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PMID: 17636889 Published · ppublish English Comparative Study Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Review

Comparative genomic reconstruction of transcriptional regulatory networks in bacteria.

Chemical reviews ·Vol. 107 ·No. 8 ·2007-08-00 ·Pages 3467-97

Rodionov DA

Abstract

暂无摘要

MeSH Terms
Bacteria/genetics,metabolism Computational Biology Databases, Genetic Gene Regulatory Networks/genetics Genome, Bacterial/genetics Genomics
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Rodionov Dmitry A
Burnham Institute for Medical Research, La Jolla, California 92037, USA. rodionov@burnham.org
References (275)
275 references, click to expand
  1. Transcription factor distribution in Escherichia coli: studies with FNR protein.
    Nucleic Acids Res. 2007;35(1):269-78 PMID: 17164287
  2. Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes.
    Nucleic Acids Res. 2004;32(1):143-50 PMID: 14704351
  3. A biophysical approach to transcription factor binding site discovery.
    Genome Res. 2003 Nov;13(11):2381-90 PMID: 14597652
  4. Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes.
    J Biol Chem. 2003 Oct 17;278(42):41148-59 PMID: 12869542
  5. Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea.
    Comput Biol Chem. 2004 Dec;28(5-6):341-50 PMID: 15556475
  6. Methods for calculating the probabilities of finding patterns in sequences.
    Comput Appl Biosci. 1989 Apr;5(2):89-96 PMID: 2720468
  7. DNA binding sites: representation and discovery.
    Bioinformatics. 2000 Jan;16(1):16-23 PMID: 10812473
  8. From genomics to chemical genomics: new developments in KEGG.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7 PMID: 16381885
  9. The cobZ gene of Methanosarcina mazei Go1 encodes the nonorthologous replacement of the alpha-ribazole-5'-phosphate phosphatase (CobC) enzyme of Salmonella enterica.
    J Bacteriol. 2006 Apr;188(7):2740-3 PMID: 16547066
  10. Evolution of sensory complexity recorded in a myxobacterial genome.
    Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15200-5 PMID: 17015832
  11. Global analysis of bacterial transcription factors to predict cellular target processes.
    Trends Genet. 2004 Mar;20(3):126-31 PMID: 15049306
  12. Iron and metal regulation in bacteria.
    Curr Opin Microbiol. 2001 Apr;4(2):172-7 PMID: 11282473
  13. Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.
    Genome Res. 2001 Mar;11(3):356-72 PMID: 11230160
  14. Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics.
    J Mol Biol. 2004 Apr 23;338(2):207-15 PMID: 15066426
  15. RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D407-12 PMID: 17142223
  16. Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?
    Nucleic Acids Res. 2003 Dec 1;31(23):6748-57 PMID: 14627808
  17. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes.
    Nucleic Acids Res. 2001 Feb 1;29(3):774-82 PMID: 11160901
  18. Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis.
    J Biol Chem. 2006 Oct 6;281(40):29872-85 PMID: 16857666
  19. The S(MK) box is a new SAM-binding RNA for translational regulation of SAM synthetase.
    Nat Struct Mol Biol. 2006 Mar;13(3):226-33 PMID: 16491091
  20. Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters.
    J Bacteriol. 2006 Jan;188(1):317-27 PMID: 16352848
  21. Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints.
    J Mol Biol. 1988 Sep 20;203(2):439-55 PMID: 3199442
  22. Structural classification of bacterial response regulators: diversity of output domains and domain combinations.
    J Bacteriol. 2006 Jun;188(12):4169-82 PMID: 16740923
  23. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria.
    Cell. 2002 Nov 27;111(5):747-56 PMID: 12464185
  24. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression.
    Nature. 2002 Oct 31;419(6910):952-6 PMID: 12410317
  25. Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D132-6 PMID: 17088283
  26. Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling.
    Trends Genet. 2005 Jul;21(7):385-9 PMID: 15949864
  27. Regulation of aromatic amino acid biosynthesis in gamma-proteobacteria.
    J Mol Microbiol Biotechnol. 2001 Oct;3(4):529-43 PMID: 11545272
  28. Catabolism of phenylalanine by Pseudomonas putida: the NtrC-family PhhR regulator binds to two sites upstream from the phhA gene and stimulates transcription with sigma70.
    J Mol Biol. 2007 Mar 9;366(5):1374-86 PMID: 17217960
  29. Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book.
    Nat Methods. 2004 Dec;1(3):195-202 PMID: 15789030
  30. Archaeal transcription and its regulators.
    Mol Microbiol. 2005 Jun;56(6):1397-407 PMID: 15916593
  31. Reconciling gene expression data with known genome-scale regulatory network structures.
    Genome Res. 2003 Nov;13(11):2423-34 PMID: 14559784
  32. Regulation of NAD synthesis by the trifunctional NadR protein of Salmonella enterica.
    J Bacteriol. 2005 Apr;187(8):2774-82 PMID: 15805524
  33. Identification of TogMNAB, an ABC transporter which mediates the uptake of pectic oligomers in Erwinia chrysanthemi 3937.
    Mol Microbiol. 2001 Sep;41(5):1113-23 PMID: 11555291
  34. Genome-wide survey of transcription factors in prokaryotes reveals many bacteria-specific families not found in archaea.
