Identification and enrichment of SECReTE cis-acting RNA elements in the Coronaviridae and other (+) single-strand RNA viruses

Gal Haimovich; Tsviya Olender; Camila Baez; Jeffrey E Gerst

Although RdRp is not a secreted protein per se, it does need to be translated on ER membranes and localizes to the DMV. Hence, we suspect that the high number of SECReTE motifs in the RdRp sequence may facilitate better RNA localization to, and translation at, ER membranes/DMVs. The hemaglutinin esterase (HE) gene, which is present only in the hCoV-OC43 and hCoV-HKU1 genomes, also contains a large number (e.g. 7-8) of SECReTE elements. Only three of the hCoVs examined have SECReTE elements in their 5'UTRs and only one has a motif in the 3'UTR. Since the non-structural proteins are translated as two long polypeptides (pp1a and pp1ab), we scored the total number of SECReTE of pp1ab for each virus. As expected, pp1ab contains the largest number of SECReTEs, with a high variability between the different CoVs. The only exception is hCoV-HKU1, which contains more SECReTE sequences in S as compared to pp1ab.