Functional investigations in diatoms need more than a transcriptomic approach

References

• Allen A.E., Vardi A. & Bowler C. 2006. An ecological and evolutionary context for integrated nitrogen metabolism and related signalling pathways in marine diatoms. Current Opinion in Plant Biology 9: 264–273.
   Google Scholar
• Allen A., Laroche J., Maheswari U., Lommer M., Schauer N., Lopez P., Finazzi G., Fernie A. & Bowler C. 2008. Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation. Proceedings of the National Academy of Sciences, U.S.A. 105: 10438–10443.
   Google Scholar
• Allen A.W., Dupont C.L., Obornik M., Horak A, Nunes-Nesi A., McCrow J.P., Zheng H., Johnson D.A., Fernie A.R. & Bowler C. 2011. Evolution and metabolic significance of the urea cycle in photosynthetic diatoms. Nature 473: 203–207.
   Google Scholar
• Arabidopsis Interactome Mapping Consortium. 2011. Evidence for network Evolution in an Arabidopsis interactome map. Science 333: 601–607.
   Google Scholar
• Archibald J.M. 2012. The evolution of algae by secondary and tertiary endosymbiosis. Advances in Botanical Research 64: 87–118.
   Google Scholar
• Armbrust E.V., Berges J.A., Bowler C., Green B.R., Martinez D., Putnam N.H., Zhou S., Allen A.E., Apt K.E., Bechner M. Brzezinski M.A., Chaal B.K., Chiovitti A., Davis A.K., Demarest M.S., Detter J.C., Glavina T., Goodstein D., Hadi M.Z., Hellsten U., Hildebrand M., Jenkins B.D., Kurka J., Kapitonov V.V., Kroger N., Lau W.W.Y., Lane S., Larimer F.W., Lippmeier J.C., Lucas S., Medina M., Montsant A., Obornik M., Schitzler Parker M., Palenik B., Pazour G.J., Richardson P.M., Rynearson T.A., Saito M.A., Schwartz D.C., Thamatrakoln K., Valentin K., Vardi A., Wilkerson F.P. & Rokhsar D.S. 2004. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306: 79–86.
   Google Scholar
• Arrivault S., Guenther M., Ivakov A., Feil R., Vosloh D., Van Dongen J.T., Sulpice R. & Stitt M. 2009. Use of reverse-phase liquid chromatography, linked to tandem mass spectrometry, to profile the Calvin cycle and other metabolic intermediates in Arabidopsis rosettes at different carbon dioxide concentrations. Plant Journal 59: 826–839.
   Google Scholar
• Avalos J.L., Fink G.R. & Stephanopoulos G. 2013. Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols. Nature Biotechnology 31: 335–341.
   Google Scholar
• Baiet B., Burel C., Saint-Jean B., Louvet R., Menu-Bouaouiche L., Kiefer-Meyer M.C., Mathieu-Rivet E., Lefebvre T., Castel H., Carlier A., Cadoret J.P., Lerouge P. & Bardor M. 2011. N-glycans of Phaeodactylum tricornutum diatom and functional characterization of its N-acetylglucosaminyltransferase I enzyme. Journal of Biological Chemistry 286: 6152–6164.
   Google Scholar
• Bartulos C.R., Scherer A.S. & Kroth P.G. 2013. Isolation of mitochondria from diatoms. Book of abstracts of the EMBO Workshop ‘The Molecular Life of Diatoms’. Pp. 69.
   Google Scholar
• Beadle G.W. & Tatum E.L. 1941. Genetic control of biochemical reactions in Neurospora. Proceedings of the National Academy of Sciences, U.S.A. 27: 499–506.
   Google Scholar
• Beardall J., Mukerji D., Glover H.E. & Morris I. 1976. The path of carbon in photosynthesis by marine phytoplankton. Journal of Phycology 12: 409–417.
   Google Scholar
• Becker F. & Rhiel E. 2006. Immuno-electron microscopic quantification of the fucoxanthin chlorophyll a/c binding polypeptides Fcp2, Fcp4, and Fcp6 of Cyclotella cryptica grown under low- and high-light intensities. International Microbiology 9: 29–36.
   Google Scholar
• Beebo A., Thomas D., Der C., Sanchez L., Leborgne-Castel N., Marty F., Schoefs B. & Bouhidel K. 2009. Life with and without AtTIP1;1, an aquaporin preferentially localized in the apposing tonoplasts of adjacent vacuoles. Plant Molecular Biology 70: 193–209.
   Google Scholar
• Beebo A., Schoefs B. & Spetea C. 2013. Assessment of the requirement for aquaporins in the thylakoid membrane of plant chloroplasts to sustain photosynthetic water oxidation. FEBS Letters 587: 2083–2089.
