The genetic marker adjacent to the chloramphenicol biosynthesis gene cluster in ISP5230: functional characterization

The GenBank accession number for the sequence reported in this paper is AF286159.

Free

Abstract

The mutation in ISP5230 confers a growth requirement for pyridoxal (pdx) and is a marker for the genetically mapped cluster of genes associated with chloramphenicol biosynthesis. A gene regulating salvage synthesis of vitamin B6 cofactors in was cloned by transforming a mutant host with the plasmid vector pDQ101 carrying a library of wild-type genomic DNA fragments, and by selecting for complementation of the host’s pdx requirement. However, the corresponding replicative plasmid could not be isolated. Southern hybridizations and transduction analysis indicated that the complementing plasmid had integrated into the chromosome; after excision by a second crossover, the plasmid failed to propagate. To avoid loss of the recombinant vector, a pdx-dependent mutant, KAA1, with a phenotype matching that of , was isolated for use as the cloning host. Introduction of pIJ702 carrying an genomic library into KAA1, and selection of prototrophic transformants, led to the isolation of a stable recombinant vector containing a 25 kb DNA fragment that complemented requirements for pdx in both and mutants. Sequence analysis of the cloned DNA located an intact ORF with a deduced amino acid sequence that, in its central and C-terminal regions resembled type-I aminotransferases. The N-terminal region of the cloned DNA fragment aligned closely with distinctive helix–turn–helix motifs found near the N termini of GntR family transcriptional regulators. The overall deduced amino acid sequence of the cloned DNA showed 73% end-to-end identity to a putative GntR-type regulator cloned in cosmid 6D7 from the A3(2) genome. This location is close to that of , the first marker in A3(2) identified and mapped genetically in Sir David Hopwood’s laboratory. The gene and are postulated to be homologues regulating vitamin B6 coenzyme synthesis from pdx.

Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-147-8-2103
2001-08-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/micro/147/8/1472103a.html?itemId=/content/journal/micro/10.1099/00221287-147-8-2103&mimeType=html&fmt=ahah

