1887

Abstract

The chromosome of shares 154 kb homology with one end of the linear plasmid SLP2, consisting of a 101 kb terminal sequence followed by the 53 kb transposable element Tn. The 101 kb terminal sequence was determined. The mean G+C content of this sequence is 679 mol% with a striking G vs C bias in the last kb. The terminal 232 nt contained 10 palindromic sequences with potential to form complex secondary structures. One typical coding sequence (designated ORF1) of 2643 bp was predicted in the determined sequence. The amino acid sequence of the ORF1 product contained a DEAH helicase motif, and exhibited similarity to type I restriction enzyme HsdR subunits in the database, suggesting a possible role in replication of the telomeres. However, all the ORF1 sequences on the chromosome and SLP2 could be simultaneously knocked out by targeted recombination without affecting the viability of the cells and the linearity of the chromosome and SLP2. This ruled out ORF1 as an essential component in the maintenance of the linear chromosome and plasmids.

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2000-04-01
2024-11-12
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References

  1. Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. 1997; Gapped b last and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [CrossRef]
    [Google Scholar]
  2. Baylis H. A., Bibb M. J. 1988; Transcriptional analysis of the 16S rRNA gene of the rrnD gene set of Streptomyces coelicolor A3(2). Mol Microbiol 2:569–579 [CrossRef]
    [Google Scholar]
  3. Bey S.-J. 2000 The terminal DNA and the terminally located gene of the Streptomyces lividans chromosome PhD thesis National Yan-Ming University; Taiwan:
    [Google Scholar]
  4. Bibb M. J., Findlay P. R., Johnson M. W. 1984; 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 30:157–166 [CrossRef]
    [Google Scholar]
  5. Calcutt M. J., Schmidt F. J. 1992; Conserved gene arrangement in the origin region of the Streptomyces coelicolor chromosome. J Bacteriol 174:3220–3226
    [Google Scholar]
  6. Chambers S. P., Prior S. E., Barstow D. A., Minton N. P. 1988; The pMTL nic - cloning vectors. I. Improved pUC polylinker regions to facilitate the use of sonicated DNA for nucleotide sequencing. Gene 68:139–149 [CrossRef]
    [Google Scholar]
  7. Chang P. C., Cohen S. N. 1994; Bidirectional replication from an internal origin in a linear Streptomyces plasmid. Science 265:952–954 [CrossRef]
    [Google Scholar]
  8. Chen C. W. 1996; Complications and implications of linear bacterial chromosomes. Trends Genet 12:192–196 [CrossRef]
    [Google Scholar]
  9. Chen C. W., Yu T.-W., Chung H.-M., Chou C.-F. 1992; Discovery and characterization of a new transposable element, Tn4811, in Streptomyces lividans 66. J Bacteriol 174:7762–7769
    [Google Scholar]
  10. Chen C. W., Yu T.-W., Lin Y. S., Kieser H. M., Hopwood D. A. 1993; The conjugative plasmid SLP2 of Streptomyces lividans is a 50 kb linear molecule. Mol Microbiol 7:925–932 [CrossRef]
    [Google Scholar]
  11. Chou S.-H., Zhu L., Reid B. R. 1994; The unusual structure of the human centromere (GGA)2 motif. J Mol Biol 244:250–268
    [Google Scholar]
  12. Chou S.-H., Zhu L., Reid B. R. 1997; Sheared purine–purine pairing in biology. J Mol Biol 267:1055–1067 [CrossRef]
    [Google Scholar]
  13. Cole S. T., Brosch R., Parkhill J.39 other authors 1998; Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537–544 [CrossRef]
    [Google Scholar]
  14. Fawcett T. W., Bartlett G. 1990; An effective method for eliminating ‘‘artifact banding’’ when sequencing double-stranded DNA templates. Biotechniques 9:46–48
    [Google Scholar]
  15. Gonzalez A., Talavera A., Almendral J. M., Vinuela E. 1986; Hairpin loop structure of African swine fever virus DNA. Nucleic Acids Res 14:6835–6844 [CrossRef]
    [Google Scholar]
  16. Gorbalenya A. E., Koonin E. V. 1993; Helicases: amino acid sequence comparisons and stucture–function relationships. Curr Opin Struct Biol 3:419–429 [CrossRef]
    [Google Scholar]
  17. Gordon S. V., Brosch R., Billault A., Garnier T., Eiglmeier K., Cole S. T. 1999; Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays. Mol Microbiol 32:643–655 [CrossRef]
    [Google Scholar]
  18. Gravius B., Glocker D., Pandza K., Hranueli D., Cullum J. 1994; The 387 kb linear plasmid pPZG101 of Streptomyces rimosus and its interactions with the chromosome. Microbiology 140:2271–2277 [CrossRef]
