1887

Abstract

The open reading frame located at 485 min (2254 kb) in the region of the chromosome was predicted to encode a CRP and FNR paralogue capable of forming inter- or intra-molecular disulphide bonds and incorporating one iron–sulphur centre per 25 kDa subunit. Purified MBP–YeiL (a maltose-binding-protein–YeiL fusion protein) was a high-molecular-mass oligomer or aggregate which released unstable monomers (68 kDa) under reducing conditions. The MBP–YeiL protein contained substoichiometric amounts of iron and acid-labile sulphide, and an average of one disulphide bond per monomer. The iron and sulphide contents increased consistent with the acquisition of one [4Fe–4S] cluster per monomer after anaerobic NifS-catalysed reconstitution. By analogy with FNR and FLP (the FNR-like protein of ) it was suggested that the transcription-regulatory activity of YeiL might be modulated by a sensory iron–sulphur cluster and/or by reversible disulphide bond formation. A transcriptional fusion showed that aerobic expression increases at least sixfold during stationary phase, requires RpoS, and is positively autoregulated by YeiL, positively activated by Lrp (and IHF in the absence of FNR) and negatively regulated by FNR. A regulatory link between the synthesis of YeiK (a potential nucleoside hydrolase) and YeiL was inferred by showing that the and genes are divergently transcribed from overlapping promoters. A 10–15% deficiency in aerobic growth yield and an enhanced loss of viability under nitrogen starvation conditions were detected with a :: mutant, suggesting that YeiL might function as a post-exponential-phase nitrogen-starvation regulator.

Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-146-12-3157
2000-12-01
2020-12-04
Loading full text...

Full text loading...

/deliver/fulltext/micro/146/12/1463157a.html?itemId=/content/journal/micro/10.1099/00221287-146-12-3157&mimeType=html&fmt=ahah