    DNA Res. 2005;12(5):269-80 PMID: 16769689
  35. Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria.
    FEMS Microbiol Lett. 2001 Dec 18;205(2):305-14 PMID: 11750820
  36. Regulation of bacterial gene expression by riboswitches.
    Annu Rev Microbiol. 2005;59:487-517 PMID: 16153177
  37. Riboswitches: the oldest mechanism for the regulation of gene expression?
    Trends Genet. 2004 Jan;20(1):44-50 PMID: 14698618
  38. Mass spectral analysis in proteomics.
    Annu Rev Biophys Biomol Struct. 2004;33:297-316 PMID: 15139815
  39. Cyclic AMP-independent catabolite repression in bacteria.
    FEMS Microbiol Lett. 1996 May 1;138(2-3):97-103 PMID: 9026456
  40. Comparative analysis of regulatory patterns in bacterial genomes.
    Brief Bioinform. 2000 Nov;1(4):357-71 PMID: 11465053
  41. Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module.
    Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2909-14 PMID: 17301237
  42. Promoters largely determine the efficiency of repressor action.
    Proc Natl Acad Sci U S A. 1988 Dec;85(23):8973-7 PMID: 3057497
  43. The zinc-responsive regulator Zur controls a zinc uptake system and some ribosomal proteins in Streptomyces coelicolor A3(2).
    J Bacteriol. 2007 Jun;189(11):4070-7 PMID: 17416659
  44. The evolution of two-component systems in bacteria reveals different strategies for niche adaptation.
    PLoS Comput Biol. 2006 Nov 3;2(11):e143 PMID: 17083272
  45. Genome update: distribution of two-component transduction systems in 250 bacterial genomes.
    Microbiology. 2005 Nov;151(Pt 11):3447-52 PMID: 16272367
  46. Tandem riboswitch architectures exhibit complex gene control functions.
    Science. 2006 Oct 13;314(5797):300-4 PMID: 17038623
  47. [Purine regulon of gamma-proteobacteria: a detailed description].
    Genetika. 2002 Sep;38(9):1203-14 PMID: 12391881
  48. Scaling laws in the functional content of genomes.
    Trends Genet. 2003 Sep;19(9):479-84 PMID: 12957540
  49. GntP is the Escherichia coli Fructuronic acid transporter and belongs to the UxuR regulon.
    J Bacteriol. 2004 Nov;186(22):7690-6 PMID: 15516583
  50. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes.
    Genome Res. 2000 Jun;10(6):744-57 PMID: 10854408
  51. The TetR family of transcriptional repressors.
    Microbiol Mol Biol Rev. 2005 Jun;69(2):326-56 PMID: 15944459
  52. Catabolite repression and activation in Bacillus subtilis: dependency on CcpA, HPr, and HprK.
    J Bacteriol. 2005 Nov;187(22):7826-39 PMID: 16267306
  53. Rfam: annotating non-coding RNAs in complete genomes.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4 PMID: 15608160
  54. Computational identification of the Spo0A-phosphate regulon that is essential for the cellular differentiation and development in Gram-positive spore-forming bacteria.
    Nucleic Acids Res. 2003 Dec 1;31(23):6891-903 PMID: 14627822
  55. The Rhizobium etli bioMNY operon is involved in biotin transport.
    FEMS Microbiol Lett. 2005 Sep 15;250(2):209-19 PMID: 16099603
  56. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control.
    Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6421-6 PMID: 15096624
  57. Riboswitch finder--a tool for identification of riboswitch RNAs.
    Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W154-9 PMID: 15215370
  58. Identification of a glycolytic regulon in the archaea Pyrococcus and Thermococcus.
    FEMS Microbiol Lett. 2006 Jul;260(1):69-76 PMID: 16790020
  59. MtaR, a regulator of methionine transport, is critical for survival of group B streptococcus in vivo.
    J Bacteriol. 2003 Nov;185(22):6592-9 PMID: 14594832
  60. Living without Fur: the subtlety and complexity of iron-responsive gene regulation in the symbiotic bacterium Rhizobium and other alpha-proteobacteria.
    Biometals. 2007 Jun;20(3-4):501-11 PMID: 17310401
  61. Transcript analysis reveals an extended regulon and the importance of protein-protein co-operativity for the Escherichia coli methionine repressor.
    Biochem J. 2006 Jun 1;396(2):227-34 PMID: 16515535
  62. The use of gene clusters to infer functional coupling.
    Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2896-901 PMID: 10077608
  63. The statistical significance of nucleotide position-weight matrix matches.
    Comput Appl Biosci. 1996 Oct;12(5):431-9 PMID: 8996792
  64. RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W690-2 PMID: 15980564
  65. Gibbs Recursive Sampler: finding transcription factor binding sites.
    Nucleic Acids Res. 2003 Jul 1;31(13):3580-5 PMID: 12824370
  66. The small RNA regulators of Escherichia coli: roles and mechanisms*.
    Annu Rev Microbiol. 2004;58:303-28 PMID: 15487940
  67. The IclR family of transcriptional activators and repressors can be defined by a single profile.
    Protein Sci. 2006 May;15(5):1207-13 PMID: 16597823
  68. Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling.
