tetano
Editor, Senior Moderator
J Gen Virol
. 2020 Jul 15.
doi: 10.1099/jgv.0.001469. Online ahead of print.
A putative new SARS-CoV protein, 3c, encoded in an ORF overlapping ORF3a
Andrew E Firth[SUP] 1 [/SUP]
Affiliations
Abstract
Identification of the full complement of genes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a crucial step towards gaining a fuller understanding of its molecular biology. However, short and/or overlapping genes can be difficult to detect using conventional computational approaches, whereas high-throughput experimental approaches - such as ribosome profiling - cannot distinguish translation of functional peptides from regulatory translation or translational noise. By studying regions showing enhanced conservation at synonymous sites in alignments of SARS-CoV-2 and related viruses (subgenus Sarbecovirus) and correlating the results with the conserved presence of an open reading frame (ORF) and a plausible translation mechanism, a putative new gene - ORF3c - was identified. ORF3c overlaps ORF3a in an alternative reading frame. A recently published ribosome profiling study confirmed that ORF3c is indeed translated during infection. ORF3c is conserved across the subgenus Sarbecovirus, and encodes a 40-41 amino acid predicted transmembrane protein.
Keywords: 3c; ORF3c; SARS-CoV; coronavirus; overlapping gene; sarbecovirus.
. 2020 Jul 15.
doi: 10.1099/jgv.0.001469. Online ahead of print.
A putative new SARS-CoV protein, 3c, encoded in an ORF overlapping ORF3a
Andrew E Firth[SUP] 1 [/SUP]
Affiliations
- PMID: 32667280
- DOI: 10.1099/jgv.0.001469
Abstract
Identification of the full complement of genes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a crucial step towards gaining a fuller understanding of its molecular biology. However, short and/or overlapping genes can be difficult to detect using conventional computational approaches, whereas high-throughput experimental approaches - such as ribosome profiling - cannot distinguish translation of functional peptides from regulatory translation or translational noise. By studying regions showing enhanced conservation at synonymous sites in alignments of SARS-CoV-2 and related viruses (subgenus Sarbecovirus) and correlating the results with the conserved presence of an open reading frame (ORF) and a plausible translation mechanism, a putative new gene - ORF3c - was identified. ORF3c overlaps ORF3a in an alternative reading frame. A recently published ribosome profiling study confirmed that ORF3c is indeed translated during infection. ORF3c is conserved across the subgenus Sarbecovirus, and encodes a 40-41 amino acid predicted transmembrane protein.
Keywords: 3c; ORF3c; SARS-CoV; coronavirus; overlapping gene; sarbecovirus.