References

  1. Aiba H., Adhya S., de Crombrugghe B.. 1981; Evidence for two functional gal promoters in intact Escherichia coli cells. J Biol Chem256:11905–11910
    [Google Scholar]
  2. Artymiuk P. J., Poirrette A. R., Grindley H. M., Rice D. W., Willett P.. 1994; A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. J Mol Biol243:327–344[CrossRef]
    [Google Scholar]
  3. Aviv M., Giladi H., Schreiber G., Oppenheim A. B., Glaser G.. 1994; Expression of the genes coding for the Escherichia coli integration host factor are controlled by growth phase, rpoS, ppGpp and by autoregulation. . Mol Microbiol14:1021–1031[CrossRef]
    [Google Scholar]
  4. Beinert H.. 1983; Semi-micro methods for analysis of labile sulfide and of labile sulfide plus sulfane sulfur in unusually stable iron sulfur proteins. Anal Biochem131:373–378[CrossRef]
    [Google Scholar]
  5. Benson D. E., Wisz M. S., Liu W., Hellinga H. W.. 1998; Construction of a novel redox protein by rational design: conversion of a disulfide bridge into a mononuclear iron–sulfur center. Biochemistry37:7070–7076[CrossRef]
    [Google Scholar]
  6. Blattner F. R., Plunkett G. III, Bloch C. A..14 other authors 1997; The complete genome sequence of Escherichia coli K-12. Science277:1453–1470[CrossRef]
    [Google Scholar]
  7. Busby S., Ebright R. H.. 1997; Transcription activation at class II CAP-dependent promoters. Mol Microbiol23:853–859[CrossRef]
    [Google Scholar]
  8. Busby S., Kolb A.. 1996; The CAP modulon. In Regulation of Gene Expression in Escherichia coli pp.255–279Edited by Lin E. C. C., Lynch S. A.. Austin, TX: R. G. Landes;
    [Google Scholar]
  9. Cui Y., Wang Q., Stormo G. D., Calvo J. M.. 1995; A consensus sequence for binding of Lrp to DNA. J Bacteriol177:4872–4880
    [Google Scholar]
  10. Cunningham L., Gruer M. J., Guest J. R.. 1997; Transcriptional regulation of the aconitase genes (acnA and acnB) of Escherichia coli. Microbiology143:3795–3805[CrossRef]
    [Google Scholar]
  11. Davis B. D., Luger S. M., Tai P. C.. 1986; Role of ribosome degradation in the death of starved Escherichia coli cells. . J Bacteriol166:439–445
    [Google Scholar]
  12. Degano M., Gopaul D. N., Scapin G., Schramm V. L., Sacchettini J. C.. 1996; Three-dimensional structure of the inosine-uridine nucleoside N-ribohydrolase from Crithidia fasciculata. Biochemistry35:5971–5981[CrossRef]
    [Google Scholar]
  13. Freundlich M., Ramani N., Mathew E., Sirko A., Tsui P.. 1992; The role of integration host factor in gene expression in Escherichia coli. Mol Microbiol6:2557–2563[CrossRef]
    [Google Scholar]
  14. Gamer J., Multhaup G., Tomoyasu T., McCarty J. S., Rãdiger S., Schönfeld H. J., Schirra C., Bujard H., Bukau B.. 1996; A cycle of binding and release of the DnaK, DnaJ and GrpE chaperones regulates activity of the Escherichia coli heat shock transcription factor σ32. EMBO J15:607–617
    [Google Scholar]
  15. Goosen N., van de Putte P.. 1995; The regulation of transcription initiation by integration host factor. Mol Microbiol16:1–7[CrossRef]
    [Google Scholar]
  16. Gostick D. O., Green J., Gasson M. J., Guest J. R.. 1997; Redox-mediated regulation by an FNR homologue. In International Anaerobic Metabolism and Regulation Workshop (Marseille) abstract A12
    [Google Scholar]
  17. Gostick D. O., Green J., Irvine A. S., Gasson M. J., Guest J. R.. 1998; A novel regulatory switch mediated by the FNR-like protein of Lactobacillus casei. Microbiology144:705–717[CrossRef]
    [Google Scholar]
  18. Gostick D. O., Griffin H. G., Shearman C. A., Scott C., Green J., Gasson M. J., Guest J. R.. 1999; Two operons that encode FNR-like proteins in Lactococcus lactis. . Mol Microbiol31:1523–1535[CrossRef]
    [Google Scholar]
  19. Green J., Sharrocks A. D., Green B., Geisow M., Guest J. R.. 1993; Properties of FNR proteins substituted at each of the five cysteine residues. . Mol Microbiol8:61–68[CrossRef]
    [Google Scholar]
  20. Green J., Bennett B., Jordan P., Ralph E. T., Thomson A. J., Guest J. R.. 1996; Reconstitution of the [4Fe–4S] cluster in FNR and demonstration of the aerobic–anaerobic transcription switch in vitro. Biochem J316:887–892
    [Google Scholar]
  21. Green J., Anjum M. F., Guest J. R.. 1997; Regulation of the ndh gene of Escherichia coli by IHF and a novel regulator, Arr. Microbiology143:2865–2875[CrossRef]
    [Google Scholar]
  22. Guest J. R., Green J., Irvine A. S., Spiro S.. 1996; The FNR modulon and FNR regulated gene expression. In Regulation of Gene Expression in Escherichia coli pp.317–342Edited by Lin E. C. C., Lynch S. A.. Austin, TX: R. G. Landes;
    [Google Scholar]
  23. Holm R. H., Ibers J. A.. 1977; Synthetic analogues of active sites of iron–sulfur proteins. In Iron–Sulfur Proteins III pp.205–281Edited by Lovenberg W.. London: Academic Press;
    [Google Scholar]
  24. Hurme R., Berndt K. D., Normark S. J., Rhen M.. 1997; A proteinaceous gene regulatory thermometer in Salmonella. Cell90:55–64[CrossRef]
    [Google Scholar]
  25. Khoroshilova N., Popescu C., Munck E., Beinert H., Kiley P. J.. 1997; Iron–sulfur cluster disassembly in the FNR protein of Escherichia coli by O2: [4Fe–4S] to [2Fe–2S] conversion with loss of biological activity. Proc Natl Acad Sci USA94:6087–6092[CrossRef]
    [Google Scholar]
  26. Kiley P. J., Beinert H.. 1999; Oxygen sensing by the global regulator, FNR: the role of the iron–sulfur cluster. . FEMS Microbiol Rev22:341–352
    [Google Scholar]
  27. Kolter R., Siegele D. A., Tormo A.. 1993; The stationary-phase of the bacterial life cycle. Annu Rev Microbiol47:855–874[CrossRef]
    [Google Scholar]
