Proteogenomic analysis of Cyprinid herpesvirus 2 using high-resolution mass spectrometry.

IF 4 2区 医学 Q2 VIROLOGY
Chen Xu, Fangxing Yu, Mingyang Xue, Zhenyu Huang, Nan Jiang, Yiqun Li, Yan Meng, Wenzhi Liu, Ya Zheng, Yuding Fan, Yong Zhou
{"title":"Proteogenomic analysis of Cyprinid herpesvirus 2 using high-resolution mass spectrometry.","authors":"Chen Xu, Fangxing Yu, Mingyang Xue, Zhenyu Huang, Nan Jiang, Yiqun Li, Yan Meng, Wenzhi Liu, Ya Zheng, Yuding Fan, Yong Zhou","doi":"10.1128/jvi.01960-24","DOIUrl":null,"url":null,"abstract":"<p><p>Cyprinid herpesvirus 2 (CyHV-2) is the main pathogen responsible for the development of herpesviral hematopoietic necrosis disease (HVHND) in crucian carp (<i>Carassius auratus</i>). The CyHV-2 genome encodes approximately 150 genes that are expressed in a well-defined manner during productive infection. However, CyHV-2 open reading frames (ORFs) are primarily derived from sequence and homology analyses, and most lack protein-level evidence to support their properties. In this study, we used high-resolution mass spectrometry followed by proteogenomic mapping to achieve genome re-annotation of CyHV-2. Based on our results, a total of 1,683 MS/MS spectra could be mapped to the CyHV-2 genome through six-frame translation, with 1,665 corresponding to 117 currently annotated protein-coding ORFs. Three of the remaining 18 peptides were mapped to the N-terminal extension region of known ORFs. However, 12 novel CyHV-2 ORFs, designated nORF1-12, were identified and characterized for the first time based on the remaining 15 peptides that could be mapped to previously unannotated regions of the viral genome. And the sequence differences of the novel phosphorylated nORF1, also referred to as ORF25E, in different CyHV-2 strains indicated that the nORF1 is a prospective molecular marker that can monitor the evolution from the Japan (J) to the China (C) genotype of CyHV-2. These findings further validate existing annotations, expand the genomic landscape of CyHV-2, and provide a rich resource for aquatic virology research.IMPORTANCECyHV-2 is a viral pathogen that poses a significant threat to crucian carp farming. CyHV-2 has a large genome with complex sequence features and diverse coding mechanisms, which complicates accurate genome annotation in the absence of protein-level evidence. Here, we employed various protein extraction and separation methods to increase viral protein coverage and performed an integrated proteogenomic analysis to refine the CyHV-2 genome annotation. A total of 129 viral genes were confidently identified, including 117 currently annotated genes and 12 novel genes. For the first time, we present large-scale evidence of peptide presence and levels in the genome of aquatic viruses and confirm the majority of the predicted proteins in CyHV-2. Our findings enhance the understanding of the CyHV-2 genome structure and provide valuable insights for future studies on CyHV-2 biology.</p>","PeriodicalId":17583,"journal":{"name":"Journal of Virology","volume":" ","pages":"e0196024"},"PeriodicalIF":4.0000,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Virology","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1128/jvi.01960-24","RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"VIROLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Cyprinid herpesvirus 2 (CyHV-2) is the main pathogen responsible for the development of herpesviral hematopoietic necrosis disease (HVHND) in crucian carp (Carassius auratus). The CyHV-2 genome encodes approximately 150 genes that are expressed in a well-defined manner