Conservation of Expression and Sequence of Metabolic Genes Is Reflected by Activity Across Metabolic States
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{"title"=>"Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states", "type"=>"journal", "authors"=>[{"first_name"=>"Yonatan", "last_name"=>"Bilu", "scopus_author_id"=>"55933387400"}, {"first_name"=>"Tomer", "last_name"=>"Shlomi", "scopus_author_id"=>"8592513400"}, {"first_name"=>"Naama", "last_name"=>"Barkai", "scopus_author_id"=>"6701315190"}, {"first_name"=>"Eytan", "last_name"=>"Ruppin", "scopus_author_id"=>"7005381250"}], "year"=>2006, "source"=>"PLoS Computational Biology", "identifiers"=>{"isbn"=>"1553-7358 (Electronic)", "pmid"=>"16933982", "pui"=>"44298481", "issn"=>"1553734X", "scopus"=>"2-s2.0-33748049452", "sgr"=>"33748049452", "doi"=>"10.1371/journal.pcbi.0020106"}, "id"=>"80444421-e6ee-3af7-8bc1-4b2093b06368", "abstract"=>"Variation in gene expression levels on a genomic scale has been detected among different strains, among closely related species, and within populations of genetically identical cells. What are the driving forces that lead to expression divergence in some genes and conserved expression in others? Here we employ flux balance analysis to address this question for metabolic genes. We consider the genome-scale metabolic model of Saccharomyces cerevisiae, and its entire space of optimal and near-optimal flux distributions. We show that this space reveals underlying evolutionary constraints on expression regulation, as well as on the conservation of the underlying gene sequences. Genes that have a high range of optimal flux levels tend to display divergent expression levels among different yeast strains and species. This suggests that gene regulation has diverged in those parts of the metabolic network that are less constrained. In addition, we show that genes that are active in a large fraction of the space of optimal solutions tend to have conserved sequences. This supports the possibility that there is less selective pressure to maintain genes that are relevant for only a small number of metabolic states.", "link"=>"http://www.mendeley.com/research/conservation-expression-sequence-metabolic-genes-reflected-activity-across-metabolic-states", "reader_count"=>69, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>11, "Researcher"=>20, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>3, "Student > Master"=>7, "Student > Bachelor"=>3, "Professor"=>2, "Other"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>11, "Researcher"=>20, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>3, "Student > Master"=>7, "Student > Bachelor"=>3, "Professor"=>2, "Other"=>2}, "reader_count_by_subject_area"=>{"Engineering"=>3, "Biochemistry, Genetics and Molecular Biology"=>7, "Mathematics"=>2, "Agricultural and Biological Sciences"=>48, "Medicine and Dentistry"=>1, "Physics and Astronomy"=>3, "Computer Science"=>5}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>48}, "Computer Science"=>{"Computer Science"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Mathematics"=>{"Mathematics"=>2}}, "reader_count_by_country"=>{"United States"=>5, "Japan"=>1, "United Kingdom"=>1, "Switzerland"=>1, "Portugal"=>1, "Spain"=>1, "India"=>1, "Sweden"=>1, "Netherlands"=>1, "Iran"=>2, "Luxembourg"=>2, "Lithuania"=>1, "Chile"=>1, "Germany"=>2}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/958069"], "description"=>"<div><p>(A) Reactions with flux equal to zero in all optimal solutions.</p><p>(B) Reactions with the same, nonzero value in all optimal solutions.</p><p>(C) Reactions with low variability among optimal solutions <i>(flexbility score between 0 and 10<sup>−2</sup>)</i>.</p><p>(D) Reactions with medium variability among optimal solutions <i>(flexbility score between 10<sup>−2</sup> and 1/2)</i>.</p><p>(E) Reactions with high variability among optimal solutions <i>(flexibility score at least 1/2)</i>.</p></div>", "links"=>[], "tags"=>["modelled", "metabolic", "reactions", "variability", "optimal", "solutions"], "article_id"=>628107, "categories"=>["Biological Sciences", "Medicine", "Evolutionary Biology"], "users"=>["Yonatan Bilu", "Tomer Shlomi", "Naama Barkai", "Eytan Ruppin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0020106.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_the_1_149_Modelled_Metabolic_Reactions_according_to_Their_Variability_within_the_Space_of_Optimal_Solutions_for_YPD_/628107", "title"=>"Distribution of the 1,149 Modelled Metabolic Reactions according to Their Variability within the Space of Optimal Solutions for YPD", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:31:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/958093"], "description"=>"<div><p>(A) Mean expression divergence (from Townsend et al.) as a function of the gene's flexibility score;</p><p>(B) Mean promoter conservation score (based on Harbison et al.) as a function of the gene's flexibility score;</p><p>(C) Mean expression variance (from Ihmels et al.) as a function of the gene's flexibility score.