    J Biol Chem. 2004 Mar 26;279(13):12588-97 PMID: 14711822
  69. Damage-repair error-prone polymerases of eubacteria: association with mobile genome elements.
    Gene. 2002 Jun 26;293(1-2):133-40 PMID: 12137951
  70. Information content of binding sites on nucleotide sequences.
    J Mol Biol. 1986 Apr 5;188(3):415-31 PMID: 3525846
  71. DNA binding sites for the Mlc and NagC proteins: regulation of nagE, encoding the N-acetylglucosamine-specific transporter in Escherichia coli.
    Nucleic Acids Res. 2001 Jan 15;29(2):506-14 PMID: 11139621
  72. Whole-genome analysis of the chromosome partitioning and sporulation protein Spo0J (ParB) reveals spreading and origin-distal sites on the Bacillus subtilis chromosome.
    Mol Microbiol. 2007 May;64(3):703-18 PMID: 17462018
  73. Comparative genomics of NAD biosynthesis in cyanobacteria.
    J Bacteriol. 2006 Apr;188(8):3012-23 PMID: 16585762
  74. Molecular mechanism of tryptophan-dependent transcriptional regulation in Chlamydia trachomatis.
    J Bacteriol. 2006 Jun;188(12):4236-43 PMID: 16740930
  75. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.
    Proc Natl Acad Sci U S A. 1999 Apr 13;96(8):4285-8 PMID: 10200254
  76. [Regulation of respiration in enterobacteria: comparison of microarray and comparative genomic data].
    Mol Biol (Mosk). 2007 May-Jun;41(3):556-71 PMID: 17685233
  77. Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element.
    RNA. 2003 Sep;9(9):1084-97 PMID: 12923257
  78. Nitrogen assimilation and global regulation in Escherichia coli.
    Annu Rev Microbiol. 2003;57:155-76 PMID: 12730324
  79. PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.
    PLoS Comput Biol. 2005 Dec;1(7):e67 PMID: 16477324
  80. Bacterial regulatory networks are extremely flexible in evolution.
    Nucleic Acids Res. 2006;34(12):3434-45 PMID: 16840530
  81. Genomic analysis of protein kinases, protein phosphatases and two-component regulatory systems of the cyanobacterium Anabaena sp. strain PCC 7120.
    FEMS Microbiol Lett. 2002 Dec 17;217(2):155-65 PMID: 12480098
  82. The origin of prokaryotic C2H2 zinc finger regulators.
    Trends Microbiol. 2000 Feb;8(2):77-81 PMID: 10664601
  83. High-throughput methods of regulatory element discovery.
    Biotechniques. 2006 Dec;41(6):673, 675, 677 passim PMID: 17191608
  84. Whole genome plasticity in pathogenic bacteria.
    Curr Opin Microbiol. 2001 Oct;4(5):550-7 PMID: 11587932
  85. The riboflavin transporter RibU in Lactococcus lactis: molecular characterization of gene expression and the transport mechanism.
    J Bacteriol. 2006 Apr;188(8):2752-60 PMID: 16585736
  86. Activation and repression of transcription initiation in bacteria.
    Essays Biochem. 2001;37:17-31 PMID: 11758454
  87. The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria.
    Mol Microbiol. 1998 Nov;30(4):737-49 PMID: 10094622
  88. Cra and the control of carbon flux via metabolic pathways.
    Res Microbiol. 1996 Jul-Sep;147(6-7):489-93 PMID: 9084760
  89. NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes.
    J Bacteriol. 2007 Jul;189(14):5012-21 PMID: 17496099
  90. The Iron control element, acting in positive and negative control of iron-regulated Bradyrhizobium japonicum genes, is a target for the Irr protein.
    J Bacteriol. 2006 Jan;188(2):733-44 PMID: 16385063
  91. Liberation of zinc-containing L31 (RpmE) from ribosomes by its paralogous gene product, YtiA, in Bacillus subtilis.
    J Bacteriol. 2006 Apr;188(7):2715-20 PMID: 16547061
  92. Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups.
    Nucleic Acids Res. 2006;34(7):1947-58 PMID: 16614445
  93. Computer methods to locate signals in nucleic acid sequences.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):505-19 PMID: 6364039
  94. Heterologous production and characterization of bacterial nickel/cobalt permeases.
    FEMS Microbiol Lett. 2004 Jan 15;230(1):129-35 PMID: 14734175
  95. The RhaS activator controls the Erwinia chrysanthemi 3937 genes rhiN, rhiT and rhiE involved in rhamnogalacturonan catabolism.
    Mol Microbiol. 2004 Mar;51(5):1361-74 PMID: 14982630
  96. The Lactococcus lactis CodY regulon: identification of a conserved cis-regulatory element.
    J Biol Chem. 2005 Oct 7;280(40):34332-42 PMID: 16040604
  97. Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria.
    Genome Biol. 2004;5(11):R90 PMID: 15535866
  98. Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA.
