Holospora are intranuclear symbionts of ciliates Paramecium spp. with strict species and nuclear specificity. Comparative metabolic reconstruction based on the ... Read more >>

Front Microbiol (Frontiers in microbiology)
[2018, 9:738]

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Neanderthal and Denisovan ancestry in Papuans: A functional study.

Evgeny E Akkuratov, Mikhail S Gelfand, Ekaterina E Khrameeva,

Sequencing of complete nuclear genomes of Neanderthal and Denisovan stimulated studies about their relationship with modern humans demonstrating, in particular, that DNA alleles from both Neanderthal and Denisovan genomes are present in genomes of modern humans. The Papuan genome is a unique object because it contains both Neanderthal and Denisovan ... Read more >>

J Bioinform Comput Biol (Journal of bioinformatics and computational biology)
[2018, 16(2):1840011]

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Comparative genomic analysis of fungal TPP-riboswitches.

Mikhail A Moldovan, Svetlana A Petrova, Mikhail S Gelfand,

Riboswitches are conserved RNA structures located in non-coding regions of mRNA and able to bind small molecules (e.g. metabolites) changing conformation upon binding. This feature enables them to function as regulators of gene expression. The thiamin pyrophosphate (TPP) riboswitch is the only type of riboswitches found not only in bacteria, ... Read more >>

Fungal Genet. Biol. (Fungal genetics and biology : FG & B)
[2018, 114:34-41]

Cited: 3 times

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Genome rearrangements and phylogeny reconstruction in Yersinia pestis.

Olga O Bochkareva, Natalia O Dranenko, Elena S Ocheredko, German M Kanevsky, Yaroslav N Lozinsky, Vera A Khalaycheva, Irena I Artamonova, Mikhail S Gelfand,

Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, ... Read more >>

PeerJ (PeerJ)
[2018, 6:e4545]

Cited: 1 time

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Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki.

Pavel V Mazin, Elena Shagimardanova, Olga Kozlova, Alexander Cherkasov, Roman Sutormin, Vita V Stepanova, Alexey Stupnikov, Maria Logacheva, Aleksey Penin, Yoichiro Sogame, Richard Cornette, Shoko Tokumoto, Yugo Miyata, Takahiro Kikawada, Mikhail S Gelfand, Oleg Gusev,

Polypedilum vanderplanki is a striking and unique example of an insect that can survive almost complete desiccation. Its genome and a set of dehydration-rehydration transcriptomes, together with the genome of Polypedilum nubifer (a congeneric desiccation-sensitive midge), were recently released. Here, using published and newly generated datasets reflecting detailed transcriptome changes ... Read more >>

Proc. Natl. Acad. Sci. U.S.A. (Proceedings of the National Academy of Sciences of the United States of America)
[2018, 115(10):E2477-E2486]

Cited: 4 times

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Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp.

Mikhail A Moldovan, Mikhail S Gelfand,

The pangenome is the collection of all groups of orthologous genes (OGGs) from a set of genomes. We apply the pangenome analysis to propose a definition of prokaryotic species based on identification of lineage-specific gene sets. While being similar to the classical biological definition based on allele flow, it does ... Read more >>

Front Microbiol (Frontiers in microbiology)
[2018, 9:428]

Cited: 5 times

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The genes of the sulphoquinovose catabolism in Escherichia coli are also associated with a previously unknown pathway of lactose degradation.

Anna Kaznadzey, Pavel Shelyakin, Evgeniya Belousova, Aleksandra Eremina, Uliana Shvyreva, Darya Bykova, Vera Emelianenko, Anastasiya Korosteleva, Maria Tutukina, Mikhail S Gelfand,

Comparative genomics analysis of conserved gene cassettes demonstrated resemblance between a recently described cassette of genes involved in sulphoquinovose degradation in Escherichia coli K-12 MG1655 and a Bacilli cassette linked with lactose degradation. Six genes from both cassettes had similar functions related to carbohydrate metabolism, namely, hydrolase, aldolase, kinase, isomerase, ... Read more >>

Sci Rep (Scientific reports)
[2018, 8(1):3177]

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Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci.

Anna Kaznadzey, Pavel Shelyakin, Mikhail S Gelfand,

Bacterial carbohydrate metabolism is extremely diverse, since carbohydrates serve as a major energy source and are involved in a variety of cellular processes. Bacterial genes belonging to same metabolic pathway are often co-localized in the chromosome, but it is not a strict rule. Gene co-localization in linked to co-evolution and ... Read more >>

Biol. Direct (Biology direct)
[2017, 12(1):28]

Cited: 1 time

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Conservation, evolution, and regulation of splicing during prefrontal cortex development in humans, chimpanzees, and macaques.

Pavel V Mazin, Xi Jiang, Ning Fu, Dingding Han, Meng Guo, Mikhail S Gelfand, Philipp Khaitovich,

Changes in splicing are known to affect the function and regulation of genes. We analyzed splicing events that take place during the postnatal development of the prefrontal cortex in humans, chimpanzees, and rhesus macaques based on data obtained from 168 individuals. Our study revealed that among the 38,822 quantified alternative ... Read more >>

RNA (RNA (New York, N.Y.))
[2018, 24(4):585-596]

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Genome analysis of E. coli isolated from Crohn's disease patients.

Daria V Rakitina, Alexander I Manolov, Alexandra V Kanygina, Sofya K Garushyants, Julia P Baikova, Dmitry G Alexeev, Valentina G Ladygina, Elena S Kostryukova, Andrei K Larin, Tatiana A Semashko, Irina Y Karpova, Vladislav V Babenko, Ruzilya K Ismagilova, Sergei Y Malanin, Mikhail S Gelfand, Elena N Ilina, Roman B Gorodnichev, Eugenia S Lisitsyna, Gennady I Aleshkin, Petr L Scherbakov, Igor L Khalif, Marina V Shapina, Igor V Maev, Dmitry N Andreev, Vadim M Govorun,

BACKGROUND:Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn's disease (CD). The phylogeny of E. coli isolated from Crohn's disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related. RESULTS:We performed the shotgun ... Read more >>

BMC Genomics (BMC genomics)
[2017, 18(1):544]

Cited: 4 times

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Application of sorting and next generation sequencing to study 5΄-UTR influence on translation efficiency in Escherichia coli.

Sergey A Evfratov, Ilya A Osterman, Ekaterina S Komarova, Alexandra M Pogorelskaya, Maria P Rubtsova, Timofei S Zatsepin, Tatiana A Semashko, Elena S Kostryukova, Andrey A Mironov, Evgeny Burnaev, Ekaterina Krymova, Mikhail S Gelfand, Vadim M Govorun, Alexey A Bogdanov, Petr V Sergiev, Olga A Dontsova,

Yield of protein per translated mRNA may vary by four orders of magnitude. Many studies analyzed the influence of mRNA features on the translation yield. However, a detailed understanding of how mRNA sequence determines its propensity to be translated is still missing. Here, we constructed a set of reporter plasmid ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2017, 45(6):3487-3502]

Cited: 6 times

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Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota.

Ilya V Kublanov, Olga M Sigalova, Sergey N Gavrilov, Alexander V Lebedinsky, Christian Rinke, Olga Kovaleva, Nikolai A Chernyh, Natalia Ivanova, Chris Daum, T B K Reddy, Hans-Peter Klenk, Stefan Spring, Markus Göker, Oleg N Reva, Margarita L Miroshnichenko, Nikos C Kyrpides, Tanja Woyke, Mikhail S Gelfand, Elizaveta A Bonch-Osmolovskaya,

The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen ... Read more >>

Front Microbiol (Frontiers in microbiology)
[2017, 8:195]

Cited: 9 times

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Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110.

Julia Hahn, Olga V Tsoy, Sebastian Thalmann, Jelena Čuklina, Mikhail S Gelfand, Elena Evguenieva-Hackenberg,

Small open reading frames (sORFs) and genes for non-coding RNAs are poorly investigated components of most genomes. Our analysis of 1391 ORFs recently annotated in the soybean symbiont Bradyrhizobium japonicum USDA 110 revealed that 78% of them contain less than 80 codons. Twenty-one of these sORFs are conserved in or ... Read more >>

PLoS ONE (PloS one)
[2016, 11(10):e0165429]

Cited: 1 time

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Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria.

Olga V Tsoy, Dmitry A Ravcheev, Jelena Čuklina, Mikhail S Gelfand,

Biological nitrogen fixation plays a crucial role in the nitrogen cycle. An ability to fix atmospheric nitrogen, reducing it to ammonium, was described for multiple species of Bacteria and Archaea. The transcriptional regulatory network for nitrogen fixation was extensively studied in several representatives of the class Alphaproteobacteria. This regulatory network ... Read more >>

Front Microbiol (Frontiers in microbiology)
[2016, 7:1343]

Cited: 6 times

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Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors.

Yuriy D Korostelev, Ilya A Zharov, Andrey A Mironov, Alexandra B Rakhmaininova, Mikhail S Gelfand,

The large and increasing volume of genomic data analyzed by comparative methods provides information about transcription factors and their binding sites that, in turn, enables statistical analysis of correlations between factors and sites, uncovering mechanisms and evolution of specific protein-DNA recognition. Here we present an online tool, Prot-DNA-Korr, designed to ... Read more >>

PLoS ONE (PloS one)
[2016, 11(9):e0162681]

Cited: 2 times

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Evolution of the Exon-Intron Structure in Ciliate Genomes.

Vladyslav S Bondarenko, Mikhail S Gelfand,

A typical eukaryotic gene is comprised of alternating stretches of regions, exons and introns, retained in and spliced out a mature mRNA, respectively. Although the length of introns may vary substantially among organisms, a large fraction of genes contains short introns in many species. Notably, some Ciliates (Paramecium and Nyctotherus) ... Read more >>

PLoS ONE (PloS one)
[2016, 11(9):e0161476]

Cited: 5 times

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