Design of a Genetically Stable High Fidelity Coxsackievirus B3 Polymerase That Attenuates Virus Growth in Vivo

Positive strand RNA viruses replicate via a virally encoded RNA-dependent RNA polymerase (RdRP) that uses a unique palm domain active site closure mechanism to establish the canonical two-metal geometry needed for catalysis. This mechanism allows these viruses to evolutionarily fine-tune their repli...

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Bibliographic Details
Published in:The Journal of biological chemistry 2016-07, Vol.291 (27), p.13999-14011
Main Authors: McDonald, Seth, Block, Andrew, Beaucourt, Stéphanie, Moratorio, Gonzalo, Vignuzzi, Marco, Peersen, Olve B.
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Biocatalysis
Biochemistry
Biochemistry, Molecular Biology
Crystallization
Enterovirus B, Human
Enterovirus B, Human - enzymology
Enterovirus B, Human - physiology
Kinetics
Life Sciences
Models, Molecular
Molecular Bases of Disease
Molecular biology
plus-stranded RNA virus
polymerase fidelity
Protein Conformation
protein engineering
RNA Replicase
RNA-Dependent RNA Polymerase - chemistry
RNA-Dependent RNA Polymerase - genetics
RNA-Dependent RNA Polymerase - metabolism
Sequence Homology, Amino Acid
Structural Biology
vaccine development
viral polymerase
virology
Virus Replication
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Summary:Positive strand RNA viruses replicate via a virally encoded RNA-dependent RNA polymerase (RdRP) that uses a unique palm domain active site closure mechanism to establish the canonical two-metal geometry needed for catalysis. This mechanism allows these viruses to evolutionarily fine-tune their replication fidelity to create an appropriate distribution of genetic variants known as a quasispecies. Prior work has shown that mutations in conserved motif A drastically alter RdRP fidelity, which can be either increased or decreased depending on the viral polymerase background. In the work presented here, we extend these studies to motif D, a region that forms the outer edge of the NTP entry channel where it may act as a nucleotide sensor to trigger active site closure. Crystallography, stopped-flow kinetics, quench-flow reactions, and infectious virus studies were used to characterize 15 engineered mutations in coxsackievirus B3 polymerase. Mutations that interfere with the transport of the metal A Mg2+ ion into the active site had only minor effects on RdRP function, but the stacking interaction between Phe364 and Pro357, which is absolutely conserved in enteroviral polymerases, was found to be critical for processive elongation and virus growth. Mutating Phe364 to tryptophan resulted in a genetically stable high fidelity virus variant with significantly reduced pathogenesis in mice. The data further illustrate the importance of the palm domain movement for RdRP active site closure and demonstrate that protein engineering can be used to alter viral polymerase function and attenuate virus growth and pathogenesis.
ISSN:0021-9258
1083-351X
DOI:10.1074/jbc.M116.726596