Genome Sequence of the Plant-Pathogenic Bacterium Dickeya dadantii 3937

Abstract

Dickeya dadantii is a plant-pathogenic enterobacterium responsible for the soft rot disease of many plants of economic importance. We present here the sequence of strain 3937, a strain widely used as a model system for research on the molecular biology and pathogenicity of this group of bacteria. Dickeya dadantii, formerly Erwinia chrysanthemi (11), is the causative agent of soft rot disease in a wide range of plant species, including many economically important crops (10). Soft rot results from the maceration of plant tissues following degradation of pectin, the major component of primary cell walls (7). D. dadantii is a devastating opportunistic pathogen in storage organs and fleshy tissues, particularly when compromised by bruising, excess water, low oxygen levels, or high temperatures. D. dadantii is also associated with systemic infections, vascular disorders, foliar necroses, and latent infections in growing plants. We sequenced and annotated the complete genome of Dickeya dadantii strain 3937, a strain widely used as a model system for research on the molecular biology and pathogenicity of this group of bacteria. Two whole-genome shotgun libraries were prepared with plasmid pHOS2 with target insert sizes of 2 to 3 kb and 10 to 12 kb. We collected approximately 67,000 dual-end sequences, 67% from small-insert clones and 33% from the larger insert library. Sequences were assembled into contigs using the Celera assembler (9), and this assembly was transferred to SeqMan II (Lasergene) for finishing. Primer walking was employed to close gaps covered by clones available from the shotgun libraries. The remaining gaps were closed by sequencing PCR products generated using primers designed from the ends of assembled and ordered contigs. PCR products spanning each rRNA operon were sequenced separately to resolve sequence differences between copies. We used Glimmer 2.0 (3) for initial prediction of protein coding regions. We added, deleted, and revised endpoints of genes based on comparisons to other genomes, genes, and proteins in the NCBI databases. tRNA sequences were identified using tRNAscan-SE (8) with additional examination to identify specific tRNAs not distinguishable by their anticodons alone. rRNA genes were identified by comparison to other enterobacterial sequences using

Inactivation of pecS restores the virulence of mutants devoid of osmoregulated periplasmic glucans in the phytopathogenic bacterium Dickeya dadantii

“…This pathogen devastates economically important crops in storage facilities or growing plants (Glasner et al, 2011). Maceration, an apparent symptom of the disease, is the result of the synthesis and secretion of a set of plant cell wall-degrading enzymes (PCWDEs), particularly pectinases (Barras et al, 1994;Collmer & Keen, 1986), but many additional factors are required for full virulence.…”

A family 3 glycosyl hydrolase of Dickeya dadantii 3937 is involved in the cleavage of aromatic glucosides

“…The genome of strain 3937 (Glasner et al, 2011) was analysed for the presence of genes encoding potential glycosidases. One of these genes (ID 20203) encodes a protein of the GH3 family that is homologous to the bgxA product of the Dickeya strain D1 (92 % identity) (Vroemen et al, 1995).…”

“…Preparation of plasmid DNA, restriction digestions, ligations, DNA electrophoresis and transformations were carried out as described by Sambrook & Russell (2001). Sequence data were obtained from the genome sequencing project of D. dadantii strain 3937 (Glasner et al, 2011). PCR primers (23-and 27-mers) were designed to amplify 2 kb of D. dadantii 3937 chromosomal DNA overlapping bgxA (Table 1).…”

“…The D. dadantii strain 3937 was isolated from the dicot plant S. ionantha. Several genes encoding potential glycosidases were predicted from its genome sequence (Glasner et al, 2011); one of these genes is homologous to bgxA of strain D1. In the present work, we further analysed bgxA expression and BgxA specificity to understand the biological role of this enzyme in the model dicot strain D. dadantii 3937.…”

“…In the genus Dickeya, most studies have been performed on the D. dadantii strain 3937 isolated from African violet (Saintpaulia ionantha). This strain has been chosen as a model by the Dickeya international community for complete genome sequencing (Glasner et al, 2011).…”