John W. Stiller
Title: Associate Professor
Area of Study: Molecular Evolution and Algal Genomics
Office: Howell Science S301A
Address: Department of Biology
East Carolina University
Greenville, NC 27858
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.
Stiller, J.W., Schreiber, J., Yue, J., Guo, H., Ding, Q. and Huang, J. 2014. The evolution of photosynthesis in chromist algae through serial endosymbiosis. Nature Communications. DOI:10.1038/ncomm6764
Yang, C., Hager, P.W. and Stiller, J.W. 2014. The identification of putative RNA polymerase II C-terminal domain associated proteins in red and green algae. Transcription. DOI:10.4161/21541264.2014.970944
Yang, C. and Stiller J.W. 2014. Evolutionary diversity and taxon-specific modifications of the RNA polymerase II C-terminal domain. Proceedings of the National Academy of Sciences, USA. 111:5920-5925.
Stiller, J.W. 2014. Toward an empirical framework for interpreting plastid evolution. Journal of Phycology. 50:462-473.
Chan, C.X., Blouin, N.A., Zhuang, Y., Zäuner, S., Prochnik, S.E., Lindquist, E. Lin, S., Benning, C., Lohr, M., Yarish, C., Gantt, E., Grossman, A.R., Lu, S., Müller, K., Stiller, J.W., Brawley, S.H. 2012. Porphyra (Bangiophyceae) transcriptomes provide insights into red algal development and metabolism. Journal of Phycology. 48:1328-1342.
Stiller, J.W., Perry, J., Rymarquis, L.A., Green, P.J., Prochnik, S., Lindquist, E., Chan, C.X., Yarish, C., Lin, S., Zhuang, Y., Blouin, N.A. and Brawley, S.H. 2012. Major developmental regulators and their expression in two closely related species of Porphyra (Rhodophyta). Journal of Phycology 48:883-896.
Xie F.L., Sun G.L., Stiller J.W. and Zhang B.H. 2011. Genome-wide functional analysis of the cotton transcriptome by creating an integrated EST database. PLoS ONE, 6(11) e26980 doi: 10.1371/journal.pone.0026980
Stiller, J.W. 2011. Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer. BMC Evolutionary Biology 11:259. Featured Article.
Liu, P., Kenney, J. Stiller, J.W. and Greenleaf, A. 2010. Sequence organization, length conservation and evolution of yeast RNA polymerase II carboxyl-terminal domain. Molecular Biology and Evolution. 27(11): 2628-2641.
Rogers, C., Guo, Z. and Stiller J.W. 2010. Combined gene expression and network analyses indicate a role for the RNA polymerase II C-terminal domain in mitotic segregation. PLoS ONE 5(6): e11386. doi:10.1371/journal.pone.0011386
Stiller, J.W., Huang, J., Ding, Q., Tian, J. and Goodwillie, C. 2009. Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses? BMC Genomics 10:484.
Bodył, A., Mackiewicz, P. and Stiller, J.W. 2009. Early steps in plastid evolution: current ideas and controversies. BioEssays. 31: 1219-1232
Bodył, A., Stiller, J.W. and Mackiewicz, P. 2009. Chromalveolate plastids: direct descent or multiple endosymbioses? Trends in Ecology and Evolution. 24: 119-121.
Liu, P., Greenleaf, A.R. and Stiller J.W. 2008. The essential sequence elements required for RNAP II carboxyl-terminal domainfunction 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.
All publications through Google Scholar
Some Interesting Websites
BIOL1100. Principles of Biology
BIOL 5230, 5231. The Biology of Algae
BIOL 4240, 7240. Genome Evolution
BIOL 4210. Phylogenetic Theory
HNRS 2014. Honors College Seminar: Science and Society in the Age of Genomics
Evolution of RNAP CTD and comparative proteomics of CTD-associated proteins in red and green algae.
Comparing student-centered learning to traditional lecture in introductory biology courses
Comparative genomics of endosymbiotic transfer in chromes algae
Evolution of eukaryotes based on core transcriptional genes
Optimal between-meal foraging strategies