2009, Gruber, Ansgar, Weber, Till, Río Bártulos, Carolina, Vugrinec, Sascha, Kroth, Peter G.

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.

2008, Bowler, Chris, Allen, Andrew E., Badger, Jonathan H., Grimwood, Jane, Jabbari, Kamel, Kuo, Alan, Maheswari, Uma, Martens, Cindy, Maumus, Florian, Otillar, Robert P., Rayko, Edda, Salamov, Asaf, Vandepoele, Klaas, Beszteri, Bank, Gruber, Ansgar, Heijde, Marc, Katinka, Michael, Mock, Thomas, Valentin, Klaus, Verret, Fréderic, Berges, John A., Brownlee, Colin, Cadoret, Jean-Paul, Chiovitti, Anthony, Choi, Chang Jae, Coesel, Sacha, De Martino, Alessandra, Detter, John Chris, Durkin, Colleen, Falciatore, Angela, Fournet, Jérome, Haruta, Miyoshi, Huysman, Marie J. J., Jenkins, Bethany D., Jiroutova, Katerina, Jorgensen, Richard E., Joubert, Yolaine, Kaplan, Aaron, Kröger, Nils, Kroth, Peter G., La Roche, Julie, Lindquist, Erica, Lommer, Markus, Martin Jézéquel, Véronique, Lopez, Pascal J., Lucas, Susan, Mangogna, Manuela, McGinnis, Karen, Medlin, Linda K., Montsant, Anton, Oudot Le Secq, Marie-Pierre, Napoli, Carolyn, Obornik, Miroslav, Schnitzler Parker, Micaela, Petit, Jean-Louis, Porcel, Betina M., Poulsen, Nicole, Robison, Matthew, Rychlewski, Leszek, Rynearson, Tatiana A., Schmutz, Jeremy, Shapiro, Harris, Siaut, Magali, Stanley, Michele S., Sussman, Michael R., Taylor, Alison R., Vardi, Assaf, Dassow, Peter von, Vyverman, Wim, Willis, Anusuya, Wyrwicz, Lucjan S., Rokhsar, Daniel S., Weissenbach, Jean, Armbrust, E. Virginia, Green, Beverley R., Van de Peer, Yves, Grigoriev, Igor V.

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

2009, Ast, Michelle, Gruber, Ansgar, Schmitz-Esser, Stephan, Neuhaus, Horst Ekkehard, Kroth, Peter G., Horn, Matthias, Haferkamp, Ilka

Diatoms are ecologically important algae that acquired their plastids by secondary endosymbiosis, resulting in a more complex cell structure and an altered distribution of metabolic pathways when compared with organisms with primary plastids. Diatom plastids are surrounded by 4 membranes; the outermost membrane is continuous with the endoplasmic reticulum. Genome analyses suggest that nucleotide biosynthesis is, in contrast to higher plants, not located in the plastid, but in the cytosol. As a consequence, nucleotides have to be imported into the organelle. However, the mechanism of nucleotide entry into the complex plastid is unknown. We identified a high number of putative nucleotide transporters (NTTs) in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum and characterized the first 2 isoforms (NTT1 and NTT2). GFP-based localization studies revealed that both investigated NTTs are targeted to the plastid membranes, and that NTT1 most likely enters the innermost plastid envelope via the stroma. Heterologously expressed NTT1 acts as a proton-dependent adenine nucleotide importer, whereas NTT2 facilitates the counter exchange of (deoxy-)nucleoside triphosphates. Therefore, these transporters functionally resemble NTTs from obligate intracellular bacteria with an impaired nucleotide metabolism rather than ATP/ADP exchanging NTTs from primary plastids. We suggest that diatoms harbor a specifically-adapted nucleotide transport system and that NTTs are the key players in nucleotide supply to the complex plastid.

