Multi-dimensional interplay between Xanthomonas oryzae TALEs and the rice genome

米黄单胞菌 TALE 与水稻基因组之间的多维相互作用

• 批准号: 261742732
• 负责人: Professor Dr. Jens Boch
• 金额: --
• 依托单位: Institut für Pflanzengenetik
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2014
• 资助国家: 德国
• 起止时间: 2013-12-31 至 2022-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/261742732?language=en
• 关键词: Multi; dimensional; interplay; between; Xanthomonas

This proposal aims at studying the interaction between plant-pathogenic Xanthomonas oryzae bacteria and the host plant rice (Oryza sativa) in multiple dimensions by a interdisciplinary approach between biology and bioinformatics. The project will focus on TALEs (transcription activator-like effectors) which are key virulence factors of X. oryzae. TALEs function as transcription factors inside plant cells to induce expression of target genes. First, specific TALE targets in rice will be studied for their role in bacterial virulence. Second, genome-wide predictions of TAL-boxes will be combined with total RNA-seq data to detect novel TALE targets not only in protein-coding genes, but also in non-coding RNAs. Third, TALE-mediated gene activation will be studied in a time-dependent manner. While primary TALE targets are activated within the first 24-48 hours after infection, the number of differentially expressed genes increases dramatically between 24 h and 48 h. Defined sets of secondary TALE targets should be attributable to the activity of regulatory TALE targets, e.g., those that function as transcription factors. Unravelling these networks will deepen our understanding of TALEs on the whole infection process. Finally, the evolutionary dimension of TALEs in the pathogen - host interaction will be analyzed by challenging X. oryzae strains with resistant plants that have been generated by genome editing. Selection and analysis of bacteria that overcome these resistances will give insights into the adaptive changes that are possible in TALE genes. This will help to develop strategies for breeding plants with durable resistances. The project will further explore very long-read sequencing technologies to assemble the highly repetitive X. oryzae genomes and extend the successful AnnoTALE bioinformatics toolbox for studying TALEs.

本研究旨在利用生物学和生物信息学的交叉学科方法，从多个维度研究水稻白叶枯病菌与寄主植物水稻的相互作用。该项目将专注于TALE(转录激活因子样效应器)，这是稻瘟病菌的关键毒力因子。TALE作为植物细胞内的转录因子，诱导靶基因的表达。首先，将研究大米中特定的TALL靶标在细菌毒力中的作用。其次，TAL盒的全基因组预测将与总的RNA序列数据相结合，不仅在蛋白质编码基因中检测新的TALE靶标，而且在非编码RNA中也检测新的TALE靶标。第三，将以时间依赖的方式研究TALE介导的基因激活。虽然初级TALE靶标在感染后24-48小时内被激活，但差异表达基因的数量在24小时到48小时之间急剧增加。确定的次要TALE靶标集合应归因于调节TALE靶标的活性，例如，那些发挥转录因子功能的靶标。解开这些网络将加深我们对整个感染过程的故事的理解。最后，通过用通过基因组编辑产生的抗性植物来挑战稻瘟病菌菌株，将分析病原体-宿主相互作用中TALS的进化维度。对克服这些耐药性的细菌的选择和分析将使人们对童话基因可能发生的适应性变化有更深入的了解。这将有助于制定培育具有持久抗性的植物的策略。该项目将进一步探索非常长的阅读测序技术，以组装高度重复的稻瘟病菌基因组，并扩展成功的AnnoTALE生物信息学工具箱，用于研究故事。