CRISPR screening reveals a dependency on ribosome recycling for efficient SARS-CoV-2 programmed ribosomal frameshifting and viral replication
Frederick Rehfeld,
Jennifer L. Eitson,
Maikke B. Ohlson,
Tsung-Cheng Chang,
John W. Schoggins,
Joshua T. Mendell
Affiliations
Frederick Rehfeld
Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Jennifer L. Eitson
Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Maikke B. Ohlson
Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Tsung-Cheng Chang
Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
John W. Schoggins
Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Joshua T. Mendell
Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Corresponding author
Summary: During translation of the genomic RNA of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus in the COVID-19 pandemic, host ribosomes undergo programmed ribosomal frameshifting (PRF) at a conserved structural element. Although PRF is essential for coronavirus replication, host factors that regulate this process have not yet been identified. Here we perform genome-wide CRISPR-Cas9 knockout screens to identify regulators of SARS-CoV-2 PRF. These screens reveal that loss of ribosome recycling factors markedly decreases frameshifting efficiency and impairs SARS-CoV-2 viral replication. Mutational studies support a model wherein efficient removal of ribosomal subunits at the ORF1a stop codon is required for frameshifting of trailing ribosomes. This dependency upon ribosome recycling is not observed with other non-pathogenic human betacoronaviruses and is likely due to the unique position of the ORF1a stop codon in the SARS clade of coronaviruses. These findings therefore uncover host factors that support efficient SARS-CoV-2 translation and replication.
