Skip to main content
NCBI home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1995 Oct;177(19):5485–5494. doi: 10.1128/jb.177.19.5485-5494.1995

Identification of Rhizobium-specific intergenic mosaic elements within an essential two-component regulatory system of Rhizobium species.

M Osterås 1, J Stanley 1, T M Finan 1
PMCID: PMC177356  PMID: 7559334

Abstract

Analysis of the DNA regions upstream of the phosphoenolpyruvate carboxykinase gene (pckA) in Rhizobium meliloti and Rhizobium sp. strain NGR234 identified an open reading frame which was highly homologous to the Agrobacterium tumefaciens chromosomal virulence gene product ChvI. A second gene product, 500 bp downstream of the chvI-like gene in R. meliloti, was homologous to the A. tumefaciens ChvG protein. The homology between the R. meliloti and A. tumefaciens genes was confirmed, because the R. meliloti chvI and chvG genes complemented A. tumefaciens chvI and chvG mutants for growth on complex media. We were unable to construct chvI or chvG insertion mutants of R. meliloti, whereas mutants carrying insertions outside of these genes were readily obtained. A 108-bp repeat element characterized by two large palindromes was identified in the chvI and chvG intergenic regions of both Rhizobium species. This element was duplicated in Rhizobium sp. strain NGR234. Another structurally similar element with a size of 109 bp was present in R. meliloti but not in Rhizobium sp. strain NGR234. These elements were named rhizobium-specific intergenic mosaic elements (RIMEs), because their distribution seems to be limited to members of the family Rhizobiaceae. A homology search in GenBank detected six more copies of the first element (RIME1), all in Rhizobium species, and three extra copies of the second element (RIME2), only in R. meliloti. Southern blot analysis with a probe specific to RIME1 showed the presence of several copies of the element in the genome of R. meliloti, Rhizobium sp. strain NGR234, Rhizobium leguminosarum, and Agrobacterium rhizogenes, but none was present in A. tumefaciens and Bradyrhizobium japonicum.

Full Text

The Full Text of this article is available as a PDF (438.3 KB).

