Skip to main content
PMC home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1995 Apr;177(7):1850–1859. doi: 10.1128/jb.177.7.1850-1859.1995

A carbon starvation survival gene of Pseudomonas putida is regulated by sigma 54.

Y Kim 1, L S Watrud 1, A Matin 1
PMCID: PMC176816  PMID: 7896711

Abstract

By using mini-Tn5 transposon mutagenesis, two mutants of Pseudomonas putida ATCC 12633 were isolated which showed a marked increase in their sensitivity to carbon starvation; these mutants are presumably affected in the Pex type of proteins that P. putida induces upon carbon starvation (M. Givskov, L. Eberl, and S. Molin, J. Bacteriol. 176:4816-4824, 1994). The affected genes in our mutants were induced about threefold upon carbon starvation. The promoter region of the starvation gene in the mutant MK107 possessed a strong sigma 54-type-promoter sequence, and deletion analysis suggested that this was the major promoter regulating expression; this was confirmed by transcript mapping in rpoN+ and rpoN mutant backgrounds. The deletion analysis implicated a sequence upstream of the sigma 54 promoter, as well as a region downstream of the transcription start site, in the functioning of the promoter. Two sigma 70-type Pribnow boxes were also detected in the promoter region, but their transcriptional activity in the wild type was very weak. However, in a sigma 54-deficient background, these promoters became stronger. The mechanism and possible physiological role of this phenomenon and the possibility that the sequence upstream of the sigma 54 promoter may have a role in carbon sensing are discussed.

Full Text

The Full Text of this article is available as a PDF (365.5 KB).