   Google Scholar
• Benemann J.R. 1997. CO2 mitigation with microalgae systems. Energy Conversion and Management 38: 475–479.
   Google Scholar
• Bertrand M. 2010. Carotenoid biosynthesis in diatoms. Photosynthesis Research 106: 89–102.
   Google Scholar
• Bertrand M., Schoefs B., Siffel P., Rohacek K. & Molnar I. 2001. Cadmium inhibits epoxidation of diatoxanthin to diadinoxanthin in the xanthophyll cycle of the marine diatom Phaeodactylum tricornutum. FEBS Letters 508: 153–156.
   Google Scholar
• Bowler C., Allen A.E., Badger J.H., Grimwood J., Jabbari K., Kuo A., Maheswari U., Martens C., Maumus F., Otillar R.P., Rayko E., Salamov A., Vandepoele K., Beszteri B., Gruber A., Heijde M., Katinka M., Mock T., Valentin K., Verret F., Berges J.A., Brownlee C., Cadoret J.-P., Chiovitti A., Choi C.J., Coesel S., De Martino A., Detter J.C., Durkin C., Falciatore A., Fournet J., Haruta M., Huysman M.J.J., Jenkins B.D., Jiroutova K., Jorgensen R.E., Joubert Y., Kaplan A., Kröger N., Kroth P.G., La Roche J., Lindquist E., Lommer M., Martin-Jèzèquel V., Lopez P.J., Lucas S., Mangogna M., Mcginnis K., Medlin L.K., Montsant A., Oudot-Le Secq M.-P., Napoli C., Obornik M., Schnitzler Parker M., Petit J.-L., Porcel B.M., Poulsen N., Robison M., Rychlewski L., Rynearson T.A., Schmutz J., Shapiro H., Siaut M., Stanley M., Sussman M.R., Taylor A.R., Vardi A., Von Dassow P., Vyverman W., Willis A., Wyrwicz L.S., Rokhsar D.S., Weissenbach J., Armbrust E.V., Green B.R., Van De Peer Y. & Grigoriev. 2008. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456: 239–244.
   Google Scholar
• Bowler C., Vardi A. & Allen A.E. 2010. Oceanographic and biogeochemical insights from diatom genomes. Annual Review of Marine Science 2: 333–363.
   Google Scholar
• Bruce B.D. 2001. The paradox of plastid transit peptides: conservation of function despite divergence in primary structure. Biochimica et Biophysica Acta 1541: 2–21.
   Google Scholar
• Cadoret J.-P., Garnier M. & Saint-Jean B. 2012. Microalgae, functional genomics and biotechnology. Advances in Botanical Research 64: 285–341.
   Google Scholar
• Chaudhuri B., Hormann F. & Frommer W.B. 2011. Dynamic imaging of glucose flux impedance using Fret sensors in wild-type Arabidopsis plants. Journal of Experimental Botany 62: 2411–2417.
   Google Scholar
• Chaumont F. & Boutry M. 1995. Protein import into plant mitochondria. In: The molecular biology of plant mitochondria (Ed. by C.S. Levings & I.K. Vasil), pp. 207–235. Kluwer Academic Publishers, Dordrecht, The Netherlands.
   Google Scholar
• Coesel S., Mangogna M., Ishikawa T., Heijde M., Rogato A., Finazzi G., Todo T., Bowler C. & Falciatore A. 2009. Diatom PtCPF1 is a new cryptochrome/photolyase family member with DNA repair and transcription regulation activity. EMBO reports 10: 655–661.
   Google Scholar
• Cogne G., Rugen M., Bockmayr A., Titica M., Dussap C.G., Cornet J.F. & Legrand J. 2011. A model-based method for investigating bioenergetic processes in autotrophically growing eukaryotic microalgae: application to the green algae Chlamydomonas reinhardtii. Biotechnology Progress 27: 631–640.
   Google Scholar
• Crawley A. Kline D.I., Dunn S., Anthony K. & Dove S. 2010. The effect of ocean acidification on symbiont photorespiration and productivity in Acrophora formosa. Global Change Biology 16: 851–863.
   Google Scholar
• Curnow P., Senior L., Knight M.J., Thamatrakoln K., Hildebrand M. & Booth P.J. 2012. Expression, purification, and reconstitution of a diatom silicon transporter. Biochemistry 51: 3776–3785.
   Google Scholar
• Curtis B.A., Tanifuji G., Burki F., Gruber A., Irimia M., Maruyama S., Arias M.C., Ball S.G., Gile G.H., Hirakawa Y., Hopkins J.F., Kuo A., Rensing S.A., Schmutz J., Symeonidi A., Elias M., Eveleigh R.J.M., Herman E.K., Klute M.J., Nakayama T., Oborni M., Reyes-Prieto A., Armbrust E.V., Aves S.J., Beiko R.G., Coutinho P., Dacks J.B., Durnford D.G., Fast N.M., Green B.R., Grisdale C.J., Hempel F., Henrissat B., Hoppner M.P., Ishida K.-I., Kim M., Koreny L., Kroth P.G., Liu Y., Malik S.B., Maier U.G., Mcrose D., Mock T., Neilson J.A.D., Onodera N.T., Poole A.M., Pritham E.J., Richards T.A., Rocap G., Roy S.W., Sarai C., Schaack S., Shirato S., Slamovits C.H., Spencer D.F., Suzuki S., Worden A.Z., Zauner S., Barry K., Bell C., Bharti A.K., Crow J.A., Grimwood J., Kramer R., Lindquist E., Lucas S., Salamov A., Mcfadden G.I., Lane C.E., Keeling P.J., Gray M.W., Grigoriev I.W. & Archibald J.M. 2012. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492: 59–65.
   Google Scholar
• Daher Z., Recorbet G., Valot B., Robert F., Balliau T., Potin S., Schoefs B. & Dumas-Gaudot E. 2010. A first root plastid proteome survey identifying novel putative plastidic proteins candidates as plant cell guards in the model legume Medicago truncatula. Proteomics 10: 2123–2137.
   Google Scholar
• De Geyter N., Gholami A., Goormachtig S. & Goosens A. 2012. Transcriptional machineries in jasmonate-elicited plant secondary metabolism. Trends in Plant Sciences 17: 349–359.
   Google Scholar
• Deloache W.C. & Dueber J.E. 2013. Compartmentalizing metabolic pathways inorganelle. Nature Biotechnology 31: 320–321.
   Google Scholar
• Del Rio L.A., Sandalio L.M., Altomare D.A. & Zilinskas B.A. 2003. Mitochondrial and peroxisomal manganese superoxide dismutase: differential expression during leaf senescence. Journal of Experimental Botany 54: 923–933.
   Google Scholar
• De Martino A., Amato A. & Bowler C. 2009. Mitosis in diatoms: rediscovering an old model for cell division. BioEssays 31: 874–884.
   Google Scholar
• Deschamps P. & Moreira D. 2012. Reevaluating the green contribution to diatom genomes. Genome Biology and Evolution 4: 795–800.
   Google Scholar
• Doney S.C., Ruckelshaus M., Duffy J.E., Barry J.P., Chan F., English C.A., Galindo H.M., Grebmeier J.M., Hollowed A.B., Knowlton N., Polovina J., Rabalais N.N., Sydeman W.J. & Talley L.D. 2012. Climate change impacts on marine ecosystems. Annual Review of Marine Science 4: 11–37.
   Google Scholar
• Dukes J.S. 2003. Burning buried sunshine: human consumption of ancient solar energy. Climatic Change 61: 31–44.
   Google Scholar
• Fabris M., Matthijs M., Rombauts S., Vyverman W., Goossens A. & Baart G.J. 2012. The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway. Plant Journal 70: 1004–1014.
   Google Scholar
• Falkowski P.G., Matz M.E., Knoll A.H., Quigg A., Raven J.A., Schofield O. & Taylor F.J.R. 2004. The evolution of modern eukaryotic phytoplankton. Science 305: 354–360.
   Google Scholar
• Feely R.A., Sabine C.L., Hernbandez-Ayon J.M., Ianson D. & Hales B. 2008. Evidence for upwelling of corrosive ‘acidified’ water onto the continental shelf. Science 320: 1490–1492.
   Google Scholar
• Feller A., Machemer K., Braun E.L. & Grotewold E. 2011. Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. The Plant Journal 66: 94–116.
   Google Scholar
• Fernie A. & Schauer N. 2009. Metabolomics-assisted breeding: a viable option for crop improvement? Trends in Genetics 25: 39–48.
   Google Scholar
• Fernie A.R., Obata T., Allen A.E., Araujo W.L. & Bowler C. 2012. Leveraging metabolomics for functional investigations in sequenced marine diatoms. Trends in Plant Science 17: 395–403.
   Google Scholar
• Field C.B., Behrenfeld M.J., Randerson J.T. & Falkowski P.G. 1998. Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281: 237–240.
   Google Scholar
• Fiers W., Contreras R., Duerinck F., Haegeman G., Iserentant D., Merregaert J., Min Jou W., Molemans F., Raeymaekers A., Van Den Berghe A., Volckaert G. & Isebaert M. 1976. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. Nature 260: 500–507.
   Google Scholar
• Gastineau R., Carrier G., Hermann D., Maumus F., Jacquette B., Hardivillier Y., Leignel V., Cariso A., Casse N., Kaczmarsk I., Davidovich N., Meleder V., Saint-Jean B., Cadoret J.-P. & Mouget J-M. 2013. Book of abstracts of the EMBO Workshop ‘The Molecular Life of Diatoms’. Pp 74.
