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Deciphering diatom biochemical pathways via whole-cell proteomics


Nunn, BL and Aker, JR and Shaffer, SA and Tsai, Y and Strzepek, RF and Boyd, PW and Freeman, TL and Brittnacher, M and Malmstrom, L and Goodlett, DR, Deciphering diatom biochemical pathways via whole-cell proteomics, Aquatic Microbial Ecology, 55, (3) pp. 241-253. ISSN 0948-3055 (2009) [Refereed Article]

Copyright Statement

Copyright 2009 Inter-Research

DOI: doi:10.3354/ame01284


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.

Item Details

Item Type:Refereed Article
Keywords:nitrogen cycle, carbon cycle, fatty acids, protein, carbon fixation, clathrin-coated vesicles
Research Division:Biological Sciences
Research Group:Ecology
Research Field:Marine and estuarine ecology (incl. marine ichthyology)
Objective Division:Environmental Policy, Climate Change and Natural Hazards
Objective Group:Adaptation to climate change
Objective Field:Climate change adaptation measures (excl. ecosystem)
UTAS Author:Boyd, PW (Professor Philip Boyd)
ID Code:95566
Year Published:2009
Web of Science® Times Cited:36
Deposited By:IMAS Research and Education Centre
Deposited On:2014-10-03
Last Modified:2015-02-02

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