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Ping J, Keleta L, Forbes NE, Dankar S, Stecho W, Tyler S, Zhou Y, Babiuk L, Weingartl H, Halpin RA, Boyne A, Bera J, Hostetler J, Fedorova NB, Proudfoot K, Katzel DA, Stockwell TB, Ghedin E, Spiro DJ, Brown EG. Genomic and protein structural maps of adaptive evolution of human influenza A virus to increased virulence in the mouse. PLoS One 2011; 6:e21740. [PMID: 21738783 PMCID: PMC3128085 DOI: 10.1371/journal.pone.0021740] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 06/10/2011] [Indexed: 12/11/2022] Open
Abstract
Adaptive evolution is characterized by positive and parallel, or repeated selection of mutations. Mouse adaptation of influenza A virus (IAV) produces virulent mutants that demonstrate positive and parallel evolution of mutations in the hemagglutinin (HA) receptor and non-structural protein 1 (NS1) interferon antagonist genes. We now present a genomic analysis of all 11 genes of 39 mouse adapted IAV variants from 10 replicate adaptation experiments. Mutations were mapped on the primary and structural maps of each protein and specific mutations were validated with respect to virulence, replication, and RNA polymerase activity. Mouse adapted (MA) variants obtained after 12 or 20–21 serial infections acquired on average 5.8 and 7.9 nonsynonymous mutations per genome of 11 genes, respectively. Among a total of 115 nonsynonymous mutations, 51 demonstrated properties of natural selection including 27 parallel mutations. The greatest degree of parallel evolution occurred in the HA receptor and ribonucleocapsid components, polymerase subunits (PB1, PB2, PA) and NP. Mutations occurred in host nuclear trafficking factor binding sites as well as sites of virus-virus protein subunit interaction for NP, NS1, HA and NA proteins. Adaptive regions included cap binding and endonuclease domains in the PB2 and PA polymerase subunits. Four mutations in NS1 resulted in loss of binding to the host cleavage and polyadenylation specificity factor (CPSF30) suggesting that a reduction in inhibition of host gene expression was being selected. The most prevalent mutations in PB2 and NP were shown to increase virulence but differed in their ability to enhance replication and demonstrated epistatic effects. Several positively selected RNA polymerase mutations demonstrated increased virulence associated with >300% enhanced polymerase activity. Adaptive mutations that control host range and virulence were identified by their repeated selection to comprise a defined model for studying IAV evolution to increased virulence in the mouse.
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Affiliation(s)
- Jihui Ping
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| | - Liya Keleta
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| | - Nicole E. Forbes
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| | - Samar Dankar
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| | - William Stecho
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada
| | - Shaun Tyler
- National Microbiology Laboratory, Canadian Science Centre for Human and Animal Health, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Yan Zhou
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| | - Lorne Babiuk
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| | - Hana Weingartl
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| | - Rebecca A. Halpin
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Alex Boyne
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jayati Bera
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jessicah Hostetler
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Nadia B. Fedorova
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Katie Proudfoot
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Dan A. Katzel
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Tim B. Stockwell
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Elodie Ghedin
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
- Center for Vaccine Research, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - David J. Spiro
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
- Viral Genomics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Earl G. Brown
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
- * E-mail:
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153
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Foeglein Á, Loucaides EM, Mura M, Wise HM, Barclay WS, Digard P. Influence of PB2 host-range determinants on the intranuclear mobility of the influenza A virus polymerase. J Gen Virol 2011; 92:1650-1661. [PMID: 21471313 PMCID: PMC3167894 DOI: 10.1099/vir.0.031492-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Avian influenza A viruses often do not propagate efficiently in mammalian cells. The viral polymerase protein PB2 is important for this host restriction, with amino-acid polymorphisms at residue 627 and other positions acting as ‘signatures’ of avian- or human-adapted viruses. Restriction is hypothesized to result from differential interactions (either positive or inhibitory) with unidentified cellular factors. We applied fluorescence recovery after photobleaching (FRAP) to investigate the mobility of the viral polymerase in the cell nucleus using A/PR/8/34 and A/Turkey/England/50-92/91 as model strains. As expected, transcriptional activity of a polymerase with the avian PB2 protein was strongly dependent on the identity of residue 627 in human but not avian cells, and this correlated with significantly slower diffusion of the inactive polymerase in human but not avian nuclei. In contrast, the activity and mobility of the PR8 polymerase was affected much less by residue 627. Sequence comparison followed by mutagenic analyses identified residues at known host-range-specific positions 271, 588 and 701 as well as a novel determinant at position 636 as contributors to host-specific activity of both PR8 and Turkey PB2 proteins. Furthermore, the correlation between poor transcriptional activity and slow diffusional mobility was maintained. However, activity did not obligatorily correlate with predicted surface charge of the 627 domain. Overall, our data support the hypothesis of a host nuclear factor that interacts with the viral polymerase and modulates its activity. While we cannot distinguish between positive and inhibitory effects, the data have implications for how such factors might operate.
