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The Genome Sequence of the Tomato-Pathogenic Actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 Reveals a Large Island Involved in Pathogenicity ^,

Karl-Heinz Gartemann,^1,2 Birte Abt,¹ Thomas Bekel,² Annette Burger,¹ Jutta Engemann,¹ Monika Flügel,¹ Lars Gaigalat,^2,3 Alexander Goesmann,² Ines Gräfen,^1, Jörn Kalinowski,^2,3 Olaf Kaup,¹ Oliver Kirchner,^1, Lutz Krause,² Burkhard Linke,² Alice McHardy,^2,¶ Folker Meyer,^2,|| Sandra Pohle,¹ Christian Rückert,^2,3 Susanne Schneiker,^2,3 Eva-Maria Zellermann,¹ Alfred Pühler,^2,3 Rudolf Eichenlaub,^1,2* Olaf Kaiser,^2,3,# and Daniela Bartels^2,||

Lehrstuhl für Gentechnologie/Mikrobiologie,¹ Center for Biotechnology (Cebitec),² Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany³

Received 2 October 2007/ Accepted 23 December 2007

Clavibacter michiganensis subsp. michiganensis is a plant-pathogenic actinomycete that causes bacterial wilt and canker of tomato. The nucleotide sequence of the genome of strain NCPPB382 was determined. The chromosome is circular, consists of 3.298 Mb, and has a high G+C content (72.6%). Annotation revealed 3,080 putative protein-encoding sequences; only 26 pseudogenes were detected. Two rrn operons, 45 tRNAs, and three small stable RNA genes were found. The two circular plasmids, pCM1 (27.4 kbp) and pCM2 (70.0 kbp), which carry pathogenicity genes and thus are essential for virulence, have lower G+C contents (66.5 and 67.6%, respectively). In contrast to the genome of the closely related organism Clavibacter michiganensis subsp. sepedonicus, the genome of C. michiganensis subsp. michiganensis lacks complete insertion elements and transposons. The 129-kb chp/tomA region with a low G+C content near the chromosomal origin of replication was shown to be necessary for pathogenicity. This region contains numerous genes encoding proteins involved in uptake and metabolism of sugars and several serine proteases. There is evidence that single genes located in this region, especially genes encoding serine proteases, are required for efficient colonization of the host. Although C. michiganensis subsp. michiganensis grows mainly in the xylem of tomato plants, no evidence for pronounced genome reduction was found. C. michiganensis subsp. michiganensis seems to have as many transporters and regulators as typical soil-inhabiting bacteria. However, the apparent lack of a sulfate reduction pathway, which makes C. michiganensis subsp. michiganensis dependent on reduced sulfur compounds for growth, is probably the reason for the poor survival of C. michiganensis subsp. michiganensis in soil.

Published ahead of print on 11 January 2008.

Supplemental material for this article may be found at http://jb.asm.org/.

Present address: Herz- und Diabeteszentrum NRW, Georgstr. 11, 32545 Bad Oeynhausen, Germany.

Present address: Schott Jenaer Glas GmbH, Otto-Schott-Str. 13, 07745 Jena, Germany.

^¶ Present address: Max Planck Institut für Informatik, Stuhlsatzenhausweg 85, 66123 Saarbruecken, Germany.

^|| Present address: Mathematics and Computer Science, Argonne National Laboratory, Argonne, IL 60439.

^# Present address: Roche Diagnostics GmbH, Werk Penzberg, Nonnenwald 2, 82372 Penzberg, Germany.