1887

Abstract

The K-12 operon, coding for a predicted oxidoreductase complex, is activated under anaerobic conditions and repressed in the presence of nitrate or nitrite. Anaerobic activation is mediated by the transcription factor FNR, and nitrate/nitrite repression is mediated by NarXL and NarQP. transcription reactions revealed that the DNA upstream of contains sufficient information for RNA polymerase alone to initiate transcription from five locations. FNR severely inhibited synthesis of two of these transcripts (located upstream of, and within, the FNR binding site) and activated the FNR-dependent promoter previously identified . Enhanced expression of in an mutant was consistent with the location of within a promoter island and the FNR-independent transcription observed . FNR-dependent transcription was decreased in the presence of NarL~P. DNaseI footprinting indicated that FNR and NarL~P simultaneously bound at the promoter region and that NarL~P-mediated repression was due to occupation of the 7-2-7 site located downstream of the FNR-dependent promoter. Expression of during the anaerobic growth cycle was repressed when nitrate was present but less so in the presence of nitrite. transcription measurements indicated that the alternative electron acceptors, DMSO and fumarate, could also lower expression, whereas trimethylamine-N-oxide (TMAO) permitted high expression. Therefore, expression of is subject to complex regulation in response to electron acceptor availability that involves at least three transcription factors, FNR (anaerobic activation), NarL~P (nitrate repression) and H-NS (repression in the absence of an antagonist; e.g. FNR).

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2017-04-01
2024-12-07
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References

