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Deciphering diatom biochemical pathways via whole-cell proteomics.

Type Information
Nr 20 (Research article)
Authors Nunn, Brook; Aker, Jocelyn; Shaffer, Scott; Tsai, Shannon; Strzepek, Robert; Boyd, Philip; Freeman, Theodore; Brittnacher, Mitchell; Malmström, Lars; Goodlett, David
Title Deciphering diatom biochemical pathways via whole-cell proteomics.
Journal Aquat Microb Ecol (2009) 55 241-253
DOI 10.3354/ame01284
Citations 57 citations (journal impact: 2.19)
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 diatoms 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 describing the 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.