| [1] | Martinez-Antonio A, Collado-Vides J (2003) Identifying global regulators in transcriptional regulatory networks in bacteria. Curr Opin Microbiol 6: 482–489.
|
| [2] | Dillon SC, Dorman CJ (2010) Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol 8: 185–195.
|
| [3] | Kahramanoglou C, Seshasayee AS, Prieto AI, Ibberson D, Schmidt S, et al. (2011) Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res 39: 2073–2091.
|
| [4] | Cho BK, Knight EM, Barrett CL, Palsson BO (2008) Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A？/AT-tracts. Genome Res 18: 900–910.
|
| [5] | Dorman CJ, Kane KA (2009) DNA bridging and antibridging: a role for bacterial nucleoid-associated proteins in regulating the expression of laterally acquired genes. FEMS Microbiol Rev 33: 587–592.
|
| [6] | Bokal AJ, Ross W, Gaal T, Johnson RC, Gourse RL (1997) Molecular anatomy of a transcription activation patch: FIS-RNA polymerase interactions at the Escherichia coli rrnB P1 promoter. EMBO J 16: 154–162.
|
| [7] | Kelly A, Goldberg MD, Carroll RK, Danino V, Hinton JC, et al. (2004) A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium. Microbiology 150: 2037–2053.
|
| [8] | Finkel SE, Johnson RC (1992) The Fis protein: it's not just for DNA inversion anymore. Mol Microbiol 6: 3257–3265.
|
| [9] | Ussery D, Larsen TS, Wilkes KT, Friis C, Worning P, et al. (2001) Genome organisation and chromatin structure in Escherichia coli. Biochimie 83: 201–212.
|
| [10] | Morett E, Bork P (1998) Evolution of new protein function: recombinational enhancer Fis originated by horizontal gene transfer from the transcriptional regulator NtrC. FEBS Lett 433: 108–112.
|
| [11] | Schneider R, Lurz R, Luder G, Tolksdorf C, Travers A, et al. (2001) An architectural role of the Escherichia coli chromatin protein FIS in organising DNA. Nucleic Acids Res 29: 5107–5114.
|
| [12] | Baracchini E, Bremer H (1991) Control of rRNA synthesis in Escherichia coli at increased rrn gene dosage. J Biol Chem 266: 11753–11760.
|
| [13] | Grainger DC, Hurd D, Goldberg MD, Busby SJ (2006) Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. Nucleic Acids Res 34: 4642–4652.
|
| [14] | Zhi H, Wang X, Cabrera JE, Johnson RC, Jin DJ (2003) Fis stabilizes the interaction between RNA polymerase and the ribosomal promoter rrnB P1, leading to transcriptional activation. J Biol Chem 278: 47340–47349.
|
| [15] | Browning DF, Grainger DC, Busby SJ (2010) Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression. Curr Opin Microbiol 13: 773–780.
|
| [16] | Hengen PN, Bartram SL, Stewart LE, Schneider TD (1997) Information analysis of Fis binding sites. Nucleic Acids Res 25: 4994–5002.
|
| [17] | Gonzalez-Gil G, Bringmann P, Kahmann R (1996) FIS is a regulator of metabolism in Escherichia coli. Mol Microbiol 22: 21–29.
|
| [18] | Browning DF, Beatty CM, Sanstad EA, Gunn KE, Busby SJ, et al. (2004) Modulation of CRP-dependent transcription at the Escherichia coli acsP2 promoter by nucleoprotein complexes: anti-activation by the nucleoid proteins FIS and IHF. Mol Microbiol 51: 241–254.
|
| [19] | Nasser W, Rochman M, Muskhelishvili G (2002) Transcriptional regulation of fis operon involves a module of multiple coupled promoters. EMBO J 21: 715–724.
|
| [20] | Weinstein-Fischer D, Altuvia S (2007) Differential regulation of Escherichia coli topoisomerase I by Fis. Mol Microbiol 63: 1131–1144.