   Google Scholar
• Giavalisco P., Hummel J., Lisec J., Inostroza A.C., Catchpole G. & Willmitzer L. 2008. High-resolution direct infusion-based mass spectrometry in combination with whole 13C metabolome isotope labeling allows unambiguously assigment of chemical sum formulas. Analytical Chemistry 80: 9417–9425.
   Google Scholar
• Gierasch L.M. & Gershenson A. 2009. Post-reductionist protein science, or putting Humpty Dumpty back together again. Nature Chemical Biology 5: 774–777.
   Google Scholar
• Gonzalez N.H., Felsner G., Schramm F.D., Klingl A., Maier U.-G. & Bolte K. 2011. A single peroxisomal targeting signal mediated matrix protein import in diatoms. PlosOne 6(9): e25316.
   Google Scholar
• Gould S.B. 2012. Algae's complex origins. Nature 492: 46–48.
   Google Scholar
• Granum E., Raven J.A. & Leegood R.C. 2005. How do marine diatoms fix 10 bilion tons of inorganic carbon per year. Canadian Journal of Botany 83: 898–908.
   Google Scholar
• Grossmann G., Opekarova M., Novakova L., Stolz J. & Tanner W. 2006. Lipid raft-based membrane compartmentation of a plant transport protein expressed in Saccharomyces cerevisiae. Eukaryotic Cell. 5: 945–953.
   Google Scholar
• Grouneva I., Rokka A. & Aro E.-M. 2011. The thylakoid membrane proteome of two marine diatoms outlines both diatom-specific and species-specific features of the photosynthetic machinery. Journal of Proteome Research 10: 5338–5353.
   Google Scholar
• Guiheneuf F., Ulmann L., Tremblin G. & Mimouni V. 2011. Light-dependent utilization of two radiolabelled carbon sources, sodium bicarbonate and sodium acetate, and relationships with long chain polyunsaturated fatty acid synthesis in the microalga Pavlova lutheri (Haptophyta). European Journal of Phycology 46: 143–152.
   Google Scholar
• Hanson A.D., Pribat A., Waller J.C. & de Crécy-Lagard V. 2010. ‘Unknown’ proteins and ‘orphan’ enzymes: the missing half of the engineering parts list – and how to find it. Biochemical Journal 425: 1–11.
   Google Scholar
• Harada H., Nakatsuma D., Ishida M. & Matsuda Y. 2005. Regulation of the expression of intracellular β-carbonic anhydrase in response to CO2 and light in the marine diatom Phaeodactylum tricornutum. Plant Physiology 139: 1041–1050.
   Google Scholar
• Harada H., Nakajima K., Sakaue K. & Matsuda Y. 2006. CO2 sensing at ocean surface mediated by cAMP in marine diatom. Plant Physiology 142: 1318–1328.
   Google Scholar
• Hester K.C., Peltzer E.T., Kirkwood W.J. & Brewer P.G. 2008. Unanticipated consequences of ocean acidification: a noisier ocean at lower pH. Geophysical Research Letters 35: L19601.
   Google Scholar
• Heydarizadeh P., Poirier I., Loizeau D., Ulmann L., Mimounii V., Schoefs B. & Bertrand M. 2013. Plastids of marine phytoplankton produce bioactive pigments and lipids. Marine Drugs 11: 3425–3471.
   Google Scholar
• Hibberd J. & Weber A. 2012. Plant metabolism and physiology. Current Opinion in Plant Biology 15: 225–227.
   Google Scholar
• Hockin N.L., Mock T., Mulholland F., Kopriva S. & Malin G. 2012. The response of diatom central carbon metabolism to nitrogen starvation is different from that of green algae and higher plants. Plant Physiology 158: 299–312.
   Google Scholar
• Huysman M.J., Fortunato A.E., Matthijs M., Costa B.S., Vanderhaeghen R., Van Den Daele H., Sachse M., Inze D., Bowler C., Kroth P.G., Wilhelm C., Falciatore A., Vyverman W. & De Veylder L. 2013. AUREOCHROME1a-mediated induction of the diatom-specific cyclin dsCYC2 controls the onset of cell division in diatoms (Phaeodactylum tricornutum). Plant Cell 25: 215–228.
   Google Scholar
• Iijima Y., Nakamura Y., Ogata Y., Tanaka K., Sakurai N., Suda K., Suzuki T., Suzuki H., Okazaki K., Kitajima M. Kanaya S., Aoki K. & Shibata D. 2008. Metabolite annotations based on the integration of mass spectral information. Plant Journal 54: 949–962.
   Google Scholar
• Inze D. & de Veylder L. 2006. Cell cycle regulation in plant development. Annual Review of Genetics 40: 77–105.