2006, Wiencke, Christian, Roleda, Michael Y., Gruber, Ansgar, Clayton, Margaret N., Bischof, Kai

1. The UV susceptibility of zoospores of the brown seaweeds Saccorhiza dermato- dea, Alaria esculenta and Laminaria digitata (Laminariales) was determined in field experiments in June 2004 on Spitsbergen (78° 55' N, 11° 56' E).
2. Freshly released zoospores were exposed for one or two days at various water depths to ambient solar radiation, ambient solar radiation depleted of UVB radiation (UVBR) and ambient solar radiation depleted of both UVBR and UVAR. Subsequently, germination rates were determined after exposure to favourable light and temperature conditions in the laboratory.
3. The radiation regime was monitored at the water surface and in the water adjacent to the exposure platforms for the duration of the field exposure.
4. Under ambient solar radiation the tolerance of zoospores to UVR was highest in the shallow water species S. dermatodea, intermediate in the upper to mid sublittoral A. esculenta and lowest in the upper to mid sublittoral L. digitata. There was, however, no difference in the susceptibility of the zoospores to ambient solar radiation or to solar radiation depleted of UVBR.
5. The water body was relatively UV transparent especially in the upper water layers. The 1 % UVB depth mostly varied between 5.35 and 6.87 m. On one stormy day the 1 % UVB depth was only 3.57 m indicating resuspension of sediments.
6. We propose that as the zoospores are the developmental stages most susceptible to UVR their UVR tolerance is a major if not the most important factor for the determination of the upper depth distribution limit of these species on the shore. The results are discussed with respect to enhanced UVBR due to stratospheric ozone depletion.

2009, Weber, Till, Gruber, Ansgar, Kroth, Peter G.

Diatoms are unicellular algae of great ecological importance. So far, very little is known about the regulation of carbon fixation in these algae; however, there are strong indications that in diatom plastids, the ferredoxin/thioredoxin system might play a minor role in redox regulation of the photosynthetic reactions compared to land plants. Until now, it is unknown whether there are fewer or other target enzymes of thioredoxins in diatoms. Only a single potential target enzyme for thioredoxin, the plastidic fructose-1,6-bisphosphatase, has yet been identified. Nevertheless, during the annotation of the genome of the diatom Phaeodactylum tricornutum, we identified several genes encoding different thioredoxins. Utilizing in vivo expression of GFP:presequence fusion proteins in P. tricornutum, we were able to show that these thioredoxins are targeted either into plastids, mitochondria, or remain in the cytosol. Surprisingly, two of the three usually cytosolic thioredoxin h proteins are apparently plastid associated and, together with a thioredoxin reductase, putatively located in the periplastidic compartment. This is one of the few indications for so far unknown enzymatic reactions in the space between the two pairs of diatom plastid envelope membranes.

2005, Roleda, Michael Y., Wiencke, Christian, Hanelt, Dieter, van de Poll, Willem H., Gruber, Ansgar

Depth distribution of kelp species in Helgoland (North Sea) is characterized by occurrence of Laminaria digitata in the upper sublittoral, whereas L. saccharina and L. hyperborea dominate the mid and lower sublittoral region. Laminaria digitata is fertile in summer whereas both other species are fertile in autumn/winter. To determine the light sensitivity of the propagules, zoospores of L. digitata, L. saccharina and L. hyperborea were exposed in the laboratory to different exposure times of photosynthetically active radiation (PAR; 400 700 nm), PAR + UVA radiation (UVAR; 320 400 nm) and PAR + UVAR + UVB radiation (UVBR; 280 320 nm). Optimum quantum yield of PSII and DNA damage were measured after exposure. Subsequently, recovery of photosynthetic efficiency and DNA damage repair, as well as germination rate were measured after 2 and 3 d cultivation in dim white light. Photosynthetic efficiency of all species was photoinhibited already at 20 µmol photons m−2 s−1 PAR, whereas UV radiation (UVR) had a significant additional effect on photoinhibition. Recovery of the PSII function was observed in all species but not in spores exposed to irradiation longer than 4 h of PAR + UVA + UVB and 8 h of PAR + UVA. The amount of UVB-induced DNA damage measured as cyclobutane pyrimidine dimers (CPDs) increased with exposure time and highest damage was detected in the spores of lower subtidal L. hyperborea relative to the other two species. Significant removal of CPDs indicating repair of DNA damage was observed in all species after 2 d in low white light especially in the spores of upper subtidal L. digitata. Therefore, efficient DNA damage repair and recovery of PSII damage contributed to the germination success but not in spores exposed to 16 h of UVBR. UV absorption of zoospore suspension in L. digitata is based both on the absorption by the zoospores itself as well as by exudates in the medium. In contrast, the absorption of the zoospore suspension in L. saccharina and L. hyperborea is based predominantly on the absorption by the exudates in the medium. This study indicates that UVR sensitivity of zoospores is related to the seasonal zoospore production as well as the vertical distribution pattern of the large sporophytes.