Skip to main content
NCBI home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1996 Aug;178(15):4344–4366. doi: 10.1128/jb.178.15.4344-4366.1996

Global analysis of proteins synthesized during phosphorus restriction in Escherichia coli.

R A VanBogelen 1, E R Olson 1, B L Wanner 1, F C Neidhardt 1
PMCID: PMC178200  PMID: 8755861

Abstract

The pattern of proteins synthesized in Escherichia coli during steady-state growth in media with ample inorganic phosphate (Pi), upon limitation for Pi (without an alternative phosphorous compound), and during steady-state growth in media containing phosphonate (PHN) as the sole P source was examined by two-dimensional gel electrophoresis. Of 816 proteins monitored in these experiments, all those with differential synthesis rates greater than 2.0 or less than 0.5 upon phosphate limitation (P limitation) or during growth on PHN compared with their rates in the cultures with Pi were classified as belonging to the PL or PHN stimulon, respectively. The PL stimulon included 413 proteins, 208 showing induced synthesis and 205 showing repressed synthesis. The PHN stimulon was smaller: it included 257 proteins; 227 showed induced synthesis and 30 showed repressed synthesis. The overlap of the two stimulons included 137 proteins: most (118) were ones showing induced synthesis. The promoter regions of genes for several of the proteins with induced or repressed synthesis contained sequences which resembled the consensus sequence for PhoB binding. The aggregate mass of proteins responding to P limitation or growth on PHN was 30 to 40% of the cells' total mass. By comparing the proteins responding to P limitation with those responding to growth on PHN, one can speculate which proteins are likely involved in adapting cells to new P sources or in preparing cells to survive stationary phase.

Full Text

The Full Text of this article is available as a PDF (989.0 KB).

