1887

Abstract

SlyA is a member of the MarR family of bacterial transcriptional regulators. Previously, SlyA has been shown to directly regulate only two operons in Escherichia coli K-12 MG1655, fimB and hlyE (clyA). In both cases, SlyA activates gene expression by antagonizing repression by the nucleoid-associated protein H-NS. Here, the transcript profiles of aerobic glucose-limited steady-state chemostat cultures of E. coli K-12 MG1655, slyA mutant and slyA over-expression strains are reported. The transcript profile of the slyA mutant was not significantly different from that of the parent; however, that of the slyA expression strain was significantly different from that of the vector control. Transcripts representing 27 operons were increased in abundance, whereas 3 were decreased. Of the 30 differentially regulated operons, 24 have previously been associated with sites of H-NS binding, suggesting that antagonism of H-NS repression is a common feature of SlyA-mediated transcription regulation. Direct binding of SlyA to DNA located upstream of a selection of these targets permitted the identification of new operons likely to be directly regulated by SlyA. Transcripts of four operons coding for cryptic adhesins exhibited enhanced expression, and this was consistent with enhanced biofilm formation associated with the SlyA over-producing strain.

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2017-03-29
2019-09-23
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References

  1. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY et al. Pfam: the protein families database. Nucleic Acids Res 2014;42:D222–D230 [CrossRef][PubMed]
    [Google Scholar]
  2. Perera IC, Grove A. Molecular mechanisms of ligand-mediated attenuation of DNA binding by MarR family transcriptional regulators. J Mol Cell Biol 2010;2:243–254 [CrossRef][PubMed]
    [Google Scholar]
  3. Martin RG, Rosner JL. Binding of purified multiple antibiotic-resistance repressor protein (MarR) to mar operator sequences. Proc Natl Acad Sci USA 1995;92:5456–5460 [CrossRef]
    [Google Scholar]
  4. Oh SY, Shin JH, Roe JH. Dual role of OhrR as a repressor and an activator in response to organic hydroperoxides in Streptomyces coelicolor. J Bacteriol 2007;189:6284–6292 [CrossRef][PubMed]
    [Google Scholar]
  5. Cathelyn JS, Ellison DW, Hinchliffe SJ, Wren BW, Miller VL. The RovA regulons of Yersinia enterocolitica and Yersinia pestis are distinct: evidence that many RovA-regulated genes were acquired more recently than the core genome. Mol Microbiol 2007;66:189–205 [CrossRef][PubMed]
    [Google Scholar]
  6. Wilkinson SP, Grove A. Ligand-responsive transcriptional regulation by members of the MarR family of winged helix proteins. Curr Issues Mol Biol 2006;8:51–62[PubMed]
    [Google Scholar]
  7. Buchmeier N, Bossie S, Chen CY, Fang FC, Guiney DG et al. SlyA, a transcriptional regulator of Salmonella typhimurium, is required for resistance to oxidative stress and is expressed in the intracellular environment of macrophages. Infect Immun 1997;65:3725–3730[PubMed]
    [Google Scholar]
  8. Libby SJ, Goebel W, Ludwig A, Buchmeier N, Bowe F et al. A cytolysin encoded by Salmonella is required for survival within macrophages. Proc Natl Acad Sci USA 1994;91:489–493 [CrossRef][PubMed]
    [Google Scholar]
  9. Haider F, Lithgow JK, Stapleton MR, Norte VA, Roberts RE et al. DNA recognition by the Salmonella enterica serovar Typhimurium transcription factor SlyA. Intl Microbiol 2008;11:245–250
    [Google Scholar]
  10. Stapleton MR, Norte VA, Read RC, Green J. Interaction of the Salmonella typhimurium transcription and virulence factor SlyA with target DNA and identification of members of the SlyA regulon. J Biol Chem 2002;277:17630–17637 [CrossRef][PubMed]
    [Google Scholar]
  11. Colgan AM, Kröger C, Diard M, Hardt WD, Puente JL et al. The impact of 18 ancestral and horizontally-acquired regulatory proteins upon the transcriptome and sRNA landscape of Salmonella enterica serovar Typhimurium. PLoS Genet 2016;12:e1006258 [CrossRef][PubMed]
    [Google Scholar]
  12. Navarre WW, Halsey TA, Walthers D, Frye J, Mcclelland M et al. Co-regulation of Salmonella enterica genes required for virulence and resistance to antimicrobial peptides by SlyA and PhoP/PhoQ. Mol Microbiol 2005;56:492–508 [CrossRef][PubMed]
    [Google Scholar]
  13. Norte VA, Stapleton MR, Green J. PhoP-responsive expression of the Salmonella enterica serovar Typhimurium slyA gene. J Bacteriol 2003;185:3508–3514 [CrossRef][PubMed]
    [Google Scholar]
  14. Perez JC, Latifi T, Groisman EA. Overcoming H-NS-mediated transcriptional silencing of horizontally acquired genes by the PhoP and SlyA proteins in Salmonella enterica. J Biol Chem 2008;283:10773–10783 [CrossRef][PubMed]
    [Google Scholar]
  15. Spory A, Bosserhoff A, von Rhein C, Goebel W, Ludwig A. Differential regulation of multiple proteins of Escherichia coli and Salmonella enterica serovar Typhimurium by the transcriptional regulator SlyA. J Bacteriol 2002;184:3549–3559 [CrossRef][PubMed]
    [Google Scholar]
  16. Dalebroux ZD, Swanson MS. ppGpp: magic beyond RNA polymerase. Nat Rev Microbiol 2012;10:203–212 [CrossRef][PubMed]
    [Google Scholar]
  17. Zhao G, Weatherspoon N, Kong W, Curtiss R, Shi Y. A dual-signal regulatory circuit activates transcription of a set of divergent operons in Salmonella typhimurium. Proc Natl Acad Sci USA 2008;105:20924–20929 [CrossRef][PubMed]
    [Google Scholar]
  18. Chalabaev S, Chauhan A, Novikov A, Iyer P, Szczesny M et al. Biofilms formed by Gram-negative bacteria undergo increased lipid a palmitoylation, enhancing in vivo survival. MBio 2014;5:e01116-14 [CrossRef][PubMed]
    [Google Scholar]
  19. Corbett D, Bennett HJ, Askar H, Green J, Roberts IS. SlyA and H-NS regulate transcription of the Escherichia coli K5 capsule gene cluster, and expression of slyA in Escherichia coli is temperature-dependent, positively autoregulated, and independent of H-NS. J Biol Chem 2007;282:33326–33335 [CrossRef][PubMed]
    [Google Scholar]
  20. Lithgow JK, Haider F, Roberts IS, Green J. Alternate SlyA and H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12. Mol Microbiol 2007;66:685–698 [CrossRef][PubMed]
    [Google Scholar]
  21. Mcvicker G, Sun L, Sohanpal BK, Gashi K, Williamson RA et al. SlyA protein activates fimB gene expression and type 1 fimbriation in Escherichia coli K-12. J Biol Chem 2011;286:32026–32035 [CrossRef][PubMed]
    [Google Scholar]
  22. Xue P, Corbett D, Goldrick M, Naylor C, Roberts IS. Regulation of expression of the region 3 promoter of the Escherichia coli K5 capsule gene cluster involves H-NS, SlyA, and a large 5' untranslated region. J Bacteriol 2009;191:1838–1846 [CrossRef][PubMed]
    [Google Scholar]
  23. Wyborn NR, Stapleton MR, Norte VA, Roberts RE, Grafton J et al. Regulation of Escherichia coli hemolysin E expression by H-NS and Salmonella SlyA. J Bacteriol 2004;186:1620–1628 [CrossRef][PubMed]
    [Google Scholar]
  24. Sambrook J, Russell DW. Molecular Cloning – a Laboratory Manual, 3rd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 2001
    [Google Scholar]
  25. Evans CGT, Herbert D, Tempest DW. The continuous cultivation of micro-organisms. Meth Microbiol 1970;2:278–327
    [Google Scholar]
  26. Studier FW. Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 2005;41:207–234 [CrossRef][PubMed]
    [Google Scholar]
  27. Tagliabue L, Antoniani D, Maciag A, Bocci P, Raffaelli N et al. The diguanylate cyclase YddV controls production of the exopolysaccharide poly-N-acetylglucosamine (PNAG) through regulation of the PNAG biosynthetic pgaABCD operon. Microbiology 2010;156:2901–2911 [CrossRef][PubMed]
    [Google Scholar]
  28. Rolfe MD, Ter Beek A, Graham AI, Trotter EW, Asif HM et al. Transcript profiling and inference of Escherichia coli K-12 ArcA activity across the range of physiologically relevant oxygen concentrations. J Biol Chem 2011;286:10147–10154 [CrossRef][PubMed]
    [Google Scholar]
  29. Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976;72:248–254 [CrossRef][PubMed]
    [Google Scholar]
  30. Braun V, Mahren S, Sauter A. Gene regulation by transmembrane signaling. Biometals 2006;19:103–113 [CrossRef][PubMed]
    [Google Scholar]
  31. Reizer J, Reizer A, Saier MH. Is the ribulose monophosphate pathway widely distributed in bacteria?. Microbiology 1997;143:2519–2520 [CrossRef][PubMed]
    [Google Scholar]
