Dmitry A Rodionov

Summary

Affiliation: The Burnham Institute
Country: USA

Publications

  1. 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
  2. pmc Genomic encyclopedia of sugar utilization pathways in the Shewanella genus
    Dmitry A Rodionov
    Burnham Institute for Medical Research, La Jolla, California 92037, USA
    BMC Genomics 11:494. 2010
  3. pmc Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum
    Marat D Kazanov
    Sanford Burnham Medical Research Institute, La Jolla, CA 92037, USA
    Nucleic Acids Res 41:790-803. 2013
  4. 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
  5. pmc Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks
    Dmitry A Ravcheev
    Sanford Burnham Medical Research Institute, La Jolla, California 92037, USA
    BMC Genomics 14:873. 2013
  6. pmc Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria
    Eric I Sun
    Sanford Burnham Medical Research Institute, 92037 La Jolla, CA, USA
    BMC Genomics 14:597. 2013
  7. pmc RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes
    Michael J Cipriano
    Department of Microbiology, University of California Davis, Davis, CA 95616, USA
    BMC Genomics 14:213. 2013
  8. doi request reprint Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima
    Irina A Rodionova
    Sanford Burnham Medical Research Institute, La Jolla, CA 92037, USA
    Environ Microbiol 14:2920-34. 2012
  9. pmc A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life
    Crysten E Haas
    Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
    BMC Genomics 10:470. 2009
  10. pmc Reconstruction of xylose utilization pathway and regulons in Firmicutes
    Yang 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

Collaborators

Detail Information

Publications60

  1. 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
    ....
  2. pmc Genomic encyclopedia of sugar utilization pathways in the Shewanella genus
    Dmitry A Rodionov
    Burnham Institute for Medical Research, La Jolla, California 92037, USA
    BMC Genomics 11:494. 2010
    ....
  3. pmc Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum
    Marat 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...
  4. 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...
  5. pmc Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks
    Dmitry A Ravcheev
    Sanford Burnham Medical Research Institute, La Jolla, California 92037, USA
    BMC Genomics 14:873. 2013
    ..The availability of genomic sequences for multiple Bacteroides species opens an opportunity for their comparative analysis to enable characterization of their metabolic and regulatory networks...
  6. pmc Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria
    Eric I Sun
    Sanford Burnham Medical Research Institute, 92037 La Jolla, CA, USA
    BMC Genomics 14:597. 2013
    ..High conservation of these RNA motifs provides a unique advantage for their genomic identification and comparative analysis...
  7. pmc RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes
    Michael J Cipriano
    Department of Microbiology, University of California Davis, Davis, CA 95616, USA
    BMC Genomics 14:213. 2013
    ..Additionally, confirming computationally inferred regulons by experimental data is critically important...
  8. doi request reprint Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima
    Irina 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...
  9. pmc A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life
    Crysten 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...
  10. pmc Reconstruction of xylose utilization pathway and regulons in Firmicutes
    Yang 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...
  11. pmc Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization
    Yan 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...
  12. pmc The Zur regulon of Corynebacterium glutamicum ATCC 13032
    Jasmin Schröder
    Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universitat Bielefeld, D 33615 Bielefeld, Germany
    BMC Genomics 11:12. 2010
    ....
  13. ncbi request reprint 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...
  14. pmc Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus
    Dmitry 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...
  15. pmc A novel class of modular transporters for vitamins in prokaryotes
    Dmitry 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...
  16. 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...
  17. 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...
  18. 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
  19. pmc RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach
    Pavel S Novichkov
    Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Nucleic Acids Res 38:W299-307. 2010
    ..An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov...
  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 central carbon and energy metabolism in bacteria by redox-responsive repressor Rex
    Dmitry 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...
  22. 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...
  23. 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...
  24. pmc Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes
    Alexey 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)...
  25. ncbi request reprint 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...
  26. ncbi request reprint 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...
  27. ncbi request reprint 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...
  28. 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...
  29. pmc Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis
    Semen 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)...
  30. pmc Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis
    Semen A Leyn
    Sanford Burnham Medical Research Institute, La Jolla, California, USA
    J Bacteriol 195:2463-73. 2013
    ..The inferred collection of regulons is available in the RegPrecise database (http://regprecise.lbl.gov/) and can be used in genetic experiments, metabolic modeling, and evolutionary analysis...
  31. ncbi request reprint Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria
    Pavel S Novichkov
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
    Environ Microbiol 16:1-8. 2014
    ..The effector-sensing domain in SahR is related to SAM-dependent methylases that are able to tightly bind SAH. SahR represents a novel type of transcriptional regulators for the control of sulphur amino acid metabolism. ..
  32. pmc Diversity and versatility of the Thermotoga maritima sugar kinome
    Irina 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...
  33. 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...
  34. 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...
  35. pmc RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics
    Pavel 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...
  36. doi request reprint Novel inositol catabolic pathway in Thermotoga maritima
    Irina A Rodionova
    Sanford Burnham Medical Research Institute, La Jolla, CA 92037, USA
    Environ Microbiol 15:2254-66. 2013
    ..The determined in vitro specificity of the InoEFGK (TM0418-TM0421) transporter to myo-inositol-phosphate suggests that the novel pathway in Thermotoga utilizes a phosphorylated derivative of inositol. ..
  37. pmc Nicotinamide mononucleotide synthetase is the key enzyme for an alternative route of NAD biosynthesis in Francisella tularensis
    Leonardo 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
    ....
  38. 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...
  39. ncbi request reprint 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...
  40. ncbi request reprint 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...
  41. doi request reprint Evolution of regulatory motifs of bacterial transcription factors
    Konstantin 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...
  42. pmc Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteria
    Inna 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...
  43. pmc Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence
    Dmitry 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)...
  44. pmc Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria
    Dmitry 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...
  45. pmc Zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for GTP cyclohydrolase IB
    Banumathi Sankaran
    Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
    J Bacteriol 191:6936-49. 2009
    ..Notably, while humans possess the canonical GCYH-IA enzyme, many clinically important human pathogens possess only the GCYH-IB enzyme, suggesting that this enzyme is a potential new molecular target for antibacterial development...
  46. pmc RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria
    Pavel S Novichkov
    Lawrence Berkeley National Laboratory, Berkeley 94710, CA, USA
    BMC Genomics 14:745. 2013
    ..The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches)...
  47. pmc New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria
    Alexey E Kazakov
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    J Bacteriol 195:4466-75. 2013
    ..To our knowledge, this is a unique case of a family of bacterial transcriptional factors evolved from site-specific recombinases. ..
  48. pmc N-acetylgalactosamine utilization pathway and regulon in proteobacteria: genomic reconstruction and experimental characterization in Shewanella
    Semen 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...
  49. 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
    ....
  50. ncbi request reprint 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...
  51. ncbi request reprint 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...
  52. 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...
  53. 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...
  54. 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...
  55. 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
    ....
  56. 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...
  57. ncbi request reprint 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...
  58. 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...
  59. doi request reprint 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
    ....