Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase

Deng, Zengqin; Lehmann, Kathleen C.; Li, Xiaorong; Feng, Chong; Wang, Guoqiang; Zhang, Qi; Qi, Xiaoxuan; Yu, Lin; Zhang, Xingliang; Feng, Wenhai; Wu, Wei; Gong, Peng; Tao, Ye; Posthuma, Clara C.; Snijder, Eric J.; Gorbalenya, Alexander E.; Chen, Zhongzhou

Compared with other +RNA viruses, nidovirus replicase genes encode an exceptionally large number of nonstructural proteins (nsps) (19, 24, 25, 28) . Nidovirus nsps are expressed from open reading frames (ORFs) 1a and 1b, which make up the 5 0 -proximal 65-75% of the genome RNA. ORF1a encodes polyprotein 1a (pp1a; size ranging from 1728 to 4550 aa) and following a -1 ribosomal frameshift pp1a can be extended with the ORF1bencoded polyprotein to give pp1ab (3175-7183 aa) (29) (Supplementary Figure S1 ). Both polyproteins are subject to extensive proteolytic processing by multiple, internally encoded proteinases (19, 30) . The nidovirus replicase backbone consists of a conserved array of domains, arranged in a nidovirus-specific order and including the ORF1b-encoded RNA-dependent RNA polymerase (RdRp) and HEL1 domains, the core enzymes needed for genome RNA synthesis (replication) and subgenomic (sg) mRNA production (transcription). The latter process yields an extensive nested set of sg mRNAs, which are used to express up to a dozen structural and accessory proteins from smaller ORFs in the 3 0 -proximal part of the genome (31) (32) (33) . In both corona-and arteriviruses, sg mRNAs contain a common leader sequence that is identical to the 5 0 end of the genome. Their generation from sg negative-stranded templates involves a mechanism of discontinuous negative strand RNA synthesis (31, 32) .