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Comparative Sequence Analysis of the Symbiosis Island of Mesorhizobium loti Strain R7A

John T. Sullivan,¹ Jodi R. Trzebiatowski,^2, Ruth W. Cruickshank,^1, Jerome Gouzy,³ Steven D. Brown,¹ Rachel M. Elliot,¹ Damien J. Fleetwood,¹ Nadine G. McCallum,^1, Uwe Rossbach,² Gabriella S. Stuart,¹ Julie E. Weaver,¹ Richard J. Webby,^1,|| Frans J. de Bruijn,^2,3 and Clive W. Ronson^1*

Department of Microbiology, University of Otago, Dunedin, New Zealand,¹ MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824,² Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, Unité Mixte de Recherche (UMR) 215, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique, F-31326 Castanet Tolosan Cedex, France³

Received 3 December 2001/ Accepted 5 February 2002

The Mesorhizobium loti strain R7A symbiosis island is a 502-kb chromosomally integrated element which transfers to nonsymbiotic mesorhizobia in the environment, converting them to Lotus symbionts. It integrates into a phenylalanine tRNA gene in a process mediated by a P4-type integrase encoded at the left end of the element. We have determined the nucleotide sequence of the island and compared its deduced genetic complement with that reported for the 611-kb putative symbiosis island of M. loti strain MAFF303099. The two islands share 248 kb of DNA, with multiple deletions and insertions of up to 168 kb interrupting highly conserved colinear DNA regions in the two strains. The shared DNA regions contain all the genes likely to be required for Nod factor synthesis, nitrogen fixation, and island transfer. Transfer genes include a trb operon and a cluster of potential tra genes which are also present on the strain MAFF303099 plasmid pMLb. The island lacks plasmid replication genes, suggesting that it is a site-specific conjugative transposon. The R7A island encodes a type IV secretion system with strong similarity to the vir pilus from Agrobacterium tumefaciens that is deleted from MAFF303099, which in turn encodes a type III secretion system not found on the R7A island. The 414 genes on the R7A island also include putative regulatory genes, transport genes, and an array of metabolic genes. Most of the unique hypothetical genes on the R7A island are strain-specific and clustered, suggesting that they may represent other acquired genetic elements rather than symbiotically relevant DNA.

Present address: Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201.

Present address: Genesis Research and Development Corporation, Auckland, New Zealand.

Present address: Institute of Medical Microbiology, University of Zürich, 8028 Zürich, Switzerland.

^|| Present address: Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105-2794.

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