Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1985 Jan 25;13(2):557–572. doi: 10.1093/nar/13.2.557

Comparison of the nucleotide sequences of the vegetative replication origins of broad host range IncP plasmids R751 and RK2 reveals conserved features of probable functional importance.

C A Smith, C M Thomas
PMCID: PMC341014  PMID: 4000925

Abstract

An 864 bp EcoRI fragment carrying oriVR751, the vegetative replication origin of broad host range IncP plasmid R751, was cloned and sequenced. Only the trfA gene of the IncP plasmid RK2 was required in trans for the function of oriVR751. The sequence of oriVR751 showed 65% overall homology to that of oriVRK2 determined previously. Highly conserved regions of probable functional importance were apparent, including two sets of direct repeats postulated to be interaction sites for the trfA protein(s), a putative dnaA protein binding site and a downstream inverted repeat of unknown function.

Full text

PDF
557

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Beringer J. E. R factor transfer in Rhizobium leguminosarum. J Gen Microbiol. 1974 Sep;84(1):188–198. doi: 10.1099/00221287-84-1-188. [DOI] [PubMed] [Google Scholar]
  2. Beringer J. E. R factor transfer in Rhizobium leguminosarum. J Gen Microbiol. 1974 Sep;84(1):188–198. doi: 10.1099/00221287-84-1-188. [DOI] [PubMed] [Google Scholar]
  3. Bolivar F., Rodriguez R. L., Greene P. J., Betlach M. C., Heyneker H. L., Boyer H. W., Crosa J. H., Falkow S. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 1977;2(2):95–113. [PubMed] [Google Scholar]
  4. Burkardt H. J., Riess G., Pühler A. Relationship of group P1 plasmids revealed by heteroduplex experiments: RP1, RP4, R68 and RK2 are identical. J Gen Microbiol. 1979 Oct;114(2):341–348. doi: 10.1099/00221287-114-2-341. [DOI] [PubMed] [Google Scholar]
  5. Chang A. C., Cohen S. N. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol. 1978 Jun;134(3):1141–1156. doi: 10.1128/jb.134.3.1141-1156.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chesney R. H., Scott J. R. Suppression of a thermosensitive dnaA mutation of Escherichia coli by bacteriophage P1 and P7. Plasmid. 1978 Feb;1(2):145–163. doi: 10.1016/0147-619x(78)90035-5. [DOI] [PubMed] [Google Scholar]
  7. Cho J. J., Panopoulos N. J., Schroth M. N. Genetic transfer of Pseudomonas aeruginosa R factors to plant pathogenic Erwinia species. J Bacteriol. 1975 Apr;122(1):192–198. doi: 10.1128/jb.122.1.192-198.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cleary J. M., Smith D. W., Harding N. E., Zyskind J. W. Primary structure of the chromosomal origins (oriC) of Enterobacter aerogenes and Klebsiella pneumoniae: comparisons and evolutionary relationships. J Bacteriol. 1982 Jun;150(3):1467–1471. doi: 10.1128/jb.150.3.1467-1471.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Covey C., Richardson D., Carbon J. A method for the deletion of restriction sites in bacterial plasmid deoxyribonucleic acid. Mol Gen Genet. 1976 May 7;145(2):155–158. doi: 10.1007/BF00269587. [DOI] [PubMed] [Google Scholar]
  10. Datta N., Hedges R. W. Host ranges of R factors. J Gen Microbiol. 1972 May;70(3):453–460. doi: 10.1099/00221287-70-3-453. [DOI] [PubMed] [Google Scholar]
  11. Figurski D. H., Meyer R. J., Helinski D. R. Suppression of Co1E1 replication properties by the Inc P-1 plasmid RK2 in hybrid plasmids constructed in vitro. J Mol Biol. 1979 Sep 25;133(3):295–318. doi: 10.1016/0022-2836(79)90395-4. [DOI] [PubMed] [Google Scholar]
  12. Frey J., Chandler M., Caro L. The effects of an Escherichia coli dnaAts mutation on the replication of the plasmids colE1 pSC101, R100.1 and RTF-TC. Mol Gen Genet. 1979 Jul 13;174(2):117–126. doi: 10.1007/BF00268349. [DOI] [PubMed] [Google Scholar]
  13. Friedman A. M., Long S. R., Brown S. E., Buikema W. J., Ausubel F. M. Construction of a broad host range cosmid cloning vector and its use in the genetic analysis of Rhizobium mutants. Gene. 1982 Jun;18(3):289–296. doi: 10.1016/0378-1119(82)90167-6. [DOI] [PubMed] [Google Scholar]
  14. Fuller R. S., Kornberg A. Purified dnaA protein in initiation of replication at the Escherichia coli chromosomal origin of replication. Proc Natl Acad Sci U S A. 1983 Oct;80(19):5817–5821. doi: 10.1073/pnas.80.19.5817. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Germino J., Bastia D. Interaction of the plasmid R6K-encoded replication initiator protein with its binding sites on DNA. Cell. 1983 Aug;34(1):125–134. doi: 10.1016/0092-8674(83)90142-3. [DOI] [PubMed] [Google Scholar]
  16. Guiney D. G. Host range of conjugation and replication functions of the Escherichia coli sex plasmid Flac. Comparison with the broad host-range plasmid RK2. J Mol Biol. 1982 Dec 15;162(3):699–703. doi: 10.1016/0022-2836(82)90397-7. [DOI] [PubMed] [Google Scholar]
  17. Hawley D. K., McClure W. R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 1983 Apr 25;11(8):2237–2255. doi: 10.1093/nar/11.8.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Ingram L. C., Richmond M. H., Sykes R. B. Molecular characterization of the R factors implicated in the carbenicillin resistance of a sequence of Pseudomonas aeruginosa strains isolated from burns. Antimicrob Agents Chemother. 1973 Feb;3(2):279–288. doi: 10.1128/aac.3.2.279. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Jacoby G. A., Weiss R., Korfhagen T. R., Krishnapillai V., Jacob A. E., Hedges R. W. An explanation for the apparent host specificity of Pseudomonas plasmid R91 expression. J Bacteriol. 1978 Dec;136(3):1159–1164. doi: 10.1128/jb.136.3.1159-1164.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Jobanputra R. S., Datta N. Trimethoprim R factors in enterobacteria from clinical specimens. J Med Microbiol. 1974 May;7(2):169–177. doi: 10.1099/00222615-7-2-169. [DOI] [PubMed] [Google Scholar]
  21. Kahn M., Kolter R., Thomas C., Figurski D., Meyer R., Remaut E., Helinski D. R. Plasmid cloning vehicles derived from plasmids ColE1, F, R6K, and RK2. Methods Enzymol. 1979;68:268–280. doi: 10.1016/0076-6879(79)68019-9. [DOI] [PubMed] [Google Scholar]
  22. Kolter R., Helinski D. R. Construction of plasmid R6K derivatives in vitro: characterization of the R6K replication region. Plasmid. 1978 Sep;1(4):571–580. doi: 10.1016/0147-619x(78)90014-8. [DOI] [PubMed] [Google Scholar]
  23. Kolter R., Helinski D. R. Plasmid R6K DNA replication. II. Direct nucleotide sequence repeats are required for an active gamma-origin. J Mol Biol. 1982 Oct 15;161(1):45–56. doi: 10.1016/0022-2836(82)90277-7. [DOI] [PubMed] [Google Scholar]
  24. Lanka E., Lurz R., Fürste J. P. Molecular cloning and mapping of SphI restriction fragments of plasmid RP4. Plasmid. 1983 Nov;10(3):303–307. doi: 10.1016/0147-619x(83)90047-1. [DOI] [PubMed] [Google Scholar]
  25. Latreille J., Barlogie B., Dosik G., Johnston D. A., Drewinko B., Alexanian R. Cellular DNA content as a marker of human multiple myeloma. Blood. 1980 Mar;55(3):403–408. [PubMed] [Google Scholar]
  26. Lindahl G., Lindahl T. Initiation of DNA replication in Escherichia coli: RNase H-deficient mutants do not require the dnaA function. Mol Gen Genet. 1984;196(2):283–289. doi: 10.1007/BF00328061. [DOI] [PubMed] [Google Scholar]
  27. Matthew M., Hedges R. W. Analytical isoelectric focusing of R factor-determined beta-lactamases: correlation with plasmid compatibility. J Bacteriol. 1976 Feb;125(2):713–718. doi: 10.1128/jb.125.2.713-718.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  29. Meyer R. J., Helinski D. R. Unidirectional replication of the P-group plasmid RK2. Biochim Biophys Acta. 1977 Sep 6;478(1):109–113. doi: 10.1016/0005-2787(77)90249-0. [DOI] [PubMed] [Google Scholar]
  30. Meyer R. J., Shapiro J. A. Genetic organization of the broad-host-range IncP-1 plasmid R751. J Bacteriol. 1980 Sep;143(3):1362–1373. doi: 10.1128/jb.143.3.1362-1373.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Nishimura Y., Caro L., Berg C. M., Hirota Y. Chromosome replication in Escherichia coli. IV. Control of chromosome replication and cell division by an integrated episome. J Mol Biol. 1971 Feb 14;55(3):441–456. doi: 10.1016/0022-2836(71)90328-7. [DOI] [PubMed] [Google Scholar]
  32. Norrander J., Kempe T., Messing J. Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis. Gene. 1983 Dec;26(1):101–106. doi: 10.1016/0378-1119(83)90040-9. [DOI] [PubMed] [Google Scholar]
  33. Olsen R. H., Shipley P. Host range and properties of the Pseudomonas aeruginosa R factor R1822. J Bacteriol. 1973 Feb;113(2):772–780. doi: 10.1128/jb.113.2.772-780.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Selzer G., Som T., Itoh T., Tomizawa J. The origin of replication of plasmid p15A and comparative studies on the nucleotide sequences around the origin of related plasmids. Cell. 1983 Jan;32(1):119–129. doi: 10.1016/0092-8674(83)90502-0. [DOI] [PubMed] [Google Scholar]
  35. Shinger V., Thomas C. M. Transcription in the trfA region of broad host range plasmid RK2 is regulated by trfB and korB. Mol Gen Genet. 1984;195(3):523–529. doi: 10.1007/BF00341457. [DOI] [PubMed] [Google Scholar]
  36. Shingler V., Thomas C. M. Analysis of the trfA region of broad host-range plasmid RK2 by transposon mutagenesis and identification of polypeptide products. J Mol Biol. 1984 May 25;175(3):229–249. doi: 10.1016/0022-2836(84)90346-2. [DOI] [PubMed] [Google Scholar]
  37. Smith C. A., Thomas C. M. Deletion mapping of kil and kor functions in the trfA and trfB regions of broad host range plasmid RK2. Mol Gen Genet. 1983;190(2):245–254. doi: 10.1007/BF00330647. [DOI] [PubMed] [Google Scholar]
  38. Smith C. A., Thomas C. M. Molecular gentic analysis of the trfB and korB region of broad host range plasmid RK2. J Gen Microbiol. 1984 Jul;130(7):1651–1663. doi: 10.1099/00221287-130-7-1651. [DOI] [PubMed] [Google Scholar]
  39. Smith C. A., Thomas C. M. Nucleotide sequence of the trfA gene of broad host-range plasmid RK2. J Mol Biol. 1984 May 25;175(3):251–262. doi: 10.1016/0022-2836(84)90347-4. [DOI] [PubMed] [Google Scholar]
  40. Stalker D. M., Thomas C. M., Helinski D. R. Nucleotide sequence of the region of the origin of replication of the broad host range plasmid RK2. Mol Gen Genet. 1981;181(1):8–12. doi: 10.1007/BF00338997. [DOI] [PubMed] [Google Scholar]
  41. Stokes H. W., Moore R. J., Krishnapillai V. Complementation analysis in Pseudomonas aeruginosa of the transfer genes of the wide host range R plasmid R18. Plasmid. 1981 Mar;5(2):202–212. doi: 10.1016/0147-619x(81)90021-4. [DOI] [PubMed] [Google Scholar]
  42. Thomas C. M. Complementation analysis of replication and maintenance functions of broad host range plasmids RK2 and RP1. Plasmid. 1981 May;5(3):277–291. doi: 10.1016/0147-619x(81)90005-6. [DOI] [PubMed] [Google Scholar]
  43. Thomas C. M., Cross M. A., Hussain A. A., Smith C. A. Analysis of copy number control elements in the region of the vegetative replication origin of the broad host range plasmid RK2. EMBO J. 1984 Jan;3(1):57–63. doi: 10.1002/j.1460-2075.1984.tb01761.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Thomas C. M., Hussain A. A. The korB gene of broad host range plasmid RK2 is a major copy number control element which may act together with trfB by limiting trfA expression. EMBO J. 1984 Jul;3(7):1513–1519. doi: 10.1002/j.1460-2075.1984.tb02004.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Thomas C. M., Meyer R., Helinski D. R. Regions of broad-host-range plasmid RK2 which are essential for replication and maintenance. J Bacteriol. 1980 Jan;141(1):213–222. doi: 10.1128/jb.141.1.213-222.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Thomas C. M., Stalker D. M., Helinski D. R. Replication and incompatibility properties of segments of the origin region of replication of the broad host range plasmid RK2. Mol Gen Genet. 1981;181(1):1–7. doi: 10.1007/BF00338996. [DOI] [PubMed] [Google Scholar]
  47. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  48. Villarroel R., Hedges R. W., Maenhaut R., Leemans J., Engler G., Van Montagu M., Schell J. Heteroduplex analysis of P-plasmid evolution: the role of insertion and deletion of transposable elements. Mol Gen Genet. 1983;189(3):390–399. doi: 10.1007/BF00325900. [DOI] [PubMed] [Google Scholar]
  49. Ward J. M., Grinsted J. Analysis of the Inc P-1 group plasmids R906 and R751 and their relationship to RP1. Plasmid. 1982 Nov;8(3):244–252. doi: 10.1016/0147-619x(82)90062-2. [DOI] [PubMed] [Google Scholar]
  50. Watson J. M., Holloway B. W. Linkage map of Pseudomonas aeruginosa PAT. J Bacteriol. 1978 Nov;136(2):507–521. doi: 10.1128/jb.136.2.507-521.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Windass J. D., Worsey M. J., Pioli E. M., Pioli D., Barth P. T., Atherton K. T., Dart E. C., Byrom D., Powell K., Senior P. J. Improved conversion of methanol to single-cell protein by Methylophilus methylotrophus. Nature. 1980 Oct 2;287(5781):396–401. doi: 10.1038/287396a0. [DOI] [PubMed] [Google Scholar]
  52. Yakobson E., Guiney G. Homology in the transfer origins of broad host range IncP plasmids: definition of two subgroups of P plasmids. Mol Gen Genet. 1983;192(3):436–438. doi: 10.1007/BF00392187. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES