Picornaviral polymerase structure, function, and fidelity modulation

Peersen, Olve B.

doi:10.1016/j.virusres.2017.01.026

Cited by 75 publications

(87 citation statements)

References 94 publications

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“…The GII.17 isolate displays evolutionary rates at least 1 order of magnitude higher than those seen with GII.4, further establishing the role of the RdRp in the emergence of new epidemic strains (Chan et al, 2015). The hypothesis that RdRp-driven genetic diversity is vital for viral fitness and pathogenesis is not unique to norovirus, and has been well documented for other virus families such as Picornaviruses (Vignuzzi et al, 2006;Peersen, 2017). Consistent with reports on the poliovirus polymerase, Arias et al reported a high-fidelity MNV polymerase variant associated with the I391L mutation (Arias et al, 2016).…”

Section: Role Of Norovirus Rdrp In Pathogenesis and Epidemiologymentioning

confidence: 80%

Structure(s), function(s), and inhibition of the RNA-dependent RNA polymerase of noroviruses

Deval¹,

Zhang²,

Chuang

et al. 2017

Virus Research

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Noroviruses belong to the Caliciviridae family of single-stranded positive-sense RNA viruses. The genus Norovirus includes seven genogroups (designated GI-GVII), of which GI, GII and GIV infect humans. Human noroviruses are responsible for widespread outbreaks of acute gastroenteritis and represent one of the most common causes of foodborne illness. No vaccine or antiviral treatment options are available for norovirus infection. The RNA-dependent RNA polymerase (RdRp) of noroviruses is a key enzyme responsible for transcription and replication of the viral genome. Here, we review the progress made in understanding the structures and functions of norovirus RdRp and its use as a target for small molecule inhibitors. Crystal structures of the RdRp at different stages of substrate interaction have been determined, which shed light on its multi-step catalytic cycle. The in vitro assays and in vivo animal models that have been developed to identify and characterize inhibitors of norovirus RdRp are also summarized, followed by an update on the current antiviral research targeting different regions of norovirus RdRp. In the future, structure-based drug design and rational optimization of known nucleoside and non-nucleoside inhibitors of norovirus RdRp may pave the way towards the next generation of direct-acting antivirals.

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Section: Role Of Norovirus Rdrp In Pathogenesis and Epidemiologymentioning

confidence: 80%

Structure(s), function(s), and inhibition of the RNA-dependent RNA polymerase of noroviruses

Deval¹,

Zhang²,

Chuang

et al. 2017

Virus Research

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“…As mentioned before, the Lys159 residue is located in motif F of the RdRp, which has been reported to play an important role in NTP binding during viral RNA synthesis (10). NTP binding is known to be a major fidelity checkpoint, and point mutations in this motif could annihilate polymerase activity or slow down catalysis (18). Mutating this lysine residue to an arginine or methionine resulted in reduced polymerization efficiency, which is likely the consequence of less efficient access of the incoming NTPs to the active site of RdRp.…”

Section: Discussionmentioning

confidence: 96%

“…(19,20), the residue Ala239 participates in a tetrahedral hydrogen bond network. This network helps position the Asp238 residue to the active site of the RdRp, providing a direct link between the properly positioned NTP and a set of structural interactions that promote catalysis by stabilizing the closed active site (18). Based on structural analysis of CVB3 polymerase, the residues Lys159 and Ala239 are closely located in the channel of the incoming NTP.…”

Section: Discussionmentioning

confidence: 99%

Understanding the Mechanism of the Broad-Spectrum Antiviral Activity of Favipiravir (T-705): Key Role of the F1 Motif of the Viral Polymerase

