Isolation and characterization of functional insertion sequences of rhizobia

FEMS Microbiology Letters

Volumn 261, Issue 1, 2006, Pages 25-31

  Hernandez Lucas, Ismael ^a   Ramirez Trujillo, Jose Augusto ^a   Gaitan, Miguel Angel ^a   Guo, Xianwu ^b   Flores, Margarita ^b   Martinez Romero, Esperanza ^b   Perez Rueda, Ernesto ^a   Mavingui, Patrick ^c  

^a INSTITUTO DE BIOTECNOLOGÍA   (Mexico)

^b INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

^c University of Lyon   (France)

Author keywords

Insertion sequences; Rhizobia; Transposition

Indexed keywords

ARTICLE; BACTERIAL GENETICS; COMPUTER ANALYSIS; DNA SEQUENCE; FUNCTIONAL GENOMICS; GENE FUNCTION; GENE INSERTION SEQUENCE; GENE ISOLATION; GENE TRANSFER; GENETIC ANALYSIS; GENETIC PROCEDURES; GENOME ANALYSIS; LEGUME; NODULATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; RHIZOBIACEAE; RHIZOBIUM; RHIZOBIUM TROPICI; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SINORHIZOBIUM MELILOTI;

RHIZOBIUM; RHIZOBIUM SP.; RHIZOBIUM TROPICI; SINORHIZOBIUM MELILOTI;

EID: 33745684181     PISSN: 03781097     EISSN: 15746968     Source Type: Journal    
DOI: 10.1111/j.1574-6968.2006.00319.x     Document Type: Article

References (46)

