Comparative genomic hybridisation and ultrafast pyrosequencing revealed remarkable differences between the Sinorhizobium meliloti genomes of the model strain Rm1021 and the field isolate SM11

Journal of Biotechnology

Volumn 136, Issue 1-2, 2008, Pages 31-37

  Stiens, Michael ^a   Becker, Anke ^a   Bekel, Thomas ^a   Gödde, Victoria ^a   Goesmann, Alexander ^a   Niehaus, Karsten ^a   Schneiker Bekel, Susanne ^a   Selbitschka, Werner ^a   Weidner, Stefan ^a   Schlüter, Andreas ^a   Pühler, Alfred ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

Bacterial genome evolution; Comparative genomic hybridisation; Megaplasmid; Microarray hybridisation; Nitrogen fixation; Nodulation; Symbiosis

Indexed keywords

BIOCHEMICAL ENGINEERING; BIOCHEMISTRY; CARBOHYDRATES; CELL MEMBRANES; CHROMOSOMES; COMPLEXATION; GENES; OLIGONUCLEOTIDES; ORGANIC COMPOUNDS; SYNTHESIS (CHEMICAL);

BACTERIAL GENOME EVOLUTION; CARBOHYDRATE SYNTHESIS; CELL SURFACES; COMPARATIVE GENOMIC HYBRIDISATION; CONTIGS; GENE CLUSTERING; GENOME SEQUENCING; GENOMIC VARIATION; IN-DEPTH ANALYSIS; INSERTION SEQUENCES; MEGAPLASMID; MICROARRAY HYBRIDISATION; NITROGEN FIXATION; NODULATION; OLIGONUCLEOTIDE MICROARRAY; PYROSEQUENCING; SIDEROPHORE; SINORHIZOBIUM MELILOTI; SYMBIOSIS; ULTRA-FAST;

CHLORINE COMPOUNDS;

SIDEROPHORE;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; BIOSYNTHESIS; CARBOHYDRATE SYNTHESIS; CELL SURFACE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTIG MAPPING; DENITRIFICATION; DEVICE; DNA MICROARRAY; GENE CLUSTER; GENE IDENTIFICATION; GENE INSERTION; MICROARRAY ANALYSIS; MICROBIAL DIVERSITY; NONHUMAN; OPERON; PLASMID; PRIORITY JOURNAL; PYROSEQUENCING; SEQUENCE ANALYSIS; SINORHIZOBIUM MELILOTI; STRAIN DIFFERENCE; TRANSPOSON;

BASE SEQUENCE; CHROMOSOME MAPPING; CONSERVED SEQUENCE; GENOME, BACTERIAL; IN SITU HYBRIDIZATION; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; OPEN READING FRAMES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SINORHIZOBIUM MELILOTI; SPECIES SPECIFICITY;

BACTERIA (MICROORGANISMS); SINORHIZOBIUM MELILOTI;

EID: 49949110306     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2008.04.014     Document Type: Article

References (25)

