title: A topological map of the compartmentalized Arabidopsis thaliana leaf metabolome.
abstract: BACKGROUND
  The extensive subcellular compartmentalization of metabolites and metabolism in eukaryotic cells is widely acknowledged and represents a key factor of metabolic activity and functionality. In striking contrast, the knowledge of actual compartmental distribution of metabolites from experimental studies is surprisingly low. However, a precise knowledge of, possibly all, metabolites and their subcellular distributions remains a key prerequisite for the understanding of any cellular function.
  
  
  RESULTS
  Here we describe results for the subcellular distribution of 1,117 polar and 2,804 lipophilic mass spectrometric features associated to known and unknown compounds from leaves of the model plant Arabidopsis thaliana. Using an optimized non-aqueous fractionation protocol in conjunction with GC/MS- and LC/MS-based metabolite profiling, 81.5% of the metabolic data could be associated to one of three subcellular compartments: the cytosol (including the mitochondria), vacuole, or plastids. Statistical analysis using a marker-'free' approach revealed that 18.5% of these metabolites show intermediate distributions, which can either be explained by transport processes or by additional subcellular compartments.
  
  
  CONCLUSIONS
  Next to a functional and conceptual workflow for the efficient, highly resolved metabolite analysis of the fractionated Arabidopsis thaliana leaf metabolome, a detailed survey of the subcellular distribution of several compounds, in the graphical format of a topological map, is provided. This complex data set therefore does not only contain a rich repository of metabolic information, but due to thorough validation and testing by statistical methods, represents an initial step in the analysis of metabolite dynamics and fluxes within and between subcellular compartments.
authors.affiliation: Botanical Institute, University of Cologne, Cologne, Germany.
authors.forename: Stephan
authors.initials: S
authors.lastname: Krueger
authors.forename: Patrick
authors.initials: P
authors.lastname: Giavalisco
authors.forename: Leonard
authors.initials: L
authors.lastname: Krall
authors.forename: Marie-Caroline
authors.initials: MC
authors.lastname: Steinhauser
authors.forename: Dirk
authors.initials: D
authors.lastname: Büssis
authors.forename: Bjoern
authors.initials: B
authors.lastname: Usadel
authors.forename: Ulf-Ingo
authors.initials: UI
authors.lastname: Flügge
authors.forename: Alisdair R
authors.initials: AR
authors.lastname: Fernie
authors.forename: Lothar
authors.initials: L
authors.lastname: Willmitzer
authors.forename: Dirk
authors.initials: D
authors.lastname: Steinhauser
mesh_terms: D017360:Arabidopsis / Q000166:cytology* / Q000378:metabolism*; D015415:Biomarkers / Q000378:metabolism; D002451:Cell Compartmentation; D002458:Cell Fractionation; D016000:Cluster Analysis; D055442:Metabolome; D008954:Models, Biological; D015233:Models, Statistical; D018515:Plant Leaves / Q000166:cytology* / Q000378:metabolism*; D025341:Principal Component Analysis; D015203:Reproducibility of Results; D013347:Subcellular Fractions / Q000378:metabolism
chemical_list: D015415:Biomarkers