title: A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis.
abstract: BACKGROUND
  Diatoms are unicellular algae responsible for approximately 20% of global carbon fixation. Their evolution by secondary endocytobiosis resulted in a complex cellular structure and metabolism compared to algae with primary plastids.
  
  
  RESULTS
  The whole genome sequence of the diatom Phaeodactylum tricornutum has recently been completed. We identified and annotated genes for enzymes involved in carbohydrate pathways based on extensive EST support and comparison to the whole genome sequence of a second diatom, Thalassiosira pseudonana. Protein localization to mitochondria was predicted based on identified similarities to mitochondrial localization motifs in other eukaryotes, whereas protein localization to plastids was based on the presence of signal peptide motifs in combination with plastid localization motifs previously shown to be required in diatoms. We identified genes potentially involved in a C4-like photosynthesis in P. tricornutum and, on the basis of sequence-based putative localization of relevant proteins, discuss possible differences in carbon concentrating mechanisms and CO(2) fixation between the two diatoms. We also identified genes encoding enzymes involved in photorespiration with one interesting exception: glycerate kinase was not found in either P. tricornutum or T. pseudonana. Various Calvin cycle enzymes were found in up to five different isoforms, distributed between plastids, mitochondria and the cytosol. Diatoms store energy either as lipids or as chrysolaminaran (a beta-1,3-glucan) outside of the plastids. We identified various beta-glucanases and large membrane-bound glucan synthases. Interestingly most of the glucanases appear to contain C-terminal anchor domains that may attach the enzymes to membranes.
  
  
  CONCLUSIONS
  Here we present a detailed synthesis of carbohydrate metabolism in diatoms based on the genome sequences of Thalassiosira pseudonana and Phaeodactylum tricornutum. This model provides novel insights into acquisition of dissolved inorganic carbon and primary metabolic pathways of carbon in two different diatoms, which is of significance for an improved understanding of global carbon cycles.
authors.affiliation: Fachbereich Biologie, University of Konstanz, Konstanz, Germany. Peter.Kroth@uni-konstanz.de
authors.forename: Peter G
authors.initials: PG
authors.lastname: Kroth
authors.forename: Anthony
authors.initials: A
authors.lastname: Chiovitti
authors.forename: Ansgar
authors.initials: A
authors.lastname: Gruber
authors.forename: Veronique
authors.initials: V
authors.lastname: Martin-Jezequel
authors.forename: Thomas
authors.initials: T
authors.lastname: Mock
authors.forename: Micaela Schnitzler
authors.initials: MS
authors.lastname: Parker
authors.forename: Michele S
authors.initials: MS
authors.lastname: Stanley
authors.forename: Aaron
authors.initials: A
authors.lastname: Kaplan
authors.forename: Lise
authors.initials: L
authors.lastname: Caron
authors.forename: Till
authors.initials: T
authors.lastname: Weber
authors.forename: Uma
authors.initials: U
authors.lastname: Maheswari
authors.forename: E Virginia
authors.initials: EV
authors.lastname: Armbrust
authors.forename: Chris
authors.initials: C
authors.lastname: Bowler
mesh_terms: D050260:Carbohydrate Metabolism; D002245:Carbon Dioxide / Q000378:metabolism; D017377:Diatoms / Q000378:metabolism*; D016678:Genome; D008954:Models, Biological
chemical_list: D002245:Carbon Dioxide