Skip to main content
PMC home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1991 May;173(9):2864–2871. doi: 10.1128/jb.173.9.2864-2871.1991

Two divergently transcribed genes, soxR and soxS, control a superoxide response regulon of Escherichia coli.

J Wu 1, B Weiss 1
PMCID: PMC207867  PMID: 1708380

Abstract

soxR governs a superoxide response regulon that contains the genes for endonuclease IV, Mn2(+)-superoxide dismutase, and glucose 6-phosphate dehydrogenase. The soxR gene encodes a 17-kDa protein; some mutations of this gene cause constitutive overexpression of the regulon. Induction by paraquat (methyl viologen) requires both soxR and a new gene, soxS. soxS is adjacent to soxR, it encodes a 13-kDa protein, and it is required for paraquat resistance. These functions were revealed by studies in which the sequence of the 1.1-kb soxR-soxS region was determined, the 5' ends of the mRNAs were mapped, and complementation tests were performed with soxRS plasmids containing deletions of known sequence. The two genes are divergently transcribed, and the transcripts overlap. The soxS promoter is within the 85-nucleotide intergenic region, whereas the soxR promoter is within soxS. soxS mRNA increases after induction. Both protein products have possible DNA-binding (helix-turn-helix) domains. SoxR contains four cysteines (CX2CXCX5C) that might be part of a sensor region. SoxS shows 17 to 31% homology to the C-terminal portions of members of the AraC family of positive regulators.

