Identification Of Rhizobiumspecific Protein Families By Comparative Genomics

Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, INRA/CNRS, BP 27, 31326 Castanet-Tolosan Cedex, France

Two complete Rhizobium genome sequences have now been determined, for Sinorhizobium meliloti (Galibert et al. 2001) and Mesorhizobium loti (Kaneko et al. 2000). It thus becomes possible (i) to compare the structures of the genomes; (ii) to systematically investigate which genes are shared between different rhizobia; and (iii) to identify which genes may be considered as Rhizobium-specific.

The comparison of the S. meliloti and M. loti genome structures showed limited macrosynteny between their chromosomes and no synteny between S. meliloti pSym plasmids and the M. loti genome. In particular no synteny was found between S. meliloti pSymA and the M. loti symbiotic island. Similarly no synteny was observed between pSymA and the symbiotic region of the Bradyrhizobium japonicum genome (GĂ´ttfert et al. 2001).

Clustering of homologous proteins coded by the S. meliloti and M. loti genomes generated 2347 protein families. Among these, 131 families were found in S. meliloti only, and 142 families in M. loti only. Two-hundred and seventeen protein families were Rhizobium-specific. The CyaG family of nucleotide cyclases was identified among these. Rhizobium nucleotide cyclases were systematically analyzed using the mkdom program (Gouzy et al. 1999) in order to identify the various types of domain arrangements. Forty-three cyclase related proteins were found in both genomes, which represents a considerable expansion when compared to other genomes. Four families are shared by the two rhizobia, including the CyaF, CyaG and CyaH families which appeared Rhizobium specific. The CyaF class appears to have expanded remarkably in rhizobia, with seven paralogs in S. meliloti and four paralogs in M. loti. CyaF cyclases can be defined structurally by an N-terminal catalytic domain and C-terminal TPR repeats. The role of this novel, Rhizobium-specific cyclase family remains to be defined.

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