Homology-based classification of accessory proteins in coronavirus genomes uncovers extremely dynamic evolution of gene content.
Homology-based classification of accessory proteins in coronavirus genomes uncovers extremely dynamic evolution of gene content.
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冠状病毒基因组中辅助蛋白的基于同源性的分类揭示了基因内容的极其动态的进化。
DOI：
10.1111/mec.16531
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发表时间：
2022-07
影响因子：
4.9
通讯作者：
Sironi, Manuela
中科院分区：
文献类型：
--
作者：
Forni, Diego;Cagliani, Rachele;Molteni, Cristian;Arrigoni, Federica;Mozzi, Alessandra;Clerici, Mario;De Gioia, Luca;Sironi, Manuela
冠状病毒（CoV）具有复杂的基因组，编码一系列固定的结构和非结构组分，以及各种辅助蛋白，即使在密切相关的病毒之间也存在差异。辅助蛋白通常在抑制免疫应答中起作用，并且可能代表毒力因子。尽管它们与CoV表型变异相关，但关于辅助蛋白的信息是零碎的。我们应用了一种基于同源性检测的系统方法来创建由CoV编码的辅助蛋白的全面目录。我们的分析将辅助蛋白分为379个正群和12个超群。四个CoV属之间没有正群共享，并且在同一属的所有或大多数病毒中存在很少的正群，反映了CoV基因组的动态进化。我们观察到CoV属中辅助蛋白的分布差异。α冠状病毒的辅助开放阅读框（ORF）多样性最大，δ冠状病毒最小。然而，每个基因组的辅助蛋白的平均数量在β冠状病毒中最高。一些正群的进化历史分析表明，不同的CoV属采取了类似的进化策略。因此，呼吸道冠状病毒和β冠状病毒独立地获得磷酸二酯酶和刺突样辅助蛋白，而来自呼肠孤病毒的水平基因转移赋予β冠状病毒和δ冠状病毒融合相关小跨膜（FAST）蛋白。最后，对注释的CoV基因组中的辅助ORF的分析表明它们的命名存在歧义。这使得研究人员之间的交叉交流变得复杂，并阻碍了大型数据集的自动搜索（例如，PubMed，GenBank）。我们建议，orthoggroupmembership一起使用的命名系统，以提供信息的蛋白质功能。
Coronaviruses (CoVs) have complex genomes that encode a fixed array of structural and nonstructural components, as well as a variety of accessory proteins that differ even among closely related viruses. Accessory proteins often play a role in the suppression of immune responses and may represent virulence factors. Despite their relevance for CoV phenotypic variability, information on accessory proteins is fragmentary. We applied a systematic approach based on homology detection to create a comprehensive catalogue of accessory proteins encoded by CoVs. Our analyses grouped accessory proteins into 379 orthogroups and 12 super‐groups. No orthogroup was shared by the four CoV genera and very few were present in all or most viruses in the same genus, reflecting the dynamic evolution of CoV genomes. We observed differences in the distribution of accessory proteins in CoV genera. Alphacoronaviruses harboured the largest diversity of accessory open reading frames (ORFs), deltacoronaviruses the smallest. However, the average number of accessory proteins per genome was highest in betacoronaviruses. Analysis of the evolutionary history of some orthogroups indicated that the different CoV genera adopted similar evolutionary strategies. Thus, alphacoronaviruses and betacoronaviruses acquired phosphodiesterases and spike‐like accessory proteins independently, whereas horizontal gene transfer from reoviruses endowed betacoronaviruses and deltacoronaviruses with fusion‐associated small transmembrane (FAST) proteins. Finally, analysis of accessory ORFs in annotated CoV genomes indicated ambiguity in their naming. This complicates cross‐communication among researchers and hinders automated searches of large data sets (e.g., PubMed, GenBank). We suggest that orthogroup membership is used together with a naming system to provide information on protein function.
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影响因子：
14.9
作者：
NCBI Resource Coordinators
通讯作者：
NCBI Resource Coordinators
影响因子：
16.6
作者：
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通讯作者：
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影响因子：
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作者：
Huang C;Liu WJ;Xu W;Jin T;Zhao Y;Song J;Shi Y;Ji W;Jia H;Zhou Y;Wen H;Zhao H;Liu H;Li H;Wang Q;Wu Y;Wang L;Liu D;Liu G;Yu H;Holmes EC;Lu L;Gao GF
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影响因子：
5.4
作者：
Guan, Hongxin;Wang, Youwang;Ouyang, Songying
通讯作者：
Ouyang, Songying
影响因子：
28.3
作者：
Gorbalenya, Alexander E.;Baker, Susan C.;Ziebuhr, John
通讯作者：
Ziebuhr, John