    J Biol Chem. 2005 Apr 15;280(15):15084-96 PMID: 15699038
  99. Differences in LexA regulon structure among Proteobacteria through in vivo assisted comparative genomics.
    Nucleic Acids Res. 2004;32(22):6617-26 PMID: 15604457
  100. Prediction of transcription regulatory sites in Archaea by a comparative genomic approach.
    Nucleic Acids Res. 2000 Feb 1;28(3):695-705 PMID: 10637320
  101. Phylogenetic shadowing of primate sequences to find functional regions of the human genome.
    Science. 2003 Feb 28;299(5611):1391-4 PMID: 12610304
  102. Evolution of the NadR regulon in Enterobacteriaceae.
    J Bioinform Comput Biol. 2005 Aug;3(4):1007-19 PMID: 16078372
  103. Detecting protein function and protein-protein interactions from genome sequences.
    Science. 1999 Jul 30;285(5428):751-3 PMID: 10427000
  104. Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation.
    Nucleic Acids Res. 2002 Jul 15;30(14):3141-51 PMID: 12136096
  105. Regulation of biosynthesis and transport of aromatic amino acids in low-GC Gram-positive bacteria.
    FEMS Microbiol Lett. 2003 May 28;222(2):211-20 PMID: 12770710
  106. Evolution of transcriptional regulatory networks in microbial genomes.
    Curr Opin Struct Biol. 2006 Jun;16(3):420-9 PMID: 16650982
  107. Identifying global regulators in transcriptional regulatory networks in bacteria.
    Curr Opin Microbiol. 2003 Oct;6(5):482-9 PMID: 14572541
  108. [Computer analysis of regulatory signals in bacterial genomes. Fnr binding segments].
    Mol Biol (Mosk). 2001 Nov-Dec;35(6):1001-9 PMID: 11771123
  109. Combining microarray and genomic data to predict DNA binding motifs.
    Microbiology. 2005 Oct;151(Pt 10):3197-213 PMID: 16207904
  110. The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum.
    BMC Genomics. 2006;7:21 PMID: 16469103
  111. Comparative analysis of iron regulated genes in mycobacteria.
    FEBS Lett. 2006 May 15;580(11):2567-76 PMID: 16631750
  112. The regulation of bacterial transcription initiation.
    Nat Rev Microbiol. 2004 Jan;2(1):57-65 PMID: 15035009
  113. Comparative analysis of FUR regulons in gamma-proteobacteria.
    Nucleic Acids Res. 2001 Dec 15;29(24):5195-206 PMID: 11812853
  114. Network motifs in the transcriptional regulation network of Escherichia coli.
    Nat Genet. 2002 May;31(1):64-8 PMID: 11967538
  115. [Bacterial cis-regulatory RNA structures].
    Mol Biol (Mosk). 2006 Jul-Aug;40(4):609-19 PMID: 16913220
  116. DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D75-7 PMID: 14681362
  117. Conservation of the binding site for the arginine repressor in all bacterial lineages.
    Genome Biol. 2001;2(4):RESEARCH0013 PMID: 11305941
  118. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles.
    PLoS Biol. 2007 Jan;5(1):e8 PMID: 17214507
  119. From "simple" DNA-protein interactions to the macromolecular machines of gene expression.
    Annu Rev Biophys Biomol Struct. 2007;36:79-105 PMID: 17477836
  120. Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes--a genomic approach.
    BMC Genomics. 2006;7:147 PMID: 16772031
  121. Global analysis of gene transcription regulation in prokaryotes.
    Cell Mol Life Sci. 2006 Oct;63(19-20):2260-90 PMID: 16927028
  122. The biosynthesis of adenosylcobalamin (vitamin B12).
    Nat Prod Rep. 2002 Aug;19(4):390-412 PMID: 12195810
  123. Beyond the Fur paradigm: iron-controlled gene expression in rhizobia.
    FEMS Microbiol Rev. 2006 Jul;30(4):631-48 PMID: 16774589
  124. Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome.
    Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17933-8 PMID: 17101990
  125. Comparative studies of transcriptional regulation mechanisms in a group of eight gamma-proteobacterial genomes.
    J Mol Biol. 2005 Nov 18;354(1):184-99 PMID: 16236313
  126. Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis.
    FEMS Microbiol Lett. 2004 May 15;234(2):357-70 PMID: 15135544
  127. An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences.
    Proteins. 1990;7(1):41-51 PMID: 2184437
  128. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.
    Science. 1993 Oct 8;262(5131):208-14 PMID: 8211139
  129. AraC-XylS database: a family of positive transcriptional regulators in bacteria.
    Nucleic Acids Res. 2002 Jan 1;30(1):318-21 PMID: 11752325
  130. Pfam: clans, web tools and services.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51 PMID: 16381856
  131. Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions.
    Genome Biol. 2001;2(9):RESEARCH0034 PMID: 11820254
  132. Bioinformatic identification of novel regulatory DNA sequence motifs in Streptomyces coelicolor.
    BMC Microbiol. 2004 Apr 8;4:14 PMID: 15072583
  133. Finding composite regulatory patterns in DNA sequences.
    Bioinformatics. 2002;18 Suppl 1:S354-63 PMID: 12169566
  134. In silico analysis of the sigma54-dependent enhancer-binding proteins in Pirellula species strain 1.
    FEMS Microbiol Lett. 2004 Jan 30;230(2):215-25 PMID: 14757243
  135. Proteomic analysis reveals the wide-ranging effects of the novel, iron-responsive regulator RirA in Rhizobium leguminosarum bv. viciae.