    [Google Scholar]
  19. Hinnebusch J., Tilly K. 1993; Linear plasmids and chromosomes in bacteria. Mol Microbiol 10:917–922 [CrossRef]
    [Google Scholar]
  20. Hirochika H., Nakamura K., Sakaguchi K. 1985; A linear DNA plasmid from Streptomyces rochei with an inverted repetition of 614 base pairs. EMBO J 3:761–766
    [Google Scholar]
  21. Hopwood D. A., Kieser T., Wright H. M., Bibb M. J. 1983; Plasmids, recombination and chromosomal mapping in Streptomyces lividans 66. J Gen Microbiol 129:2257–2269
    [Google Scholar]
  22. Hopwood D. A., Bibb M. J., Chater K. F.7 other authors 1985 Genetic Manipulation of Streptomyces: a Laboratory Manual Norwich: John Innes Foundation;
    [Google Scholar]
  23. Huang C.-H. 1997 The terminal DNA of Streptomyces chromosomes and linear plasmids MSc thesis National Yang-Ming University; Taiwan:
    [Google Scholar]
  24. Huang C.-H., Lin Y.-S., Yang Y.-L., Huang S.-w., Chen C. W. 1998; The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures. Mol Microbiol 28:905–926 [CrossRef]
    [Google Scholar]
  25. Illana B., Blanco L., Salas M. 1996; Functional characterization of the genes coding for the terminal protein and DNA polymerase from bacteriophage GA-1. Evidence for a sliding-back mechanism during protein-primed GA-1 DNA replication. J Mol Biol 264:453–464 [CrossRef]
    [Google Scholar]
  26. Jung G. H., Leavitt M. C., Hsieh J. C., Ito J. 1987; Bacteriophage PRD1 DNA polymerase: evolution of DNA polymerases. Proc Natl Acad Sci USA 84:8287–8291 [CrossRef]
    [Google Scholar]
  27. 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]
  28. Kinashi H., Shimaji M. 1987; Detection of giant linear plasmids in antibiotic producing strains of Streptomyces by the OFAGE technique. J Antibiot 40:913–916 [CrossRef]
    [Google Scholar]
  29. Kinashi H., Shimaji M., Sakai A. 1987; Giant linear plasmids in Streptomyces which code for antibiotic biosynthesis genes. Nature 328:454–456 [CrossRef]
    [Google Scholar]
  30. Kinashi H., Shimaji-Murayama M., Hanafusa T. 1991; Nucleotide sequence analysis of the unusually long terminal inverted repeats of a giant linear plasmid, SCP1. Plasmid 26:123–130 [CrossRef]
    [Google Scholar]
  31. Leblond P., Fischer G., Francou F., Berger F., Guerineau M., Decaris B. 1996; The unstable region of Streptomyces ambofaciens includes 210 kb terminal inverted repeats flanking the extremities of the linear chromosomal DNA. Mol Microbiol 19:261–271 [CrossRef]
    [Google Scholar]
  32. Lezhava A. L., Mizukami T., Kajitani T., Kameoka D., Redenbach M., Shinkawa H., Nimi O., Kinashi H. 1995; Physical map of the linear chromosome of Streptomyces griseus. J Bacteriol 177:6492–6498
    [Google Scholar]
  33. Lin Y.-S. 1995 The linear chromosome and the linear plasmid of Streptomyces lividans 66 PhD thesis National Yang-Ming University; Taiwan:
    [Google Scholar]
  34. Lin Y.-S., Chen C. W. 1997; Instability of artificially circularized chromosomes of Streptomyces lividans. Mol Microbiol 26:709–719 [CrossRef]
    [Google Scholar]
  35. Lin Y.-S., Kieser H. M., Hopwood D. A., Chen C. W. 1993; The chromosomal DNA of Streptomyces lividans 66 is linear. Mol Microbiol 10:923–933 [CrossRef]
    [Google Scholar]
  36. Murray N. E., Daniel A. S., Cowan G. M., Sharp P. M. 1993; Conservation of motifs within the unusually variable polypeptide sequences of type I restriction and modification enzymes. Mol Microbiol 9:133–143 [CrossRef]
    [Google Scholar]
  37. Musialowski M. S., Flett F., Scott G. B., Hobbs G., Smith C. P., Oliver S. G. 1994; Functional evidence that the principal DNA replication origin of the Streptomyces coelicolor chromosome is close to the dnaA–gyrB region. J Bacteriol 176:5123–5125
    [Google Scholar]
  38. Netolitzky D. J., Wu X., Jensen S. E., Roy K. L. 1995; Giant linear plasmids of β-lactam antibiotic producing Streptomyces. FEMS Microbiol Lett 131:27–34
    [Google Scholar]
  39. Oh S. H., Chater K. F. 1997; Denaturation of circular or linear DNA facilitates targeted integrative transformation of Streptomyces coelicolor A3(2): possible relevance to other organisms. J Bacteriol 179:122–127
    [Google Scholar]
  40. Qin Z., Cohen S. N. 1998; Replication at the telomeres of the Streptomyces linear plasmid pSLA2. Mol Microbiol 28:893–904 [CrossRef]
    [Google Scholar]
  41. Rauland U., Glocker I., Redenbach M., Cullum J. 1995; DNA amplifications and deletions in Streptomyces lividans 66 and the loss of one end of the linear chromosome. Mol Gen Genet 246:37–44 [CrossRef]
    [Google Scholar]
  42. Redenbach M., Flett F., Piendl W., Glocker I., Rauland U., Wafzig O., Leblond P., Cullum J. 1993; The Streptomyces lividans 66 chromosome contains a 1 Mb deletogenic region flanked by two amplifiable regions. Mol Gen Genet 241:255–262
    [Google Scholar]
  43. Sakaguchi K. 1990; Invertrons, a class of structurally and functionally related genetic elements that includes linear plasmids, transposable elements, and genomes of adeno-type viruses. Microbiol Rev 54:66–74
    [Google Scholar]
  44. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory;
    [Google Scholar]
  45. SantaLucia J. J., Allawi H. T., Seneviratne P. A. 1996; Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35:3555–3562 [CrossRef]
    [Google Scholar]
  46. Shiffman D., Cohen S. N. 1992; Reconstruction of a Streptomyces linear plasmid replicon from separately cloned DNA fragments: existence of a cryptic origin of circular replication within the linear plasmid. Proc Natl Acad Sci USA 89:6129–6133 [CrossRef]
    [Google Scholar]
  47. Southern E. 1975; Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503–517 [CrossRef]
    [Google Scholar]
  48. Stark M. J., Mileham A. J., Romanos M. A., Boyd A. 1984; Nucleotide sequence and transcription analysis of a linear DNA plasmid associated with the killer character of the yeast Kluyveromyces lactis. Nucleic Acids Res 12:6011–6030 [CrossRef]
    [Google Scholar]
  49. Thompson C. J., Skinner R. H., Thompson J., Ward J. M., Hopwood D. A., Cundliffe E. 1982; Biochemical characterization of resistance determinants cloned from antibiotic-producing streptomycetes. J Bacteriol 151:678–685
    [Google Scholar]
  50. Tomb J. F., White O., Kerlavage A. R.39 other authors 1997; The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388:539–547 [CrossRef]
    [Google Scholar]
  51. Tommasino M., Ricci S., Galeotti C. L. 1988; Genome organization of the killer plasmid pGK12 from Kluyveromyces lactis. Nucleic Acids Res 16:5863–5878 [CrossRef]
    [Google Scholar]
  52. de la Vega I., Gonzalez A., Blasco R., Calvo V., Vinuela E. 1994; Nucleotide sequence and variability of the inverted terminal repetitions of African swine fever virus DNA. Virology 201:152–156 [CrossRef]
    [Google Scholar]
  53. Wang S.-J., Chang H.-M., Lin Y.-S., Huang C.-H., Chen C. W. 1999; Streptomyces genomes: circular genetic maps from the linear chromosomes. Microbiology 145:2209–2220
    [Google Scholar]
  54. Wu X., Roy K. L. 1992; Complete nucleotide sequence of a linear plasmid from Streptomyces clavuligerus and characterization of its RNA transcripts. J Bacteriol 175:32–52
    [Google Scholar]
  55. Yamakawa H., Nakajima D., Ohara O. 1996; Identification of sequence motifs causing band compressions on human cDNA sequencing. DNA Res 3:81–86 [CrossRef]
    [Google Scholar]
  56. Yoshikawa H., Ito J. 1982; Nucleotide sequence of the major early region of bacteriophage ϕ29. Gene 17:323–335 [CrossRef]
    [Google Scholar]
  57. Zakrzewska-Czerwinska J., Schrempf H. 1992; Characterization of an autonomously replicating region from the Streptomyces lividans chromosome. J Bacteriol 147:2688–2693
    [Google Scholar]
  58. Zhang Z., Schaffer A. A., Miller W., Madden T. L., Lipman D. J., Koonin E. V., Altschul S. F. 1998; Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res 26:3986–3990 [CrossRef]
    [Google Scholar]
  59. Zhou X., Deng Z., Firmin J. L., Hopwood D. A., Kieser T. 1988; Site-specific degradation of Streptomyces lividans DNA during electrophoresis in buffers contaminated with ferrous iron. Nucleic Acids Res 16:4341–4354 [CrossRef]
    [Google Scholar]
  60. Zhu L., Chou S.-H., Reid B. R. 1995a; The structure of a novel DNA duplex formed by human centromere d(TGGAA) repeats with possible implication for chromosome attachment during mitosis. J Mol Biol 254:623–637 [CrossRef]
    [Google Scholar]
  61. Zhu L., Chou S.-H., Xu J., Reid B. R. 1995b; Structure of a single-cytidine hairpin loop formed by the DNA triplet GCA. Nature Struct Biol 2:1012–1017 [CrossRef]
    [Google Scholar]
  62. Zuker M. 1989; On finding all suboptimal foldings of an RNA molecule. Science 244:48–52 [CrossRef]
    [Google Scholar]
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