AME 55:241-253 (2009)  -  doi:10.3354/ame01284

Deciphering diatom biochemical pathways via whole-cell proteomics

Brook L. Nunn1,*, Jocelyn R. Aker1, Scott A. Shaffer1, Yihsuan Tsai1, Robert F. Strzepek2, Philip W. Boyd3, Theodore Larson Freeman1,4, Mitchell Brittnacher4, Lars Malmström1, David R. Goodlett1

1Medicinal Chemistry Department, University of Washington, Box 335351, Seattle, Washington 98195, USA
2Chemistry Department, University of Otago, Box 56, Dunedin, New Zealand
3NIWA Centre for Chemical and Physical Oceanography, Department of Chemistry, University of Otago, Dunedin, New Zealand
4Department of Genomic Sciences, University of Washington, Box 355065, Seattle, Washington 98195, USA

ABSTRACT: Diatoms play a critical role in the oceans’ carbon and silicon cycles; however, a mechanistic understanding of the biochemical processes that contribute to their ecological success remains elusive. Completion of the Thalassiosira pseudonana genome provided ‘blueprints’ for the potential biochemical machinery of diatoms, but offers only a limited insight into their biology under various environmental conditions. Using high-throughput shotgun proteomics, we identified a total of 1928 proteins expressed by T. pseudonana cultured under optimal growth conditions, enabling us to analyze this diatom’s primary metabolic and biosynthetic pathways. Of the proteins identified, 70% are involved in cellular metabolism, while 11% are involved in the transport of molecules. We identified all of the enzymes involved in the urea cycle, thereby presenting a complete pathway to convert ammonia to urea, along with urea transporters, and the urea-degrading enzyme urease. Although metabolic exchange between these pathways remains ambiguous, their constitutive presence suggests complex intracellular nitrogen recycling. In addition, all C4-related enzymes for carbon fixation have been identified to be in abundance, with high protein sequence coverage. Quantification of mass spectra acquisitions demonstrated that the 20 most abundant proteins included an unexpectedly high expression of clathrin, which is the primary structural protein involved in endocytic transport. This result highlights a previously overlooked mechanism for the inter- and intra-cellular transport of nutrients and macromolecules in diatoms, potentially providing a missing link to organelle communication and metabolite exchange. Our results demonstrate the power of proteomics, and lay the groundwork for future comparative proteomic studies and directed analyses of specifically expressed proteins and biochemical pathways of oceanic diatoms.

KEY WORDS: Nitrogen cycle · Carbon cycle · Fatty acids · Protein · Carbon fixation · Clathrin-coated vesicles

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Cite this article as: Nunn BL, Aker JR, Shaffer SA, Tsai Y and others (2009) Deciphering diatom biochemical pathways via whole-cell proteomics. Aquat Microb Ecol 55:241-253

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