  32. Sundararaj S, Guo A, Habibi-Nazhad B, Rouani M, Stothard P et al. The CyberCell database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res 2004;32:293D–295 [CrossRef][PubMed]
    [Google Scholar]
  33. Navarre WW. The impact of gene silencing on horizontal gene transfer and bacterial evolution. Adv Microb Physiol 2016;69:157–186 [CrossRef][PubMed]
    [Google Scholar]
  34. Huang Q, Cheng X, Cheung MK, Kiselev SS, Ozoline ON et al. High-density transcriptional initiation signals underline genomic islands in bacteria. PLoS One 2012;7:e33759 [CrossRef][PubMed]
    [Google Scholar]
  35. Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science 2010;327:167–170 [CrossRef][PubMed]
    [Google Scholar]
  36. Brinkkötter A, Klöss H, Alpert C, Lengeler JW. Pathways for the utilization of N-acetyl-galactosamine and galactosamine in Escherichia coli. Mol Microbiol 2000;37:125–135 [CrossRef][PubMed]
    [Google Scholar]
  37. Eichhorn E, van der Ploeg JR, Leisinger T. Deletion analysis of the Escherichia coli taurine and alkanesulfonate transport systems. J Bacteriol 2000;182:2687–2695 [CrossRef][PubMed]
    [Google Scholar]
  38. Ismail W, El-Said Mohamed M, Wanner BL, Datsenko KA, Eisenreich W et al. Functional genomics by NMR spectroscopy. phenylacetate catabolism in Escherichia coli. Eur J Biochem 2003;270:3047–3054[PubMed][CrossRef]
    [Google Scholar]
  39. Sampaio MM, Chevance F, Dippel R, Eppler T, Schlegel A et al. Phosphotransferase-mediated transport of the osmolyte 2-O-alpha-mannosyl-d-glycerate in Escherichia coli occurs by the product of the mngA (hrsA) gene and is regulated by the mngR (farR) gene product acting as repressor. J Biol Chem 2004;279:5537–5548 [CrossRef][PubMed]
    [Google Scholar]
  40. Holdsworth SR, Law CJ. Multidrug resistance protein MdtM adds to the repertoire of antiporters involved in alkaline pH homeostasis in Escherichia coli. BMC Microbiol 2013;13:113 [CrossRef][PubMed]
    [Google Scholar]
  41. Francetic O, Belin D, Badaut C, Pugsley AP. Expression of the endogenous type II secretion pathway in Escherichia coli leads to chitinase secretion. EMBO J 2000;19:6697–6703 [CrossRef][PubMed]
    [Google Scholar]
  42. Francetic O, Pugsley AP. The cryptic general secretory pathway (gsp) operon of Escherichia coli K-12 encodes functional proteins. J Bacteriol 1996;178:3544–3549 [CrossRef][PubMed]
    [Google Scholar]
  43. Korea C-G, Badouraly R, Prevost M-C, Ghigo J-M, Beloin C. Escherichia coli K-12 possesses multiple cryptic but functional chaperone-usher fimbriae with distinct surface specificities. Environ Microbiol 2010;12:1957–1977 [CrossRef]
    [Google Scholar]
  44. Shimada T, Bridier A, Briandet R, Ishihama A. Novel roles of LeuO in transcription regulation of E. coli genome: antagonistic interplay with the universal silencer H-NS. Mol Microbiol 2011;82:378–397 [CrossRef][PubMed]
    [Google Scholar]
  45. Stratmann T, Madhusudan S, Schnetz K. Regulation of the yjjQ-bglJ operon, encoding LuxR-type transcription factors, and the divergent yjjP gene by H-NS and LeuO. J Bacteriol 2008;190:926–935 [CrossRef][PubMed]
    [Google Scholar]
  46. Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S et al. EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res 2013;41:D605–D612 [CrossRef][PubMed]
    [Google Scholar]
  47. Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V et al. The complete genome sequence of Escherichia coli K-12. Science 1997;277:1453–1462 [CrossRef][PubMed]
    [Google Scholar]
  48. Datsenko KA, Wanner BL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 2000;97:6640–6645 [CrossRef][PubMed]
    [Google Scholar]
  49. Grainger DC, Hurd D, Goldberg MD, Busby SJ. Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. Nucleic Acids Res 2006;34:4642–4652 [CrossRef][PubMed]
    [Google Scholar]
  50. Kahramanoglou C, Seshasayee AS, Prieto AI, Ibberson D, Schmidt S et al. Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res 2011;39:2073–2091 [CrossRef][PubMed]
    [Google Scholar]
  51. Oshima T, Ishikawa S, Kurokawa K, Aiba H, Ogasawara N. Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res 2006;13:141–153 [CrossRef][PubMed]
    [Google Scholar]
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