Skip to main content
NCBI home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1993 Feb;175(4):1019–1025. doi: 10.1128/jb.175.4.1019-1025.1993

Specific binding of Thiobacillus ferrooxidans RbcR to the intergenic sequence between the rbc operon and the rbcR gene.

T Kusano 1, K Sugawara 1
PMCID: PMC193014  PMID: 8432695

Abstract

The presence of two sets (rbcL1-rbcS1 and rbcL2-rbcS2) of rbc operons has been demonstrated in Thiobacillus ferrooxidans Fe1 (T. Kusano, T. Takeshima, C. Inoue, and K. Sugawara, J. Bacteriol. 173:7313-7323, 1991). A possible regulatory gene, rbcR, 930 bp long and possibly translated into a 309-amino-acid protein, was found upstream from the rbcL1 gene as a single copy. The gene is located divergently to rbcL1 with a 144-bp intergenic sequence. As in the cases of the Chromatium vinosum RbcR and Alcaligenes eutrophus CfxR, T. ferrooxidans RbcR is thought to be a new member of the LysR family, and these proteins share 46.5 and 42.8% identity, respectively. Gel mobility shift assays showed that T. ferrooxidans RbcR, produced in Escherichia coli, binds specifically to the intergenic sequence between rbcL1 and rbcR. Footprinting and site-directed mutagenesis experiments further demonstrated that RbcR binds to overlapping promoter elements of the rbcR and rbcL1 genes. The above data strongly support the participation of RbcR in regulation of the rbcL1-rbcS1 operon and the rbcR gene in T. ferrooxidans.

