Species code:	CLAMS
Taxonomy:	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Micrococcineae; Microbacteriaceae; Clavibacter (TaxID: 31964) [NEWT/ NCBI]
Description:	Clavibacter michiganensis subsp. sepedonicus is a plant-pathogenic actinomycete that causes the bacterial ring rot, a devastating agricultural disease. Its genome is made up of a circular chromosome and two plasmids, one circular pCS1 and one linear pCSL1. It contains 106 insertion elements that appear to be randomly distributed. Only five IS are inserted directly into CDSs. It contains 110 pseudogenes, accounting for 3.4% of the CDSs. This high level of nonfunctional genes suggests that there has been genome decay, a phenomenon often associated with bacterial lineages that have recently acquired a new niche. Their distribution shows an overrepresentation in transport and degradation of carbohydrates, regulation and functions related to pathogenicity and adaptation. Intriguingly, the cellulase gene celB, an important determinant in pathogenicity, is disrupted. However, it should be noted that the plasmid-borne cellulase gene celA is intact. These genomic features suggest a recent adaptation for life in a restricted niche. Clavibacter michiganensis subsp. sepedonicus appears indeed to be largely restricted to an endophytic lifestyle, proliferating within plant tissues and unable to survive in the absence of plant material. The bacterium spreads easily within potato farms during seed cutting and can be readily disseminated in latently infected tubers by contaminated farm equipment, in storage facilities or in packing materials. The main economic loss occurs in the seed industry but losses can also occur in the fresh and processed potato industries. Bacterial ring rot is normally associated with the temperate climates of North America, Scandinavia, Northern Europe and Asia.
Properties:	Presence of flagella: No Interaction: Plant pathogen Number of membranes: 1 Number of inteins:0
Statistics:	Number of CLAMS entries in the UniProt Knowledgebase: 3057 (147 in UniProtKB/Swiss-Prot + 2910 in UniProtKB/TrEMBL)

Genome structure:	• Chromosome EMBL accession number AM849034 (circular; 3,258,645 bp) (download entry) (download Genome Reviews). • Plasmid pCS1 EMBL accession number AM849035 (circular; 50,350 bp) (download entry) (download Genome Reviews). • Plasmid pCSL1 EMBL accession number AM849036 (circular; 94,791 bp) (download entry) (download Genome Reviews).
Reference(s):	[1] PubMed=18192393; [ NCBI , EBI , Israel , Japan ] Bentley S.D., Corton C., Brown S.E., Barron A., Clark L., Doggett J., Harris B., Ormond D., Quail M.A., May G., Francis D., Knudson D., Parkhill J., Ishimaru C.A. ; "Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation."; J. Bacteriol. 190:2150-2160(2008).
Web links:	Official genome site(s): http://www.sanger.ac.uk/Projects/C_michiganensis/ Other web sites: Entrez Genome Project: http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=184 GIB (DDBJ): http://gib.genes.nig.ac.jp/single/index.php?spid=Cmic_sepedonicus  EBI Proteome Analysis page

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