   Google Scholar
• Jochem F.J., Smith G.J., Gao Y., Zimmerman R.C., Cabello-Pasini A., Kohrs D.G. & Alberte R.S. 2000. Cytometric quantification of nitrate reductase by immunolabeling in the marine diatom Skeletonema costatum. Cytometry 39: 173–178.
   Google Scholar
• Keeling P.J. & Palmer J.D. 2008. Horizontal gene transfer in eukaryotic evolution. Nature Review in Genetics 9: 605–618.
   Google Scholar
• Keys A.J., Bird I.F., Cornelius M.J., Lea P.J., Wallsgrove R.M. & Miflin B.J. 1978. Photorespiratory nitrogen cycle. Nature 275: 741–743.
   Google Scholar
• Krall L., Huege J., Catchpole G., Steinhauser D. & Willmitzer L. 2009. Assessment of sampling strategies for gas chromatography-mass spectrometry (GC-MS) based metabolomics of cyanobacteria. Journal of Chromatography 877B: 2952–2960.
   Google Scholar
• Kroger N. & Poulsen N. 2008. Diatoms – from cell wall biogenesis to nanotechnology. Annual Review of Genetics 42: 83–107.
   Google Scholar
• Kroth P.G. 2007. Genetic transformation: a tool to study protein targeting in diatoms. Methods in Molecular Biology 390: 257–267.
   Google Scholar
• Kroth P., Chiovitti A., Gruber A., Martin-Jezequel V., Mock T., Parker M., Stanley M., Kaplan A., Caron L., Weber T., Maheswari U., Armbrust V. & Bowler C. 2008. A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis. PLoS ONE 3: e1426.
   Google Scholar
• Lang M., Apt K.E. & Kroth P. 1998. Protein transport into ‘complex’ diatom plastids utilizes two different targeting signals. Journal of Biological Chemistry 273: 30973–30978.
   Google Scholar
• Lemoine Y. & Schoefs B. 2010. Secondary ketocarotenoid astaxanthin biosynthesis in algae: a multifunctional response to stress. Photosynthesis Research 106: 155–177.
   Google Scholar
• Liaud M.-F., Lichtle C., Apt K., Martin W. & Cerff R. 2000. Compartment-specific isoforms of TP1 and GAPDH are imported into diatom mitochondria as a fusion protein: evidence in favor of a mitochondrial origin of the eukaryotic glycolytic pathway. Molecular Biology and Evolution 17: 213–223.
   Google Scholar
• Lommer M., Specht M., Roy A.S., Kraemer L., Andreson R., Gutowska M.A., Wolf J., Bergner S.V., Schilhabel M.B., Klostermeier U.C., Beiko R.G., Rosenstiel P., Hippler M. & Laroche J. 2012. Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation. Genome Biology 13: R66.
   Google Scholar
• Maheswari U., Montsant A., Goll J., Krishnasamy S., Rajyashri K.R., Patel V.M. & Bowler C. 2005. The diatom EST database. Nucleic Acids Research 33: D344–347.
   Google Scholar
• Maheswari U., Mock T., Armbrust E.V. & Bowler C. 2009. Update of the Diatom EST Database:a new tool for digital transcriptomics. Nucleic Acids Research 37: D1001–1005.
   Google Scholar
• Maheswari U., Jabbari K., Petit J.L., Porcel B.M., Allen A.E., Cadoret J.P., De Martino A., Heijde M., Kaas R., La Roche J., Lopez P.J., Martin-Jezequel V., Meichenin A., Mock T., Schnitzler-Parker M., Vardi A., Armbrust E.V., Weissenbach J., Katinka M. & Bowler C. 2010. Digital expression profiling of novel diatom transcripts provides insight into their biological functions. Genome Biology 11: R85.
   Google Scholar
• Malinsky J., Opekarová M., Grossmann G. & Tanner W. 2013. Membrane microdomains, rafts, and detergent-resistant membranes in plants and fungi. Annual Review of Plant Biology 64: 501–529.
   Google Scholar
• Maniatis T. & Reed R. 2002. An extensive network of coupling among gene expression machines. Nature 416: 499–506.
   Google Scholar
• Mathieu-Rivet E., Scholz M., Arias C., Dardelle F., Schulze S., Le Mauff F., Teo G., Hochmal A.K., Blanco-Rivero A., Loutelier-Bourhis C., Kiefer-Meyer M.C., Fufezan C., Burel C., Lerouge P., Martinez F., Bardor M. & Hippler M. 2013. Exploring the N-glycosylation pathway in Chlamydomonas reinhardtii unravels novel complex structures. Molecular and Cell Proteomics, 12: 3160–3163.
   Google Scholar
• May P., Wienkoop S., Kempa S., Usadel B., Christian N., Rupprecht J., Weiss J., Recuenco-Munoz L., Ebenhöh O., Weckwerth W. & Walther D. 2008. Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. Genetics, 179: 157–166.
   Google Scholar
• Michels A., Wedel N. & Kroth P. 2005. Diatom plastids possess a phosphoribulokinase with an altered regulation and no oxidative pentose phosphate pathway. Plant Physiology 137: 911–920.
   Google Scholar
• Mimouni V., Ulmann L., Pasquet V., Mathieu M., Picot L., Bougaran G., Cadoret J.P., Morant-Manceau A. & Schoefs B. 2012. The potential of microalgae for the production of bioactive molecules of pharmaceutical interest. Current Pharmaceutical Biotechnology 13: 2733–2750.
   Google Scholar
• Mock T. & Medlin L.K. 2012. Genomics and genetics of diatoms. Advances in Botanical Research 64: 245–284.
   Google Scholar
• Mock T., Manoj Pratim S., Iverson V., Berthiaume C., Robison M., Holtermann K., Durkin C., Splinter Bondurant C., Richmond K., Rodesch M., Kallas T., Huttlin E.L., Cerrina F., Sussman M.R. & Armbrust E.V. 2008. Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses. Proceedings of the National Academy of Sciences, U.S.A. 105: 1579–1584.
   Google Scholar
• Montsant A., Jabbari K., Maheswari U. & Bowler C. 2005. Comparative genomics of the diatom Phaeodactylum tricornutum. Plant Physiology 137: 500–513.
   Google Scholar
• Mouget J.L., Rosa P., Vachoux C. & Tremblin G. 2005. Enhancement of marennine production by blue light in the diatom Haslea ostrearia. Journal of Applied Phycology 17: 437–445.
   Google Scholar
• Muto M., Fukuda Y., Nemoto M., Yoshino T., Matsunaga T. & Tanaka T. 2012. Establishment of a genetic transformation system for the marine pennate diatom Fistulifera sp. Strain JPCC DA0580 – A high triglyceride producer. Marine Biotechnology. Accepted for publication.
   Google Scholar
• Nagao R., Ishii A., Tada O., Suzuki T., Dohmae N., Okumura A., Iwai M., Takahashi T., Kashino Y. & Enami I. 2007. Isolation and characterization of oxygen-evolving thylakoid membranes and photosystem II particles from a marine diatom Chaetoceros gracilis. Biochimica and Biophysica Acta 1767: 1353–1362.
   Google Scholar
• Nguyen-Deroche T.L.N., Le T.T., Bui T.V., Rince Y., Tremblin G. & Morant-Manceau A. 2009. Effects of copper on growth and photosynthesis in marine diatoms: a comparison between species from two different geographical areas. Cryptogamie, Algologie 30: 97–109.
   Google Scholar
• Nguyen-Deroche T.L.N., Caruso A., Le T.T., Bui T.V., Schoefs B., Tremblin G. & Morant-Manceau A. 2012. Zinc affects differently growth, photosynthesis, antioxidant enzyme activities and phytochelatin synthase expression of four marine diatoms. The ScientificWorld Journal 2012, Article ID 982957, 15 pages.
   Google Scholar
• Nymark M., Valle K., Brembu T., Hancke K., Winge P., Andresen K., Johnsen G. & Bones A. 2009. An integrated analysis of molecular acclimation to high light in the marine diatom Phaeodactylum tricornutum. Plos One 4: e7743.
   Google Scholar
• Oberhardt M.A., Palsson B.Ø. & Papin J.A. 2009. Applications of genome-scale metabolic reconstructions. Molecular System Biology 5: 320.
   Google Scholar
• Ohno N., Inoue T., Yamashiki R., Nakajima K., Kitahara Y., Ishibashi M. & Matsuda Y. 2012. CO2-cAMP-responsive cis-elements targeted by a transcription factor with CREB/ATF-like basic zipper domain in the marine diatom Phaeodactylum tricornutum. Plant Physiology 158: 499–513.
   Google Scholar
• Orr J.C., Fabry V.J., Aumont O., Bopp L., Doney S.C., Feely R.A., Gnanadesikan A., Gruber N., Ishida A., Joos F., Key R.M., Lindsay K., Maier-Reimer E., Matear R., Monfray P., Mouchet A., Najiar R.G., Plattner G.K., Rodgers K.B., Sabine C.L., Sarmiento J.L., Schlitzer R., Slater R.D., Totterdell I.J., Weirig M.F., Yamanaka Y. & Yool A. 2005. Anthropogenic ocean acidification over the twenty-first century and its impact on calcifying organisms. Nature 437: 681–686.
   Google Scholar
• Pabo C.O. & Sauer R.T. 1992. Transcription factors: structural families and principles of DNA recognition. Annual Review of Biochemistry 61: 1053–1095.
   Google Scholar
• Palmer J.D. & Delwiche C.F. 1998. The origin and evolution of plastids and their genomes. In: Molecular systematics in plants: DNA sequencing (Ed. by D.E. Soltis, P.S. Soltis & J.J. Doyle), pp. 375–409. Kluwer Academic Publishers, Boston, USA.
   Google Scholar
• Parker M. & Armbrust V. 2005. Synergistic effects of light, temperature, and nitrogen source on transcription of genes for carbon and nitrogen metabolism in the centric diatom Thalassiosira pseudonana (Bacillariophyceae). Journal of Phycology, 41: 1142–1153.
   Google Scholar
• Parker M.S., Maumus F. & Armbrust E.V. 2013. Pseudo-Nitzschia multiseries: a coastal bloom-forming diatom with a fat genome. Book of abstracts of the EMBO Workshop ‘The Molecular Life of Diatoms’. Pp 24.
   Google Scholar
• Patron N., Rogers M. & Keeling P. 2004. Gene replacement of fructose 1,6-bisphosphate aldolase supports the hypothesis of a single photosynthetic ancestor of chromatoalveolates. Eukaryotic Cell 3: 1169–1175.
   Google Scholar
• Paul J.S. & Volcani B.E. 1976. Photorespiration in diatoms. 4. 2 pathways of glycolate metabolism in synchronized cultures of Cylindrotheca fusiformis. Archives of Microbiology 110: 247–252.
   Google Scholar
• Pfeil B., Schoefs B. & Spetea C. 2013. Function and evolution of channels and transporters in photosynthetic membranes. Cellular and Molecular Life Science. In press.
   Google Scholar
• Poulsen N. & Kröger N. 2005. A new molecular tool for transgenic diatoms: control of mRNA and protein biosynthesis by an inducible promoter-terminator cassette. FEBS Journal 272: 3413–3423.
   Google Scholar
• Prouse M.B. & Campbell M.M. 2012. The interaction between MYB proteins and their target DNA binding sites. Biochimica et Biophysica Acta, Gene Regulatory Mechanisms 1819: 67–77.
   Google Scholar
• Raven J.A. 1993. Limits on growth rates. Nature 361: 209–210.
   Google Scholar
• Raven J.A. & Beardall J. 1981. Respiration and photorespiration. Canadian Bulletin of Fisheries and Aquatic Sciences 210: 55–82.
   Google Scholar
• Rayko E., Maumus F., Maheswari U., Jabbari K. & Bowler C. 2010. Transcription factor families inferred from genome sequences of photosynthetic stramenopiles. New Phytologist 188: 52–66.
   Google Scholar
• Rech M., Morant-Manceau A. & Tremblin G. 2008. Carbon fixation and carbonic anhydrase activity in Haslea ostrearia (Bacillariophyceae) in relation to growth irradiance. Photosynthetica 46: 56–62.
   Google Scholar
• Remington S.J. 2011. Green fluorescent protein: a perspective. Protein Science 20: 1509–1519.
   Google Scholar
• Robertson D.L. & Alberte R.S. 1996. Isolation and characterization of glutamine synthase from the marine diatom Skeletonema costatum. Plant Physiology 111: 1169–1175.
   Google Scholar
• Sage R.F., Sage T.L. & Kocacinar F. 2012. Photorespiration and the evolution of C4 photosynthesis. Annual Review Plant Biology 63: 19–47.
   Google Scholar
• Satoh D., Hiraoka Y., Colman B. & Matsuda Y. 2001. Physiological and molecular biological characterization of intracellular carbonic anhydrase from the marine diatom Phaeodactylum tricornutum. Plant Physiology 126: 1459–1470.
   Google Scholar
• Schnitzler-Parker M.S., Armbrust E.V., Piovia-Scott J. & Veil R.G. 2005. Synergistic effects of light, temperature, and nitrogen source on transcription of genes for carbon and nitrogen metabolism in the centric diatom Thalassiosira pseudonana (Bacillariophyceae). Journal of Phycology 41: 1142–1153.
   Google Scholar
• Schoefs B. 2008. Plant Cell Compartments – Selected Topics. Research Signpost: Kerala, India. 450 pp.
   Google Scholar
• Schwartzbach S.D., Osafune T. & Loffelhardt W. 1998. Protein import into cyanelles and complex chloroplasts. Plant Molecular Biology 38: 247–263.
   Google Scholar
• Siaut M., Heijde M., Mangogna M., Montsant A., Coesel S., Allen A., Manfredonia A., Falciatore A. & Bowler C. 2007. Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum. Gene 406: 23–35.
