Metabolomic Analysis of Three Mollicute Species
Publication Date
March 04, 2014
Journal
PLOS ONE
Authors
Anna A. Vanyushkina, Gleb Y. Fisunov, Alexey Y. Gorbachev, Dmitri E. Kamashev, et al
Volume
9
Issue
3
Pages
e89312
DOI
https://dx.plos.org/10.1371/journal.pone.0089312
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0089312
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24595068
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3942410
Europe PMC
http://europepmc.org/abstract/MED/24595068
Web of Science
000332475500012
Scopus
84897035249
Mendeley
http://www.mendeley.com/research/metabolomic-analysis-three-mollicute-species
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1407497"], "description"=>"<p>The pathways common for three Mollicute species are represented. Abbreviations and symbols are given in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089312#pone-0089312-g001\" target=\"_blank\">figure 1</a>.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Computational biology", "systems biology", "microbiology", "bacteriology", "Bacterial physiology", "Microbial metabolism", "Microbial physiology", "metabolic"], "article_id"=>951898, "categories"=>["Biological Sciences"], "users"=>["Anna A. Vanyushkina", "Gleb Y. Fisunov", "Alexey Y. Gorbachev", "Dmitri E. Kamashev", "Vadim M. Govorun"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089312.g002", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reconstructed_metabolic_map_of_A_laidlawii_/951898", "title"=>"Reconstructed metabolic map of <i>A. laidlawii</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-04 03:44:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1407506"], "description"=>"<p>Identified metabolites of <i>S. melliferum</i>, <i>M. gallisepticum</i> and <i>A. laidlawii</i>.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Computational biology", "systems biology", "microbiology", "bacteriology", "Bacterial physiology", "Microbial metabolism", "Microbial physiology", "metabolites"], "article_id"=>951907, "categories"=>["Biological Sciences"], "users"=>["Anna A. Vanyushkina", "Gleb Y. Fisunov", "Alexey Y. Gorbachev", "Dmitri E. Kamashev", "Vadim M. Govorun"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089312.t001", "stats"=>{"downloads"=>1, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identified_metabolites_of_S_melliferum_M_gallisepticum_and_A_laidlawii_/951907", "title"=>"Identified metabolites of <i>S. melliferum</i>, <i>M. gallisepticum</i> and <i>A. laidlawii</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-04 03:44:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1407505"], "description"=>"<p>Fragmentation spectra results for the detected metabolites of <i>S. melliferum</i>, <i>M. gallisepticum</i> and <i>A. laidlawii</i>, and fragmentation spectra of the analyzed ion standards from the Metlin database <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089312#pone.0089312-Yus1\" target=\"_blank\">[23]</a> in the same experimental conditions (fixed collision energy of 20 eV).</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Computational biology", "systems biology", "microbiology", "bacteriology", "Bacterial physiology", "Microbial metabolism", "Microbial physiology", "spectra", "metabolites", "fragmentation", "ion", "standards", "metlin", "collision", "20"], "article_id"=>951906, "categories"=>["Biological Sciences"], "users"=>["Anna A. Vanyushkina", "Gleb Y. Fisunov", "Alexey Y. Gorbachev", "Dmitri E. Kamashev", "Vadim M. Govorun"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089312.t002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fragmentation_spectra_results_for_the_detected_metabolites_of_S_melliferum_M_gallisepticum_and_A_laidlawii_and_fragmentation_spectra_of_the_analyzed_ion_standards_from_the_Metlin_database_23_in_the_same_experimental_conditions_fixed_collision_energy_of_2/951906", "title"=>"Fragmentation spectra results for the detected metabolites of <i>S. melliferum</i>, <i>M. gallisepticum</i> and <i>A. laidlawii</i>, and fragmentation spectra of the analyzed ion standards from the Metlin database [23] in the same experimental conditions (fixed collision energy of 20 eV).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-04 03:44:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1407500"], "description"=>"<p>Metabolites involved in the pathway are shown as circles; enzymes are shown as diamonds; and the path that we propose to convert sedoheptulose-7-phosphate is marked in green.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Computational biology", "systems biology", "microbiology", "bacteriology", "Bacterial physiology", "Microbial metabolism", "Microbial physiology", "pentose", "phosphate"], "article_id"=>951901, "categories"=>["Biological Sciences"], "users"=>["Anna A. Vanyushkina", "Gleb Y. Fisunov", "Alexey Y. Gorbachev", "Dmitri E. Kamashev", "Vadim M. Govorun"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089312.g005", "stats"=>{"downloads"=>0, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reactions_of_the_pentose_phosphate_pathway_/951901", "title"=>"Reactions of the pentose phosphate pathway.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-04 03:44:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1407499"], "description"=>"<p>Yellow circle represents metabolites of <i>M. gallisepticum</i>, violet circle represents metabolites of <i>S. melliferum</i>, and green circle represents metabolites of <i>A. laidlawii</i>. The list of identified metabolites of <i>S. melliferum</i>, <i>M. gallisepticum</i> and <i>A. laidlawii</i> is presented in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089312#pone-0089312-t001\" target=\"_blank\">Table 1</a>.