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Volume 147, Issue 2

A novel rolling-circle-replicating plasmid from P8: molecular characterization and use as vector

The EMBL and GenBank accession number for the nucleotide sequence of pPP8–1 is AJ289784.

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Abstract

In P8, three cryptic circular plasmids were detected, i.e. pPP8-1 (25 kbp), pPP8-2 (42 kbp) and pPP8-3 (100 kbp). Cloning and complete sequencing of pPP8-1 revealed a 2534 bp element harbouring four open reading frames (ORFs A, B, C and D). No function could be attributed to the latter three ORFs, whereas the predicted ORF A gene product is homologous to replication proteins known from small multicopy plasmids of Gram-positive bacteria and single-stranded (ss) phages, genetic elements replicating via a rolling circle (RC) mechanism involving characteristic ssDNA intermediates. Consistently, a double-strand origin of replication, highly conserved in rolling-circle-replicating (RCR) elements, was identified in pPP8-1, along with a putative single-strand origin. Beyond this, ss replication intermediates were confirmed by Southern analysis and mungbean-nuclease digestion. This being the first element of this type known in pseudomonads, a kanamycin-resistance gene was ligated into pPP8-1 and the resulting vector was successfully used for the transformation of both and

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Keyword(s): cloning , cryptic plasmid , ds, double-stranded; , DSO, double-strand origin; , extrachromosomal element , IR, imperfect repeat; , KmR, kanamycin resistance; , pP81–1 , RC, rolling circle; , RCR, rolling circle replicating; , repA , S/D, Shine–Dalgarno; , ss, single-stranded; , SSB, single-strand DNA-binding protein; and SSO, single-strand origin.
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2001-02-01
2024-05-02
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References

  1. Alonso J. C., Tailor R. H. 1987; Initiation of plasmid pC194 replication and its control in Bacillus subtilis. Mol Gen Genet 210:476–484 [CrossRef]
     [Google Scholar]
  2. Altenschmidt U., Bokranz M., Fuchs G. 1992; Novel aerobic 2-aminobenzoate metabolism. Nucleotide sequence of the plasmid carrying the gene for the flavoprotein 2-aminobenzoyl-CoA monooxygenase/reductase in denitrifying Pseudomonas sp. Eur J Biochem 207:715–722 [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. Baas P. D., Jansz H. S. 1988; Single stranded DNA phage origins. Curr Top Microbiol Immunol 136:31–70
     [Google Scholar]
  5. Barany F., Boeke J. D., Tomasz A. 1982; Staphylococcal plasmids that replicate and express erythromycin resistance in both Staphylococcus pneumoniae and Escherichia coli. Proc Natl Acad Sci USA 79:2991–2995 [CrossRef]
     [Google Scholar]
  6. Bettmann H., Rehm H. J. 1984; Degradation of phenol by polymer entrapped microorganisms. Appl Microbiol Biotechnol 22:389–393
     [Google Scholar]
  7. Birnboim H. C., Doly J. 1979; A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 7:1513–1522 [CrossRef]
     [Google Scholar]
  8. Boe L., Gros M. F., te Riele H., Ehrlich S. D., Gruss A. 1989; Replication origins of single-stranded-DNA plasmid pUB110. J Bacteriol 171:3366–3372
     [Google Scholar]
  9. Boronin A. M. 1992; Diversity and relationship of Pseudomonas plasmids. In Pseudomonas: Molecular Biology and Biotechnology pp. 329–340Edited by Galli E., Silver S., Witholt B. Washington, DC: American Society for Microbiology;
     [Google Scholar]
  10. Carne A., Hill D. F., Stockwell P. A., Hughes G., Petersen G. B. 1991; The putative single-stranded DNA binding protein of the filamentous bacteriophage, IF1. Amino acid sequence of the protein and structure of the gene. Proc R Soc Lond B Biol Sci 245:23–30 [CrossRef]
     [Google Scholar]
  11. Goze A., Ehrlich S. D. 1980; Replication of plasmids from Staphylococcus aureus in Escherichia coli. Proc Natl Acad Sci USA 77:733–737
     [Google Scholar]
  12. Gruss A., Ross H., Novick R. 1987; Functional analysis of a palindromic sequence required for normal replication of several staphylococcal plasmids. Proc Natl Acad Sci USA 84:2165–2169 [CrossRef]
     [Google Scholar]
  13. Hill D. F., Short N. J., Perham R. N., Petersen G. B. 1991; DNA sequence of the filamentous bacteriophage Pf1. J Mol Biol 218:349–364 [CrossRef]
     [Google Scholar]
  14. Holtwick R., Meinhardt F., Keweloh H. 1997; Cis–trans isomerisation of fatty acids: cloning and sequencing of the cti gene from Pseudomonas putida P8. Appl Environ Microbiol 63:4292–4297
     [Google Scholar]
  15. Holtwick R., Keweloh H., Meinhardt F. 1999; Cis/trans isomerase of unsaturated fatty acids of Pseudomonas putida P8: evidence for a heme protein of the cytochrome c type. Appl Environ Microbiol 65:2644–2649
     [Google Scholar]
  16. Horinouchi S., Weisblum B. 1982; Nucleotide sequence and functional map of plasmid pC194, a plasmid that specifies inducible chloramphenicol resistance. J Bacteriol 150:815–825
     [Google Scholar]
  17. Josson K., Soetaert P., Michiels F., Joos H., Mahillon J. 1990; Lactobacillus hilgardii plasmid pLAB1000 consists of two functional cassettes commonly found in other gram positive organisms. J Bacteriol 172:3089–3099
     [Google Scholar]
  18. Khan S. A. 1997; Rolling-circle replication of bacterial plasmids. Microbiol Mol Biol Rev 61:442–455
     [Google Scholar]
  19. Kramer M. G., Espinosa M., Misra T. K., Khan S. A. 1999; Characterization of a single-strand origin, ssoU, required for broad host range replication of rolling-circle plasmids. Mol Microbiol 33:466–475 [CrossRef]
     [Google Scholar]
  20. de Lorenzo V., Herrero M., Jacubzik U., Timmis K. N. 1990; Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria. J Bacteriol 172:6568–6572
     [Google Scholar]
  21. Luiten R. G., Putterman D. G., Schoenmakers J. G., Kronigs R. N., Day L. A. 1985; Nucleotide sequence of the genome of Pf3 and IncP-1 plasmid specific filamentous bacteriophage of Pseudomonas aeruginosa. J Virol 56:268–276
     [Google Scholar]
  22. Madsen S. M., Andrup L., Boe L. 1993; Fine mapping and DNA sequence of replication functions of Bacillus thuringiensis plasmid pTX14-3. Plasmid 30:119–130 [CrossRef]
     [Google Scholar]
  23. Meijer W. J., Wisman G. B., Terpstra P., Thorsted P. B., Thomas C. M., Holsappel S., Venema G., Bron S. 1998; Rolling-circle plasmids from Bacillus subtilis: complete nucleotide sequences and analyses of genes of pTA1015, pTA1040, pTA1050 and pTA1060, and comparisons with related plasmids from gram-positive bacteria. FEMS Microbiol Rev 21:337–368 [CrossRef]
     [Google Scholar]
  24. Noriot-Gros M. F., Bidnenko V., Ehrlich S. D. 1994; Active site of the replication protein of the rolling circle plasmid pC194. EMBO J 13:4412–4420
     [Google Scholar]
  25. Novick R. P. 1989; Staphylococcal plasmids and their replication. Annu Rev Microbiol 43:537–565 [CrossRef]
     [Google Scholar]
  26. te Riele H., Michel B., Ehrlich S. D. 1986; Single stranded plasmid DNA in Bacillus subtilis and Staphylococcus aureus. Proc Natl Acad Sci USA 83:2541–2545 [CrossRef]
     [Google Scholar]
  27. Rodrigues R. L., Tait R. C. 1983 Recombinant DNA Techniques: an Introduction Stanford: Addison-Wesley;
     [Google Scholar]
  28. Ronald S., Farinha M. A., Allan B. J., Kropinski A. M. 1992; Cloning and physical mapping of transcriptional regulatory (sigma) factors from Pseudomonas aeruginosa. In Pseudomonas: Molecular Biology and Biotechnology pp. 249–257Edited by Galli E., Silver S., Witholt B. Washington, DC: American Society for Microbiology;
     [Google Scholar]
  29. 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]
  30. del Solar G., Diaz R., Espinosa M. 1987a; Replication of the streptococcal plasmid pMV158 and derivatives in cell-free extracts of Escherichia coli. Mol Gen Genet 206:428–435 [CrossRef]
     [Google Scholar]
  31. del Solar G., Puyet A., Espinosa M. 1987b; Initiation signals for the conversion of single stranded to double stranded DNA forms in the streptococcal plasmid pLS1. Nucleic Acids Res 15:5561–5580 [CrossRef]
     [Google Scholar]
  32. del Solar G., Moscoso M., Espinosa M. 1993; Rolling circle-replicating plasmids from Gram-positive and Gram-negative bacteria: a wall falls. Mol Microbiol 8:789–796 [CrossRef]
     [Google Scholar]
  33. del Solar G., Giraldo R., Ruiz-Echevarria M. J., Espinosa M., Diaz-Orejas R. 1998; Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev 62:434–464
     [Google Scholar]
  34. Stassen A. P., Schonmakers E. F., Yu M., Schoenmakers J. G., Konings R. N. H. 1992; Nucleotide sequence of the genome of the filamentous bacteriophage I2-2: module evolution of the filamentous phage genome. J Mol Evol 34:141–152
     [Google Scholar]
  35. Taghavi S., van der Lelie D., Mergeay M. 1994; Electroporation of Alcaligenes eutrophus with (mega) plasmids and genomic DNA fragments. Appl Environ Microbiol 60:3585–3591
     [Google Scholar]
  36. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [CrossRef]
     [Google Scholar]
  37. Tinoco I. Jr, Borer P. N., Dengler B., Levine M. D., Uhlenbeck O. C., Crothers D. M., Gralla J. 1973; Improved estimation of secondary structure in ribonucleic acid. Nature New Biol 246:40–41 [CrossRef]
     [Google Scholar]
  38. Yamagata A., Kato J., Hirota R., Kuroda A., Ikeda T., Takiguchi N., Ohtake H. 1999; Isolation and characterization of two cryptic plasmids in the ammonia-oxidizing bacterium Nitrosomonas sp. strain ENI-11. J Bacteriol 181:3375–3381
     [Google Scholar]
  39. Yanisch-Perron C., Vieira J., Messing J. 1985; Improved M13 phage cloning vectors and host strains: nucleotide sequence of the M13mp18 and pUC19 vectors. Gene 33:103–119 [CrossRef]
     [Google Scholar]
  40. Yasukawa H., Hase T., Sakai A., Masamune Y. 1991; Rolling-circle replication of the plasmid pKYM isolated from a gram-negative bacterium. Proc Natl Acad Sci USA 88:10282–10286 [CrossRef]
     [Google Scholar]
  41. Wagner E. G., Simons R. W. 1994; Antisense RNA control in bacteria, phages and plasmids. Annu Rev Microbiol 48:713–742 [CrossRef]
     [Google Scholar]
  42. Zache G., Rehm H. J. 1989; Degradation of phenol by a coimmobilized entrapped mixed culture. Appl Microbiol Biotechnol 30:426–432 [CrossRef]
     [Google Scholar]
  43. Zhang N., Brooker J. D. 1993; Characterization, sequence, and replication of a small cryptic plasmid from Selenomonas ruminantium subspecies lactilytica. Plasmid 29:125–134 [CrossRef]
     [Google Scholar]
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A novel rolling-circle-replicating plasmid from Pseudomonas putida P8: molecular characterization and use as vectorThe EMBL and GenBank accession number for the nucleotide sequence of pPP8–1 is AJ289784.
Microbiology 147, 337 (2001); https://doi.org/10.1099/00221287-147-2-337
/content/journal/micro/10.1099/00221287-147-2-337
/content/journal/micro/10.1099/00221287-147-2-337
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