1. Barker CS, Prüß BM & Matsumura P (2004) Increased motility of Escherichia coli by insertion sequence element integration into the regulatory region of the flhD operon. J Bacteriol 186: 7529-7537.
2. Chang-Gyun H, Shiga Y, Tobe T, Sasakawa C & Ohtsubo E (2001) Structural and functional characterization of IS679 and IS66-family elements. J Bacteriol 183: 4296-4304.
3. Charles TC & Finan TM (1991) Analysis of a 1600-kilobase Rhizobium meliloti megaplasmid using defined deletions generated in vivo. Genetics 127: 5-20.
4. Cooper VS, Schneider D, Blot M & Lenski RE (2001) Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations at Escherichia coli B. J Bacteriol 183: 2834-2841.
5. Dusha I, Kovalenko S, Bonfalvi Z & Kondorosi A (1987) Rhizobium meliloti insertion element ISRm2 and its use for identification of the fixX gene. J Bacteriol 169: 1403-1409.
6. Figurski DH & Helinski DR (1979) Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc Natl Acad Sci USA 76: 1648-1652.
7. Flores M, Mavingui P, Perret X, Broughton WJ, Romero D, Hernández G, Davila G & Palacios R (2000) Prediction, identification, and artificial selection of DNA rearrangements in Rhizobium: toward a natural genomic design. Proc Natl Acad Sci USA 97: 9138-9143.
8. Freiberg C, Fellay R, Bairoch A, Broughton WJ, Rosenthal A & Perret X (1997) Molecular basis of symbiosis between Rhizobium and legumes. Nature 387: 394-401.
9. Galas DJ & Chandler M (1989) Bacterial insertion sequences. Mobile DNA (Berg DE & Howe MM, eds), pp. 109-162. American Society for Microbiology, Washington, DC.
10. Galibert F, Finan TM, Long SR, et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293: 668-672.
11. Gay P, Le coq D, Steinmetz M, Berkelman T & Kado CI (1985) Positive selection procedure for entrapment of insertion sequence elements in gram-negative bacteria. J Bacteriol 164: 918-921.
12. Gonzalez V, Bustos P, Ramirez-Romero MA, et al. (2003) The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42. Genome Biol 4: R36.
13. Gough J, Karplus K, Hughey R & Chothia C (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 313: 903-919.
14. Hynes MF & McGregor NF (1990) Two plasmids other than the nodulation plasmid are necessary for formation of nitrogen fixing nodules by Rhizobium leguminosarum. Mol Microbiol 4: 567-574.
15. Kaneko T, Nakamura Y, Sato S, et al. (2000) Complete genome sequence of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res 7: 331-338.
16. Kaneko T, Nakamura Y, Sato S, et al. (2002) Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res 9: 189-197.
17. Kosier B, Puhler A & Simon R (1993) Monitoring the diversity of Rhizobium meliloti field and microcosm isolates with a novel rapid genotyping method using insertion elements. Mol Ecol 2: 35-46.
18. Mahillon J & Chandler M (1998) Insertion sequences. Microbiol Mol Biol Rev 62: 725-774.
19. Martinez E, Pardo MA, Palacios R & Cevallos MA (1985) Reiteration of nitrogen fixation gene sequences and specificity of Rhizobium in nodulation and nitrogen fixation in Phaseolus vulgaris. J Gen Microbiol 131: 1779-1786.
20. Martinez-Romero E & Rosenblueth M (1990) Increased bean (Phaseolus vulgaris L.) nodulation competitiveness of genetically modified Rhizobium strains. Appl Environ Microbiol 56: 2384-2388.
21. Martínez-Romero E, Segovia L, Mercante M, Franco A, Graham P & Pardo MA (1991) Rhizobium tropici: a novel species nodulating Phaseolus vulgaris L. beans and Leucaena sp. trees. Int J Syst Bacteriol 41: 417-426.
22. Mavingui P, Laeremans T, Flores M, Romero D, Martínez-Romero E & Palacios R (1998) Genes essential for nod factor production and nodulation are located on a symbiotic amplicon (AMPRtrCFN299pc60) in Rhizobium tropici. J Bacteriol 180: 2866-2874.
23. Mavingui P, Flores M, Guo X, Davila G, Perret X, Broughton WJ & Palacios R (2002) Dynamics of genome architecture in Rhizobium sp. strain NGR234. J Bacteriol 184: 171-176.
24. Meade HM, Long SR, Ruvkun GB, Brown SE & Ausubel FM (1982) Physical and genetic characterisation of symbiotic and auxotrophic mutants of Rhizobium meliloti induced by transposon Tn5 mutagenesis. J Bacteriol 149: 114-122.
25. Paulus F, Canaday J & Otten L (1991) Limited host range Ti plasmids: recent origin from wide host range Ti plasmid and involvement of a novel IS element, IS868. Mol Plant Microbe Interact 4: 190-197.
26. Perret X, Viprey V, Freiberg C & Broughton WJ (1997) Structure and evolution of NGRRS-1, a complex, repeated element in the genome of Rhizobium sp. strain NGR234. J Bacteriol 179: 7488-7496.
27. Priefer UB, Burkardt HJ, Klipp W & Puhler A (1981) ISR1 an insertion element isolated from the soil bacterium Rhizobium lupini. Movable Genetic Elements, Cold Spring Harbor Symposium on Quantum Biology, Vol. XLV, pp. 87-91. Cold Spring Harbor Laboratories, Cold Spring Harbor, NY.
28. Priefer UB, Kalinowski J, Ruger B, Heumann W & Puhler A (1989) ISR1 a transposable DNA sequence resident in Rhizobium class IV strains, shows structural characteristics of classical insertion elements. Plasmid 21: 120-128.
29. Rezsohazy R, Hallet B, Delcour J & Mahillon J (1993) The IS4 family of insertion sequences: evidence for a conserved transposase motif. Mol Microbiol 9: 1283-1295.
30. Rochepeau P, Selinger LB & Hynes MF (1997) Transposon-like structure of a new plasmid-encoded restriction-modification system in Rhizobium leguminosarum VF39SM. Mol Gen Genet 256: 387-396.
31. Romanov VI, Hernández-Lucas I & Martínez-Romero E (1994) Carbon metabolism enzymes of Rhizobium tropici cultures and bacteroids. Appl Environ Microbiol 60: 2339-2342.
32. Ruvkun GB, Long SR, Meade HM, van den Bos RC & Ausubel FM (1982) ISRm1: a Rhizobium meliloti insertion sequence that transposes preferentially into nitrogen fixation genes. J Mol Appl Genet 1: 405-418.
33. Sambrook J, Fritsch EF & Maniatis T (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
34. Schneider D, Faure D, Noirclerc-Savoye M, Barriere A, Coursange E & Blot M (2000) A broad-host-range plasmid for isolating mobile genetic E1 in gram-negative bacteria. Plasmid 44: 201-207.
35. Schneiker S, Kosier B, Puhler A & Selbitschka W (1999) The Sinorhizobium meliloti insertion sequence (IS) element ISRm14 is related to a previously unrecognized IS element located adjacent to the Escherichia coli locus of enterocyte effacement (LEE) pathogenicity island. Curr Microbiol 39: 274-281.
36. Selbitschka W, Arnold W, Jording D, Kosier B, Toro N & Puhler A (1995) The insertion sequence element ISRm2011-2 belongs to the IS630-Tc1 family of transposable elements and is abundant in Rhizobium meliloti. Gene 163: 59-64.
37. Selbitschka W, Zekri S, Schroder G, Puhler A & Toro N (1999) The Sinorhizobium meliloti insertion sequence (IS) elements ISRm102F34-1/ISRm7 and ISRm220-13-5 belong to a new family of insertion sequence elements. FEMS Microbiol Lett 172: 1-7.
38. Simon R, Hotte B, Klauke B & Kosier B (1991) Isolation and characterization of insertion sequence elements from gram-negative bacteria by using new broad-host-range, positive selection vectors. J Bacteriol 173: 1502-1508.
39. Soto MJ, Zorzano O, Olivares J & Toro N (1992) Sequence of ISRm4 from Rhizobium meliloti strain GR4. Gene 120: 125-126.
40. Southern EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98: 503-517.
41. Trinick MJ (1980) Relationships among the fast-growing rhizobia of Lablab purpureus, Leucaena leucochephala, Mimosa sp., Acacia farnesiana, and Sesbania grandiflora and their affinities with other rhizobia groups. J Appl Bacteriol 49: 39-53.
42. Watson RB & Wheatcroft R (1991) Nucleotide sequence of Rhizobium meliloti insertion sequence ISRm1: homology to IS2 from Escherichia coli and IS426 from Agrobacterium tumefaciens. DNA Seq 2: 163-172.
43. Wheatcroft R & Watson RB (1988) Distribution of insertion sequence ISRm1 in Rhizobium meliloti and other gram-negative bacteria. J Gen Microbiol 134: 113-121.
44. Wood DW, Setubal JC, Kaul R, et al. (2001) The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294: 2317-2323.
45. Zekri S & Toro N (1996) Identification and nucleotide sequence of Rhizobium meliloti insertion sequence ISRm6, a small transposable element that belongs to the IS3 family. Gene 175: 43-48.
46. Zekri S, Soto MJ & Toro N (1998) ISRm4-1 and ISRm9, two novel insertion sequences from Sinorhizobium meliloti. Gene 207: 93-96.