Skip to main content
NCBI home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1989 Jan;171(1):198–204. doi: 10.1128/jb.171.1.198-204.1989

Identification and sequence analysis of Escherichia coli purE and purK genes encoding 5'-phosphoribosyl-5-amino-4-imidazole carboxylase for de novo purine biosynthesis.

W Watanabe 1, G Sampei 1, A Aiba 1, K Mizobuchi 1
PMCID: PMC209573  PMID: 2644189

Abstract

It has been shown that the Escherichia coli purE locus specifying 5'-phosphoribosyl-5-amino-4-imidazole carboxylase in de novo purine nucleotide synthesis is divided into two cistrons. We cloned and determined a 2,449-nucleotide sequence including the purE locus. This sequence contains two overlapped open reading frames, ORF-18 and ORF-39, encoding proteins with molecular weights of 18,000 and 39,000, respectively. The purE mutations of CSH57A and DCSP22 were complemented by plasmids carrying ORF-18, while that of NK6051 was complemented by plasmids carrying ORF-39. Thus, the purE locus consists of two distinct genes, designated purE and purK for ORF-18 and ORF-39, respectively. These genes constitute a single operon. A highly conserved 16-nucleotide sequence, termed the PUR box, was found in the upstream region of purE by comparing the sequences of the purF and purMN operons. We also found three entire and one partial repetitive extragenic palindromic (REP) sequences in the downstream region of purK. Roles of the PUR box and REP sequences are discussed in relation to the genesis of the purEK operon.

