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Open Access Publications from the University of California

A multi-level study of regulation in the model pennate diatom, Phaeodactylum tricornutum

  • Author(s): Tan, Maxine Hui Yan
  • Advisor(s): Allen, Andrew E
  • et al.
Abstract

Diatoms are major contributors to global photosynthesis and their populations in the modern oceans are affected by availability of iron, nitrogen, phosphate, silica, and other trace metals, vitamins, and infochemicals. However, little is known about regulation in diatoms. In this dissertation, we use the model pennate diatom, Phaeodactylum tricornutum, to highlight multi-level regulation over the diel cycle and across iron and nitrogen treatments. First, we study the global phosphoproteome of Phaeodactylum tricornutum to uncover new phosphorylation sites and gain insights into the role of phosphorylation in diel cycling and nutrient sensing. Second, we use a time course multi-omic approach to understand the dynamics between whole cell transcript expression and protein abundance. The integrated analysis of transcriptome and proteome data highlight proteins that undergo post-transcriptional and/or translational regulation, specifically immediate translation, delayed translation and transcript/protein uncoupling. Finally, we use cutting edge genetic manipulation techniques to generate gene knockouts of three putative nitrate response regulators to elucidate their roles in the regulation gene expression and the nitrate signaling cascade. Our results establish new insights into regulation in the model diatom \pt under low Fe, diel light cycling, and across a transition of N availability. We also conclude that analyses based on only one omic perspective is not sufficient to fully understand the complicated dynamics of gene expression regulation and may lead to biased conclusions of cellular responses.

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