Using machine learning to identify the functional consequences of post-translational modifications in the rice proteome

对于世界上许多穷人来说，大米提供了日常热量的大部分。由于持续的育种努力，水稻生产率在近几十年里翻了一番以上。然而，为了满足预计的人口增长带来的需求，大米产量必须继续快速增长，同时应对气候变化带来的挑战。随着最近对3000个不同品种的测序，有大量的遗传资源可用于鉴定与理想性状相关的遗传多态，如对生物或非生物胁迫的耐受性、产量、营养含量等，这些品种在适当的时候可能被培育成主要的作物品种。然而，就植物在细胞水平上如何响应不同的胁迫而言，目前在遗传变异和功能效应之间存在着很大的认识差距。在正常的田间条件下，植物可以暴露在各种生物和非生物环境胁迫下。植物对逆境的耐受性和驯化依赖于特定蛋白质翻译后修饰(PTM)的显著变化来迅速切换功能。预计未来几十年，干旱和高温等环境压力将变得更加普遍。未来成功的解决方案无疑将涉及应用下一代技术来改进对农业经济具有重要意义的作物的育种。本研究旨在鉴定和量化水稻和模式植物拟南芥中的PTMS，以提高我们对植物如何对不同类型的胁迫做出快速反应的理解。我们特别感兴趣的是研究影响蛋白质相互作用和周转的赖氨酸修饰，如SUMO化和泛素化。我们将研究这些站点的进化保护，它们在多大程度上可以在同一站点的不同PTM之间竞争，和/或与邻近站点的串扰。所获得的知识将用于挖掘植物基因组，寻找与所需特征相关的新等位基因，长期目标是改善作物育种工作。

For much of the world's poor, rice (O. sativa) provides the majority of daily calories. Rice productivity has more than doubled in recent decades, resulting from continued breeding efforts. However, to meet the demands imposed by the projected increase in population, rice production has to continue growing rapidly, while meeting challenges imposed by a changing climate. With the recent sequencing of >3000 different varieties, there is a huge genetic resource available for identifying genetic polymorphisms associated with desirable traits e.g. tolerance to biotic or abiotic stress, yield, nutritional content etc., which in due course could be bred into a major crop variety. However, there is a great knowledge gap at present between genetic variation and functional effects, in terms of how plants respond at the cellular level to different stresses.Under normal field conditions, plants can be exposed to various biotic and abiotic environmental stresses. Plant stress tolerance and acclimation depends on significant changes in post-translational modifications (PTMs) of specific proteins to switch function rapidly. It is expected that environmental stresses, such as drought and heat will become more prevalent in the coming decades. Future successful solutions will undoubtedly involve applying next-generation technologies to improve the breeding of agro-economically important crops. This study aims to identify and quantify PTMs in rice, and in the model plant Arabidopsis thaliana, to improve our understanding of how plants respond rapidly to different types of stress. We are particularly interested to study lysine modifications that affect protein-protein interactions and turnover, such as SUMOylation and ubiquitination. We will study the evolutionary conservation of these sites, the extent to which they can be competition between different PTMs for the same site, and/or crosstalk with proximal sites. The acquired knowledge will be used to mine plant genomes for new alleles associated with desirable traits, with a long term objective of improving crop breeding efforts.