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. 1988 Oct;170(10):4634–4651. doi: 10.1128/jb.170.10.4634-4651.1988

Complete nucleotide sequence of the Streptomyces lividans plasmid pIJ101 and correlation of the sequence with genetic properties.

K J Kendall 1, S N Cohen 1
PMCID: PMC211503  PMID: 3170481

Abstract

The complete nucleotide sequence of the multicopy Streptomyces plasmid pIJ101 has been determined and correlated with previously published genetic data. The circular DNA molecule is 8,830 nucleotides in length and has a G+C composition of 72.98%. The use of a computer program, FRAME, enabled identification in the sequence of seven open reading frames, four of which, tra (621 amino acids [aa]), spdA (146 aa), spdB (274 aa), and kilB (177 aa), appear to be genes involved in plasmid transfer. At least two of the above genes are predicted to be transcribed by known promoters that are regulated in trans by the products of the korA (241 aa) and korB (80 aa) loci on the plasmid. The segment of the plasmid capable of autonomous replication contains one large open reading frame (rep; 450 aa) and a noncoding region presumed to be the origin of replication. Four other small (less than 90 aa) open reading frames are also present on the plasmid, although no function can be attributed to them. The sequence of the pIJ101 replication segment present in several widely used cloning vectors (e.g., pIJ350 and pIJ702) has also been determined, so that the complete nucleotide sequences of these vectors are now known.

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Selected References

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

  1. Bankier A. T., Weston K. M., Barrell B. G. Random cloning and sequencing by the M13/dideoxynucleotide chain termination method. Methods Enzymol. 1987;155:51–93. doi: 10.1016/0076-6879(87)55009-1. [DOI] [PubMed] [Google Scholar]
  2. Bernan V., Filpula D., Herber W., Bibb M., Katz E. The nucleotide sequence of the tyrosinase gene from Streptomyces antibioticus and characterization of the gene product. Gene. 1985;37(1-3):101–110. doi: 10.1016/0378-1119(85)90262-8. [DOI] [PubMed] [Google Scholar]
  3. Bibb M. J., Bibb M. J., Ward J. M., Cohen S. N. Nucleotide sequences encoding and promoting expression of three antibiotic resistance genes indigenous to Streptomyces. Mol Gen Genet. 1985;199(1):26–36. doi: 10.1007/BF00327505. [DOI] [PubMed] [Google Scholar]
  4. Bibb M. J., Cohen S. N. Gene expression in Streptomyces: construction and application of promoter-probe plasmid vectors in Streptomyces lividans. Mol Gen Genet. 1982;187(2):265–277. doi: 10.1007/BF00331128. [DOI] [PubMed] [Google Scholar]
  5. Bibb M. J., Findlay P. R., Johnson M. W. The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences. Gene. 1984 Oct;30(1-3):157–166. doi: 10.1016/0378-1119(84)90116-1. [DOI] [PubMed] [Google Scholar]
  6. Buttner M J, Fearnley I M, Bibb M J. The agarase gene (dagA) of Streptomyces coelicolor A3(2): nucleotide sequence and transcriptional analysis. Mol Gen Genet. 1987 Aug;209(1):101–109. doi: 10.1007/BF00329843. [DOI] [PubMed] [Google Scholar]
  7. Buttner M. J., Brown N. L. RNA polymerase-DNA interactions in Streptomyces. In vitro studies of a S. lividans plasmid promoter with S. coelicolor RNA polymerase. J Mol Biol. 1985 Sep 5;185(1):177–188. doi: 10.1016/0022-2836(85)90189-5. [DOI] [PubMed] [Google Scholar]
  8. Buttner M. J., Brown N. L. Two promoters from the Streptomyces plasmid pIJ101 and their expression in Escherichia coli. Gene. 1987;51(2-3):179–186. doi: 10.1016/0378-1119(87)90306-4. [DOI] [PubMed] [Google Scholar]
  9. Chou P. Y., Fasman G. D. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol. 1978;47:45–148. doi: 10.1002/9780470122921.ch2. [DOI] [PubMed] [Google Scholar]
  10. Deng Z. X., Kieser T., Hopwood D. A. Activity of a Streptomyces transcriptional terminator in Escherichia coli. Nucleic Acids Res. 1987 Mar 25;15(6):2665–2675. doi: 10.1093/nar/15.6.2665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Deng Z., Kieser T., Hopwood D. A. Expression of a Streptomyces plasmid promoter in Escherichia coli. Gene. 1986;43(3):295–300. doi: 10.1016/0378-1119(86)90219-2. [DOI] [PubMed] [Google Scholar]
  12. Eisenberg D., Weiss R. M., Terwilliger T. C. The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature. 1982 Sep 23;299(5881):371–374. doi: 10.1038/299371a0. [DOI] [PubMed] [Google Scholar]
  13. Garnier J., Osguthorpe D. J., Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol. 1978 Mar 25;120(1):97–120. doi: 10.1016/0022-2836(78)90297-8. [DOI] [PubMed] [Google Scholar]
  14. Hopwood D. A., Kieser T., Wright H. M., Bibb M. J. Plasmids, recombination and chromosome mapping in Streptomyces lividans 66. J Gen Microbiol. 1983 Jul;129(7):2257–2269. doi: 10.1099/00221287-129-7-2257. [DOI] [PubMed] [Google Scholar]
  15. Hopwood D. A., Lydiate D. J., Malpartida F., Wright H. M. Conjugative sex plasmids of Streptomyces. Basic Life Sci. 1985;30:615–634. doi: 10.1007/978-1-4613-2447-8_43. [DOI] [PubMed] [Google Scholar]
  16. Katz E., Thompson C. J., Hopwood D. A. Cloning and expression of the tyrosinase gene from Streptomyces antibioticus in Streptomyces lividans. J Gen Microbiol. 1983 Sep;129(9):2703–2714. doi: 10.1099/00221287-129-9-2703. [DOI] [PubMed] [Google Scholar]
  17. Kendall K. J., Cohen S. N. Plasmid transfer in Streptomyces lividans: identification of a kil-kor system associated with the transfer region of pIJ101. J Bacteriol. 1987 Sep;169(9):4177–4183. doi: 10.1128/jb.169.9.4177-4183.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kieser T., Hopwood D. A., Wright H. M., Thompson C. J. pIJ101, a multi-copy broad host-range Streptomyces plasmid: functional analysis and development of DNA cloning vectors. Mol Gen Genet. 1982;185(2):223–228. doi: 10.1007/BF00330791. [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. 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]
  21. 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]
  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. Scott J. R. Regulation of plasmid replication. Microbiol Rev. 1984 Mar;48(1):1–23. doi: 10.1016/b978-0-12-048850-6.50006-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Thompson C. J., Ward J. M., Hopwood D. A. Cloning of antibiotic resistance and nutritional genes in streptomycetes. J Bacteriol. 1982 Aug;151(2):668–677. doi: 10.1128/jb.151.2.668-677.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Uchiyama H., Weisblum B. N-Methyl transferase of Streptomyces erythraeus that confers resistance to the macrolide-lincosamide-streptogramin B antibiotics: amino acid sequence and its homology to cognate R-factor enzymes from pathogenic bacilli and cocci. Gene. 1985;38(1-3):103–110. doi: 10.1016/0378-1119(85)90208-2. [DOI] [PubMed] [Google Scholar]
  26. Walker J. E., Saraste M., Runswick M. J., Gay N. J. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1982;1(8):945–951. doi: 10.1002/j.1460-2075.1982.tb01276.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. 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]
  28. Zalacain M., González A., Guerrero M. C., Mattaliano R. J., Malpartida F., Jiménez A. Nucleotide sequence of the hygromycin B phosphotransferase gene from Streptomyces hygroscopicus. Nucleic Acids Res. 1986 Feb 25;14(4):1565–1581. doi: 10.1093/nar/14.4.1565. [DOI] [PMC free article] [PubMed] [Google Scholar]

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