Metatranscriptomics analysis reveals a novel transcriptional and translational landscape during Middle East respiratory syndrome coronavirus infection
Ethan J. Fritch,
Wes Sanders,
Amy C. Sims,
Laura E. Herring,
Natalie K. Barker,
Athena A. Schepmoes,
Karl K. Weitz,
Jordan R. Texier,
Dirk P. Dittmer,
Lee M. Graves,
Richard D. Smith,
Katrina M. Waters,
Nathaniel J. Moorman,
Ralph S. Baric,
Rachel L. Graham
Affiliations
Ethan J. Fritch
Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Wes Sanders
Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Amy C. Sims
Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Laura E. Herring
Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Michael Hooker Proteomics Core Facility, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Natalie K. Barker
Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Michael Hooker Proteomics Core Facility, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Athena A. Schepmoes
Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99394, USA
Karl K. Weitz
Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99394, USA
Jordan R. Texier
Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Dirk P. Dittmer
Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Lee M. Graves
Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Michael Hooker Proteomics Core Facility, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Richard D. Smith
Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99394, USA
Katrina M. Waters
Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99394, USA
Nathaniel J. Moorman
Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Ralph S. Baric
Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Rachel L. Graham
Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Corresponding author
Summary: Among all RNA viruses, coronavirus RNA transcription is the most complex and involves a process termed “discontinuous transcription” that results in the production of a set of 3′-nested, co-terminal genomic and subgenomic RNAs during infection. While the expression of the classic canonical set of subgenomic RNAs depends on the recognition of a 6- to 7-nt transcription regulatory core sequence (TRS), here, we use deep sequence and metagenomics analysis strategies and show that the coronavirus transcriptome is even more vast and more complex than previously appreciated and involves the production of leader-containing transcripts that have canonical and noncanonical leader-body junctions. Moreover, by ribosome protection and proteomics analyses, we show that both positive- and negative-sense transcripts are translationally active. The data support the hypothesis that the coronavirus proteome is much vaster than previously noted in the literature.
