Flexibility of a Eukaryotic Lipidome – Insights from Yeast Lipidomics
Publication Date
April 18, 2012
Journal
PLOS ONE
Authors
Christian Klose, Michal A. Surma, Mathias J. Gerl, Felix Meyenhofer, et al
Volume
7
Issue
4
Pages
e35063
DOI
https://dx.plos.org/10.1371/journal.pone.0035063
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0035063
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22529973
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329542
Europe PMC
http://europepmc.org/abstract/MED/22529973
Web of Science
000305350600055
Scopus
84860014018
Mendeley
http://www.mendeley.com/research/flexibility-eukaryotic-lipidome-insights-yeast-lipidomics
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Mendeley | Further Information

{"title"=>"Flexibility of a eukaryotic lipidome - insights from yeast lipidomics", "type"=>"journal", "authors"=>[{"first_name"=>"Christian", "last_name"=>"Klose", "scopus_author_id"=>"36885252400"}, {"first_name"=>"Michal A.", "last_name"=>"Surma", "scopus_author_id"=>"26635853800"}, {"first_name"=>"Mathias J.", "last_name"=>"Gerl", "scopus_author_id"=>"15520566000"}, {"first_name"=>"Felix", "last_name"=>"Meyenhofer", "scopus_author_id"=>"23389864700"}, {"first_name"=>"Andrej", "last_name"=>"Shevchenko", "scopus_author_id"=>"7201467952"}, {"first_name"=>"Kai", "last_name"=>"Simons", "scopus_author_id"=>"7202131266"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84860014018", "sgr"=>"84860014018", "pui"=>"364660897", "isbn"=>"10.1371/journal.pone.0035063", "pmid"=>"22529973", "doi"=>"10.1371/journal.pone.0035063"}, "id"=>"d4a07192-1142-328f-b4a5-0667ae896350", "abstract"=>"Mass spectrometry-based shotgun lipidomics has enabled the quantitative and comprehensive assessment of cellular lipid compositions. The yeast Saccharomyces cerevisiae has proven to be a particularly valuable experimental system for studying lipid-related cellular processes. Here, by applying our shotgun lipidomics platform, we investigated the influence of a variety of commonly used growth conditions on the yeast lipidome, including glycerophospholipids, triglycerides, ergosterol as well as complex sphingolipids. This extensive dataset allowed for a quantitative description of the intrinsic flexibility of a eukaryotic lipidome, thereby providing new insights into the adjustments of lipid biosynthetic pathways. In addition, we established a baseline for future lipidomic experiments in yeast. Finally, flexibility of lipidomic features is proposed as a new parameter for the description of the physiological state of an organism.", "link"=>"http://www.mendeley.com/research/flexibility-eukaryotic-lipidome-insights-yeast-lipidomics", "reader_count"=>44, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>3, "Researcher"=>11, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>3, "Student > Master"=>4, "Other"=>2, "Student > Bachelor"=>5, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>3, "Researcher"=>11, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>3, "Student > Master"=>4, "Other"=>2, "Student > Bachelor"=>5, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>10, "Agricultural and Biological Sciences"=>21, "Medicine and Dentistry"=>1, "Physics and Astronomy"=>1, "Chemical Engineering"=>1, "Chemistry"=>2, "Energy"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>2}, "Energy"=>{"Energy"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>21}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}, "Unspecified"=>{"Unspecified"=>6}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"Austria"=>2, "United States"=>1, "Brazil"=>1, "Australia"=>1, "Switzerland"=>1}, "group_count"=>2}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/651664"], "description"=>"<p>Yeast cells were grown in SCglc at 15°C (T15), 24°C (T24) 30°C (T30) and 37°C (T37). A) Lipid class composition in mol% of total lipids in the sample. LysoPS and ceramides as minor constituents are not shown. B) Total double bonds of glycerophospholipids (CL omitted for clarity), given as sum of double bounds in fatty acids, in mol% of category. C) Total length of glycerophospholipids, given as sum of fatty acids, in mol% of category. Lysospecies and cardiolipin lengths are omitted for clarity. D) Phosphatidylcholine (PC) species profile in mol% of class. The least abundant species are not shown. E) Sphingolipid species profile in mol% of category. All data were calculated from n = 3 independent samples ± SD. For the lipid nomenclature, sample names and experiment description see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035063#s2\" target=\"_blank\">Materials and Methods</a>.