Full text

PDF
2864

Images in this article

2867Image
on p.2867

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Alton N. K., Vapnek D. Nucleotide sequence analysis of the chloramphenicol resistance transposon Tn9. Nature. 1979 Dec 20;282(5741):864–869. doi: 10.1038/282864a0. [DOI] [PubMed] [Google Scholar]
  2. Atlung T., Nielsen A., Hansen F. G. Isolation, characterization, and nucleotide sequence of appY, a regulatory gene for growth-phase-dependent gene expression in Escherichia coli. J Bacteriol. 1989 Mar;171(3):1683–1691. doi: 10.1128/jb.171.3.1683-1691.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bachmann B. J. Linkage map of Escherichia coli K-12, edition 8. Microbiol Rev. 1990 Jun;54(2):130–197. doi: 10.1128/mr.54.2.130-197.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bachmann B. J. Pedigrees of some mutant strains of Escherichia coli K-12. Bacteriol Rev. 1972 Dec;36(4):525–557. doi: 10.1128/br.36.4.525-557.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Beck C. F., Warren R. A. Divergent promoters, a common form of gene organization. Microbiol Rev. 1988 Sep;52(3):318–326. doi: 10.1128/mr.52.3.318-326.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Belfort M., Pedersen-Lane J., West D., Ehrenman K., Maley G., Chu F., Maley F. Processing of the intron-containing thymidylate synthase (td) gene of phage T4 is at the RNA level. Cell. 1985 Jun;41(2):375–382. doi: 10.1016/s0092-8674(85)80010-6. [DOI] [PubMed] [Google Scholar]
  7. Braus G., Argast M., Beck C. F. Identification of additional genes on transposon Tn10: tetC and tetD. J Bacteriol. 1984 Nov;160(2):504–509. doi: 10.1128/jb.160.2.504-509.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Brawn M. K., Fridovich I. Increased superoxide radical production evokes inducible DNA repair in Escherichia coli. J Biol Chem. 1985 Jan 25;260(2):922–925. [PubMed] [Google Scholar]
  9. Brendel V., Hamm G. H., Trifonov E. N. Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find them. J Biomol Struct Dyn. 1986 Feb;3(4):705–723. doi: 10.1080/07391102.1986.10508457. [DOI] [PubMed] [Google Scholar]
  10. Burke K. A., Wilcox G. The araC gene of Citrobacter freundii. Gene. 1987;61(3):243–252. doi: 10.1016/0378-1119(87)90188-0. [DOI] [PubMed] [Google Scholar]
  11. Cole S. T., Eiglmeier K., Ahmed S., Honore N., Elmes L., Anderson W. F., Weiner J. H. Nucleotide sequence and gene-polypeptide relationships of the glpABC operon encoding the anaerobic sn-glycerol-3-phosphate dehydrogenase of Escherichia coli K-12. J Bacteriol. 1988 Jun;170(6):2448–2456. doi: 10.1128/jb.170.6.2448-2456.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Cornelis G., Sluiters C., de Rouvroit C. L., Michiels T. Homology between virF, the transcriptional activator of the Yersinia virulence regulon, and AraC, the Escherichia coli arabinose operon regulator. J Bacteriol. 1989 Jan;171(1):254–262. doi: 10.1128/jb.171.1.254-262.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Cunningham R. P., Saporito S. M., Spitzer S. G., Weiss B. Endonuclease IV (nfo) mutant of Escherichia coli. J Bacteriol. 1986 Dec;168(3):1120–1127. doi: 10.1128/jb.168.3.1120-1127.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dale R. M., McClure B. A., Houchins J. P. A rapid single-stranded cloning strategy for producing a sequential series of overlapping clones for use in DNA sequencing: application to sequencing the corn mitochondrial 18 S rDNA. Plasmid. 1985 Jan;13(1):31–40. doi: 10.1016/0147-619x(85)90053-8. [DOI] [PubMed] [Google Scholar]
  15. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Engelman D. M., Steitz T. A., Goldman A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem. 1986;15:321–353. doi: 10.1146/annurev.bb.15.060186.001541. [DOI] [PubMed] [Google Scholar]
  17. Goodrich J. A., Schwartz M. L., McClure W. R. Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res. 1990 Sep 11;18(17):4993–5000. doi: 10.1093/nar/18.17.4993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Gottesman S., Squires C., Pichersky E., Carrington M., Hobbs M., Mattick J. S., Dalrymple B., Kuramitsu H., Shiroza T., Foster T. Conservation of the regulatory subunit for the Clp ATP-dependent protease in prokaryotes and eukaryotes. Proc Natl Acad Sci U S A. 1990 May;87(9):3513–3517. doi: 10.1073/pnas.87.9.3513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Greenberg J. T., Demple B. A global response induced in Escherichia coli by redox-cycling agents overlaps with that induced by peroxide stress. J Bacteriol. 1989 Jul;171(7):3933–3939. doi: 10.1128/jb.171.7.3933-3939.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Greenberg J. T., Monach P., Chou J. H., Josephy P. D., Demple B. Positive control of a global antioxidant defense regulon activated by superoxide-generating agents in Escherichia coli. Proc Natl Acad Sci U S A. 1990 Aug;87(16):6181–6185. doi: 10.1073/pnas.87.16.6181. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Gribskov M., Devereux J., Burgess R. R. The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):539–549. doi: 10.1093/nar/12.1part2.539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Inouye S., Nakazawa A., Nakazawa T. Nucleotide sequence of the regulatory gene xylS on the Pseudomonas putida TOL plasmid and identification of the protein product. Gene. 1986;44(2-3):235–242. doi: 10.1016/0378-1119(86)90187-3. [DOI] [PubMed] [Google Scholar]
