A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis

Kroth, Peter G.; Chiovitti, Anthony; Gruber, Ansgar; Martin-Jezequel, Veronique; Mock, Thomas; Parker, Micaela Schnitzler; Stanley, Michele S.; Kaplan, Aaron; Caron, Lise; Weber, Till; Maheswari, Uma; Armbrust, E. Virginia; Bowler, Chris

doi:10.1371/journal.pone.0001426

Cited by 439Photosynthetic Processes and MechanismsProtist diversity and phylogenyDiatoms and Algae Research

A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis

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Kroth, Peter G., Chiovitti, Anthony, Gruber, Ansgar, Martin-Jezequel, Veronique, Mock, Thomas, Parker, Micaela Schnitzler, Stanley, Michele S., Kaplan, Aaron +5 more·2008·PLoS ONE

DOI 10.1371/journal.pone.0001426PMC PMC2173943

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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. METHODOLOGY/PRINCIPAL FINDINGS: 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/SIGNIFICANCE: 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.

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Based on sequencing of Nannochloropsis spp. genomes, the form of carbohydrate reserve in Nannochloropsis spp. is not starch but chrysolaminaran, similar to the diatom Phaeodactylum tricornutum.
“Based on the sequencing of Nannochloropsis spp.genomes, it is proposed that the form of carbohydrate reserve in Nannochloropsis spp. is not starch but chrysolaminaran (J.Xu, personal communication), similar to the diatom Phaeodactylum triconum (Kroth et al., 2008).”
From Responses ofNannochloropsis oceanicaIMET1 to Long-Term Nitrogen Starvation and Recovery (2013) · cites this paper as Kroth et al., 2008

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Authors: Kroth, P. G., Chiovitti, A., Gruber, A., Martin-Jezequel, V., Mock, T., Parker, M. S., Stanley, M. S., Kaplan, A., Caron, L., Weber, T., Maheswari, U., Armbrust, E. V., & Bowler, C.
Affiliations: University of Konstanz (DE)
The University of Melbourne (AU)
University of Washington (US)
Scottish Association For Marine Science (GB)
Hebrew University of Jerusalem (IL)
Inserm (FR)
Centre National de la Recherche Scientifique (FR)
Corresponding author: Kroth, Peter G.
ORCID: Kroth, Peter G.
Chiovitti, Anthony
Gruber, Ansgar
Parker, Micaela Schnitzler
Stanley, Michele S.
Kaplan, Aaron
Maheswari, Uma
Armbrust, E. Virginia
Bowler, Chris
Venue: PLoS ONE
Publisher: Public Library of Science (PLoS)
Published: 2008-01-09
Volume: 3
Issue: 1
Pages: e1426
ISSN: 1932-6203 (ISSN-L)
DOI: 10.1371/journal.pone.0001426
PMC: PMC2173943
OpenAlex: W2104130360
Cited by: 439
References: 133
Citations by year: 2026: 7 · 2025: 15 · 2024: 31 · 2023: 17 · 2022: 25 · 2021: 37 · 2020: 25 · 2019: 25 · 2018: 24 · 2017: 32 · 2016: 24 · 2015: 17 · 2014: 29 · 2013: 27 · 2012: 36
FWCI: 9.18
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (unspecified)
Locations: PLoS ONE (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
KOPS (University of Konstanz) (submittedVersion, cc-by-nc-nd)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Minerva Access (University of Melbourne) (submittedVersion, cc-by)
UEA Digital Repository (University of East Anglia) (submittedVersion, cc-by)
Funders: National Science Foundation (0434087)
U.S. Department of Energy
Gordon and Betty Moore Foundation
Joint Genome Institute
Department of Defence, Australian Government
Deutscher Akademischer Austauschdienst
Deutsche Forschungsgemeinschaft (1661/4, 1661/3-2)
Agence Nationale de la Recherche
University of Melbourne
Centre National de la Recherche Scientifique
Université de Nantes
Universität Konstanz
National Institutes of Health
Australian Research Council (LP0454982)
Defence Science and Technology Group
National Institute of Environmental Health Sciences (P50ES012762)
Division of Ocean Sciences
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Photosynthetic Processes and Mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
Physical Sciences › Materials Science › Biomaterials › Diatoms and Algae Research
Keywords: Phaeodactylum tricornutum, Thalassiosira pseudonana, CO2-concentrating mechanism, photorespiration, glycerate kinase, β-glucanase, glucan synthase, chrysolaminarin, fat deposition, dissolved inorganic carbon uptake, CO2 fixation, carbon cycle
MeSH terms: Carbon Dioxide, Models, Biological, Genome, Diatoms, Carbohydrate Metabolism

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A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis

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