Regional Centre, ICAR-Central Tuber Crops Research Institute Bhubaneswar, Odisha, India.
ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India.
PLoS One. 2022 Jul 22;17(7):e0270534. doi: 10.1371/journal.pone.0270534. eCollection 2022.
Plants are constantly threatened by a virus infection, i.e., Potyviruses, the second largest genus of plant viruses which results in several million-dollar losses in various essential crops globally. Yam bean (Pachyrhizus erosus) is considered to be one of the essential tuberous legume crops holding a great potential source of starch. Yam Bean Mosaic Virus (YBMV) of Potyvirus group belonging to the family potyviridae affects Yam bean and several angiosperms both in the tropical and sub-tropical regions causing large economical losses in crops. In this study, we attempted to understand the sequence-structure relationship and mode of RNA binding mechanism in YBMV CP using in silico integrative modeling and all-atoms molecular dynamics (MD) simulations. The assembly of coat protein (CP) subunits from YBMV and the plausible mode of RNA binding were compared with the experimental structure of CP from Watermelon mosaic virus potyvirus (5ODV). The transmembrane helix region is present in the YBMV CP sequence ranging from 76 to 91 amino acids. Like the close structural-homolog, 24 CPs monomeric sub-units formed YBMV a conserved fold. Our computational study showed that ARG124, ARG155, and TYR151 orient towards the inner side of the virion, while, THR122, GLN125, SER92, ASP94 reside towards the outer side of the virion. Despite sharing very low sequence similarity with CPs from other plant viruses, the strongly conserved residues Ser, Arg, and Asp within the RNA binding pocket of YBMV CP indicate the presence of a highly conserved RNA binding site in CPs from different families. Using several bioinformatics tools and comprehensive analysis from MD simulation, our study has provided novel insights into the RNA binding mechanism in YBMV CP. Thus, we anticipate that our findings from this study will be useful for the development of new therapeutic agents against the pathogen, paving the way for researchers to better control this destructive plant virus.
植物不断受到病毒感染的威胁，例如马铃薯 Y 病毒属（Potyviruses），这是植物病毒的第二大属，在全球范围内导致了数百万美元的损失。山药豆（Pachyrhizus erosus）被认为是一种重要的块茎豆科作物，拥有巨大的淀粉潜在来源。属于马铃薯 Y 病毒属（Potyviridae）的山药豆花叶病毒（Yam Bean Mosaic Virus，YBMV）会影响山药豆和热带及亚热带地区的几种被子植物，导致作物的巨大经济损失。在这项研究中，我们试图通过整合计算建模和全原子分子动力学（MD）模拟来了解 YBMV CP 的序列-结构关系和 RNA 结合机制的模式。通过比较 YBMV CP 亚基的组装和可能的 RNA 结合模式与西瓜花叶病毒马铃薯 Y 病毒属（5ODV）CP 的实验结构，发现 YBMV CP 序列中存在从 76 到 91 个氨基酸的跨膜螺旋区。与结构密切同源的类似物一样，24 个 CP 单体亚基形成了 YBMV 的保守折叠。我们的计算研究表明，ARG124、ARG155 和 TYR151 朝向病毒的内侧，而 THR122、GLN125、SER92 和 ASP94 位于病毒的外侧。尽管与其他植物病毒的 CP 共享非常低的序列相似性，但 YBMV CP 的 RNA 结合口袋内强烈保守的残基 Ser、Arg 和 Asp 表明，不同家族的 CP 中存在高度保守的 RNA 结合位点。使用几种生物信息学工具和 MD 模拟的综合分析，我们的研究为 YBMV CP 的 RNA 结合机制提供了新的见解。因此，我们预计，我们从这项研究中获得的发现将有助于开发针对病原体的新治疗剂，为研究人员更好地控制这种破坏性植物病毒铺平道路。
