Transcription and transcript processing in the sdh CDAB-sucABCD operon of Escherichia coli Free

Abstract

The genes encoding succinate dehydrogenase , the specific components of the 2-oxoglutarate dehydrogenase complex (ODH, E1o and E2o; ) and succinyl-CoA synthetase form a cluster containing two promoters at 16 · 3 min in the chromosome of . The gene encoding the lipoamide dehydrogenase component of both the 2-oxoglutarate and pyruvate dehydrogenase complexes (E3; ) is the distal gene of another cluster containing two promoters located at 2 · 7 min: . The responses of the suc and promoters to different environmental conditions and to regulator defects were investigated with appropriate fusions, in order to understand how expression of the genes is co-regulated with other genes in the cluster and with expression. Expression from the promoter was repressed by IHF and partially activated by s but it was not regulated by ArcA, FNR, CRP, FruR or Fis, and not repressed by glucose or anaerobiosis, indicating that the well-established catabolite and anaerobic repression of ODH synthesis is imposed elsewhere. In contrast, the promoter was repressed by both glucose (via a CRP-independent mechanism) and anaerobiosis (mediated by ArcA), and activated by Fis, but it was not regulated by FNR, FruR, IHF or s. These observations support the view that transcription of the genes is primarily initiated and regulated at the upstream promoter, and that the promoter is independently co-regulated with (primarily by ArcA-mediated repression) rather than with Direct evidence for co-transcription of the entire region from was obtained by detecting a 10 kb transcript in and mutants, but not in the parental strains. Three RNaseIII-specific processing sites, which contribute to the extreme instability of the readthrough transcript, were identified in the intergenic region. Other sites of endonuclease processing were located by interpreting the patterns of transcript subfragments observed in Northern blotting.

Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-144-8-2113
1998-08-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/micro/144/8/mic-144-8-2113.html?itemId=/content/journal/micro/10.1099/00221287-144-8-2113&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 chem 256:11905–11910
    [Google Scholar]
  2. Amarasingham C.R., Davis B.D. 1965; Regulation of ɑ- ketoglutarate dehydrogenase formation in Escherichia coli. . J Biol Chem 240:3664–3668
    [Google Scholar]
  3. Ball C.A., Osuna R., Ferguson K.C., Johnson R.C. 1992; Dramatic changes in fis levels upon nutrient upshift in Escherichia coli. . J Bacteriol 174:8043–8056
    [Google Scholar]
  4. Bonnefoy V., Pascal M.-C., Ratouchniak J., Chippaux M. 1986; Alteration by mutation of the control by oxygen of the nar operon in Escherichia coli. . Mol Gen Genet 205:349–352
    [Google Scholar]
  5. Bradford M.M. 1976; A rapid and sensitive method for the quantitation of microgram quantities of protein utilising the principle of protein-dye binding. . Anal Biochem 72:248–253
    [Google Scholar]
  6. Buck D., Spencer M.E., Guest J.R. 1986; Cloning and expression of the succinyl-CoA synthetase genes of Escherichia coli K12. . J Gen Microbiol 132:1753–1762
    [Google Scholar]
  7. Buck M., Woodcock J., Cannon W., Mitchenall L., Drummond M. 1987; Positional requirements for the function of NIF- specific upstream activator sequences. . Mol Gen Genet 210:140–144
    [Google Scholar]
  8. Cohen S.N., McDowall K.J. 1997; RNaseE: still a wonderfully mysterious enzyme. . Mol Microbiol 23:1099–1106
    [Google Scholar]
  9. Compan I., Touati D. 1994; Anaerobic activation of arc A transcription in Escherichia coli: roles for Fnr and ArcA. . Mol Microbiol 11:955–964
    [Google Scholar]
  10. Cronan J.E. JR LaPorte D. 1996; Tricarboxylic acid cycle and glyoxylate bypass.. In Escherichia coli and Salmonella typhi- murium: Cellular and Molecular Biology pp. 206–216 Neidhardt F.C. others Edited by Washington, DC: American Society for Microbiology;
    [Google Scholar]
  11. Cunningham L, Guest J.R., Guest J.R. 1997; Transcriptional regulation of the aconitase genes (acnA and acnB) of Escherichia coli. . Microbiology 143:3795–3805
    [Google Scholar]
  12. Finkel S.E., Johnson R.C. 1992; The Fis protein: it̒s not just for DNA inversion anymore. . Mol Microbiol 6:3257–3265
    [Google Scholar]
  13. Gerischer U., Dürre P. 1992; mRNA analysis of the adc gene region of Clostridium acetobutylicum during the shift to solvento- genesis. . J Bacteriol 174:426–433
    [Google Scholar]
  14. Goldblum K., Apirion D. 1981; Inactivation of the ribonucleic acid-processing enzyme ribonuclease E blocks cell division. . J Bacteriol 146:128–132
    [Google Scholar]
  15. Greene R.C. 1996; Biosynthesis of methionine.. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology pp. 542–560 Neidhardt F.C. others Edited by Washington, DC: American Society for Microbiology;
    [Google Scholar]
  16. Guest J.R., Russell G.C. 1992; Complexes and complexities of the citric acid cycle in Escherichia coli. . Curr Top Cell Regulation 33:231–247
    [Google Scholar]
  17. Guest J.R., Angier S.J., Russell G.C. 1989; Structure, expression and protein engineering of the pyruvate dehydrogenase complex of Escherichia coli. . Ann N Y Acad Sei 573:76–99
    [Google Scholar]
  18. Iuchi S., Lin E.C.C. 1988; arc A (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. . Proc Natl Acad Sei USA 85:1888–1892
    [Google Scholar]
  19. Iuchi S., Aristarkov G., Dong J.M., Taylor J.S., Lin E.C.C. 1994; Effects of nitrate respiration on expression of the Arc- controlled operons encoding succinate dehydrogenase and flavin- linked L-lactate dehydrogenase. . J Bacteriol 176:1695–1701
    [Google Scholar]
  20. Krinke L., Wulff D.L. 1990; The cleavage specificity of RNaseIII. . Nucleic Acids Res 18:4809–4815
    [Google Scholar]
  21. Kushner S.R. 1996; mRNA decay. . In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology pp. 849–860 Neidhardt F.C. others Edited by Washington, DC: American Society for Microbiology;
    [Google Scholar]
  22. Meganathan R. 1996; Biosynthesis of the isoprenoid quinones menaquinone (vitamin K2) and ubiquinone (Coenzyme Q).. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology pp. 642–664 Neidhardt F.C. others Edited by Washington, DC: American Society for Microbiology;
    [Google Scholar]
  23. Miller J.H. 1972 Experiments in Molecular Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  24. Miller J.H., Albertini A.M. 1983; Effects of surrounding sequence on the suppression of nonsense codons. . J Mol Biol 164:59–71
    [Google Scholar]
  25. Park S.-J., Tseng C.-P., Gunsalus R.P. 1995; Regulation of succinate dehydrogenase (sdhCDAB) operon expression in Escherichia coli in response to carbon supply and anaerobiosis: role of ArcA and Fnr. . Mol Microbiol 15:473–482
    [Google Scholar]
  26. Park S.-J., Chao G., Gunsalus R.P. 1997; Aerobic regulation of the sucABCD genes of Escherichia coli, which encode ɑ- ketoglutarate dehydrogenase and succinyl coenzyme A synthetase: roles of ArcA, Fnr, and the upstream sdhCDAB promoter. . J Bacteriol 179:4138–4142
    [Google Scholar]
  27. Patte J.-C. 1996; Biosynthesis of threonine and lysine.. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology pp. 528–541 Neidhardt F.C. others Edited by Washington, DC: American Society for Microbiology;
    [Google Scholar]
  28. Perham R.N. 1991; Domains, motifs and linkers in 2-oxo acid dehydrogenase multienzyme complexes: a paradigm in the design of a multifunctional protein. . Biochemistry 30:8501–8512
    [Google Scholar]
  29. Philips-Jones M.K., Watson F.J., Martin R. 1993; The 3ʹcodon effect on UAG suppressor tRNA in different Escherichia coli and human cells. . J Mol Biol 233:1–6
    [Google Scholar]
  30. Quail M.A., Haydon D.J., Guest J.R. 1994; The pdhR- aceEE-lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex. . Mol Microbiol 12:95–104
    [Google Scholar]
  31. 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]
  32. Schröder I., Darie S., Gunsalus R.P. 1993; Activation of the Escherichia coli nitrate reductase (narGHJI) operon by NarL and Fnr requires integration host factor. . J Biol Chem 268:771–774
    [Google Scholar]
  33. Silhavy T.J., Barman M.L., Enquist L.W. 1984 Experiments with Gene Fusions. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  34. Simons R.W., Houman F., Kleckner N. 1987; Improved single and multicopy lac-based cloning vectors for protein and operon fusions. . Gene 53:85–96
    [Google Scholar]
  35. Smith M.W., Neidhardt F.C. 1983; 2-Oxoacid dehydrogenase complexes of Escherichia coli: cellullar amounts and patterns of synthesis. . J Bacteriol 156:81–88
    [Google Scholar]
  36. Spencer M.E., Guest J.R. 1982; Molecular cloning of four tricarboxylic acid cycle genes of Escherichia coli. . J Bacteriol 151:542–552
    [Google Scholar]
  37. Spencer M.E., Guest J.R. 1985; Transcription analysis of the sucAB, aceEF and Ipd genes of Escherichia coli. . Mol Gen Genet 200:145–154
    [Google Scholar]
  38. Spencer M.E., Guest J.R. 1987; Regulation of citric acid cycle genes in facultative bacteria. . Microbiol Sci 4:164–168
    [Google Scholar]
  39. Spencer M.E., Wilde R.J., Guest J.R. 1986; Transcription and regulation of TCA cycle genes of E. coli. . Soc Gen Microbiol Q 13:M9
    [Google Scholar]
  40. Spiro S., Roberts R.E., Guest J.R. 1989; FNR-dependent repression of the ndh gene of Escherichia coli and metal ion requirement for FNR-regulated gene expression. . Mol Microbiol 3:601–608
    [Google Scholar]
  41. Stephens P.E., Lewis H.M., Dariison M.G., Guest J.R. 1983; Nucleotide sequence of the lipoamide dehydrogenase gene of Escherichia coli K12. . Eur J Chem 135:519–527
    [Google Scholar]
  42. Wilde R.J., Guest J.R. 1986; Transcript analysis of the citrate synthase and succinate dehydrogenase genes of Escherichia coli K12. . J Gen Microbiol 132:3239–3251
    [Google Scholar]
  43. Xu J., Johnson R.C. 1995; Identification of genes negatively regulated by Fis: Fis and RpoS comodulate growth-phase- dependent gene expression in Escherichia coli. . J Bacteriol 177:938–947
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-144-8-2113
Loading
/content/journal/micro/10.1099/00221287-144-8-2113
Loading

Data & Media loading...

Most cited Most Cited RSS feed