Full text

PDF
198

Images in this article

202Image
on p.202
202Image
on p.202

Selected References

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

  1. Bachmann B. J. Linkage map of Escherichia coli K-12, edition 7. Microbiol Rev. 1983 Jun;47(2):180–230. doi: 10.1128/mr.47.2.180-230.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Casadaban M. J. Transposition and fusion of the lac genes to selected promoters in Escherichia coli using bacteriophage lambda and Mu. J Mol Biol. 1976 Jul 5;104(3):541–555. doi: 10.1016/0022-2836(76)90119-4. [DOI] [PubMed] [Google Scholar]
  3. Clarke L., Carbon J. A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome. Cell. 1976 Sep;9(1):91–99. doi: 10.1016/0092-8674(76)90055-6. [DOI] [PubMed] [Google Scholar]
  4. Clarke L., Carbon J. Selection of specific clones from colony banks by suppression or complementation tests. Methods Enzymol. 1979;68:396–408. doi: 10.1016/0076-6879(79)68029-1. [DOI] [PubMed] [Google Scholar]
  5. Ebbole D. J., Zalkin H. Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide synthesis. J Biol Chem. 1987 Jun 15;262(17):8274–8287. [PubMed] [Google Scholar]
  6. Fuller R. S., Kaguni J. M., Kornberg A. Enzymatic replication of the origin of the Escherichia coli chromosome. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7370–7374. doi: 10.1073/pnas.78.12.7370. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gilson E., Clément J. M., Brutlag D., Hofnung M. A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. EMBO J. 1984 Jun;3(6):1417–1421. doi: 10.1002/j.1460-2075.1984.tb01986.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gots J. S., Benson C. E., Jochimsen B., Koduri K. R. Microbial models and regulatory elements in the control of purine metabolism. Ciba Found Symp. 1977;(48):23–41. doi: 10.1002/9780470720301.ch3. [DOI] [PubMed] [Google Scholar]
  9. Hamilton P. T., Reeve J. N. Sequence divergence of an archaebacterial gene cloned from a mesophilic and a thermophilic methanogen. J Mol Evol. 1985;22(4):351–360. doi: 10.1007/BF02115691. [DOI] [PubMed] [Google Scholar]
  10. Hamilton P. T., Reeve J. N. Structure of genes and an insertion element in the methane producing archaebacterium Methanobrevibacter smithii. Mol Gen Genet. 1985;200(1):47–59. doi: 10.1007/BF00383311. [DOI] [PubMed] [Google Scholar]
  11. Henikoff S. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene. 1984 Jun;28(3):351–359. doi: 10.1016/0378-1119(84)90153-7. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. LENNOX E. S. Transduction of linked genetic characters of the host by bacteriophage P1. Virology. 1955 Jul;1(2):190–206. doi: 10.1016/0042-6822(55)90016-7. [DOI] [PubMed] [Google Scholar]
  14. LUKENS L. N., BUCHANAN J. M. Biosynthesis of the purines. XXIV. The enzymatic synthesis of 5-amino-1-ribosyl-4-imidazolecarboxylic acid 5'-phosphate from 5-amino-1-ribosylimidazole 5'-phosphate and carbon dioxide. J Biol Chem. 1959 Jul;234(7):1799–1805. [PubMed] [Google Scholar]
  15. 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]
  16. Makaroff C. A., Zalkin H. Regulation of Escherichia coli purF. Analysis of the control region of a pur regulon gene. J Biol Chem. 1985 Aug 25;260(18):10378–10387. [PubMed] [Google Scholar]
  17. Masai H., Kaziro Y., Arai K. Definition of oriR, the minimum DNA segment essential for initiation of R1 plasmid replication in vitro. Proc Natl Acad Sci U S A. 1983 Nov;80(22):6814–6818. doi: 10.1073/pnas.80.22.6814. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Mead D. A., Szczesna-Skorupa E., Kemper B. Single-stranded DNA 'blue' T7 promoter plasmids: a versatile tandem promoter system for cloning and protein engineering. Protein Eng. 1986 Oct-Nov;1(1):67–74. doi: 10.1093/protein/1.1.67. [DOI] [PubMed] [Google Scholar]
  19. Messing J. New M13 vectors for cloning. Methods Enzymol. 1983;101:20–78. doi: 10.1016/0076-6879(83)01005-8. [DOI] [PubMed] [Google Scholar]
  20. Messing J., Vieira J. A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene. 1982 Oct;19(3):269–276. doi: 10.1016/0378-1119(82)90016-6. [DOI] [PubMed] [Google Scholar]
  21. Reiner A. M. Characterization of polynucleotide phosphorylase mutants of Escherichia coli. J Bacteriol. 1969 Mar;97(3):1437–1443. doi: 10.1128/jb.97.3.1437-1443.1969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. 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]
  23. Shine J., Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342–1346. doi: 10.1073/pnas.71.4.1342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Smith J. M., Daum H. A., 3rd Identification and nucleotide sequence of a gene encoding 5'-phosphoribosylglycinamide transformylase in Escherichia coli K12. J Biol Chem. 1987 Aug 5;262(22):10565–10569. [PubMed] [Google Scholar]
  25. Smith J. M., Daum H. A., 3rd Nucleotide sequence of the purM gene encoding 5'-phosphoribosyl-5-aminoimidazole synthetase of Escherichia coli K12. J Biol Chem. 1986 Aug 15;261(23):10632–10636. [PubMed] [Google Scholar]
  26. Staudenbauer W. L. Replication of small plasmids in extracts of Escherichia coli. Mol Gen Genet. 1976 Jun 15;145(3):273–280. doi: 10.1007/BF00325823. [DOI] [PubMed] [Google Scholar]
  27. Stern M. J., Ames G. F., Smith N. H., Robinson E. C., Higgins C. F. Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell. 1984 Jul;37(3):1015–1026. doi: 10.1016/0092-8674(84)90436-7. [DOI] [PubMed] [Google Scholar]
  28. Tiedeman A. A., Smith J. M. Nucleotide sequence of the guaB locus encoding IMP dehydrogenase of Escherichia coli K12. Nucleic Acids Res. 1985 Feb 25;13(4):1303–1316. doi: 10.1093/nar/13.4.1303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Tiedeman A. A., Smith J. M., Zalkin H. Nucleotide sequence of the guaA gene encoding GMP synthetase of Escherichia coli K12. J Biol Chem. 1985 Jul 25;260(15):8676–8679. [PubMed] [Google Scholar]
  30. Tinoco I., Jr, Borer P. N., Dengler B., Levin M. D., Uhlenbeck O. C., Crothers D. M., Bralla J. Improved estimation of secondary structure in ribonucleic acids. Nat New Biol. 1973 Nov 14;246(150):40–41. doi: 10.1038/newbio246040a0. [DOI] [PubMed] [Google Scholar]
  31. Tso J. Y., Zalkin H., van Cleemput M., Yanofsky C., Smith J. M. Nucleotide sequence of Escherichia coli purF and deduced amino acid sequence of glutamine phosphoribosylpyrophosphate amidotransferase. J Biol Chem. 1982 Apr 10;257(7):3525–3531. [PubMed] [Google Scholar]
  32. Vieira J., Messing J. Production of single-stranded plasmid DNA. Methods Enzymol. 1987;153:3–11. doi: 10.1016/0076-6879(87)53044-0. [DOI] [PubMed] [Google Scholar]

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

RESOURCES