Identification of a Nidovirales Orf1a N7-guanine cap methyltransferase signature-sequence as a genetic marker of large RNA genome Tobaniviridae

Members of the Nidovirales order have (+)RNA genomes amongst the largest in size in the RNA virus world. Expression of their genes is promoted through reading of genomic RNA and mRNA transcripts by the ribosome of the infected cell. The 5-end of these RNAs is supposedly protected by an RNA-cap structure (m7GpppNm) whose most synthesis steps remain elusive. In Eukaryotes, the RNA-cap structure is methylated by RNA methyltransferases (MTases) at the RNA-cap N7-guanine position as well as the 2-O methyl position of the first transcribed nucleotide. In Coronaviridae, two separate enzymes (nsp14 and nsp16) perform the N7-guanine and the 2-OH methylation, respectively. One salient feature of the Nidovirales N7-guanine MTase nsp14 is that it is the only example of non-Rossman fold viral MTase known so far. Conversely, all other Nidovirales nsp16-like MTases have a canonical Rossman fold. Many Nidovirales members lack either any RNA MTase signature sequence (e.g., Arteriviridae), or lack a N7-guanine MTase signature sequence (e.g., Tobaniviridae, Euroniviridae, Roniviridae, Medioniviridae). Both nsp14-and nsp16-like enzyme genes are usually located in Orf1b encoding for the replication machinery. Here, we report the discovery of a putative Rossman fold RNA MTase in the Orf1a of ten Tobaniviridae members. Multiple sequence alignments and structural analyses identify this novel gene as a typical RNA-cap N7-guanine MTase with substrate specificity and active-site organization similar to the canonical eukaryotic RNA-cap N7-guanine MTase.