Identification of the protein coding capability of coronavirus defective viral genomes by mass spectrometry

During coronavirus infection, in addition to the well-known coronavirus genomes and subgenomic mRNAs, an abundance of defective viral genomes (DVGs) can also be synthesized. In this study, we aimed to examine whether DVGs can encode proteins in infected cells. Nanopore direct RNA sequencing and liqu...

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Published inVirology journal Vol. 20; no. 1; p. 290
Main Authors Lin, Ching-Hung, Hsieh, Feng-Cheng, Lai, Chien-Chen, Wang, Wei-Chen, Kuo, Cheng-Yu, Yang, Chun-Chun, Hsu, Hsuan-Wei, Tam, Hon-Man-Herman, Yang, Cheng-Yao, Wu, Hung-Yi
Format Journal Article
LanguageEnglish
Published England BioMed Central Ltd 07.12.2023
BioMed Central
BMC
Subjects
Amino acids
Chromatography
Chromatography, Liquid
Coronavirus
Coronavirus - genetics
Coronavirus Infections
Coronaviruses
Defective viral genome
Dengue fever
Development and progression
Disease transmission
Gene expression
Genetic aspects
Genome, Viral
Genomes
Humans
Infections
Influenza
Liquid chromatography
Lysates
Mass spectrometry
Mass spectroscopy
Pathogenesis
Peptides
Protein coding
Proteins
Proteins - genetics
Ribonucleic acid
RNA
RNA, Viral - genetics
Scientific imaging
Severe acute respiratory syndrome coronavirus 2
Tandem Mass Spectrometry
Viral proteins
Virus research
Viruses
Taiwan
United States > US
Protein coding
Defective viral genome
Coronavirus
Gene expression
Pathogenesis
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Summary:During coronavirus infection, in addition to the well-known coronavirus genomes and subgenomic mRNAs, an abundance of defective viral genomes (DVGs) can also be synthesized. In this study, we aimed to examine whether DVGs can encode proteins in infected cells. Nanopore direct RNA sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis were employed. With the protein databases generated by nanopore direct RNA sequencing and the cell lysates derived from the RNA-protein pull-down assay, six DVG-encoded proteins were identified by LC-MS/MS based on the featured fusion peptides caused by recombination during DVG synthesis. The results suggest that the coronavirus DVGs have the capability to encode proteins. Consequently, future studies determining the biological function of DVG-encoded proteins may contribute to the understanding of their roles in coronavirus pathogenesis and the development of antiviral strategies.
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ISSN:1743-422X
1743-422X
DOI:10.1186/s12985-023-02252-3