Genomic Diversity of Erwinia carotovora subsp. carotovora and Its Correlation with Virulence

Abstract

We used genetic and biochemical methods to examine the genomic diversity of the enterobacterial plant pathogen Erwinia carotovora subsp. carotovora. The results obtained with each method showed that E. carotovora subsp. carotovora strains isolated from one ecological niche, potato plants, are surprisingly diverse compared to related pathogens. A comparison of 23 partial mdh sequences revealed a maximum pairwise difference of 10.49% and an average pairwise difference of 2.13%, values which are much greater than the maximum variation (1.81%) and average variation (0.75%) previously reported for Escherichia coli. Pulsed-field gel electrophoresis analysis of I-CeuI-digested genomic DNA revealed seven rrn operons in all E. carotovora subsp. carotovora strains examined except strain WPP17, which had only six copies. We identified 26 I-CeuI restriction fragment length polymorphism patterns and observed significant polymorphism in fragment sizes ranging from 100 to 450 kb for all strains. We detected large plasmids in two strains, including the model strain E. carotovora subsp. carotovora 71. The two least virulent strains had an unusual chromosomal structure, suggesting that a particular pulsotype is correlated with virulence. To compare chromosomal organization of multiple enterobacterial genomes, several genes were mapped onto I-CeuI fragments. We identified portions of the genome that appear to be conserved across enterobacteria and portions that have undergone genome rearrangements. We found that the least virulent strain, WPP17, failed to oxidize cellobiose and was missing several hrp and hrc genes. The unexpected variability among isolates obtained from clonal hosts in one region and in one season suggests that factors other than the host plant, potato, drive the evolution of this common environmental bacterium and key plant pathogen.The plant-pathogenic species Erwinia carotovora is a complex taxon consisting of strains with a range of different phenotypic, biochemical, host range, and genetic characteristics. This species is well suited for studying the ecology, speciation, and pathogenicity of enterobacterial pathogens since it is widespread in the environment, it can infect numerous plant species (42), and many of its virulence genes have been identified, including genes encoding degradative enzymes, diverse regulatory systems, and the type III secretion system (TTSS) (42). E. carotovora is considered a broad-host-range soft rot pathogen because under laboratory conditions it can macerate plant tissues from numerous species. However, in nature, E. carotovora subspecies are associated with particular plant species, showing subspecies adaptation to specific hosts. None of the genetic differences responsible for host specialization in E. carotovora, which is one of the world's most economically important bacterial plant pathogens, have been identified yet.The taxonomy of the soft rot Erwinia is in flux. Recently, Hauben et al. (16) proposed resurrecting the name Pectobacterium, but the majority of the Erwinia r...

Pectobacterium carotovorum subsp. carotovorum - the causal agent of broccoli soft rot in Serbia

“…Previously, P. c. ssp. carotovorum strains had been shown to vary in their ability to cause HR in tobacco and the presence of type III secretion system (Yap et al, 2004;Kim et al, 2009;Baghaee-Ravari et al, 2011;Nabhan et al, 2012).…”

The Lectin Receptor Kinase-VI.2 Is Required for Priming and Positively Regulates Arabidopsis Pattern-Triggered Immunity

“…To test the role of LecRK-VI.2 during the PTI response induced by Pcc, expression of LecRK-VI.2 was evaluated after infection with Pcc strain WPP17 that is deficient in several HRP and HRC genes (Yap et al, 2004). Similarly to Pst DC3000 hrcC mutant bacteria (see Supplemental Figure 4B online), LecRK-VI.2 mRNA transcripts accumulated at 6 h after inoculation with Pcc WPP17 (see Supplemental Figure 7 online).…”

“…Pst bacteria were cultivated at 288C and 340 rpm in King's B medium containing rifampicin (Pst DC3000), rifampicin, spectinomycin, and kanamycin (DB29) or rifampicin and kanamycin (CB200). We obtained Pcc hp-and hrc-deficient strain WPP17 (Yap et al, 2004) from Amy Charkowski (University of Wisconsin, Madison, WI), and Pcc SCC1 (Kariola et al, 2005) expressing the green fluorescent protein (Kwon et al, 2009) were a gift from Ohkmae Park (Korea University, Seoul, Korea). Pcc bacteria were cultivated at 288C and 340 rpm in Luria-Bertani medium (Bioman Scientific) for 16 to 18 h without selection (Pcc WPP17) or with ampicillin (Pcc SCC1).…”

First report of Dickeya dianthicola and Pectobacterium wasabiae causing aerial stem rot of potato in Michigan, USA

“…Additionally partial sequences of 16S rRNA (1,276 bp), acnA (404 bp) and mdh (563 bp) genes (KT626462, KT932316 and KT932315, respectively) showed 99% identities with Pectobacterium wasabiae strain WPP163. Maximum parsimony analysis (Yap et al, 2004) using concatenated 16S rRNA and mdh sequences from this study and Dickeya spp. and Pectobacterium spp.…”

“…Dickeya and Pectobacterium spp. have been recovered from potato production fields in parts of the USA (Dickey, 1979;Ma et al, 2007) DNA analysis of the bacteria was done with 16S rRNA, aconitase (acnA) and malate dehydrogenase (mdh) coding sequences as described previously (Yap et al, 2004). Partial sequences of 16S rRNA (1,219 bp) and acnA (407 bp) genes (GenBank Accession Nos.…”