A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189
Publication Date
February 13, 2009
Journal
PLOS Computational Biology
Authors
Patrick F. Suthers, Madhukar S. Dasika, Vinay Satish Kumar, Gennady Denisov, et al
Volume
5
Issue
2
Pages
e1000285
DOI
https://dx.plos.org/10.1371/journal.pcbi.1000285
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1000285
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/19214212
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2633051
Europe PMC
http://europepmc.org/abstract/MED/19214212
Web of Science
000263924500010
Scopus
61449115916
Mendeley
http://www.mendeley.com/research/genomescale-metabolic-reconstruction-mycoplasma-genitalium-ips189
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Mendeley | Further Information

{"title"=>"Genome-scale metabolic reconstruction Of mycoplasma genitalium, iPS189", "type"=>"journal", "authors"=>[{"first_name"=>"Patrick F.", "last_name"=>"Suthers", "scopus_author_id"=>"6504538741"}, {"first_name"=>"Madhukar S.", "last_name"=>"Dasika", "scopus_author_id"=>"6507969846"}, {"first_name"=>"Vinay Satish", "last_name"=>"Kumar", "scopus_author_id"=>"26040852400"}, {"first_name"=>"Gennady", "last_name"=>"Denisov", "scopus_author_id"=>"7101858887"}, {"first_name"=>"John I.", "last_name"=>"Glass", "scopus_author_id"=>"7201603522"}, {"first_name"=>"Costas D.", "last_name"=>"Maranas", "scopus_author_id"=>"7005248717"}], "year"=>2009, "source"=>"PLoS Computational Biology", "identifiers"=>{"pui"=>"354253453", "issn"=>"1553734X", "isbn"=>"1553-7358 (Electronic)", "doi"=>"10.1371/journal.pcbi.1000285", "scopus"=>"2-s2.0-61449115916", "pmid"=>"19214212", "sgr"=>"61449115916"}, "id"=>"32ad1f02-762a-342d-a8d4-1951b65c48f6", "abstract"=>"With a genome size of approximately 580 kb and approximately 480 protein coding regions, Mycoplasma genitalium is one of the smallest known self-replicating organisms and, additionally, has extremely fastidious nutrient requirements. The reduced genomic content of M. genitalium has led researchers to suggest that the molecular assembly contained in this organism may be a close approximation to the minimal set of genes required for bacterial growth. Here, we introduce a systematic approach for the construction and curation of a genome-scale in silico metabolic model for M. genitalium. Key challenges included estimation of biomass composition, handling of enzymes with broad specificities, and the lack of a defined medium. Computational tools were subsequently employed to identify and resolve connectivity gaps in the model as well as growth prediction inconsistencies with gene essentiality experimental data. The curated model, M. genitalium iPS189 (262 reactions, 274 metabolites), is 87% accurate in recapitulating in vivo gene essentiality results for M. genitalium. Approaches and tools described herein provide a roadmap for the automated construction of in silico metabolic models of other organisms.", "link"=>"http://www.mendeley.com/research/genomescale-metabolic-reconstruction-mycoplasma-genitalium-ips189", "reader_count"=>208, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>11, "Researcher"=>53, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>65, "Student > Postgraduate"=>6, "Student > Master"=>35, "Other"=>3, "Student > Bachelor"=>13, "Lecturer"=>2, "Professor"=>11}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>11, "Researcher"=>53, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>65, "Student > Postgraduate"=>6, "Student > Master"=>35, "Other"=>3, "Student > Bachelor"=>13, "Lecturer"=>2, "Professor"=>11}, "reader_count_by_subject_area"=>{"Unspecified"=>11, "Agricultural and Biological Sciences"=>132, "Chemical Engineering"=>3, "Chemistry"=>3, "Computer Science"=>16, "Engineering"=>12, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>17, "Mathematics"=>1, "Medicine and Dentistry"=>3, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Physics and Astronomy"=>3, "Social Sciences"=>1, "Immunology and Microbiology"=>2, "Veterinary Science and Veterinary Medicine"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>11}, "Environmental Science"=>{"Environmental Science"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Chemical Engineering"=>{"Chemical Engineering"=>3}, "Engineering"=>{"Engineering"=>12}, "Chemistry"=>{"Chemistry"=>3}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>132}, "Computer Science"=>{"Computer Science"=>16}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>17}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"United States"=>10, "Japan"=>1, "United Kingdom"=>9, "Portugal"=>2, "Switzerland"=>1, "Spain"=>1, "Russia"=>2, "India"=>3, "Austria"=>1, "Sweden"=>1, "Iran"=>2, "Brazil"=>1, "France"=>2, "Germany"=>4}, "group_count"=>12}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/908228"], "description"=>"<p>The four steps used in the present work are 1) identification of biotransformations using automated homology searches 2) assembly of reaction sets into a genome-scale metabolic model 3) automated network connectivity analysis and restoration, and 4) automated evaluation and improvement of model performance when compared to <i>in vivo</i> gene essentiality data.</p>", "links"=>[], "tags"=>["reconstruction"], "article_id"=>578688, "categories"=>["Computational Biology", "Genetics", "Medicine"], "users"=>["Patrick F. Suthers", "Madhukar S. Dasika", "Vinay Satish Kumar", "Gennady Denisov", "John I. Glass", "Costas D. Maranas"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000285.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Steps_used_in_the_semi_automated_reconstruction_process_/578688", "title"=>"Steps used in the (semi)-automated reconstruction process.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-02-13 02:24:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/908302"], "description"=>"<p>The percent assigned to each class refers to the coverage of the total number in the genome accounted for in the model. Some of the ORFs in <i>Mycoplasma genitalium</i> do not currently have a COG functional category assignment (here represented as N/A). Note that although each ORF is only counted once within each COG functional category, some ORFs have multiple COG category assignments.</p>", "links"=>[], "tags"=>["orfs", "included", "grouped", "cog"], "article_id"=>578754, "categories"=>["Computational Biology", "Genetics", "Medicine"], "users"=>["Patrick F. Suthers", "Madhukar S. Dasika", "Vinay Satish Kumar", "Gennady Denisov", "John I. Glass", "Costas D. Maranas"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000285.g003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Classification_of_the_ORFs_included_in_i_PS189_grouped_into_COG_functional_categories_/578754", "title"=>"Classification of the ORFs included in <i>i</i>PS189 grouped into COG functional categories.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-02-13 02:25:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/908588"], "description"=>"a<p>All ribosome-associated proteins are counted as a single complex. The number for protein complexes and isozymes is not on a reaction basis but rather a protein basis.</p>b<p>Distinct species ignoring the compartment of the metabolites.</p>c<p>Includes minor adjustments to compartment assignment.</p>d<p>Based on 482 protein-encoding ORFs.</p>e<p>After additional BLASTP matches, specificity adjustments and conversion to computations-ready form.</p>", "links"=>[], "tags"=>["computational biology/metabolic networks", "computational biology/systems biology", "genetics and genomics/bioinformatics"], "article_id"=>579043, "categories"=>["Computational Biology", "Genetics", "Medicine"], "users"=>["Patrick F. Suthers", "Madhukar S. Dasika", "Vinay Satish Kumar", "Gennady Denisov", "John I. Glass", "Costas D. Maranas"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000285.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Composition_of_the_model_after_each_step_/579043", "title"=>"Composition of the model after each step.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-02-13 02:30:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/908554"], "description"=>"a<p>Amino acids were incorporated as charged and unchanged tRNA molecules in the equation as reactants and products, respectively. The charged gln-tRNA becomes an uncharged glu-tRNA and the charged fmet-tRNA becomes an uncharged met-tRNA through the biomass equation.</p>b<p>Added during GrowMatch procedure.</p>", "links"=>[], "tags"=>["components"], "article_id"=>579013, "categories"=>["Computational Biology", "Genetics", "Medicine"], "users"=>["Patrick F. Suthers", "Madhukar S. Dasika", "Vinay Satish Kumar", "Gennady Denisov", "John I. Glass", "Costas D. Maranas"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000285.t003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Biomass_components_used_in_i_PS189_/579013", "title"=>"Biomass components used in <i>i</i>PS189.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-02-13 02:30:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/908627"], "description"=>"a<p>This component was not predicted as essential for growth, but its inclusion improved biomass yield.</p>", "links"=>[], "tags"=>["computationally", "supplements", "modified", "c5"], "article_id"=>579083, "categories"=>["Computational Biology", "Genetics", "Medicine"], "users"=>["Patrick F. Suthers", "Madhukar S. Dasika", "Vinay Satish Kumar", "Gennady Denisov", "John I. Glass", "Costas D. Maranas"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000285.t004", "stats"=>{"downloads"=>4, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Metabolites_computationally_predicted_as_necessary_supplements_to_the_modified_C5_medium_in_order_to_support_growth_of_M_genitalium_/579083", "title"=>"Metabolites computationally predicted as necessary supplements to the modified C5 medium in order to support growth of <i>M. genitalium</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-02-13 02:31:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/908380"], "description"=>"<p>During biomass formation unblocking, most metabolites that could not be produced (disconnected metabolites) were reconnected through the addition of transport reactions. Metabolites not directly connected to biomass were mostly reconnected through the addition of reactions from KEGG and Metacyc.</p>", "links"=>[], "tags"=>["gapfind", "gapfill", "procedures", "biomass"], "article_id"=>578830, "categories"=>["Computational Biology", "Genetics", "Medicine"], "users"=>["Patrick F. Suthers", "Madhukar S. Dasika", "Vinay Satish Kumar", "Gennady Denisov", "John I. Glass", "Costas D. Maranas"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000285.g004", "stats"=>{"downloads"=>2, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_the_GapFind_and_GapFill_procedures_after_biomass_unblocking_/578830", "title"=>"Summary of the GapFind and GapFill procedures after biomass unblocking.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-02-13 02:27:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/908192"], "description"=>"<p>The numbers of both metabolic models and completed genome sequences have been growing exponentially. Despite the increase in the number of metabolic models, their total remains smaller than 1% of that of sequenced genomes.</p>", "links"=>[], "tags"=>["sequenced", "genomes", "generated"], "article_id"=>578645, "categories"=>["Computational Biology", "Genetics", "Medicine"], "users"=>["Patrick F. Suthers", "Madhukar S. Dasika", "Vinay Satish Kumar", "Gennady Denisov", "John I. Glass", "Costas D. Maranas"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000285.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gap_between_sequenced_genomes_and_generated_models_/578645", "title"=>"Gap between sequenced genomes and generated models.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-02-13 02:24:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/908441"], "description"=>"<p>The ORFs included in the comparisons are ordered within each COG functional category (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000285#pcbi-1000285-g003\" target=\"_blank\">Figure 3</a> for abbreviations). If an ORF belongs to more than one category only the first one is used. The dark shading indicates an ORF that was essential, and the light shading indicates a non-essential ORF. Before the application of GrowMatch, 79% of the model predictions on gene essentiality agreed with <i>in vivo</i> experiments. Nearly all incorrect predictions occurred when the model predicted growth, but no growth was observed in the <i>in vivo</i> experiment (termed GNG mismatches). GrowMatch was able to rectify eighteen of these mismatches. This increased the percent agreement to 87%. The rightmost heat-map and the number of resolved mismatches also include the removal of one gene to correct a GNG experiment and three genes to resolve NGG mismatches.</p>", "links"=>[], "tags"=>["growmatch"], "article_id"=>578903, "categories"=>["Computational Biology", "Genetics", "Medicine"], "users"=>["Patrick F. Suthers", "Madhukar S. Dasika", "Vinay Satish Kumar", "Gennady Denisov", "John I. Glass", "Costas D. Maranas"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000285.g005", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_the_GrowMatch_reconciliations_/578903", "title"=>"Summary of the GrowMatch reconciliations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-02-13 02:28:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/449032", "https://ndownloader.figshare.com/files/449056", "https://ndownloader.figshare.com/files/449072", "https://ndownloader.figshare.com/files/449085", "https://ndownloader.figshare.com/files/449100"], "description"=>"<div><p>With a genome size of ∼580 kb and approximately 480 protein coding regions, <em>Mycoplasma genitalium</em> is one of the smallest known self-replicating organisms and, additionally, has extremely fastidious nutrient requirements. The reduced genomic content of <em>M. genitalium</em> has led researchers to suggest that the molecular assembly contained in this organism may be a close approximation to the minimal set of genes required for bacterial growth. Here, we introduce a systematic approach for the construction and curation of a genome-scale <em>in silico</em> metabolic model for <em>M. genitalium</em>. Key challenges included estimation of biomass composition, handling of enzymes with broad specificities, and the lack of a defined medium. Computational tools were subsequently employed to identify and resolve connectivity gaps in the model as well as growth prediction inconsistencies with gene essentiality experimental data. The curated model, <em>M. genitalium i</em>PS189 (262 reactions, 274 metabolites), is 87% accurate in recapitulating <em>in vivo</em> gene essentiality results for <em>M. genitalium</em>. Approaches and tools described herein provide a roadmap for the automated construction of <em>in silico</em> metabolic models of other organisms.</p></div>", "links"=>[], "tags"=>["genome-scale", "metabolic", "reconstruction"], "article_id"=>148503, "categories"=>["Biological Sciences", "Genetics", "Medicine"], "users"=>["Patrick F. Suthers", "Madhukar S. Dasika", "Vinay Satish Kumar", "Gennady Denisov", "John I. Glass", "Costas D. Maranas"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000285.s001", "https://dx.doi.org/10.1371/journal.pcbi.1000285.s002", "https://dx.doi.org/10.1371/journal.pcbi.1000285.s003", "https://dx.doi.org/10.1371/journal.pcbi.1000285.s004", "https://dx.doi.org/10.1371/journal.pcbi.1000285.s005"], "stats"=>{"downloads"=>6, "page_views"=>32, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Genome_Scale_Metabolic_Reconstruction_of_Mycoplasma_genitalium_i_PS189/148503", "title"=>"A Genome-Scale Metabolic Reconstruction of <em>Mycoplasma genitalium</em>, <em>i</em>PS189", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-02-13 02:21:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/908515"], "description"=>"a<p>Encodes the phosphocarrier protein. The phosphoenolpyruvate-protein phosphotransferase component (MG429) was already included in the model.</p><p><sup>b</sup> Forward referes to using the <i>M. genitalium</i> locus as the input sequence to be searched against other genomes.</p><p><sup>c</sup> Reverse referes to using the locus of the other organism as the input sequence to be searched against the genome of <i>M. genitalium</i>.</p>", "links"=>[], "tags"=>["genes", "reactions", "bi-directional", "blastp", "homology"], "article_id"=>578969, "categories"=>["Computational Biology", "Genetics", "Medicine"], "users"=>["Patrick F. Suthers", "Madhukar S. Dasika", "Vinay Satish Kumar", "Gennady Denisov", "John I. Glass", "Costas D. Maranas"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000285.t002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Additional_genes_and_associated_reactions_added_to_the_model_through_bi_directional_BLASTp_homology_searches_/578969", "title"=>"Additional genes and associated reactions added to the model through bi-directional BLASTp homology searches.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-02-13 02:29:29"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"14", "full-text"=>"18", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"1", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"13", "full-text"=>"9", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"25", "full-text"=>"18", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

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