Eric Baggs, Ph.D.

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2004-2010: B.S., Chemistry: Biochemistry Emphasis | Advisor: Professor Henry Charlier | Boise State University, Boise ID

2010-2018: Ph.D., Microbiology and Molecular Genetics | Advisor: Bert Semler | University of California, Irvine CA

The burgeoning realization that RNA serves not only as an information intermediary, but also a highly complex biochemical mediator has reshaped our understanding of the scale of biological complexity. RNAs are able to regulate gene expression in cis and in trans, are critical structural components of ribonucleoproteins, serve as signaling molecules, effect enzymatic functions, and serve as bait for other enzymes! The vast possibilities as to what RNA can do, we are only beginning to understand. My research has focused primarily on cis-acting RNA elements in viral and eukaryotic mRNAs and how they drive different biological outcomes, with an eye to finding innovative therapeutic targets.

Collagen mRNA: Collagen (type I) represents the most abundant protein in the human body as a central component of the extra-cellular matrix. Upon injury or disease, the over-deposition of collagen (fibrosis) can lead to negative outcomes; from cosmetic scarring to acute organ failure. Understanding the underlying mechanisms behind pathological fibrosis may help us to develop treatments applicable to a vast spectrum disease states. The mRNA of collagen type I has a small RNA hairpin structure right at the 5’ translation start site. Upon investigation, it was found that this hairpin was critical to efficient gene expression, and it was subsequently determined that this gene regulation was imparted by the binding of a protein (Larp6) to this RNA structure. My laboratory is focused on characterizing this binding interaction as a potential
target for developing broad-spectrum anti-fibrotic therapeutics.

As an undergraduate I started my research career right here! In this very department! I conducted research, under the supervision of Professor Charlier, into the enzymatic activity of recombinant human Carbonyl Reductase (r-hCBR) relative to endogenous hCBR.
Subsequently, I received an internship with the National Institute of Allergy and Infectious Diseases (NIAID/NIH) to study the epidemiology of Borrelia hermsii (tick-borne relapsing fever), by trapping and sampling of wildlife. Animal blood samples and ticks were analyzed by microscopy, serology, and qPCR to map a shift in endemicity.
My doctoral research centered on understanding the mechanism of IRES mediated translation, in particular the mechanism by which eukaryotic IRES elements function. Distinctly from the Picornavirus IRESs (as well as other viral IRESs), the mechanism and purpose of these eukaryotic IRESs function remains fairly unclear. I set out to determine if any trans-acting factors (ITAFs) were involved in regulating translation from my model system, the Kv1.4 IRES. Using a parallel biochemical and genetic approach, I identified many specific IRES RNA binding proteins. I used RNA affinity chromatography to purify proteins from tissue extract, and identified them by LC/MS. I also screened the entire Kv1.4 5’NCR by yeast 3-hybrid assays and identified RNA binding proteins by transcriptional activation and sequence analysis. Candidate trans-acting factors were investigated by a variety of means to determine the role that each of these proteins plays in IRES mediated translation. This included many in vitro and cell-based biochemical assays examining transcription, translation, and macromolecular assembly and function. These studies identified a compendium of novel players in this little understood process of Internal Ribosome Entry Site mediated translation. These results add to the idea that translation regulation is much more complex and tailored than first thought.
My post-doctoral work has mainly focused on the regulatory function/mechanism of the Collagen type I mRNA 5’SL (see Research Interests). I began developing a “tool-kit” for dissecting the biophysical, biochemical, and biomolecular constraints behind this RNAs regulatory activity. Additionally, I collaborated with others in the optimized purification of bioactive and isotopically labeled proteins for in vitro and NMR experiments.

F Matosin, S., Fischer, P.D., Droemer, M.A., Baggs, E., Chowdhury, A.S., Tavares, I., Ficarro, S.B., Warner, L., Arthanari, H., Nagarajan, R. 1H, 13C and 15N backbone and sidechain assignment of the Burkholderia mallei acyl carrier protein J. Biomolecular NMR assign. (2023)

Rizzo, M., Baggs, E.L., Chowdhury, A.S., Nagarajan, R., and Warner, L.R. Backbone 1H, 13C and 15N assignments of the apo-acyl carrier protein of Pseudomonas aeruginosa. J. Biomolecular NMR assign. (2023)

Fischer PD, Chowdhury AS, Bartholow T, Basu S, Baggs E, Cox HS 3rd, Matošin S, Burkart MD, Warner L, Nagarajan R, Arthanari H. Carrier protein mediated cargo sensing in quorum signal synthases. Chem Commun (Camb). 2023 Jan 24; 59(8):1014-1017. PubMed Central PMCID: PMC9931420.

Flather D, Cathcart AL, Cruz C, Baggs E, Ngo T, Gershon PD, Semler BL. Generation of Recombinant Polioviruses Harboring RNA Affinity Tags in the 5' and 3' Noncoding Regions of Genomic RNAs. Viruses. 2016 Feb 4; 8(2) PubMed Central PMCID: PMC4776194.

Cathcart AL, Baggs EL, Semler BL. Picornaviruses: Pathogenesis and Molecular Biology. Reference Module in Biomedical Sciences [Internet] Online: Elsevier; (2015). Available from: http://www.sciencedirect.com/science/article/pii/B9780128012383002725 DOI:
10.1016/B978-0-12-801238-3.00272-5