Skip to main content
PMC home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1988 Feb;170(2):757–768. doi: 10.1128/jb.170.2.757-768.1988

Structure of the Caulobacter crescentus trpFBA operon.

C M Ross 1, M E Winkler 1
PMCID: PMC210719  PMID: 2828322

Abstract

The DNA sequences of the Caulobacter crescentus trpF, trpB, and trpA genes were determined, along with 500 base pairs (bp) of 5'-flanking sequence and 320 bp of 3'-flanking sequence. An open reading frame, designated usg, occurs upstream of trpF and encodes a polypeptide of 89 amino acids which seems to be expressed in a coupled transcription-translation system. Interestingly, the usg polypeptide is not homologous to any known tryptophan biosynthetic enzyme. S1 nuclease mapping of in vivo transcripts indicated that usg, trpF, trpB, and trpA are arranged into a single operon, with the transcription initiation site located 30 bp upstream from the start of usg. Sequences centered at -30 and -6 bp upstream from the transcription initiation site are somewhat homologous to the Escherichia coli promoter consensus sequence and are homologous to sequences found upstream of genes from several organisms which are evolutionarily related to C. crescentus. Furthermore, the trpFBA operon promoter sequence lacks homology to promoter sequences identified for certain developmentally regulated C. crescentus genes. The structures of the C. crescentus usg, trpF, trpB, and trpA genes were further analyzed in terms of codon usage, G+C content, and genetic signals and were related to genetic signals previously identified in C. crescentus and other bacteria. Taken together, these results are relevant to the analysis of gene expression in C. crescentus and the study of trp gene structure and regulation.

