Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains
Giuntini E, Mengoni A, De Filippo C, Cavalieri D, Aubin-Horth N, Landry CR, Becker A, Bazzicalupo M (2005)
BMC Genomics 6(1): 158.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Giuntini, Elisa;
Mengoni, Alessio;
De Filippo, Carlotta;
Cavalieri, Duccio;
Aubin-Horth, Nadia;
Landry, Christian R.;
Becker, Anke;
Bazzicalupo, Marco
Einrichtung
Abstract / Bemerkung
Background: Sinorhizobium meliloti is a soil bacterium that forms nitrogen-fixing nodules on the roots of leguminous plants such as alfalfa ( Medicago sativa). This species occupies different ecological niches, being present as a free-living soil bacterium and as a symbiont of plant root nodules. The genome of the type strain Rm 1021 contains one chromosome and two megaplasmids for a total genome size of 6 Mb. We applied comparative genomic hybridisation (CGH) on an oligonucleotide microarrays to estimate genetic variation at the genomic level in four natural strains, two isolated from Italian agricultural soil and two from desert soil in the Aral Sea region. Results: From 4.6 to 5.7 percent of the genes showed a pattern of hybridisation concordant with deletion, nucleotide divergence or ORF duplication when compared to the type strain Rm 1021. A large number of these polymorphisms were confirmed by sequencing and Southern blot. A statistically significant fraction of these variable genes was found on the pSymA megaplasmid and grouped in clusters. These variable genes were found to be mainly transposases or genes with unknown function. Conclusion: The obtained results allow to conclude that the symbiosis-required megaplasmid pSymA can be considered the major hot-spot for intra-specific differentiation in S. meliloti.
Erscheinungsjahr
2005
Zeitschriftentitel
BMC Genomics
Band
6
Ausgabe
1
Art.-Nr.
158
ISSN
1471-2164
Page URI
https://pub.uni-bielefeld.de/record/1773618
Zitieren
Giuntini E, Mengoni A, De Filippo C, et al. Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains. BMC Genomics. 2005;6(1): 158.
Giuntini, E., Mengoni, A., De Filippo, C., Cavalieri, D., Aubin-Horth, N., Landry, C. R., Becker, A., et al. (2005). Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains. BMC Genomics, 6(1), 158. https://doi.org/10.1186/1471-2164-6-158
Giuntini, Elisa, Mengoni, Alessio, De Filippo, Carlotta, Cavalieri, Duccio, Aubin-Horth, Nadia, Landry, Christian R., Becker, Anke, and Bazzicalupo, Marco. 2005. “Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains”. BMC Genomics 6 (1): 158.
Giuntini, E., Mengoni, A., De Filippo, C., Cavalieri, D., Aubin-Horth, N., Landry, C. R., Becker, A., and Bazzicalupo, M. (2005). Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains. BMC Genomics 6:158.
Giuntini, E., et al., 2005. Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains. BMC Genomics, 6(1): 158.
E. Giuntini, et al., “Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains”, BMC Genomics, vol. 6, 2005, : 158.
Giuntini, E., Mengoni, A., De Filippo, C., Cavalieri, D., Aubin-Horth, N., Landry, C.R., Becker, A., 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, : 158 (2005).
Giuntini, Elisa, Mengoni, Alessio, De Filippo, Carlotta, Cavalieri, Duccio, Aubin-Horth, Nadia, Landry, Christian R., Becker, Anke, and Bazzicalupo, Marco. “Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains”. BMC Genomics 6.1 (2005): 158.
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Rhizobium meliloti carries two megaplasmids.
Banfalvi Z, Kondorosi E, Kondorosi A., Plasmid 13(2), 1985
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Banfalvi Z, Kondorosi E, Kondorosi A., Plasmid 13(2), 1985
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Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid.
Barnett MJ, Fisher RF, Jones T, Komp C, Abola AP, Barloy-Hubler F, Bowser L, Capela D, Galibert F, Gouzy J, Gurjal M, Hong A, Huizar L, Hyman RW, Kahn D, Kahn ML, Kalman S, Keating DH, Palm C, Peck MC, Surzycki R, Wells DH, Yeh KC, Davis RW, Federspiel NA, Long SR., Proc. Natl. Acad. Sci. U.S.A. 98(17), 2001
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PMID: 11481432
The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti.
Finan TM, Weidner S, Wong K, Buhrmester J, Chain P, Vorholter FJ, Hernandez-Lucas I, Becker A, Cowie A, Gouzy J, Golding B, Puhler A., Proc. Natl. Acad. Sci. U.S.A. 98(17), 2001
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Finan TM, Weidner S, Wong K, Buhrmester J, Chain P, Vorholter FJ, Hernandez-Lucas I, Becker A, Cowie A, Gouzy J, Golding B, Puhler A., Proc. Natl. Acad. Sci. U.S.A. 98(17), 2001
PMID: 11481431
Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021.
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, Puhler A, Purnelle B, Ramsperger U, Renard C, Thebault P, Vandenbol M, Weidner S, Galibert F., Proc. Natl. Acad. Sci. U.S.A. 98(17), 2001
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Location of nodulation and nitrogen fixation genes on a high molecular weight plasmid of R. meliloti.
Banfalvi Z, Sakanyan V, Koncz C, Kiss A, Dusha I, Kondorosi A., Mol. Gen. Genet. 184(2), 1981
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Genes controlling early and late functions in symbiosis are located on a megaplasmid in Rhizobium meliloti.
Rosenberg C, Boistard P, Denarie J, Casse-Delbart F., Mol. Gen. Genet. 184(2), 1981
PMID: 6949001
Rosenberg C, Boistard P, Denarie J, Casse-Delbart F., Mol. Gen. Genet. 184(2), 1981
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Genetic relationship of Sinorhizobium meliloti and Sinorhizobium medicae strains isolated from Caucasian region.
Biondi EG, Pilli E, Giuntini E, Roumiantseva ML, Andronov EE, Onichtchouk OP, Kurchak ON, Simarov BV, Dzyubenko NI, Mengoni A, Bazzicalupo M., FEMS Microbiol. Lett. 220(2), 2003
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Genetic diversity and dynamics of Sinorhizobium meliloti populations nodulating different alfalfa cultivars in Italian soils.
Carelli M, Gnocchi S, Fancelli S, Mengoni A, Paffetti D, Scotti C, Bazzicalupo M., Appl. Environ. Microbiol. 66(11), 2000
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Diversity of Sinorhizobium meliloti from the Central Asian Alfalfa Gene Center.
Roumiantseva ML, Andronov EE, Sharypova LA, Dammann-Kalinowski T, Keller M, Young JP, Simarov BV., Appl. Environ. Microbiol. 68(9), 2002
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Genetic diversity of Sinorhizobium populations recovered from different medicago varieties cultivated in Tunisian soils.
Jebara M, Mhamdi R, Aouani ME, Ghrir R, Mars M., Can. J. Microbiol. 47(2), 2001
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Jebara M, Mhamdi R, Aouani ME, Ghrir R, Mars M., Can. J. Microbiol. 47(2), 2001
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Genetic diversity of an Italian Rhizobium meliloti population from different Medicago sativa varieties.
Paffetti D, Scotti C, Gnocchi S, Fancelli S, Bazzicalupo M., Appl. Environ. Microbiol. 62(7), 1996
PMID: 8779566
Paffetti D, Scotti C, Gnocchi S, Fancelli S, Bazzicalupo M., Appl. Environ. Microbiol. 62(7), 1996
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Hierarchical analysis of linkage disequilibrium in Rhizobium populations: evidence for sex?
Souza V, Nguyen TT, Hudson RR, Pinero D, Lenski RE., Proc. Natl. Acad. Sci. U.S.A. 89(17), 1992
PMID: 1518873
Souza V, Nguyen TT, Hudson RR, Pinero D, Lenski RE., Proc. Natl. Acad. Sci. U.S.A. 89(17), 1992
PMID: 1518873
The insertion sequence element ISRm2011-2 belongs to the IS630-Tc1 family of transposable elements and is abundant in Rhizobium meliloti.
Selbitschka W, Arnold W, Jording D, Kosier B, Toro N, Puhler A., Gene 163(1), 1995
PMID: 7557479
Selbitschka W, Arnold W, Jording D, Kosier B, Toro N, Puhler A., Gene 163(1), 1995
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ISRm10: a new insertion sequence of Sinorhizobium meliloti: nucleotide sequence and geographic distribution.
Biondi EG, Fancelli S, Bazzicalupo M., FEMS Microbiol. Lett. 181(1), 1999
PMID: 10564804
Biondi EG, Fancelli S, Bazzicalupo M., FEMS Microbiol. Lett. 181(1), 1999
PMID: 10564804
IS Rm31, a new insertion sequence of the IS 66 family in Sinorhizobium meliloti.
Biondi EG, Femia AP, Favilli F, Bazzicalupo M., Arch. Microbiol. 180(2), 2003
PMID: 12819859
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PMID: 12819859
Global transcriptional analysis of the phosphate starvation response in Sinorhizobium meliloti strains 1021 and 2011.
Krol E, Becker A., Mol. Genet. Genomics 272(1), 2004
PMID: 15221452
Krol E, Becker A., Mol. Genet. Genomics 272(1), 2004
PMID: 15221452
Shaping bacterial genomes with integrative and conjugative elements.
Burrus V, Waldor MK., Res. Microbiol. 155(5), 2004
PMID: 15207870
Burrus V, Waldor MK., Res. Microbiol. 155(5), 2004
PMID: 15207870
Megaplasmid pRme2011a of Sinorhizobium meliloti is not required for viability.
Oresnik IJ, Liu SL, Yost CK, Hynes MF., J. Bacteriol. 182(12), 2000
PMID: 10852892
Oresnik IJ, Liu SL, Yost CK, Hynes MF., J. Bacteriol. 182(12), 2000
PMID: 10852892
The composite genome of the legume symbiont Sinorhizobium meliloti.
Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J., Science 293(5530), 2001
PMID: 11474104
Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J., Science 293(5530), 2001
PMID: 11474104
Genome-wide analysis of DNA copy-number changes using cDNA microarrays.
Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO., Nat. Genet. 23(1), 1999
PMID: 10471496
Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO., Nat. Genet. 23(1), 1999
PMID: 10471496
AUTHOR UNKNOWN, 2004
Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
Smyth GK., 2004
Smyth GK., 2004
Bradley JV., 1968
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