Research Topics
Genomes and Genes | Dmitry A RodionovSummaryAffiliation: The Burnham Institute Country: USA Publications
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Publications
Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuationAlexey G Vitreschak
Institute for Problems of Information Transmission, Moscow, 101447, Russia
Nucleic Acids Res 30:3141-51. 2002....
Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteriaDmitry A Ravcheev
Sanford Burnham Medical Research Institute, La Jolla, CA 92037, USA
BMC Genomics 14:94. 2013..Nonetheless, no systematic genome-wide analysis of transcriptional regulation has been previously made for this taxonomic group...- A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of lifeCrysten E Haas
Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
BMC Genomics 10:470. 2009..Even though the first COG0523-encoding gene, cobW, was identified almost 20 years ago, little is known concerning the function of other members belonging to this ubiquitous family... - Reconstruction of xylose utilization pathway and regulons in FirmicutesYang Gu
Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
BMC Genomics 11:255. 2010..Moreover, the regulatory mechanisms of xylose catabolism in many Firmicutes except Bacillus spp. still remained unclear... - Comparative genomic analyses of nickel, cobalt and vitamin B12 utilizationYan Zhang
Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, NE 68588 0664, USA
BMC Genomics 10:78. 2009..Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited... - The Zur regulon of Corynebacterium glutamicum ATCC 13032Jasmin Schröder
Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universitat Bielefeld, D 33615 Bielefeld, Germany
BMC Genomics 11:12. 2010.... - Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transportersDmitry A Rodionov
The Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
J Bacteriol 188:317-27. 2006..Experimental analysis confirmed metal transport activity for three members of this family and demonstrated significant activity for a basic module (CbiMN) of the Salmonella enterica serovar Typhimurium transporter... - Comparative genomic reconstruction of transcriptional regulatory networks in bacteriaDmitry A Rodionov
Burnham Institute for Medical Research, La Jolla, California 92037, USA
Chem Rev 107:3467-97. 2007 
Computational identification of BioR, a transcriptional regulator of biotin metabolism in Alphaproteobacteria, and of its binding signalDmitry A Rodionov
Institute for Information Transmission Problems RAS, Moscow, Russia
FEMS Microbiol Lett 255:102-7. 2006..Thus, in Alphaproteobacteria, BioR seems to have assumed the role of the biotin regulator that in most other bacteria is fulfilled by the dual function biotin-protein ligase BirA having the DNA-binding helix-turn-helix domain...- A novel class of modular transporters for vitamins in prokaryotesDmitry A Rodionov
Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
J Bacteriol 191:42-51. 2009..The shared use of energy-coupling modules was experimentally confirmed for folate, thiamine, and riboflavin transporters. We propose the name energy-coupling factor transporters for the new class of membrane transporters... - Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genusDmitry A Rodionov
Sanford Burnham Medical Research Institute, La Jolla, California, USA
BMC Genomics 12:S3. 2011..The comparative genomics approaches and computational identification of regulatory sites are useful for the in silico reconstruction of transcriptional regulatory networks in bacteria... - Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulonDmitry A Rodionov
Burnham Institute for Medical Research, La Jolla, CA 92037, USA
Nucleic Acids Res 36:2032-46. 2008..Overall, the analysis of the NiaR and NrtR regulons (described in the accompanying paper) revealed mechanisms of transcriptional regulation of NAD metabolism in nearly a hundred diverse bacteria... - Genomic encyclopedia of sugar utilization pathways in the Shewanella genusDmitry A Rodionov
Burnham Institute for Medical Research, La Jolla, California 92037, USA
BMC Genomics 11:494. 2010.... - RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotesPavel S Novichkov
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, State Scientific Center GosNIIGenetika, Moscow 117545, Russia
Nucleic Acids Res 38:D111-8. 2010..Another section in the database represents the results of accurate regulon propagation to the closely related genomes... - Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulatorsDmitry A Rodionov
Burnham Institute for Medical Research, La Jolla, CA 92037, USA
Nucleic Acids Res 36:2047-59. 2008..This work and the accompanying study of NiaR regulon demonstrate significant variability of regulatory strategies for control of NAD metabolic pathway in bacteria... - Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomesAlexey E Kazakov
Lawrence Berkeley National Laboratory, Berkeley, California, USA
J Bacteriol 195:29-38. 2013..The collection of reconstructed regulons is available at the RegPrecise database (http://regprecise.lbl.gov/RegPrecise/Desulfovibrionales.jsp)... - Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor RexDmitry A Ravcheev
Sanford Burnham Medical Research Institute, La Jolla, California, USA
J Bacteriol 194:1145-57. 2012..The novel functional role of Rex in the control of the central carbon metabolism and hydrogen production genes was validated by in vitro DNA binding assays using the TM0169 protein in the hydrogen-producing bacterium Thermotoga maritima... - Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networksDmitry A Rodionov
Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
PLoS Comput Biol 1:e55. 2005..As the result, we demonstrate considerable interconnection between various nitrogen-oxides-responsive regulatory systems for the denitrification and NO detoxification genes and evolutionary plasticity of this transcriptional network... - Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?Dmitry A Rodionov
State Scientific Center GosNIIGenetika, Moscow, 113545, Russia
Nucleic Acids Res 31:6748-57. 2003..Finally, the most likely candidates for genes of lysine biosynthesis missing in Gram- positive bacteria were identified using the genome context analysis... - Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylumMarat D Kazanov
Sanford Burnham Medical Research Institute, La Jolla, CA 92037, USA
Nucleic Acids Res 41:790-803. 2013..Observed correlations between signature residues and the sugar-ligand specificities provide the framework for structure functional classification of the entire ROK family... - Diversity and versatility of the Thermotoga maritima sugar kinomeIrina A Rodionova
Sanford Burnham Medical Research Institute, La Jolla, California, USA
J Bacteriol 194:5552-63. 2012..Use of the integrated genomic and experimental approach greatly speeds up the identification of the biochemical function of unknown proteins and improves the quality of reconstructed pathways... - Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensisSemen A Leyn
Sanford Burnham Medical Research Institute, La Jolla, California 92037, USA
J Biol Chem 286:35782-94. 2011..oneidensis using [(13)C]lactate labeling and GC-MS analysis confirmed the hypothesized HexR role as a master regulator of gluconeogenic flux from pyruvate via the transcriptional activation of phosphoenolpyruvate synthase (PpsA)... - Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathwaysChen Yang
Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
J Bacteriol 190:1773-82. 2008..Both enzymatic activities were experimentally verified, and the entire pathway was validated by its in vitro reconstitution... - Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteriaAlexey E Kazakov
Institute for Information Transmission Problems, RAS, Moscow, Russia
J Bacteriol 191:52-64. 2009..The remarkable variability of the regulatory systems associated with the FA degradation pathway is discussed from functional and evolutionary points of view... - Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteriaDmitry A Rodionov
State Scientific Centre GosNIIGenetika, Moscow, 117545, Russia
Microbiology 150:3571-90. 2004..In particular, possible non-orthologous substitutes of isomerase KduI and a new oligogalacturonide transporter in the Vibrio species were detected... - Nicotinamide mononucleotide synthetase is the key enzyme for an alternative route of NAD biosynthesis in Francisella tularensisLeonardo Sorci
Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
Proc Natl Acad Sci U S A 106:3083-8. 2009.... - Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphateDmitry A Rodionov
Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
Proc Natl Acad Sci U S A 104:4279-84. 2007..The genomic survey confirmed its presence in the species known to use DIP for osmoprotection. Among several newly identified species with a postulated DIP pathway, Aeropyrum pernix was directly proven to produce this osmolyte... - Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profilingDmitry A Rodionov
Institute for Information Transmission Problems, RAS, Bolshoi Karetny per 19, Moscow, 127994, Russia
Trends Genet 21:385-9. 2005..The method of simultaneous phylogenetic profiling of genes and conserved regulatory signals introduced in this study could be used to identify transcriptional factors regulating orphan regulons... - Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidenceDmitry A Ravcheev
Sanford Burnham Medical Research Institute, La Jolla, CA 92037, USA
J Bacteriol 193:3228-40. 2011..aureus to assess relationships between the inferred regulons and gene expression patterns. The predicted reference set of regulons is captured within the Staphylococcus collection in the RegPrecise database (http://regprecise.lbl.gov)... - Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensisChen Yang
Burnham Institute for Medical Research, La Jolla, California 92037, USA
J Biol Chem 281:29872-85. 2006..unambiguously identifies several genes involved in chitin metabolism, and describes a novel variant of the classical three-step biochemical conversion of GlcNAc to fructose 6-phosphate first described in Escherichia coli... - Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteriaInna A Suvorova
State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIGenetika, Moscow, Russia
J Bacteriol 193:3956-63. 2011..We provide experimental evidence that two predicted members of the UxuR regulon, yjjM and yjjN, are the subject of complex regulation by this transcription factor in E. coli... - N-acetylgalactosamine utilization pathway and regulon in proteobacteria: genomic reconstruction and experimental characterization in ShewanellaSemen A Leyn
Sanford Burnham Medical Research Institute, La Jolla, California 92037, USA
J Biol Chem 287:28047-56. 2012..This study provides comprehensive insights into the common and distinctive features of the GalNAc/GalN catabolism and its regulation in diverse Proteobacteria... - Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteriaDmitry A Rodionov
Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
PLoS Comput Biol 2:e163. 2006.... - RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomicsPavel S Novichkov
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Nucleic Acids Res 40:W604-8. 2012..The RegPrecise web services API is freely accessible at http://regprecise.lbl.gov/RegPrecise/services.jsp with no login requirements... - Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritimaIrina A Rodionova
Sanford Burnham Medical Research Institute, La Jolla, CA, 92037, USA
Environ Microbiol 14:2920-34. 2012..The genomic context of respective genes and reconstruction of associated pathways suggest that UxaE enzymatic and biological function remains conserved in all of these species... - Evolution of regulatory motifs of bacterial transcription factorsKonstantin Y Gorbunov
Institute for Information Transmission Problems of the Russian Academy of Sciences Kharkevich Institute, Moscow, Russia
In Silico Biol 10:163-83. 2010..In most transcription factor families the changes in binding motifs are limited to several branches. Changes in consensus nucleotides proceed via an intermediate stage when the respective position is not conserved... - Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotesDmitry A Rodionov
State Scientific Center GosNIIGenetika, Moscow 113545, Russia
J Biol Chem 278:41148-59. 2003..Moreover, B12 regulons of various bacteria are thought to include enzymes from known B12-dependent or alternative pathways... - Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and ArchaeaDmitry A Rodionov
State Scientific Center GosNIIGenetika, Moscow 113545, Russia
Genome Res 12:1507-16. 2002..BirA is the first example of a transcriptional regulator with a conserved binding signal in eubacteria and archaea... - Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systemsDmitry A Rodionov
Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny pereulok 19, Moscow 127994, Russia
Nucleic Acids Res 32:3340-53. 2004..In particular, Oceanobacillus iheyensis possibly uses a homolog of the betaine-homocysteine methyltransferase bhmT gene from vertebrates to substitute missing bacterial-type methionine synthases... - Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteriaDmitry A Rodionov
Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny per, 19, Moscow 127994, Russia
Genome Biol 5:R90. 2004.... - Living without Fur: the subtlety and complexity of iron-responsive gene regulation in the symbiotic bacterium Rhizobium and other alpha-proteobacteriaAndrew W B Johnston
School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
Biometals 20:501-11. 2007..Thus, their "iron-omes" may be more accurately linked to the real-time needs for the metal and not just to its absolute concentration in the environment... - Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing modulePeter Hebbeln
Institut für Biologie Mikrobiologie, Humboldt Universitat zu Berlin, Chausseestrasse 117, 10115 Berlin, Germany
Proc Natl Acad Sci U S A 104:2909-14. 2007..The results substantiate our earlier suggestion of a mechanistically novel group of membrane transporters... - The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotationLeslie Klis McNeil
National Center for Supercomputing Applications, Urbana, IL 61801, USA
Nucleic Acids Res 35:D347-53. 2007..Essentiality data collated from genome-wide studies have been curated. Drug target identification and high-throughput, in silico, compound screening are in development... - Definition of a consensus DNA-binding site for PecS, a global regulator of virulence gene expression in Erwinia chrysanthemi and identification of new members of the PecS regulonCarine Rouanet
, , 69622 Villeurbanne, France
J Biol Chem 279:30158-67. 2004..Accordingly, PecS directly represses fliE expression. Thus, PecS seems to control the synthesis of virulence factors required for the key steps of plant infection... - The subsystems approach to genome annotation and its use in the project to annotate 1000 genomesRoss Overbeek
Fellowship for Interpretation of Genomes, 15W155 81st Street, Burr Ridge, IL 60527, USA
Nucleic Acids Res 33:5691-702. 2005..The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms... - The Rhizobium leguminosarum regulator IrrA affects the transcription of a wide range of genes in response to Fe availabilityJonathan D Todd
School of Biological Sciences, University of East Anglia, NR4 7TJ, Norwich, UK
Mol Genet Genomics 275:564-77. 2006..g. Escherichia coli) in which the ferric uptake regulator Fur is the global Fe-responsive gene regulator... - Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanismsDmitry A Rodionov
State Scientific Center GosNIIGenetika, Moscow 113545, Russia
J Biol Chem 277:48949-59. 2002..Based on analysis of co-occurrence of the thiamin biosynthetic genes in complete genomes, we predict that eubacteria, archaea, and eukaryota have different pathways for the HMP and hydroxyethylthiazole biosynthesis... - Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural elementAlexey G Vitreschak
Integrated Genomics-Moscow, 117333, Russia
RNA 9:1084-97. 2003..These lineage-specific duplications of RNA regulatory elements seem to be a major evolutionary mechanism for expansion of the vitamin B(12) regulon... - Towards environmental systems biology of ShewanellaJames K Fredrickson
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Nat Rev Microbiol 6:592-603. 2008....