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. 1996 Feb;178(4):1003–1011. doi: 10.1128/jb.178.4.1003-1011.1996

Ribose catabolism of Escherichia coli: characterization of the rpiB gene encoding ribose phosphate isomerase B and of the rpiR gene, which is involved in regulation of rpiB expression.

K I Sørensen 1, B Hove-Jensen 1
PMCID: PMC177759  PMID: 8576032

Abstract

Escherichia coli strains defective in the rpiA gene, encoding ribose phosphate isomerase A, are ribose auxotrophs, despite the presence of the wild-type rpiB gene, which encodes ribose phosphate isomerase B. Ribose prototrophs of an rpiA genetic background were isolated by two different approaches. Firstly, spontaneous ribose-independent mutants were isolated. The locus for this lesion, rpiR, was mapped to 93 min on the linkage map, and the gene order zje::Tn10-rpiR-mel-zjd::Tn10-psd-purA was established. Secondly, ribose prototrophs resulted from the cloning of the rpiB gene on a multicopy plasmid. The rpiB gene resided on a 4.6-kbp HindIII-EcoRV DNA fragment from phage lambda 10H5 (642) of the Kohara gene library and mapped at 92.85 min. Consistent with this map position, the cloned DNA fragment contained two divergent open reading frames of 149 and 296 codons, encoding ribose phosphate isomerase B (molecular mass, 16,063 Da) and a negative regulator of rpiB gene expression, RpiR (molecular mass, 32,341 Da), respectively. The 5' ends of rpiB- and rpiR-specified transcripts were located by primer extension analysis. No significant amino acid sequence similarity was found between ribose phosphate isomerases A and B, but ribose phosphate isomerase B exhibited high-level similarity to both LacA and LacB subunits of the galactose 6-phosphate isomerases of several gram-positive bacteria. Analyses of strains containing rpiA, rpiB, or rpiA rpiB mutations revealed that both enzymes were equally efficient in catalyzing the isomerization step in either direction and that the construction of rpiA rpiB double mutants was a necessity to fully prevent this reaction.