Full text

PDF
761

Images in this article

764Image
on p.764
765Image
on p.765

Selected References

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

  1. Akiyoshi D. E., Regier D. A., Jen G., Gordon M. P. Cloning and nucleotide sequence of the tzs gene from Agrobacterium tumefaciens strain T37. Nucleic Acids Res. 1985 Apr 25;13(8):2773–2788. doi: 10.1093/nar/13.8.2773. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Amemiya K., Wu C. W., Shapiro L. Caulobacter crescentus RNA polymerase. Purification and characterization of holoenzyme and core polymerase. J Biol Chem. 1977 Jun 25;252(12):4157–4165. [PubMed] [Google Scholar]
  3. Barrett J. T., Croft R. H., Ferber D. M., Gerardot C. J., Schoenlein P. V., Ely B. Genetic mapping with Tn5-derived auxotrophs of Caulobacter crescentus. J Bacteriol. 1982 Aug;151(2):888–898. doi: 10.1128/jb.151.2.888-898.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Barrett J. T., Rhodes C. S., Ferber D. M., Jenkins B., Kuhl S. A., Ely B. Construction of a genetic map for Caulobacter crescentus. J Bacteriol. 1982 Mar;149(3):889–896. doi: 10.1128/jb.149.3.889-896.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bendis I. K., Shapiro L. Deoxyribonucleic acid-dependent ribonucleic acid polymerase of Caulobacter crescentus. J Bacteriol. 1973 Sep;115(3):848–857. doi: 10.1128/jb.115.3.848-857.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Berk A. J., Sharp P. A. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell. 1977 Nov;12(3):721–732. doi: 10.1016/0092-8674(77)90272-0. [DOI] [PubMed] [Google Scholar]
  7. Chory J., Kaplan S. The in vitro transcription-translation of DNA and RNA templates by extracts of Rhodopseudomonas sphaeroides. Optimization and comparison of template specificity with Escherichia coli extracts and in vivo synthesis. J Biol Chem. 1982 Dec 25;257(24):15110–15121. [PubMed] [Google Scholar]
  8. Ciampi M. S., Schmid M. B., Roth J. R. Transposon Tn10 provides a promoter for transcription of adjacent sequences. Proc Natl Acad Sci U S A. 1982 Aug;79(16):5016–5020. doi: 10.1073/pnas.79.16.5016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Coleman J., Green P. J., Inouye M. The use of RNAs complementary to specific mRNAs to regulate the expression of individual bacterial genes. Cell. 1984 Jun;37(2):429–436. doi: 10.1016/0092-8674(84)90373-8. [DOI] [PubMed] [Google Scholar]
  10. Crawford I. P. Comparative studies on the regulation of tryptophan synthesis. CRC Crit Rev Biochem. 1980;8(2):175–189. doi: 10.3109/10409238009105468. [DOI] [PubMed] [Google Scholar]
  11. Crawford I. P., Stauffer G. V. Regulation of tryptophan biosynthesis. Annu Rev Biochem. 1980;49:163–195. doi: 10.1146/annurev.bi.49.070180.001115. [DOI] [PubMed] [Google Scholar]
  12. Donohue T. J., Hoger J. H., Kaplan S. Cloning and expression of the Rhodobacter sphaeroides reaction center H gene. J Bacteriol. 1986 Nov;168(2):953–961. doi: 10.1128/jb.168.2.953-961.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Donohue T. J., McEwan A. G., Kaplan S. Cloning, DNA sequence, and expression of the Rhodobacter sphaeroides cytochrome c2 gene. J Bacteriol. 1986 Nov;168(2):962–972. doi: 10.1128/jb.168.2.962-972.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Feingold J., Bellofatto V., Shapiro L., Amemiya K. Organization and nucleotide sequence analysis of an rRNA and tRNA gene cluster from Caulobacter crescentus. J Bacteriol. 1985 Jul;163(1):155–166. doi: 10.1128/jb.163.1.155-166.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Fox G. E., Stackebrandt E., Hespell R. B., Gibson J., Maniloff J., Dyer T. A., Wolfe R. S., Balch W. E., Tanner R. S., Magrum L. J. The phylogeny of prokaryotes. Science. 1980 Jul 25;209(4455):457–463. doi: 10.1126/science.6771870. [DOI] [PubMed] [Google Scholar]
  16. Gill P. R., Agabian N. The nucleotide sequence of the Mr = 28,500 flagellin gene of Caulobacter crescentus. J Biol Chem. 1983 Jun 25;258(12):7395–7401. [PubMed] [Google Scholar]
  17. 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]
  18. Gosule L. C., Schellman J. A. DNA condensation with polyamines I. Spectroscopic studies. J Mol Biol. 1978 May 25;121(3):311–326. doi: 10.1016/0022-2836(78)90366-2. [DOI] [PubMed] [Google Scholar]
  19. Gouy M., Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 1982 Nov 25;10(22):7055–7074. doi: 10.1093/nar/10.22.7055. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Hadero A., Crawford I. P. Nucleotide sequence of the genes for tryptophan synthase in Pseudomonas aeruginosa. Mol Biol Evol. 1986 May;3(3):191–204. doi: 10.1093/oxfordjournals.molbev.a040388. [DOI] [PubMed] [Google Scholar]
  21. Inouye S., Asai Y., Nakazawa A., Nakazawa T. Nucleotide sequence of a DNA segment promoting transcription in Pseudomonas putida. J Bacteriol. 1986 Jun;166(3):739–745. doi: 10.1128/jb.166.3.739-745.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Iserentant D., Fiers W. Secondary structure of mRNA and efficiency of translation initiation. Gene. 1980 Apr;9(1-2):1–12. doi: 10.1016/0378-1119(80)90163-8. [DOI] [PubMed] [Google Scholar]
