What we know but do not understand about nidovirus helicases

Abstract

Helicases are versatile NTP-dependent motor proteins of monophyletic origin that are found in all kingdoms of life. Their functions range from nucleic acid duplex unwinding to protein displacement and double-strand translocation. This explains their participation in virtually every metabolic process that involves nucleic acids, including DNA replication, recombination and repair, transcription, translation, as well as RNA processing. Helicases are encoded by all plant and animal viruses with a positive-sense RNA genome that is larger than 7 kb, indicating a link to genome size evolution in this virus class. Viral helicases belong to three out of the six currently recognized superfamilies, SF1, SF2, and SF3. Despite being omnipresent, highly conserved and essential, only a few viral helicases, mostly from SF2, have been studied extensively. In general, their specific roles in the viral replication cycle remain poorly understood at present. The SF1 helicase protein of viruses classified in the order Nidovirales is encoded in replicase open reading frame 1b (ORF1b), which is translated to give rise to a large polyprotein following a ribosomal frameshift from the upstream ORF1a. Proteolytic processing of the replicase polyprotein yields a dozen or so mature proteins, one of which includes a helicase. Its hallmark is the presence of an N-terminal multi-nuclear zinc-binding domain, the nidoviral genetic marker and one of the most conserved domains across members of the order. This review summarizes biochemical, structural, and genetic data, including drug development studies, obtained using helicases originating from several mammalian nidoviruses, along with the results of the genomics characterization of a much larger number of (putative) helicases of vertebrate and invertebrate nidoviruses. In the context of our knowledge of related helicases of cellular and viral origin, it discusses the implications of these results for the protein's emerging critical function(s) in nidovirus evolution, genome replication and expression, virion biogenesis, and possibly also post-transcriptional processing of viral RNAs. Using our accumulated knowledge and highlighting gaps in our data, concepts and approaches, it concludes with a perspective on future research aimed at elucidating the role of helicases in the nidovirus replication cycle.

Nidovirus RNA polymerases: Complex enzymes handling exceptional RNA genomes

“…However, it remains unclear how AV nsp1 interacts with e.g. the network of TRS signals, the viral RNA polymerase (AV nsp9), or the helicase (AV nsp10), which has also been implicated in transcriptional control (Deng et al, 2014;Lehmann et al, 2015b). The protein could e.g.…”

Biogenesis and architecture of arterivirus replication organelles

“…The ORF1b-encoded subunits include the main enzymatic activities required for RNA replication, such as the RNA-dependent RNA polymerase (RdRp) and the helicase (den Boon et al, 1991;Fang and Snijder, 2010;Gorbalenya et al, 2006;Lehmann et al, 2015a;Lehmann et al, 2015b;Snijder et al, 2013). The pp1a subunits seem to support the viral RNA replication more indirectly.…”

The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing

“…However, despite their abundance and conservation, the specific role of helicases in +RNA virus replication remains poorly understood. For an extensive recent review of nidovirus helicases, the reader is referred to Lehmann et al (2015c).…”

“…The N-terminal part of nsp13 is formed by a multinuclear ZBD, one of the most conserved domains across the order Nidovirales (Gorbalenya, 2001;Nga et al, 2011). This qualification also applies to the helicase-containing subunit as a whole, despite considerable size differences between, e.g., CoV nsp13 and its arterivirus homolog (designated nsp10) (Lehmann et al, 2015c). The ZBD and HEL1 domains occupy a conserved position downstream of the RdRp domain in all nidovirus replicase polyproteins studied so far.…”