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σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough

Alexey E. Kazakov, Lara Rajeev, Amy Chen, Eric G. Luning, Inna Dubchak, Aindrila Mukhopadhyay, Pavel S. Novichkov
2015 BMC Genomics  
The σ 54 subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequenced bacteria. The cellular processes regulated by many of these EBPs remain unknown. Results: To characterize the σ 54 -dependent regulome of D. vulgaris Hildenborough, we identified EBP
more » ... ng motifs and regulated genes by a combination of computational and experimental techniques. These predictions were supported by our reconstruction of σ 54 -dependent promoters by comparative genomics. We reassessed and refined the results of earlier studies on regulation in D. vulgaris Hildenborough and consolidated them with our new findings. It allowed us to reconstruct the σ 54 regulome in D. vulgaris Hildenborough. This regulome includes 36 regulons that consist of 201 coding genes and 4 non-coding RNAs, and is involved in nitrogen, carbon and energy metabolism, regulation, transmembrane transport and various extracellular functions. To the best of our knowledge, this is the first report of direct regulation of alanine dehydrogenase, pyruvate metabolism genes and type III secretion system by σ 54 -dependent regulators. Conclusions: The σ 54 -dependent regulome is an important component of transcriptional regulatory network in D. vulgaris Hildenborough and related free-living Deltaproteobacteria. Our study provides a representative collection of σ 54 -dependent regulons that can be used for regulation prediction in Deltaproteobacteria and other taxa.
doi:10.1186/s12864-015-2176-y pmid:26555820 pmcid:PMC4641369 fatcat:ymsugevel5h43knwetqdcbiine

PHOG: a database of supergenomes built from proteome complements

Igor V Merkeev, Pavel S Novichkov, Andrey A Mironov
2006 BMC Evolutionary Biology  
Orthologs and paralogs are widely used terms in modern comparative genomics. Existing procedures for resolving orthologous/paralogous relationships are often based on manual revision of clusters of orthologous groups and/or lack any rigorous evolutionary base. We developed a completely automated procedure that creates clusters of orthologous groups at each node of the taxonomy tree (PHOGs--Phylogenetic Orthologous Groups). As a result of this procedure, a tree of orthologous groups was
more » ... Each cluster is a "supergene" and it is represented by an "ancestral" sequence obtained from the multiple alignment of orthologous and paralogous genes. The procedure has been applied to the taxonomy tree of organisms from all three domains of life. Protein complements from 50 bacterial, archaeal and eukaryotic species were used to create PHOGs at all tree nodes. 51367 PHOGs were obtained at the root node. The PHOG database demonstrates that it is possible to automatically process any number of sequenced genomes and to reconstruct orthologous and paralogous relationships between genomes using a rigorous evolutionary approach. This database can become a very useful tool in various areas of comparative genomics.
doi:10.1186/1471-2148-6-52 pmid:16792803 pmcid:PMC1523204 fatcat:hmam2wqyxbbohe24vapwnmdx5i

A dual functioning small RNA/Riboswitch controls the expression of the methionine biosynthesis regulator SahR in Desulfovibrio vulgaris Hildenborough [article]

Megan L Kempher, Andrew S. Burns, Pavel S. Novichkov, Kelly S. Bender
2019 bioRxiv   pre-print
Riboswitches are cis-acting RNA regulatory elements that control expression of a downstream gene(s) by directly binding to a specific metabolite.  ...  Here we report a S-adenosylmethionine (SAM)-I riboswitch in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) that plays an additional regulatory role as a trans small noncoding  ...  Tomsic, J., McDaniel, B.A., Grundy, F.J. and Henkin, T.M. (2008) Natural 688 variability in S-adenosylmethionine (SAM)-dependent riboswitches: S-box 689 elements in Bacillus subtilis exhibit differential  ... 
doi:10.1101/803072 fatcat:csbp66bicjhpdgttab4zj2xmxm

Comparative Genomics of Transcriptional Regulation of Methionine Metabolism in Proteobacteria

Semen A. Leyn, Inna A. Suvorova, Tatiana D. Kholina, Sofia S. Sherstneva, Pavel S. Novichkov, Mikhail S. Gelfand, Dmitry A. Rodionov, Oscar P. Kuipers
2014 PLoS ONE  
Alternatively, SAH is first converted into S-ribosylhomocysteine by SAH nucleosidase Mtn and then utilized to homocysteine and 4,5-dihydroxypentan-2,3-dione by S-ribosylhomocysteine lyase LuxS.  ...  Less abundant riboswitches responding to SAM and/or SAH molecules include SAM-III (or S MK -box) that controls metK in Lactobacillus spp.  ... 
doi:10.1371/journal.pone.0113714 pmid:25411846 pmcid:PMC4239095 fatcat:duknaddhujgcjfpl7kqfi7dqr4