Selected References

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

  1. Andersen K., Wilke-Douglas M. Construction and use of a gene bank of Alcaligenes eutrophus in the analysis of ribulose bisphosphate carboxylase genes. J Bacteriol. 1984 Sep;159(3):973–978. doi: 10.1128/jb.159.3.973-978.1984. [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. Boyer H. W., Roulland-Dussoix D. A complementation analysis of the restriction and modification of DNA in Escherichia coli. J Mol Biol. 1969 May 14;41(3):459–472. doi: 10.1016/0022-2836(69)90288-5. [DOI] [PubMed] [Google Scholar]
  4. Boyle-Vavra S., So M., Seifert H. S. Transcriptional control of gonococcal pilE expression: involvement of an alternate sigma factor. Gene. 1993 Dec 31;137(2):233–236. doi: 10.1016/0378-1119(93)90012-r. [DOI] [PubMed] [Google Scholar]
  5. Bryan R., Champer R., Gomes S., Ely B., Shapiro L. Separation of temporal control and trans-acting modulation of flagellin and chemotaxis genes in Caulobacter. Mol Gen Genet. 1987 Feb;206(2):300–306. doi: 10.1007/BF00333588. [DOI] [PubMed] [Google Scholar]
  6. Carpenter P. B., Hanlon D. W., Ordal G. W. flhF, a Bacillus subtilis flagellar gene that encodes a putative GTP-binding protein. Mol Microbiol. 1992 Sep;6(18):2705–2713. doi: 10.1111/j.1365-2958.1992.tb01447.x. [DOI] [PubMed] [Google Scholar]
  7. Feng J., Atkinson M. R., McCleary W., Stock J. B., Wanner B. L., Ninfa A. J. Role of phosphorylated metabolic intermediates in the regulation of glutamine synthetase synthesis in Escherichia coli. J Bacteriol. 1992 Oct;174(19):6061–6070. doi: 10.1128/jb.174.19.6061-6070.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Fürste J. P., Pansegrau W., Frank R., Blöcker H., Scholz P., Bagdasarian M., Lanka E. Molecular cloning of the plasmid RP4 primase region in a multi-host-range tacP expression vector. Gene. 1986;48(1):119–131. doi: 10.1016/0378-1119(86)90358-6. [DOI] [PubMed] [Google Scholar]
  9. Ghiorse W. C., Wilson J. T. Microbial ecology of the terrestrial subsurface. Adv Appl Microbiol. 1988;33:107–172. doi: 10.1016/s0065-2164(08)70206-5. [DOI] [PubMed] [Google Scholar]
  10. Givskov M., Eberl L., Molin S. Responses to nutrient starvation in Pseudomonas putida KT2442: two-dimensional electrophoretic analysis of starvation- and stress-induced proteins. J Bacteriol. 1994 Aug;176(16):4816–4824. doi: 10.1128/jb.176.16.4816-4824.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Givskov M., Eberl L., Møller S., Poulsen L. K., Molin S. Responses to nutrient starvation in Pseudomonas putida KT2442: analysis of general cross-protection, cell shape, and macromolecular content. J Bacteriol. 1994 Jan;176(1):7–14. doi: 10.1128/jb.176.1.7-14.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Groat R. G., Schultz J. E., Zychlinsky E., Bockman A., Matin A. Starvation proteins in Escherichia coli: kinetics of synthesis and role in starvation survival. J Bacteriol. 1986 Nov;168(2):486–493. doi: 10.1128/jb.168.2.486-493.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hengge-Aronis R. Survival of hunger and stress: the role of rpoS in early stationary phase gene regulation in E. coli. Cell. 1993 Jan 29;72(2):165–168. doi: 10.1016/0092-8674(93)90655-a. [DOI] [PubMed] [Google Scholar]
  14. Herrero M., de Lorenzo V., Timmis K. N. Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria. J Bacteriol. 1990 Nov;172(11):6557–6567. doi: 10.1128/jb.172.11.6557-6567.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Huisman G. W., Kolter R. Sensing starvation: a homoserine lactone--dependent signaling pathway in Escherichia coli. Science. 1994 Jul 22;265(5171):537–539. doi: 10.1126/science.7545940. [DOI] [PubMed] [Google Scholar]
  16. Ishimoto K. S., Lory S. Identification of pilR, which encodes a transcriptional activator of the Pseudomonas aeruginosa pilin gene. J Bacteriol. 1992 Jun;174(11):3514–3521. doi: 10.1128/jb.174.11.3514-3521.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Jenkins D. E., Auger E. A., Matin A. Role of RpoH, a heat shock regulator protein, in Escherichia coli carbon starvation protein synthesis and survival. J Bacteriol. 1991 Mar;173(6):1992–1996. doi: 10.1128/jb.173.6.1992-1996.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Jenkins D. E., Chaisson S. A., Matin A. Starvation-induced cross protection against osmotic challenge in Escherichia coli. J Bacteriol. 1990 May;172(5):2779–2781. doi: 10.1128/jb.172.5.2779-2781.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Jenkins D. E., Schultz J. E., Matin A. Starvation-induced cross protection against heat or H2O2 challenge in Escherichia coli. J Bacteriol. 1988 Sep;170(9):3910–3914. doi: 10.1128/jb.170.9.3910-3914.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kolter R., Siegele D. A., Tormo A. The stationary phase of the bacterial life cycle. Annu Rev Microbiol. 1993;47:855–874. doi: 10.1146/annurev.mi.47.100193.004231. [DOI] [PubMed] [Google Scholar]
  21. Kustu S., Santero E., Keener J., Popham D., Weiss D. Expression of sigma 54 (ntrA)-dependent genes is probably united by a common mechanism. Microbiol Rev. 1989 Sep;53(3):367–376. doi: 10.1128/mr.53.3.367-376.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Köhler T., Alvarez J. F., Harayama S. Regulation of the rpoN, ORF102 and ORF154 genes in Pseudomonas putida. FEMS Microbiol Lett. 1994 Jan 15;115(2-3):177–184. doi: 10.1111/j.1574-6968.1994.tb06634.x. [DOI] [PubMed] [Google Scholar]
  23. Köhler T., Harayama S., Ramos J. L., Timmis K. N. Involvement of Pseudomonas putida RpoN sigma factor in regulation of various metabolic functions. J Bacteriol. 1989 Aug;171(8):4326–4333. doi: 10.1128/jb.171.8.4326-4333.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lange R., Hengge-Aronis R. Identification of a central regulator of stationary-phase gene expression in Escherichia coli. Mol Microbiol. 1991 Jan;5(1):49–59. doi: 10.1111/j.1365-2958.1991.tb01825.x. [DOI] [PubMed] [Google Scholar]
  25. Loewen P. C., von Ossowski I., Switala J., Mulvey M. R. KatF (sigma S) synthesis in Escherichia coli is subject to posttranscriptional regulation. J Bacteriol. 1993 Apr;175(7):2150–2153. doi: 10.1128/jb.175.7.2150-2153.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Lomovskaya O. L., Kidwell J. P., Matin A. Characterization of the sigma 38-dependent expression of a core Escherichia coli starvation gene, pexB. J Bacteriol. 1994 Jul;176(13):3928–3935. doi: 10.1128/jb.176.13.3928-3935.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Matin A., Auger E. A., Blum P. H., Schultz J. E. Genetic basis of starvation survival in nondifferentiating bacteria. Annu Rev Microbiol. 1989;43:293–316. doi: 10.1146/annurev.mi.43.100189.001453. [DOI] [PubMed] [Google Scholar]
  28. Matin A. Starvation promoters of Escherichia coli. Their function, regulation, and use in bioprocessing and bioremediation. Ann N Y Acad Sci. 1994 May 2;721:277–291. doi: 10.1111/j.1749-6632.1994.tb47401.x. [DOI] [PubMed] [Google Scholar]
  29. Matin A. The molecular basis of carbon-starvation-induced general resistance in Escherichia coli. Mol Microbiol. 1991 Jan;5(1):3–10. doi: 10.1111/j.1365-2958.1991.tb01819.x. [DOI] [PubMed] [Google Scholar]
  30. McCann M. P., Fraley C. D., Matin A. The putative sigma factor KatF is regulated posttranscriptionally during carbon starvation. J Bacteriol. 1993 Apr;175(7):2143–2149. doi: 10.1128/jb.175.7.2143-2149.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. McCann M. P., Kidwell J. P., Matin A. The putative sigma factor KatF has a central role in development of starvation-mediated general resistance in Escherichia coli. J Bacteriol. 1991 Jul;173(13):4188–4194. doi: 10.1128/jb.173.13.4188-4194.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Merrick M. J. In a class of its own--the RNA polymerase sigma factor sigma 54 (sigma N). Mol Microbiol. 1993 Dec;10(5):903–909. doi: 10.1111/j.1365-2958.1993.tb00961.x. [DOI] [PubMed] [Google Scholar]
  33. Morett E., Buck M. In vivo studies on the interaction of RNA polymerase-sigma 54 with the Klebsiella pneumoniae and Rhizobium meliloti nifH promoters. The role of NifA in the formation of an open promoter complex. J Mol Biol. 1989 Nov 5;210(1):65–77. doi: 10.1016/0022-2836(89)90291-x. [DOI] [PubMed] [Google Scholar]
  34. Ninfa A. J., Reitzer L. J., Magasanik B. Initiation of transcription at the bacterial glnAp2 promoter by purified E. coli components is facilitated by enhancers. Cell. 1987 Sep 25;50(7):1039–1046. doi: 10.1016/0092-8674(87)90170-x. [DOI] [PubMed] [Google Scholar]
  35. Nyström T., Flärdh K., Kjelleberg S. Responses to multiple-nutrient starvation in marine Vibrio sp. strain CCUG 15956. J Bacteriol. 1990 Dec;172(12):7085–7097. doi: 10.1128/jb.172.12.7085-7097.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Parales R. E., Harwood C. S. Construction and use of a new broad-host-range lacZ transcriptional fusion vector, pHRP309, for gram- bacteria. Gene. 1993 Oct 29;133(1):23–30. doi: 10.1016/0378-1119(93)90220-w. [DOI] [PubMed] [Google Scholar]
  37. 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]
  38. Schultz J. E., Latter G. I., Matin A. Differential regulation by cyclic AMP of starvation protein synthesis in Escherichia coli. J Bacteriol. 1988 Sep;170(9):3903–3909. doi: 10.1128/jb.170.9.3903-3909.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Schultz J. E., Matin A. Molecular and functional characterization of a carbon starvation gene of Escherichia coli. J Mol Biol. 1991 Mar 5;218(1):129–140. doi: 10.1016/0022-2836(91)90879-b. [DOI] [PubMed] [Google Scholar]
  40. Spector M. P., Cubitt C. L. Starvation-inducible loci of Salmonella typhimurium: regulation and roles in starvation-survival. Mol Microbiol. 1992 Jun;6(11):1467–1476. doi: 10.1111/j.1365-2958.1992.tb00867.x. [DOI] [PubMed] [Google Scholar]
  41. Thomas A. W., Topping A. W., Slater J. H., Weightman A. J. Localization and functional analysis of structural and regulatory dehalogenase genes carried on DEH from Pseudomonas putida PP3. J Bacteriol. 1992 Mar;174(6):1941–1947. doi: 10.1128/jb.174.6.1941-1947.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Totten P. A., Lara J. C., Lory S. The rpoN gene product of Pseudomonas aeruginosa is required for expression of diverse genes, including the flagellin gene. J Bacteriol. 1990 Jan;172(1):389–396. doi: 10.1128/jb.172.1.389-396.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Wozniak D. J. Integration host factor and sequences downstream of the Pseudomonas aeruginosa algD transcription start site are required for expression. J Bacteriol. 1994 Aug;176(16):5068–5076. doi: 10.1128/jb.176.16.5068-5076.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Zielinski N. A., Maharaj R., Roychoudhury S., Danganan C. E., Hendrickson W., Chakrabarty A. M. Alginate synthesis in Pseudomonas aeruginosa: environmental regulation of the algC promoter. J Bacteriol. 1992 Dec;174(23):7680–7688. doi: 10.1128/jb.174.23.7680-7688.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. de Lorenzo V., Herrero M., Metzke M., Timmis K. N. An upstream XylR- and IHF-induced nucleoprotein complex regulates the sigma 54-dependent Pu promoter of TOL plasmid. EMBO J. 1991 May;10(5):1159–1167. doi: 10.1002/j.1460-2075.1991.tb08056.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES