Journal Article

RNA-seq pinpoints a Xanthomonas TAL-effector activated resistance gene in a large-crop genome

Minsavage, Gerald V, Parniske, Martin, van Poecke, Remco M. P, Strauß, Tina, Römer, Patrick, Strauß, Axel, Yeom, Seon-In, Strauß, Annett, Stall, Robert E, Choi, Doil, Wolf, Christina, Lee, Hyun-Ah, Lahaye, Thomas, Jones, Jeffrey B, Kim, Seungill, Singh, Sylvia, Prins, Marcel

2012

Overview

Transcription activator-like effector (TALE) proteins of the plant pathogenic bacterial genus Xanthomonas bind to and transcriptionally activate host susceptibility genes, promoting disease. Plant immune systems have taken advantage of this mechanism by evolving TALE binding sites upstream of resistance (R) genes. For example, the pepper Bs3 and rice Xa27 genes are hypersensitive reaction plant R genes that are transcriptionally activated by corresponding TALEs. Both R genes have a hallmark expression pattern in which their transcripts are detectable only in the presence and not the absence of the corresponding TALE. By transcriptome profiling using next-generation sequencing (RNA-seq), we tested whether we could avoid laborious positional cloning for the isolation of TALE-induced R genes. In a proof-of-principle experiment, RNA-seq was used to identify a candidate for Bs4C , an R gene from pepper that mediates recognition of the Xanthomonas TALE protein AvrBs4. We identified one major Bs4C candidate transcript by RNA-seq that was expressed exclusively in the presence of AvrBs4. Complementation studies confirmed that the candidate corresponds to the Bs4C gene and that an AvrBs4 binding site in the Bs4C promoter directs its transcriptional activation. Comparison of Bs4C with a nonfunctional allele that is unable to recognize AvrBs4 revealed a 2-bp polymorphism within the TALE binding site of the Bs4C promoter. Bs4C encodes a structurally unique R protein and Bs4C -like genes that are present in many solanaceous genomes seem to be as tightly regulated as pepper Bs4C . These findings demonstrate that TALE-specific R genes can be cloned from large-genome crops with a highly efficient RNA-seq approach.

• Publisher: National Academy of Sciences,National Acad Sciences
• Subject: Alleles / Bacteria / Bacterial Proteins - chemistry / Bacterial Proteins - metabolism / Binding sites / Biological Sciences / Capsicum - drug effects / Capsicum - genetics / Capsicum - immunology / Capsicum - microbiology / Cloning / crops / Crops, Agricultural - drug effects / Crops, Agricultural - genetics / Crops, Agricultural - microbiology / Cycloheximide - pharmacology / Disease Resistance - drug effects / Disease Resistance - genetics / DNA / Gene expression / Gene Expression Profiling - methods / Gene Expression Regulation, Plant - drug effects / Genes / Genes, Plant - genetics / Genetic Association Studies / Genomes / high-throughput nucleotide sequencing / hypersensitive response / immune system / Memory interference / molecular cloning / pepper / Peppers / Plant diseases / Plant Diseases - genetics / Plant Diseases - microbiology / plant proteins / Plant resistance / Plants / Promoter Regions, Genetic - genetics / Protein Structure, Tertiary / Protein Synthesis Inhibitors - pharmacology / Proteins / Ribonucleic acid / rice / RNA / RNA, Messenger - genetics / RNA, Messenger - metabolism / RNA, Plant - genetics / Simultaneous interpretation / transcription (genetics) / Transcription Activator-Like Effectors / Transcriptional activation / Transcriptional Activation - drug effects / Transcriptional Activation - genetics / Transcriptome - genetics / transcriptomics / Xanthomonas / Xanthomonas - drug effects / Xanthomonas - physiology