Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome

Roux Brice, Bolot Stéphanie, Guy Endrick, Denancé Nicolas, Lautier Martine, Jardinaud Marie-Françoise, Fischer-Le-Caux Marion, Portier Perrine, Jacques Marie Agnès, Gagnevin Lionel, Pruvost Olivier, Lauber Emmanuelle, Arlat Mathieu, Carrère Sébastien, Koebnik Ralf, Noel Laurent D.. 2015. Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome. BMC Genomics, 16 (975), 19 p.

https://doi.org/10.1186/s12864-015-2190-0

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Url - jeu de données - Entrepôt autre : https://lipm-browsers.toulouse.inra.fr/pub/xanthomix/

Quartile : Q1, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q2, Sujet : GENETICS & HEREDITY

Résumé : Background The 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). Results In 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. Conclusions This 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.

Mots-clés Agrovoc : Xanthomonas campestris, maladie des plantes, bactérie pathogène, génomique, génome, séquence d'adn, sécrétion, protéine bactérienne, Transcription génique, transcription d'ADN

Mots-clés libres : Xanthomonas campestris, Type III secretion, Effector, Xanthomonas outer protein, RNA-seq, Transcriptome

Classification Agris : H20 - Maladies des plantes

Champ stratégique Cirad : Axe 4 (2014-2018) - Santé des animaux et des plantes

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