Graduate Faculty Directory
Tilman Baumstark
Department of Biological Sciences
Education
- MS, PhD (Heinrich-Heine University, Germany)
Faculty Appointments
Assistant Professor of Biology
Research Interest
RNA viruses and subviral RNA pathogens
BMV replication complex assembly
Turnip crinkle virus associated Satellite C
Potato spindle tuber viroid (PSTVD)
Synopsis
RNA viruses and subviral RNA pathogens
Plus-strand RNA viruses are responsible for many diseases in humans, animals, and plants. Hepatitis C, influenza, and SARS, for example, are caused by viruses from this important group. Our efforts are focused on an early step in the viral life cycle within the host cell, the recruitment of the viral RNA genome into a replication complex with viral and cellular proteins. Satellites and viroids are subviral RNAs that do not encode their own proteins, but that rely entirely on factors provided by the associated helper virus or the host cell. The smaller size and simpler organization of their genome makes them convenient model systems to study the role of RNA structure in recognition by viral and host proteins, structural changes involved in these interactions, and intracellular transport. We use yeast as a model host, which allows us to apply the full range of experimental tools from genetics, biochemistry, biophysics, cell and molecular biology, bioinformatics, and proteomics to our study. Since these pathogens have intimately adapted to the cellular machinery for their survival, our increased understanding of their structure and function is also enhancing our knowledge of the molecular and cell biology of the host cell system.
BMV replication complex assembly
Brome mosaic virus RNA contains several conserved regions essential for replication that mimic the structure and some of the unctions of tRNA. We have identified a host factor from yeast that appears to bind and stabilize one of these regions, and we are currently in the process of characterizing this complex in vitro and in vivo using recombinant protein expression, affinity purification, electrophoretic mobility shift assays, and 2D liquid chromatography (LC). We plan to use UVcrosslinking, footprinting studies, and mass spectrometry (MS) to identify the components of this complex and the elements on both protein and RNA involved in the interaction. The second region of tRNA mimicry, the intergenic replication enhancer, has been studied using chemical mapping and temperature gradient gel electrophoresis (TGGE). We have designed and characterized small segments of this region that are suitable for NMR high resolution structural analysis.
Turnip crinkle virus associated Satellite C
SatC is a 356 nt RNA with extensive homology to the virus 3’-end. It serves as a model system for the investigation of a conformational
switch by the (+)-strand template shown to be necessary for initiation of (?)-strand synthesis by the viral RNA-dependent RNA polymerase (RdRp). While satC secondary and tertiary structure is being analyzed using TGGE and other biophysical methods, we are also working to overexpress and purify viral RdRp in bacterial and novel yeast systems. Future experiments will focus on how the replicase recognizes the RNA template, and whether the RNA structural switch is prerequisite
or consequence of RdRp binding.
Potato Spindle Tuber Viroid (PSTVD)
Viroids infect, replicate and spread within plant systems in the absence of a helper virus, using host factors instead for almost every single step of their life cycle. Loop E, an RNA element found also in 5S rRNA, has been implicated for both viroid processing and intracellular transport. We intend to study these functions in yeast by launching self-cleaving PSTVd modules of (+)- or (-)-polarity from modified BMV constructs, either from nuclear or cytoplasmic starting points. Crosslinking, LC-MS, yeast knock-outs, cDNA libraries, and confocal microscopy will be used to identify cellular proteins responsible for realization of particular viroid functions.
Publications & Presentations
- Zhang, G., Zhang, J., George, A.T., Baumstark, T., and Simon, A.E. (2006). Conformational Changes Involved in Initiation of Minus-Strand Synthesis of a Virus-Associated RNA. RNA 12, 147–162.
- Schrader, O., Baumstark, T., and Riesner, D. (2003). A mini-RNA containing the tetraloop, wobble-pair and loop E motifs of the central conserved region of potato spindle tuber viroid is processed into a minicircle. Nucleic Acids Res. 31, 988–998.
- Baumstark, T. and Ahlquist P. (2001). The brome mosaic virus RNA3 intergenic replication enhancer folds to mimic a tRNA TYC-stem loop and is modified in vivo. RNA 7, 1652–1670.
Contact Information
Office:
Science & Technology Center
Room # 348
Box # 38
Phone: 215.596.7531
Email: t.baumst@usp.edu