  23. Jacobs T. W., Egelhoff T. T., Long S. R. Physical and genetic map of a Rhizobium meliloti nodulation gene region and nucleotide sequence of nodC. J Bacteriol. 1985 May;162(2):469–476. doi: 10.1128/jb.162.2.469-476.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Johnson R. C., Ely B. Isolation of spontaneously derived mutants of Caulobacter crescentus. Genetics. 1977 May;86(1):25–32. doi: 10.1093/genetics/86.1.25. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Leong S. A., Williams P. H., Ditta G. S. Analysis of the 5' regulatory region of the gene for delta-aminolevulinic acid synthetase of Rhizobium meliloti. Nucleic Acids Res. 1985 Aug 26;13(16):5965–5976. doi: 10.1093/nar/13.16.5965. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Looman A. C., Bodlaender J., de Gruyter M., Vogelaar A., van Knippenberg P. H. Secondary structure as primary determinant of the efficiency of ribosomal binding sites in Escherichia coli. Nucleic Acids Res. 1986 Jul 11;14(13):5481–5497. doi: 10.1093/nar/14.13.5481. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Losick R., Pero J. Cascades of Sigma factors. Cell. 1981 Sep;25(3):582–584. doi: 10.1016/0092-8674(81)90164-1. [DOI] [PubMed] [Google Scholar]
  28. Messing J., Crea R., Seeburg P. H. A system for shotgun DNA sequencing. Nucleic Acids Res. 1981 Jan 24;9(2):309–321. doi: 10.1093/nar/9.2.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Minnich S. A., Newton A. Promoter mapping and cell cycle regulation of flagellin gene transcription in Caulobacter crescentus. Proc Natl Acad Sci U S A. 1987 Mar;84(5):1142–1146. doi: 10.1073/pnas.84.5.1142. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Mullin D., Minnich S., Chen L. S., Newton A. A set of positively regulated flagellar gene promoters in Caulobacter crescentus with sequence homology to the nif gene promoters of Klebsiella pneumoniae. J Mol Biol. 1987 Jun 20;195(4):939–943. doi: 10.1016/0022-2836(87)90497-9. [DOI] [PubMed] [Google Scholar]
  31. Oppenheim D. S., Yanofsky C. Translational coupling during expression of the tryptophan operon of Escherichia coli. Genetics. 1980 Aug;95(4):785–795. doi: 10.1093/genetics/95.4.785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. POINDEXTER J. S. BIOLOGICAL PROPERTIES AND CLASSIFICATION OF THE CAULOBACTER GROUP. Bacteriol Rev. 1964 Sep;28:231–295. doi: 10.1128/br.28.3.231-295.1964. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Ross C. M., Winkler M. E. Regulation of tryptophan biosynthesis in Caulobacter crescentus. J Bacteriol. 1988 Feb;170(2):769–774. doi: 10.1128/jb.170.2.769-774.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Rossen L., Ma Q. S., Mudd E. A., Johnston A. W., Downie J. A. Identification and DNA sequence of fixZ, a nifB-like gene from Rhizobium leguminosarum. Nucleic Acids Res. 1984 Sep 25;12(18):7123–7134. doi: 10.1093/nar/12.18.7123. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Saari G. C., Kumar A. A., Kawasaki G. H., Insley M. Y., O'Hara P. J. Sequence of the Ampullariella sp. strain 3876 gene coding for xylose isomerase. J Bacteriol. 1987 Feb;169(2):612–618. doi: 10.1128/jb.169.2.612-618.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Sanger F., Coulson A. R. The use of thin acrylamide gels for DNA sequencing. FEBS Lett. 1978 Mar 1;87(1):107–110. doi: 10.1016/0014-5793(78)80145-8. [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. Schofield P. R., Watson J. M. DNA sequence of Rhizobium trifolii nodulation genes reveals a reiterated and potentially regulatory sequence preceding nodABC and nodFE. Nucleic Acids Res. 1986 Apr 11;14(7):2891–2903. doi: 10.1093/nar/14.7.2891. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Scott K. F. Conserved nodulation genes from the non-legume symbiont Bradyrhizobium sp. (Parasponia). Nucleic Acids Res. 1986 Apr 11;14(7):2905–2919. doi: 10.1093/nar/14.7.2905. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Widom J., Baldwin R. L. Cation-induced toroidal condensation of DNA studies with Co3+(NH3)6. J Mol Biol. 1980 Dec 25;144(4):431–453. doi: 10.1016/0022-2836(80)90330-7. [DOI] [PubMed] [Google Scholar]
  41. Winkler M. E., Schoenlein P. V., Ross C. M., Barrett J. T., Ely B. Genetic and physical analyses of Caulobacter crescentus trp genes. J Bacteriol. 1984 Oct;160(1):279–287. doi: 10.1128/jb.160.1.279-287.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Yanofsky C. Comparison of regulatory and structural regions of genes of tryptophan metabolism. Mol Biol Evol. 1984 Feb;1(2):143–161. doi: 10.1093/oxfordjournals.molbev.a040307. [DOI] [PubMed] [Google Scholar]
  43. Yanofsky C., Platt T., Crawford I. P., Nichols B. P., Christie G. E., Horowitz H., VanCleemput M., Wu A. M. The complete nucleotide sequence of the tryptophan operon of Escherichia coli. Nucleic Acids Res. 1981 Dec 21;9(24):6647–6668. doi: 10.1093/nar/9.24.6647. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES