Skip to main content
NCBI home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1988 Jan;170(1):330–334. doi: 10.1128/jb.170.1.330-334.1988

DNA sequence of the D-serine deaminase activator gene dsdC.

S Palchaudhuri 1, V Patel 1, E McFall 1
PMCID: PMC210646  PMID: 3275618

Abstract

We have determined the DNA sequence of dsdC, the gene that encodes the D-serine deaminase activator protein of Escherichia coli K-12. The sequence contains a single open reading frame that terminates in a UGA codon. One the basis of the size of the protein, 33 kilodaltons, and the amino acid sequence encoded by the open reading frame, we identified a likely translation initiation codon 731 base pairs upstream of the translation initiation codon for the divergently transcribed D-serine deaminase gene. There is a broad range of codon usage, not surprising in view of the weak expression of the gene. The N-terminal two-thirds of the activator is arginine-lysine rich and quite polar; the remainder is more neutral. The segment of the protein that seems most likely to have potential to form the helix-turn-helix structure characteristic of DNA-regulatory proteins is located near the end of the polar region. The protein contains a region with significant homology to lambda attB.

Full text

PDF
330

Selected References

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

  1. Bloom F. R., McFall E., Young M. C., Carothers A. M. Positive control in the D-serine deaminase system of Escherichia coli K-12. J Bacteriol. 1975 Mar;121(3):1092–1101. doi: 10.1128/jb.121.3.1092-1101.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bornstein-Forst S. M., McFall E., Palchaudhuri S. In vivo D-serine deaminase transcription start sites in wild-type Escherichia coli and in dsdA promoter mutants. J Bacteriol. 1987 Mar;169(3):1056–1060. doi: 10.1128/jb.169.3.1056-1060.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cole S. T., Raibaud O. The nucleotide sequence of the malT gene encoding the positive regulator of the Escherichia coli maltose regulon. Gene. 1986;42(2):201–208. doi: 10.1016/0378-1119(86)90297-0. [DOI] [PubMed] [Google Scholar]
  4. Cossart P., Gicquel-Sanzey B. Cloning and sequence of the crp gene of Escherichia coli K 12. Nucleic Acids Res. 1982 Feb 25;10(4):1363–1378. doi: 10.1093/nar/10.4.1363. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Franklin N. C. "N" transcription antitermination proteins of bacteriophages lambda, phi 21 and P22. J Mol Biol. 1985 Jan 5;181(1):85–91. doi: 10.1016/0022-2836(85)90326-2. [DOI] [PubMed] [Google Scholar]
  6. 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]
  7. Grosjean H., Fiers W. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene. 1982 Jun;18(3):199–209. doi: 10.1016/0378-1119(82)90157-3. [DOI] [PubMed] [Google Scholar]
  8. Gunsalus R. P., Yanofsky C. Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor. Proc Natl Acad Sci U S A. 1980 Dec;77(12):7117–7121. doi: 10.1073/pnas.77.12.7117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Heincz M. C., Bornstein S. M., McFall E. Purification and characterization of D-serine deaminase activator protein. J Bacteriol. 1984 Oct;160(1):42–49. doi: 10.1128/jb.160.1.42-49.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hendrickson W., Schleif R. A dimer of AraC protein contacts three adjacent major groove regions of the araI DNA site. Proc Natl Acad Sci U S A. 1985 May;82(10):3129–3133. doi: 10.1073/pnas.82.10.3129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kelley R. L., Yanofsky C. Mutational studies with the trp repressor of Escherichia coli support the helix-turn-helix model of repressor recognition of operator DNA. Proc Natl Acad Sci U S A. 1985 Jan;82(2):483–487. doi: 10.1073/pnas.82.2.483. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. McFall E., Heincz M. C. Identification and control of synthesis of the dsdC activator protein. J Bacteriol. 1983 Feb;153(2):872–877. doi: 10.1128/jb.153.2.872-877.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. McFall E. Role of adenosine 3',5'-cyclic monophosphate and its specific binding protein in the regulation of D-serine deaminase synthesis. J Bacteriol. 1973 Feb;113(2):781–785. doi: 10.1128/jb.113.2.781-785.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. McFall E. cis-acting proteins. J Bacteriol. 1986 Aug;167(2):429–432. doi: 10.1128/jb.167.2.429-432.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Platt T. Transcription termination and the regulation of gene expression. Annu Rev Biochem. 1986;55:339–372. doi: 10.1146/annurev.bi.55.070186.002011. [DOI] [PubMed] [Google Scholar]
  16. Rosenberg M., Court D. Regulatory sequences involved in the promotion and termination of RNA transcription. Annu Rev Genet. 1979;13:319–353. doi: 10.1146/annurev.ge.13.120179.001535. [DOI] [PubMed] [Google Scholar]
  17. Sanger F., Coulson A. R. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol. 1975 May 25;94(3):441–448. doi: 10.1016/0022-2836(75)90213-2. [DOI] [PubMed] [Google Scholar]
  18. Weber I. T., McKay D. B., Steitz T. A. Two helix DNA binding motif of CAP found in lac repressor and gal repressor. Nucleic Acids Res. 1982 Aug 25;10(16):5085–5102. doi: 10.1093/nar/10.16.5085. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. 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]
  20. von Wilcken-Bergmann B., Müller-Hill B. Sequence of galR gene indicates a common evolutionary origin of lac and gal repressor in Escherichia coli. Proc Natl Acad Sci U S A. 1982 Apr;79(8):2427–2431. doi: 10.1073/pnas.79.8.2427. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES