1887

Abstract

Previous reports showed that the large linear plasmid SCP1 of A3(2) contains a 5.4 kb centrally located replication locus. We report here that SCP1 actually contains three internal replication loci. Subcloning of the 5.4 kb sequence identified a 3.2 kb minimal locus (//iteron) that determined propagation in The two newly identified replication genes, and , resembled the gene of circular plasmid pZL12. Transcription start points of the three replication genes were determined. The three replication loci could independently determine propagation in linear mode in . Individual and sequential deletions of the and genes were successful. The SCP1-derived linear plasmids with deletions of the and/or genes still propagated in similar copy numbers, were inherited largely stable and were transferred efficiently by conjugation in . Interestingly, SCP1 can be artificially circularized to yield a 280 kb circular plasmid, circular SCP-1 (C-SCP1), which contains the three replication loci. Strikingly, the copy numbers, inheritance and transfer of C-SCP1 resembled that of the linear SCP1 plasmids. Transcripts of the and genes in linear or artificially circularized SCP1 were detected at all the time points of strain growth.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.067363-0
2013-10-01
2020-01-20
Loading full text...

Full text loading...

/deliver/fulltext/micro/159/10/2127.html?itemId=/content/journal/micro/10.1099/mic.0.067363-0&mimeType=html&fmt=ahah

References

  1. Bao K., Cohen S. N..( 2001;). Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces. Genes Dev15:1518–1527 [CrossRef][PubMed]
    [Google Scholar]
  2. Bao K., Cohen S. N..( 2003;). Recruitment of terminal protein to the ends of Streptomyces linear plasmids and chromosomes by a novel telomere-binding protein essential for linear DNA replication. Genes Dev17:774–785 [CrossRef][PubMed]
    [Google Scholar]
  3. Bentley S. D., Brown S., Murphy L. D., Harris D. E., Quail M. A., Parkhill J., Barrell B. G., McCormick J. R., Santamaria R. I..& other authors ( 2004;). SCP1, a 356,023 bp linear plasmid adapted to the ecology and developmental biology of its host, Streptomyces coelicolor A3(2). Mol Microbiol51:1615–1628 [CrossRef][PubMed]
    [Google Scholar]
  4. Bibb M. J., Ward J. M., Kieser T., Cohen S. N., Hopwood D. A..( 1981;). Excision of chromosomal DNA sequences from Streptomyces coelicolor forms a novel family of plasmids detectable in Streptomyces lividans. Mol Gen Genet184:230–240[PubMed]
    [Google Scholar]
  5. Boidol W., Siewert G., Lindenmaier W., Luibrand G., Goebel W..( 1977;). Properties of hybrid plasmids, consisting of parts of the mini-R1 factor Rsc11 and ColE1. Mol Gen Genet152:231–237 [CrossRef][PubMed]
    [Google Scholar]
  6. Cabello F., Timmis K., Cohen S. N..( 1976;). Replication control in a composite plasmid constructed by in vitro linkage of two distinct replicons. Nature259:285–290 [CrossRef][PubMed]
    [Google Scholar]
  7. Chang P. C., Cohen S. N..( 1994;). Bidirectional replication from an internal origin in a linear Streptomyces plasmid. Science265:952–954 [CrossRef][PubMed]
    [Google Scholar]
  8. Chang P. C., Kim E. S., Cohen S. N..( 1996;). Streptomyces linear plasmids that contain a phage-like, centrally located, replication origin. Mol Microbiol22:789–800 [CrossRef][PubMed]
    [Google Scholar]
  9. Chater K. F., Bruton C. J..( 1985;). Resistance, regulatory and production genes for the antibiotic methylenomycin are clustered. EMBO J4:1893–1897[PubMed]
    [Google Scholar]
  10. Chater K. F., Kinashi H..( 2007;). Streptomyces linear plasmids: their discovery, functions, interactions with other replicons, and evolutionary significance. Microbial Linear Plasmids1–31 Meinhardt F., Klassen R.. Berlin: Springer; [CrossRef]
    [Google Scholar]
  11. Chen C. W..( 1996;). Complications and implications of linear bacterial chromosomes. Trends Genet12:192–196 [CrossRef][PubMed]
