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.

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.

Figure 1. Model of carbon concentrating mechanisms (CCM) in diatoms based on annotations of the Phaeodactylum tricornutum and Thalassiosira pseudonana genomes.

For discussion of the pathways see text. Enzyme abbreviations: CA: carbonic anhydrase; MDH: malate dehydrogenase; ME1: NAD malic enzyme, mitochondrial; PEPC: phosphoenolpyruvate carboxylase; PEPCK: phosphenolpyruvate carboxykinase; PK: pyruvate kinase; PPDK: pyruvate-phosphate dikinase; PYC: pyruvate carboxylase; RUBISCO: ribulose-1,5-bisphosphate carboxylase.

Figure 2. Model for photorespiration and associated pathways in diatoms based on the annotations of the Phaeodactylum tricornutum and Thalassiosira pseudonana genomes.

For simplicity, the number of oragenelle membranes has been reduced in this figure. A gene model for glycerate kinase (GK) could not be found in either genome. The bacterial-type glyoxylate to glycerate metabolism is not shown due to uncertainty in the localization of the enzymes. Enzyme Abbreviations: ACS: acetyl CoA synthetase; CTS: citrate synthase; GDC: glycine decarboxylase; GOX: glycolate oxidase; GK: glycerate kinase; HPR: hydroxypyruvate reductase /glycerate dehydrogenase; ICL: isocitrate lyase; ME1: NAD malic enzyme; MLS: malate synthase; PDH: pyruvate dehydrogenase; PGP: 2-phosphoglycolate phosphatase; RUBISCO: ribulose-1,5-bisphosphate carboxylase; SHMT: serine hydroxymethyltransferase; SPT/AGT: serine-pyruvate/alanine-glyoxylate aminotransferase.

Figure 3. Model of the oxidative and reductive pentose phosphate pathways and related reactions in P. tricornutum.

For simplicity, the number of organelle membranes has been reduced in this figure. The superscript numbers attached to the enzyme names indicate the number of isoenzymes within the respective compartment. Enzyme abbreviations: AL: aldolase; FBA: fructose-1,6-bisphosphate aldolase; FBP: fructose-1,6-bisphosphatase; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GPI: Glucose-6-phosphate isomerase; GPDH: glucose-6-phosphate dehydrogenase; PGL: phosphor-gluconate lactonase; PRK: Phosphoribulokinase; RUBISCO: ribulose-1,5-bisphosphate carboxylase; PGDH: 6-phospho-gluconolactone dehydrogenase, PGK: phospho-glycerate kinase; RPI: ribose-5-phosphate isomerase; RPE: ribulose-phosphate epimerase; RPI: ribose-5-phosphate isomerase; TKL: transketolase; TAL: transaldolase; TPI: triose-phosphate isomerase; SBP: seduheptulose-1,7-bisphosphatase.

Figure 4. Model of the glycolytic reactions in the cytosol and related pathways within mitochondria and plastids of P. tricornutum.

Enzyme abbreviations: PGM: phosphoglucomutase; GPI: Glucose-6-phosphate isomerase; PFK: Phosphofructokinase; FBA: fructose-1,6-bisphosphate aldolase; GAPDH: glyceraldehyde-phosphate dehydrogenase; PGK phospho-glycerate kinase; PGAM: phosphor-glycerate mutase; PK: pyruvate kinase; PPDK: pyruvate-phosphate dikinase.