Poxvirus-encoded noncanonical open reading frames

痘病毒是一个大的病毒家族，包括对人类和动物具有高致病性的物种，包括天花和猴痘病毒。一些痘病毒被开发为疫苗载体和溶瘤病毒疗法，以对抗其他传染病和癌症。痘苗病毒是痘病毒的原型，在其200kbp的基因组中编码了200多个开放阅读框。我们使用rna测序对牛痘病毒基因表达进行全基因组分析，发现许多意想不到的mrna被转录。此外，我们之前的研究使用核糖体分析发现了大量（bbbb500）个新的翻译起始位点，这些位点与以前未被识别的非规范开放阅读框架（orf）相关。关于这些非规范orf的生物学相关性仍有许多未知之处。本研究的目的是表征非典型牛痘病毒orf编码的肽，并探讨其生物学相关性和功能。核心假设是肽/蛋白质是由非规范orf产生的，这可能在VACV复制中起重要作用。在Specific Aim 1中，将鉴定由牛痘病毒非规范orf编码的肽/蛋白。在特异性目标2中，将确定具有代表性的非规范orf在牛痘病毒复制中的作用。该项目的完成预计将提供以前未被识别的非规范痘病毒orf的表达和功能的知识。这对解释痘病毒的遗传研究具有深远的意义，因为过去的研究主要集中在先前注释的大orf上。这一结果可能会改变人们对痘病毒基因表达的认识，并为该领域开辟新的方向。更好地了解这些新发现的orf可能最终导致新的干预策略和改进痘病毒作为疫苗载体和癌症治疗剂。因此，研究结果预计将对痘病毒以外的生物产生广泛影响，因为包括人类在内的各种生物的基因组也编码了许多以前未被识别的orf。

Poxviruses are a large family of viruses including species that are highly pathogenic for humans and animals, including smallpox and monkeypox viruses. Some poxviruses are developed as vaccine vectors and oncolytic virotherapies to fight other infectious diseases and cancers. Vaccinia virus, the prototype poxvirus, has previously been annotated to encode over 200 open reading frames in its 200kbp genome. Our genome-wide analysis of vaccinia virus gene expression using RNA-sequencing uncovered that numerous unexpected mRNAs are transcribed. Furthermore, our previous study discovered a large number of (>500) novel translation initiation sites associated with previously unrecognized non-canonical open reading frames (ORFs) using ribosome profiling. Much remains unknown about the biological relevance of these non-canonical ORFs. The objective of this proposal is to characterize the peptides encoded by the non-canonical vaccinia virus ORFs and explore the biological relevance and functions. The central hypothesis is that peptides/proteins are produced from the non-canonical ORFs, which may play important roles in VACV replication. In Specific Aim 1, peptides/proteins encoded by vaccinia virus non-canonical ORFs will be identified. In Specific Aim 2, the roles of representative non-canonical ORFs in vaccinia virus replication will be determined. Completion of the project is expected to provide knowledge of the expression and functions of the non-canonical poxvirus ORFs that are previously unrecognized. It has profound implications in interpreting poxvirus genetic studies since the past studies have been focusing on previously annotated large ORFs. The outcomes may transform the understanding of poxvirus gene expression and break ground toward new directions in the field. Better understanding these newly identified ORFs may ultimately lead to novel intervening strategies and improving poxviruses as vaccine vectors and cancer therapeutics agents. Therefore, the outcomes are also expected to have a broad impact beyond the poxviruses, as the genomes of various organisms, including humans, also encoded many previously unrecognized ORFs.