D A Rodionov

Summary

Affiliation: State Research Institute of Genetics and Selection of Industrial Microorganisms
Country: Russia

Publications

  1. pmc Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module
    Peter 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
  2. ncbi Riboswitches: the oldest mechanism for the regulation of gene expression?
    Alexey G Vitreschak
    Institute for Problems of Information Transmission RAS, Bolshoi Karetnyi per 19, Moscow, 127994, Russia
    Trends Genet 20:44-50. 2004
  3. ncbi Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria
    D A Rodionov
    State Scientific Center GosNIIGenetika, Moscow, 113545, Russia
    Mol Microbiol 38:673-83. 2000
  4. pmc Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems
    Dmitry 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
  5. pmc Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria
    Dmitry A Rodionov
    Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny per, 19, Moscow 127994, Russia
    Genome Biol 5:R90. 2004
  6. pmc 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
  7. ncbi Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes
    Dmitry A Rodionov
    State Scientific Center GosNIIGenetika, Moscow 113545, Russia
    J Biol Chem 278:41148-59. 2003
  8. ncbi Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms
    Dmitry A Rodionov
    State Scientific Center GosNIIGenetika, Moscow 113545, Russia
    J Biol Chem 277:48949-59. 2002
  9. pmc Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea
    Dmitry A Rodionov
    State Scientific Center GosNIIGenetika, Moscow 113545, Russia
    Genome Res 12:1507-16. 2002
  10. ncbi Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria
    D A Rodionov
    State Scientific Center GosNIIGenetika, Moscow, Russia
    FEMS Microbiol Lett 205:305-14. 2001

Collaborators

Detail Information

Publications33

  1. pmc Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module
    Peter 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...
  2. ncbi Riboswitches: the oldest mechanism for the regulation of gene expression?
    Alexey G Vitreschak
    Institute for Problems of Information Transmission RAS, Bolshoi Karetnyi per 19, Moscow, 127994, Russia
    Trends Genet 20:44-50. 2004
    ....
  3. ncbi Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria
    D A Rodionov
    State Scientific Center GosNIIGenetika, Moscow, 113545, Russia
    Mol Microbiol 38:673-83. 2000
    ..The former is likely to be the transport system for the products of pectin degradation, oligogalacturonides...
  4. pmc Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems
    Dmitry 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...
  5. pmc Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria
    Dmitry A Rodionov
    Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny per, 19, Moscow 127994, Russia
    Genome Biol 5:R90. 2004
    ....
  6. pmc 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...
  7. ncbi Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes
    Dmitry 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...
  8. ncbi Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms
    Dmitry 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...
  9. pmc Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea
    Dmitry 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...
  10. ncbi Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria
    D A Rodionov
    State Scientific Center GosNIIGenetika, Moscow, Russia
    FEMS Microbiol Lett 205:305-14. 2001
    ..Moreover, candidate catabolite responsive elements found upstream of most pentose-utilising genes suggest CcpA-mediated catabolite repression...
  11. ncbi Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria
    Dmitry 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...
  12. ncbi Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria
    D A Rodionov
    State Scientific Center GosNIIGenetika, Moscow, Russia
    J Mol Microbiol Biotechnol 3:319-24. 2001
    ..New candidate members of the MarA regulon were detected. Putative binding sites for EmrR and AcrR were suggested. A new hypothetical MarX regulon was described that includes some multidrug transporters and porins...
  13. pmc Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation
    Alexey G Vitreschak
    Institute for Problems of Information Transmission, Moscow, 101447, Russia
    Nucleic Acids Res 30:3141-51. 2002
    ....
  14. pmc Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks
    Dmitry 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...
  15. ncbi Computational identification of BioR, a transcriptional regulator of biotin metabolism in Alphaproteobacteria, and of its binding signal
    Dmitry 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...
  16. ncbi Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling
    Dmitry 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...
  17. pmc Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria
    Alexey 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...
  18. pmc RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes
    Pavel 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...
  19. pmc Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria
    Dmitry A Rodionov
    Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
    PLoS Comput Biol 2:e163. 2006
    ....
  20. pmc Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators
    Dmitry 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...
  21. pmc Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon
    Dmitry 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...
  22. pmc Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways
    Chen 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...
  23. pmc Comparative genomic reconstruction of transcriptional regulatory networks in bacteria
    Dmitry A Rodionov
    Burnham Institute for Medical Research, La Jolla, California 92037, USA
    Chem Rev 107:3467-97. 2007
  24. pmc Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate
    Dmitry 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...
  25. ncbi Living without Fur: the subtlety and complexity of iron-responsive gene regulation in the symbiotic bacterium Rhizobium and other alpha-proteobacteria
    Andrew 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...
  26. pmc The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
    Leslie 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...
  27. pmc Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters
    Dmitry 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...
  28. pmc Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element
    Alexey 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...
  29. pmc The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    Ross 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...
  30. ncbi 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 regulon
    Carine Rouanet
    Unité de Microbiologie et Génétique CNRS Institut National des Sciences Appliquées Université Claude Bernard Lyon, Unité Mixte de Recherche 5122 Université Claude Bernard Lyon, 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...
  31. ncbi Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis
    Chen 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...
  32. ncbi The Rhizobium leguminosarum regulator IrrA affects the transcription of a wide range of genes in response to Fe availability
    Jonathan 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...
  33. doi Towards environmental systems biology of Shewanella
    James K Fredrickson
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Nat Rev Microbiol 6:592-603. 2008
    ....