The Genome Sequence of the Tomato-Pathogenic ActinomyceteClavibacter michiganensissubsp.michiganensisNCPPB382 Reveals a Large Island Involved in Pathogenicity

Abstract

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.

Organization of the biosynthetic genes encoding deoxyactagardine B (DAB), a new lantibiotic produced by Actinoplanes liguriae NCIMB41362

“…This is consistent with the arrangement described for the lantibiotic clusters of actagardine A, 12 cinnamycin 6 and michiganin A. 27 The apparent lack of a discrete protease or protease domain encoded amongst the genes identified in this work suggests that cleavage of the leader peptide is carried out by an enzyme encoded by a gene or genes elsewhere on the host's genomic DNA or alternatively occurs by a novel cleavage mechanism. The organization and degree of similarity between the genes of the actagardine A biosynthetic cluster and DAB significantly decreases beyond the boundaries of their respective structural gene (lanA) and lanR, falling from around 76% (65% including ORF14) within this boundary to between 30-42% at the flanking regions.…”

The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation

“…In some cases the manual curation corrected structural features, such as placement of start codons, (e.g. Clavibacter michiganensis [20]) while others appraised the data used to infer function (e.g. hits to various databases, performing of protein alignments) in order to identify erroneous functional assignments [14,21].…”

The influence of the accessory genome on bacterial pathogen evolution

“…GIs are also important in the pathogenicity of plant pathogens: for example, Clavibacter michiganensis, a pathogen of tomato, contains a 129 kb island that is necessary for pathogenicity. 49 Also, plant pathogenic Streptomyces species contain a large mobile PAI that encodes multiple virulence-associated genes, including the nitrated dipeptide phytotoxin thaxtomin biosynthetic genes and the virulence factor nec1, whose transfer to other Streptomyces species is responsible for the emergence of new pathogens in agricultural settings. 50 A common PAI found in a number of animal and plant pathogenic bacteria is the T3SS PAI.…”