疫霉属的卵菌包括迄今为止描述的几种最成功的植物病原体。疫霉感染的成功归因于病原体分泌改变宿主生理过程的效应蛋白的能力。主要来自细菌和病毒病原体的效应蛋白的结构分析已经揭示了宿主短线性基序(SLiMs)的内在无序区域的存在。这些基序通过促进蛋白质-蛋白质相互作用以及蛋白质易位而发挥重要的生物学作用。尽管如此,疫霉物种RxLR效应子中的SLiM以前尚未研究过,它们的作用仍然未知。使用生物信息学管道,我们在寄生疫霉INRA310菌株中鉴定了333个候选RxLR效应子。其中,还发现有71个(21%)存在于寄生假单胞菌的其他10个基因组中,因此,这些被指定为核心RxLR效应器(CREs)。在CRE序列中,与C末端相比,N末端表现出内在无序区域的富集,提示疾病在效应物易位中的潜在作用。尽管C端区域的无序含量降低,值得一提的是,大多数SLiM都在这个终点站。PpRxLR1是本研究中确定的71个CRE之一,其基因在C末端编码6个氨基酸(aa)长的SLiM。我们表明PpRxLR1与几种参与防御的宿主蛋白相互作用。使用同源建模对该效应物进行结构分析揭示了潜在配体结合位点的存在。在预测对配体结合至关重要的关键残基中,L102和Y106是感兴趣的,因为它们形成6-aa长的PpRxLR1SLiM的一部分。预测这两个残基到丙氨酸的硅置换对PpRxLR1效应子的功能和结构具有显著影响。分子对接模拟揭示了PpRxLR1效应子和泛素相关蛋白之间可能的相互作用。该效应物中携带的泛素样SLiM被证明是这些相互作用的潜在介质。需要进一步的研究来验证和阐明潜在的分子作用机制。重要性RxLR效应子的连续得失使得对疫霉菌属的控制成为可能。困难。因此,在这项研究中,我们努力确定在物种之间高度保守的RxLR效应子,也称为“核心”RxLR效应器(CREs)。我们认为这些高度保守的效应子靶向保守的蛋白质或过程;因此,它们可以用于植物的持久抗性育种。为了进一步了解CREs的作用机制,这些蛋白质的结构解剖是至关重要的。内在无序区域(IDR)不采用固定的,三维折叠携带介导蛋白质生物学功能的短线性基序(SLiMs)。这些SLiM在疫霉CRE中的存在和潜在作用。被忽视了。据我们所知,我们已经有效地鉴定了具有促进效应毒力潜力的CRE和SLiM。一起,这项工作提高了我们对疫霉菌RxLR效应子功能的理解,可能有助于开发创新和有效的控制策略。
Oomycetes of the genus
Phytophthora encompass several of the most successful plant pathogens described to date. The success of infection by
Phytophthora species is attributed to the pathogens\' ability to secrete effector proteins that alter the host\'s physiological processes. Structural analyses of effector proteins mainly from bacterial and viral pathogens have revealed the presence of intrinsically disordered regions that host short linear motifs (SLiMs). These motifs play important biological roles by facilitating protein-protein interactions as well as protein translocation. Nonetheless, SLiMs in
Phytophthora species RxLR effectors have not been investigated previously and their roles remain unknown. Using a bioinformatics pipeline, we identified 333 candidate RxLR effectors in the strain INRA 310 of Phytophthora parasitica. Of these, 71 (21%) were also found to be present in 10 other genomes of P. parasitica, and hence, these were designated core RxLR effectors (CREs). Within the CRE sequences, the N terminus exhibited enrichment in intrinsically disordered regions compared to the C terminus, suggesting a potential role of disorder in effector translocation. Although the disorder content was reduced in the C-terminal regions, it is important to mention that most SLiMs were in this terminus. PpRxLR1 is one of the 71 CREs identified in this study, and its genes encode a 6-amino acid (aa)-long SLiM at the C terminus. We showed that PpRxLR1 interacts with several host proteins that are implicated in defense. Structural analysis of this effector using homology modeling revealed the presence of potential ligand-binding sites. Among key residues that were predicted to be crucial for ligand binding, L102 and Y106 were of interest since they form part of the 6-aa-long PpRxLR1 SLiM. In silico substitution of these two residues to alanine was predicted to have a significant effect on both the function and the structure of PpRxLR1 effector. Molecular docking simulations revealed possible interactions between PpRxLR1 effector and ubiquitin-associated proteins. The ubiquitin-like SLiM carried in this effector was shown to be a potential mediator of these interactions. Further studies are required to validate and elucidate the underlying molecular mechanism of action. IMPORTANCE The continuous gain and loss of RxLR effectors makes the control of
Phytophthora spp. difficult. Therefore, in this study, we endeavored to identify RxLR effectors that are highly conserved among species, also known as \"core\" RxLR effectors (CREs). We reason that these highly conserved effectors target conserved proteins or processes; thus, they can be harnessed in breeding for durable resistance in plants. To further understand the mechanisms of action of CREs, structural dissection of these proteins is crucial. Intrinsically disordered regions (IDRs) that do not adopt a fixed, three-dimensional fold carry short linear motifs (SLiMs) that mediate biological functions of proteins. The presence and potential role of these SLiMs in CREs of
Phytophthora spp. have been overlooked. To our knowledge, we have effectively identified CREs as well as SLiMs with the potential of promoting effector virulence. Together, this work has advanced our comprehension of Phytophthora RxLR effector function and may facilitate the development of innovative and effective control strategies.