Frequency and Fitness Consequences of Bacteriophage Φ6 Host Range Mutations
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{"title"=>"Frequency and fitness consequences of bacteriophage 6 host range mutations", "type"=>"journal", "authors"=>[{"first_name"=>"Brian E.", "last_name"=>"Ford", "scopus_author_id"=>"50261653800"}, {"first_name"=>"Bruce", "last_name"=>"Sun", "scopus_author_id"=>"56431780300"}, {"first_name"=>"James", "last_name"=>"Carpino", "scopus_author_id"=>"18041948100"}, {"first_name"=>"Elizabeth S.", "last_name"=>"Chapler", "scopus_author_id"=>"56433483700"}, {"first_name"=>"Jane", "last_name"=>"Ching", "scopus_author_id"=>"56432427900"}, {"first_name"=>"Yoon", "last_name"=>"Choi", "scopus_author_id"=>"56173169700"}, {"first_name"=>"Kevin", "last_name"=>"Jhun", "scopus_author_id"=>"56433556300"}, {"first_name"=>"Jung D.", "last_name"=>"Kim", "scopus_author_id"=>"56431791400"}, {"first_name"=>"Gregory G.", "last_name"=>"Lallos", "scopus_author_id"=>"56433391200"}, {"first_name"=>"Rachelle", "last_name"=>"Morgenstern", "scopus_author_id"=>"56432362900"}, {"first_name"=>"Shalini", "last_name"=>"Singh", "scopus_author_id"=>"57199223887"}, {"first_name"=>"Sai", "last_name"=>"Theja", "scopus_author_id"=>"56433372500"}, {"first_name"=>"John J.", "last_name"=>"Dennehy", "scopus_author_id"=>"6701577521"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84913528575", "doi"=>"10.1371/journal.pone.0113078", "pui"=>"600550272", "pmid"=>"25409341", "scopus"=>"2-s2.0-84913528575", "issn"=>"19326203", "isbn"=>"1932-6203"}, "id"=>"6f4e09df-657b-3144-a6e3-de87db2f8cab", "abstract"=>"Viruses readily mutate and gain the ability to infect novel hosts, but few data are available regarding the number of possible host range-expanding mutations allowing infection of any given novel host, and the fitness consequences of these mutations on original and novel hosts. To gain insight into the process of host range expansion, we isolated and sequenced 69 independent mutants of the dsRNA bacteriophage Φ6 able to infect the novel host, Pseudomonas pseudoalcaligenes. In total, we found at least 17 unique suites of mutations among these 69 mutants. We assayed fitness for 13 of 17 mutant genotypes on P. pseudoalcaligenes and the standard laboratory host, P. phaseolicola. Mutants exhibited significantly lower fitnesses on P. pseudoalcaligenes compared to P. phaseolicola. Furthermore, 12 of the 13 assayed mutants showed reduced fitness on P. phaseolicola compared to wildtype Φ6, confirming the prevalence of antagonistic pleiotropy during host range expansion. Further experiments revealed that the mechanistic basis of these fitness differences was likely variation in host attachment ability. In addition, using computational protein modeling, we show that host-range expanding mutations occurred in hotspots on the surface of the phage's host attachment protein opposite a putative hydrophobic anchoring domain.", "link"=>"http://www.mendeley.com/research/frequency-fitness-consequences-bacteriophage-6-host-range-mutations", "reader_count"=>15, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>1, "Student > Master"=>1, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>1, "Student > Master"=>1, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>8, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United States"=>3}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/4345357"], "description"=>"<p>Host Range Substitution Hotspots in φ6 P3 Protein<sup><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113078#nt103\" target=\"_blank\">a</a></sup>.</p>", "links"=>[], "tags"=>["dsRNA bacteriophage Φ6", "host range expansion", "mutation", "novel host", "host attachment ability", "novel hosts", "host attachment protein", "fitness"], "article_id"=>2681086, "categories"=>["Biophysics", "Biochemistry", "Medicine", "Microbiology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Virology"], "users"=>["Brian E. Ford", "Bruce Sun", "James Carpino", "Elizabeth S. Chapler", "Jane Ching", "Yoon Choi", "Kevin Jhun", "Jung D. Kim", "Gregory G. Lallos", "Rachelle Morgenstern", "Shalini Singh", "Sai Theja", "John J. Dennehy"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113078.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Host_Range_Substitution_Hotspots_in_6_P3_Protein_sup_a_sup_/2681086", "title"=>"Host Range Substitution Hotspots in φ6 P3 Protein<sup>a</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-19 16:54:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/4345321"], "description"=>"<p>Panel A: Absolute fitness of 13 Φ6 host range mutants on the novel host, ERA. Each point is the mean of 5 replicate measurements of fitness. Bars are ±1SE. Panel B: Absolute fitness of 13 Φ6 host range mutants on the canonical host, PP. Each point is the mean of 5 replicate measurements of fitness. Fitness of wildtype Φ6 is shown by the dotted line for comparison. Bars are ±1SE.</p>", "links"=>[], "tags"=>["dsRNA bacteriophage Φ6", "host range expansion", "mutation", "novel host", "host attachment ability", "novel hosts", "host attachment protein", "fitness"], "article_id"=>2681050, "categories"=>["Biophysics", "Biochemistry", "Medicine", "Microbiology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Virology"], "users"=>["Brian E. Ford", "Bruce Sun", "James Carpino", "Elizabeth S. Chapler", "Jane Ching", "Yoon Choi", "Kevin Jhun", "Jung D. Kim", "Gregory G. Lallos", "Rachelle Morgenstern", "Shalini Singh", "Sai Theja", "John J. Dennehy"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113078.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Mutant_absolute_fitness_on_canonical_and_novel_hosts_/2681050", "title"=>"Mutant absolute fitness on canonical and novel hosts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-19 16:54:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/4345333"], "description"=>"<p>Attachment to ERA was correlated with fitness on ERA for Φ6 host range mutants. Each point is the mean of 3 replicate measurements. Dotted lines show 95% confidence intervals.</p>", "links"=>[], "tags"=>["dsRNA bacteriophage Φ6", "host range expansion", "mutation", "novel host", "host attachment ability", "novel hosts", "host attachment protein", "fitness"], "article_id"=>2681062, "categories"=>["Biophysics", "Biochemistry", "Medicine", "Microbiology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Virology"], "users"=>["Brian E. Ford", "Bruce Sun", "James Carpino", "Elizabeth S. Chapler", "Jane Ching", "Yoon Choi", "Kevin Jhun", "Jung D. Kim", "Gregory G. Lallos", "Rachelle Morgenstern", "Shalini Singh", "Sai Theja", "John J. Dennehy"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113078.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Mean_ERA_attachment_rate_k_is_plotted_against_phage_6_fitness_on_ERA_/2681062", "title"=>"Mean ERA attachment rate (k) is plotted against phage Φ6 fitness on ERA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-19 16:54:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/4345315"], "description"=>"<p>Panel A: Three host range mutation hotspots (accounting for 86% of all mutations) are highlighted in this linear representation of the 648 amino acid sequence of the Φ6 P3 gene. The remaining 14% of mutations are not shown. Panel B: Space-filling representations of the Φ6 P3 protein are shown as predicted by I-TASSER. Colored regions correspond to the mutation hotspots depicted in Panel A. A putative hydrophobic anchoring domain (HAD) is shown in orange. In our model, the hydrophobic anchoring domain penetrates Φ6's outer lipid membrane to bind inner membrane protein P6. Panel C: Surface electrical charges of E8G mutant contrasted with ancestor. Space-filling representations showing predicted surface electrical charges for the Φ6 E8G host range mutant and its ancestor were estimated using I-TASSER. Positively- and negatively-charged regions are depicted in blue and red respectively. Arrows indicate the predicted location of the mutated 8<sup>th</sup> residue. The most prominent difference between the mutant and the ancestor is the greater surface positive charge at the presumed host binding domain.</p>", "links"=>[], "tags"=>["dsRNA bacteriophage Φ6", "host range expansion", "mutation", "novel host", "host attachment ability", "novel hosts", "host attachment protein", "fitness"], "article_id"=>2681044, "categories"=>["Biophysics", "Biochemistry", "Medicine", "Microbiology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Virology"], "users"=>["Brian E. Ford", "Bruce Sun", "James Carpino", "Elizabeth S. Chapler", "Jane Ching", "Yoon Choi", "Kevin Jhun", "Jung D. Kim", "Gregory G. Lallos", "Rachelle Morgenstern", "Shalini Singh", "Sai Theja", "John J. Dennehy"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113078.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Spatial_models_of_6_P3_protein_mutants_/2681044", "title"=>"Spatial models of Φ6 P3 protein mutants.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-19 16:54:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/4345369"], "description"=>"<p>Amino Acid Substitutions Associated with φ6 Host Range Expansion on ERA.</p>", "links"=>[], "tags"=>["dsRNA bacteriophage Φ6", "host range expansion", "mutation", "novel host", "host attachment ability", "novel hosts", "host attachment protein", "fitness"], "article_id"=>2681098, "categories"=>["Biophysics", "Biochemistry", "Medicine", "Microbiology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Virology"], "users"=>["Brian E. Ford", "Bruce Sun", "James Carpino", "Elizabeth S. Chapler", "Jane Ching", "Yoon Choi", "Kevin Jhun", "Jung D. Kim", "Gregory G. Lallos", "Rachelle Morgenstern", "Shalini Singh", "Sai Theja", "John J. Dennehy"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113078.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Amino_Acid_Substitutions_Associated_with_6_Host_Range_Expansion_on_ERA_/2681098", "title"=>"Amino Acid Substitutions Associated with φ6 Host Range Expansion on ERA.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-19 16:54:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/4345351"], "description"=>"<p>Phage φ6 Mutations Allowing Infection of Novel Host ERA.</p>", "links"=>[], "tags"=>["dsRNA bacteriophage Φ6", "host range expansion", "mutation", "novel host", "host attachment ability", "novel hosts", "host attachment protein", "fitness"], "article_id"=>2681080, "categories"=>["Biophysics", "Biochemistry", "Medicine", "Microbiology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Virology"], "users"=>["Brian E. Ford", "Bruce Sun", "James Carpino", "Elizabeth S. Chapler", "Jane Ching", "Yoon Choi", "Kevin Jhun", "Jung D. Kim", "Gregory G. Lallos", "Rachelle Morgenstern", "Shalini Singh", "Sai Theja", "John J. Dennehy"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113078.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Phage_6_Mutations_Allowing_Infection_of_Novel_Host_ERA_/2681080", "title"=>"Phage φ6 Mutations Allowing Infection of Novel Host ERA.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-19 16:54:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/4345378"], "description"=>"<p>Phenotypic Characteristics of Bacteriophage φ6 Mutants.</p>", "links"=>[], "tags"=>["dsRNA bacteriophage Φ6", "host range expansion", "mutation", "novel host", "host attachment ability", "novel hosts", "host attachment protein", "fitness"], "article_id"=>2681107, "categories"=>["Biophysics", "Biochemistry", "Medicine", "Microbiology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Virology"], "users"=>["Brian E. Ford", "Bruce Sun", "James Carpino", "Elizabeth S. Chapler", "Jane Ching", "Yoon Choi", "Kevin Jhun", "Jung D. Kim", "Gregory G. Lallos", "Rachelle Morgenstern", "Shalini Singh", "Sai Theja", "John J. Dennehy"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113078.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Phenotypic_Characteristics_of_Bacteriophage_6_Mutants_/2681107", "title"=>"Phenotypic Characteristics of Bacteriophage φ6 Mutants.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-19 16:54:11"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2015", "month"=>"10"}
  • {"unique-ip"=>"11", "full-text"=>"11", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
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  • {"unique-ip"=>"10", "full-text"=>"5", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2015", "month"=>"11"}
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  • {"unique-ip"=>"6", "full-text"=>"8", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"7"}
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  • {"unique-ip"=>"5", "full-text"=>"3", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
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  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
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  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"2"}
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  • {"unique-ip"=>"11", "full-text"=>"11", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"6"}
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  • {"unique-ip"=>"3", "full-text"=>"1", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
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  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2018", "month"=>"3"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"1"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
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Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[282]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[292, 461]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[310]}, {"subject_area"=>"/Medicine and health sciences/Infectious diseases", "average_usage"=>[319]}, {"subject_area"=>"/Medicine and health sciences/Pathology and laboratory medicine", "average_usage"=>[287]}]}
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