title: Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality.
abstract: Viruses often encode proteins with multiple functions due to their compact genomes. Existing approaches to identify functional residues largely rely on sequence conservation analysis. Inferring functional residues from sequence conservation can produce false positives, in which the conserved residues are functionally silent, or false negatives, where functional residues are not identified since they are species-specific and therefore non-conserved. Furthermore, the tedious process of constructing and analyzing individual mutations limits the number of residues that can be examined in a single study. Here, we developed a systematic approach to identify the functional residues of a viral protein by coupling experimental fitness profiling with protein stability prediction using the influenza virus polymerase PA subunit as the target protein. We identified a significant number of functional residues that were influenza type-specific and were evolutionarily non-conserved among different influenza types. Our results indicate that type-specific functional residues are prevalent and may not otherwise be identified by sequence conservation analysis alone. More importantly, this technique can be adapted to any viral (and potentially non-viral) protein where structural information is available.
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America,; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America.
authors.forename: Nicholas C
authors.initials: NC
authors.lastname: Wu
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America.
authors.forename: C Anders
authors.initials: CA
authors.lastname: Olson
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America.
authors.forename: Yushen
authors.initials: Y
authors.lastname: Du
authors.affiliation: Department of Microbiology, Third Military Medical University, Chongqing, 400038, China.
authors.forename: Shuai
authors.initials: S
authors.lastname: Le
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America.
authors.forename: Kevin
authors.initials: K
authors.lastname: Tran
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America.
authors.forename: Roland
authors.initials: R
authors.lastname: Remenyi
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America.
authors.forename: Danyang
authors.initials: D
authors.lastname: Gong
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America.
authors.forename: Laith Q
authors.initials: LQ
authors.lastname: Al-Mawsawi
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America.
authors.forename: Hangfei
authors.initials: H
authors.lastname: Qi
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America.
authors.forename: Ting-Ting
authors.initials: TT
authors.lastname: Wu
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America,; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America,; AIDS Institute, University of California, Los Angeles, Los Angeles, California, United States of America.
authors.forename: Ren
authors.initials: R
authors.lastname: Sun
mesh_terms: D001483:Base Sequence; D005075:Biological Evolution; D002460:Cell Line; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D015723:Gene Library; D057809:HEK293 Cells; D006801:Humans; D009980:Influenza A virus / Q000235:genetics*; D009981:Influenza B virus / Q000235:genetics*; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000235:genetics*
chemical_list: C061290:PA protein, influenza viruses; D014764:Viral Proteins; D012324:RNA-Dependent RNA Polymerase