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Affiliation(s)
- Ágnes Foeglein
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Eva M Loucaides
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | | | - Helen M Wise
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | | | - Paul Digard
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
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154
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An Y, Meresse P, Mas PJ, Hart DJ. CoESPRIT: a library-based construct screening method for identification and expression of soluble protein complexes. PLoS One 2011; 6:e16261. [PMID: 21364980 PMCID: PMC3043051 DOI: 10.1371/journal.pone.0016261] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Accepted: 12/13/2010] [Indexed: 11/29/2022] Open
Abstract
Structural and biophysical studies of protein complexes require multi-milligram quantities of soluble material. Subunits are often unstable when expressed separately so co-expression strategies are commonly employed since in vivo complex formation can provide stabilising effects. Defining constructs for subunit co-expression experiments is difficult if the proteins are poorly understood. Even more problematic is when subunit polypeptide chains co-fold since individually they do not have predictable domains. We have developed CoESPRIT, a modified version of the ESPRIT random library construct screen used previously on single proteins, to express soluble protein complexes. A random library of target constructs is screened against a fixed bait protein to identify stable complexes. In a proof-of-principle study, C-terminal fragments of the influenza polymerase PB2 subunit containing folded domains were isolated using importin alpha as bait. Separately, a C-terminal fragment of the PB1 subunit was used as bait to trap N-terminal fragments of PB2 resulting in co-folded complexes. Subsequent expression of the target protein without the bait indicates whether the target is independently stable, or co-folds with its partner. This highly automated method provides an efficient strategy for obtaining recombinant protein complexes at yields compatible with structural, biophysical and functional studies.
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Affiliation(s)
- Yingfeng An
- Grenoble Outstation, European Molecular Biology Laboratory, BP181, Grenoble, France
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI3265, Grenoble, France
| | - Patrick Meresse
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI3265, Grenoble, France
| | - Philippe J. Mas
- Grenoble Outstation, European Molecular Biology Laboratory, BP181, Grenoble, France
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI3265, Grenoble, France
| | - Darren J. Hart
- Grenoble Outstation, European Molecular Biology Laboratory, BP181, Grenoble, France
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI3265, Grenoble, France
- * E-mail:
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155
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Boivin S, Hart DJ. Interaction of the influenza A virus polymerase PB2 C-terminal region with importin alpha isoforms provides insights into host adaptation and polymerase assembly. J Biol Chem 2011; 286:10439-48. [PMID: 21216958 DOI: 10.1074/jbc.m110.182964] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the adaptation of avian viruses to mammalian hosts, mutations in the viral polymerase, notably in the PB2 subunit, play an important role. A PB2 C-terminal domain rich in putative host adaptation residues has been shown to bind importin α nuclear import receptors. Adaptation has been proposed to involve binding of PB2 to importins of the new host. To date PB2-importin complexes have been characterized semiquantitatively with no precise measurement of binding parameters. To investigate the effects of adaptive mutations on importin interaction and selectivity, surface plasmon resonance was used to compare the binding rate constants and affinities of avian H5N1 and human H3N2 PB2 C-terminal variants with importin isoforms human α 1, 3, 5 and 7, and avian α 1. Using purified proteins eliminates host environment effects and permits measurement of intrinsic affinities and rates of complex formation and dissociation. Two effects were observed: first, adaptive mutations D701N, R702K, and S714R in the nuclear localization signal domain increased 2-4-fold the association rates with avian and human importins; second, measurement of different structural forms of the PB2 C terminus demonstrated that the upstream 627 domain reduced binding affinity, consistent with a steric clash predicted from crystal structures. From these kinetic data, structural analyses, and the data of others, a model is proposed in which an increase in charged surface residues during host adaptation increases the association rate of PB2 to cytoplasmic importins and where the C-terminal 627-nuclear localization signal domain may reorganize upon importin binding, consistent with a role in active polymerase assembly.
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Affiliation(s)
- Stephane Boivin
- Unit of Virus Host-Cell Interactions, UMI 3265, UJF-EMBL-CNRS and the Grenoble Outstation, European Molecular Biology Laboratory, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
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