    [Google Scholar]
  12. 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 Microbiol7:925–932 [CrossRef][PubMed]
    [Google Scholar]
  13. Chen Z., Zhong L., Shen M., Fang P., Qin Z..( 2012;). Characterization of Streptomyces plasmid-phage pFP4 and its evolutionary implications. Plasmid68:170–178 [CrossRef][PubMed]
    [Google Scholar]
  14. Evans R. P. Jr, Macrina F. L..( 1983;). Streptococcal R plasmid pIP501: endonuclease site map, resistance determinant location, and construction of novel derivatives. J Bacteriol154:1347–1355[PubMed]
    [Google Scholar]
  15. Haug I., Weissenborn A., Brolle D., Bentley S., Kieser T., Altenbuchner J..( 2003;). Streptomyces coelicolor A3(2) plasmid SCP2*: deductions from the complete sequence. Microbiology149:505–513 [CrossRef][PubMed]
    [Google Scholar]
  16. Hayakawa T., Yanaka T., Sakaguchi K., Otake N., Yonehara H..( 1979;). A linear plasmid-like DNA in Streptomyces sp. producing lankacidin group antibiotics. J Gen Appl Microbiol25:255–260 [CrossRef]
    [Google Scholar]
  17. Hiratsu K., Mochizuki S., Kinashi H..( 2000;). Cloning and analysis of the replication origin and the telomeres of the large linear plasmid pSLA2-L in Streptomyces rochei. Mol Gen Genet263:1015–1021 [CrossRef][PubMed]
    [Google Scholar]
  18. Hopwood D. A..( 1999;). Forty years of genetics with Streptomyces: from in vivo through in vitro to in silico. Microbiology145:2183–2202[PubMed]
    [Google Scholar]
  19. Hopwood D. A., Kieser T..( 1993;). Conjugative plasmids of Streptomyces. Bacterial Conjugation293–311 Clewell D. B.. New York: Plenum; [CrossRef]
    [Google Scholar]
  20. Hopwood D. A., Wright H. M..( 1976;). Genetic studies on SCP1-prime strains of Streptomyces coelicolor A3(2). J Gen Microbiol95:107–120 [CrossRef][PubMed]
    [Google Scholar]
  21. Hopwood D. A., Harold R. J., Vivian A., Ferguson H. M..( 1969;). A new kind of fertility variant in Streptomyces coelicolor. Genetics62:461–477[PubMed]
    [Google Scholar]
  22. 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 Microbiol28:905–916 [CrossRef][PubMed]
    [Google Scholar]
  23. Huang C. H., Chen C. Y., Tsai H. H., Chen C., Lin Y. S., Chen C. W..( 2003;). Linear plasmid SLP2 of Streptomyces lividans is a composite replicon. Mol Microbiol47:1563–1576 [CrossRef][PubMed]
    [Google Scholar]
  24. Huang C. H., Tsai H. H., Tsay Y. G., Chien Y. N., Wang S. L., Cheng M. Y., Ke C. H., Chen C. W..( 2007;). The telomere system of the Streptomyces linear plasmid SCP1 represents a novel class. Mol Microbiol63:1710–1718 [CrossRef][PubMed]
    [Google Scholar]
  25. Keen C. L., Mendelovitz S., Cohen G., Aharonowitz Y., Roy K. L..( 1988;). Isolation and characterization of a linear DNA plasmid from Streptomyces clavuligerus. Mol Gen Genet212:172–176 [CrossRef][PubMed]
    [Google Scholar]
  26. Kieser T..( 1984;). Factors affecting the isolation of CCC DNA from Streptomyces lividans and Escherichia coli. Plasmid12:19–36 [CrossRef][PubMed]
    [Google Scholar]
  27. Kieser T., Bibb M. J., Buttner M. J., Chater K. F., Hopwood D. A..( 2000;). Practical Streptomyces Genetics Norwich: John Innes Foundation Press;
    [Google Scholar]
  28. Kinashi H., Shimaji-Murayama M..( 1991;). Physical characterization of SCP1, a giant linear plasmid from Streptomyces coelicolor. J Bacteriol173:1523–1529[PubMed]
    [Google Scholar]
  29. Kinashi H., Shimaji M., Sakai A..( 1987;). Giant linear plasmids in Streptomyces which code for antibiotic biosynthesis genes. Nature328:454–456 [CrossRef][PubMed]
    [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. Plasmid26:123–130 [CrossRef][PubMed]
    [Google Scholar]
  31. Lin Y. S., Chen C. W..( 1997;). Instability of artificially circularized chromosomes of Streptomyces lividans. Mol Microbiol26:709–719 [CrossRef][PubMed]
    [Google Scholar]
