Abstract
The nucleotide sequence is described of a region of the Escherichia coli chromosome extending from oriC to phoS that also includes the loci gid, unc and glmS. Taken with known sequences for asnA and phoS this completes the sequence of a segment of about 17 kilobases or 0.4 min of the E. coli genome. Sequences that are probably transcriptional promoters for unc and phoS can be detected and the identity of the unc promoter has been confirmed by experiments in vitro with RNA polymerase. Upstream of the promoter sequence is an extensive region that appears to be non-coding. Conserved sequences are found that may serve to concentrate RNA polymerase in the vicinity of the unc promoter. Hairpin loop structures resembling known rho-independent transcription termination signals are evident following the unc operon and glmS. The glmS gene encoding the amidotransferase, glucosamine synthetase, has been identified by homology with glutamine 5-phosphoribosylpyrophosphate amidotransferase.
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- 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]
- Biggin M. D., Gibson T. J., Hong G. F. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3963–3965. doi: 10.1073/pnas.80.13.3963. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brusilow W. S., Klionsky D. J., Simoni R. D. Differential polypeptide synthesis of the proton-translocating ATPase of Escherichia coli. J Bacteriol. 1982 Sep;151(3):1363–1371. doi: 10.1128/jb.151.3.1363-1371.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brusilow W. S., Porter A. C., Simoni R. D. Cloning and expression of uncI, the first gene of the unc operon of Escherichia coli. J Bacteriol. 1983 Sep;155(3):1265–1270. doi: 10.1128/jb.155.3.1265-1270.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Buchanan J. M. The amidotransferases. Adv Enzymol Relat Areas Mol Biol. 1973;39:91–183. doi: 10.1002/9780470122846.ch2. [DOI] [PubMed] [Google Scholar]
- DAWID I. B., FRENCH T. C., BUCHANAN J. M. Azaserine-reactive sulfhydryl group of 2-formamido-N-ribosylacetamide 5'-phosphate: L-glutamine amido-ligase (adenosine diphosphate). II. Degradation of azaserine-C-14-labeled enzyme. J Biol Chem. 1963 Jun;238:2178–2185. [PubMed] [Google Scholar]
- Deininger P. L. Random subcloning of sonicated DNA: application to shotgun DNA sequence analysis. Anal Biochem. 1983 Feb 15;129(1):216–223. doi: 10.1016/0003-2697(83)90072-6. [DOI] [PubMed] [Google Scholar]
- Doolittle R. F. Similar amino acid sequences: chance or common ancestry? Science. 1981 Oct 9;214(4517):149–159. doi: 10.1126/science.7280687. [DOI] [PubMed] [Google Scholar]
- Duckworth M. L., Gait M. J., Goelet P., Hong G. F., Singh M., Titmas R. C. Rapid synthesis of oligodeoxyribonucleotides VI. Efficient, mechanised synthesis of heptadecadeoxyribonucleotides by an improved solid phase phosphotriester route. Nucleic Acids Res. 1981 Apr 10;9(7):1691–1706. doi: 10.1093/nar/9.7.1691. [DOI] [PMC free article] [PubMed] [Google Scholar]
- GHOSH S., BLUMENTHAL H. J., DAVIDSON E., ROSEMAN S. Glucosamine metabolism. V. Enzymatic synthesis of glucosamine 6-phosphate. J Biol Chem. 1960 May;235:1265–1273. [PubMed] [Google Scholar]
- Gay N. J., Walker J. E. The atp operon: nucleotide sequence of the promoter and the genes for the membrane proteins, and the delta subunit of Escherichia coli ATP-synthase. Nucleic Acids Res. 1981 Aug 25;9(16):3919–3926. doi: 10.1093/nar/9.16.3919. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gay N. J., Walker J. E. The atp operon: nucleotide sequence of the region encoding the alpha-subunit of Escherichia coli ATP-synthase. Nucleic Acids Res. 1981 May 11;9(9):2187–2194. doi: 10.1093/nar/9.9.2187. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hansen F. G., Nielsen J., Riise E., von Meyenburg K. The genes for the eight subunits of the membrane bound ATP synthase of Escherichia coli. Mol Gen Genet. 1981;183(3):463–472. doi: 10.1007/BF00268766. [DOI] [PubMed] [Google Scholar]
- Kanazawa H., Kayano T., Kiyasu T., Futai M. Nucleotide sequence of the genes for beta and epsilon subunits of proton-translocating ATPase from Escherichia coli. Biochem Biophys Res Commun. 1982 Apr 29;105(4):1257–1264. doi: 10.1016/0006-291x(82)90922-6. [DOI] [PubMed] [Google Scholar]
- Kanazawa H., Mabuchi K., Futai M. Nucleotide sequence of the promoter region of the gene cluster for proton-translocating ATPase from Escherichia coli and identification of the active promotor. Biochem Biophys Res Commun. 1982 Jul 30;107(2):568–575. doi: 10.1016/0006-291x(82)91529-7. [DOI] [PubMed] [Google Scholar]
- Kanazawa H., Tamura F., Mabuchi K., Miki T., Futai M. Organization of unc gene cluster of Escherichia coli coding for proton-translocating ATPase of oxidative phosphorylation. Proc Natl Acad Sci U S A. 1980 Dec;77(12):7005–7009. doi: 10.1073/pnas.77.12.7005. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kaplan J. B., Nichols B. P. Nucleotide sequence of Escherichia coli pabA and its evolutionary relationship to trp(G)D. J Mol Biol. 1983 Aug 15;168(3):451–468. doi: 10.1016/s0022-2836(83)80295-2. [DOI] [PubMed] [Google Scholar]
- Kawamura M., Keim P. S., Goto Y., Zalkin H., Heinrikson R. L. Anthranilate synthetase component II from Pseudomonas putida. Covalent structure and identification of the cysteine residue involved in catalysis. J Biol Chem. 1978 Jul 10;253(13):4659–4668. [PubMed] [Google Scholar]
- Kyte J., Doolittle R. F. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982 May 5;157(1):105–132. doi: 10.1016/0022-2836(82)90515-0. [DOI] [PubMed] [Google Scholar]
- Lichtenstein C., Brenner S. Unique insertion site of Tn7 in the E. coli chromosome. Nature. 1982 Jun 17;297(5867):601–603. doi: 10.1038/297601a0. [DOI] [PubMed] [Google Scholar]
- Lother H., Messer W. Promoters in the E. coli replication origin. Nature. 1981 Nov 26;294(5839):376–378. doi: 10.1038/294376a0. [DOI] [PubMed] [Google Scholar]
- Lu P., Rich A. The nature of the polypeptide chain termination signal. J Mol Biol. 1971 Jun 14;58(2):513–531. doi: 10.1016/0022-2836(71)90368-8. [DOI] [PubMed] [Google Scholar]
- Mabuchi K., Kanazawa H., Kayano T., Futai M. Nucleotide sequence of the gene coding for the delta subunit of proton translocating ATPase of Escherichia coli. Biochem Biophys Res Commun. 1981 Sep 16;102(1):172–179. doi: 10.1016/0006-291x(81)91504-7. [DOI] [PubMed] [Google Scholar]
- Magota K., Otsuji N., Miki T., Horiuchi T., Tsunasawa S., Kondo J., Sakiyama F., Amemura M., Morita T., Shinagawa H. Nucleotide sequence of the phoS gene, the structural gene for the phosphate-binding protein of Escherichia coli. J Bacteriol. 1984 Mar;157(3):909–917. doi: 10.1128/jb.157.3.909-917.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Makaroff C. A., Zalkin H., Switzer R. L., Vollmer S. J. Cloning of the Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase gene in Escherichia coli. Nucleotide sequence determination and properties of the plasmid-encoded enzyme. J Biol Chem. 1983 Sep 10;258(17):10586–10593. [PubMed] [Google Scholar]
- Meijer M., Beck E., Hansen F. G., Bergmans H. E., Messer W., von Meyenburg K., Schaller H. Nucleotide sequence of the origin of replication of the Escherichia coli K-12 chromosome. Proc Natl Acad Sci U S A. 1979 Feb;76(2):580–584. doi: 10.1073/pnas.76.2.580. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Nakamura M., Yamada M., Hirota Y., Sugimoto K., Oka A., Takanami M. Nucleotide sequence of the asnA gene coding for asparagine synthetase of E. coli K-12. Nucleic Acids Res. 1981 Sep 25;9(18):4669–4676. doi: 10.1093/nar/9.18.4669. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nielsen J., Hansen F. G., Hoppe J., Friedl P., von Meyenburg K. The nucleotide sequence of the atp genes coding for the F0 subunits a, b, c and the F1 subunit delta of the membrane bound ATP synthase of Escherichia coli. Mol Gen Genet. 1981;184(1):33–39. doi: 10.1007/BF00271191. [DOI] [PubMed] [Google Scholar]
- Nyunoya H., Lusty C. J. Sequence of the small subunit of yeast carbamyl phosphate synthetase and identification of its catalytic domain. J Biol Chem. 1984 Aug 10;259(15):9790–9798. [PubMed] [Google Scholar]
- Ohnoki S., Hong B. S., Buchanan J. M. Glutamine active site of formylglycinamide ribonucleotide amidotransferase. 2. Amino acid sequence of labeled peptides. Biochemistry. 1977 Mar 22;16(6):1070–1076. doi: 10.1021/bi00625a007. [DOI] [PubMed] [Google Scholar]
- Piette J., Nyunoya H., Lusty C. J., Cunin R., Weyens G., Crabeel M., Charlier D., Glansdorff N., Piérard A. DNA sequence of the carA gene and the control region of carAB: tandem promoters, respectively controlled by arginine and the pyrimidines, regulate the synthesis of carbamoyl-phosphate synthetase in Escherichia coli K-12. Proc Natl Acad Sci U S A. 1984 Jul;81(13):4134–4138. doi: 10.1073/pnas.81.13.4134. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Porter A. C., Brusilow W. S., Simoni R. D. Promoter for the unc operon of Escherichia coli. J Bacteriol. 1983 Sep;155(3):1271–1278. doi: 10.1128/jb.155.3.1271-1278.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sanger F., Coulson A. R., Hong G. F., Hill D. F., Petersen G. B. Nucleotide sequence of bacteriophage lambda DNA. J Mol Biol. 1982 Dec 25;162(4):729–773. doi: 10.1016/0022-2836(82)90546-0. [DOI] [PubMed] [Google Scholar]
- 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]
- Saraste M., Gay N. J., Eberle A., Runswick M. J., Walker J. E. The atp operon: nucleotide sequence of the genes for the gamma, beta, and epsilon subunits of Escherichia coli ATP synthase. Nucleic Acids Res. 1981 Oct 24;9(20):5287–5296. doi: 10.1093/nar/9.20.5287. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schechtman M. G., Yanofsky C. Structure of the trifunctional trp-1 gene from Neurospora crassa and its aberrant expression in Escherichia coli. J Mol Appl Genet. 1983;2(1):83–99. [PubMed] [Google Scholar]
- Sekiya T., Contreras R., Takeya T., Khorana H. G. Total synthesis of a tyrosine suppressor transfer RNA gene. XVII. Transcription, in vitro, of the synthetic gene and processing of the primary transcript to transfer RNA. J Biol Chem. 1979 Jul 10;254(13):5802–5816. [PubMed] [Google Scholar]
- 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]
- Staden R. An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. Nucleic Acids Res. 1982 May 11;10(9):2951–2961. doi: 10.1093/nar/10.9.2951. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Staden R. Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. Nucleic Acids Res. 1982 Aug 11;10(15):4731–4751. doi: 10.1093/nar/10.15.4731. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Staden R. Graphic methods to determine the function of nucleic acid sequences. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):521–538. doi: 10.1093/nar/12.1part2.521. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Staden R., McLachlan A. D. Codon preference and its use in identifying protein coding regions in long DNA sequences. Nucleic Acids Res. 1982 Jan 11;10(1):141–156. doi: 10.1093/nar/10.1.141. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sugimoto K., Oka A., Sugisaki H., Takanami M., Nishimura A., Yasuda Y., Hirota Y. Nucleotide sequence of Escherichia coli K-12 replication origin. Proc Natl Acad Sci U S A. 1979 Feb;76(2):575–579. doi: 10.1073/pnas.76.2.575. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Surin B. P., Jans D. A., Fimmel A. L., Shaw D. C., Cox G. B., Rosenberg H. Structural gene for the phosphate-repressible phosphate-binding protein of Escherichia coli has its own promoter: complete nucleotide sequence of the phoS gene. J Bacteriol. 1984 Mar;157(3):772–778. doi: 10.1128/jb.157.3.772-778.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Travers A. A. A tRNATyr promoter with an altered in vitro response to ppgpp. J Mol Biol. 1980 Jul 25;141(1):91–97. doi: 10.1016/s0022-2836(80)80030-1. [DOI] [PubMed] [Google Scholar]
- Travers A. A. Conserved features of coordinately regulated E. coli promoters. Nucleic Acids Res. 1984 Mar 26;12(6):2605–2618. doi: 10.1093/nar/12.6.2605. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Travers A. A., Lamond A. I., Mace H. A., Berman M. L. RNA polymerase interactions with the upstream region of the E. coli tyrT promoter. Cell. 1983 Nov;35(1):265–273. doi: 10.1016/0092-8674(83)90229-5. [DOI] [PubMed] [Google Scholar]
- Tso J. Y., Hermodson M. A., Zalkin H. Glutamine phosphoribosylpyrophosphate amidotransferase from cloned Escherichia coli purF. NH2-terminal amino acid sequence, identification of the glutamine site, and trace metal analysis. J Biol Chem. 1982 Apr 10;257(7):3532–3536. [PubMed] [Google Scholar]
- Tso J. Y., Hermodson M. A., Zalkin H. Primary structure of Serratia marcescens anthranilate synthase component II. J Biol Chem. 1980 Feb 25;255(4):1451–1457. [PubMed] [Google Scholar]
- 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]
- Vollmer S. J., Switzer R. L., Hermodson M. A., Bower S. G., Zalkin H. The glutamine-utilizing site of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase. J Biol Chem. 1983 Sep 10;258(17):10582–10585. [PubMed] [Google Scholar]
- Walker J. E., Auffret A. D., Carne A., Gurnett A., Hanisch P., Hill D., Saraste M. Solid-phase sequence analysis of polypeptides eluted from polyacrylamide gels. An aid to interpretation of DNA sequences exemplified by the Escherichia coli unc operon and bacteriophage lambda. Eur J Biochem. 1982 Apr 1;123(2):253–260. doi: 10.1111/j.1432-1033.1982.tb19761.x. [DOI] [PubMed] [Google Scholar]
- Walker J. E., Gay N. J. Analysis of Escherichia coli ATP synthase subunits by DNA and protein sequencing. Methods Enzymol. 1983;97:195–218. doi: 10.1016/0076-6879(83)97133-1. [DOI] [PubMed] [Google Scholar]
- Walker J. E., Saraste M., Gay N. J. The unc operon. Nucleotide sequence, regulation and structure of ATP-synthase. Biochim Biophys Acta. 1984 Sep 6;768(2):164–200. doi: 10.1016/0304-4173(84)90003-x. [DOI] [PubMed] [Google Scholar]
- Wilbur W. J., Lipman D. J. Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci U S A. 1983 Feb;80(3):726–730. doi: 10.1073/pnas.80.3.726. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wolf-Watz H. Affinity of two different regions of the chromosome to the outer membrane of Escherichia coli. J Bacteriol. 1984 Mar;157(3):968–970. doi: 10.1128/jb.157.3.968-970.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wolf-Watz H., Masters M. Deoxyribonucleic acid and outer membrane: strains diploid for the oriC region show elevated levels of deoxyribonucleic acid-binding protein and evidence for specific binding of the oriC region to outer membrane. J Bacteriol. 1979 Oct;140(1):50–58. doi: 10.1128/jb.140.1.50-58.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wolf-Watz H., Norqvist A. Deoxyribonucleic acid and outer membrane: binding to outer membrane involves a specific protein. J Bacteriol. 1979 Oct;140(1):43–49. doi: 10.1128/jb.140.1.43-49.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wu H. C., Wu T. C. Isolation and characterization of a glucosamine-requiring mutant of Escherichia coli K-12 defective in glucosamine-6-phosphate synthetase. J Bacteriol. 1971 Feb;105(2):455–466. doi: 10.1128/jb.105.2.455-466.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- von Meyenburg K., Jørgensen B. B., Nielsen J., Hansen F. G. Promoters of the atp operon coding for the membrane-bound ATP synthase of Escherichia coli mapped by Tn10 insertion mutations. Mol Gen Genet. 1982;188(2):240–248. doi: 10.1007/BF00332682. [DOI] [PubMed] [Google Scholar]