</p>", "links"=>[], "tags"=>["yeast", "grown"], "article_id"=>322153, "categories"=>["Chemistry", "Biochemistry", "Cell Biology", "Microbiology"], "users"=>["Christian Klose", "Michal A. Surma", "Mathias J. Gerl", "Felix Meyenhofer", "Andrej Shevchenko", "Kai Simons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035063.g002", "stats"=>{"downloads"=>2, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Lipidomics_of_yeast_grown_in_different_temperatures_/322153", "title"=>"Lipidomics of yeast grown in different temperatures.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:35:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/651570"], "description"=>"<p>A) Hierarchical clustering of yeast lipidomes using lipidomic features (see text) reveals three major subclusters (underlined). Samples grown under “reference conditions” (SCglc in 30°C and OD<sub>600 nm</sub> = 1) are in bold. B) Principal component analysis of yeast lipidomes using lipidomic features separates three major conditions (encircled with dashed lines) along the first two PCA dimensions. For the abbreviations see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035063#s2\" target=\"_blank\">Materials and Methods</a>.</p>", "links"=>[], "tags"=>["clustering", "yeast", "lipidomes"], "article_id"=>322055, "categories"=>["Chemistry", "Biochemistry", "Cell Biology", "Microbiology"], "users"=>["Christian Klose", "Michal A. Surma", "Mathias J. Gerl", "Felix Meyenhofer", "Andrej Shevchenko", "Kai Simons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035063.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hierarchical_clustering_and_principal_component_analysis_PCA_of_yeast_lipidomes_from_different_growth_conditions_/322055", "title"=>"Hierarchical clustering and principal component analysis (PCA) of yeast lipidomes from different growth conditions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:34:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/651819"], "description"=>"<p>Yeast cells were grown at 30°C in full medium (YP) supplemented with different carbon sources (glucose: YPglc; raffinose: YPraf; glycerol: YPgly) A) Lipid class composition in mol% of total lipids in the sample. LysoPS and ceramides as minor constituents are not shown. B) Total double bonds of glycerophospholipids (CL omitted for clarity), given as sum of double bounds in fatty acids, in mol% of category. C) Total length of glycerophospholipids, given as sum of fatty acids, in mol% of category. Lysospecies and cardiolipin lengths are omitted for clarity. D) Phosphatidic acid (PA) species profile in mol% of class. E) Sphingolipid species profile in mol% of category. All data were calculated from n = 3 independent samples ± SD. For the lipid nomenclature, sample names and experiment description see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035063#s2\" target=\"_blank\">Materials and Methods</a>.</p>", "links"=>[], "tags"=>["yeast", "grown", "carbon"], "article_id"=>322310, "categories"=>["Chemistry", "Biochemistry", "Cell Biology", "Microbiology"], "users"=>["Christian Klose", "Michal A. Surma", "Mathias J. Gerl", "Felix Meyenhofer", "Andrej Shevchenko", "Kai Simons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035063.g004", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Lipidomics_of_yeast_grown_on_different_carbon_sources_/322310", "title"=>"Lipidomics of yeast grown on different carbon sources.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:38:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/652049"], "description"=>"<p>The flexibility is expressed as the variance-to-mean ratio (VMR). For details see text.