References

  1. Aidoo D. A. 1989; Approaches to the cloning of genes for chloramphenicol biosynthesis in Streptomyces venezuelae ISP5230. PhD thesis Dalhousie University; Halifax, NS, Canada:
    [Google Scholar]
  2. Aidoo D. A., Barrett K., Vining L. C. 1990; Plasmid transformation of Streptomyces venezuelae : modified procedures used to introduce the genes for p -aminobenzoate synthetase. J Gen Microbiol 136:657–662 [CrossRef]
    [Google Scholar]
  3. Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [CrossRef]
    [Google Scholar]
  4. Baltz R. H., Seno E. T. 1988; Genetics of Streptomyces fradiae and tylosin biosynthesis. Annu Rev Microbiol 42:547–574 [CrossRef]
    [Google Scholar]
  5. Brennan R. G., Matthews B. W. 1989; The helix–turn–helix DNA binding motif. J Biol Chem 264:1903–1906
    [Google Scholar]
  6. Cosmina P., Rodriguez F., Grandi G., Perego M., Venema G., de Ferra F., van Sinderen D. 1993; Sequence and analysis of the genetic locus responsible for surfactin synthesis in Bacillus subtilis. Mol Microbiol 8821–831 [CrossRef]
    [Google Scholar]
  7. Delic V., Hopwood D. A., Friend E. J. 1970; Mutagenesis by N -methyl- N -nitro- N -nitrosoguanidine. Mutat Res 9:167–182 [CrossRef]
    [Google Scholar]
  8. Dempsey W. B. 1966; Synthesis of pyridoxine by a pyridoxal auxotroph of Escherichia coli. J Bacteriol 92:333–337
    [Google Scholar]
  9. Dempsey W. B. 1987; Synthesis of pyridoxal phosphate . In Escherichia coli and Salmonella typhimurium pp 539–543 Edited by Neidhardt F. C., Ingraham D. L., Brooks K., Low, Magasanik B., Schaechter M., Umbarger H. E. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  10. Denhardt D. T. 1966; A membrane filter technique for the detection of complementary DNA. Biochem Biophys Res Commun 23:641–646 [CrossRef]
    [Google Scholar]
  11. Devereux J., Haeberli P., Smithies O. 1984; A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12:387–395 [CrossRef]
    [Google Scholar]
  12. Doull J., Ahmed Z., Stuttard C., Vining L. C. 1985; Isolation and characterization of Streptomyces venezuelae mutants blocked in chloramphenicol biosynthesis. J Gen Microbiol 131:97–104
    [Google Scholar]
  13. Doull J. L., Vats S., Chaliciopoulos M., Stuttard C., Wong K., Vining L. C. 1986; Conjugational fertility and location of chloramphenicol biosynthesis genes on the chromosomal linkage map of Streptomyces venezuelae. J Gen Microbiol 132:1327–1338
    [Google Scholar]
  14. Facey S. J., Gross F., Vining L. C., Yang K., van Pee K. H. 1996; Cloning, sequencing and disruption of a bromoperoxidase-catalase gene in Streptomyces venezuelae. Microbiology 142:657–665 [CrossRef]
    [Google Scholar]
  15. Han L., Yang K., Ramalingam E., Mosher R. H., Vining L. C. 1994; Cloning and characterization of polyketide synthase genes for jadomycin B biosynthesis in Streptomyces venezuelae ISP5230. Microbiology 140:3379–3389 [CrossRef]
    [Google Scholar]
  16. Haydon D. J., Guest J. R. 1991; A new family of bacterial regulatory proteins. FEMS Microbiol Lett 79:291–296 [CrossRef]
    [Google Scholar]
  17. Henikoff S. 1984; Unidirectional deletion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene 28:351–359 [CrossRef]
    [Google Scholar]
  18. Holmes D. S., Quigley M. 1981; A rapid boiling method for the preparation of bacterial plasmids. Anal Biochem 114:193–200 [CrossRef]
    [Google Scholar]
  19. Hopwood D. A. 1967; Genetic analysis and genome structure in Streptomyces coelicolor . Bacteriol Rev 31:373–403
    [Google Scholar]
  20. Hopwood D. A., Kieser T. 1990; The Streptomyces genome. In The Bacterial Chromosome pp 147–162 Edited by Drlica K., Riley M. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  21. Hopwood D. A., Bibb M. J., Chater K. F. and 7 other authors 1985 Genetic Manipulation of Streptomyces: a Laboratory Manual Norwich: John Innes Foundation;
    [Google Scholar]
  22. Ishikawa J., Hotta K. 1999; Frameplot: a new implementation of the frame analysis for predicting protein-coding regions in bacterial DNA with a high G+C content. FEMS Microbiol Lett 174:251–253 [CrossRef]
    [Google Scholar]
  23. Katz E., Thompson C. J., Hopwood D. A. 1983; Cloning and expression of the tyrosinase gene from Streptomyces antibioticus in Streptomyces lividans . J Gen Microbiol 129:2703–2714
    [Google Scholar]
  24. Kendall K. J., Cohen S. N. 1988; Complete nucleotide sequence of Streptomyces lividans plasmid pIJ101 and correlation of the sequence with genetic properties. J Bacteriol 170:4634–4651
    [Google Scholar]
  25. Kieser T. 1984; Factors affecting the isolation of cccDNA from Streptomyces lividans and Escherichia coli . Plasmid 12:19–36 [CrossRef]
    [Google Scholar]
  26. Kieser T., Bibb M. J., Buttner M. J., Chater K. F., Hopwood D. A. 2000 Practical Streptomyces Genetics Norwich: John Innes Foundation;
    [Google Scholar]
  27. Larson J. L., Hershberger C. L. 1986; The minimal replicon of a streptomycete plasmid produces an ultrahigh level of plasmid DNA. Plasmid 15:199–209 [CrossRef]
    [Google Scholar]
  28. Lydiate D. J., Malpartida F., Hopwood D. A. 1985; The Streptomyces plasmid SCP2*: its functional analysis and development into useful cloning vectors. Gene 35:223–235 [CrossRef]
    [Google Scholar]
  29. MacNeil D. J., Gewain K. M., Rudy C. L., Dezeny G., Gibbons P. H., MacNeil T. 1992; Analysis of Streptomyces avermitilis genes required for avermectin biosynthesis utilizing a novel integration vector. Gene 111:61–68 [CrossRef]
    [Google Scholar]
  30. Neidle E. L., Kaplan S. 1992; Rhodobacter sphaeroides rdxA , a homolog of Rhizobium meliloti fixG , encodes a membrane protein which may bind cytoplasmic [4Fe–4S] clusters. J Bacteriol 174:6444–6454
    [Google Scholar]
  31. Pabo C. O., Sauer R. T. 1984; Protein–DNA recognition. Annu Rev Biochem 53:293–321 [CrossRef]
    [Google Scholar]
  32. Paradkar A. S., Jensen S. E. 1995; Functional analysis of the gene encoding the clavaminate synthase 2 isoenzyme involved in clavulanic acid biosynthesis in Streptomyces clavuligerus . J Bacteriol 177:1307–1314
    [Google Scholar]
  33. Paradkar A. S., Stuttard C., Vining L. C. 1993; Location of the genes for anthranilate synthase in Streptomyces venezuelae ISP5230: genetic mapping after integration of the cloned genes. J Gen Microbiol 139:687–694 [CrossRef]
    [Google Scholar]
  34. Redenbach M., Kieser H. M., Denapaite D., Eichner A., Cullum L., Kinashi H., Hopwood D. A. 1996; A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome. Mol Microbiol 21:77–96 [CrossRef]
    [Google Scholar]
  35. Rossbach S., Kulpa D. A., Rossbach U., de Bruijn F. J. 1994; Molecular and genetic characterization of the rhizopine catabolism ( mocABRC) genes of Rhizobium meliloti L5-30. Mol Gen Genet 245:11–24 [CrossRef]
    [Google Scholar]
  36. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual , 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  37. Sanger F., Nicklen S., Coulson A. R. 1977; DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467 [CrossRef]
    [Google Scholar]
  38. Southern E. M. 1975; Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503–517 [CrossRef]
    [Google Scholar]
  39. Stuttard C. 1982; Temperate phages of Streptomyces venezuelae : lysogeny and host specificity shown by SV1 and SV2. J Gen Microbiol 128:115–121
    [Google Scholar]
  40. Stuttard C. 1988; Transduction and genome structure in Streptomyces. . Dev Ind Microbiol 29:69–75
    [Google Scholar]
  41. Stuttard C. 1989; Generalized transduction in Streptomyces species. In Genetics and Molecular Biology of Industrial Microorganisms pp 157–162 Edited by Hershberger C. L., Queener S. W., Hegeman G. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  42. Stuttard C., Atkinson L., Vats S. 1987; Genome structure in Streptomyces spp.: adjacent genes on the S. coelicolor A3(2) linkage map have cotransducible analogs in S. venezuelae . J Bacteriol 169:3809–3813
    [Google Scholar]
  43. Thompson C. J., Ward J. M., Hopwood D. A. 1982; Cloning of antibiotic resistance and nutritional genes in streptomycetes. J Bacteriol 151:668–672
    [Google Scholar]
  44. Titgemeyer F., Reizer J., Reizer A., Tang J., Parr T. R. Jr, Saier H. M. Jr 1995; Nucleotide sequence of the region between crr and cysM in Salmonella typhimurium : five novel ORFs, including one encoding a putative transcriptional regulator of the phosphotransferase system. DNA Seq 5:145–152
    [Google Scholar]
  45. Vats S. 1987; The fine structure mapping of chloramphenicol biosynthesis genes in Streptomyces venezuelae. PhD thesis Dalhousie University; Halifax, NS, Canada:
    [Google Scholar]
  46. Vats S., Atkinson L., Stuttard C. 1987a; Genome structure in Streptomyces spp.: adjacent genes on the S. coelicolor A3(2) linkage map have transducible analogs in S.venezuelae. J Bacteriol 169:3814–3816
    [Google Scholar]
  47. Vats S., Stuttard C., Vining L. C. 1987b; Transductional analysis of chloramphenicol biosynthesis genes in Streptomyces venezuelae. J Bacteriol 169:3809–3813
    [Google Scholar]
  48. Vining L. C., Stuttard C. 1994; Chloramphenicol. In Genetics and Biochemistry of Antibiotic Production pp 505–530 Edited by Vining L. C., Stuttard C. Boston: Butterworth-Heinemann;
    [Google Scholar]
  49. Vining L. C., Westlake D. W. S. 1984; Chloramphenicol: properties, biosynthesis and fermentation. In Biotechnology of Industrial Antibiotics pp 387–411 Edited by Vandamme S. J. New York & Basel: Marcel Dekker;
    [Google Scholar]
  50. Vivian A., Charles H. P. 1970; The occurrence and genetics of some CO2 mutants in Streptomyces coelicolor . J Gen Microbiol 61:263–271 [CrossRef]
    [Google Scholar]
  51. Wright F., Bibb M. J. 1992; Codon usage in the G+C-rich Streptomyces genome. Gene 113:55–65 [CrossRef]
    [Google Scholar]
  52. Wu C., Zhao S., Chen H. L., Lo C. J., McLarty J. 1996; Motif identification neural design for rapid and sensitive protein family search. CABIOS 12:109–118
    [Google Scholar]
  53. Wu C., Shivakumar S., Shivakumar C. V., Chen S. 1998; GeneFIND web server for protein family identification and information retrieval. Bioinformatics 14:223–224 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-147-8-2103
Loading
/content/journal/micro/10.1099/00221287-147-8-2103
Loading

Data & Media loading...

Most cited Most Cited RSS feed