|
| [21] | Husnain SI, Thomas MS (2008) Downregulation of the Escherichia coli guaB promoter by FIS. Microbiology 154: 1729–1738.
|
| [22] | Stella S, Cascio D, Johnson RC (2010) The shape of the DNA minor groove directs binding by the DNA-bending protein Fis. Genes Dev 24: 814–826.
|
| [23] | Shultzaberger RK, Roberts LR, Lyakhov IG, Sidorov IA, Stephen AG, et al. (2007) Correlation between binding rate constants and individual information of E. coli Fis binding sites. Nucleic Acids Res 35: 5275–5283.
|
| [24] | McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, et al. (2001) Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413: 852–856.
|
| [25] | Fass E, Groisman EA (2009) Control of Salmonella pathogenicity island-2 gene expression. Curr Opin Microbiol 12: 199–204.
|
| [26] | Cameron AD, Stoebel DM, Dorman CJ (2011) DNA supercoiling is differentially regulated by environmental factors and FIS in Escherichia coli and Salmonella enterica. Mol Microbiol 80: 85–101.
|
| [27] | Weinstein-Fischer D, Elgrably-Weiss M, Altuvia S (2000) Escherichia coli response to hydrogen peroxide: a role for DNA supercoiling, topoisomerase I and Fis. Mol Microbiol 35: 1413–1420.
|
| [28] | Schneider R, Travers A, Muskhelishvili G (1997) FIS modulates growth phase-dependent topological transitions of DNA in Escherichia coli. Mol Microbiol 26: 519–530.
|
| [29] | Goldberg MD, Johnson M, Hinton JC, Williams PH (2001) Role of the nucleoid-associated protein Fis in the regulation of virulence properties of enteropathogenic Escherichia coli. Mol Microbiol 41: 549–559.
|
| [30] | Wilson RL, Libby SJ, Freet AM, Boddicker JD, Fahlen TF, et al. (2001) Fis, a DNA nucleoid-associated protein, is involved in Salmonella typhimurium SPI-1 invasion gene expression. Mol Microbiol 39: 79–88.
|
| [31] | Karambelkar S, Swapna G, Nagaraja V (2012) Silencing of toxic gene expression by Fis. Nucleic Acids Res 40: 4358–4367.
|
| [32] | Ellermeier JR, Slauch JM (2007) Adaptation to the host environment: regulation of the SPI1 type III secretion system in Salmonella enterica serovar Typhimurium. Curr Opin Microbiol 10: 24–29.
|
| [33] | Eichelberg K, Galan JE (1999) Differential regulation of Salmonella typhimurium type III secreted proteins by pathogenicity island 1 (SPI-1)-encoded transcriptional activators InvF and HilA. Infect Immun 67: 4099–4105.
|
| [34] | Feng X, Oropeza R, Kenney LJ (2003) Dual regulation by phospho-OmpR of ssrA/B gene expression in Salmonella pathogenicity island 2. Mol Microbiol 48: 1131–1143.
|
| [35] | Rychlik I, Karasova D, Sebkova A, Volf J, Sisak F, et al. (2009) Virulence potential of five major pathogenicity islands (SPI-1 to SPI-5) of Salmonella enterica serovar Enteritidis for chickens. BMC Microbiol 9: 268.
|
| [36] | Gerlach RG, Claudio N, Rohde M, Jackel D, Wagner C, et al. (2008) Cooperation of Salmonella pathogenicity islands 1 and 4 is required to breach epithelial barriers. Cell Microbiol 10: 2364–2376.
|
| [37] | Marcus SL, Brumell JH, Pfeifer CG, Finlay BB (2000) Salmonella pathogenicity islands: big virulence in small packages. Microbes Infect 2: 145–156.
|
| [38] | Blanc-Potard AB, Solomon F, Kayser J, Groisman EA (1999) The SPI-3 pathogenicity island of Salmonella enterica. J Bacteriol 181: 998–1004.
|
| [39] | Cameron AD, Dorman CJ (2012) A fundamental regulatory mechanism operating through OmpR and DNA topology controls expression of Salmonella pathogenicity islands SPI-1 and SPI-2. PLoS Genet 8: e1002615.
|
| [40] | Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97: 6640–6645.
|
| [41] | Ju H, Zou R, Venema VJ, Venema RC (1997) Direct interaction of endothelial nitric-oxide synthase and caveolin-1 inhibits synthase activity. J Biol Chem 272: 18522–18525.
|
| [42] | Wang RF, Kushner SR (1991) Construction of versatile low-copy-number vectors for cloning, sequencing and gene expression in E.coli. Gene 100: 195–199.
|
| [43] | Bowden SD, Ramachandran VK, Knudsen GM, Hinton JC, Thompson A (2010) An incomplete TCA cycle increases survival of Salmonella Typhimurium during infection of resting and activated murine macrophages. PLoS One 5: e13871.
|
| [44] | Penheiter KL, Mathur N, Giles D, Fahlen T, Jones BD (1997) Non-invasive Salmonella typhimurium mutants are avirulent because of an inability to enter and destroy M cells of ileal Peyer's patches. Mol Microbiol 24: 697–709.
|
| [45] | Jing D, Agnew J, Patton WF, Hendrickson J, Beechem JM (2003) A sensitive two-color electrophoretic mobility shift assay for detecting both nucleic acids and protein in gels. Proteomics 3: 1172–1180.
|
| [46] | Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621–628.
|
| [47] | Cox MP, Peterson DA, Biggs PJ (2010) SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11: 485.
|
| [48] | Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105–1111.
|
| [49] | Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L (2011) Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol 12: R22.
|
| [50] | Bailey TL, Boden M, Buske FA, Frith M, Grant CE, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202–W208.
|
| [51] | Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34: W369–W373.
|
| [52] | Machanick P, Bailey TL (2011) MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27: 1696–1697.
|
| [53] | Osuna R, Lienau D, Hughes KT, Johnson RC (1995) Sequence, regulation, and functions of Fis in Salmonella typhimurium. J Bacteriol 177: 2021–2032.
|
| [54] | Ramseier TM, Bledig S, Michotey V, Feghali R, Saier MJ (1995) The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli. Mol Microbiol 16: 1157–1169.
|
| [55] | Chen YM, Zhu Y, Lin EC (1987) The organization of the fuc regulon specifying L-fucose dissimilation in Escherichia coli K12 as determined by gene cloning. Mol Gen Genet 210: 331–337.
|
| [56] | Liu X, Matsumura P (1994) The FlhD/FlhC complex, a transcriptional activator of the Escherichia coli flagellar class II operons. J Bacteriol 176: 7345–7351.
|
| [57] | Yamada M, Saier MJ (1988) Positive and negative regulators for glucitol (gut) operon expression in Escherichia coli. J Mol Biol 203: 569–583.
|
| [58] | Lee SK, Newman JD, Keasling JD (2005) Catabolite repression of the propionate catabolic genes in Escherichia coli and Salmonella enterica: evidence for involvement of the cyclic AMP receptor protein. J Bacteriol 187: 2793–2800.
|
| [59] | Jeter RM, Olivera BM, Roth JR (1984) Salmonella typhimurium synthesizes cobalamin (vitamin B12) de novo under anaerobic growth conditions. J Bacteriol 159: 206–213.
|
| [60] | Raux E, Lanois A, Levillayer F, Warren MJ, Brody E, et al. (1996) Salmonella typhimurium cobalamin (vitamin B12) biosynthetic genes: functional studies in S. typhimurium and Escherichia coli. J Bacteriol 178: 753–767.
|
| [61] | Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM (1993) Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. J Bacteriol 175: 3303–3316.
|
| [62] | Martens JH, Barg H, Warren MJ, Jahn D (2002) Microbial production of vitamin B12. Appl Microbiol Biotechnol 58: 275–285.
|
| [63] | Bobik TA, Ailion M, Roth JR (1992) A single regulatory gene integrates control of vitamin B12 synthesis and propanediol degradation. J Bacteriol 174: 2253–2266.
|
| [64] | Sittka A, Pfeiffer V, Tedin K, Vogel J (2007) The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium. Mol Microbiol 63: 193–217.
|
| [65] | Thompson A, Rolfe MD, Lucchini S, Schwerk P, Hinton JC, et al. (2006) The bacterial signal molecule, ppGpp, mediates the environmental regulation of both the invasion and intracellular virulence gene programs of Salmonella. J Biol Chem 281: 30112–30121.
|
| [66] | Schechter LM, Lee CA (2001) AraC/XylS family members, HilC and HilD, directly bind and derepress the Salmonella typhimurium hilA promoter. Mol Microbiol 40: 1289–1299.
|
| [67] | Akbar S, Schechter LM, Lostroh CP, Lee CA (2003) AraC/XylS family members, HilD and HilC, directly activate virulence gene expression independently of HilA in Salmonella typhimurium. Mol Microbiol 47: 715–728.
|
| [68] | Bajaj V, Hwang C, Lee CA (1995) hilA is a novel ompR/toxR family member that activates the expression of Salmonella typhimurium invasion genes. Mol Microbiol 18: 715–727.
|
| [69] | Walthers D, Carroll RK, Navarre WW, Libby SJ, Fang FC, et al. (2007) The response regulator SsrB activates expression of diverse Salmonella pathogenicity island 2 promoters and counters silencing by the nucleoid-associated protein H-NS. Mol Microbiol 65: 477–493.
|
| [70] | Linehan SA, Rytkonen A, Yu XJ, Liu M, Holden DW (2005) SlyA regulates function of Salmonella pathogenicity island 2 (SPI-2) and expression of SPI-2-associated genes. Infect Immun 73: 4354–4362.
|
| [71] | Ellermeier CD, Ellermeier JR, Slauch JM (2005) HilD, HilC and RtsA constitute a feed forward loop that controls expression of the SPI1 type three secretion system regulator hilA in Salmonella enterica serovar Typhimurium. Mol Microbiol 57: 691–705.
|
| [72] | Carroll RK, Liao X, Morgan LK, Cicirelli EM, Li Y, et al. (2009) Structural and functional analysis of the C-terminal DNA binding domain of the Salmonella typhimurium SPI-2 response regulator SsrB. J Biol Chem 284: 12008–12019.
|
| [73] | Dillon SC, Cameron AD, Hokamp K, Lucchini S, Hinton JC, et al. (2010) Genome-wide analysis of the H-NS and Sfh regulatory networks in Salmonella Typhimurium identifies a plasmid-encoded transcription silencing mechanism. Mol Microbiol 76: 1250–1265.
|
| [74] | Shimada T, Ishihama A, Busby SJ, Grainger DC (2008) The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions. Nucleic Acids Res 36: 3950–3955.
|
| [75] | Navarre WW, Porwollik S, Wang Y, McClelland M, Rosen H, et al. (2006) Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science 313: 236–238.
|
| [76] | Nagarajavel V, Madhusudan S, Dole S, Rahmouni AR, Schnetz K (2007) Repression by binding of H-NS within the transcription unit. J Biol Chem 282: 23622–23630.
|
| [77] | Reppas NB, Wade JT, Church GM, Struhl K (2006) The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol Cell 24: 747–757.
|
| [78] | Postow L, Hardy CD, Arsuaga J, Cozzarelli NR (2004) Topological domain structure of the Escherichia coli chromosome. Genes Dev 18: 1766–1779.
|
| [79] | Lee CA, Falkow S (1990) The ability of Salmonella to enter mammalian cells is affected by bacterial growth state. Proc Natl Acad Sci U S A 87: 4304–4308.
|
| [80] | Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, et al. (2008) Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet 4: e1000163.
|
| [81] | Lobry JR (1996) Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 13: 660–665.
|
