Genome of the Actinomycete Plant Pathogen Clavibacter michiganensis subsp. sepedonicus Suggests Recent Niche Adaptation

Abstract

Clavibacter michiganensis subsp. sepedonicus is a plant-pathogenic bacterium and the causative agent of bacterial ring rot, a devastating agricultural disease under strict quarantine control and zero tolerance in the seed potato industry. This organism appears to be largely restricted to an endophytic lifestyle, proliferating within plant tissues and unable to persist in the absence of plant material. Analysis of the genome sequence of C. michiganensis subsp. sepedonicus and comparison with the genome sequences of related plant pathogens revealed a dramatic recent evolutionary history. The genome contains 106 insertion sequence elements, which appear to have been active in extensive rearrangement of the chromosome compared to that of Clavibacter michiganensis subsp. michiganensis. There are 110 pseudogenes with overrepresentation in functions associated with carbohydrate metabolism, transcriptional regulation, and pathogenicity. Genome comparisons also indicated that there is substantial gene content diversity within the species, probably due to differential gene acquisition and loss. These genomic features and evolutionary dating suggest that there was recent adaptation for life in a restricted niche where nutrient diversity and perhaps competition are low, correlated with a reduced ability to exploit previously occupied complex niches outside the plant. Toleration of factors such as multiplication and integration of insertion sequence elements, genome rearrangements, and functional disruption of many genes and operons seems to indicate that there has been general relaxation of selective pressure on a large proportion of the genome.High-GϩC-content gram-positive coryneform bacteria cause economic losses in several crops worldwide, yet the relatively slow in vitro and in planta growth and general genetic intractability of these bacteria have long been deterrents to successful identification of the specific molecular mechanisms by which they cause diseases in plants. Consequently, there is a clear disparity between the amount of scientific research on plant-pathogenic coryneform bacteria and the amount of scientific research on their gramnegative counterparts. Recent advances in this field have coincided with the availability of transformation systems and complete genome sequences for representatives of the genera Clavibacter and Leifsonia, two of the major coryneform plant-pathogenic genera (14,32,48,56,74). Importantly, these advances allowed breakthrough identification of a novel set of pathogenicity-related genes in the tomato pathogen Clavibacter michiganensis subsp. michiganensis and identification of homologues in other coryneform plant pathogens (15, 27, 32; see the accompanying paper). Because methodologies created for functional analysis of C. michiganensis subsp. michiganensis are generally applicable to other members of the genus, additional advances in this field can be expected in the near future (40, 46).The genus Clavibacter provides an excellent resource for obtaining a more comprehensive underst...

An Environmental Model Predicting Bacterial Ring Rot Symptom Expression

“…This supports previous observations and our understanding of conditions that influence the severity of symptoms of BRR infection (Manzer et al 1987). Warmer temperatures especially later in the season have been reported to increase disease symptom expression probably due to the impact of restricted water availability caused by the destruction or blockage of vascular xylem tissues by bacteria such as Cms in infected plants (Bentley et al 2008;De Boer and Slack 1984;Inglis et al 2000;Laine et al 2000;Westra and Slack 1992). Extracellular polysacharides and macerating enzymes such as cellulase capable of contributing to the disruption observed plant cell vascular tissues have been identified in Cms.…”

Diversity of Plant Associated Actinobacteria

“…michiganensis and subsp. sepedonicus have occurred 53,000 to 1,120,000 years ago (Bentley et al 2008).…”

The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

“…This could occur once every 46 million years, assuming a mutation rate of one nucleotide every 95,000 years and 2,085 generations per year ( S. lividans reproduces every 4.2 hours; Palacin et al 2003); this didactic estimate is based on an average mutation rate of 5.0 base pairs every 10 10 nucleotides per generation (Drake 1991; Drake et al 1998; Lynch 2006; Bentley et al 2008; note that our estimate disregards the tetrameric configuration of KcsA, whose structural and functional assemblage must have required additional time-consuming evolution). But mutations are complex, occur in clusters, occur at different rates within and between genes (= “hot spots” in the genome); and networks of genes can coevolve (e.g., interacting ion-channel genes), thus increasing and maintaining informational complexity, decreasing uncertainty, and expediting evolution (for detailed discussions on computational methods and theoretical implications see Schneider 2000; Lynch 2005, 2006; Durrett and Schmidt 2008; Stern and Orgogozo 2009).…”