Full text

PDF
1019

Images in this article

1022Image
on p.1022
1023Image
on p.1023
1023Image
on p.1023
1024Image
on p.1024

Selected References

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

  1. Andersen K., Caton J. Sequence analysis of the Alcaligenes eutrophus chromosomally encoded ribulose bisphosphate carboxylase large and small subunit genes and their gene products. J Bacteriol. 1987 Oct;169(10):4547–4558. doi: 10.1128/jb.169.10.4547-4558.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bohannon D. E., Sonenshein A. L. Positive regulation of glutamate biosynthesis in Bacillus subtilis. J Bacteriol. 1989 Sep;171(9):4718–4727. doi: 10.1128/jb.171.9.4718-4727.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chang M., Hadero A., Crawford I. P. Sequence of the Pseudomonas aeruginosa trpI activator gene and relatedness of trpI to other procaryotic regulatory genes. J Bacteriol. 1989 Jan;171(1):172–183. doi: 10.1128/jb.171.1.172-183.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Hattori M., Sakaki Y. Dideoxy sequencing method using denatured plasmid templates. Anal Biochem. 1986 Feb 1;152(2):232–238. doi: 10.1016/0003-2697(86)90403-3. [DOI] [PubMed] [Google Scholar]
  6. Henikoff S., Haughn G. W., Calvo J. M., Wallace J. C. A large family of bacterial activator proteins. Proc Natl Acad Sci U S A. 1988 Sep;85(18):6602–6606. doi: 10.1073/pnas.85.18.6602. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Honoré N., Nicolas M. H., Cole S. T. Inducible cephalosporinase production in clinical isolates of Enterobacter cloacae is controlled by a regulatory gene that has been deleted from Escherichia coli. EMBO J. 1986 Dec 20;5(13):3709–3714. doi: 10.1002/j.1460-2075.1986.tb04704.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Inoue H., Nojima H., Okayama H. High efficiency transformation of Escherichia coli with plasmids. Gene. 1990 Nov 30;96(1):23–28. doi: 10.1016/0378-1119(90)90336-p. [DOI] [PubMed] [Google Scholar]
  9. Kobayashi H., Viale A. M., Takabe T., Akazawa T., Wada K., Shinozaki K., Kobayashi K., Sugiura M. Sequence and expression of genes encoding the large and small subunits of ribulose 1,5-bisphosphate carboxylase/oxygenase from Chromatium vinosum. Gene. 1991 Jan 2;97(1):55–62. doi: 10.1016/0378-1119(91)90009-z. [DOI] [PubMed] [Google Scholar]
  10. Kusano T., Takeshima T., Inoue C., Sugawara K. Evidence for two sets of structural genes coding for ribulose bisphosphate carboxylase in Thiobacillus ferrooxidans. J Bacteriol. 1991 Nov;173(22):7313–7323. doi: 10.1128/jb.173.22.7313-7323.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kuwabara M. D., Sigman D. S. Footprinting DNA-protein complexes in situ following gel retardation assays using 1,10-phenanthroline-copper ion: Escherichia coli RNA polymerase-lac promoter complexes. Biochemistry. 1987 Nov 17;26(23):7234–7238. doi: 10.1021/bi00397a006. [DOI] [PubMed] [Google Scholar]
  12. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  13. Mares R., Urbanowski M. L., Stauffer G. V. Regulation of the Salmonella typhimurium metA gene by the metR protein and homocysteine. J Bacteriol. 1992 Jan;174(2):390–397. doi: 10.1128/jb.174.2.390-397.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Maxon M. E., Wigboldus J., Brot N., Weissbach H. Structure-function studies on Escherichia coli MetR protein, a putative prokaryotic leucine zipper protein. Proc Natl Acad Sci U S A. 1990 Sep;87(18):7076–7079. doi: 10.1073/pnas.87.18.7076. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Meijer W. G., Arnberg A. C., Enequist H. G., Terpstra P., Lidstrom M. E., Dijkhuizen L. Identification and organization of carbon dioxide fixation genes in Xanthobacter flavus H4-14. Mol Gen Genet. 1991 Feb;225(2):320–330. doi: 10.1007/BF00269865. [DOI] [PubMed] [Google Scholar]
  16. Miziorko H. M., Lorimer G. H. Ribulose-1,5-bisphosphate carboxylase-oxygenase. Annu Rev Biochem. 1983;52:507–535. doi: 10.1146/annurev.bi.52.070183.002451. [DOI] [PubMed] [Google Scholar]
  17. Mizusawa S., Nishimura S., Seela F. Improvement of the dideoxy chain termination method of DNA sequencing by use of deoxy-7-deazaguanosine triphosphate in place of dGTP. Nucleic Acids Res. 1986 Feb 11;14(3):1319–1324. doi: 10.1093/nar/14.3.1319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Pulgar V., Gaete L., Allende J., Orellana O., Jordana X., Jedlicki E. Isolation and nucleotide sequence of the Thiobacillus ferrooxidans genes for the small and large subunits of ribulose 1,5-bisphosphate carboxylase/oxygenase. FEBS Lett. 1991 Nov 4;292(1-2):85–89. doi: 10.1016/0014-5793(91)80840-y. [DOI] [PubMed] [Google Scholar]
  19. Renault P., Gaillardin C., Heslot H. Product of the Lactococcus lactis gene required for malolactic fermentation is homologous to a family of positive regulators. J Bacteriol. 1989 Jun;171(6):3108–3114. doi: 10.1128/jb.171.6.3108-3114.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Rothmel R. K., Aldrich T. L., Houghton J. E., Coco W. M., Ornston L. N., Chakrabarty A. M. Nucleotide sequencing and characterization of Pseudomonas putida catR: a positive regulator of the catBC operon is a member of the LysR family. J Bacteriol. 1990 Feb;172(2):922–931. doi: 10.1128/jb.172.2.922-931.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988 Jan 29;239(4839):487–491. doi: 10.1126/science.2448875. [DOI] [PubMed] [Google Scholar]
  22. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Schell M. A., Poser E. F. Demonstration, characterization, and mutational analysis of NahR protein binding to nah and sal promoters. J Bacteriol. 1989 Feb;171(2):837–846. doi: 10.1128/jb.171.2.837-846.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Stragier P., Patte J. C. Regulation of diaminopimelate decarboxylase synthesis in Escherichia coli. III. Nucleotide sequence and regulation of the lysR gene. J Mol Biol. 1983 Aug 5;168(2):333–350. doi: 10.1016/s0022-2836(83)80022-9. [DOI] [PubMed] [Google Scholar]
  25. Sung Y. C., Fuchs J. A. The Escherichia coli K-12 cyn operon is positively regulated by a member of the lysR family. J Bacteriol. 1992 Jun;174(11):3645–3650. doi: 10.1128/jb.174.11.3645-3650.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Tabita F. R. Molecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms. Microbiol Rev. 1988 Jun;52(2):155–189. doi: 10.1128/mr.52.2.155-189.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Tabor S., Richardson C. C. A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. Proc Natl Acad Sci U S A. 1985 Feb;82(4):1074–1078. doi: 10.1073/pnas.82.4.1074. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Viale A. M., Kobayashi H., Akazawa T. Distinct properties of Escherichia coli products of plant-type ribulose-1,5-bisphosphate carboxylase/oxygenase directed by two sets of genes from the photosynthetic bacterium Chromatium vinosum. J Biol Chem. 1990 Oct 25;265(30):18386–18392. [PubMed] [Google Scholar]
  29. Viale A. M., Kobayashi H., Akazawa T. Expressed genes for plant-type ribulose 1,5-bisphosphate carboxylase/oxygenase in the photosynthetic bacterium Chromatium vinosum, which possesses two complete sets of the genes. J Bacteriol. 1989 May;171(5):2391–2400. doi: 10.1128/jb.171.5.2391-2400.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Viale A. M., Kobayashi H., Akazawa T., Henikoff S. rbcR [correction of rcbR], a gene coding for a member of the LysR family of transcriptional regulators, is located upstream of the expressed set of ribulose 1,5-bisphosphate carboxylase/oxygenase genes in the photosynthetic bacterium Chromatium vinosum. J Bacteriol. 1991 Aug;173(16):5224–5229. doi: 10.1128/jb.173.16.5224-5229.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Wek R. C., Hatfield G. W. Nucleotide sequence and in vivo expression of the ilvY and ilvC genes in Escherichia coli K12. Transcription from divergent overlapping promoters. J Biol Chem. 1986 Feb 15;261(5):2441–2450. [PubMed] [Google Scholar]
  32. Windhövel U., Bowien B. Identification of cfxR, an activator gene of autotrophic CO2 fixation in Alcaligenes eutrophus. Mol Microbiol. 1991 Nov;5(11):2695–2705. doi: 10.1111/j.1365-2958.1991.tb01978.x. [DOI] [PubMed] [Google Scholar]
  33. 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]
  34. You I. S., Ghosal D., Gunsalus I. C. Nucleotide sequence of plasmid NAH7 gene nahR and DNA binding of the nahR product. J Bacteriol. 1988 Dec;170(12):5409–5415. doi: 10.1128/jb.170.12.5409-5415.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES