The complete genome sequence of Dickeya zeae EC1 reveals substantial divergence from other Dickeya strains and species

Abstract

BackgroundDickeya zeae is a bacterial species that infects monocotyledons and dicotyledons. Two antibiotic-like phytotoxins named zeamine and zeamine II were reported to play an important role in rice seed germination, and two genes associated with zeamines production, i.e., zmsA and zmsK, have been thoroughly characterized. However, other virulence factors and its molecular mechanisms of host specificity and pathogenesis are hardly known.ResultsThe complete genome of D. zeae strain EC1 isolated from diseased rice plants was sequenced, annotated, and compared with the genomes of other Dickeya spp.. The pathogen contains a chromosome of 4,532,364 bp with 4,154 predicted protein-coding genes. Comparative genomics analysis indicates that D. zeae EC1 is most co-linear with D. chrysanthemi Ech1591, most conserved with D. zeae Ech586 and least similar to D. paradisiaca Ech703. Substantial genomic rearrangement was revealed by comparing EC1 with Ech586 and Ech703. Most virulence genes were well-conserved in Dickeya strains except Ech703. Significantly, the zms gene cluster involved in biosynthesis of zeamines, which were shown previously as key virulence determinants, is present in D. zeae strains isolated from rice, and some D. solani strains, but absent in other Dickeya species and the D. zeae strains isolated from other plants or sources. In addition, a DNA fragment containing 9 genes associated with fatty acid biosynthesis was found inserted in the fli gene cluster encoding flagellar biosynthesis of strain EC1 and other two rice isolates but not in other strains. This gene cluster shares a high protein similarity to the fatty acid genes from Pantoea ananatis.ConlusionOur findings delineate the genetic background of D. zeae EC1, which infects both dicotyledons and monocotyledons, and suggest that D. zeae strains isolated from rice could be grouped into a distinct pathovar, i.e., D. zeae subsp. oryzae. In addition, the results of this study also unveiled that the zms gene cluster presented in the genomes of D. zeae rice isolates and D. solani strains, and the fatty acid genes inserted in the fli gene cluster of strain EC1 were likely derived from horizontal gene transfer during later stage of bacterial evolution.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1545-x) contains supplementary material, which is available to authorized users.

SlyA regulates phytotoxin production and virulence in Dickeya zeae EC1

“…Table S3 (see Supporting Information) shows the selected genes under the regulation of SlyA, most of which were reported to be associated with the virulence of Dickeya species. As expected, of the 18 genes in the zms gene cluster associated with the biosynthesis of zeamines (Cheng et al ., ; Zhou et al ., ), 14 were significantly reduced in transcript level by 2.3–23.3‐fold, and the remaining four were reduced by over 1.4‐fold (Table S3). The other affected genes include those encoding cell wall‐degrading enzymes, exopolysaccharide (EPS) biosynthesis, five types of secretion system, QS signals, cyclic‐di‐GMP signalling systems, transporters, transcriptional regulators and proteins involved in cell motility, stress and toxin resistance (Table S3).…”

“…The hallmark of this disease is an area of ‘mushy’ tissues at the site of infection, which may eventually lead to the collapse of the entire plant (Barras et al ., ; Collmer and Bauer, ). As expected for soft rot symptoms, the pathogens produce a large array of plant cell wall‐degrading enzymes, including different types of pectinases (Collmer and Bauer, ; Hugouvieux‐Cotte‐Pattat et al ., ; Robert‐Baudouy et al ., ), proteases (Boyd and Keen, ; Ghigo and Wandersman, ; Shevchik et al ., ), feruloyl esterases (Hassan and Hugouvieux‐Cotte‐Pattat, ) and cellulases (Reverchon et al ., ), which collectively contribute to bacterial infections (Reverchon and Nasser, ; Zhou et al ., ). In addition, a catechol‐type siderophore and a blue pigment indigoidine are also implicated in bacterial systemic invasion (Enard and Expert, ; Enard et al ., ; Expert and Toussaint, ; Reverchon et al ., ).…”

Genetic Modulation of c-di-GMP Turnover Affects Multiple Virulence Traits and Bacterial Virulence in Rice Pathogen Dickeya zeae

“…dadantii genome, including 12 genes with GGDEF-subclass domain, four with EAL-subclass domain and 2 with dual-function domains (ASAP website; https://asap.ahabs.wisc.edu/asap/home.php). Based on the genome sequence released recently[26], we predicted same number of c-di-GMP turnover genes in D . zeae EC1, except that the one ( W909_14520 ) belongs to the HD domain superfamily[65].…”

“…zeae , we recently completed the genome sequencing of D . zeae strain EC1[26]. In this study, we constructed in-frame deletion mutants targeting all the predicted c-di-GMP related genes by using strain EC1 as a parental strain.…”

A Sfp-type phosphopantetheinyl transferase ZmsO is essential for zeamines production and the virulence of Dickeya zeae

“…Given that mutation of either zmsA or zmsO leads to null production of zeamines, we are tempted to speculate that ZmsO may likely be involved in post-translational activation of ZmsA but not ZmsK. It is interesting to note that within the gene cluster for zeamines production, there are 5 ORFs encoding for polyketide synthases (Masschelein et al 2013;Masschelein et al 2015;Zhou et al 2015). Obviously, further experiments are needed to identify the molecular target(s) of ZmsO.…”