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. 1991 Feb;173(3):1168–1174. doi: 10.1128/jb.173.3.1168-1174.1991

An unusual correlation between ppGpp pool size and rate of ribosome synthesis during partial pyrimidine starvation of Escherichia coli.

U Vogel 1, S Pedersen 1, K F Jensen 1
PMCID: PMC207238  PMID: 1704003

Abstract

Escherichia coli was exposed to partial pyrimidine starvation by feeding a pyrBI strain orotate as the only pyrimidine source. Subsequently, differential rates of synthesis of rRNA and of a few ribosome-associated proteins as well as the pool sizes of nucleoside triphosphates and ppGpp were measured. As the orotate concentration in the medium was reduced, the growth rate decreased and the pools of pyrimidine nucleotides, particularly UTP, declined. We did not observe the normal inverse relation between concentration of ppGpp and growth rate; rather, we observed that the ppGpp pool was low at slow growth rates. Upshifts in growth rate were made by adding uracil to a culture growing slowly on orotate. Downshifts could be provoked by adding aspartate plus glutamate to a culture growing at a high concentration of orotate. Following the upshift, both the rates of synthesis of the ribosomal components and the pool of ppGpp increased rapidly, while they all decreased after the downshift. These results are discussed in relation to the role of ppGpp in the growth rate control and the stringent response.

