University of Liège (ULg), Department of Integrated and Urban Phytopathology, Gembloux, Belgium.
Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Merelbeke, Belgium.
Prog Mol Biol Transl Sci. 2021;183:355-409. doi: 10.1016/bs.pmbts.2021.06.007. Epub 2021 Sep 23.
Intrinsically disordered proteins and regions (IDPs/IDRs) make up a large part of viral proteomes, but their real prevalence across the global plant virome is still murky, partly because of their massive diversity. Here, we propose an evolutionary quantitative proteomic approach to foray into genomic signatures that are preserved in the amino acid sequences of orthologous IDRs. Markedly, we found that relatively abundant IDP varies substantially in viral species among and within plant virus families, including according to genome size, partition or replication strategies. We also demonstrate that most encoded proteomic modules of the plant virome contain multiple disordered features that are phylogenomically preserved, and can be correlated to genomic, bio-physical and evolutionary strategies. Furthermore, our focused interactome-wide analysis highlights lines of evidence indicating that various IDPs with similar evolutionary signatures modulate viral multifunctionality. Moreover, estimated fractions of IDR in the vicinity of pivotal evolutionary structural domains embedded in interaction modules are strongly enriched with affinity binding functional annotations and relate to vector-borne virus transmission modes. Importantly, molecular recognition features (MoRFs) are abundantly widespread in IDRs of viral hallmark modules and their binding partners. Finally, we propose a coarse-grained conceptual framework in which evolutionary proteome-wide IDP/IDRs patterns can be, rather, reliably exploited to elucidate their foundational fine-tuning role in plant virus transmission mechanisms. While opening unexplored avenues for consistently predicting virus-host functions for many new or uncharacterized viruses based on their proteomic repertoire, other considerations advocating further structural IDP research in Plant Virology are thoroughly discussed in light of viral modular evolution.
无规卷曲蛋白质和区域（IDPs/IDRs）构成了病毒蛋白质组的很大一部分，但它们在全球植物病毒组中的实际流行程度仍然不清楚，部分原因是它们的多样性很大。在这里，我们提出了一种进化定量蛋白质组学方法，深入研究在同源 IDR 的氨基酸序列中保留的基因组特征。值得注意的是，我们发现相对丰富的 IDP 在植物病毒科内和科间的病毒物种中变化很大，包括根据基因组大小、分区或复制策略。我们还证明，植物病毒组的大多数编码蛋白质组模块都包含多个无序特征，这些特征在系统发育上是保守的，可以与基因组、生物物理和进化策略相关联。此外，我们的重点是互作组广泛分析强调了各种具有相似进化特征的 IDP 调节病毒多功能性的证据。此外，在嵌入交互模块中的关键进化结构域附近的 IDR 中估计的 IDR 分数强烈富集了亲和力结合功能注释，并与载体传播病毒的传播模式有关。重要的是，分子识别特征（MoRFs）在病毒标志性模块及其结合伴侣的 IDR 中广泛存在。最后，我们提出了一个粗粒度的概念框架，其中进化蛋白质组范围内的 IDP/IDRs 模式可以可靠地用于阐明它们在植物病毒传播机制中的基础微调作用。虽然为许多新的或未表征的病毒基于其蛋白质组谱一致地预测病毒-宿主功能开辟了未知的途径，但在考虑病毒模块进化时，彻底讨论了其他支持进一步进行植物病毒学中结构 IDP 研究的考虑因素。