Abdelnabi

Morais

Leyssen

et al. 2017

J Virol

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Favipiravir (T-705) is a broad-spectrum antiviral agent that has been approved in Japan for the treatment of influenza virus infections. T-705 also inhibits the replication of various RNA viruses, including chikungunya virus (CHIKV). We demonstrated earlier that the K291R mutation in the F1 motif of the RNA-dependent RNA polymerase (RdRp) of CHIKV is responsible for low-level resistance to T-705. Interestingly, this lysine is highly conserved in the RdRp of positive-sense singlestranded RNA (ϩssRNA) viruses. To obtain insights into the unique broad-spectrum antiviral activity of T-705, we explored the role of this lysine using another ϩssRNA virus, namely, coxsackievirus B3 (CVB3). Introduction of the corresponding K-to-R substitution in the CVB3 RdRp (K159R) resulted in a nonviable virus. Replication competence of the K159R variant was restored by spontaneous acquisition of an A239G substitution in the RdRp. A mutagenesis analysis at position K159 identified the K159M variant as the only other viable variant which had also acquired the A239G substitution. The K159 substitutions markedly decreased the processivity of the purified viral RdRp, which was restored by the introduction of the A239G mutation. The K159R A239G and K159M A239G variants proved, surprisingly, more susceptible than the wild-type virus to T-705 and exhibited lower fidelity in polymerase assays. Furthermore, the K159R A239G variant was found to be highly attenuated in mice. We thus demonstrate that the conserved lysine in the F1 motif of the RdRp of ϩssRNA viruses is involved in the broad-spectrum antiviral activity of T-705 and that it is a key amino acid for the proper functioning of the enzyme.IMPORTANCE In this study, we report the key role of a highly conserved lysine residue of the viral polymerase in the broad-spectrum antiviral activity of favipiravir (T-705) against positive-sense single-stranded RNA viruses. Substitutions of this conserved lysine have a major negative impact on the functionality of the RdRp. Furthermore, we show that this lysine is involved in the fidelity of the RdRp and that the RdRp fidelity influences the sensitivity of the virus for the antiviral efficacy of T-705. Consequently, these results provide insights into the mechanism of the antiviral activity of T-705 and may lay the basis for the design of novel chemical scaffolds that may be endowed with a more potent broad-spectrum antiviral activity than that of T-705.KEYWORDS favipiravir, fidelity, mutagenesis, RdRp, CVB3

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“…A number of culture-independent methods exist now to characterize the novel viruses and their genes. Biochemical assays for RdRp, proteases, helicases, capsids, and internal ribosome entry sites all exist and synthetic biology allows for easy cloning from a database to test these new proteins found through metagenomics (Ladd Effio et al, 2016;O'Donoghue et al, 2012;Peersen, 2017). Profiling known functions across the new viral species, such as RNA binding strength and sequence specificity of novel RNA phage proteins related to MS2 phage or viral protease specificity and kinetics, might be a place to start (O'Donoghue et al, 2012).…”

Section: Experimenting With Functionmentioning

confidence: 99%

A decade of RNA virus metagenomics is (not) enough

2018

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It is hard to overemphasize the role that metagenomics has had on our recent understanding of RNA virus diversity. Metagenomics in the 21st century has brought with it an explosion in the number of RNA virus species, genera, and families far exceeding that following the discovery of the microscope in the 18th century for eukaryotic life or culture media in the 19th century for bacteriology or the 20th century for virology. When the definition of success in organism discovery is measured by sequence diversity and evolutionary distance, RNA viruses win. This review explores the history of RNA virus metagenomics, reasons for the successes so far in RNA virus metagenomics, and methodological concerns. In addition, the review briefly covers clinical metagenomics and environmental metagenomics and highlights some of the critical accomplishments that have defined the fast pace of RNA virus discoveries in recent years. Slightly more than a decade in, the field is exhausted from its discoveries but knows that there is yet even more out there to be found.

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Picornaviral polymerase structure, function, and fidelity modulation

Cited by 75 publications

References 94 publications

Structure(s), function(s), and inhibition of the RNA-dependent RNA polymerase of noroviruses

Structure(s), function(s), and inhibition of the RNA-dependent RNA polymerase of noroviruses

Understanding the Mechanism of the Broad-Spectrum Antiviral Activity of Favipiravir (T-705): Key Role of the F1 Motif of the Viral Polymerase

A decade of RNA virus metagenomics is (not) enough

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