    Mol Genet Genomics. 2005 Apr;273(2):197-206 PMID: 15856304
  136. Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms.
    J Biol Chem. 2002 Dec 13;277(50):48949-59 PMID: 12376536
  137. Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and sigmaR.
    J Bacteriol. 2007 Jun;189(11):4078-86 PMID: 17400736
  138. Evolutionary dynamics of prokaryotic transcriptional regulatory networks.
    J Mol Biol. 2006 Apr 28;358(2):614-33 PMID: 16530225
  139. MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes.
    Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W366-8 PMID: 16845027
  140. Discovery of novel transcription factor binding sites by statistical overrepresentation.
    Nucleic Acids Res. 2002 Dec 15;30(24):5549-60 PMID: 12490723
  141. Sulfur amino acid metabolism and its control in Lactococcus lactis IL1403.
    J Bacteriol. 2005 Jun;187(11):3762-78 PMID: 15901700
  142. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.
    Bioinformatics. 1999 Jul-Aug;15(7-8):563-77 PMID: 10487864
  143. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
    Nucleic Acids Res. 2005;33(17):5691-702 PMID: 16214803
  144. Making connections between novel transcription factors and their DNA motifs.
    Genome Res. 2005 Feb;15(2):312-20 PMID: 15653829
  145. RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D394-7 PMID: 16381895
  146. A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain.
    Nat Struct Mol Biol. 2007 Apr;14(4):308-17 PMID: 17384645
  147. Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR.
    J Biol Chem. 2003 Aug 8;278(32):29837-55 PMID: 12754220
  148. Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis.
    J Bacteriol. 2004 Dec;186(24):8385-400 PMID: 15576789
  149. Computational identification of BioR, a transcriptional regulator of biotin metabolism in Alphaproteobacteria, and of its binding signal.
    FEMS Microbiol Lett. 2006 Feb;255(1):102-7 PMID: 16436068
  150. Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome.
    Proc Natl Acad Sci U S A. 2005 Dec 6;102(49):17693-8 PMID: 16301522
  151. Ribosylnicotinamide kinase domain of NadR protein: identification and implications in NAD biosynthesis.
    J Bacteriol. 2002 Dec;184(24):6906-17 PMID: 12446641
  152. WebLogo: a sequence logo generator.
    Genome Res. 2004 Jun;14(6):1188-90 PMID: 15173120
  153. TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D274-9 PMID: 17135193
  154. DNA-dependent renaturation of an insoluble DNA binding protein. Identification of the RhaS binding site at rhaBAD.
    J Mol Biol. 1994 Nov 11;243(5):821-9 PMID: 7966303
  155. Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12.
    Bioinformatics. 1998 Jun;14(5):391-400 PMID: 9682052
  156. Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli.
    Nucleic Acids Res. 1982 May 11;10(9):2997-3011 PMID: 7048259
  157. [Study of the phenotypic occurrence of ura gene inactivation in Bacillus subtilis].
    Genetika. 2000 Aug;36(8):1166-8 PMID: 11033791
  158. Transcriptional regulation of the Escherichia coli rhaT gene.
    Microbiology. 1996 Jul;142 ( Pt 7):1833-40 PMID: 8757746
  159. Conserved regulatory motifs in bacteria: riboswitches and beyond.
    Trends Genet. 2004 Oct;20(10):475-9 PMID: 15363900
  160. Identifying protein-binding sites from unaligned DNA fragments.
    Proc Natl Acad Sci U S A. 1989 Feb;86(4):1183-7 PMID: 2919167
  161. Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes.
    Nucleic Acids Res. 1999 Jul 15;27(14):2981-9 PMID: 10390542
  162. An mRNA structure in bacteria that controls gene expression by binding lysine.
    Genes Dev. 2003 Nov 1;17(21):2688-97 PMID: 14597663
  163. Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria.
    PLoS Comput Biol. 2006 Dec 15;2(12):e163 PMID: 17173478
  164. Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle.
    Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4632-7 PMID: 11930012
  165. Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea.
    Genome Res. 2002 Oct;12(10):1507-16 PMID: 12368242
  166. Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins.
    Proc Natl Acad Sci U S A. 2003 Aug 19;100(17):9912-7 PMID: 12904577
  167. Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis.
    Nucleic Acids Res. 2005;33(16):5156-71 PMID: 16157864
  168. Application of global analysis techniques to Corynebacterium glutamicum: new insights into nitrogen regulation.
    J Biotechnol. 2006 Oct 20;126(1):101-10 PMID: 16698104
  169. Missing genes in metabolic pathways: a comparative genomics approach.
    Curr Opin Chem Biol. 2003 Apr;7(2):238-51 PMID: 12714058
  170. Zinc is a key factor in controlling alternation of two types of L31 protein in the Bacillus subtilis ribosome.
    Mol Microbiol. 2004 Apr;52(1):273-83 PMID: 15049826
  171. Computation-directed identification of OxyR DNA binding sites in Escherichia coli.
    J Bacteriol. 2001 Aug;183(15):4571-9 PMID: 11443092
  172. Genetic regulation of biological nitrogen fixation.
    Nat Rev Microbiol. 2004 Aug;2(8):621-31 PMID: 15263897
  173. Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli.
    Microbiol Mol Biol Rev. 2001 Sep;65(3):422-44, table of contents PMID: 11528004
  174. Computational analysis of the transcriptional regulation of pentose utilization systems in the gamma subdivision of Proteobacteria.
    FEMS Microbiol Lett. 2001 Dec 18;205(2):315-22 PMID: 11750821
  175. EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae.
    Nucleic Acids Res. 2003 Jul 1;31(13):3527-32 PMID: 12824359
  176. Prediction of co-regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related species.
    Genome Biol. 2001;2(11):RESEARCH0048 PMID: 11737947
  177. PhyloScan: identification of transcription factor binding sites using cross-species evidence.
    Algorithms Mol Biol. 2007 Jan 23;2:1 PMID: 17244358
  178. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria.
    Genome Biol. 2005;6(8):R70 PMID: 16086852
  179. ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms.
    BMC Microbiol. 2006;6:29 PMID: 16539733
  180. Differential analysis of DNA microarray gene expression data.
    Mol Microbiol. 2003 Feb;47(4):871-7 PMID: 12581345
  181. Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA.
    Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3083-8 PMID: 12626738
  182. The phosphate-starvation response in Vibrio cholerae O1 and phoB mutant under proteomic analysis: disclosing functions involved in adaptation, survival and virulence.
    Proteomics. 2006 Mar;6(5):1495-511 PMID: 16447160
  183. The enigmatic Escherichia coli fadE gene is yafH.
    J Bacteriol. 2002 Jul;184(13):3759-64 PMID: 12057976
  184. Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus.
    Genome Res. 2004 Jul;14(7):1362-73 PMID: 15231752
  185. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation.
    Nat Biotechnol. 1998 Oct;16(10):939-45 PMID: 9788350
  186. cTFbase: a database for comparative genomics of transcription factors in cyanobacteria.
    BMC Genomics. 2007;8:104 PMID: 17439663
  187. Global iron-dependent gene regulation in Escherichia coli. A new mechanism for iron homeostasis.
    J Biol Chem. 2003 Aug 8;278(32):29478-86 PMID: 12746439
  188. An mRNA structure that controls gene expression by binding FMN.
    Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15908-13 PMID: 12456892
  189. Co-evolution of transcription factors and their targets depends on mode of regulation.
    Genome Biol. 2006;7(7):R62 PMID: 16859509
  190. A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes.
    Trends Genet. 1999 Nov;15(11):439-42 PMID: 10529804
  191. Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria.
    Microbiology. 2004 Nov;150(Pt 11):3571-90 PMID: 15528647
  192. Members of the IclR family of bacterial transcriptional regulators function as activators and/or repressors.
    FEMS Microbiol Rev. 2006 Mar;30(2):157-86 PMID: 16472303
  193. The DtxR regulon of Corynebacterium glutamicum.
    J Bacteriol. 2006 Apr;188(8):2907-18 PMID: 16585752
  194. Identification of the binding sites of regulatory proteins in bacterial genomes.
    Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11772-7 PMID: 12181488
  195. The extracytoplasmic function (ECF) sigma factors.
    Adv Microb Physiol. 2002;46:47-110 PMID: 12073657
  196. Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
    Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36 PMID: 7584402
  197. Mining genome databases to identify and understand new gene regulatory systems.
    Curr Opin Microbiol. 2002 Apr;5(2):149-53 PMID: 11934610
  198. Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis.
    Annu Rev Genet. 2005;39:47-68 PMID: 16285852
  199. Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.
    J Mol Biol. 1987 Feb 20;193(4):723-50 PMID: 3612791
  200. Identification of the CRP regulon using in vitro and in vivo transcriptional profiling.
    Nucleic Acids Res. 2004;32(19):5874-93 PMID: 15520470
  201. In Staphylococcus aureus, fur is an interactive regulator with PerR, contributes to virulence, and Is necessary for oxidative stress resistance through positive regulation of catalase and iron homeostasis.
    J Bacteriol. 2001 Jan;183(2):468-75 PMID: 11133939
  202. Combining evidence using p-values: application to sequence homology searches.
    Bioinformatics. 1998;14(1):48-54 PMID: 9520501
  203. Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites.
    Nat Biotechnol. 2003 Apr;21(4):435-9 PMID: 12627170
  204. Transcription attenuation.
    Biochim Biophys Acta. 2002 Sep 13;1577(2):240-50 PMID: 12213655
  205. [Regulation of nitrogen metabolism in gram-positive bacteria].
    Mol Biol (Mosk). 2006 Sep-Oct;40(5):919-26 PMID: 17086994
  206. Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes.
    Nucleic Acids Res. 2004;32(16):4725-31 PMID: 15353560
  207. MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis.
    Bioinformatics. 2005 May 15;21(10):2563-5 PMID: 15722376
  208. Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems.