</p><p>Genes are binned according to their flexibility score into five bins, such that each bin contains the same number of genes. Plot-points represent mean <i>y</i>-axis values over these bins. Error bars depict mean standard error.</p><p>Importantly, the correlations reported in the main text are computed from the raw data. The Spearman rank correlation of the binned data displayed here is 0.9 (A and C), and −1 (B).</p></div>", "links"=>[], "tags"=>["ypd", "reflecting", "constraints"], "article_id"=>628132, "categories"=>["Biological Sciences", "Medicine", "Evolutionary Biology"], "users"=>["Yonatan Bilu", "Tomer Shlomi", "Naama Barkai", "Eytan Ruppin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0020106.g002", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_of_YPD_Flexibility_Score_with_Biological_Measurements_Reflecting_Constraints_on_Regulation_/628132", "title"=>"Correlation of YPD Flexibility Score with Biological Measurements Reflecting Constraints on Regulation", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:32:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/958119"], "description"=>"<div><p>Genes are binned by multiplying their evolutionary rate by 50, and rounding to the closest integer. The mean YPD activity score over each subset is depicted. Error bars describe mean standard deviation.</p><p>Importantly, the correlations reported in the main text are computed from the raw data. The Spearman Rank correlation of the binned data displayed here is −0.71.</p></div>", "links"=>[], "tags"=>["ypd", "evolutionary"], "article_id"=>628159, "categories"=>["Biological Sciences", "Medicine", "Evolutionary Biology"], "users"=>["Yonatan Bilu", "Tomer Shlomi", "Naama Barkai", "Eytan Ruppin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0020106.g003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_YPD_Activity_Score_as_a_Function_of_a_Gene_s_Evolutionary_Rate_/628159", "title"=>"Average YPD Activity Score as a Function of a Gene's Evolutionary Rate", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:32:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/471706", "https://ndownloader.figshare.com/files/471716", "https://ndownloader.figshare.com/files/471775", "https://ndownloader.figshare.com/files/471848", "https://ndownloader.figshare.com/files/471895"], "description"=>"<div><p>Variation in gene expression levels on a genomic scale has been detected among different strains, among closely related species, and within populations of genetically identical cells. What are the driving forces that lead to expression divergence in some genes and conserved expression in others? Here we employ flux balance analysis to address this question for metabolic genes. We consider the genome-scale metabolic model of <em>Saccharomyces cerevisiae,</em> and its entire space of optimal and near-optimal flux distributions. We show that this space reveals underlying evolutionary constraints on expression regulation, as well as on the conservation of the underlying gene sequences. Genes that have a high range of optimal flux levels tend to display divergent expression levels among different yeast strains and species. This suggests that gene regulation has diverged in those parts of the metabolic network that are less constrained. In addition, we show that genes that are active in a large fraction of the space of optimal solutions tend to have conserved sequences. This supports the possibility that there is less selective pressure to maintain genes that are relevant for only a small number of metabolic states.</p></div>", "links"=>[], "tags"=>["metabolic", "genes", "reflected", "states"], "article_id"=>153007, "categories"=>["Biological Sciences", "Medicine", "Evolutionary Biology"], "users"=>["Yonatan Bilu", "Tomer Shlomi", "Naama Barkai", "Eytan Ruppin"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.0020106.sd001", "https://dx.doi.org/10.1371/journal.pcbi.0020106.sd002", "https://dx.doi.org/10.1371/journal.pcbi.0020106.sd003", "https://dx.doi.org/10.1371/journal.pcbi.0020106.sd004", "https://dx.doi.org/10.1371/journal.pcbi.0020106.st001"], "stats"=>{"downloads"=>5, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Conservation_of_Expression_and_Sequence_of_Metabolic_Genes_Is_Reflected_by_Activity_Across_Metabolic_States/153007", "title"=>"Conservation of Expression and Sequence of Metabolic Genes Is Reflected by Activity Across Metabolic States", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2006-08-18 00:50:07"}

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Relative Metric

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