1. Baek S.H., Rajashekara G., Splitter G.A., and Shapleigh J.P. Denitrification genes regulate Brucella virulence in mice. J. Bacteriol. 186 (2004) 6025-6031
2. Barnett M.J., Fisher R.F., Jones T., Komp C., Abola A.P., Barloy-Hubler F., Bowser L., Capela D., Galibert F., Gouzy J., Gurjal M., Hong A., Huizar L., Hyman R.W., Kahn D., Kahn M.L., Kalman S., Keating D.H., Palm C., Peck M.C., Surzycki R., Wells D.H., Yeh K.C., Davis R.W., Federspiel N.A., and Long S.R. Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 9883-9888
3. Becker A., Berges H., Krol E., Bruand C., Rüberg S., Capela D., Lauber E., Meilhoc E., Ampe F., de Bruijn F.J., Fourment J., Francez-Charlot A., Kahn D., Küster H., Liebe C., Pühler A., Weidner S., and Batut J. Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions. Mol. Plant Microbe Interact. 17 (2004) 292-303
4. Capela D., Barloy-Hubler F., Gouzy J., Bothe G., Ampe F., Batut J., Boistard P., Becker A., Boutry M., Cadieu E., Dreano S., Gloux S., Godrie T., Goffeau A., Kahn D., Kiss E., Lelaure V., Masuy D., Pohl T., Portetelle D., Pühler A., Purnelle B., Ramsperger U., Renard C., Thebault P., Vandenbol M., Weidner S., and Galibert F. Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 9877-9882
5. Chan Y.K., and McCormick W.A. Experimental evidence for plasmid-borne nor-nir genes in Sinorhizobium meliloti JJ1c10. Can. J. Microbiol. 50 (2004) 657-667
6. Charles T.C., and Finan T.M. Analysis of a 1600-kilobase Rhizobium meliloti megaplasmid using defined deletions generated in vivo. Genetics 127 (1991) 5-20
7. de Boer A.P., van der Oost J., Reijnders W.N., Westerhoff H.V., Stouthamer A.H., and van Spanning R.J. Mutational analysis of the nor gene cluster which encodes nitric-oxide reductase from Paracoccus denitrificans. Eur. J. Biochem. 242 (1996) 592-600
8. Dondrup M., Goesmann A., Bartels D., Kalinowski J., Krause L., Linke B., Rupp O., Sczyrba A., Pühler A., and Meyer F. EMMA: a platform for consistent storage and efficient analysis of microarray data. J. Biotechnol. 106 (2003) 135-146
9. 2-fixing endosymbiont Sinorhizobium meliloti. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 9889-9894
10. Galibert F., Finan T.M., Long S.R., Pühler A., Abola P., Ampe F., Barloy-Hubler F., Barnett M.J., Becker A., Boistard P., Bothe G., Boutry M., Bowser L., Buhrmester J., Cadieu E., Capela D., Chain P., Cowie A., Davis R.W., Dreano S., Federspiel N.A., Fisher R.F., Gloux S., Godrie T., Goffeau A., Golding B., Gouzy J., Gurjal M., Hernandez-Lucas I., Hong A., Huizar L., Hyman R.W., Jones T., Kahn D., Kahn M.L., Kalman S., Keating D.H., Kiss E., Komp C., Lalaure V., Masuy D., Palm C., Peck M.C., Pohl T.M., Portetelle D., Purnelle B., Ramsperger U., Surzycki R., Thebault P., Vandenbol M., Vorhölter F.J., Weidner S., Wells D.H., Wong K., Yeh K.C., and Batut J. The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293 (2001) 668-672
11. Giuntini E., Mengoni A., De Filippo C., Cavalieri D., Aubin-Horth N., Landry C.R., Becker A., and Bazzicalupo M. Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains. BMC Genomics 6 (2005) 158
12. Guo H., Sun S., Finan T.M., and Xu J. Novel DNA sequences from natural strains of the nitrogen-fixing symbiotic bacterium Sinorhizobium meliloti. Appl. Environ. Microbiol. 71 (2005) 7130-7138
13. Hopwood D.A., Bibb M.J., Chater K.F., Kieser T., Bruton C.J., Kieser D.J., Lydiate C.P., Smith J.M., Ward H., and Schrempf H. Genetic Manipulations of Streptomyces. A Laboratory Manual (1985), John Innes Foundation, Norwich, UK
14. Kobayashi I. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res. 29 (2001) 3742-3756
15. Kuhn S., Stiens M., Pühler A., and Schlüter A. Prevalence of pSmeSM11a-like plasmids in indigenous Sinorhizobium meliloti strains isolated in the course of a deliberate release experiment with genetically modified S. meliloti strains. FEMS Microbiol. Ecol. 63 (2008) 118-131
16. Kwiatkowski A.V., Laratta W.P., Toffanin A., and Shapleigh J.P. Analysis of the role of the nnrR gene product in the response of Rhodobacter sphaeroides 2.4.1 to exogenous nitric oxide. J. Bacteriol. 179 (1997) 5618-5620
17. Lynch D., O'Brien J., Welch T., Clarke P., Cuiv P.O., Crosa J.H., and O'Connell M. Genetic organization of the region encoding regulation, biosynthesis, and transport of rhizobactin 1021, a siderophore produced by Sinorhizobium meliloti. J. Bacteriol. 183 (2001) 2576-2585
18. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Godwin B.C., He W., Helgesen S., Ho C.H., Irzyk G.P., Jando S.C., Alenquer M.L., Jarvie T.P., Jirage K.B., Kim J.B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., McDade K.E., McKenna M.P., Myers E.W., Nickerson E., Nobile J.R., Plant R., Puc B.P., Ronan M.T., Roth G.T., Sarkis G.J., Simons J.F., Simpson J.W., Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.F., and Rothberg J.M. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437 (2005) 376-380
19. Meyer F., Goesmann A., McHardy A.C., Bartels D., Bekel T., Clausen J., Kalinowski J., Linke B., Rupp O., Giegerich R., and Pühler A. GenDB-an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 31 (2003) 2187-2195
20. Murray N.E. Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle). Microbiol. Mol. Biol. Rev. 64 (2000) 412-434
21. Oresnik I.J., Liu S.L., Yost C.K., and Hynes M.F. Megaplasmid pRme2011a of Sinorhizobium meliloti is not required for viability. J. Bacteriol. 182 (2000) 3582-3586
22. Selbitschka W., Keller M., Miethling-Graff R., Dresing U., Schwieger F., Krahn I., Homann I., Dammann-Kalinowski T., Pühler A., and Tebbe C.C. Long-term field release of bioluminescent Sinorhizobium meliloti strains to assess the influence of a recA mutation on the strains' survival. Microb. Ecol. 52 (2006) 583-595
23. Stiens M., Schneiker S., Pühler A., and Schlüter A. Sequence analysis of the 181-kb accessory plasmid pSmeSM11b, isolated from a dominant Sinorhizobium meliloti strain identified during a long-term field release experiment. FEMS Microbiol. Lett. 271 (2007) 297-309
24. Stiens M., Schneiker S., Keller M., Kuhn S., Pühler A., and Schlüter A. Sequence analysis of the 144-kilobase accessory plasmid pSmeSM11a, isolated from a dominant Sinorhizobium meliloti strain identified during a long-term field release experiment. Appl. Environ. Microbiol. 72 (2006) 3662-3672
25. Zumft W.G. Cell biology and molecular basis of denitrification. Microbiol. Mol. Biol. Rev. 61 (1997) 533-616