  1. Guest JR, Green J, Irvine AS, Spiro S. The FNR modulon and FNR-regulated gene expression. In Lin ECC, Lynch AS. (editors) Regulation of Gene Expression in Escherichia coli Austin, TX: RG Landes Company; 1996 pp. 317–342 [CrossRef]
    [Google Scholar]
  2. Unden G, Bongaerts J. Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochim Biophys Acta 1997; 1320:217–234 [View Article][PubMed]
    [Google Scholar]
  3. Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW et al. 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; 281:4802–4815 [View Article][PubMed]
    [Google Scholar]
  4. Crack JC, Green J, Thomson AJ, Le Brun NE. Iron-sulfur cluster sensor-regulators. Curr Opin Chem Biol 2012; 16:35–44 [View Article][PubMed]
    [Google Scholar]
  5. Spiro S, Guest JR. FNR and its role in oxygen-regulated gene expression in Escherichia coli. FEMS Microbiol Rev 1990; 6:399–428[PubMed]
    [Google Scholar]
  6. Gross R, Aricò B, Rappuoli R. Families of bacterial signal-transducing proteins. Mol Microbiol 1989; 3:1661–1667 [View Article][PubMed]
    [Google Scholar]
  7. Rabin RS, Stewart V. Dual response regulators (NarL and NarP) interact with dual sensors (NarX and NarQ) to control nitrate- and nitrite-regulated gene expression in Escherichia coli K-12. J Bacteriol 1993; 175:3259–3268 [View Article][PubMed]
    [Google Scholar]
  8. Stewart V. Dual interacting two-component regulatory systems mediate nitrate- and nitrite-regulated gene expression in Escherichia coli. Res Microbiol 1994; 145:450–454 [View Article][PubMed]
    [Google Scholar]
  9. Stewart V. Nitrate- and nitrite-responsive sensors NarX and NarQ of proteobacteria. Biochem Soc Trans 2003; 31:1–10 [View Article]
    [Google Scholar]
  10. Schröder I, Wolin CD, Cavicchioli R, Gunsalus RP. Phosphorylation and dephosphorylation of the NarQ, NarX, and NarL proteins of the nitrate-dependent two-component regulatory system of Escherichia coli. J Bacteriol 1994; 176:4985–4992 [View Article][PubMed]
    [Google Scholar]
  11. Walker MS, DeMoss JA. Phosphorylation and dephosphorylation catalyzed in vitro by purified components of the nitrate sensing system, NarX and NarL. J Biol Chem 1993; 268:8391–8393[PubMed]
    [Google Scholar]
  12. Lee AI, Delgado A, Gunsalus RP. Signal-dependent phosphorylation of the membrane-bound NarX two-component sensor-transmitter protein of Escherichia coli: nitrate elicits a superior anion ligand response compared to nitrite. J Bacteriol 1999; 181:5309–5316[PubMed]
    [Google Scholar]
  13. Williams SB, Stewart V. Discrimination between structurally related ligands nitrate and nitrite controls autokinase activity of the NarX transmembrane signal transducer of Escherichia coli K-12. Mol Microbiol 1997; 26:911–925 [View Article][PubMed]
    [Google Scholar]
  14. Williams SB, Stewart V. Nitrate- and nitrite-sensing protein NarX of Escherichia coli K-12: mutational analysis of the amino-terminal tail and first transmembrane segment. J Bacteriol 1997; 179:721–729 [View Article][PubMed]
    [Google Scholar]
  15. Darwin AJ, Tyson KL, Busby SJ, Stewart V. Differential regulation by the homologous response regulators NarL and NarP of Escherichia coli K-12 depends on DNA binding site arrangement. Mol Microbiol 1997; 25:583–595 [View Article][PubMed]
    [Google Scholar]
  16. Tyson KL, Cole JA, Busby SJ. Nitrite and nitrate regulation at the promoters of two Escherichia coli operons encoding nitrite reductase: identification of common target heptamers for both NarP- and NarL-dependent regulation. Mol Microbiol 1994; 13:1045–1055 [View Article][PubMed]
    [Google Scholar]
  17. Darwin AJ, Stewart V. The NAR modulon systems: nitrate and nitrite regulation of anaerobic gene expression. In Lin ECC, Lynch AS. (editors) Regulation of Gene Expression in Escherichia coli Austin, TX: RG Landes Company; 1996 pp. 343–359 [CrossRef]
    [Google Scholar]
  18. Partridge JD, Browning DF, Xu M, Newnham LJ, Scott C et al. Characterization of the Escherichia coli K-12 ydhYVWXUT operon: regulation by FNR, NarL and NarP. Microbiology 2008; 154:608–618 [View Article][PubMed]
    [Google Scholar]
  19. Evans CGT, Herbert D, Tempest DW. The continuous cultivation of micro-organisms. Meth Microbiol 1970; 2:278–327
    [Google Scholar]
  20. Sambrook JW, Russell DW. Molecular Cloning: A Laboratory Manual, 3rd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 2001
    [Google Scholar]
  21. Miller JH. Assay of β-galactosidase. In Miller JH. editor Experiments in Molecular Genetics Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1972 pp. 352–354
    [Google Scholar]
  22. Xu J, Xu X, Verstraete W. Adaptation of E. coli cell method for micro-scale nitrate measurement with the Griess reaction in culture media. J Microbiol Methods 2000; 41:23–33 [View Article][PubMed]
    [Google Scholar]
  23. Ziegelhoffer EC, Kiley PJ. In vitro analysis of a constitutively active mutant form of the Escherichia coli global transcription factor FNR. J Mol Biol 1995; 245:351–361 [View Article][PubMed]
    [Google Scholar]
  24. Maxam AM, Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol 1980; 65:499–560[PubMed] [CrossRef]
    [Google Scholar]
  25. Panyukov VV, Ozoline ON. Promoters of Escherichia coli versus promoter islands: function and structure comparison. PLoS One 2013; 8:e62601 [View Article][PubMed]
    [Google Scholar]
  26. 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 [View Article][PubMed]
    [Google Scholar]
  27. Kahramanoglou C, Seshasayee ASN, 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 [View Article][PubMed]
    [Google Scholar]
  28. 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 [View Article][PubMed]
    [Google Scholar]
  29. Myers KS, Yan H, Ong IM, Chung D, Liang K et al. Genome-scale analysis of Escherichia coli FNR reveals complex features of transcription factor binding. PLoS Genet 2013; 9:e1003565 [View Article][PubMed]
    [Google Scholar]
  30. Curran T, Abacha F, Hibberd S, Rolfe M, Lacey M et al. Identification of new members of the Escherichia coli K-12 MG1655 SlyA regulon. Microbiology 2017; 163:400–409 [View Article][PubMed]
    [Google Scholar]
  31. Reese MG, Harris NL, Eeckman FH. Large scale sequencing specific neural networks for promoter and splice site recognition. In Hunter L, Klein TE. (editors) Biocomputing: Proceedings of the 1996 Pacific Symposium Singapore: World Scientific Publishing Co; 1996 pp. 737–738
    [Google Scholar]
  32. Solovyev V, Salamov A. Automatic annotation of microbial genomes and metagenomic sequences. In RW Li. (editor) Metagenomics and Its Applications in Agriculture, Biomedicine and Environmental Studies Hauppauge, New York: Nova Science Publishers; 2011 pp. 61–78
    [Google Scholar]
  33. Gennis RB, Stewart V. Respiration. In Neidardt FC. (editor) Escherichia Coli and Salmonella, 2nd ed. Washington, DC: ASM Press; 1996 pp. 217–261
    [Google Scholar]
  34. Zumft WG. Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 1997; 61:533–616[PubMed]
    [Google Scholar]
  35. 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 [View Article][PubMed]
    [Google Scholar]
  36. Meng W, Green J, Guest JR. FNR-dependent repression of ndh gene expression requires two upstream FNR-binding sites. Microbiology 1997; 143:1521–1532 [View Article][PubMed]
    [Google Scholar]
  37. Li J, Kustu S, Stewart V. In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12. J Mol Biol 1994; 241:150–165 [View Article][PubMed]
    [Google Scholar]
  38. Darwin AJ, Stewart V. Nitrate and nitrite regulation of the Fnr-dependent aeg-46.5 promoter of Escherichia coli K-12 is mediated by competition between homologous response regulators (NarL and NarP) for a common DNA-binding site. J Mol Biol 1995; 251:15–29 [View Article][PubMed]
    [Google Scholar]
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