Selected References

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

  1. Albright L. M., Ronson C. W., Nixon B. T., Ausubel F. M. Identification of a gene linked to Rhizobium meliloti ntrA whose product is homologous to a family to ATP-binding proteins. J Bacteriol. 1989 Apr;171(4):1932–1941. doi: 10.1128/jb.171.4.1932-1941.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  3. Archdeacon J., Talty J., Boesten B., Danchin A., O'Gara F. Cloning of the second adenylate cyclase gene (cya2) from Rhizobium meliloti F34: sequence similarity to eukaryotic cyclases. FEMS Microbiol Lett. 1995 May 1;128(2):177–184. doi: 10.1111/j.1574-6968.1995.tb07519.x. [DOI] [PubMed] [Google Scholar]
  4. Bachellier S., Saurin W., Perrin D., Hofnung M., Gilson E. Structural and functional diversity among bacterial interspersed mosaic elements (BIMEs). Mol Microbiol. 1994 Apr;12(1):61–70. doi: 10.1111/j.1365-2958.1994.tb00995.x. [DOI] [PubMed] [Google Scholar]
  5. Brown C. M., Stockwell P. A., Dalphin M. E., Tate W. P. The translational termination signal database (TransTerm) now also includes initiation contexts. Nucleic Acids Res. 1994 Sep;22(17):3620–3624. doi: 10.1093/nar/22.17.3620. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Charles T. C., Nester E. W. A chromosomally encoded two-component sensory transduction system is required for virulence of Agrobacterium tumefaciens. J Bacteriol. 1993 Oct;175(20):6614–6625. doi: 10.1128/jb.175.20.6614-6625.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Colonna-Romano S., Riccio A., Guida M., Defez R., Lamberti A., Iaccarino M., Arnold W., Priefer U., Pühler A. Tight linkage of glnA and a putative regulatory gene in Rhizobium leguminosarum. Nucleic Acids Res. 1987 Mar 11;15(5):1951–1964. doi: 10.1093/nar/15.5.1951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Correia F. F., Inouye S., Inouye M. A 26-base-pair repetitive sequence specific for Neisseria gonorrhoeae and Neisseria meningitidis genomic DNA. J Bacteriol. 1986 Sep;167(3):1009–1015. doi: 10.1128/jb.167.3.1009-1015.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dimri G. P., Rudd K. E., Morgan M. K., Bayat H., Ames G. F. Physical mapping of repetitive extragenic palindromic sequences in Escherichia coli and phylogenetic distribution among Escherichia coli strains and other enteric bacteria. J Bacteriol. 1992 Jul;174(14):4583–4593. doi: 10.1128/jb.174.14.4583-4593.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Ditta G., Stanfield S., Corbin D., Helinski D. R. Broad host range DNA cloning system for gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc Natl Acad Sci U S A. 1980 Dec;77(12):7347–7351. doi: 10.1073/pnas.77.12.7347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Eardly B. D., Materon L. A., Smith N. H., Johnson D. A., Rumbaugh M. D., Selander R. K. Genetic structure of natural populations of the nitrogen-fixing bacterium Rhizobium meliloti. Appl Environ Microbiol. 1990 Jan;56(1):187–194. doi: 10.1128/aem.56.1.187-194.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Finan T. M., Hartweig E., LeMieux K., Bergman K., Walker G. C., Signer E. R. General transduction in Rhizobium meliloti. J Bacteriol. 1984 Jul;159(1):120–124. doi: 10.1128/jb.159.1.120-124.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Finan T. M., Kunkel B., De Vos G. F., Signer E. R. Second symbiotic megaplasmid in Rhizobium meliloti carrying exopolysaccharide and thiamine synthesis genes. J Bacteriol. 1986 Jul;167(1):66–72. doi: 10.1128/jb.167.1.66-72.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Finan T. M., Oresnik I., Bottacin A. Mutants of Rhizobium meliloti defective in succinate metabolism. J Bacteriol. 1988 Aug;170(8):3396–3403. doi: 10.1128/jb.170.8.3396-3403.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Finan T. M., Wood J. M., Jordan D. C. Succinate transport in Rhizobium leguminosarum. J Bacteriol. 1981 Oct;148(1):193–202. doi: 10.1128/jb.148.1.193-202.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Forrai T., Vincze E., Bánfalvi Z., Kiss G. B., Randhawa G. S., Kondorosi A. Localization of symbiotic mutations in Rhizobium meliloti. J Bacteriol. 1983 Feb;153(2):635–643. doi: 10.1128/jb.153.2.635-643.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Frey J., Krisch H. M. Omega mutagenesis in gram-negative bacteria: a selectable interposon which is strongly polar in a wide range of bacterial species. Gene. 1985;36(1-2):143–150. doi: 10.1016/0378-1119(85)90078-2. [DOI] [PubMed] [Google Scholar]
  18. 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]
  19. Fujitani S., Komano T., Inouye S. A unique repetitive DNA sequence in the Myxococcus xanthus genome. J Bacteriol. 1991 Mar;173(6):2125–2127. doi: 10.1128/jb.173.6.2125-2127.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Gilson E., Clément J. M., Brutlag D., Hofnung M. A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. EMBO J. 1984 Jun;3(6):1417–1421. doi: 10.1002/j.1460-2075.1984.tb01986.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Gilson E., Perrin D., Hofnung M. DNA polymerase I and a protein complex bind specifically to E. coli palindromic unit highly repetitive DNA: implications for bacterial chromosome organization. Nucleic Acids Res. 1990 Jul 11;18(13):3941–3952. doi: 10.1093/nar/18.13.3941. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Gilson E., Saurin W., Perrin D., Bachellier S., Hofnung M. Palindromic units are part of a new bacterial interspersed mosaic element (BIME). Nucleic Acids Res. 1991 Apr 11;19(7):1375–1383. doi: 10.1093/nar/19.7.1375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Higgins C. F., McLaren R. S., Newbury S. F. Repetitive extragenic palindromic sequences, mRNA stability and gene expression: evolution by gene conversion? A review. Gene. 1988 Dec 10;72(1-2):3–14. doi: 10.1016/0378-1119(88)90122-9. [DOI] [PubMed] [Google Scholar]
  24. Higgins D. G., Bleasby A. J., Fuchs R. CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci. 1992 Apr;8(2):189–191. doi: 10.1093/bioinformatics/8.2.189. [DOI] [PubMed] [Google Scholar]
  25. Hulton C. S., Higgins C. F., Sharp P. M. ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol Microbiol. 1991 Apr;5(4):825–834. doi: 10.1111/j.1365-2958.1991.tb00755.x. [DOI] [PubMed] [Google Scholar]
  26. Jacoby G. A., Jacob A. E., Hedges R. W. Recombination between plasmids of incompatibility groups P-1 and P-2. J Bacteriol. 1976 Sep;127(3):1278–1285. doi: 10.1128/jb.127.3.1278-1285.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Jones J. D., Gutterson N. An efficient mobilizable cosmid vector, pRK7813, and its use in a rapid method for marker exchange in Pseudomonas fluorescens strain HV37a. Gene. 1987;61(3):299–306. doi: 10.1016/0378-1119(87)90193-4. [DOI] [PubMed] [Google Scholar]
  28. Kuykendall L. D., Elkan G. H. Rhizobium japonicum derivatives differing in nitrogen-fixing efficiency and carbohydrate utilization. Appl Environ Microbiol. 1976 Oct;32(4):511–519. doi: 10.1128/aem.32.4.511-519.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Laguerre G., Allard M. R., Revoy F., Amarger N. Rapid Identification of Rhizobia by Restriction Fragment Length Polymorphism Analysis of PCR-Amplified 16S rRNA Genes. Appl Environ Microbiol. 1994 Jan;60(1):56–63. doi: 10.1128/aem.60.1.56-63.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Lennon E., Gutman P. D., Yao H. L., Minton K. W. A highly conserved repeated chromosomal sequence in the radioresistant bacterium Deinococcus radiodurans SARK. J Bacteriol. 1991 Mar;173(6):2137–2140. doi: 10.1128/jb.173.6.2137-2140.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Lupski J. R., Weinstock G. M. Short, interspersed repetitive DNA sequences in prokaryotic genomes. J Bacteriol. 1992 Jul;174(14):4525–4529. doi: 10.1128/jb.174.14.4525-4529.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Mantis N. J., Winans S. C. The chromosomal response regulatory gene chvI of Agrobacterium tumefaciens complements an Escherichia coli phoB mutation and is required for virulence. J Bacteriol. 1993 Oct;175(20):6626–6636. doi: 10.1128/jb.175.20.6626-6636.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Meade H. M., Long S. R., Ruvkun G. B., Brown S. E., Ausubel F. M. Physical and genetic characterization of symbiotic and auxotrophic mutants of Rhizobium meliloti induced by transposon Tn5 mutagenesis. J Bacteriol. 1982 Jan;149(1):114–122. doi: 10.1128/jb.149.1.114-122.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Miksch G., Arnold W., Lentzsch P., Priefer U. B., Pühler A. A 4.6 kb DNA region of Rhizobium meliloti involved in determining urease and hydrogenase activities carries the structural genes for urease (ureA, ureB, ureC) interrupted by other open reading frames. Mol Gen Genet. 1994 Mar;242(5):539–550. doi: 10.1007/BF00285277. [DOI] [PubMed] [Google Scholar]
  35. Morrison N. A., Hau C. Y., Trinick M. J., Shine J., Rolfe B. G. Heat curing of a sym plasmid in a fast-growing Rhizobium sp. that is able to nodulate legumes and the nonlegume Parasponia sp. J Bacteriol. 1983 Jan;153(1):527–531. doi: 10.1128/jb.153.1.527-531.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Newbury S. F., Smith N. H., Higgins C. F. Differential mRNA stability controls relative gene expression within a polycistronic operon. Cell. 1987 Dec 24;51(6):1131–1143. doi: 10.1016/0092-8674(87)90599-x. [DOI] [PubMed] [Google Scholar]
