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. 1995 Dec;177(23):6854–6860. doi: 10.1128/jb.177.23.6854-6860.1995

Principal sigma subunit of the Caulobacter crescentus RNA polymerase.

J Malakooti 1, B Ely 1
PMCID: PMC177553  PMID: 7592478

Abstract

We have identified the gene encoding the Caulobacter crescentus principal sigma subunit, RpoD. The rpoD gene codes for a polypeptide of 653 amino acids with a predicted molecular mass of 72,623 Da (sigma 73). The C. crescentus sigma subunit has extensive amino acid sequence homology with the principal sigma factors of a number of divergent procaryotes. In particular, the segments designated region 2 that are involved in core polymerase binding and promoter recognition were identical among these bacteria despite the fact that the -10 region recognized by the C. crescentus sigma 73 differs significantly from that of the other bacteria. Thus, it appears that additional sigma factor regions must be involved in -10 region recognition. This conclusion was strengthened by a heterologous complementation assay in which C. crescentus sigma 73 was capable of complementing the Escherichia coli rpoD285 temperature-sensitive mutant. Furthermore, C. crescentus sigma 73 conferred new specificity on the E. coli RNA polymerase, allowing the expression of C. crescentus promoters in E. coli. Thus, the C. crescentus sigma 73 appears to have a broader specificity than does the sigma 70 of the enteric bacteria.

