Abstract
BackgroundThe bacterial species Xanthomonas campestris infects a wide range of Brassicaceae. Specific pathovars of this species cause black rot (pv. campestris), bacterial blight of stock (pv. incanae) or bacterial leaf spot (pv. raphani).ResultsIn this study, we extended the genomic coverage of the species by sequencing and annotating the genomes of strains from pathovar incanae (CFBP 1606R and CFBP 2527R), pathovar raphani (CFBP 5828R) and a pathovar formerly named barbareae (CFBP 5825R). While comparative analyses identified a large core ORFeome at the species level, the core type III effectome was limited to only three putative type III effectors (XopP, XopF1 and XopAL1). In Xanthomonas, these effector proteins are injected inside the plant cells by the type III secretion system and contribute collectively to virulence. A deep and strand-specific RNA sequencing strategy was adopted in order to experimentally refine genome annotation for strain CFBP 5828R. This approach also allowed the experimental definition of novel ORFs and non-coding RNA transcripts. Using a constitutively active allele of hrpG, a master regulator of the type III secretion system, a HrpG-dependent regulon of 141 genes co-regulated with the type III secretion system was identified. Importantly, all these genes but seven are positively regulated by HrpG and 56 of those encode components of the Hrp type III secretion system and putative effector proteins.ConclusionsThis dataset is an important resource to mine for novel type III effector proteins as well as for bacterial genes which could contribute to pathogenicity of X. campestris.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2190-0) contains supplementary material, which is available to authorized users.
Highlights
The bacterial species Xanthomonas campestris infects a wide range of Brassicaceae
Type III-secreted proteins (T3SP) include type III effector (T3E) proteins which are injected inside the plant cells where many of them interfere with cell physiology and plant immunity
Genome sequencing and properties Four X. campestris strains belonging to pathovars not or poorly characterized at the genomic levels were selected for this study (Table 1)
Summary
The bacterial species Xanthomonas campestris infects a wide range of Brassicaceae. Specific pathovars of this species cause black rot While strains of pathovars campestris and incanae use the hydathodes (and wounds) to initiate a vascular infection of the plant, strains of the pathovar raphani seem to preferentially use stomata (and wounds) to enter the leaf and colonize the mesophyll. Two master regulators of the hrp systems which are both required for virulence and hrp gene expression in minimal medium have been identified: HrpX is an AraC-type transcriptional activator inducing the expression of all hrp operons but hrpA upon binding to the plant-inducible promoter (PIP) box (TTCGB-N15-TTCGB; B represents C, G, or T) in the promoter region [11, 12]. Several point mutations in hrpG (hrpG*) can render its activity constitutive in the absence of inducing condition and result in an increased aggressiveness on plants [18]
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