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Microbial Linear Plasmids pp 33–61Cite as

Streptomyces Linear Plasmids: Replication and Telomeres

Part of the Microbiology Monographs book series (MICROMONO,volume 7)

Abstract

Vegetative replication of terminal protein (TP)-capped linear plasmids (and linear chromosomes) of Streptomyces proceeds in two steps: a classical bidirectional replication from an internal origin followed by a novel TP-primed DNA synthesis that patches the resulting single-strand gaps at the 3′ ends (“end patching”). Replication initiation systems found on different linear Streptomyces plasmids consist of helicase-like genes and iterons of relatively diverse origins. In contrast, the end patching system (including the telomeres and the TPs) is highly conserved in most linear replicons in Streptomyces with only a single exception so far. Both the TPs and the telomeric DNAs have evolved structural features to serve replication as well as protection of the telomeres. Interaction of TPs shapes the linear replicon into a circular form, which would allow generation of biologically important superhelicity in terminal DNA, but would also create complications during postreplicational segregation of the daughter DNA. TPs may also be involved in priming initiation of replication during conjugal transfer. Like the T-DNA transfer system in Agrobacterium tumefaciens, the TPs can target themselves and the attached DNA into eukaryotic nuclei, thus suggesting a possibility of interkingdom conjugal transfer.

Keywords

  • Terminal Inverted Repeat
  • Telomere Sequence
  • Linear Plasmid
  • Conjugal Transfer
  • Linear Chromosome

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. Adams DE, Shekhtman EM, Zechiedrich EL, Schmid MB, Cozzarelli NR (1992) The role of topoisomerase IV in partitioning bacterial replicons and the structure of catenated intermediates in DNA replication. Cell 71:277–288

    PubMed  CrossRef  CAS  Google Scholar 

  2. Arnberg A, Arwert F (1976) DNA–protein complex in circular DNA from Bacillus bacteriophage GA-1. J Virol 18:783–784

    PubMed  CAS  Google Scholar 

  3. Astell CR, Smith M, Chow MB, Ward DC (1979) Structure of the 3′ hairpin termini of four rodent parvovirus genomes: nucleotide sequence homology at origins of DNA replication. Cell 17:691–703

    PubMed  CrossRef  CAS  Google Scholar 

  4. Astell CR, Chow MB, Ward DC (1985) Sequence analysis of the termini of virion and replicative forms of minute virus of mice suggests a modified rolling hairpin model for autonomous parvovirus DNA replication. J Virol 54:171–177

    PubMed  CAS  Google Scholar 

  5. Bao K, Cohen SN (2001) Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces. Genes Dev 15:1518–1527

    PubMed  CrossRef  CAS  Google Scholar 

  6. Bao K, Cohen SN (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 Dev 17:774–785

    PubMed  CrossRef  CAS  Google Scholar 

  7. Bao K, Cohen SN (2004) Reverse transcriptase activity innate to DNA polymerase I and DNA topoisomerase I proteins of Streptomyces telomere complex. Proc Natl Acad Sci USA 101:14361–14366

    PubMed  CrossRef  CAS  Google Scholar 

  8. Barre FX, Soballe B, Michel B, Aroyo M, Robertson M, Sherratt D (2001) Circles: the replication–recombination–chromosome segregation connection. Proc Natl Acad Sci USA 98:8189–8195

    PubMed  CrossRef  CAS  Google Scholar 

  9. Bentley SD et al (2004) SCP1, a 356,023 base pair linear plasmid adapted to the ecology and developmental biology of its host, Streptomyces coelicolor A3(2). Mol Microbiol 51:1615–1628

    PubMed  CrossRef  CAS  Google Scholar 

  10. Bey S-J, Tsou M-F, Huang C-H, Yang C-C, Chen CW (2000) The homologous terminal sequence of the Streptomyces lividans chromosome and SLP2 plasmid. Microbiology 146:911–922

    PubMed  CAS  Google Scholar 

  11. Bignell C, Thomas CM (2001) The bacterial ParA–ParB partitioning proteins. J Biotechnol 91:1–34

    PubMed  CrossRef  CAS  Google Scholar 

  12. Bravo A, Salas M (1997) Initiation of bacteriophage 29 DNA replication in vivo: assembly of a membrane-associated multiprotein complex. J Mol Biol 269:102–112

    PubMed  CrossRef  CAS  Google Scholar 

  13. Chaconas G, Chen CW (2005) Linear chromosomes in bacteria: no longer going around in circles. In: Higgins NP (ed) The bacterial chromosome. American Society for Microbiology, Washington, DC, pp 525–539

    Google Scholar 

  14. Chang P-C, Cohen SN (1994) Bidirectional replication from an internal origin in a linear Streptomyces plasmid. Science 265:952–954

    PubMed  CrossRef  CAS  Google Scholar 

  15. Chang P-C, Kim ES, Cohen SN (1996) Streptomyces linear plasmids that contain a phagelike, centrally located replication origin. Mol Microbiol 22:789–800

    PubMed  CrossRef  CAS  Google Scholar 

  16. Chater K, Kinashi H (2007) Streptomyces Linear Plasmids: Their Discovery, Functions, Interactions with other Replicons, and Evolutionary Significance. Microbiol Monogr 7. Springer, Heidelberg

    Google Scholar 

  17. Chen CW (1996) Complications and implications of linear bacterial chromosomes. Trends Genet 12:192–196

    PubMed  CrossRef  CAS  Google Scholar 

  18. Chen CW, Yu T-W, Lin Y-S, Kieser HM, Hopwood DA (1993) The conjugative plasmid SLP2 of Streptomyces lividans is a 50-kb linear molecule. Mol Microbiol 7:925–932

    PubMed  CrossRef  CAS  Google Scholar 

  19. Chen CW, Huang C-H, Lee H-H, Tsai H-H, Kirby R (2002) Once the circle has been broken: dynamics and evolution of Streptomyces chromosomes. Trends Genet 18:522–529

    PubMed  CrossRef  CAS  Google Scholar 

  20. Chen Y-T (2000) Linear chromosomes and linear plasmids in actinomycetes. In: Institute of Genetics. National Yang-Ming University, Taipei

    Google Scholar 

  21. Chou S-H, Zhu L, Reid BR (1997) Sheared purine–purine pairing in biology. J Mol Biol 267:1055–1067

    PubMed  CrossRef  CAS  Google Scholar 

  22. Fetzner S, Kolkenbrock S, Parschat K (2007) Catabolic Linear Plasmids. Microbiol Monogr 7. Springer, Heidelberg

    Google Scholar 

  23. Fischer G, Wenner T, Decaris B, Leblond P (1998) Chromosomal arm replacement generates a high level of intraspecific polymorphism in the terminal inverted repeats of the linear chromosomal DNA of Streptomyces ambofaciens. Proc Natl Acad Sci USA 95:14296–14301

    PubMed  CrossRef  CAS  Google Scholar 

  24. Flett F, Platt J, Oliver SG (1992) Isolation and characterization of temperature-sensitive mutants of Streptomyces coelicolor A3(2) blocked in macromolecular synthesis. J Gen Microbiol 138:579–585

    PubMed  CAS  Google Scholar 

  25. Flett F, de Mello Jungmann-Campello D, Mersinias V, Koh SL, Godden R, Smith CP (1999) A “gram-negative-type” DNA polymerase III is essential for replication of the linear chromosome of Streptomyces coelicolor A3(2). Mol Microbiol 31:949–958

    PubMed  CrossRef  CAS  Google Scholar 

  26. Gerdes K, Moller-Jensen J, Jensen RB (2000) Plasmid and chromosome partitioning: surprises from phylogeny. Mol Microbiol 37:455–466

    PubMed  CrossRef  CAS  Google Scholar 

  27. Goshi K et al (2002) Cloning and analysis of the telomere and terminal inverted repeat of the linear chromosome of Streptomyces griseus. J Bacteriol 184:3411–3415

    PubMed  CrossRef  CAS  Google Scholar 

  28. 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 Genet 263:1015–1021

    PubMed  CrossRef  CAS  Google Scholar 

  29. 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 

  30. Hopwood DA (1967) Genetic analysis and genome structure in Streptomyces coelicolor. Bacteriol Rev 31:373–403

    PubMed  CAS  Google Scholar 

  31. Hopwood DA (2006) Soil to genomics: the Streptomyces chromosome. Annu Rev Genet 40:123

    CrossRef  CAS  Google Scholar 

  32. Hopwood DA, Kieser T (1993) Conjugative plasmids of Streptomyces. In: Clewell DB (ed) Bacterial conjugation. Plenum, New York, pp 293–311

    Google Scholar 

  33. Huang C-H (2002) Structures and functions of Streptomyces telomeres. PhD-Thesis. In: Institute of Genetics. National Yang-Ming University, Taipei, p 111

    Google Scholar 

  34. Huang C-H, Lin Y-S, Yang Y-L, Huang S-W, Chen CW (1998) The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures. Mol Microbiol 28:905–926

    PubMed  CrossRef  CAS  Google Scholar 

  35. Huang C-H, Chen C-Y, Tsai H-H, Chen C, Lin Y-S, Chen CW (2003) Linear plasmid SLP2 of Streptomyces lividans is a composite replicon. Mol Microbiol 47:1563–1576

