Novel DNA sequences from natural strains of the nitrogen-fixing symbiotic bacterium Sinorhizobium meliloti

Applied and Environmental Microbiology

Volumn 71, Issue 11, 2005, Pages 7130-7138

  Guo, Hong ^a,b   Sun, Sheng ^a   Finan, Turlough M ^a   Xu, Jianping ^a,b  

^a MCMASTER UNIVERSITY   (Canada)

^b HAINAN MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOLOGY; BIODIVERSITY; DATABASE SYSTEMS; ECOLOGY; ELECTROPHORESIS; GENES;

ENZYME ELECTROPHORESIS; GENOME EVOLUTION; SHINORHIZOBIUM MELILOTI;

DNA;

BACTERIAL DNA; DNA FRAGMENT;

GENOME;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BRADYRHIZOBIUM JAPONICUM; CONTROLLED STUDY; DNA SEQUENCE; DNA SYNTHESIS; GENE IDENTIFICATION; GENE LOSS; GENE SEQUENCE; GENETIC DATABASE; GENOME SIZE; GENOTYPE; MULTILOCUS ENZYME ELECTROPHORESIS; NITROGEN FIXATION; NONHUMAN; POLYMERASE CHAIN REACTION; PSEUDOMONAS; RHIZOBIUM ETLI; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SINORHIZOBIUM MELILOTI; STRAIN DIFFERENCE; SYMBIOSIS;

BASE SEQUENCE; DNA, BACTERIAL; GENE LIBRARY; GENOME, BACTERIAL; GENOTYPE; NITROGEN FIXATION; PHYLOGENY; SINORHIZOBIUM MELILOTI; SYMBIOSIS;

BACTERIA (MICROORGANISMS); BRADYRHIZOBIUM JAPONICUM; PSEUDOMONAS; PSEUDOMONAS SP.; RHIZOBIUM ETLI; SINORHIZOBIUM MELILOTI;

EID: 32044473964     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.71.11.7130-7138.2005     Document Type: Article

References (36)