  32. Lin Y. S., Kieser H. M., Hopwood D. A., Chen C. W..( 1993;). The chromosomal DNA of Streptomyces lividans 66 is linear. Mol Microbiol10:923–933 [CrossRef][PubMed]
    [Google Scholar]
  33. Medema M. H., Trefzer A., Kovalchuk A., van den Berg M., Müller U., Heijne W., Wu L., Alam M. T., Ronning C. M..& other authors ( 2010;). The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways. Genome Biol Evol2:212–224 [CrossRef][PubMed]
    [Google Scholar]
  34. Omer C. A., Cohen S. N..( 1984;). Plasmid formation in Streptomyces: excision and integration of the SLP1 replicon at a specific chromosomal site. Mol Gen Genet196:429–438 [CrossRef][PubMed]
    [Google Scholar]
  35. Pagotto F., Dillon J. A..( 2001;). Multiple origins and replication proteins influence biological properties of beta-lactamase-producing plasmids from Neisseria gonorrhoeae. J Bacteriol183:5472–5481 [CrossRef][PubMed]
    [Google Scholar]
  36. Pandza S., Biuković G., Paravić A., Dadbin A., Cullum J., Hranueli D..( 1998;). Recombination between the linear plasmid pPZG101 and the linear chromosome of Streptomyces rimosus can lead to exchange of ends. Mol Microbiol28:1165–1176 [CrossRef][PubMed]
    [Google Scholar]
  37. Pettis G. S., Cohen S. N..( 1994;). Transfer of the plJ101 plasmid in Streptomyces lividans requires a cis-acting function dispensable for chromosomal gene transfer. Mol Microbiol13:955–964 [CrossRef][PubMed]
    [Google Scholar]
  38. Possoz C., Ribard C., Gagnat J., Pernodet J. L., Guérineau M..( 2001;). The integrative element pSAM2 from Streptomyces: kinetics and mode of conjugal transfer. Mol Microbiol42:159–166 [CrossRef][PubMed]
    [Google Scholar]
  39. Pujol C., Chédin F., Ehrlich S. D., Jannière L..( 1998;). Inhibition of a naturally occurring rolling-circle replicon in derivatives of the theta-replicating plasmid pIP501. Mol Microbiol29:709–718 [CrossRef][PubMed]
    [Google Scholar]
  40. Qin Z., Cohen S. N..( 1998;). Replication at the telomeres of the Streptomyces linear plasmid pSLA2. Mol Microbiol28:893–903 [CrossRef][PubMed]
    [Google Scholar]
  41. Qin Z., Cohen S. N..( 2002;). Survival mechanisms for Streptomyces linear replicons after telomere damage. Mol Microbiol45:785–794 [CrossRef][PubMed]
    [Google Scholar]
  42. Qin Z., Shen M., Cohen S. N..( 2003;). Identification and characterization of a pSLA2 plasmid locus required for linear DNA replication and circular plasmid stable inheritance in Streptomyces lividans. J Bacteriol185:6575–6582 [CrossRef][PubMed]
    [Google Scholar]
  43. Redenbach M., Bibb M., Gust B., Seitz B., Spychaj A..( 1999;). The linear plasmid SCP1 of Streptomyces coelicolor A3(2) possesses a centrally located replication origin and shows significant homology to the transposon Tn4811. Plasmid42:174–185 [CrossRef][PubMed]
    [Google Scholar]
  44. Reuther J., Gekeler C., Tiffert Y., Wohlleben W., Muth G..( 2006;). Unique conjugation mechanism in mycelial streptomycetes: a DNA-binding ATPase translocates unprocessed plasmid DNA at the hyphal tip. Mol Microbiol61:436–446 [CrossRef][PubMed]
    [Google Scholar]
  45. Robinson N. P., Dionne I., Lundgren M., Marsh V. L., Bernander R., Bell S. D..( 2004;). Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus. Cell116:25–38 [CrossRef][PubMed]
    [Google Scholar]
  46. Salas M..( 1991;). Protein-priming of DNA replication. Annu Rev Biochem60:39–71 [CrossRef][PubMed]
    [Google Scholar]
  47. Sambrook J., Fritsch E. F., Maniatis T..( 1989;). Molecular Cloning: a Laboratory Manual Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press;
    [Google Scholar]
  48. Shiffman D., Cohen S. N..( 1992;). Reconstruction of a Streptomyces linear replicon from separately cloned DNA fragments: existence of a cryptic origin of circular replication within the linear plasmid. Proc Natl Acad Sci U S A89:6129–6133 [CrossRef][PubMed]
    [Google Scholar]