  23. Kohara Y., Akiyama K., Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. doi: 10.1016/0092-8674(87)90503-4. [DOI] [PubMed] [Google Scholar]
  24. Lundrigan M. D., Friedrich M. J., Kadner R. J. Nucleotide sequence of the Escherichia coli porin thermoregulatory gene envY. Nucleic Acids Res. 1989 Jan 25;17(2):800–800. doi: 10.1093/nar/17.2.800. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Mulligan M. E., Hawley D. K., Entriken R., McClure W. R. Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):789–800. doi: 10.1093/nar/12.1part2.789. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Mulligan M. E., McClure W. R. Analysis of the occurrence of promoter-sites in DNA. Nucleic Acids Res. 1986 Jan 10;14(1):109–126. doi: 10.1093/nar/14.1.109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Ohtsubo H., Ohtsubo E. Nucleotide sequence of an insertion element, IS1. Proc Natl Acad Sci U S A. 1978 Feb;75(2):615–619. doi: 10.1073/pnas.75.2.615. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Ramos J. L., Rojo F., Zhou L., Timmis K. N. A family of positive regulators related to the Pseudomonas putida TOL plasmid XylS and the Escherichia coli AraC activators. Nucleic Acids Res. 1990 Apr 25;18(8):2149–2152. doi: 10.1093/nar/18.8.2149. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Ronson C. W., Nixon B. T., Ausubel F. M. Conserved domains in bacterial regulatory proteins that respond to environmental stimuli. Cell. 1987 Jun 5;49(5):579–581. doi: 10.1016/0092-8674(87)90530-7. [DOI] [PubMed] [Google Scholar]
  31. Saporito S. M., Cunningham R. P. Nucleotide sequence of the nfo gene of Escherichia coli K-12. J Bacteriol. 1988 Nov;170(11):5141–5145. doi: 10.1128/jb.170.11.5141-5145.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Schmeissner U., Court D., Shimatake H., Rosenberg M. Promoter for the establishment of repressor synthesis in bacteriophage lambda. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3191–3195. doi: 10.1073/pnas.77.6.3191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Schollmeier K., Hillen W. Transposon Tn10 contains two structural genes with opposite polarity between tetA and IS10R. J Bacteriol. 1984 Nov;160(2):499–503. doi: 10.1128/jb.160.2.499-503.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Shaw J. H., Clewell D. B. Complete nucleotide sequence of macrolide-lincosamide-streptogramin B-resistance transposon Tn917 in Streptococcus faecalis. J Bacteriol. 1985 Nov;164(2):782–796. doi: 10.1128/jb.164.2.782-796.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Spooner R. A., Lindsay K., Franklin F. C. Genetic, functional and sequence analysis of the xylR and xylS regulatory genes of the TOL plasmid pWW0. J Gen Microbiol. 1986 May;132(5):1347–1358. doi: 10.1099/00221287-132-5-1347. [DOI] [PubMed] [Google Scholar]
  36. Stoner C. M., Schleif R. Is the amino acid but not the nucleotide sequence of the Escherichia coli araC gene conserved? J Mol Biol. 1982 Feb 5;154(4):649–652. doi: 10.1016/s0022-2836(82)80020-x. [DOI] [PubMed] [Google Scholar]
  37. Tobin J. F., Schleif R. F. Positive regulation of the Escherichia coli L-rhamnose operon is mediated by the products of tandemly repeated regulatory genes. J Mol Biol. 1987 Aug 20;196(4):789–799. doi: 10.1016/0022-2836(87)90405-0. [DOI] [PubMed] [Google Scholar]
  38. Touati D. Transcriptional and posttranscriptional regulation of manganese superoxide dismutase biosynthesis in Escherichia coli, studied with operon and protein fusions. J Bacteriol. 1988 Jun;170(6):2511–2520. doi: 10.1128/jb.170.6.2511-2520.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Tsaneva I. R., Weiss B. soxR, a locus governing a superoxide response regulon in Escherichia coli K-12. J Bacteriol. 1990 Aug;172(8):4197–4205. doi: 10.1128/jb.172.8.4197-4205.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Walkup L. K., Kogoma T. Escherichia coli proteins inducible by oxidative stress mediated by the superoxide radical. J Bacteriol. 1989 Mar;171(3):1476–1484. doi: 10.1128/jb.171.3.1476-1484.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Ward D. F., Murray N. E. Convergent transcription in bacteriophage lambda: interference with gene expression. J Mol Biol. 1979 Sep 15;133(2):249–266. doi: 10.1016/0022-2836(79)90533-3. [DOI] [PubMed] [Google Scholar]
  42. Webster C., Gardner L., Busby S. The Escherichia coli melR gene encodes a DNA-binding protein with affinity for specific sequences located in the melibiose-operon regulatory region. Gene. 1989 Nov 30;83(2):207–213. doi: 10.1016/0378-1119(89)90106-6. [DOI] [PubMed] [Google Scholar]
  43. Webster C., Kempsell K., Booth I., Busby S. Organisation of the regulatory region of the Escherichia coli melibiose operon. Gene. 1987;59(2-3):253–263. doi: 10.1016/0378-1119(87)90333-7. [DOI] [PubMed] [Google Scholar]
  44. White B. J., Hochhauser S. J., Cintron N. M., Weiss B. Genetic mapping of xthA, the structural gene for exonuclease III in Escherichia coli K-12. J Bacteriol. 1976 Jun;126(3):1082–1088. doi: 10.1128/jb.126.3.1082-1088.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]
  46. Zhang X. P., Ebright R. H. Identification of a contact between arginine-180 of the catabolite gene activator protein (CAP) and base pair 5 of the DNA site in the CAP-DNA complex. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4717–4721. doi: 10.1073/pnas.87.12.4717. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES