Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression
Authors
Shang, Pengcheng
Li, Yanhua
Soday, Lior
Tumescheit, Charlotte
Mockett, Adrian
Fang, Ying
Publication Date
2022-02-28Journal Title
eLife
ISSN
2050-084X
Publisher
eLife Sciences Publications Ltd
Volume
11
Language
en
Type
Article
This Version
VoR
Metadata
Show full item recordCitation
Cook, G., Brown, K., Shang, P., Li, Y., Soday, L., Dinan, A., Tumescheit, C., et al. (2022). Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression. eLife, 11 https://doi.org/10.7554/eLife.75668
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is an arterivirus which causes significant economic losses to the swine industry worldwide. Here, we use ribosome profiling (RiboSeq) and parallel RNA sequencing (RNASeq) to characterise the transcriptome and translatome of both species of PRRSV and analyse the host response to infection. We quantified viral gene expression over a timecourse of infection, and calculated the efficiency of programmed ribosomal frameshifting (PRF) at both sites on the viral genome. At the nsp2 frameshift site (a rare example of protein-stimulated frameshifting), −2 PRF efficiency increases over time, likely facilitated by accumulation of the PRF stimulatory viral protein (nsp1β) during infection. This marks arteriviruses as the second example of temporally regulated PRF. Surprisingly, we also found PRF efficiency at the canonical ORF1ab frameshift site increases over time, in apparent contradiction of the common assumption that RNA structure-directed frameshift sites operate at a fixed efficiency. This has potential implications for the numerous other viruses with canonical PRF sites. Furthermore, we discovered several highly translated additional viral ORFs, the translation of which may be facilitated by multiple novel viral transcripts. For example, we found a 125-codon ORF overlapping nsp12, which is expressed as highly as nsp12 itself at late stages of replication, and is likely translated from novel subgenomic (sg) RNA transcripts that overlap the 3′ end of ORF1b. Similar transcripts were discovered for both PRRSV-1 and PRRSV- 2, suggesting a potential conserved mechanism for temporal regulation of expression of the 3′-proximal region of ORF1b. In addition, we identified a highly translated, short upstream ORF (uORF) in the 5′ UTR, the presence of which is highly conserved amongst PRRSV-2 isolates. This is the first application of RiboSeq to arterivirus-infected cells, and reveals new features which add to the complexity of gene expression programmes in this important family of nidoviruses.
Keywords
Research Article, Chromosomes and Gene Expression, Microbiology and Infectious Disease, arterivirus, porcine reproductive, PRRSV, ribosome profiling, programmed ribosomal frameshifting, subgenomic mRNAs, RNA sequencing, transcriptome, translatome, gene expression regulation, respiratory syndrome virus, Nidovirus
Sponsorship
Biotechnology and Biological Sciences Research Council (BB/L000334/1)
Wellcome Trust (202797/Z/16/Z)
Wellcome Trust (106207/Z/14/Z)
European Research Council (646891)
Wellcome Trust (203864/Z/16/Z)
Wellcome Trust (102163/B/13/Z)
Identifiers
75668
External DOI: https://doi.org/10.7554/eLife.75668
This record's URL: https://www.repository.cam.ac.uk/handle/1810/336013
Rights
Licence:
http://creativecommons.org/licenses/by/4.0/
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