during productive infection. However, CyHV-2 open reading frames (ORFs) are primarily derived from sequence and homology analyses, and most lack protein-level evidence to support their properties. In this study, we used high-resolution mass spectrometry followed by proteogenomic mapping to achieve genome re-annotation of CyHV-2. Based on our results, a total of 1,683 MS/MS spectra could be mapped to the CyHV-2 genome through six-frame translation, with 1,665 corresponding to 117 currently annotated protein-coding ORFs. Three of the remaining 18 peptides were mapped to the N-terminal extension region of known ORFs. However, 12 novel CyHV-2 ORFs, designated nORF1-12, were identified and characterized for the first time based on the remaining 15 peptides that could be mapped to previously unannotated regions of the viral genome. And the sequence differences of the novel phosphorylated nORF1, also referred to as ORF25E, in different CyHV-2 strains indicated that the nORF1 is a prospective molecular marker that can monitor the evolution from the Japan (J) to the China (C) genotype of CyHV-2. These findings further validate existing annotations, expand the genomic landscape of CyHV-2, and provide a rich resource for aquatic virology research.IMPORTANCECyHV-2 is a viral pathogen that poses a significant threat to crucian carp farming. CyHV-2 has a large genome with complex sequence features and diverse coding mechanisms, which complicates accurate genome annotation in the absence of protein-level evidence. Here, we employed various protein extraction and separation methods to increase viral protein coverage and performed an integrated proteogenomic analysis to refine the CyHV-2 genome annotation. A total of 129 viral genes were confidently identified, including 117 currently annotated genes and 12 novel genes. For the first time, we present large-scale evidence of peptide presence and levels in the genome of aquatic viruses and confirm the majority of the predicted proteins in CyHV-2. Our findings enhance the understanding of the CyHV-2 genome structure and provide valuable insights for future studies on CyHV-2 biology.

鲤科疱疹病毒 2(CyHV-2)是导致鲫鱼(Carassius auratus)发生疱疹病毒造血坏死病(HVHND)的主要病原体。CyHV-2 基因组编码约 150 个基因,这些基因在生产性感染期间以明确的方式表达。然而,CyHV-2 开放阅读框(ORF)主要来自序列和同源性分析,大多数缺乏蛋白质水平的证据来支持其特性。在本研究中,我们利用高分辨率质谱技术和蛋白质基因组图谱实现了对 CyHV-2 基因组的重新标注。根据我们的结果,通过六框架翻译,共有 1,683 条 MS/MS 图谱可以映射到 CyHV-2 基因组,其中 1,665 条对应于目前注释的 117 个蛋白质编码 ORF。其余 18 个肽段中有 3 个被映射到已知 ORF 的 N 端延伸区域。然而,根据剩余的 15 条肽链,首次发现并鉴定了 12 个新的 CyHV-2 ORF(命名为 nORF1-12),这些肽链可以映射到以前未注释的病毒基因组区域。新型磷酸化 nORF1(又称 ORF25E)在不同 CyHV-2 株系中的序列差异表明,nORF1 是一种前瞻性分子标记,可监测 CyHV-2 基因型从日本(J)向中国(C)的演变。这些发现进一步验证了现有的注释,扩展了 CyHV-2 的基因组图谱,为水生病毒学研究提供了丰富的资源。CyHV-2 基因组庞大,序列特征复杂,编码机制多样,在缺乏蛋白质水平证据的情况下,准确的基因组注释非常复杂。在此,我们采用了多种蛋白质提取和分离方法来提高病毒蛋白质的覆盖率,并进行了综合蛋白质基因组分析,以完善CyHV-2基因组注释。共确定了 129 个病毒基因,包括 117 个当前已注释的基因和 12 个新基因。我们首次提出了水生病毒基因组中肽的存在和水平的大规模证据,并确认了 CyHV-2 中的大多数预测蛋白。我们的发现加深了人们对 CyHV-2 基因组结构的了解,为今后研究 CyHV-2 生物学提供了宝贵的见解。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Journal of Virology
Journal of Virology 医学-病毒学
CiteScore
10.10
自引率
7.40%
发文量
906
审稿时长
1 months
期刊介绍: Journal of Virology (JVI) explores the nature of the viruses of animals, archaea, bacteria, fungi, plants, and protozoa. We welcome papers on virion structure and assembly, viral genome replication and regulation of gene expression, genetic diversity and evolution, virus-cell interactions, cellular responses to infection, transformation and oncogenesis, gene delivery, viral pathogenesis and immunity, and vaccines and antiviral agents.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信