</p>", "links"=>[], "tags"=>["lipid", "categories"], "article_id"=>322539, "categories"=>["Chemistry", "Biochemistry", "Cell Biology", "Microbiology"], "users"=>["Christian Klose", "Michal A. Surma", "Mathias J. Gerl", "Felix Meyenhofer", "Andrej Shevchenko", "Kai Simons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035063.t001", "stats"=>{"downloads"=>5, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flexibility_of_the_lipid_categories_and_classes_/322539", "title"=>"Flexibility of the lipid categories and classes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-18 00:42:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/334684"], "description"=>"<div><p>Mass spectrometry-based shotgun lipidomics has enabled the quantitative and comprehensive assessment of cellular lipid compositions. The yeast <em>Saccharomyces cerevisiae</em> has proven to be a particularly valuable experimental system for studying lipid-related cellular processes. Here, by applying our shotgun lipidomics platform, we investigated the influence of a variety of commonly used growth conditions on the yeast lipidome, including glycerophospholipids, triglycerides, ergosterol as well as complex sphingolipids. This extensive dataset allowed for a quantitative description of the intrinsic flexibility of a eukaryotic lipidome, thereby providing new insights into the adjustments of lipid biosynthetic pathways. In addition, we established a baseline for future lipidomic experiments in yeast. Finally, flexibility of lipidomic features is proposed as a new parameter for the description of the physiological state of an organism.</p> </div>", "links"=>[], "tags"=>["eukaryotic", "lipidome", "insights", "yeast", "lipidomics"], "article_id"=>126123, "categories"=>["Chemistry", "Biochemistry", "Cell Biology", "Microbiology"], "users"=>["Christian Klose", "Michal A. Surma", "Mathias J. Gerl", "Felix Meyenhofer", "Andrej Shevchenko", "Kai Simons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035063", "stats"=>{"downloads"=>4, "page_views"=>39, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Flexibility_of_a_Eukaryotic_Lipidome_Insights_from_Yeast_Lipidomics/126123", "title"=>"Flexibility of a Eukaryotic Lipidome – Insights from Yeast Lipidomics", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-18 01:42:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/651999"], "description"=>"<p>The internal variability was calculated by averaging the variance-to-mean ratio (VMR) of the length and DB features of the respective lipid classes across the entire sample set (“overall”). Individual calculation of the average VMR of the length and DB features, respectively, reveals that the overall internal variability of a lipid class is largely determined by changes in the DB features (“DB” vs. “length”).</p>", "links"=>[], "tags"=>["variability", "lipid"], "article_id"=>322488, "categories"=>["Chemistry", "Biochemistry", "Cell Biology", "Microbiology"], "users"=>["Christian Klose", "Michal A. Surma", "Mathias J. Gerl", "Felix Meyenhofer", "Andrej Shevchenko", "Kai Simons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035063.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Internal_variability_of_lipid_classes_/322488", "title"=>"Internal variability of lipid classes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:41:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/651753"], "description"=>"<p>Yeast cells were grown in SCglc at 30°C and harvested in early logarithmic (OD1), middle logarithmic (OD3.5) and early stationary (OD6) phase as well as after overnight growth (ODstat). A) Lipid class composition in mol% of total lipids in the sample. LysoPS and ceramides as minor constituents are not shown. Inset: Growth curve with data points indicated by arrowheads. B) Total length of glycerophospholipids in mol% of category. Lysospecies and cardiolipin lengths are omitted for clarity. C) Sphingolipid species profile in mol% of category. All data were calculated from n = 3 independent samples ± SD. For the lipid nomenclature, sample names and experiment description see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035063#s2\" target=\"_blank\">Materials and Methods</a>.</p>", "links"=>[], "tags"=>["yeast"], "article_id"=>322245, "categories"=>["Chemistry", "Biochemistry", "Cell Biology", "Microbiology"], "users"=>["Christian Klose", "Michal A. Surma", "Mathias J. Gerl", "Felix Meyenhofer", "Andrej Shevchenko", "Kai Simons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035063.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Lipidomics_of_yeast_in_different_growth_phases_/322245", "title"=>"Lipidomics of yeast in different growth phases.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-18 00:37:25"}

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Relative Metric

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