Research Program                  

Molecular evolution and function of RNA polymerase II

Our laboratory takes 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.

In an effort to understand the evolutionary distribution of the CTD, and the functional significance of differences found among eukaryotic organisms, we have employed methods ranging from phylogenetic and bioinformatic comparisons, to genetic analyses of yeast CTD mutants, to biochemical assays on mutated CTDs. Currently we are exploring experimental comparative proteomics of CTD-associated proteins in red algae.

Algal Genomics

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 and green 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 first meeting of the Porphyra RCN was held in May of 2008 at University of Maine's Darling Marine Center and an upcoming meeting is planned for East Carolina University. The draft genome is expected to be complete in early 2009, and offers exciting opportunities in comparative genomics of a wide variety of biological processes.

Courses Taught

BIOL1100. Principles of Biology

BIOL 5230, 5231. The Biology of Algae.

BIOL 4240, 7240. Genome Evolution

BIOL 4210. Phylogenetic Theory

Recent Publications

Bodyl, A., Stiller, J.W. and Mackiewicz, P. 2009. Chromalveolate plastids: direct descent or multiple endosymbioses? Trends in Ecology and Evolution. (in press…on-line early, 2/4/09)

Stiller, J.W. 2008. Unravelling the algae: the past, present and future of algal systematics. Brodie, J. and Lewis, J. Eds. CRC Press, London. 386 pp. Review for The Systematist 30:15-19.

Liu, P., Greenleaf, A.R. and Stiller J.W. 2008. The essential sequence elements required for RNAP II carboxyl-terminal domain function in yeastand their evolutionary conservation. Molecular Biology and Evolution 25: 719-727.

Stiller, J.W. 2007. Plastid endosymbiosis, genome evolution, and the origin of plants. Trends in Plant Science 12: 391-396.

Bodyl, A., Mackiewicz,P. and Stiller, J.W. 2007. The intracellular cyanobacteria of Paulinella chromatophora: endosymbionts or organelles? Trends in Microbiology. 15: 295-296.

Bertournay, S., Marsh, A.C., Donello, N. and Stiller, J.W. 2007. Selective recovery of microalgae from diverse habitats using "phyto-specific" 16S rDNA primers. Journal of Phycology. 43: 609-613.

Mattos, C., Stiller, J.W., Postava-Davignon, M. and Rosengaus, R.B. 2006. Estimation and identification of bacterial and fungal loads in the termite species Nasutitermes corniger using molecular methods. Explorations: The Journal of Undergraduate Research and Creative Activities for the State of North Carolina. 1:107-121.

Stiller, J.W. and Coggins, T.C. 2006. Teaching molecular biological techniques in a research context. American Biology Teacher. January: 595-601.

Stiller, J.W. and Harrell, L. 2005. The largest subunit of RNA polymerase II from the Glaucocystophyta: functional constraint and short-branch exclusion in deep eukaryotic phylogeny. BMC Evolutionary Biology 5:71.

Guo, Z. and Stiller, J.W. 2005. Comparative genomics and evolution of proteins associated with RNA polymerase II C-terminal domain. Molecular Biology and Evolution 22:2166-2178.

Powell, K. and Stiller, J.W. 2005. What's Living in Your World? Building research partnerships for inquiry-based learning. The Science Teacher.  December: 20-25.

Stiller, J.W. and McClanahan, A. 2005. Phyto-specific 16S rDNA PCR primers for recovering algal and plant sequences from mixed samples. Molecular Ecology Notes  5:1-3.

Stiller, J.W. 2004. Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms. Genomics, Proteomics and Bioinformatics  2:69-75.

Guo, Z. and Stiller, J.W. 2004. Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs. BMC Genomics 5:69.

Stiller, J.W. and Cook, M.S. 2004. Functional unit of the RNA polymerase II C-terminal domain lies within heptapeptide pairs. Eukaryotic Cell 3:735-740.

Zhu, Y., Stiller, J.W., Shaner, M.P., Baldini, A., Scemama, J-L and Capehart, A.A. 2004. Cloning of somatolactin aand bcDNAs in zebrafish and phylogenetic analysis of two distinct somatolactin subtypes in fish. Journal of Endocrinology 182:509-518.

Waaland, J.R., Stiller J.W. and Cheney, D. 2004. Macroalgal candidates for genomics. Journal of Phycology  40:26-33.

Stiller, J.W. 2004. Eukaryotic phylogeny in the age of genomics: evolutionary implications of functional differences. In: Organelles, Genomes and Eukaryotic Phylogeny: An Evolutionary Synthesis in the Age of Genomics. Hirt, R.P and Horner, D.S. Eds. CRC Press London. pp. 171-188.

Laboratory Personnel