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. 1985 May;162(2):535–542. doi: 10.1128/jb.162.2.535-542.1985

Repeated sequences similar to insertion elements clustered around the nif region of the Rhizobium japonicum genome.

K Kaluza, M Hahn, H Hennecke
PMCID: PMC218881  PMID: 2985537

Abstract

Two different repeated sequences (RSs) were discovered in the Rhizobium japonicum genome: RSRj alpha is 1126 base pairs long and is repeated 12 times; RSRj beta is approximately 950 base pairs long and is repeated at least 6 times. Their arrangement in root nodule bacteroid DNA is the same as in DNA from bacteria grown in culture. Deletion analysis showed that many copies of alpha and beta are clustered around the nitrogenase genes nifDK and nifH, or, in general, they are found within a genomic region harboring genes that are nonessential for growth. One copy each of alpha and beta are located upstream of nifDK and are adjacent to each other. Neither of them, however, is involved in the expression of nifDK. Nucleotide sequence analysis of three copies of RS alpha revealed many characteristics of procaryotic insertion sequence elements: potential inverted repeats at their ends, potential target site duplication, and large open reading frames. Despite this, their genomic positions appear to be stable. One possible function of these RSs is in deletion formation probably via recombination between them.

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Selected References

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  1. Adams T. H., Chelm B. K. The nifH and nifDK promoter regions from Rhizobium japonicum share structural homologies with each other and with nitrogen-regulated promoters from other organisms. J Mol Appl Genet. 1984;2(4):392–405. [PubMed] [Google Scholar]
  2. Adams T. H., McClung C. R., Chelm B. K. Physical organization of the Bradyrhizobium japonicum nitrogenase gene region. J Bacteriol. 1984 Sep;159(3):857–862. doi: 10.1128/jb.159.3.857-862.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Auerswald E. A., Ludwig G., Schaller H. Structural analysis of Tn5. Cold Spring Harb Symp Quant Biol. 1981;45(Pt 1):107–113. doi: 10.1101/sqb.1981.045.01.019. [DOI] [PubMed] [Google Scholar]
  4. Better M., Lewis B., Corbin D., Ditta G., Helinski D. R. Structural relationships among Rhizobium meliloti symbiotic promoters. Cell. 1983 Dec;35(2 Pt 1):479–485. doi: 10.1016/0092-8674(83)90181-2. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. 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]
  7. Danna K. J. Determination of fragment order through partial digests and multiple enzyme digests. Methods Enzymol. 1980;65(1):449–467. doi: 10.1016/s0076-6879(80)65055-1. [DOI] [PubMed] [Google Scholar]
  8. Denhardt D. T. A membrane-filter technique for the detection of complementary DNA. Biochem Biophys Res Commun. 1966 Jun 13;23(5):641–646. doi: 10.1016/0006-291x(66)90447-5. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. Engler J. A., van Bree M. P. The nucleotide sequence and protein-coding capability of the transposable element IS5. Gene. 1981 Aug;14(3):155–163. doi: 10.1016/0378-1119(81)90111-6. [DOI] [PubMed] [Google Scholar]
  11. Fuhrmann M., Hennecke H. Rhizobium japonicum nitrogenase Fe protein gene (nifH). J Bacteriol. 1984 Jun;158(3):1005–1011. doi: 10.1128/jb.158.3.1005-1011.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Gray C. P., Sommer R., Polke C., Beck E., Schaller H. Structure of the orgin of DNA replication of bacteriophage fd. Proc Natl Acad Sci U S A. 1978 Jan;75(1):50–53. doi: 10.1073/pnas.75.1.50. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hennecke H., Günther I., Binder F. A novel cloning vector for the direct selection of recombinant DNA in E. coli. Gene. 1982 Sep;19(2):231–234. doi: 10.1016/0378-1119(82)90011-7. [DOI] [PubMed] [Google Scholar]
  14. Heumann W. Conjugation in starforming Rhizobium lupini. Mol Gen Genet. 1968;102(2):132–144. doi: 10.1007/BF01789140. [DOI] [PubMed] [Google Scholar]
  15. Messing J., Crea R., Seeburg P. H. A system for shotgun DNA sequencing. Nucleic Acids Res. 1981 Jan 24;9(2):309–321. doi: 10.1093/nar/9.2.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Messing J. New M13 vectors for cloning. Methods Enzymol. 1983;101:20–78. doi: 10.1016/0076-6879(83)01005-8. [DOI] [PubMed] [Google Scholar]
  17. Murphy E., Löfdahl S. Transposition of Tn554 does not generate a target duplication. Nature. 1984 Jan 19;307(5948):292–294. doi: 10.1038/307292a0. [DOI] [PubMed] [Google Scholar]
  18. Regensburger B., Hennecke H. RNA polymerase from Rhizobium japonicum. Arch Microbiol. 1983 Aug;135(2):103–109. doi: 10.1007/BF00408017. [DOI] [PubMed] [Google Scholar]
  19. Ruvkun G. B., Long S. R., Meade H. M., van den Bos R. C., Ausubel F. M. ISRm1: A Rhizobium meliloti insertion sequence that transposes preferentially into nitrogen fixation genes. J Mol Appl Genet. 1982;1(5):405–418. [PubMed] [Google Scholar]
  20. 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]
  21. Schnabel H., Palm P., Dick K., Grampp B. Sequence analysis of the insertion element ISH1.8 and of associated structural changes in the genome of phage PhiH of the archaebacterium Halobacterium halobium. EMBO J. 1984 Aug;3(8):1717–1722. doi: 10.1002/j.1460-2075.1984.tb02037.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Scott D. B., Hennecke H., Lim S. T. The biosynthesis of nitrogenase MoFe protein polypeptides in free-living cultures of Rhizobium japonicum. Biochim Biophys Acta. 1979 Dec 17;565(2):365–378. doi: 10.1016/0005-2787(79)90212-0. [DOI] [PubMed] [Google Scholar]
  23. Shepherd J. C. Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1596–1600. doi: 10.1073/pnas.78.3.1596. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Shine J., Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342–1346. doi: 10.1073/pnas.71.4.1342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Skogen-Hagenson M. J., Atherly A. G. High-frequency induction of nodulation and nitrogen fixation mutants of Rhizobium japonicum. J Bacteriol. 1983 Nov;156(2):937–940. doi: 10.1128/jb.156.2.937-940.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Smith G. E., Summers M. D. The bidirectional transfer of DNA and RNA to nitrocellulose or diazobenzyloxymethyl-paper. Anal Biochem. 1980 Nov 15;109(1):123–129. doi: 10.1016/0003-2697(80)90019-6. [DOI] [PubMed] [Google Scholar]
  27. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  28. Sundaresan V., Jones J. D., Ow D. W., Ausubel F. M. Klebsiella pneumoniae nifA product activates the Rhizobium meliloti nitrogenase promoter. Nature. 1983 Feb 24;301(5902):728–732. doi: 10.1038/301728a0. [DOI] [PubMed] [Google Scholar]

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