  49. Vivian A., Hopwood D. A..( 1973;). Genetic control of fertility in Streptomyces coelicolor A3(2): new kinds of donor strains. J Gen Microbiol76:147–162 [CrossRef]
    [Google Scholar]
  50. Wang L., Tian X., Wang J., Yang H., Fan K., Xu G., Yang K., Tan H..( 2009;). Autoregulation of antibiotic biosynthesis by binding of the end product to an atypical response regulator. Proc Natl Acad Sci U S A106:8617–8622 [CrossRef][PubMed]
    [Google Scholar]
  51. Wu X., Roy K. L..( 1993;). Complete nucleotide sequence of a linear plasmid from Streptomyces clavuligerus and characterization of its RNA transcripts. J Bacteriol175:37–52[PubMed]
    [Google Scholar]
  52. Wu W., Leblanc S. K., Piktel J., Jensen S. E., Roy K. L..( 2006;). Prediction and functional analysis of the replication origin of the linear plasmid pSCL2 in Streptomyces clavuligerus. Can J Microbiol52:293–300 [CrossRef][PubMed]
    [Google Scholar]
  53. Xia H., Huang J., Hu M., Shen M., Xie P., Zhang L., Wang H., Qin Z..( 2009;). Construction of an ordered cosmid library of S. avermitilis for genetic modification of the industrial strains. Chin J Antibiot34:340–343
    [Google Scholar]
  54. Xu M., Zhu Y., Zhang R., Shen M., Jiang W., Zhao G., Qin Z..( 2006a;). Characterization of the genetic components of Streptomyces lividans linear plasmid SLP2 for replication in circular and linear modes. J Bacteriol188:6851–6857 [CrossRef][PubMed]
    [Google Scholar]
  55. Xu M., Zhu Y., Shen M., Jiang W., Zhao G., Qin Z..( 2006b;). Characterization of the essential gene components for conjugal transfer of Streptomyces lividans linear plasmid SLP2. Prog Biochem Biophys33:986–993
    [Google Scholar]
  56. Yamasaki M., Kinashi H..( 2004;). Two chimeric chromosomes of Streptomyces coelicolor A3(2) generated by single crossover of the wild-type chromosome and linear plasmid scp1. J Bacteriol186:6553–6559 [CrossRef][PubMed]
    [Google Scholar]
  57. Yamasaki M., Ikuto Y., Ohira A., Chater K., Kinashi H..( 2003;). Limited regions of homology between linear and circular plasmids encoding methylenomycin biosynthesis in two independently isolated streptomycetes. Microbiology149:1351–1356 [CrossRef][PubMed]
    [Google Scholar]
  58. Yang C. C., Huang C. H., Li C. Y., Tsay Y. G., Lee S. C., Chen C. W..( 2002;). The terminal proteins of linear Streptomyces chromosomes and plasmids: a novel class of replication priming proteins. Mol Microbiol43:297–305 [CrossRef][PubMed]
    [Google Scholar]
  59. Zhang R., Yang Y., Fang P., Jiang C., Xu L., Zhu Y., Shen M., Xia H., Zhao J..& other authors ( 2006;). Diversity of telomere palindromic sequences and replication genes among Streptomyces linear plasmids. Appl Environ Microbiol72:5728–5733 [CrossRef][PubMed]
    [Google Scholar]
  60. Zhang R., Zeng A., Fang P., Qin Z..( 2008;). Characterization of replication and conjugation of Streptomyces circular plasmids pFP1 and pFP11 and their ability to propagate in linear mode with artificially attached telomeres. Appl Environ Microbiol74:3368–3376 [CrossRef][PubMed]
    [Google Scholar]
  61. Zhang R., Xia H., Guo P., Qin Z..( 2009;). Variation in the replication loci of Streptomyces linear plasmids. FEMS Microbiol Lett290:209–216 [CrossRef][PubMed]
    [Google Scholar]
  62. Zhang R., Peng S., Qin Z..( 2010;). Two internal origins of replication in Streptomyces linear plasmid pFRL1. Appl Environ Microbiol76:5676–5683 [CrossRef][PubMed]
    [Google Scholar]
  63. Zhong L., Cheng Q., Tian X., Zhao L., Qin Z..( 2010;). Characterization of the replication, transfer, and plasmid/lytic phage cycle of the Streptomyces plasmid-phage pZL12. J Bacteriol192:3747–3754 [CrossRef][PubMed]
    [Google Scholar]
  64. 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 Res16:4341–4352 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.067363-0
Loading
/content/journal/micro/10.1099/mic.0.067363-0
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error