   Google Scholar
• Sirpio S., Suorsa M., Paakharinen V. & Aro E.-M. 2011. Optimized native gel systems for separating thylakoid protein complexes: novel super- and mega-complexes. Biochemical Journal 439: 207–214.
   Google Scholar
• Solymosi K. 2012. Plastid Structure, Diversification and Interconversions I. Algae. Current Chemical Biology 6: 167–186 (Special issue: Plastids: a family of crucial actors in plant physiology. Schoefs, B. Ed).
   Google Scholar
• Solymosi K. & Bertrand M. 2012. Soil metals, chloroplasts, and secure crop production: a review. Agronomy for Sustainable Environment 32: 245–272.
   Google Scholar
• Spetea C., Pfeil B.E. & Schoefs B. 2012. Phylogenetic analysis of the thylakoid ATP/ADP carrier reveals new insights into its function restricted to green plants. Frontiers in Plant Science 2: article 110.
   Google Scholar
• Stitt M., Wirtz W. & Heldt H.W. 1980. Metabolite levels during induction in the chloroplast and extrachloroplast compartments of spinach protoplasts. Biochimica Biophysica Acta 593: 85–102.
   Google Scholar
• Sullivan C.W., Volcani B.E., Lum D. & Chiappin M.L. 1974. Isolation and characterization of plasma and smooth membranes of marine diatom Nitzschia alba. Archives of Biochemistry and Biophysics 163: 29–45.
   Google Scholar
• Sweetlove L.J. & Fernie A.R. 2013. The spatial organization of metabolism within plant cell. Annual Review of Plant Biology 64: In press.
   Google Scholar
• Tachibana M., Allen A.E., Kikutani S., Endo Y., Bowler C. & Matsuda Y. 2011. Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana. Photosynthesis Research 109: 205–221.
   Google Scholar
• Takahashi F., Yamagata D., Ishikawa M., Fukumatsu Y., Ogura Y., Kasahara M., Kiyosue T., Kikuyama M., Wada M. & Kataoka H. 2007. Aureochrome, a photoreceptor required for photomorphogenesis in stramenopiles. Proceedings of the National Academy of Sciences, U.S.A. 104: 19625–19630.
   Google Scholar
• Tanaka Y., Nakatsuma D., Harada H., Ishida M. & Matsuda Y. 2005. Localization of soluble beta-carbonic anhydrase in the marine diatom Phaeodactylum tricornutum. Sorting to the chloroplast and cluster formation on the girdle lamellae. Plant Physiology 138: 207–217.
   Google Scholar
• Timmis J.N., Ayliffe M.A., Huang C.Y. & Martin W. 2004. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nature Review in Genetics 5: 13–135.
   Google Scholar
• Trethewey R. 2004. Metabolite profiling as an aid to metabolic engineering in plants. Current Opinion in Plant Biology 7: 196–201.
   Google Scholar
• Valenzuela J., Mazurie A., Carlson R., Gerlach R., Cooksey K., Peyton B. & Fields M. 2012. Potential role of multiple carbon fixation pathways during lipid accumulation in Phaeodactylum tricornutum. Biotechnology for Biofuels 5: 40.
   Google Scholar
• Vasseur C., Bougaran G., Garnier M., Hamelin J., Leboulanger C., Le Chevanton M., Mostajir B., Sialve B., Steyer J.P. & Fouilland E. 2012. Carbon conversion efficiency and population dynamics of a marine algae-bacteria consortium growing on simplified synthetic digestate: first step in a bioprocess coupling algal production and anaerobic digestion. Bioressource Technology 119: 79–87.
   Google Scholar
• Vitkin E. & Shlomi T. 2012. MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks. Genome Biology 13: R111.
   Google Scholar
• Wolfe-Simon F., Starovoytov V., Reinfelder J.R., Schofield O. & Falkowski P.G. 2006. Localization and role of manganese superoxide dismutase in a marine diatom. Plant Physiology 142: 1701–1709.
   Google Scholar
• Wordeman L., Mcdonald K.L. & Cande W.Z. 1986. The distribution of cytoplasmic microtubules throughout the cell cycle of the centric diatom Stephanopyxis turris: their role in nuclear migration and positioning the mitotic spindle during cytokinesis. Journal of Cell Biology 102: 1688–1698.
   Google Scholar
• Wu Y., Gao K. & Riebesell U. 2010. CO2-induced seawater acidification effects physiological performance of the marine diatom Phaeodactylum tricornutum. Biogeosciences 7: 2915–2923.
   Google Scholar
• Zhang J. 2012. Genetic redundancies and their evolutionary maintenance. Advances in Experimental Medicine and Biology 751: 279–300.
   Google Scholar
• Zhang H.X. & Blumwald E. 2001. Transgenic salt-tolerant tomato plants accumulate salt in foliage but not in fruit. Nature Biotechnology 19: 765–768.
   Google Scholar