SGER-Comparative proteomics of the RNAP II CTD in red and green algae.

East Carolina University, Greenville NC

Investigators

Abstract

Intellectual merit: The marriage of molecular biology to informatics brought about a revolution in broad scale eukaryotic evolutionary biology. To date, interpretations of how organisms themselves have evolved, along with their key cellular and metabolic features, have relied almost exclusively on sequence-based phylogenetic reconstruction. At the same time, genome-level comparisons continue to reveal new sources of bias that can mislead tree-building computations. As phylogenomic investigations converge on a single framework for understanding eukaryotic diversity, a universal "Tree of Life", it essential to develop new, experimental methodologies to test and extend computation-based hypotheses. This project develops an innovative approach to address one of the most vexing problems in comparative evolution, genomics and proteomics; that is, the origin of green plants and, specifically, whether they share a sister relationship with red algae. Comparative sets of proteins that bind the RNA polymerase II C-terminal domain (CTD), a key organizing platform for complex gene expression, will be identified experimentally in respective green plant and red algal models. Phospho-CTD associated proteins (PCAPs) will be isolated and identified from the rhodophyte Cyanidioschyzon merolae and chlorophyte Chlamydomonas rheinhardii; both of these unicellular algae have complete and well-annotated genomes, permitting direct identification of specific isolated proteins through mass spectrometry. They represent, at present, the best system for experimental comparative proteomics of CTD-based transcription in the red and green lineages. Broader impacts: As an example of how empirical approaches can be used to test computational hypotheses directly, this research can be transformative in the broader fields of evolutionary proteomics and genomics. The work fosters development of interdisciplinary collaborative research, supports training of a Masters-level student, and provides research opportunities for multiple undergraduates. The research will integrate with ongoing collaborations within the Porphyra (Rhodophyta) Genome Research Coordinating Network, and raise public awareness of science through a high school outreach program and public symposia that accompany annual meetings. The goals and preliminary results from this project are scheduled to be highlighted for developing network collaborations, both at a Porphyra RCN symposium at the 2009 joint meeting of the American Society of Plant Biologists and the Phycological Society of America, and at the subsequent RCN meeting scheduled at East Carolina University for spring 2010.