Selected References

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

  1. Backendorf C., Brandsma J. A., Kartasova T., van de Putte P. In vivo regulation of the uvrA gene: role of the "-10" and "-35" promoter regions. Nucleic Acids Res. 1983 Sep 10;11(17):5795–5810. doi: 10.1093/nar/11.17.5795. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bairoch A., Boeckmann B. The SWISS-PROT protein sequence data bank: current status. Nucleic Acids Res. 1994 Sep;22(17):3578–3580. [PMC free article] [PubMed] [Google Scholar]
  3. Chuang S. E., Daniels D. L., Blattner F. R. Global regulation of gene expression in Escherichia coli. J Bacteriol. 1993 Apr;175(7):2026–2036. doi: 10.1128/jb.175.7.2026-2036.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cordaro J. C., Melton T., Stratis J. P., Atagün M., Gladding C., Hartman P. E., Roseman S. Fosfomycin resistance: selection method for internal and extended deletions of the phosphoenolpyruvate:sugar phosphotransferase genes of Salmonella typhimurium. J Bacteriol. 1976 Dec;128(3):785–793. doi: 10.1128/jb.128.3.785-793.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Daldal F. Nucleotide sequence of gene pfkB encoding the minor phosphofructokinase of Escherichia coli K-12. Gene. 1984 Jun;28(3):337–342. doi: 10.1016/0378-1119(84)90151-3. [DOI] [PubMed] [Google Scholar]
  6. Egan S. E., Fliege R., Tong S., Shibata A., Wolf R. E., Jr, Conway T. Molecular characterization of the Entner-Doudoroff pathway in Escherichia coli: sequence analysis and localization of promoters for the edd-eda operon. J Bacteriol. 1992 Jul;174(14):4638–4646. doi: 10.1128/jb.174.14.4638-4646.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Falconi M., Higgins N. P., Spurio R., Pon C. L., Gualerzi C. O. Expression of the gene encoding the major bacterial nucleotide protein H-NS is subject to transcriptional auto-repression. Mol Microbiol. 1993 Oct;10(2):273–282. [PubMed] [Google Scholar]
  8. Garrels J. I. Two dimensional gel electrophoresis and computer analysis of proteins synthesized by clonal cell lines. J Biol Chem. 1979 Aug 25;254(16):7961–7977. [PubMed] [Google Scholar]
  9. 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]
  10. Gutierrez C., Barondess J., Manoil C., Beckwith J. The use of transposon TnphoA to detect genes for cell envelope proteins subject to a common regulatory stimulus. Analysis of osmotically regulated genes in Escherichia coli. J Mol Biol. 1987 May 20;195(2):289–297. doi: 10.1016/0022-2836(87)90650-4. [DOI] [PubMed] [Google Scholar]
  11. Inokuchi K., Mutoh N., Matsuyama S., Mizushima S. Primary structure of the ompF gene that codes for a major outer membrane protein of Escherichia coli K-12. Nucleic Acids Res. 1982 Nov 11;10(21):6957–6968. doi: 10.1093/nar/10.21.6957. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kennedy K. E., Thompson G. A., Jr Phosphonolipids: localization in surface membranes of Tetrahymena. Science. 1970 May 22;168(3934):989–991. doi: 10.1126/science.168.3934.989. [DOI] [PubMed] [Google Scholar]
  13. Kröger M., Wahl R., Rice P. Compilation of DNA sequences of Escherichia coli (update 1993). Nucleic Acids Res. 1993 Jul 1;21(13):2973–3000. doi: 10.1093/nar/21.13.2973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lawther R. P., Wek R. C., Lopes J. M., Pereira R., Taillon B. E., Hatfield G. W. The complete nucleotide sequence of the ilvGMEDA operon of Escherichia coli K-12. Nucleic Acids Res. 1987 Mar 11;15(5):2137–2155. doi: 10.1093/nar/15.5.2137. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lee K. S., Metcalf W. W., Wanner B. L. Evidence for two phosphonate degradative pathways in Enterobacter aerogenes. J Bacteriol. 1992 Apr;174(8):2501–2510. doi: 10.1128/jb.174.8.2501-2510.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Leung H. B., Kvalnes-Krick K. L., Meyer S. L., deRiel J. K., Schramm V. L. Structure and regulation of the AMP nucleosidase gene (amn) from Escherichia coli. Biochemistry. 1989 Oct 31;28(22):8726–8733. doi: 10.1021/bi00448a008. [DOI] [PubMed] [Google Scholar]
  17. Lindquist S., Craig E. A. The heat-shock proteins. Annu Rev Genet. 1988;22:631–677. doi: 10.1146/annurev.ge.22.120188.003215. [DOI] [PubMed] [Google Scholar]
  18. Martin J. F., Demain A. L. Control of antibiotic biosynthesis. Microbiol Rev. 1980 Jun;44(2):230–251. doi: 10.1128/mr.44.2.230-251.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Metcalf W. W., Wanner B. L. Evidence for a fourteen-gene, phnC to phnP locus for phosphonate metabolism in Escherichia coli. Gene. 1993 Jul 15;129(1):27–32. doi: 10.1016/0378-1119(93)90692-v. [DOI] [PubMed] [Google Scholar]
  20. Miller J. F., Mekalanos J. J., Falkow S. Coordinate regulation and sensory transduction in the control of bacterial virulence. Science. 1989 Feb 17;243(4893):916–922. doi: 10.1126/science.2537530. [DOI] [PubMed] [Google Scholar]
  21. Nasoff M. S., Baker H. V., 2nd, Wolf R. E., Jr DNA sequence of the Escherichia coli gene, gnd, for 6-phosphogluconate dehydrogenase. Gene. 1984 Mar;27(3):253–264. doi: 10.1016/0378-1119(84)90070-2. [DOI] [PubMed] [Google Scholar]
  22. Neidhardt F. C., Bloch P. L., Smith D. F. Culture medium for enterobacteria. J Bacteriol. 1974 Sep;119(3):736–747. doi: 10.1128/jb.119.3.736-747.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Neidhardt F. C., VanBogelen R. A. Positive regulatory gene for temperature-controlled proteins in Escherichia coli. Biochem Biophys Res Commun. 1981 May 29;100(2):894–900. doi: 10.1016/s0006-291x(81)80257-4. [DOI] [PubMed] [Google Scholar]
  24. O'Farrell P. H. High resolution two-dimensional electrophoresis of proteins. J Biol Chem. 1975 May 25;250(10):4007–4021. [PMC free article] [PubMed] [Google Scholar]
  25. Patterson S. D., Latter G. I. Evaluation of storage phosphor imaging for quantitative analysis of 2-D gels using the Quest II system. Biotechniques. 1993 Dec;15(6):1076–1083. [PubMed] [Google Scholar]
  26. Pedersen S., Bloch P. L., Reeh S., Neidhardt F. C. Patterns of protein synthesis in E. coli: a catalog of the amount of 140 individual proteins at different growth rates. Cell. 1978 May;14(1):179–190. doi: 10.1016/0092-8674(78)90312-4. [DOI] [PubMed] [Google Scholar]
  27. Rödel W., Plaga W., Frank R., Knappe J. Primary structures of Escherichia coli pyruvate formate-lyase and pyruvate-formate-lyase-activating enzyme deduced from the DNA nucleotide sequences. Eur J Biochem. 1988 Oct 15;177(1):153–158. doi: 10.1111/j.1432-1033.1988.tb14356.x. [DOI] [PubMed] [Google Scholar]
  28. Sankar P., Hutton M. E., VanBogelen R. A., Clark R. L., Neidhardt F. C. Expression analysis of cloned chromosomal segments of Escherichia coli. J Bacteriol. 1993 Aug;175(16):5145–5152. doi: 10.1128/jb.175.16.5145-5152.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Siegele D. A., Kolter R. Life after log. J Bacteriol. 1992 Jan;174(2):345–348. doi: 10.1128/jb.174.2.345-348.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Sinai A. P., Bavoil P. M. Hyper-invasive mutants define a novel Pho-regulated invasion pathway in Escherichia coli. Mol Microbiol. 1993 Dec;10(5):1125–1137. doi: 10.1111/j.1365-2958.1993.tb00982.x. [DOI] [PubMed] [Google Scholar]
  31. Smith D. R., Calvo J. M. Nucleotide sequence of the E coli gene coding for dihydrofolate reductase. Nucleic Acids Res. 1980 May 24;8(10):2255–2274. doi: 10.1093/nar/8.10.2255. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Spence J., Cegielska A., Georgopoulos C. Role of Escherichia coli heat shock proteins DnaK and HtpG (C62.5) in response to nutritional deprivation. J Bacteriol. 1990 Dec;172(12):7157–7166. doi: 10.1128/jb.172.12.7157-7166.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Tanaka S., Matsushita Y., Yoshikawa A., Isono K. Cloning and molecular characterization of the gene rimL which encodes an enzyme acetylating ribosomal protein L12 of Escherichia coli K12. Mol Gen Genet. 1989 Jun;217(2-3):289–293. doi: 10.1007/BF02464895. [DOI] [PubMed] [Google Scholar]
  34. VanBogelen R. A., Hutton M. E., Neidhardt F. C. Gene-protein database of Escherichia coli K-12: edition 3. Electrophoresis. 1990 Dec;11(12):1131–1166. doi: 10.1002/elps.1150111205. [DOI] [PubMed] [Google Scholar]
  35. VanBogelen R. A., Kelley P. M., Neidhardt F. C. Differential induction of heat shock, SOS, and oxidation stress regulons and accumulation of nucleotides in Escherichia coli. J Bacteriol. 1987 Jan;169(1):26–32. doi: 10.1128/jb.169.1.26-32.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. VanBogelen R. A., Neidhardt F. C. Ribosomes as sensors of heat and cold shock in Escherichia coli. Proc Natl Acad Sci U S A. 1990 Aug;87(15):5589–5593. doi: 10.1073/pnas.87.15.5589. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. VanBogelen R. A., Sankar P., Clark R. L., Bogan J. A., Neidhardt F. C. The gene-protein database of Escherichia coli: edition 5. Electrophoresis. 1992 Dec;13(12):1014–1054. doi: 10.1002/elps.11501301203. [DOI] [PubMed] [Google Scholar]
  38. Wanner B. L., Boline J. A. Mapping and molecular cloning of the phn (psiD) locus for phosphonate utilization in Escherichia coli. J Bacteriol. 1990 Mar;172(3):1186–1196. doi: 10.1128/jb.172.3.1186-1196.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Wanner B. L., McSharry R. Phosphate-controlled gene expression in Escherichia coli K12 using Mudl-directed lacZ fusions. J Mol Biol. 1982 Jul 5;158(3):347–363. doi: 10.1016/0022-2836(82)90202-9. [DOI] [PubMed] [Google Scholar]
  40. Wanner B. L., Metcalf W. W. Molecular genetic studies of a 10.9-kb operon in Escherichia coli for phosphonate uptake and biodegradation. FEMS Microbiol Lett. 1992 Dec 15;100(1-3):133–139. doi: 10.1111/j.1574-6968.1992.tb14031.x. [DOI] [PubMed] [Google Scholar]
  41. Weichart D., Lange R., Henneberg N., Hengge-Aronis R. Identification and characterization of stationary phase-inducible genes in Escherichia coli. Mol Microbiol. 1993 Oct;10(2):407–420. [PubMed] [Google Scholar]

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

RESOURCES