    Nucleic Acids Res. 2004;32(11):3340-53 PMID: 15215334
  209. In vivo hydrolysis of S-adenosylmethionine induces the met regulon of Escherichia coli.
    Microbiology. 2006 May;152(Pt 5):1451-9 PMID: 16622061
  210. Comparative genomics of regulation of heavy metal resistance in Eubacteria.
    BMC Microbiol. 2006;6:49 PMID: 16753059
  211. A DNA element recognised by the molybdenum-responsive transcription factor ModE is conserved in Proteobacteria, green sulphur bacteria and Archaea.
    BMC Microbiol. 2003 Dec 2;3:24 PMID: 14641908
  212. Assessing computational tools for the discovery of transcription factor binding sites.
    Nat Biotechnol. 2005 Jan;23(1):137-44 PMID: 15637633
  213. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements.
    Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W429-34 PMID: 16845041
  214. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria.
    Cell. 2003 May 30;113(5):577-86 PMID: 12787499
  215. PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences.
    BMC Bioinformatics. 2004 Oct 28;5:170 PMID: 15511292
  216. Approaches to the automatic discovery of patterns in biosequences.
    J Comput Biol. 1998 Summer;5(2):279-305 PMID: 9672833
  217. Discovery of regulatory elements by a computational method for phylogenetic footprinting.
    Genome Res. 2002 May;12(5):739-48 PMID: 11997340
  218. Sentra: a database of signal transduction proteins for comparative genome analysis.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D271-3 PMID: 17135204
  219. Genome wide identification of regulatory motifs in Bacillus subtilis.
    BMC Bioinformatics. 2003 May 16;4:18 PMID: 12749771
  220. Alternative sigma factors and their roles in bacterial virulence.
    Microbiol Mol Biol Rev. 2005 Dec;69(4):527-43 PMID: 16339734
  221. The McbR repressor modulated by the effector substance S-adenosylhomocysteine controls directly the transcription of a regulon involved in sulphur metabolism of Corynebacterium glutamicum ATCC 13032.
    Mol Microbiol. 2005 May;56(4):871-87 PMID: 15853877
  222. Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102.
    Nucleic Acids Res. 2006;34(3):1050-65 PMID: 16473855
  223. Reconstruction of microbial transcriptional regulatory networks.
    Curr Opin Biotechnol. 2004 Feb;15(1):70-7 PMID: 15102470
  224. Matrix formalism to describe functional states of transcriptional regulatory systems.
    PLoS Comput Biol. 2006 Aug 11;2(8):e101 PMID: 16895435
  225. BacTregulators: a database of transcriptional regulators in bacteria and archaea.
    Bioinformatics. 2004 Nov 1;20(16):2787-91 PMID: 15166024
  226. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data.
    Bioinformatics. 2004 Dec 12;20(18):3682-6 PMID: 15256401
  227. Functional determinants of transcription factors in Escherichia coli: protein families and binding sites.
    Trends Genet. 2003 Feb;19(2):75-9 PMID: 12547514
  228. Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes.
    Bioinformatics. 2005 Nov 15;21(22):4187-9 PMID: 16109747
  229. Regulation of nif expression in Methanococcus maripaludis: roles of the euryarchaeal repressor NrpR, 2-oxoglutarate, and two operators.
    J Biol Chem. 2005 Feb 18;280(7):5236-41 PMID: 15590692
  230. Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification.
    J Comput Biol. 2000;7(3-4):345-62 PMID: 11108467
  231. [Software for analyzing bacterial genomes].
    Mol Biol (Mosk). 2000 Mar-Apr;34(2):253-62 PMID: 10779952
  232. Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae).
    BMC Genomics. 2007;8:54 PMID: 17313674
  233. VISTA family of computational tools for comparative analysis of DNA sequences and whole genomes.
    Methods Mol Biol. 2006;338:69-89 PMID: 16888351
  234. Factors influencing the identification of transcription factor binding sites by cross-species comparison.
    Genome Res. 2002 Oct;12(10):1523-32 PMID: 12368244
  235. A glycine-dependent riboswitch that uses cooperative binding to control gene expression.
    Science. 2004 Oct 8;306(5694):275-9 PMID: 15472076
  236. Global analysis of iron assimilation and fur regulation in Yersinia pestis.
    FEMS Microbiol Lett. 2006 May;258(1):9-17 PMID: 16630248
  237. Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks.
    PLoS Comput Biol. 2005 Oct;1(5):e55 PMID: 16261196
  238. A comparative genomics approach to prediction of new members of regulons.
    Genome Res. 2001 Apr;11(4):566-84 PMID: 11282972
  239. MetaCyc: a multiorganism database of metabolic pathways and enzymes.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D511-6 PMID: 16381923
  240. Coenzyme B12 controls transcription of the Streptomyces class Ia ribonucleotide reductase nrdABS operon via a riboswitch mechanism.
    J Bacteriol. 2006 Apr;188(7):2512-20 PMID: 16547038
  241. Who's your neighbor? New computational approaches for functional genomics.
    Nat Biotechnol. 2000 Jun;18(6):609-13 PMID: 10835597
  242. A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli.
    Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4620-5 PMID: 11917098
  243. The Vibrio cholerae chitin utilization program.
    Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2524-9 PMID: 14983042
  244. Sequence logos: a new way to display consensus sequences.
    Nucleic Acids Res. 1990 Oct 25;18(20):6097-100 PMID: 2172928
  245. Genetic composition of the Bacillus subtilis SOS system.
    J Bacteriol. 2005 Nov;187(22):7655-66 PMID: 16267290
  246. The Streptomyces NrdR transcriptional regulator is a Zn ribbon/ATP cone protein that binds to the promoter regions of class Ia and class II ribonucleotide reductase operons.
    J Bacteriol. 2006 Nov;188(21):7635-44 PMID: 16950922
  247. A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth.
    J Biol Chem. 2006 Feb 24;281(8):4802-15 PMID: 16377617
  248. Genomic position analyses and the transcription machinery.
    J Mol Biol. 1998 Jan 16;275(2):165-70 PMID: 9466899
  249. Evolutionary population genetics of promoters: predicting binding sites and functional phylogenies.
    Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15936-41 PMID: 16236723
  250. Heat shock (sigma32 and HrcA/CIRCE) regulons in beta-, gamma- and epsilon-proteobacteria.
    J Mol Microbiol Biotechnol. 2003;6(3-4):174-81 PMID: 15153770
  251. An algorithm for finding signals of unknown length in DNA sequences.
    Bioinformatics. 2001;17 Suppl 1:S207-14 PMID: 11473011
  252. A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.
    Bioinformatics. 2005 May 15;21(10):2240-5 PMID: 15728117
  253. Recognition of regulatory sites by genomic comparison.
    Res Microbiol. 1999 Nov-Dec;150(9-10):755-71 PMID: 10673013
  254. [Comparative genomics analysis of nitrate and nitrite respiration in gamma proteobacteria].
    Mol Biol (Mosk). 2005 Sep-Oct;39(5):832-46 PMID: 16240717
  255. Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria.
    Nucleic Acids Res. 2006;34(9):2686-97 PMID: 16717279
  256. CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks.
    BMC Genomics. 2006;7:24 PMID: 16478536
  257. Microbial genome analyses: global comparisons of transport capabilities based on phylogenies, bioenergetics and substrate specificities.
    J Mol Biol. 1998 Apr 3;277(3):573-92 PMID: 9533881
  258. The FabR (YijC) transcription factor regulates unsaturated fatty acid biosynthesis in Escherichia coli.
    J Biol Chem. 2002 May 3;277(18):15558-65 PMID: 11859088
  259. Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria.
    Mol Microbiol. 2000 Nov;38(4):673-83 PMID: 11115104
  260. Chromatin immunoprecipitation and microarray-based analysis of protein location.
    Nat Protoc. 2006;1(2):729-48 PMID: 17406303
  261. The Spo0A regulon of Bacillus subtilis.
    Mol Microbiol. 2003 Dec;50(5):1683-701 PMID: 14651647
  262. Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes.
    Appl Environ Microbiol. 2005 Nov;71(11):7442-52 PMID: 16269786
  263. How does DNA sequence motif discovery work?
    Nat Biotechnol. 2006 Aug;24(8):959-61 PMID: 16900144
  264. Connecting protein structure with predictions of regulatory sites.
    Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7068-73 PMID: 17438293
  265. Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box.
    Mol Microbiol. 2003 Jul;49(1):157-65 PMID: 12823818
  266. The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12.
    Nucleic Acids Res. 2000 Apr 15;28(8):1838-47 PMID: 10734204
  267. DBD: a transcription factor prediction database.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D74-81 PMID: 16381970
  268. DNA microarrays: experimental issues, data analysis, and application to bacterial systems.
    Biotechnol Prog. 2004 Sep-Oct;20(5):1309-24 PMID: 15458312
  269. Control site location and transcriptional regulation in Escherichia coli.
    Microbiol Rev. 1991 Sep;55(3):371-94 PMID: 1943993
  270. The Fnr regulon of Bacillus subtilis.
    J Bacteriol. 2006 Feb;188(3):1103-12 PMID: 16428414
  271. Transcriptome analysis of Crp-dependent catabolite control of gene expression in Escherichia coli.
    J Bacteriol. 2004 Jun;186(11):3516-24 PMID: 15150239
  272. Global protein expression pattern of Bradyrhizobium japonicum bacteroids: a prelude to functional proteomics.
    Proteomics. 2005 Nov;5(16):4170-84 PMID: 16254929
  273. YrxA is the transcriptional regulator that represses de novo NAD biosynthesis in Bacillus subtilis.
    J Bacteriol. 2005 Oct;187(20):7155-60 PMID: 16199587
  274. Defining the Bacillus subtilis sigma(W) regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches.
    J Mol Biol. 2002 Feb 22;316(3):443-57 PMID: 11866510
  275. The SUPERFAMILY database in 2007: families and functions.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D308-13 PMID: 17098927
Article Info
Journal
Chemical reviews
Abbr.
Chem Rev
ISSN
0009-2665
Published
2007-08-00
Epub
2007-00-18
Pages
3467-97
Language
English
Region
United States
NLM ID
2985134R
PMCID
PMC2643304
Subset
IM
Grants
NIAID NIH HHS · R01 AI066244 · United States
NIAID NIH HHS · R01 AI066244-01A2 · United States
NIAID NIH HHS · 1R01AI066244-01A2 · United States
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