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Selected References

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

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Bachmann B. J. Linkage map of Escherichia coli K-12, edition 8. Microbiol Rev. 1990 Jun;54(2):130–197. doi: 10.1128/mr.54.2.130-197.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. 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]
  4. Buxton R. S., Hammer-Jespersen K., Valentin-Hansen P. A second purine nucleoside phosphorylase in Escherichia coli K-12. I. Xanthosine phosphorylase regulatory mutants isolated as secondary-site revertants of a deoD mutant. Mol Gen Genet. 1980;179(2):331–340. doi: 10.1007/BF00425461. [DOI] [PubMed] [Google Scholar]
  5. Canard B., Garnier T., Saint-Joanis B., Cole S. T. Molecular genetic analysis of the nagH gene encoding a hyaluronidase of Clostridium perfringens. Mol Gen Genet. 1994 Apr;243(2):215–224. doi: 10.1007/BF00280319. [DOI] [PubMed] [Google Scholar]
  6. Chan B., Spassky A., Busby S. The organization of open complexes between Escherichia coli RNA polymerase and DNA fragments carrying promoters either with or without consensus -35 region sequences. Biochem J. 1990 Aug 15;270(1):141–148. doi: 10.1042/bj2700141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. David J., Wiesmeyer H. Regulation of ribose metabolism in Escherichia coli. II. Evidence for two ribose-5-phosphate isomerase activities. Biochim Biophys Acta. 1970 Apr 14;208(1):56–67. doi: 10.1016/0304-4165(70)90048-6. [DOI] [PubMed] [Google Scholar]
  8. Essenberg M. K., Cooper R. A. Two ribose-5-phosphate isomerases from Escherichia coli K12: partial characterisation of the enzymes and consideration of their possible physiological roles. Eur J Biochem. 1975 Jul 1;55(2):323–332. doi: 10.1111/j.1432-1033.1975.tb02166.x. [DOI] [PubMed] [Google Scholar]
  9. Gold L., Pribnow D., Schneider T., Shinedling S., Singer B. S., Stormo G. Translational initiation in prokaryotes. Annu Rev Microbiol. 1981;35:365–403. doi: 10.1146/annurev.mi.35.100181.002053. [DOI] [PubMed] [Google Scholar]
  10. Gough J. A., Murray N. E. Sequence diversity among related genes for recognition of specific targets in DNA molecules. J Mol Biol. 1983 May 5;166(1):1–19. doi: 10.1016/s0022-2836(83)80047-3. [DOI] [PubMed] [Google Scholar]
  11. Groarke J. M., Mahoney W. C., Hope J. N., Furlong C. E., Robb F. T., Zalkin H., Hermodson M. A. The amino acid sequence of D-ribose-binding protein from Escherichia coli K12. J Biol Chem. 1983 Nov 10;258(21):12952–12956. [PubMed] [Google Scholar]
  12. Hawley D. K., McClure W. R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 1983 Apr 25;11(8):2237–2255. doi: 10.1093/nar/11.8.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hawrot E., Kennedy E. P. Conditional lethal phosphatidylserine decarboxylase mutants of Escherichia coli. Mapping of the structural gene for phosphatidylserine decarboxylase. Mol Gen Genet. 1976 Nov 17;148(3):271–279. doi: 10.1007/BF00332901. [DOI] [PubMed] [Google Scholar]
  14. Horton R. M., Hunt H. D., Ho S. N., Pullen J. K., Pease L. R. Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene. 1989 Apr 15;77(1):61–68. doi: 10.1016/0378-1119(89)90359-4. [DOI] [PubMed] [Google Scholar]
  15. Hove-Jensen B. Chromosomal location of the gene encoding phosphoribosylpyrophosphate synthetase in Escherichia coli. J Bacteriol. 1983 Apr;154(1):177–184. doi: 10.1128/jb.154.1.177-184.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hove-Jensen B. Cloning and characterization of the prs gene encoding phosphoribosylpyrophosphate synthetase of Escherichia coli. Mol Gen Genet. 1985;201(2):269–276. doi: 10.1007/BF00425670. [DOI] [PubMed] [Google Scholar]
  17. Hove-Jensen B., Maigaard M. Escherichia coli rpiA gene encoding ribose phosphate isomerase A. J Bacteriol. 1993 Sep;175(17):5628–5635. doi: 10.1128/jb.175.17.5628-5635.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hove-Jensen B. Mutation in the phosphoribosylpyrophosphate synthetase gene (prs) that results in simultaneous requirements for purine and pyrimidine nucleosides, nicotinamide nucleotide, histidine, and tryptophan in Escherichia coli. J Bacteriol. 1988 Mar;170(3):1148–1152. doi: 10.1128/jb.170.3.1148-1152.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Hove-Jensen B., Nygaard P. Phosphoribosylpyrophosphate synthetase of Escherichia coli, Identification of a mutant enzyme. Eur J Biochem. 1982 Aug;126(2):327–332. doi: 10.1111/j.1432-1033.1982.tb06782.x. [DOI] [PubMed] [Google Scholar]
  20. Hove-Jensen B., Nygaard P. Role of guanosine kinase in the utilization of guanosine for nucleotide synthesis in Escherichia coli. J Gen Microbiol. 1989 May;135(5):1263–1273. doi: 10.1099/00221287-135-5-1263. [DOI] [PubMed] [Google Scholar]
  21. Hove-Jensen B. Phosphoribosylpyrophosphate (PRPP)-less mutants of Escherichia coli. Mol Microbiol. 1989 Nov;3(11):1487–1492. doi: 10.1111/j.1365-2958.1989.tb00134.x. [DOI] [PubMed] [Google Scholar]
