Research Interest/Area of Expertise
Molecular systems biology
RNA mediated gene regulation
Genomics/high-throughput methods in bacteria
Mechanisms of non-Shine-Dalgarno translation initiation
The mechanism of translation initiation in bacteria was first examined in E. coli, where the presence of a Shine-Dalgarno site preceding the start codon leads to the initiation of translation in the proper reading frame. Now with thousands of sequenced bacterial genomes it was discovered that less than 1/2 of all bacterial protein coding genes are preceded by a Shine-Dalgarno site. Additionally, individual bacterial species including many cyanobacteria and bacteroidetes, lack Shine-Dalgarno sites in nearly 90% of their genes! We are therefore investigating the mechanisms of non-Shine-Dalgarno initiation by utilizing Caulobacter crescentus. Caulobacter contains Shine-Dalgarno sites in only 23.5% of its genes, has a doubling time of less than 2 hours, has well established genetic tools, and has a well annotated transcriptome. We are currently utilizing ribosome profiling, translation reporters, and in vitro reconstituted translation initiation assays to dissect the factors required for non-Shine-Dalgarno initiation in Caulobacter.
Sub-cellular organization of mRNA decay in bacteria
In eukaryotic cells, mRNA decay is often organized in ribonucleoprotein granules like RNA processing-bodies or stress granules. We found that bacteria can also make similar ribonucleoprotein granules that we termed bacterial ribonucleoprotein bodies (BR-bodies) composed of Ribonuclease E, protein components of the RNA degradosome, and RNA. These BR-bodies appear to be important for mRNA degradation and are assembled by liquid-liquid phase separation from the cytoplasm forming a compartment with high concentrations of the RNA degradosome and RNA. Here were's currently utilizing high-throughput mRNA decay assays and cell biology experiments to probe the role of these granules in mRNA decay.
RNA-mediated mechanisms of cell cycle-regulation
The Caulobacter cell cycle is controlled by a genetic and biochemical circuit that functions in space and time to control the the transcription of ~20% of the entire genome. We recently found that approximately half of these mRNAs contained translational control to regulate the timing of expression. We are interested in the regulatory logic of RNA-mediated control and how it is integrated with the cell cycle-regulatory circuit.
Education – Degrees, Licenses, Certifications
- Postdoctoral Fellowship, Stanford University 2011-2015
- Ph.D. Biophysical Chemistry, Northwestern University 2011
- B.S. Microbiology, Colorado State University 2005
Awards and Grants
Schrader, J.M., Li, G.W., Childers, W.S., Perez, A., Weissman, J.S., Shapiro, L., McAdams, H.H. Dynamic translational regulation in Caulobacter cell cycle control. Proceedings of the National Academy of Sciences 2016
Schrader, J.M., Zhou, B., Li, G., Lasker, K., Childers, W.S., Williams, B., Long, T., Crosson, S., McAdams, H.H., Weissman, J.S., Shapiro, L. The coding and noncoding architecture of the Caulobacter crescentus genome. PLOS Genetics 2014
Bio 2200 - Introductory Microbiology (Fall)
Bio 5060/8000 - Molecular Systems Biology (Winter)
Bio 6994 - Technical Communication in Molecular Biotechnology
Bio 2200 - Introductory Microbiology
Bio 5060/8000 - Molecular Systems Biology
Other qualifications directly relevant to courses taught
Board Member - Michigan Branch of the American Society of Microbiology