The celC gene, a new phylogenetic marker useful for taxonomic studies in Rhizobium

Systematic and Applied Microbiology

Volumn 34, Issue 6, 2011, Pages 393-399

  Robledo, Marta ^a   Velázquez, Encarna ^a   Ramírez Bahena, Martha Helena ^a,b   García Fraile, Paula ^a   Pérez Alonso, Ana ^a   Rivas, Raúl ^a   Martínez Molina, Eustoquio ^a   Mateos, Pedro F ^a  

^a UNIVERSITY OF SALAMANCA   (Spain)

^b University of Lyon   (France)

Author keywords

CelC; Cellulose; Endoglucanases; Phylogeny; Taxonomy

Indexed keywords

ARTICLE; ATPD GENE; BACTERIAL GENE; BACTERIAL GENETICS; BACTERIAL GENOME; CELC GENE; GENE SEQUENCE; GENETIC ANALYSIS; LEGUME; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT TUMOR; PLASMID; PRIORITY JOURNAL; RECA GENE; RHIZOBIUM; RHIZOBIUM ALAMII; RHIZOBIUM ETLI; RHIZOBIUM FABAE; RHIZOBIUM GALLICUM; RHIZOBIUM GIARDINI; RHIZOBIUM GIARDINII; RHIZOBIUM HAINANENSE; RHIZOBIUM INDIGOFERAE; RHIZOBIUM LEGUMINOSARUM; RHIZOBIUM MONGOLENSE; RHIZOBIUM PHASEOLI; RHIZOBIUM PISI; RHIZOBIUM RADIOBACTER; RHIZOBIUM RHIZOGENES; RHIZOBIUM TIBETICUM; RHIZOBIUM TROPICI; RRS GENE; SPECIES DIFFERENTIATION; TAXONOMY;

BACTERIAL PROTEINS; BETA-GLUCOSIDASE; DNA, BACTERIAL; FABACEAE; PHYLOGENY; RHIZOBIUM; SEQUENCE ANALYSIS, DNA; SYMBIOSIS; TRIFOLIUM; VIRULENCE;

AGROBACTERIUM TUMEFACIENS; RHIZOBIUM; RHIZOBIUM ETLI; RHIZOBIUM LEGUMINOSARUM; TRIFOLIUM;

EID: 80051690647     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2011.01.010     Document Type: Article

References (36)

1. Alschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
2. Álvarez-Martínez E.R., Valverde A., Ramírez-Bahena M.H., García-Fraile P., Tejedor C., Mateos P.F., Santillana N., Zuñiga D., Peix A., Velázquez E. The analysis of core and symbiotic genes of rhizobia nodulating Vicia from different continents reveals their common phylogenetic origin and suggests the distribution of Rhizobium leguminosarum strains together with Vicia seeds. Arch. Microbiol. 2009, 191:659-668.
3. Amarger N., Macheret V., Laguerre G. Rhizobium gallicum sp. nov. and Rhizobium giardinii sp. nov., from Phaseolus vulgaris nodules. Int. J. Syst. Bacteriol. 1997, 47:996-1006.
4. An J.M., Lim W.J., Hong S.Y., Shin E.C., Kim E.J., Kim Y.K., Park S.R., Yun H.D. Cloning and characterization of ce/8A gene from Rhizobium leguminosarum bv. trifolii 1536. Lett. Appl. Microbiol. 2004, 38:296-300.
5. Ausmees N., Jonsson H., Hoglund S., Ljunggren H., Lindberg M. Structural and putative regulatory genes involved in cellulose synthesis in Rhizobium leguminosarum bv. trifolii. Microbiology 1999, 145:1253-1262.
6. Farrand S.K., van Berkum P., Oger P. Agrobacterium is a definable genus of the family Rhizobiaceae. Int. J. Syst. Evol. Microbiol. 2003, 53:1681-1687.
7. García-Fraile P., Mulas-García D., Peix A., Rivas R., González-Andres F., Velázquez E. Phaseolus vulgaris is nodulated in northern Spain by Rhizobium leguminosarum strains harboring two nodC alleles present in American Rhizobium etli strains: biogeographical and evolutionary implications. Can. J. Microbiol. 2010, 56:657-666.
8. Gaunt M.W., Turner S.L., Rigottier-Gois L., Lloyd-Macgilp S.A., Young J.P. Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. Int. J. Syst. Evol. Microbiol. 2001, 51:2037-2048.
9. González V., Acosta J.L., Santamaría R.I., Bustos P., Fernández J.L., Hernández-González I.L., Díaz R., Flores M., Palacios R., Mora J., Dávila G. Conserved symbiotic plasmid DNA sequences in the multireplicon pangenomic structure of Rhizobium etli. Appl. Environ. Microbiol. 2010, 76:1604-1614.
10. Guiseppi C., Aymeric J.L., Cami B., Barras F., Creuzet N. Sequence analysis of the cellulase-encoding celY gene of Erwinia chrysanthemi: a possible case of interspecies gene transfer. Gene 1991, 106:109-114.
11. Iglesias O., Rivas R., García-Fraile P., Abril A., Mateos P.F., Martínez-Molina E., Velázquez E. Genetic characterization of fast-growing rhizobia able to nodulate Prosopis alba in North Spain. FEMS Microbiol. Lett. 2007, 277:210-216.
12. Jarvis B.D., Downer H.L., Young J.P. Phylogeny of fast-growing soybean-nodulating rhizobia support synonymy of Sinorhizobium and Rhizobium and assignment to Rhizobium fredii. Int. J. Syst. Bacteriol. 1992, 42:93-96.
13. Jordan D.C. Family III. Rhizobiaceae. Bergey's Manual of Systematic Bacteriology 1984, 234-242. The Williams and Wilkins Co., Baltimore. N.R. Krieg, J.G. Holt (Eds.).
14. Kersters K., de Ley J. Genus III. Agrobacterium. Bergey's Manual of Systematic Bacteriology 1984, 244-254. Williams and Wilkins Co., Baltimore. N.R. Krieg, J.G. Holt (Eds.).
15. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 1980, 16:111-120.
16. Krishnamohan A., Balaji V., Veluthambi K. Efficient vir gene induction in Agrobacterium tumefaciens requires virA, virG, and vir box from the same Ti plasmid. J. Bacteriol. 2001, 183:4079-4089.
17. AL. Bergey's Manual of Systematic Bacteriology. Part C 2005, vol. 2:324-361. Springer, New York.
18. Laguerre G., Nour S.M., Macheret V., Sanjuan J., Drouin P., Amarger N. Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. Microbiology 2001, 147:981-993.
19. Lindström K., Young J.P.W. International Committee on Systematics of Prokaryotes; Subcommittee on the taxonomy of Agrobacterium and Rhizobium: minutes of the meetings, 31 August 2008, Gent, Belgium. Int. J. Syst. Evol. Microbiol. 2009, 59:921-922.
20. Matthysse A.G., Thomas D.L., White A.R. Mechanism of cellulose synthesis in Agrobacterium tumefaciens. J. Bacteriol. 1995, 177:1076-1081.
21. Moore L.W., Warren G. Agrobacterium radiobacter strain K84 and biological control of crown gall. Annu. Rev. Phytopathol. 1979, 17:163-179.
22. Ramírez-Bahena M.H., García-Fraile P., Peix A., Valverde A., Rivas R., Igual J.M., Mateos P.F., Martínez-Molina E., Velázquez E. Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank 1889, R. phaseoli Dangeard 1926AL and R. trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the strain Rhizobium leguminosarum DSM 30132T (=NCIMB 11478T) into the new species Rhizobium pisi sp. nov. Int. J. Syst. Evol. Microbiol. 2008, 58:2484-2490.
23. Rivas R., García-Fraile P., Mateos P.F., Martínez-Molina E., Velázquez E. Characterization of xylanolytic bacteria present in the bract phyllosphere of the date palm Phoenix dactylifera. Lett. Appl. Microbiol. 2007, 44:181-187.
24. Robledo M., Jiménez-Zurdo J.I., Velázquez E., Trujillo M.E., Zurdo-Piñeiro J.L., Ramírez-Bahena M.H., Ramos B., Díaz-Mínguez J.M., Dazzo F.B., Martínez-Molina E., Mateos P.F. Rhizobium cellulase CelC2 is essential for primary symbiotic infection of legume host roots. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:7064-7069.
25. Roche P., Maillet F., Plazanet C., Debellé F., Ferro M., Truchet G., Promé J.C., Dénarié J. The common nodABC genes of Rhizobium meliloti are host-range determinants. Proc. Natl. Acad. Sci. U.S.A. 1996, 93:15305-15310.
26. Saitou N., Nei M. A neighbour-joining method: a new method for reconstructing phylogenetics trees. Mol. Biol. Evol. 1987, 44:406-425.
27. Segovia L., Young J.P.W., Martínez-Romero E. Reclassification of American Rhizobium leguminosarum biovar phaseoli type I strains as Rhizobium etli sp. nov. Int. J. Syst. Bacteriol. 1993, 43:374-377.
28. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
29. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acid Res. 1997, 24:4876-4882.
30. Turner S.L., Zhang X.X., Li F.D., Young J.P. What does a bacterial genome sequence represent? Mis-assignment of MAFF 303099 to the genospecies Mesorhizobium loti. Microbiology 2002, 148:3330-3331.
31. Valverde A., Igual J.M., Peix A., Cervantes E., Velázquez E. Rhizobium lusitanum sp. nov. a bacterium that nodulates Phaseolus vulgaris. Int. J. Syst. Evol. Microbiol. 2006, 56:2631-2637.
32. van Berkum P., Beyene D., Bao G., Campbell T.A., Eardly B.D. Rhizobium mongolense sp. nov. is one of three rhizobial genotypes identified which nodulate and form nitrogen-fixing symbioses with Medicago ruthenica [(L.) Ledebour]. Int. J. Syst. Bacteriol. 1998, 48:13-22.
33. Velázquez E., Palomo J.L., Rivas R., Guerra H., Peix A., Trujillo M.E., García-Benavides P., Mateos P.F., Wabiko H., Martínez-Molina E. Analysis of core genes supports the reclassification of strains Agrobacterium radiobacter K84 and Agrobacterium tumefaciens AKE10 into the species Rhizobium rhizogenes. Syst. Appl. Microbiol. 2010, 33:247-251.
34. Velázquez E., Peix A., Zurdo-Piñeiro J.L., Palomo J.L., Mateos P.F., Rivas R., Muñoz-Adelantado E., Toro N., García-Benavides P., Martínez-Molina E. The coexistence of symbiosis and pathogenicity-determining genes in Rhizobium rhizogenes strains enables them to induce nodules and tumours or hairy roots in plants. Mol. Plant Microbe Interact. 2005, 18:1325-1332.
35. Wang E.T., Rogel M.A., García-de los Santos A., Martínez-Romero J., Cevallos M.A., Martínez-Romero E. Rhizobium etli bv. mimosae, a novel biovar isolated from Mimosa affinis. Int. J. Syst. Bacteriol. 1999, 49(Pt 4):1479-1491.
36. Young J.M., Kuykendall L.D., Martínez-Romero E., Kerr A., Sawada H.A. A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis. Int. J. Syst. Evol. Microbiol. 2001, 51:89-103.