A2M: Exploring in-silico predicted arms-races at the plant-pathogen interface

植物-病原体界面的军备竞赛是一个迷人的生物学领域，可以为作物保护提供重要的新的细胞外策略。我们使用尖端的人工智能来预测植物-病原体界面处的新型蛋白质-蛋白质相互作用，使用Alphafold 2多聚体（A2 M）。使用A2 M筛选番茄分泌的P69 B免疫蛋白酶的新的病原体衍生的抑制剂，我们发现P69 B被由四种不同的番茄病原体产生的（至少）五种不相关的抑制剂：来自卵菌晚疫病病原体致病疫霉的Epi 1;来自细菌性斑点病原体穿孔黄单胞菌的P3; Ecp 36来自真菌叶霉菌病原体黄枝孢菌（Cladosporium fulvum），TIL和Six 15来自真菌枯萎病病原体尖孢镰刀菌（Fusarium oxysporum）。P69 B是番茄病原菌的主要靶标，这与以下事实相一致：i）P69 B在受感染植物的质外体中被诱导并高度丰富：ii）P69 B在野生番茄中可能与抑制剂相互作用的残基处受到正选择; iii）P69 B具有由快速进化的基因簇编码的9个旁系同源物，其主要不同在于底物结合沟周围的残基，抑制剂相互作用的地方在这项提案中，我们的目标是阐明这种军备竞赛，并利用这些知识来工程细胞外免疫。我们将首先解决的抑制机制，并确定与P69 B旁系同源物和同源物，也从非宿主植物的相互作用的特异性。其次，我们将确定P69在免疫中的作用和抑制剂在病原体毒力中的作用，利用番茄和病原体的反向遗传学。第三，我们将阐明P69基因家族在茄科植物中的进化，并工程化不敏感的P69基因，以建立持久的胞外抵抗质外体病原体的策略。

The arms race at the plant-pathogen interface is a fascinating field of biology that can deliver important new, extracellular strategies for crop protection. We have used cutting edge artificial intelligence to predict novel protein-protein interactions at the plant-pathogen interface using Alphafold2 Multimer (A2M). Using an A2M screen for novel, pathogen-derived inhibitors of the secreted P69B immune protease of tomato, we discovered that P69B is targeted by (at least) five unrelated inhibitors produced by four different tomato pathogens: Epi1 from the oomycete late blight pathogen Phytophthora infestans; P3 from the bacterial spot pathogen Xanthomonas perforans; Ecp36 from the fungal leaf mould pathogen Cladosporium fulvum and TIL and Six15 from the fungal Fusarium wilt pathogen Fusarium oxysporum. That P69B is a major target for tomato pathogens is consistent with the facts that: i) P69B is induced and highly abundant in the apoplast of infected plants; ii) P69B is under positive selection in wild tomato at residues that probably interact with inhibitors; iii) P69B has nine paralogs encoded from a fast evolving gene cluster, that differ mostly in residues surrounding the substrate binding groove, where inhibitors interact. In this proposal, we aim to elucidate this arms-race and use this knowledge to engineer extracellular immunity. We will first resolve the inhibition mechanisms and determine the specificities of interactions with P69B paralogs and homologs, also from non-host plants. Second, we will determine the role of P69s in immunity and the role of inhibitors in pathogen virulence using reverse genetics on tomato and the pathogens. Third, we will elucidate the evolution of the P69 gene family in solanaceous plants and engineer inhibitor-insensitive P69s to build a strategy for durable extracellular resistance to apoplastic pathogens.