Pan Gong, Qingtang Shen, Mingzhen Zhang, Rui Qiao, Jing Jiang, Lili Su, Siwen Zhao, Shuai Fu, Yu Ma, Linhao Ge, Yaqin Wang, Rosa Lozano-Duran, Aimign Wang, Fangfang Li*, Xueping Zhou*. Plant and animal positive-sense single-stranded RNA viruses encode small proteins important for viral infection in their negative-sense strand. Molecular Plant, 2023, https://doi.org/10.1016/j.molp.2023.09.020

Abstract

Positive-sense single-stranded RNA (+ssRNA) viruses, the most abundant viruses of eukaryotes in nature, require the synthesis of negative-sense RNA (-RNA) using their genomic (positive-sense) RNA (+RNA) as a template for replication. Based on the current evidence, viral proteins are translated via viral positive sense RNAs, whereas -RNA is considered to be a viral replication intermediate without coding capacity. Here, we report that plant and animal +ssRNA viruses contain small open reading frames (ORFs) in their -RNA (rORFs). Using turnip mosaic virus (TuMV) as a model for plant +ssRNA viruses, we demonstrate that small proteins encoded by rORFs display specific subcellular localizations, and confirm the presence of rORF2 in infected cells through mass spectrometry analysis. The protein encoded by TuMV rORF2 forms punctuate granules that localize in the perinuclear region and co-localize with viral replication complexes. The rORF2 protein can directly interact with the viral RNA-dependent RNA polymerase; mutation of rORF2 completely abolishes virus infection, and ectopic expression of rORF2 rescues the mutant virus. Furthermore, we show that several rORFs in the -RNA of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have the ability to suppress type-I interferon (IFN-I) production and facilitate vesicular stomatitis virus (VSV) infection. Additionally, we provide evidence that TuMV might utilize internal ribosome entry sites to translate these small rORFs. Our findings reveal that the -RNA of +ssRNA viruses can also have coding capacity and that small proteins encoded therein play critical roles in viral infection, unveiling a larger viral proteome than previously thought.

Molecular Plant, IF=27.5

https://www.sciencedirect.com/science/article/pii/S16742052230