Intracellular distribution of the reductive and oxidative pentose phosphate pathways in two diatoms

Abstract

Diatoms contribute a large proportion to the worldwide primary production and are particularly effective in fixing carbon dioxide. Possibly because diatom plastids originate from a secondary endocytobiosis, their cellular structure is more complex and metabolic pathways are rearranged within diatom cells compared to cells containing primary plastids. We annotated genes encoding isozymes of the reductive and oxidative pentose phosphate pathways in the genomes of the centric diatom Thalassiosira pseudonana and the pennate diatom Phaeodactylum tricornutum and bioinformatically inferred their intracellular distribution. Prediction results were confirmed by fusion of selected presequences to Green Fluorescent Protein and expression of these constructs in P. tricornutum. Calvin cycle enzymes for the carbon fixation and reduction of 3-phosphoglycerate are present in single isoforms, while we found multiple isoenzymes involved in the regeneration of ribulose-1,5-bisphosphate. We only identified one cytosolic sedoheptulose-1,7-bisphosphatase in both investigated diatoms. The oxidative pentose phosphate pathway seems to be restricted to the cytosol in diatoms, since we did not find stromal glucose-6-phosphate dehydrogenase and 6-phosphogluconolactone dehydrogenase isoforms. However, the two species apparently possess a plastidic phosphogluconolactonase. A 6-phosphogluconolactone dehydrogenase is apparently plastid associated in P. tricornutum and might be active in the periplastidic compartment, suggesting that this compartment might be involved in metabolic processes in diatoms.

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation

“…First, genes were identified with keyword searches of both existing and de novo gene catalog annotations, and published pathway annotations specific to P . tricornutum [85–86,90–92,132]. To identify all desired isozymes of individual steps in desired pathways, we used BLASTP against the P .…”

In Silico and In Vivo Investigations of Proteins of a Minimized Eukaryotic Cytoplasm

“…Enzymes for housekeeping biochemistry, such as glycolysis, oxidative, and reductive pentose phosphate pathway, were investigated by another group (Gruber et al 2009). However, with 6PGDH, only one PPC-localized protein was verified by in vivo localization studies (Gruber et al 2009).…”

“…s, symbiontic (PPC-localized); sDer1-1/1-2, degradation at the ER; sUfd1, ubiquitin fusion degradation; sUba1, ubiquitin activating E1; sUbc, ubiquitin conjugating E2; ptE3P, P. tricornutum ubiquitin ligase E3 of the PPC; Ub, ubiquitin; ptDUP, P. tricornutum deubiquitinating enzyme of the PPC; sCdc48-1/2, cell division cycle protein; sPUB, PUB and thioredoxin domain containing protein; sHsp70, heat shock protein; sDTC, DnaJ and TPR domain-containing protein; sDPC, DnaJ and PDI domain-containing protein; sSec14, putative lipid transfer protein sTrxH, thioredoxin; sNTRC, NADPH depending thioredoxin reductase containing N-terminal thioredoxin domain; sDrp, dynamin-related protein; sα7/sβ2/6/7, proteasomal 20S components of the alpha and beta type; sTLP-1, trypsin-like serine protease; sSMC, structural maintenance of the chromosome-like protein; sPRP, pentapeptide repeats containing protein; sPEL, pectin esterase domain-containing protein; sP4H, prolyl-4-hydroxylase; 6PGDH, 6-phosphogluconolactone dehydrogenase; sαCA-1/2, alpha carbonic anhydrase; sORF139/261/532a/534, open reading frame ( Guillardia theta nucleomorph-encoded ORF homolog); ptOmp85, outer membrane protein. Superscript numbers indicate proteins localized in previous studies: 1, (Gould et al 2006a); 2, (Sommer et al 2007); 3, (Hempel et al 2010); 4, (Gruber et al 2009); 5, (Weber et al 2009); 6, (Bullmann et al 2010). ( B ) Phaeodactylum tricornutum possesses an aliform-shaped secondary plastid surrounded by four membranes.…”

The place of diatoms in the biofuels industry

“…These include differences in the homology and distribution in enzymes of carbohydrate metabolism, the pentose phosphate pathway and carbonic anhydrases [59,68,[169][170][171]. Differences in these core pathways are likely to affect metabolism and/or cellular energetics.…”