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Selected References

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  1. Amemiya K., Shapiro L. Differential template recognition by the Caulobacter crescentus and the escherichia coli RNA polymerases. J Biol Chem. 1983 Jul 25;258(14):8984–8992. [PubMed] [Google Scholar]
  2. Bender R. A., Refson C. M., O'Neill E. A. Role of the flagellum in cell-cycle-dependent expression of bacteriophage receptor activity in Caulobacter crescentus. J Bacteriol. 1989 Feb;171(2):1035–1040. doi: 10.1128/jb.171.2.1035-1040.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bendis I. K., Shapiro L. Deoxyribonucleic acid-dependent ribonucleic acid polymerase of Caulobacter crescentus. J Bacteriol. 1973 Sep;115(3):848–857. doi: 10.1128/jb.115.3.848-857.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Berk A. J., Sharp P. A. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell. 1977 Nov;12(3):721–732. doi: 10.1016/0092-8674(77)90272-0. [DOI] [PubMed] [Google Scholar]
  5. Brun Y. V., Shapiro L. A temporally controlled sigma-factor is required for polar morphogenesis and normal cell division in Caulobacter. Genes Dev. 1992 Dec;6(12A):2395–2408. doi: 10.1101/gad.6.12a.2395. [DOI] [PubMed] [Google Scholar]
  6. Burton Z. F., Gross C. A., Watanabe K. K., Burgess R. R. The operon that encodes the sigma subunit of RNA polymerase also encodes ribosomal protein S21 and DNA primase in E. coli K12. Cell. 1983 Feb;32(2):335–349. doi: 10.1016/0092-8674(83)90453-1. [DOI] [PubMed] [Google Scholar]
  7. Burton Z., Burgess R. R., Lin J., Moore D., Holder S., Gross C. A. The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12. Nucleic Acids Res. 1981 Jun 25;9(12):2889–2903. doi: 10.1093/nar/9.12.2889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Daniels D., Zuber P., Losick R. Two amino acids in an RNA polymerase sigma factor involved in the recognition of adjacent base pairs in the -10 region of a cognate promoter. Proc Natl Acad Sci U S A. 1990 Oct;87(20):8075–8079. doi: 10.1073/pnas.87.20.8075. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. 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]
  10. Ely B. DNA sequence of the 3' end of the Caulobacter crescentus 16S rRNA gene. Nucleic Acids Res. 1992 Mar 25;20(6):1423–1423. doi: 10.1093/nar/20.6.1423. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Erickson B. D., Burton Z. F., Watanabe K. K., Burgess R. R. Nucleotide sequence of the rpsU-dnaG-rpoD operon from Salmonella typhimurium and a comparison of this sequence with the homologous operon of Escherichia coli. Gene. 1985;40(1):67–78. doi: 10.1016/0378-1119(85)90025-3. [DOI] [PubMed] [Google Scholar]
  12. Gardella T., Moyle H., Susskind M. M. A mutant Escherichia coli sigma 70 subunit of RNA polymerase with altered promoter specificity. J Mol Biol. 1989 Apr 20;206(4):579–590. doi: 10.1016/0022-2836(89)90567-6. [DOI] [PubMed] [Google Scholar]
  13. Helmann J. D., Chamberlin M. J. Structure and function of bacterial sigma factors. Annu Rev Biochem. 1988;57:839–872. doi: 10.1146/annurev.bi.57.070188.004203. [DOI] [PubMed] [Google Scholar]
  14. Johnson R. C., Ely B. Isolation of spontaneously derived mutants of Caulobacter crescentus. Genetics. 1977 May;86(1):25–32. doi: 10.1093/genetics/86.1.25. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lai C. Y., Baumann P. Sequence analysis of a DNA fragment from Buchnera aphidicola (an endosymbiont of aphids) containing genes homologous to dnaG, rpoD, cysE, and secB. Gene. 1992 Sep 21;119(1):113–118. doi: 10.1016/0378-1119(92)90074-y. [DOI] [PubMed] [Google Scholar]
  16. Liebke H., Gross C., Walter W., Burgess R. A new mutation rpoD800, affecting the sigma subunit of E. coli RNA polymerase is allelic to two other sigma mutants. Mol Gen Genet. 1980 Jan;177(2):277–282. doi: 10.1007/BF00267439. [DOI] [PubMed] [Google Scholar]
  17. Lonetto M., Gribskov M., Gross C. A. The sigma 70 family: sequence conservation and evolutionary relationships. J Bacteriol. 1992 Jun;174(12):3843–3849. doi: 10.1128/jb.174.12.3843-3849.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Malakooti J., Ely B. Identification and characterization of the ilvR gene encoding a LysR-type regulator of Caulobacter crescentus. J Bacteriol. 1994 Mar;176(5):1275–1281. doi: 10.1128/jb.176.5.1275-1281.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Malakooti J., Wang S. P., Ely B. A consensus promoter sequence for Caulobacter crescentus genes involved in biosynthetic and housekeeping functions. J Bacteriol. 1995 Aug;177(15):4372–4376. doi: 10.1128/jb.177.15.4372-4376.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Mullin D., Minnich S., Chen L. S., Newton A. A set of positively regulated flagellar gene promoters in Caulobacter crescentus with sequence homology to the nif gene promoters of Klebsiella pneumoniae. J Mol Biol. 1987 Jun 20;195(4):939–943. doi: 10.1016/0022-2836(87)90497-9. [DOI] [PubMed] [Google Scholar]
  21. Newton A., Ohta N., Ramakrishnan G., Mullin D., Raymond G. Genetic switching in the flagellar gene hierarchy of Caulobacter requires negative as well as positive regulation of transcription. Proc Natl Acad Sci U S A. 1989 Sep;86(17):6651–6655. doi: 10.1073/pnas.86.17.6651. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Newton A., Ohta N. Regulation of the cell division cycle and differentiation in bacteria. Annu Rev Microbiol. 1990;44:689–719. doi: 10.1146/annurev.mi.44.100190.003353. [DOI] [PubMed] [Google Scholar]
  23. Newton A. Role of transcription in the temporal control of development in Caulobacter crescentus (stalk-rifampin-RNA synthesis-DNA synthesis-motility). Proc Natl Acad Sci U S A. 1972 Feb;69(2):447–451. doi: 10.1073/pnas.69.2.447. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Ramakrishnan G., Newton A. FlbD of Caulobacter crescentus is a homologue of the NtrC (NRI) protein and activates sigma 54-dependent flagellar gene promoters. Proc Natl Acad Sci U S A. 1990 Mar;87(6):2369–2373. doi: 10.1073/pnas.87.6.2369. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Reuter S. H., Shapiro L. Asymmetric segregation of heat-shock proteins upon cell division in Caulobacter crescentus. J Mol Biol. 1987 Apr 20;194(4):653–662. doi: 10.1016/0022-2836(87)90242-7. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. Schneider G. J., Hasekorn R. RNA polymerase subunit homology among cyanobacteria, other eubacteria and archaebacteria. J Bacteriol. 1988 Sep;170(9):4136–4140. doi: 10.1128/jb.170.9.4136-4140.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Segal G., Ron E. Z. Cloning, sequencing, and transcriptional analysis of the gene coding for the vegetative sigma factor of Agrobacterium tumefaciens. J Bacteriol. 1993 May;175(10):3026–3030. doi: 10.1128/jb.175.10.3026-3030.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Shapiro L. Protein localization and asymmetry in the bacterial cell. Cell. 1993 Jun 4;73(5):841–855. doi: 10.1016/0092-8674(93)90266-s. [DOI] [PubMed] [Google Scholar]
  30. Smiley B. L., Lupski J. R., Svec P. S., McMacken R., Godson G. N. Sequences of the Escherichia coli dnaG primase gene and regulation of its expression. Proc Natl Acad Sci U S A. 1982 Aug;79(15):4550–4554. doi: 10.1073/pnas.79.15.4550. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Tanaka K., Takahashi H. Cloning and analysis of the gene (rpoDA) for the principal sigma factor of Pseudomonas aeruginosa. Biochim Biophys Acta. 1991 May 2;1089(1):113–119. doi: 10.1016/0167-4781(91)90092-z. [DOI] [PubMed] [Google Scholar]
  32. Tarleton J. C., Ely B. Isolation and characterization of ilvA, ilvBN, and ilvD mutants of Caulobacter crescentus. J Bacteriol. 1991 Feb;173(3):1259–1267. doi: 10.1128/jb.173.3.1259-1267.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Tarleton J. C., Malakooti J., Ely B. Regulation of Caulobacter crescentus ilvBN gene expression. J Bacteriol. 1994 Jun;176(12):3765–3774. doi: 10.1128/jb.176.12.3765-3774.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Taylor W. E., Straus D. B., Grossman A. D., Burton Z. F., Gross C. A., Burgess R. R. Transcription from a heat-inducible promoter causes heat shock regulation of the sigma subunit of E. coli RNA polymerase. Cell. 1984 Sep;38(2):371–381. doi: 10.1016/0092-8674(84)90492-6. [DOI] [PubMed] [Google Scholar]
  35. Waldburger C., Gardella T., Wong R., Susskind M. M. Changes in conserved region 2 of Escherichia coli sigma 70 affecting promoter recognition. J Mol Biol. 1990 Sep 20;215(2):267–276. doi: 10.1016/s0022-2836(05)80345-6. [DOI] [PubMed] [Google Scholar]
  36. Wang L. F., Doi R. H. Nucleotide sequence and organization of Bacillus subtilis RNA polymerase major sigma (sigma 43) operon. Nucleic Acids Res. 1986 May 27;14(10):4293–4307. doi: 10.1093/nar/14.10.4293. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Winkler M. E., Schoenlein P. V., Ross C. M., Barrett J. T., Ely B. Genetic and physical analyses of Caulobacter crescentus trp genes. J Bacteriol. 1984 Oct;160(1):279–287. doi: 10.1128/jb.160.1.279-287.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Zhou Y. N., Walter W. A., Gross C. A. A mutant sigma 32 with a small deletion in conserved region 3 of sigma has reduced affinity for core RNA polymerase. J Bacteriol. 1992 Aug;174(15):5005–5012. doi: 10.1128/jb.174.15.5005-5012.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]

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