  22. Jagusztyn-Krynicka E. K., Hansen J. B., Crow V. L., Thomas T. D., Honeyman A. L., Curtiss R., 3rd Streptococcus mutans serotype c tagatose 6-phosphate pathway gene cluster. J Bacteriol. 1992 Oct;174(19):6152–6158. doi: 10.1128/jb.174.19.6152-6158.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Jochimsen B., Nygaard P., Vestergaard T. Location on the chromosome of Escherichia coli of genes governing purine metabolism. Adenosine deaminase (add), guanosine kinase (gsk) and hypoxanthine phosphoribosyltransferase (hpt). Mol Gen Genet. 1975 Dec 30;143(1):85–91. doi: 10.1007/BF00269424. [DOI] [PubMed] [Google Scholar]
  24. Kohara Y., Akiyama K., Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. doi: 10.1016/0092-8674(87)90503-4. [DOI] [PubMed] [Google Scholar]
  25. LOWRY O. H., ROSEBROUGH N. J., FARR A. L., RANDALL R. J. Protein measurement with the Folin phenol reagent. J Biol Chem. 1951 Nov;193(1):265–275. [PubMed] [Google Scholar]
  26. 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]
  27. Leer J. C., Hammer-Jespersen K., Schwartz M. Uridine phosphorylase from Escherichia coli. Physical and chemical characterization. Eur J Biochem. 1977 May 2;75(1):217–224. doi: 10.1111/j.1432-1033.1977.tb11520.x. [DOI] [PubMed] [Google Scholar]
  28. Lopilato J. E., Garwin J. L., Emr S. D., Silhavy T. J., Beckwith J. R. D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport. J Bacteriol. 1984 May;158(2):665–673. doi: 10.1128/jb.158.2.665-673.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Low K. B. Escherichia coli K-12 F-prime factors, old and new. Bacteriol Rev. 1972 Dec;36(4):587–607. doi: 10.1128/br.36.4.587-607.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Makino K., Kim S. K., Shinagawa H., Amemura M., Nakata A. Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12. J Bacteriol. 1991 Apr;173(8):2665–2672. doi: 10.1128/jb.173.8.2665-2672.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Mandel M., Higa A. Calcium-dependent bacteriophage DNA infection. J Mol Biol. 1970 Oct 14;53(1):159–162. doi: 10.1016/0022-2836(70)90051-3. [DOI] [PubMed] [Google Scholar]
  32. Mauzy C. A., Hermodson M. A. Structural and functional analyses of the repressor, RbsR, of the ribose operon of Escherichia coli. Protein Sci. 1992 Jul;1(7):831–842. doi: 10.1002/pro.5560010701. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Nilsson D., Hove-Jensen B. Phosphoribosylpyrophosphate synthetase of Bacillus subtilis. Cloning, characterization and chromosomal mapping of the prs gene. Gene. 1987;53(2-3):247–255. doi: 10.1016/0378-1119(87)90013-8. [DOI] [PubMed] [Google Scholar]
  34. O'Callaghan C. H., Morris A., Kirby S. M., Shingler A. H. Novel method for detection of beta-lactamases by using a chromogenic cephalosporin substrate. Antimicrob Agents Chemother. 1972 Apr;1(4):283–288. doi: 10.1128/aac.1.4.283. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Pabo C. O., Sauer R. T. Protein-DNA recognition. Annu Rev Biochem. 1984;53:293–321. doi: 10.1146/annurev.bi.53.070184.001453. [DOI] [PubMed] [Google Scholar]
  36. Rosey E. L., Oskouian B., Stewart G. C. Lactose metabolism by Staphylococcus aureus: characterization of lacABCD, the structural genes of the tagatose 6-phosphate pathway. J Bacteriol. 1991 Oct;173(19):5992–5998. doi: 10.1128/jb.173.19.5992-5998.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Rosey E. L., Stewart G. C. Nucleotide and deduced amino acid sequences of the lacR, lacABCD, and lacFE genes encoding the repressor, tagatose 6-phosphate gene cluster, and sugar-specific phosphotransferase system components of the lactose operon of Streptococcus mutans. J Bacteriol. 1992 Oct;174(19):6159–6170. doi: 10.1128/jb.174.19.6159-6170.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Singer M., Baker T. A., Schnitzler G., Deischel S. M., Goel M., Dove W., Jaacks K. J., Grossman A. D., Erickson J. W., Gross C. A. A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol Rev. 1989 Mar;53(1):1–24. doi: 10.1128/mr.53.1.1-24.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Skinner A. J., Cooper R. A. Genetic studies on ribose 5-phosphate isomerase mutants of Escherichia coli K-12. J Bacteriol. 1974 Jun;118(3):1183–1185. doi: 10.1128/jb.118.3.1183-1185.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Skinner A. J., Cooper R. A. The regulation of ribose-5-phosphate isomerisation in Escherichia coli K12. FEBS Lett. 1971 Jan 30;12(5):293–296. doi: 10.1016/0014-5793(71)80202-8. [DOI] [PubMed] [Google Scholar]
  41. Sørensen K. I., Neuhard J. Dual transcriptional initiation sites from the pyrC promoter control expression of the gene in Salmonella typhimurium. Mol Gen Genet. 1991 Feb;225(2):249–256. doi: 10.1007/BF00269856. [DOI] [PubMed] [Google Scholar]
  42. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  43. Woodson K., Devine K. M. Analysis of a ribose transport operon from Bacillus subtilis. Microbiology. 1994 Aug;140(Pt 8):1829–1838. doi: 10.1099/13500872-140-8-1829. [DOI] [PubMed] [Google Scholar]
  44. 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]
  45. de Crombrugghe B., Busby S., Buc H. Cyclic AMP receptor protein: role in transcription activation. Science. 1984 May 25;224(4651):831–838. doi: 10.1126/science.6372090. [DOI] [PubMed] [Google Scholar]
  46. van Rooijen R. J., van Schalkwijk S., de Vos W. M. Molecular cloning, characterization, and nucleotide sequence of the tagatose 6-phosphate pathway gene cluster of the lactose operon of Lactococcus lactis. J Biol Chem. 1991 Apr 15;266(11):7176–7181. [PubMed] [Google Scholar]

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