John Stiller

Education

• Ph.D., Department of Botany, University of Washington, Seattle, 1995
• B.S., Zoology, University of Washington, Seattle, 1989

Research Interests

Molecular evolution and function of RNA polymerase II

We have taken an integrated approach to comparative molecular evolution, investigating key mechanistic differences found among diverse organisms and how these differences impact inferences of patterns of evolution from molecular sequences.  The focus of our work has been RNA polymerase II, the enzyme responsible for transcribing protein-encoding genes in all eukaryotic cells; in particular, the origin, evolution and comparative function of the RNAP II C-terminal domain (CTD).  Our overall goal is to understand how CTD-protein interactions have evolved differently among major eukaryotic taxa, and how those differences have impacted patterns of diversification and developmental complexity.

To investigate the evolutionary distribution of the CTD, along with the functional significance of differences found among eukaryotic CTD sequences, we have employed methods ranging from phylogenetic and bioinformatic comparisons, to genetic analyses of yeast CTD mutants, to biochemical assays on mutated CTDs.

Algal Genomics and the evolution of eukaryotic algae

Based on well-characterized fossils, red algae related to the modern genus Porphyra (best known as the edible sea vegetable “Nori” used to wrap sushi) first appeared more than 1.2 billion years ago, making them the most ancient eukaryotic group to have achieved multicellular complexity.  Despite this impressive age and their great ecological diversity, no red alga has ever managed to attain the kinds of true tissue development that characterize animals and green plants.  In addition, whether red algae are closely related to green plants, and how red plastids (chloroplasts) have moved horizontally to other eukaryotic taxa, are among the most controversial and exciting topics in the field of broad scale eukaryotic phylogenomics.  We are investigating these issues through both experimental analyses and comparative genomics.

We are one of four laboratories that initiated the “Porphyra Genome Project” through the Department of Energy’s Joint Genomics Institute, as well as the “Porphyra Genome Research Coordinating Network (RCN)” supported by the National Science Foundation.  The RCN has fostered diverse collaborations in algal biology, genomics and transcriptomics, including one spearheaded by our lab on major developmental genes and their expression in two species of Porphyra published in the Journal of Phycology.

Publications

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