Decoding evolution, expression, and virulence function of Xanthomonas TALEs across plant hosts

• Applicants: Professor Dr. Jens Boch; Dr. Jan Grau
• Subject Area: Organismic Interactions, Chemical Ecology and Microbiomes of Plant Systems ; Bioinformatics and Theoretical Biology
• Term: since 2014
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 261742732

Xanthomonas bacteria are plant pathogens infecting many crop plants with profound impact on human food production. This project aims at studying the interactions between plant-pathogenic Xanthomonas bacteria and the infected host plant by an interdisciplinary approach between biology and bioinformatics. The project will focus on transcription activator-like effectors (TALEs), bacterial proteins that act as transcriptional activators of host plant genes and are key virulence factors of many Xanthomonas pathogens. Previous funding periods were devoted to genome sequencing of Xanthomonas strains, prediction and validation of TALE targets in the plant cell, studies of TALE evolution and time-resolved expression of TALE targets during the infection. Based on this, we will scrutinize specific aspects of TALE organization and evolution, the function of induced host transcripts, and the effects of natural variation in promoters of TALE targets. We will first focus on the established Xanthomonas oryzae-rice pathosystem, while our scope will later be broadened to cotton pathogens, which may yield insights into general infection strategies. To achieve these project goals, we will extend our software suite AnnoTALE for annotating and analyzing TALE genes, and improve its sustainability for the rapid growth of available Xanthomonas genomes. We will further analyze previously identified TALE target genes for their role in the infection. Here, we focus on converging TALE targets that are common among different Xanthomonas oryzae sub-species or that are induced by widespread TALE classes. For studying bacterial and host transcripts during the infection, we will establish dual ONT direct RNA sequencing, which is required to resolve highly repetitive TALE genes. ONT reads are also suited to resolve partial and antisense transcripts and shifted transcription start sites that we discovered in previous transcriptomics data. We will extend our analyses to the Xanthomonas citri pv. malvacearum-cotton pathosystem with ONT-based genome sequencing of bacterial strains and infection experiments of cotton plants. Here, we hypothesize that targets with common function exist across different pathosystems and anticipate that identifying these will give insights into general infection strategies. In-depth studies of TALE evolution, including recombination and reassortment of TALE genes, may elucidate evolutionary mechanisms that shape the diversity of TALomes. Finally, we will leverage large-scale information about naturally occurring variants of target gene promoters that may provide a natural resource of resistance against Xanthomonas pathogens.

• DFG Programme: Research Grants
• International Connection: Argentina
• Cooperation Partner: Dr. Roxana Roeschlin