Richard (Rick) D Vierstra
DBBS Graduate Programs
Plant and Microbial Biosciences Program
Molecular Cell Biology Program
Light is essential to plants, providing both the necessary energy for growth and signals to entrain their life cycles to the daily and seasonal rhythms. To perceive this signal, plants employ a family of red/far-red light-absorbing photoreceptors called phytochromes. The Vierstra lab is attempting to understand how phytochromes work at the atomic level, using a variety of structure-based approaches such as X-ray crystallography and single-particle electron microscopy with both plant and microbial versions. An emerging model is that light excitation triggers an isomerization of the bilin chromophore, which induces dramatic changes within the protein that alter signaling. Based on this model, the lab is now trying to reengineer phytochromes as a novel strategy to improve agricultural yield and sustainability.
All cells have catabolic mechanisms designed to maintain proper homeostasis and influence the levels of key regulators that control growth and development. The Vierstra lab is studying two key degradative routes in plants, the ubiquitin/proteasome system (UPS) and autophagy, with the goals of understanding how they work, how they select targets, and how they function synergistically. The UPS involves tagging of unwanted proteins with the small, highly conserved protein ubiquitin. Once modified with multiple ubiquitins, these targets are individually recognized and broken down by the 26S proteasome, a self-compartmentalized proteolytic machine that also releases the ubiquitins for reuse. Over 6% of the Arabidopsis genome encodes UPS components, with as many as a 1000 factors participating in target selection alone, making it one of the most complex processes in plants. Autophagy (‘self eating’) involves encapsulating unwanted cytosolic constituents in vesicles called autophagosomes, which are delivered to the vacuole for degradation. In contrast to the UPS, autophagy is designed to handle large protein complexes, protein aggregates and even entire organelles. Genetic analyses showed that autophagy is critical for nutrient recycling, maintaining cellular homeostasis, and programmed cell death. The Vierstra lab is also studying a relative of ubiquitin called SUMO that becomes post-translationally attached to a plethora of nuclear proteins when cells are exposed to various environmental insults, presumably to provide stress protection. For all this research, the Vierstra lab combines data on the proteome, transcriptome, metabolome and interactome, using a variety of cell biological, biochemical, genetic and mass spectrometric techniques.
Diagram showing how autophagy captures cytoplasmic material and transport it to the vacuole for degradation. The background shows Arabidopsis root cells containing GFP-labeled autophagic vesicles inside the vacuole.
3-D structure of the photosensing module of a bacterial phytochrome showing the nanometer-scale conformational changes that occur during photoconversion between the inactive Pr and the active Pfr states.
Diagram of the UPS. Top diagram shows the enzymatic cascade that links ubiquitins (Ub) to targets followed by their degradation by the 26S proteasome. Bottom images show the 3-D structures of the core protease (CP) that houses the protease active sites and the 26S proteasome containing the CP capped on both ends by a regulatory particle (RP) that identifies appropriate substrates, releases the ubiquitin moieties, and transports the unfolded polypeptides into the CP lumen for breakdown.
The proteasome stress regulon is controlled by a pair of NAC transcription factors in Arabidopsis. Gladman, N.P., R.S. Marshall, K.-H. Lee, and R.D. Vierstra (2016) Plant Cell (in press).
Defining the SUMO system is maize: SUMOylation is up-regulated during endosperm development and rapidly induced by stress. Augustine, R.C., T.C. Rytz, S.L. York, and R.D. Vierstra (2016) Plant Physiol. (in press).
Crystal structure of Deinoccocus phytochrome in the photoactivated state reveals a cascade of structural rearrangements during photoconversion. Burgie, E.S., J. Zhang, and R.D. Vierstra (2016) Structure 24: 448-457.
Morpheus Spectral Counter: a computational tool for quantitative mass spectrometry using the Morpheus search engine. Gemperline, D.C., M. Scalf, L.M. Smith, and R.D. Vierstra (2016) Proteomics 16: 920-924.
Spotlight: Ubiquitin goes green. Hua, Z., and R.D. Vierstra (2016) Trends Cell Biol. 26: 3-5.
Autophagic recycling plays a central role in maize nitrogen remobilization. Li, F., T. Chung, J.G. Pennington, M.L. Federico, H.F. Kaeppler, S.M. Kaeppler, M.S. Otegui, and R.D. Vierstra (2015) Plant Cell 27: 1389-1408.
X-ray radiation induces deprotonation of the bilin chromophore in crystalline D. radiodurans phytochrome. Li, F., E.S. Burgie, T. Yu, A. Heroux, G.G. Schatz, R.D. Vierstra, and A.M. Orville (2015) J. Amer. Chem. Soc. 37: 2792-2795.
Autophagic degradation of the 26S proteasome is mediated by the dual ATG8/ubiquitin receptor RPN10 in Arabidopsis. Marshall, R.S., F. Li, D.C. Gemperline, A.J. Book, and R.D. Vierstra (2015) Mol. Cell 58: 1053-1066
Crystallographic and electron microscopic analyses of a bacterial phytochrome reveal local and global rearrangements during photoconversion. Burgie, E.S., T. Wang, A.N. Bussell, J.M. Walker, H. Li, and R.D. Vierstra (2014) J. Biol. Chem. 289: 24573-24587.
Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome. Burgie, E.S., A.N. Bussell, K. Dubiel, J.M. Walker, and R.D. Vierstra (2014) Proc. Natl. Acad. Sci. USA 111: 10179-10184.
Autophagy-related (ATG)11 plays an essential role in non-selective autophagy and senescence-induced mitophagy in Arabidopsis. Li, F., T. Chung, and R.D. Vierstra (2014) Plant Cell 26: 788-807.
Phytochromes, atomic perspectives of photoactivation and signaling. Burgie, E.S., and R.D. Vierstra (2014) Plant Cell 26: 4568-4583.
Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis. Hua, Z., J.E. Pool, R.J. Schmitz, M.D. Schultz, S.-H. Shiu, J.R. Ecker, and R.D. Vierstra (2013) Proc. Natl. Acad. Sci. USA 110: 16927-16932.
Quantitative proteomics reveal factors regulating RNA biology as dynamic targets of stress-induced SUMOylation in Arabidopsis. Miller, M.J., M. Scalf, T.C. Rytz, S.L. Hubler, L.M. Smith and R.D. Vierstra (2013) Molec. Cell. Proteomics 12: 449-463.
Structure-guided engineering of phytochrome B with altered photochemistry and light signaling. Zhang, J., R.J. Stankey, and R.D. Vierstra (2013) Plant Physiol. 161: 1445-1457.
Advanced proteomic analyses yield a deep dataset of ubiquitylation targets in Arabidopsis. Kim, D.-Y., M. Scalf, L.M. Smith, and R.D. Vierstra (2013) Plant Cell. 25: 1523-1540.
A photo-labile thioether linkage to phycoviolobilin provides the foundation for the unique blue/green photocycles in DXCF cyanobacteriochromes. Burgie, E.S., J.M. Walker, G.N. Phillips Jr, and R.D. Vierstra (2013) Structure 21: 88-97.