  37. Osterås M., Driscoll B. T., Finan T. M. Molecular and expression analysis of the Rhizobium meliloti phosphoenolpyruvate carboxykinase (pckA) gene. J Bacteriol. 1995 Mar;177(6):1452–1460. doi: 10.1128/jb.177.6.1452-1460.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Osterås M., Finan T. M., Stanley J. Site-directed mutagenesis and DNA sequence of pckA of Rhizobium NGR234, encoding phosphoenolpyruvate carboxykinase: gluconeogenesis and host-dependent symbiotic phenotype. Mol Gen Genet. 1991 Nov;230(1-2):257–269. doi: 10.1007/BF00290676. [DOI] [PubMed] [Google Scholar]
  39. Parkinson J. S., Kofoid E. C. Communication modules in bacterial signaling proteins. Annu Rev Genet. 1992;26:71–112. doi: 10.1146/annurev.ge.26.120192.000443. [DOI] [PubMed] [Google Scholar]
  40. Rastogi V. K., Watson R. J. Aspartate aminotransferase activity is required for aspartate catabolism and symbiotic nitrogen fixation in Rhizobium meliloti. J Bacteriol. 1991 May;173(9):2879–2887. doi: 10.1128/jb.173.9.2879-2887.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Ronson C. W., Nixon B. T., Albright L. M., Ausubel F. M. Rhizobium meliloti ntrA (rpoN) gene is required for diverse metabolic functions. J Bacteriol. 1987 Jun;169(6):2424–2431. doi: 10.1128/jb.169.6.2424-2431.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Ruvkun G. B., Ausubel F. M. A general method for site-directed mutagenesis in prokaryotes. Nature. 1981 Jan 1;289(5793):85–88. doi: 10.1038/289085a0. [DOI] [PubMed] [Google Scholar]
  43. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Schmid C. W., Jelinek W. R. The Alu family of dispersed repetitive sequences. Science. 1982 Jun 4;216(4550):1065–1070. doi: 10.1126/science.6281889. [DOI] [PubMed] [Google Scholar]
  45. Sciaky D., Montoya A. L., Chilton M. D. Fingerprints of Agrobacterium Ti plasmids. Plasmid. 1978 Feb;1(2):238–253. doi: 10.1016/0147-619x(78)90042-2. [DOI] [PubMed] [Google Scholar]
  46. Sharples G. J., Lloyd R. G. A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes. Nucleic Acids Res. 1990 Nov 25;18(22):6503–6508. doi: 10.1093/nar/18.22.6503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Shatters R. G., Somerville J. E., Kahn M. L. Regulation of glutamine synthetase II activity in Rhizobium meliloti 104A14. J Bacteriol. 1989 Sep;171(9):5087–5094. doi: 10.1128/jb.171.9.5087-5094.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Steffan R. J., Atlas R. M. Polymerase chain reaction: applications in environmental microbiology. Annu Rev Microbiol. 1991;45:137–161. doi: 10.1146/annurev.mi.45.100191.001033. [DOI] [PubMed] [Google Scholar]
  49. Stern M. J., Ames G. F., Smith N. H., Robinson E. C., Higgins C. F. Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell. 1984 Jul;37(3):1015–1026. doi: 10.1016/0092-8674(84)90436-7. [DOI] [PubMed] [Google Scholar]
  50. Stock J. B., Ninfa A. J., Stock A. M. Protein phosphorylation and regulation of adaptive responses in bacteria. Microbiol Rev. 1989 Dec;53(4):450–490. doi: 10.1128/mr.53.4.450-490.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Versalovic J., Koeuth T., Lupski J. R. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 1991 Dec 25;19(24):6823–6831. doi: 10.1093/nar/19.24.6823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Vieira J., Messing J. Production of single-stranded plasmid DNA. Methods Enzymol. 1987;153:3–11. doi: 10.1016/0076-6879(87)53044-0. [DOI] [PubMed] [Google Scholar]
  53. Wheatcroft R., Watson R. J. Distribution of insertion sequence ISRm1 in Rhizobium meliloti and other gram-negative bacteria. J Gen Microbiol. 1988 Jan;134(1):113–121. doi: 10.1099/00221287-134-1-113. [DOI] [PubMed] [Google Scholar]
  54. Yanagi M., Yamasato K. Phylogenetic analysis of the family Rhizobiaceae and related bacteria by sequencing of 16S rRNA gene using PCR and DNA sequencer. FEMS Microbiol Lett. 1993 Feb 15;107(1):115–120. doi: 10.1111/j.1574-6968.1993.tb06014.x. [DOI] [PubMed] [Google Scholar]
  55. Yang Y., Ames G. F. DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8850–8854. doi: 10.1073/pnas.85.23.8850. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. de Bruijn F. J. Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl Environ Microbiol. 1992 Jul;58(7):2180–2187. doi: 10.1128/aem.58.7.2180-2187.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. van Slooten J. C., Cervantes E., Broughton W. J., Wong C. H., Stanley J. Sequence and analysis of the rpoN sigma factor gene of rhizobium sp. strain NGR234, a primary coregulator of symbiosis. J Bacteriol. 1990 Oct;172(10):5563–5574. doi: 10.1128/jb.172.10.5563-5574.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES