Respiratory syncytial virus M2-1 protein associates non-specifically with viral messenger RNA and with specific cellular messenger RNA transcripts

Respiratory syncytial virus (RSV) is a major cause of respiratory disease in infants and the elderly. RSV is a non-segmented negative strand RNA virus. The viral M2-1 protein plays a key role in viral transcription, serving as an elongation factor to enable synthesis of full-length mRNAs. M2-1 contains an unusual CCCH zinc-finger motif that is conserved in the related human metapneumovirus M2-1 protein and filovirus VP30 proteins. Previous biochemical studies have suggested that RSV M2-1 might bind to specific virus RNA sequences, such as the transcription gene end signals or poly A tails, but there was no clear consensus on what RSV sequences it binds. To determine if M2-1 binds to specific RSV RNA sequences during infection, we mapped points of M2-1:RNA interactions in RSV-infected cells at 8 and 18 hours post infection using crosslinking immunoprecipitation with RNA sequencing (CLIP-Seq). This analysis revealed that M2-1 interacts specifically with positive sense RSV RNA, but not negative sense genome RNA. It also showed that M2-1 makes contacts along the length of each viral mRNA, indicating that M2-1 functions as a component of the transcriptase complex, transiently associating with nascent mRNA being extruded from the polymerase. In addition, we found that M2-1 binds specific cellular mRNAs. In contrast to the situation with RSV mRNA, M2-1 binds discrete sites within cellular mRNAs, with a preference for A/U rich sequences. These results suggest that in addition to its previously described role in transcription elongation, M2-1 might have an additional role involving cellular RNA interactions. Author summary RSV is a significant cause of respiratory disease in infants and the elderly population. As yet there are no vaccines or effective antiviral treatments to control the virus. An understanding of the viral machinery that generates viral RNA could help identify suitable targets for antiviral inhibitors. Our goal in this study was to elucidate how a key protein in RSV mRNA transcription, M2-1, functions by determining if it binds to specific RSV RNA sequences. Our findings show that while M2-1 binds RSV mRNAs, it makes contacts along the entire length of each mRNA, indicating that it is part of the RNA generating machinery. Surprisingly, we also found that M2-1 binds to specific cellular mRNAs. This finding suggests that M2-1 might have another role in infection, besides its role in RSV mRNA transcription.

Automated summary

Respiratory syncytial virus (RSV) is a significant cause of respiratory disease in infants and the elderly, with no vaccines or effective antiviral treatments available. The M2-1 protein in RSV plays a key role in viral transcription, binding to specific RSV RNA sequences and possibly having an additional role in cellular RNA interactions. This study aimed to elucidate the function of M2-1 in RSV mRNA transcription, revealing its involvement in viral RNA generation and its binding to specific cellular mRNAs, suggesting a potential dual role in infection.