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Computational biology", "systems biology", "microbiology", "bacteriology", "Bacterial physiology", "Microbial metabolism", "Microbial physiology", "metabolites", "mollicute"], "article_id"=>951900, "categories"=>["Biological Sciences"], "users"=>["Anna A. Vanyushkina", "Gleb Y. Fisunov", "Alexey Y. Gorbachev", "Dmitri E. Kamashev", "Vadim M. Govorun"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089312.g004", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overlap_of_the_detected_metabolites_for_three_Mollicute_species_/951900", "title"=>"Overlap of the detected metabolites for three Mollicute species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-04 03:44:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1407495"], "description"=>"<p>The pathways common for three Mollicute species are represented. Metabolites are shown as circles; compounds identified by LC-MS are marked in green, other predicted compounds are marked in red. Proteins that catalyze metabolic reactions are shown as diamonds, and their ID numbers are indicated. Enzymatic activities, which are not associated with annotated proteins, are indicated in italics. Abbreviations: D-F-6-P - D-fructose-6-phosphate; D-F-1,6-PP - D-fructose-1,6-bisphosphate; D-S-1,7-PP - D-sedoheptulose-1,7-bisphosphate; D-S-7-P - D-sedoheptulose-7-phosphate; GAP - glyceraldehyde-3-P).</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Computational biology", "systems biology", "microbiology", "bacteriology", "Bacterial physiology", "Microbial metabolism", "Microbial physiology", "metabolic"], "article_id"=>951896, "categories"=>["Biological Sciences"], "users"=>["Anna A. Vanyushkina", "Gleb Y. Fisunov", "Alexey Y. Gorbachev", "Dmitri E. Kamashev", "Vadim M. Govorun"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089312.g001", "stats"=>{"downloads"=>0, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reconstructed_metabolic_map_of_M_gallisepticum_/951896", "title"=>"Reconstructed metabolic map of <i>M. gallisepticum</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-04 03:44:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1407508", "https://ndownloader.figshare.com/files/1407509", "https://ndownloader.figshare.com/files/1407510", "https://ndownloader.figshare.com/files/1407511"], "description"=>"<div><p>We present a systematic study of three bacterial species that belong to the class Mollicutes, the smallest and simplest bacteria, <i>Spiroplasma melliferum</i>, <i>Mycoplasma gallisepticum</i>, and <i>Acholeplasma laidlawii</i>. To understand the difference in the basic principles of metabolism regulation and adaptation to environmental conditions in the three species, we analyzed the metabolome of these bacteria. Metabolic pathways were reconstructed using the proteogenomic annotation data provided by our lab. The results of metabolome, proteome and genome profiling suggest a fundamental difference in the adaptation of the three closely related Mollicute species to stress conditions. As the transaldolase is not annotated in Mollicutes, we propose variants of the pentose phosphate pathway catalyzed by annotated enzymes for three species. For metabolite detection we employed high performance liquid chromatography coupled with mass spectrometry. We used liquid chromatography method - hydrophilic interaction chromatography with silica column - as it effectively separates highly polar cellular metabolites prior to their detection by mass spectrometer.</p></div>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Computational biology", "systems biology", "microbiology", "bacteriology", "Bacterial physiology", "Microbial metabolism", "Microbial physiology", "mollicute"], "article_id"=>951909, "categories"=>["Biological Sciences"], "users"=>["Anna A. Vanyushkina", "Gleb Y. Fisunov", "Alexey Y. Gorbachev", "Dmitri E. Kamashev", "Vadim M. Govorun"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0089312.s001", "https://dx.doi.org/10.1371/journal.pone.0089312.s002", "https://dx.doi.org/10.1371/journal.pone.0089312.s003", "https://dx.doi.org/10.1371/journal.pone.0089312.s004"], "stats"=>{"downloads"=>2, "page_views"=>35, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Metabolomic_Analysis_of_Three_Mollicute_Species_/951909", "title"=>"Metabolomic Analysis of Three Mollicute Species", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-03-04 03:44:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1407504"], "description"=>"<p>Results are summarized for the positive and negative acquisition modes.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Computational biology", "systems biology", "microbiology", "bacteriology", "Bacterial physiology", "Microbial metabolism", "Microbial physiology", "peaks", "counting", "pairwise", "mollicute"], "article_id"=>951905, "categories"=>["Biological Sciences"], "users"=>["Anna A. Vanyushkina", "Gleb Y. Fisunov", "Alexey Y. Gorbachev", "Dmitri E. Kamashev", "Vadim M. Govorun"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089312.t003", "stats"=>{"downloads"=>0, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Metabolite_peaks_counting_and_pairwise_comparison_of_three_Mollicute_species_/951905", "title"=>"Metabolite peaks counting and pairwise comparison of three Mollicute species.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-04 03:44:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1407502"], "description"=>"<p>In this pathway, metabolites are shown as circles; enzymes are shown as diamonds; and compounds that we detected are marked in green.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Computational biology", "systems biology", "microbiology", "bacteriology", "Bacterial physiology", "Microbial metabolism", "Microbial physiology", "deiminase"], "article_id"=>951903, "categories"=>["Biological Sciences"], "users"=>["Anna A. Vanyushkina", "Gleb Y. Fisunov", "Alexey Y. Gorbachev", "Dmitri E. Kamashev", "Vadim M. Govorun"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089312.g006", "stats"=>{"downloads"=>9, "page_views"=>393, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Arginine_deiminase_ADI_pathway_/951903", "title"=>"Arginine deiminase (ADI) pathway.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-04 03:44:12"}

PMC Usage Stats | Further Information

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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/Organisms", "average_usage"=>[310]}]}
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