    PubMed  CrossRef  CAS  Google Scholar 

  36. Huang T-W, Chen CW (2006) A recA null mutation may be generated in Streptomyces coelicolor. J Bacteriol 188:6771–6779

    PubMed  CrossRef  CAS  Google Scholar 

  37. Huang C-H, Tsai H-H, Tsay Y-G, Chien Y-N, Wang S-L, Cheng M-Y, Ke C-H, Chen CW (2007) The Telomere System of the Streptomyces Linear Plasmid SCP1 Represents a Novel Class. Mol Microbiol 63:1710–1718

    PubMed  CrossRef  CAS  Google Scholar 

  38. Ikeda H et al (2003) Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol 21:526–531

    PubMed  CrossRef  Google Scholar 

  39. Jakimowicz D et al (1998) Structural elements of the Streptomyces oriC region and their interactions with the DnaA protein. Microbiology 144:1281–1290

    PubMed  CAS  CrossRef  Google Scholar 

  40. Keegstra W, Van Wielink P, Sussenbach J (1977) The visualization of a circular DNA–protein complex from adenovirions. Virology 76:444–447

    PubMed  CrossRef  CAS  Google Scholar 

  41. Klassen R, Meinhardt F (2007) Linear Protein-primed Replicating Plasmids in Eukaryotic Microbes. Microbiol Monogr 7. Springer, Heidelberg

    Google Scholar 

  42. 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

    PubMed  CrossRef  CAS  Google Scholar 

  43. Kornberg A, Baker TA (1992) DNA replication. Freeman, New York

    Google Scholar 

  44. Lin Y-S, Kieser HM, Hopwood DA, Chen CW (1993) The chromosomal DNA of Streptomyces lividans 66 is linear. Mol Microbiol 10:923–933

    PubMed  CrossRef  CAS  Google Scholar 

  45. McLeod MP et al (2006) The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci USA 103:15582–15587

    PubMed  CrossRef  Google Scholar 

  46. Mochizuki S, Hiratsu K, Akita A, Kinashi H (2001) Complete nucleotide sequence of the linear plasmid pSLA2-L revealed unusual gene organizations for secondary metabolism. In: Twelfth international symposium on the biology of actinomycetes, Vancouver, Canada, p 60

    Google Scholar 

  47. Muth G, Frese D, Kleber A, Wohlleben W (1997) Mutational analysis of the Streptomyces lividans recA gene suggests that only mutants with residual activity remain viable. Mol Gen Genet 255:420–428

    PubMed  CrossRef  CAS  Google Scholar 

  48. Ortin J, Vinuela E, Salas M, Vasquez C (1971) DNA–protein complex in circular DNA from phage 29. Nat New Biol 234:275–277

    PubMed  CrossRef  CAS  Google Scholar 

  49. Possoz C, Ribard C, Gagnat J, Pernodet JL, Guerineau M (2001) The integrative element pSAM2 from Streptomyces: kinetics and mode of conjugal transfer. Mol Microbiol 42:159–166

    PubMed  CrossRef  CAS  Google Scholar 

  50. Qin Z, Cohen SN (1998) Replication at the telomeres of the Streptomyces linear plasmid pSLA2. Mol Microbiol 28:893–904

    PubMed  CrossRef  CAS  Google Scholar 

  51. Qin Z, Cohen SN (2002) Survival mechanisms for Streptomyces linear replicons after telomere damage. Mol Microbiol 45:785–794

    PubMed  CrossRef  CAS  Google Scholar 

  52. Qin Z, Shen M, Cohen SN (2003) Identification and characterization of a pSLA2 plasmid locus required for linear DNA replication and circular plasmid stable inheritance in Streptomyces lividans. J Bacteriol 185:6575–6582

    PubMed  CrossRef  CAS  Google Scholar 

  53. 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. Plasmid 42:174–185

    PubMed  CrossRef  CAS  Google Scholar 

  54. Redenbach M, Scheel J, Schmidt U (2000) Chromosome topology and genome size of selected actinomycetes species. Antonie Van Leeuwenhoek 78:227–235

    PubMed  CrossRef  CAS  Google Scholar 

  55. 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 Microbiol 61:436–446

    PubMed  CrossRef  CAS  Google Scholar 

  56. Robinson AJ, Younghusband HB, Bellett AJ (1973) A circular DNA–protein complex from adenoviruses. Virology 56:54–69

    PubMed  CrossRef  CAS  Google Scholar 

  57. Sakaguchi K (1990) Invertrons, a class of structurally and functionally related genetic elements that include linear plasmids, transposable elements, and genomes of adeno-type viruses. Microbiol Rev 54:66–74

    PubMed  CAS  Google Scholar 

  58. Schaack J, Ho WY, Freimuth P, Shenk T (1990) Adenovirus terminal protein mediates both nuclear matrix association and efficient transcription of adenovirus DNA. Genes Dev 4:1197–1208

    PubMed  CrossRef  CAS  Google Scholar 

  59. Sekine M et al (2006) Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4. Environ Microbiol 8:334–346

    PubMed  CrossRef  CAS  Google Scholar 

  60. Shiffman D, Cohen SN (1992) Reconstruction of a Streptomyces linear plasmid replicon from separately cloned DNA fragment: existence of a cryptic origin of circular replication within the linear plasmid. Proc Natl Acad Sci USA 89:6129–6133

    PubMed  CrossRef  CAS  Google Scholar 

  61. Shih YL, Rothfield L (2006) The bacterial cytoskeleton. Microbiol Mol Biol Rev 70:729–754

    PubMed  CrossRef  CAS  Google Scholar 

  62. Stahl FW (1967) Circular genetic maps. J Cell Physiol 70:1–12

    PubMed  CrossRef  Google Scholar 

  63. Stahl FW, Steinberg CM (1964) The theory of formal phage genetics for circular maps. Genetics 50:531–538

    PubMed  CAS  Google Scholar 

  64. Uchida T, Miyawaki M, Kinashi H (2003) Chromosomal arm replacement in Streptomyces griseus. J Bacteriol 185:1120–1124

    PubMed  CrossRef  CAS  Google Scholar 

  65. Wang S-J, Chang H-M, Lin Y-S, Huang C-H, Chen CW (1999) Streptomyces genomes: circular genetic maps from the linear chromosomes. Microbiology 145:2209–2220

    PubMed  CAS  Google Scholar 

  66. Weaver D et al (2004) Genome plasticity in Streptomyces: identification of 1-Mb TIRs in the S. coelicolor A3(2) chromosome. Mol Microbiol 51:1530–1550

    CrossRef  Google Scholar 

  67. Wong M, Hsu M (1989) Linear adenovirus DNA is organized into supercoiled domains in virus particles. Nucleic Acids Res 17:3535–3550

    PubMed  CrossRef  CAS  Google Scholar 

  68. Xu M et al (2006) Characterization of the genetic components of Streptomyces lividans linear plasmid SLP2 for replication in circular and linear modes. J Bacteriol 188:6851–6857

    PubMed  CrossRef  CAS  Google Scholar 

  69. 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 Bacteriol 186:6553–6559

    PubMed  CrossRef  CAS  Google Scholar 

  70. Yang C-C, Huang C-H, Li C-Y, Tsay Y-G, Lee S-C, Chen CW (2002) The terminal proteins of linear Streptomyces chromosomes and plasmids: a novel class of replication priming proteins. Mol Microbiol 43:297–305

    PubMed  CrossRef  Google Scholar 

  71. Yang C-C, Chen Y-H, Tsai H-H, Huang C-H, Huang T-W, Chen CW (2006) In vitro deoxynucleotidylation of terminal protein of Streptomyces linear chromosomes. J Bacteriol 72:7959–7961

    CAS  Google Scholar 

  72. Zambryski P, Tempe J, Schell J (1989) Transfer and function of T-DNA genes from agrobacterium Ti and Ri plasmids in plants. Cell 56:193–201

    PubMed  CrossRef  CAS  Google Scholar 

  73. Zechiedrich EL, Cozzarelli NR (1995) Roles of topoisomerase IV and DNA gyrase in DNA unlinking during replication in Escherichia coli. Genes Dev 9:2859–2869

    PubMed  CrossRef  CAS  Google Scholar 

  74. Zhang R et al (2006) Diversity of telomere palindromic sequences and replication genes among Streptomyces linear plasmids. Appl Environ Microbiol 72:5728–5733

    PubMed  CrossRef  CAS  Google Scholar 

  75. Zhu L, Chou S-H, Xu J, Reid BR (1995) Structure of a single-cytidine hairpin loop formed by the DNA triplet GCA. Nat Struct Biol 2:1012–1017

    PubMed  CrossRef  CAS  Google Scholar 

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  1. Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Shih-Pai, 112, Taipei, Taiwan

    Carton W. Chen

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    Chen, C.W. (2007). Streptomyces Linear Plasmids: Replication and Telomeres. In: Meinhardt, F., Klassen, R. (eds) Microbial Linear Plasmids. Microbiology Monographs, vol 7. Springer, Berlin, Heidelberg. https://doi.org/10.1007/7171_2007_090

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