Skip to main content
NCBI home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1995 Feb;177(4):973–980. doi: 10.1128/jb.177.4.973-980.1995

Discrete amplifiable regions (amplicons) in the symbiotic plasmid of Rhizobium etli CFN42.

D Romero 1, J Martínez-Salazar 1, L Girard 1, S Brom 1, G Dávilla 1, R Palacios 1, M Flores 1, C Rodríguez 1
PMCID: PMC176691  PMID: 7860608

Abstract

Frequent tandem amplification of defined regions of the genome, called amplicons, is a common characteristic in the genomes of some Rhizobium species, such as Rhizobium etli. In order to map these zones in a model Rhizobium replicon, we undertook an analysis of the plasticity patterns fostered by amplicons in the pSym (390 kb) of R. etli CFN42. Data presented in this article indicate the presence of four amplicons in pSym, used for the generation of tandem amplifications and deletions. The amplicons are large, ranging from 90 to 175 kb, and they are overlapping. Each amplicon is usually flanked by specific reiterated sequences. Formation of amplifications and deletions requires an active recA gene. All the amplicons detected are concentrated in a zone of roughly one-third of pSym, covering most of the symbiotic genes detected in this plasmid. No amplicons were detected in the remaining two-thirds of pSym. These data support the idea that most of the known symbiotic genes in this plasmid are located in a genomic region that is prone to the formation of frequent tandem amplification.

Full Text

The Full Text of this article is available as a PDF (303.9 KB).

Selected References

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

  1. Anderson R. P., Roth J. R. Tandem genetic duplications in phage and bacteria. Annu Rev Microbiol. 1977;31:473–505. doi: 10.1146/annurev.mi.31.100177.002353. [DOI] [PubMed] [Google Scholar]
  2. Austin S., Ziese M., Sternberg N. A novel role for site-specific recombination in maintenance of bacterial replicons. Cell. 1981 Sep;25(3):729–736. doi: 10.1016/0092-8674(81)90180-x. [DOI] [PubMed] [Google Scholar]
  3. Boyer H. W., Roulland-Dussoix D. A complementation analysis of the restriction and modification of DNA in Escherichia coli. J Mol Biol. 1969 May 14;41(3):459–472. doi: 10.1016/0022-2836(69)90288-5. [DOI] [PubMed] [Google Scholar]
  4. Brom S., García de los Santos A., Stepkowsky T., Flores M., Dávila G., Romero D., Palacios R. Different plasmids of Rhizobium leguminosarum bv. phaseoli are required for optimal symbiotic performance. J Bacteriol. 1992 Aug;174(16):5183–5189. doi: 10.1128/jb.174.16.5183-5189.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Brom S., García de los Santos A., de Lourdes Girard M., Dávila G., Palacios R., Romero D. High-frequency rearrangements in Rhizobium leguminosarum bv. phaseoli plasmids. J Bacteriol. 1991 Feb;173(3):1344–1346. doi: 10.1128/jb.173.3.1344-1346.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Charles T. C., Finan T. M. Analysis of a 1600-kilobase Rhizobium meliloti megaplasmid using defined deletions generated in vivo. Genetics. 1991 Jan;127(1):5–20. doi: 10.1093/genetics/127.1.5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Corn P. G., Anders J., Takala A. K., Käyhty H., Hoiseth S. K. Genes involved in Haemophilus influenzae type b capsule expression are frequently amplified. J Infect Dis. 1993 Feb;167(2):356–364. doi: 10.1093/infdis/167.2.356. [DOI] [PubMed] [Google Scholar]
  8. Djordjevic M. A., Zurkowski W., Rolfe B. G. Plasmids and stability of symbiotic properties of Rhizobium trifolii. J Bacteriol. 1982 Aug;151(2):560–568. doi: 10.1128/jb.151.2.560-568.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Eckhardt T. A rapid method for the identification of plasmid desoxyribonucleic acid in bacteria. Plasmid. 1978 Sep;1(4):584–588. doi: 10.1016/0147-619x(78)90016-1. [DOI] [PubMed] [Google Scholar]
  10. Figurski D. H., Helinski D. R. Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1648–1652. doi: 10.1073/pnas.76.4.1648. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Fisher R. F., Long S. R. Rhizobium--plant signal exchange. Nature. 1992 Jun 25;357(6380):655–660. doi: 10.1038/357655a0. [DOI] [PubMed] [Google Scholar]
  12. Flores M., Brom S., Stepkowski T., Girard M. L., Dávila G., Romero D., Palacios R. Gene amplification in Rhizobium: identification and in vivo cloning of discrete amplifiable DNA regions (amplicons) from Rhizobium leguminosarum biovar phaseoli. Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):4932–4936. doi: 10.1073/pnas.90.11.4932. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Flores M., González V., Brom S., Martínez E., Piñero D., Romero D., Dávila G., Palacios R. Reiterated DNA sequences in Rhizobium and Agrobacterium spp. J Bacteriol. 1987 Dec;169(12):5782–5788. doi: 10.1128/jb.169.12.5782-5788.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Flores M., González V., Pardo M. A., Leija A., Martínez E., Romero D., Piñero D., Dávila G., Palacios R. Genomic instability in Rhizobium phaseoli. J Bacteriol. 1988 Mar;170(3):1191–1196. doi: 10.1128/jb.170.3.1191-1196.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Funnell B. E. Mini-P1 plasmid partitioning: excess ParB protein destabilizes plasmids containing the centromere parS. J Bacteriol. 1988 Feb;170(2):954–960. doi: 10.1128/jb.170.2.954-960.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Gay P., Le Coq D., Steinmetz M., Berkelman T., Kado C. I. Positive selection procedure for entrapment of insertion sequence elements in gram-negative bacteria. J Bacteriol. 1985 Nov;164(2):918–921. doi: 10.1128/jb.164.2.918-921.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Girard M. L., Flores M., Brom S., Romero D., Palacios R., Dávila G. Structural complexity of the symbiotic plasmid of Rhizobium leguminosarum bv. phaseoli. J Bacteriol. 1991 Apr;173(8):2411–2419. doi: 10.1128/jb.173.8.2411-2419.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Goldberg I., Mekalanos J. J. Effect of a recA mutation on cholera toxin gene amplification and deletion events. J Bacteriol. 1986 Mar;165(3):723–731. doi: 10.1128/jb.165.3.723-731.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Hahn M., Hennecke H. Mapping of a Bradyrhizobium japonicum DNA Region Carrying Genes for Symbiosis and an Asymmetric Accumulation of Reiterated Sequences. Appl Environ Microbiol. 1987 Sep;53(9):2247–2252. doi: 10.1128/aem.53.9.2247-2252.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Hynes M. F., McGregor N. F. Two plasmids other than the nodulation plasmid are necessary for formation of nitrogen-fixing nodules by Rhizobium leguminosarum. Mol Microbiol. 1990 Apr;4(4):567–574. doi: 10.1111/j.1365-2958.1990.tb00625.x. [DOI] [PubMed] [Google Scholar]
  21. Kaluza K., Hahn M., Hennecke H. Repeated sequences similar to insertion elements clustered around the nif region of the Rhizobium japonicum genome. J Bacteriol. 1985 May;162(2):535–542. doi: 10.1128/jb.162.2.535-542.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Krawiec S., Riley M. Organization of the bacterial chromosome. Microbiol Rev. 1990 Dec;54(4):502–539. doi: 10.1128/mr.54.4.502-539.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Kündig C., Hennecke H., Göttfert M. Correlated physical and genetic map of the Bradyrhizobium japonicum 110 genome. J Bacteriol. 1993 Feb;175(3):613–622. doi: 10.1128/jb.175.3.613-622.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lin R. J., Capage M., Hill C. W. A repetitive DNA sequence, rhs, responsible for duplications within the Escherichia coli K-12 chromosome. J Mol Biol. 1984 Jul 25;177(1):1–18. doi: 10.1016/0022-2836(84)90054-8. [DOI] [PubMed] [Google Scholar]
  25. Long S. R. Rhizobium genetics. Annu Rev Genet. 1989;23:483–506. doi: 10.1146/annurev.ge.23.120189.002411. [DOI] [PubMed] [Google Scholar]
  26. Martínez-Salazar J. M., Romero D., Girard M. L., Dávila G. Molecular cloning and characterization of the recA gene of Rhizobium phaseoli and construction of recA mutants. J Bacteriol. 1991 May;173(10):3035–3040. doi: 10.1128/jb.173.10.3035-3040.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Masterson R. V., Atherly A. G. The presence of repeated DNA sequences and a partial restriction map of the pSym of Rhizobium fredii USDA193. Plasmid. 1986 Jul;16(1):37–44. doi: 10.1016/0147-619x(86)90077-6. [DOI] [PubMed] [Google Scholar]
  28. Mekalanos J. J. Duplication and amplification of toxin genes in Vibrio cholerae. Cell. 1983 Nov;35(1):253–263. doi: 10.1016/0092-8674(83)90228-3. [DOI] [PubMed] [Google Scholar]
  29. Noel K. D., Sanchez A., Fernandez L., Leemans J., Cevallos M. A. Rhizobium phaseoli symbiotic mutants with transposon Tn5 insertions. J Bacteriol. 1984 Apr;158(1):148–155. doi: 10.1128/jb.158.1.148-155.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Peterson B. C., Rownd R. H. Drug resistance gene amplification of plasmid NR1 derivatives with various amounts of resistance determinant DNA. J Bacteriol. 1985 Mar;161(3):1042–1048. doi: 10.1128/jb.161.3.1042-1048.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Petes T. D., Hill C. W. Recombination between repeated genes in microorganisms. Annu Rev Genet. 1988;22:147–168. doi: 10.1146/annurev.ge.22.120188.001051. [DOI] [PubMed] [Google Scholar]
  32. Quinto C., De La Vega H., Flores M., Leemans J., Cevallos M. A., Pardo M. A., Azpiroz R., De Lourdes Girard M., Calva E., Palacios R. Nitrogenase reductase: A functional multigene family in Rhizobium phaseoli. Proc Natl Acad Sci U S A. 1985 Feb;82(4):1170–1174. doi: 10.1073/pnas.82.4.1170. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Rigby P. W., Dieckmann M., Rhodes C., Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol. 1977 Jun 15;113(1):237–251. doi: 10.1016/0022-2836(77)90052-3. [DOI] [PubMed] [Google Scholar]
  34. Romero D., Brom S., Martínez-Salazar J., Girard M. L., Palacios R., Dávila G. Amplification and deletion of a nod-nif region in the symbiotic plasmid of Rhizobium phaseoli. J Bacteriol. 1991 Apr;173(8):2435–2441. doi: 10.1128/jb.173.8.2435-2441.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Segovia L., Young J. P., Martínez-Romero E. Reclassification of American Rhizobium leguminosarum biovar phaseoli type I strains as Rhizobium etli sp. nov. Int J Syst Bacteriol. 1993 Apr;43(2):374–377. doi: 10.1099/00207713-43-2-374. [DOI] [PubMed] [Google Scholar]
  36. Shyamala V., Schneider E., Ames G. F. Tandem chromosomal duplications: role of REP sequences in the recombination event at the join-point. EMBO J. 1990 Mar;9(3):939–946. doi: 10.1002/j.1460-2075.1990.tb08192.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Soberón-Chávez G., Nájera R., Olivera H., Segovia L. Genetic rearrangements of a Rhizobium phaseoli symbiotic plasmid. J Bacteriol. 1986 Aug;167(2):487–491. doi: 10.1128/jb.167.2.487-491.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Sobral B. W., Honeycutt R. J., Atherly A. G., McClelland M. Electrophoretic separation of the three Rhizobium meliloti replicons. J Bacteriol. 1991 Aug;173(16):5173–5180. doi: 10.1128/jb.173.16.5173-5180.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Sonti R. V., Roth J. R. Role of gene duplications in the adaptation of Salmonella typhimurium to growth on limiting carbon sources. Genetics. 1989 Sep;123(1):19–28. doi: 10.1093/genetics/123.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Wiebauer K., Schraml S., Shales S. W., Schmitt R. Tetracycline resistance transposon Tn1721: recA-dependent gene amplification and expression of tetracycline resistance. J Bacteriol. 1981 Sep;147(3):851–859. doi: 10.1128/jb.147.3.851-859.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Williams D. R., Thomas C. M. Active partitioning of bacterial plasmids. J Gen Microbiol. 1992 Jan;138(1):1–16. doi: 10.1099/00221287-138-1-1. [DOI] [PubMed] [Google Scholar]
  42. Zurkowski W. Molecular mechanism for loss of nodulation properties of Rhizobium trifolii. J Bacteriol. 1982 Jun;150(3):999–1007. doi: 10.1128/jb.150.3.999-1007.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES