Synonymous Mutations at the Beginning of the Influenza A Virus Hemagglutinin Gene Impact Experimental Fitness

Aneth S Canale; Sergey V Venev; Troy W Whitfield; Daniel R Caffrey; Wayne A Marasco; Celia A Schiffer; Timothy F Kowalik; Jeffrey D Jensen; Robert W Finberg; Konstantin B Zeldovich; Jennifer P Wang; Daniel N A Bolon

doi:10.1016/j.jmb.2018.02.009

Synonymous Mutations at the Beginning of the Influenza A Virus Hemagglutinin Gene Impact Experimental Fitness

J Mol Biol. 2018 Apr 13;430(8):1098-1115. doi: 10.1016/j.jmb.2018.02.009. Epub 2018 Feb 18.

Affiliations

¹ Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
² Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
³ Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA.
⁴ Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA.
⁵ Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA.
⁶ Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA.
⁷ School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ. 85281, USA.
⁸ Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA. Electronic address: Jennifer.Wang@umassmed.edu.
⁹ Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA. Electronic address: Dan.Bolon@umassmed.edu.

PMID: 29466705
DOI: 10.1016/j.jmb.2018.02.009

Abstract

The fitness effects of synonymous mutations can provide insights into biological and evolutionary mechanisms. We analyzed the experimental fitness effects of all single-nucleotide mutations, including synonymous substitutions, at the beginning of the influenza A virus hemagglutinin (HA) gene. Many synonymous substitutions were deleterious both in bulk competition and for individually isolated clones. Investigating protein and RNA levels of a subset of individually expressed HA variants revealed that multiple biochemical properties contribute to the observed experimental fitness effects. Our results indicate that a structural element in the HA segment viral RNA may influence fitness. Examination of naturally evolved sequences in human hosts indicates a preference for the unfolded state of this structural element compared to that found in swine hosts. Our overall results reveal that synonymous mutations may have greater fitness consequences than indicated by simple models of sequence conservation, and we discuss the implications of this finding for commonly used evolutionary tests and analyses.

Keywords: deep mutational scanning; experimental evolution; influenza A virus; selection; synonymous mutations.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Amino Acid Substitution
Animals
Dogs
Evolution, Molecular
Genetic Fitness*
HEK293 Cells
Hemagglutinin Glycoproteins, Influenza Virus / chemistry*
Hemagglutinin Glycoproteins, Influenza Virus / genetics*
Humans
Influenza A Virus, H1N1 Subtype / genetics
Influenza A Virus, H1N1 Subtype / growth & development*
Madin Darby Canine Kidney Cells
Models, Molecular
Phylogeny
RNA Folding
Silent Mutation*
Swine
Virus Replication

Substances

H1N1 virus hemagglutinin
Hemagglutinin Glycoproteins, Influenza Virus