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Selected References

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  1. Bagnara A. S., Finch L. R. The effects of bases and nucleosides on the intracellular contents of nucleotides and 5-phosphoribosyl 1-pyrophosphate in Escherichia coli. Eur J Biochem. 1974 Feb 1;41(3):421–430. doi: 10.1111/j.1432-1033.1974.tb03283.x. [DOI] [PubMed] [Google Scholar]
  2. Baracchini E., Bremer H. Stringent and growth control of rRNA synthesis in Escherichia coli are both mediated by ppGpp. J Biol Chem. 1988 Feb 25;263(6):2597–2602. [PubMed] [Google Scholar]
  3. Bonekamp F., Clemmesen K., Karlström O., Jensen K. F. Mechanism of UTP-modulated attenuation at the pyrE gene of Escherichia coli: an example of operon polarity control through the coupling of translation to transcription. EMBO J. 1984 Dec 1;3(12):2857–2861. doi: 10.1002/j.1460-2075.1984.tb02220.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bremer H., Yuan D. RNA chain growth-rate in Escherichia coli. J Mol Biol. 1968 Dec 14;38(2):163–180. doi: 10.1016/0022-2836(68)90404-x. [DOI] [PubMed] [Google Scholar]
  5. Cashel M., Gallant J. Two compounds implicated in the function of the RC gene of Escherichia coli. Nature. 1969 Mar 1;221(5183):838–841. doi: 10.1038/221838a0. [DOI] [PubMed] [Google Scholar]
  6. Christiansen L., Pedersen S. Cloning, restriction endonuclease mapping and post-transcriptional regulation of rpsA, the structural gene for ribosomal protein S1. Mol Gen Genet. 1981;181(4):548–551. doi: 10.1007/BF00428751. [DOI] [PubMed] [Google Scholar]
  7. Clemmesen K., Bonekamp F., Karlström O., Jensen K. F. Role of translation in the UTP-modulated attenuation at the pyrBI operon of Escherichia coli. Mol Gen Genet. 1985;201(2):247–251. doi: 10.1007/BF00425666. [DOI] [PubMed] [Google Scholar]
  8. Dennis P. P., Herman R. K. Pyrimidine pools and macromolecular composition of pyrimidine-limited Escherichia coli. J Bacteriol. 1970 Apr;102(1):118–123. doi: 10.1128/jb.102.1.118-123.1970. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Edlin G., Maaloe O. Synthesis and breakdown of messenger RNA without protein synthesis. J Mol Biol. 1966 Feb;15(2):428–434. doi: 10.1016/s0022-2836(66)80118-3. [DOI] [PubMed] [Google Scholar]
  10. Fiil N. P., von Meyenburg K., Friesen J. D. Accumulation and turnover of guanosine tetraphosphate in Escherichia coli. J Mol Biol. 1972 Nov 28;71(3):769–783. doi: 10.1016/s0022-2836(72)80037-8. [DOI] [PubMed] [Google Scholar]
  11. Gaal T., Gourse R. L. Guanosine 3'-diphosphate 5'-diphosphate is not required for growth rate-dependent control of rRNA synthesis in Escherichia coli. Proc Natl Acad Sci U S A. 1990 Jul;87(14):5533–5537. doi: 10.1073/pnas.87.14.5533. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Haseltine W. A., Block R. Synthesis of guanosine tetra- and pentaphosphate requires the presence of a codon-specific, uncharged transfer ribonucleic acid in the acceptor site of ribosomes. Proc Natl Acad Sci U S A. 1973 May;70(5):1564–1568. doi: 10.1073/pnas.70.5.1564. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hernandez V. J., Bremer H. Guanosine tetraphosphate (ppGpp) dependence of the growth rate control of rrnB P1 promoter activity in Escherichia coli. J Biol Chem. 1990 Jul 15;265(20):11605–11614. [PubMed] [Google Scholar]
  14. Jensen K. F., Fast R., Karlström O., Larsen J. N. Association of RNA polymerase having increased Km for ATP and UTP with hyperexpression of the pyrB and pyrE genes of Salmonella typhimurium. J Bacteriol. 1986 Jun;166(3):857–865. doi: 10.1128/jb.166.3.857-865.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Jensen K. F., Houlberg U., Nygaard P. Thin-layer chromatographic methods to isolate 32P-labeled 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP): determination of cellular PRPP pools and assay of PRPP synthetase activity. Anal Biochem. 1979 Oct 1;98(2):254–263. doi: 10.1016/0003-2697(79)90138-6. [DOI] [PubMed] [Google Scholar]
  16. Jensen K. F., Pedersen S. Metabolic growth rate control in Escherichia coli may be a consequence of subsaturation of the macromolecular biosynthetic apparatus with substrates and catalytic components. Microbiol Rev. 1990 Jun;54(2):89–100. doi: 10.1128/mr.54.2.89-100.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Johnsen K., Molin S., Karlström O., Maaloe O. Control of protein synthesis in Escherichia coli: analysis of an energy source shift-down. J Bacteriol. 1977 Jul;131(1):18–29. doi: 10.1128/jb.131.1.18-29.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Justesen J., Lund T., Skou Pedersen F., Kjeldgaard N. O. The physiology of stringent factor (ATP:GTP 3'-diphosphotransferase) in Escherichia coli. Biochimie. 1986 May;68(5):715–722. doi: 10.1016/s0300-9084(86)80165-1. [DOI] [PubMed] [Google Scholar]
  19. Jørgensen P., Collins J., Fiil N., von Meyenbourg K. A ribosomal RNA gene, rrnC, of Escherichia coli, mapped by specialized transducing lambdadilv and lambda drbs phages. Mol Gen Genet. 1978 Jul 11;163(2):223–228. doi: 10.1007/BF00267413. [DOI] [PubMed] [Google Scholar]
  20. Kingston R. E., Chamberlin M. J. Pausing and attenuation of in vitro transcription in the rrnB operon of E. coli. Cell. 1981 Dec;27(3 Pt 2):523–531. doi: 10.1016/0092-8674(81)90394-9. [DOI] [PubMed] [Google Scholar]
  21. Kingston R. E., Nierman W. C., Chamberlin M. J. A direct effect of guanosine tetraphosphate on pausing of Escherichia coli RNA polymerase during RNA chain elongation. J Biol Chem. 1981 Mar 25;256(6):2787–2797. [PubMed] [Google Scholar]
  22. Lund E., Kjeldgaard N. O. Metabolism of guanosine tetraphosphate in Escherichia coli. Eur J Biochem. 1972 Jul 24;28(3):316–326. doi: 10.1111/j.1432-1033.1972.tb01916.x. [DOI] [PubMed] [Google Scholar]
  23. Metzger S., Schreiber G., Aizenman E., Cashel M., Glaser G. Characterization of the relA1 mutation and a comparison of relA1 with new relA null alleles in Escherichia coli. J Biol Chem. 1989 Dec 15;264(35):21146–21152. [PubMed] [Google Scholar]
  24. Molin S., Von Meyenburg K., Maaloe O., Hansen M. T., Pato M. L. Control of ribosome synthesis in Escherichia coli: analysis of an energy source shift-down. J Bacteriol. 1977 Jul;131(1):7–17. doi: 10.1128/jb.131.1.7-17.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. 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]
  26. Pedersen F. S., Lund E., Kjeldgaard N. O. Codon specific, tRNA dependent in vitro synthesis of ppGpp and pppGpp. Nat New Biol. 1973 May 2;243(122):13–15. [PubMed] [Google Scholar]
  27. Pedersen S., Reeh S. V. Analysis of the proteins synthesized in ultraviolet light-irradiated Escherichia coli following infection with the bacteriophages lambdadrifd 18 and lambdadfus-3. Mol Gen Genet. 1976 Mar 30;144(3):339–343. doi: 10.1007/BF00341733. [DOI] [PubMed] [Google Scholar]
  28. Poulsen P., Jensen K. F. Effect of UTP and GTP pools on attenuation at the pyrE gene of Escherichia coli. Mol Gen Genet. 1987 Jun;208(1-2):152–158. doi: 10.1007/BF00330436. [DOI] [PubMed] [Google Scholar]
  29. Reeh S., Pedersen S., Friesen J. D. Biosynthetic regulation of individual proteins in relA+ and relA strains of Escherichia coli during amino acid starvation. Mol Gen Genet. 1976 Dec 22;149(3):279–289. doi: 10.1007/BF00268529. [DOI] [PubMed] [Google Scholar]
  30. Rojiani M. V., Jakubowski H., Goldman E. Effect of variation of charged and uncharged tRNA(Trp) levels on ppGpp synthesis in Escherichia coli. J Bacteriol. 1989 Dec;171(12):6493–6502. doi: 10.1128/jb.171.12.6493-6502.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Roland K. L., Liu C. G., Turnbough C. L., Jr Role of the ribosome in suppressing transcriptional termination at the pyrBI attenuator of Escherichia coli K-12. Proc Natl Acad Sci U S A. 1988 Oct;85(19):7149–7153. doi: 10.1073/pnas.85.19.7149. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Roland K. L., Powell F. E., Turnbough C. L., Jr Role of translation and attenuation in the control of pyrBI operon expression in Escherichia coli K-12. J Bacteriol. 1985 Sep;163(3):991–999. doi: 10.1128/jb.163.3.991-999.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. SCHAECHTER M., MAALOE O., KJELDGAARD N. O. Dependency on medium and temperature of cell size and chemical composition during balanced grown of Salmonella typhimurium. J Gen Microbiol. 1958 Dec;19(3):592–606. doi: 10.1099/00221287-19-3-592. [DOI] [PubMed] [Google Scholar]
  34. STENT G. S., BRENNER S. A genetic locus for the regulation of ribonucleic acid synthesis. Proc Natl Acad Sci U S A. 1961 Dec 15;47:2005–2014. doi: 10.1073/pnas.47.12.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sarubbi E., Rudd K. E., Cashel M. Basal ppGpp level adjustment shown by new spoT mutants affect steady state growth rates and rrnA ribosomal promoter regulation in Escherichia coli. Mol Gen Genet. 1988 Aug;213(2-3):214–222. doi: 10.1007/BF00339584. [DOI] [PubMed] [Google Scholar]
  36. Sarubbi E., Rudd K. E., Xiao H., Ikehara K., Kalman M., Cashel M. Characterization of the spoT gene of Escherichia coli. J Biol Chem. 1989 Sep 5;264(25):15074–15082. [PubMed] [Google Scholar]
  37. Shimosaka M., Fukuda Y., Murata K., Kimura A. Purine-mediated growth inhibition caused by a pyrE mutation in Escherichia coli K-12. J Bacteriol. 1984 Dec;160(3):1101–1104. doi: 10.1128/jb.160.3.1101-1104.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Turnbough C. L., Jr, Bochner B. R. Toxicity of the pyrimidine biosynthetic pathway intermediate carbamyl aspartate in Salmonella typhimurium. J Bacteriol. 1985 Aug;163(2):500–505. doi: 10.1128/jb.163.2.500-505.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Turnbough C. L., Jr, Hicks K. L., Donahue J. P. Attenuation control of pyrBI operon expression in Escherichia coli K-12. Proc Natl Acad Sci U S A. 1983 Jan;80(2):368–372. doi: 10.1073/pnas.80.2.368. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. White M. N., Olszowy J., Switzer R. L. Regulation and mechanism of phosphoribosylpyrophosphate synthetase: repression by end products. J Bacteriol. 1971 Oct;108(1):122–131. doi: 10.1128/jb.108.1.122-131.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]

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