1. Agapow, P. M., and A. Burt. 2001. Indices of multilocus linkage disequilibrium. Mol. Ecol. Notes 1:101-102.
2. Allen, N. L., A. C. Hilton, R. Betts, and C. W. Penn. 2001. Use of representational difference analysis to identify Escherichia coli O157-specific DNA sequences. FEMS Microbiol. Lett. 197:195-201.
3. Allen, N. L., C. W. Penn, and A. C. Hilton. 2003. Representational difference analysis: critical appraisal and method development for the identification of unique DNA sequences from prokatyotes. J. Microbiol. Methods 55:73-81.
4. Bart, A., J. Dankert, and A. van der Ende. 2000. Representational difference analysis of Neisseria meningitidis identifies sequences that are specific for the hyper-virulent lineage III clone. FEMS Microbiol. Lett. 188:111-114.
5. Bart, A., Y. Pannekoek, J. Dankert, and A. van der Ende. 2001. NmeSI restriction-modification system identified by representational difference analysis of a hypervirulent Neisseria meningitides strain. Infect. Immun. 69: 1816-1820.
6. Bergthorsson, U., and H. Ochman. 1995. Heterogeneity of genome sizes among natural isolates of Escherichia coli. J. Bacteriol. 177:5784-5789.
7. Bergthorsson, U., and H. Ochman. 1998. Distribution of chromosome length variation in natural isolates of Escherichia coli. Mol. Biol. Evol. 15:6-16.
8. Bittinger, M. A., J. A. Gross, J. Widom, J. Clardy, and J. Handelsman. 2000. Rhizobium etli CE3 carries vir gene homologs on a self-transmissible plasmid. Mol. Plant-Microbe Interact. 13:1019-1021.
9. Blanc-Potard, A.-B., C. Tinsley, I. Scaletsky, C. Le Bouguenec, J. Guignot, A. L. Servin, X. Nassif, and M.-F. Bernet-Camard. 2002. Representational difference analysis between Afa/Dr diffusely adhering Escherichia coli and nonpathogenic E. coli K-12. Infect. Immun. 70:5503-5511.
10. Bonacorsi, S. P. P., O. Clermont, C. Tinsley, I. Le Gall, J.-C. Beaudoin, J. Elion, X. Nassif, and E. Bingen. 2000. Identification of regions of the Escherichia coli chromosome specific for neonatal meningitis-associated strains. Infect. Immun. 68:2096-2101.
11. Calia, K. E., M. K. Waldor, and S. B. Calderwood. 1998. Use of representational difference analysis to identify genomic differences between pathogenic strains of Vibrio cholerae. Infect. Immun. 66:849-852.
12. Charles, T., and T. M. Finan. 1991. Analysis of a 1600-kilobase Rhizobium meliloti megaplasmid using defined deletions generated in vivo. Genetics 127:5-20.
13. Eardly, B. D., L. A. Materon, N. H. Smith, D. A. Johnson, M. D. Rumbaugh, and R. K. Selander. 1990. Genetic structure of natural populations of the nitrogen-fixing bacterium Rhizobium meliloti. Appl. Environ. Microbiol. 56: 187-194.
14. Faith, D. P. 1991. Cladistic permutation tests for monophyly and nonmonophyly. Syst. Zool. 40:366-375.
15. Galibert, F., T. M. Finan, S. R. Long, A. Puhler, P. Abola, F. Ampe, F. Barloy-Hubler, M. J. Barnett, A. Becker, P. Boistard, G. Bothe, M. Boutry, L. Bowser, J. Buhrmester, E. Cadieu, D. Capela, P. Chain, A. Cowie, R. W. Davis, S. Dreano, N. A. Federspiel, R. F. Fisher, S. Gloux, T. Godrie, A. Goffeau, B. Golding, J. Gouzy, M. Gurjal, I. Hernandez-Lucas, A. Hong, L. Huizar, R. W. Hyman, T. Jones, D. Kahn, M. L. Kahn, S. Kalman, D. H. Keating, E. Kiss, C. Komp, V. Lelaure, D. Masuy, C. Palm, M. C. Peck, T. M. Pohl, D. Portetelle, B. Purnelle, U. Ramsperger, R. Surzycki, P. Thebault, M. Vandenbol, F. J. Verholter, S. Weidner, D. H. Wells, K. Wong, K. C. Yen, and J. Batut. 2001. The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293:668-672.
16. Göttfert, M., S. Röthlisberger, C. Kundig, C. Beck, R. Marty, and H. Hennecke. 2001. Potential symbiosis-specific genes uncovered by sequencing a 410-kilobase DNA region of the Bradyrhizobium japonicum chromosome. J. Bacteriol. 183:1405-1412.
17. Harsono, K. D., C. W. Kaspar, and J. B. Luchansky. 1993. Comparison and genomic sizing of Escherichia coli O157:H7 isolates by pulsed-field gel electrophoresis. Appl. Environ. Microbiol. 59:3141-3144.
18. House, B. L., M. W. Mortimer, and M. L. Kahn. 2004. New recombination methods for Sinorhizobium meliloti genetics. Appl. Environ. Microbiol. 70: 2806-2815.
19. Kanagawa, K., M. Oishi, S. Negoro, I. Urable, and H. Okada. 1993. Characterization of the 6-aminohexanoate-dimer hydrolase from Pseudomonas sp. NK87. J. Gen. Microbiol. 139:787-795.
20. Lisitsyn, N., N. Lisitsyn, and M. Wigler. 1993. Cloning the differences between two complex genomes. Science 259:946-951.
21. Liu, S.-L., A. Hessel, and K. E. Sanderson. 1993. Genomic mapping with 1-CeuI, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria. Proc. Natl. Acad. Sci. USA 90:6874-6878.
22. Mercado-Blanco, J., F. García, M. Fernández-López, and J. Olivares. 1993. Melanin production by Rhizobium meliloti GR4 is linked to nonsymbiotic plasmid pRmeGR4b: cloning, sequencing, and expression of the tyrosinase gene mepA. J. Bacteriol. 175:5403-5410.
23. Middendorf, B., and R. Gross. 1999. Representational difference analysis identifies a strain-specific LPS biosynthesis locus in Bordetella species. Mol. Gen. Genet. 262:189-198.
24. Oresnik, I. J., S.-L. Liu, C. K. Yost, and M. F. Hynes. 2000. Megaplasmid pRme2011a of Sinorhizobium meliloti is not required for viability. J. Bacteriol. 182:3582-3586.
25. Pinero, D., E. Martinez, and R. K. Selander. 1988. Genetic diversity and relationships among isolates of Rhizobium leguminosarum biovar phaseoli. Appl. Environ. Microbiol. 54:2825-2832.
26. Roumiantseva, M. L., E. E. Andronov, L. A. Sharypova, T. Dammann-Kalinowski, M. Keller, J. P. W. Young, and B. V. Simarov. 2002. Diversity of Sinorhizobium meliloti from the Central Asian alfalfa gene center. Appl. Environ. Microbiol. 68:4694-4697.
27. Sagerstrom, C. G., B. I. Sun, and H. L. Sive. 1997. Subtractive cloning: past, present, and future. Annu. Rev. Biochem. 66:751-783.
28. Schofield, P. R., A. H. Gibson, W. F. Dudman, and J. M. Watson. 1987. Evidence for genetic exchange and recombination of Rhizobium symbiotic plasmids in a soil population. Appl. Environ. Microbiol. 53:2942-2947.
29. Stêpkowski, T., and A. B. Legocki. 2001. Reduction of bacterial genome size and expansion resulting from obligate intracellular life style and adaptation to soil habitat. Acta Biochim. Pol. 48:367-381.
30. Swofford, D. L. 2004. PAUP*. Phylogenetic Analysis Using Parsimony (* and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
31. Tinsley, C. R., and X. Nassif. 1996. Analysis of the genetic differences between Neisseria meningitidis and Neisseria gonorrhoeae: two closely related bacteria expressing two different pathogenicities. Proc. Natl. Acad. Sci. USA 93:11109-11114.
32. Toro, N., F. Martinez-Abarca, M. Fernandez-Lopez, and E. Munoz-Adelantado. 2003. Diversity of group II introns in the genome of Sinorhizobium meliloti strain 1021: splicing and mobility of RmInt1. Mol. Genet. Genomics 268:628-636.
33. Wong, K., and G. B. Golding. 2003. A phylogenetic analysis of the pSymB replicon from Sinorhizobium meliloti genome reveals a complex evolutionary history. Can. J. Microbiol. 49:269-280.
34. Yomo, T., I. Urable, and H. Okada. 1992. No stop codons in the antisense strands of the genes for nylon oligomer degradation. Proc. Natl. Acad. Sci. USA 89:3780-3784.
35. Young, J. P. W., and M. Wexler. 1988. Sym plasmid and chromosomal genotypes are correlated in field populations of Rhizobium leguminosarum. J. Gen. Microbiol. 134:2731-2739.
36. Zekri, S., M. J. Soto, and N. Toro. 1998. ISRm4-1 and ISRm9, two novel insertion sequences from Sinorhizobium meliloti. Gene 207:93-96.