Comparative genomics and evolution of transcriptional regulons in Proteobacteria

Semen A. Leyn, Dmitry A. Rodionov, Pavel S. Novichkov, Vita V. Stepanova, Dmitry A. Ravcheev, Alexey E. Kazakov, Inna A. Suvorova
2016 Microbial Genomics  
In S. meliloti, hydroxyproline is imported into the cell via the ABC-family transporter HypMNPQ, which is predicted to be a part of HypR regulons only in three other genomes and thus was classified as  ... 
doi:10.1099/mgen.0.000061 pmid:28348857 pmcid:PMC5343134 fatcat:udolpyslqjesha6inmb5a4mlte

Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria

Dmitry A Ravcheev, Aaron A Best, Natalia V Sernova, Marat D Kazanov, Pavel S Novichkov, Dmitry A Rodionov
2013 BMC Genomics  
GAS 40 319 150 180 S. gallolyticus UCN34 41 328 167 199 S. mutans UA159 41 317 147 173 S. suis 05ZYH33 43 366 145 173 S. mitis B6 35 305 148 174 S. pneumoniae TIGR4 42  ...  30 263 125 141 S. agalactiae 2603 V/R 38 340 159 186 S. uberis 0140 J 42 330 156 183 S. equi MGCS10565 42 334 143 167 S. dysgalactiae GGS_124 43 356 160 189 S. pyogenes M1  ... 
doi:10.1186/1471-2164-14-94 pmid:23398941 pmcid:PMC3616900 fatcat:oppqiq4be5fr5pbotwayuv4uvm

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

Kira S Makarova, Alexander V Sorokin, Pavel S Novichkov, Yuri I Wolf, Eugene V Koonin
2007 Biology Direct  
Forterre P. and Gribaldo S.  ...  i >20s j /(10-s j ) where s i and s j stand for the species-coverage of the species-rich and species-poor descendant nodes, respectively). 4 .  ... 
doi:10.1186/1745-6150-2-33 pmid:18042280 pmcid:PMC2222616 fatcat:axyzyqfj5fgo3k4juio5ex2eni

Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome

Dmitry A. Rodionov, Aleksandr A. Arzamasov, Matvei S. Khoroshkin, Stanislav N. Iablokov, Semen A. Leyn, Scott N. Peterson, Pavel S. Novichkov, Andrei L. Osterman
2019 Frontiers in Microbiology  
or biochemical route(s) for β-alanine synthesis in these bacteria.  ...  Transcriptional regulons for transcription factors (TFs) (BirA, BioQ, NrtR, NiaR, PdxR) and riboswicthes (TPP, FMN, THF, B12) as captured in the RegPrecise database (Novichkov et al., 2013) were used  ... 
doi:10.3389/fmicb.2019.01316 pmid:31275260 pmcid:PMC6593275 fatcat:kl7wvnot6bebhhbfpb5vxt4eti

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

Pavel S. Novichkov, Olga N. Laikova, Elena S. Novichkova, Mikhail S. Gelfand, Adam P. Arkin, Inna Dubchak, Dmitry A. Rodionov
2009 Nucleic Acids Research  
The RegPrecise database (http://regprecise.lbl.gov) was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. A significant number of highquality inferences of transcriptional regulatory interactions have been already accumulated for diverse taxonomic groups of bacteria. The reconstructed regulons include transcription factors, their cognate DNA
more » ... fs and regulated genes/ operons linked to the candidate transcription factor binding sites. The RegPrecise allows for browsing the regulon collections for: (i) conservation of DNA binding sites and regulated genes for a particular regulon across diverse taxonomic lineages; (ii) sets of regulons for a family of transcription factors; (iii) repertoire of regulons in a particular taxonomic group of species; (iv) regulons associated with a metabolic pathway or a biological process in various genomes. The initial release of the database includes 11 500 candidate binding sites for 400 orthologous groups of transcription factors from over 350 prokaryotic genomes. Majority of these data are represented by genomewide regulon reconstructions in Shewanella and Streptococcus genera and a large-scale prediction of regulons for the LacI family of transcription factors. Another section in the database represents the results of accurate regulon propagation to the closely related genomes.
doi:10.1093/nar/gkp894 pmid:19884135 pmcid:PMC2808921 fatcat:yl7n7xaznbgzbodgkyf6j46ozu

Comparative genomics and evolution of regulons of the LacI-family transcription factors

Dmitry A. Ravcheev, Matvei S. Khoroshkin, Olga N. Laikova, Olga V. Tsoy, Natalia V. Sernova, Svetlana A. Petrova, Aleksandra B. Rakhmaninova, Pavel S. Novichkov, Mikhail S. Gelfand, Dmitry A. Rodionov
2014 Frontiers in Microbiology  
Rodionov, Pavel S. Novichkov, and Mikhail S. Gelfand conceived and designed the research project. Dmitry A. Ravcheev, Dmitry A. Rodionov, and Mikhail S. Gelfand wrote the manuscript. Dmitry A.  ...  Matvei S. Khoroshkin analyzed statistical properties of TF regulons. All authors read and approved the final manuscript.  ... 
doi:10.3389/fmicb.2014.00294 pmid:24966856 pmcid:PMC4052901 fatcat:2n4ngs7yh5elxerpccxdvabn3y

Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel Diseases

Stanislav N. Iablokov, Natalia S. Klimenko, Daria A. Efimova, Tatiana Shashkova, Pavel S. Novichkov, Dmitry A. Rodionov, Alexander V. Tyakht
2021 Frontiers in Molecular Biosciences  
This motivates the strict choice of S and D parameters, which leads to compact MTA descriptions.  ...  Alignment hits with value of F in the range between M and M-(1-M)/S and greater than a threshold value D were selected for MTA.  ... 
doi:10.3389/fmolb.2020.603740 pmid:33537340 pmcid:PMC7848230 fatcat:kcrro6owhfhnbbgz427q6adame

Dub-seq: dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits [article]

Vivek K Mutalik, Pavel S Novichkov, Morgan N Price, Trenton K Owens, Mark Callaghan, Sean Carim, Adam M Deutschbauer, Adam P Arkin
2018 bioRxiv   pre-print
Positive scores indicate that the gene(s) 263 contained on that fragment lead to an increase in relative fitness, while negative values 264 mean the gene(s) on the fragment reduced relative fitness.  ...  Scores near zero indicate no 265 fitness reduction or benefit for the gene(s) under the assayed condition.  ... 
doi:10.1101/387399 fatcat:fxiklifvj5c4fgczltbirwk4ge

High-throughput mapping of the phage resistance landscape in E. coli [article]

Vivek K Mutalik, Benjamin A. Adler, Harneet S. Rishi, Denish Piya, Crystal Zhong, Britt Koskella, Richard Calendar, Pavel Novichkov, Morgan N. Price, Adam M. Deutschbauer, Adam P. Arkin
2020 biorxiv/medrxiv   pre-print
Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, et al. Systematic discovery of antiphage defense systems in the microbial pangenome.  ...  Shin H, Lee J-H, Kim H, Choi Y, Heu S, Ryu S. Receptor diversity and host interaction of bacteriophages infecting Salmonella enterica serovar Typhimurium.  ... 
doi:10.1101/2020.02.15.951020 fatcat:btcaplvrwvgoxb5aztn2cpov4q

Distinct Patterns of Expression and Evolution of Intronless and Intron-Containing Mammalian Genes

Svetlana A. Shabalina, Aleksey Y. Ogurtsov, Alexey N. Spiridonov, Pavel S. Novichkov, Nikolay A. Spiridonov, Eugene V. Koonin
2010 Molecular biology and evolution  
Comparison of expression levels and breadth and evolutionary rates of intronless and intron-containing mammalian genes shows that intronless genes are expressed at lower levels, tend to be tissue specific, and evolve significantly faster than spliced genes. By contrast, monomorphic spliced genes that are not subject to detectable alternative splicing and polymorphic alternatively spliced genes show similar statistically indistinguishable patterns of expression and evolution. Alternative
more » ... is most common in ancient genes, whereas intronless genes appear to have relatively recent origins. These results imply tight coupling between different stages of gene expression, in particular, transcription, splicing, and nucleocytosolic transport of transcripts, and suggest that formation of intronless genes is an important route of evolution of novel tissue-specific functions in animals.
doi:10.1093/molbev/msq086 pmid:20360214 pmcid:PMC2908711 fatcat:xqvus3laizdfjelcnuangkhh6u

Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria

Eric I Sun, Semen A Leyn, Marat D Kazanov, Milton H Saier, Pavel S Novichkov, Dmitry A Rodionov
2013 BMC Genomics  
14 predicted RF01070 C glnA glutamine 13 known RF01739 C SAM-IV S-adenosylmethionine 13 known RF00634 C SAM-SAH S-adenosylmethionine, S-adenosylhomocysteine 13 known RF01727  ...  C Smk-box S-adenosylmethionine 13 known RF01767 C speF ?  ... 
doi:10.1186/1471-2164-14-597 pmid:24060102 pmcid:PMC3766115 fatcat:zrcmb4nshbczjeegaotfsrrocq
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