  28. Kraulis P. J.. 1991; molscript: a program to produce both detailed and schematic plots of protein structures. J Appl Cryst24:946–950[CrossRef]
    [Google Scholar]
  29. Kushner S. R., Nagaishi H., Templin A., Clark A. J.. 1971; Genetic recombination in Escherichia coli: the role of exonuclease I. Proc Natl Acad Sci USA68:824–827[CrossRef]
    [Google Scholar]
  30. Landgraf J. R., Wu J., Calvo J. M.. 1996; Effects of nutrition and growth rate on Lrp levels in Escherichia coli. . J Bacteriol178:6930–6936
    [Google Scholar]
  31. Lange R., Hengge-Aronis R.. 1991; Identification of a central regulator of stationary-phase gene expression in Escherichia coli. Mol Microbiol5:49–59[CrossRef]
    [Google Scholar]
  32. Lange R., Fischer D., Hengge-Aronis R.. 1995; Identification of transcriptional start sites and the role of ppGpp in the expression of rpoS, the structural gene for the σS subunit of RNA polymerase in Escherichia coli. J Bacteriol177:4676–4680
    [Google Scholar]
  33. Lazazzera B. A., Beinert H., Khoroshilova N., Kennedy M. C., Kiley P. J.. 1996; DNA binding and dimerization of the Fe–S-containing FNR protein from Escherichia coli are regulated by oxygen. J Biol Chem271:2762–2768[CrossRef]
    [Google Scholar]
  34. Li B., Wing H., Lee D., Wu H., Busby S.. 1998; Transcription activation by Escherichia coli FNR protein: similarities to, and differences from, the CRP paradigm. Nucleic Acid Res26:2075–2081[CrossRef]
    [Google Scholar]
  35. Marinus M. G., Morris M. R.. 1973; Isolation of deoxyribonucleic acid methylase mutants of Escherichia coli K-12. J Bacteriol114:1143–1150
    [Google Scholar]
  36. Martinez E., Bartolomé B., Delacruz F.. 1988; pACYC184-derived cloning vectors containing the multiple cloning site and lacz α reporter gene of pUC8/9 and pUC18/19 plasmids. Gene68:159–162[CrossRef]
    [Google Scholar]
  37. Miller J. H.. 1972; Assay of β-galactosidase. In Experiments in Molecular Genetics pp.352–355 Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  38. Nyström T.. 1995; Glucose starvation stimulon of Escherichia coli: role of integration host factor in starvation survival and growth phase-dependent protein synthesis. J Bacteriol177:5707–5710
    [Google Scholar]
  39. Oden K. L., De Veaux L. C., Vibat C. R. T., Cronan J. E. Jr, Gennis R. B.. 1990; Genomic replacement in Escherichia coli K-12 using covalently closed circular plasmid DNA. Gene96:29–36[CrossRef]
    [Google Scholar]
  40. Prodromou C., Haynes M. J., Guest J. R.. 1991; The aconitase of Escherichia coli: purification of the enzyme and molecular cloning and map location of the gene (acn). J Gen Microbiol137:2505–2515[CrossRef]
    [Google Scholar]
  41. Rao N. N., Liu S. J., Kornberg A.. 1998; Inorganic polyphosphate in Escherichia coli: the phosphate regulon and the stringent response. J Bacteriol180:2186–2193
    [Google Scholar]
  42. Robbins A. H., Stout C. D.. 1989; Structure of activated aconitase: formation of the [4Fe–4S] cluster in the crystal. Proc Natl Acad Sci USA86:3639–3643[CrossRef]
    [Google Scholar]
  43. Sambrook J., Fritsch E. F., Maniatis T.. 1989; Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  44. Schultz S. C., Shields G. C., Steitz T. A.. 1991; Crystal-structure of a CAP–DNA complex – the DNA is bent by 90 °. Science253:1001–1007[CrossRef]
    [Google Scholar]
  45. Simons R. W., Houman F., Kleckner N.. 1987; Improved single and multicopy lac-based cloning vectors for protein and operon fusions. . Gene53:85–96[CrossRef]
    [Google Scholar]
  46. Spiro S.. 1994; The FNR family of transcriptional regulators. Antonie Leeuwenhoek66:23–36[CrossRef]
    [Google Scholar]
  47. Staden R.. 1982; An interactive graphics package for comparing and aligning nucleic acid and amino acid sequences. . Nucleic Acid Res10:2951–2961[CrossRef]
    [Google Scholar]
  48. Straus D., Walter W., Gross C. A.. 1990; DnaK, DnaJ, and GrpE heat shock proteins negatively regulate heat shock gene expression by controlling the synthesis and stability of σ32. Genes Dev4:2202–2209[CrossRef]
    [Google Scholar]
  49. Thannhauser T. W., Konishi Y., Scheraga H. A.. 1987; Analysis for disulfide bonds in peptides and proteins. Methods Enzymol143:115–119
    [Google Scholar]
  50. Thelander L.. 1973; Physicochemical characterization of ribonucleoside diphosphate reductase from Escherichia coli. . J Biol Chem248:4591–4601
    [Google Scholar]
  51. VanBogelen R. A., Neidhardt F. C.. 1990; Ribosomes as sensors of heat and cold shock in Escherichia coli. . Proc Natl Acad Sci USA87:5589–5593[CrossRef]
    [Google Scholar]
  52. Vogel H., Bonner D. M.. 1956; A convenient growth medium for Escherichia coli and some other micro-organisms. . Microb Genet Bull13:43–44
    [Google Scholar]
  53. Vollack K. U., Hartig E., Korner H., Zumpft W. G.. 1999; Multiple transcription factors of the FNR family in denitrifying Pseudomonas stutzeri: characterization of four fnr-like genes, regulatory responses and cognate metabolic processes. Mol Microbiol31:1681–1694[CrossRef]
    [Google Scholar]
  54. Woodland M. P., Dalton H.. 1984; Purification and characterization of component A of the methane monooxygenase from Methylococcus capsulatus (Bath). J Biol Chem259:53–59
    [Google Scholar]
  55. Wu G., Cruz-Ramos H., Hill S., Green J., Sawers G., Poole R. K.. 2000; Regulation of cytochrome bd expression in the obligate aerobe Azotobacter vinelandii by CydR (Fnr): sensitivity to oxygen, reactive oxygen and nitric oxide. J Biol Chem275:4679–4686[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-146-12-3157
Loading
/content/journal/micro/10.1099/00221287-146-12-3157
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error