Uncovering the role of RNA-binding proteins in plant immunity

Thesis

RNA-binding proteins (RBPs) are essential regulators of RNA fate, from synthesis to decay. Hence, changes in the RBPome orchestrate the reprograming of RNA metabolism and gene expression that occur during plant responses to a myriad of cues, including pathogen attack. Although RBPs are known to play critical roles in plants, we lack comprehensive information on the identity and function of RBPs in different species. Moreover, it remains unknown how RBPs globally respond to different environmental, physiological and pathological cues.

Here, we have developed ‘plant RNA-interactome capture’ (ptRIC), a variant of RNA-interactome capture (RIC) optimised for plant tissues that allows efficient system-wide identification of RBPs in leaves. We used ptRIC to identify the most extensive Arabidopsis RBPome to date, which includes more than 1100 RBPs, and showed that it displays all the hallmarks expected from a high-quality RBPome. We have used ptRIC to uncover, for the first time, the RBPome of six additional plant species that span across the plant kingdom. This revealed hundreds of unconventional RBPs with no known RNA-binding domains or previously unlinked to RNA biology, including photosynthetic components and metabolic enzymes. By comparing the RBPomes discovered in these different species we have determined the ‘core plant RBPome’, which is composed by RBPs conserved from bryophytes to angiosperms. Using ptRIC we discovered that the Arabidopsis RBPome is extensively reconfigured during plant immune responses. Almost 300 RBPs displayed altered association with RNA in response to the bacterial elicitor flg22. Moreover, these alterations that cannot be explained due to changes in protein abundance, indicating that they are due to changes in RNA-binding activity. Through immunity-based mutant screens, we have discovered that several of these flg22- responsive RBPs play a role in immunity against bacterial pathogens.

Taken together, the results from this thesis provide a significant advance in the knowledge of RBPs in plants and their regulation during immunity. Hence, my results provide a framework for future studies on the role of RBPs in regulating important processes in plants.

Authors: Bach Pages, M

• Alternative title: Exploiting RNA-interactome capture to dissect plant immunity
• DOI: 10.5287/ora-korp5zbwn
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: Oryza sativa; RBP; RIC; ptRIC; RNA-binding proteins; Physcomitrella; flg22; PAMP-triggered immunity; immune system; RBPome; Solanum tuberosum; RNA-binding proteome; Marchantia; Pseudomonas syringae; Solanum lycopersicum; Zea mays; Plant pathology; Arabidopsis; Nicotiana tabacum; RNA-interactome capture; immunity; Nicotiana benthamiana; Phaseolus vulgaris; plants
• Subjects: Biology; Plant pathology; Biochemistry; Immunology; Genetics; Molecular Biology