title: Comparative genomics of the dormancy regulons in mycobacteria.
abstract: In response to stresses, Mycobacterium cells become dormant. This process is regulated by the DosR transcription factor. In Mycobacterium tuberculosis, the dormancy regulon is well characterized and contains the dosR gene itself and dosS and dosT genes encoding DosR kinases, nitroreductases (acg; Rv3131), diacylglycerol acyltransferase (DGAT) (Rv3130c), and many universal stress proteins (USPs). In this study, we apply comparative genomic analysis to characterize the DosR regulons in nine Mycobacterium genomes, Rhodococcus sp. RHA1, Nocardia farcinica, and Saccharopolyspora erythraea. The regulons are highly labile, containing eight core gene groups (regulators, kinases, USPs, DGATs, nitroreductases, ferredoxins, heat shock proteins, and the orthologs of the predicted kinase [Rv2004c] from M. tuberculosis) and 10 additional genes with more restricted taxonomic distribution that are mostly involved in anaerobic respiration. The largest regulon is observed in M. marinum and the smallest in M. abscessus. Analysis of large gene families encoding USPs, nitroreductases, and DGATs demonstrates a mosaic distribution of regulated and nonregulated members, suggesting frequent acquisition and loss of DosR-binding sites.
authors: Energy Bioscience Institute, University of California, Berkeley, California 94720, USA. AGerasimova@lbl.gov
authors: Anna
authors: A
authors: Gerasimova
authors: Alexey E
authors: AE
authors: Kazakov
authors: Adam P
authors: AP
authors: Arkin
authors: Inna
authors: I
authors: Dubchak
authors: Mikhail S
authors: MS
authors: Gelfand
references: Mol Microbiol. 2006 Jun;60(6):1432-45
references: 16796679
references: J Bacteriol. 2002 Dec;184(24):6760-7
references: 12446625
references: Extremophiles. 2001 Dec;5(6):357-73
references: 11778837
references: Tuberculosis (Edinb). 2004;84(3-4):247-55
references: 15207494
references: J Bacteriol. 2008 Oct;190(20):6795-804
references: 18708494
references: BMC Bioinformatics. 2007 Nov 22;8:460
references: 18034891
references: J Bacteriol. 2003 Dec;185(24):7247-56
references: 14645286
references: Infect Immun. 2008 Jun;76(6):2587-93
references: 18362135
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D111-8
references: 19884135
references: BMC Bioinformatics. 2004 Aug 19;5:113
references: 15318951
references: J Biomol Struct Dyn. 2009 Dec;27(3):283-92
references: 19795912
references: Biochemistry. 2011 Feb 15;50(6):1023-8
references: 21250657
references: Infect Immun. 2006 Feb;74(2):1233-42
references: 16428773
references: Bioinformatics. 2007 Nov 1;23(21):2947-8
references: 17846036
references: PLoS One. 2010 Jan 07;5(1):e8614
references: 20062806
references: J Bacteriol. 1999 Jun;181(12):3658-65
references: 10368138
references: J Mol Biol. 2003 Oct 31;333(4):781-815
references: 14568537
references: BMC Genomics. 2007 Feb 21;8:54
references: 17313674
references: Nucleic Acids Res. 2007 Jan;35(Database issue):D21-5
references: 17202161
references: Infect Immun. 2009 Aug;77(8):3258-63
references: 19487478
references: Nucleic Acids Res. 2001 Dec 15;29(24):5195-206
references: 11812853
references: Tuberculosis (Edinb). 2004;84(1-2):29-44
references: 14670344
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D401-7
references: 19900966
references: Nucleic Acids Res. 1999 Jul 15;27(14):2981-9
references: 10390542
references: Nature. 2001 Feb 22;409(6823):1007-11
references: 11234002
references: Tuberculosis (Edinb). 2004;84(3-4):218-27
references: 15207491
references: Tuberculosis (Edinb). 2010 Mar;90(2):94-118
references: 20236863
references: Science. 1997 Oct 24;278(5338):631-7
references: 9381173
references: J Biol Chem. 2004 May 28;279(22):23082-7
references: 15033981
references: Mol Microbiol. 2010 Sep;77(5):1172-85
references: 20624223
references: Mol Biol (Mosk). 2000 Mar-Apr;34(2):253-62
references: 10779952
references: Infect Immun. 2003 Sep;71(9):5332-43
references: 12933881
references: Proc Natl Acad Sci U S A. 2007 Jul 10;104(28):11568-73
references: 17609369
references: Syst Biol. 2003 Oct;52(5):696-704
references: 14530136
references: J Bacteriol. 2010 Oct;192(19):4868-75
references: 20675480
references: Genome Res. 2004 Jun;14(6):1188-90
references: 15173120
references: Proc Natl Acad Sci U S A. 1996 Feb 6;93(3):1226-31
references: 8577745
references: J Exp Med. 2003 Sep 1;198(5):693-704
references: 12953091
references: Tuberculosis (Edinb). 2009 Jul;89(4):310-6
references: 19577518
references: Tuberculosis (Edinb). 2004;84(3-4):138-43
references: 15207483
references: J Exp Med. 2003 Sep 1;198(5):705-13
references: 12953092
references: Microbiology (Reading). 2005 Dec;151(Pt 12):4045-4053
references: 16339949
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D396-400
references: 19906701
references: J Bacteriol. 2010 Dec;192(24):6447-55
references: 20952575
references: Mol Microbiol. 2003 May;48(3):833-43
references: 12694625
references: Infect Immun. 2008 Jun;76(6):2478-89
references: 18391009
references: Protein Sci. 2007 Aug;16(8):1708-19
references: 17600145
references: J Bacteriol. 2004 Aug;186(15):5017-30
references: 15262939
references: Annu Rev Microbiol. 2001;55:139-63
references: 11544352