Identification of new protein-coding genes with a potential role in the virulence of the plant pathogen Xanthomonas euvesicatoria

Abstract

BackgroundBacteria of the genus Xanthomonas are economically important plant pathogens. Pathogenicity of Xanthomonas spp. depends on the type III-secretion system and additional virulence determinants. The number of sequenced Xanthomonas genomes increases rapidly, however, accurate annotation of these genomes is difficult, because it relies on gene prediction programs. In this study, we used a mass-spectrometry (MS)-based approach to identify the proteome of Xanthomonas euvesicatoria (Xe) strain 85–10 also known as X. campestris pv. vesicatoria, a well-studied member of plant-pathogenic Xanthomonadaceae.ResultsUsing different culture conditions, MS-datasets were searched against a six-frame-translated genome database of Xe. In total, we identified 2588 proteins covering 55% of the Xe genome, including 764 hitherto hypothetical proteins. Our proteogenomic approach identified 30 new protein-coding genes and allowed correction of the N-termini of 50 protein-coding genes. For five novel and two N-terminally corrected genes the corresponding proteins were confirmed by immunoblot. Furthermore, our data indicate that two putative type VI-secretion systems encoded in Xe play no role in bacterial virulence which was experimentally confirmed.ConclusionsThe discovery and re-annotation of numerous genes in the genome of Xe shows that also a well-annotated genome can be improved. Additionally, our proteogenomic analyses validates “hypothetical” proteins and will improve annotation of Xanthomonadaceae genomes, providing a solid basis for further studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-4041-7) contains supplementary material, which is available to authorized users.

The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility

“…Boyer and collaborators [12] found that Xanthomonas axonopodis and Xantohomonas campestris both have two complementary T6SS loci. Similarly, Xanthomonas euvesicatoria 85-10 (Xeu) has two T6SS loci or clusters with 15 conserved components [22]. The T6SS has been partially characterized, through bioinformatics, in Xeu, Xanthomonas vesicatoria strain 1111 (ATCC 35937: Xv) and Xanthomonas perforans strain 91-118 (Xp) [23].…”

Interaction of the Ankyrin H Core Effector of Legionella with the Host LARP7 Component of the 7SK snRNP Complex

“…This cysteine protease-like domain (CPLD) is most similar to the outer protein D (XopD; PDB identifier [ID] 2OIX) from bacterial plant pathogen Xanthomonas campestris pv. vesicatoria (82–84) (Fig. 4C).…”

Proteome Profile and Genome Refinement of the Tomato‐Pathogenic Bacterium Clavibacter michiganensis subsp. michiganensis

“…This technique is used to refine genomes and discover protein‐coding regions that may play a role in virulence or other important biological processes. Recently it was used to identify 30 new protein coding regions and extend the N‐terminus of 50 previously annotated genes of the tomato bacterial spot pathogen Xanthomonas euvesicatoria . Six‐frame (6F) translated databases of the genome are often used in proteogenomics for identification of novel peptides.…”