Background:

• 1986-1988, NIH Postodoctoral Fellow, Yale University
• 1988-2007, Assistant, Associate and Full Professor, Texas A&M University
• 1990-1992, American Cancer Society Junior Faculty Research Awardee, Texas A&M University
• 2001-2006, Faculty Fellow, Texas A&M University

My research group is currently working in four separate areas united by their common use of the tools of biophysical chemistry, bioinorganic chemistry and structural biology to solve interesting "nucleic acid-centric" problems in biological regulation.

1) Metalloregulation of transcription. In this project, our goal is to understand the molecular mechanisms of how cells regulate the intracellular bioavailability of essential metals ions, notably Cu, Fe and Zn among others. This process, termed metal homeostasis and resistance, represents an important battleground in human host-bacterial pathogen interactions since these ions may be limiting or in excess, both detrimental to the survival of the invading microbe. Metal sensor proteins bind specific DNA sequences and regulate the expression of homeostasis genes in response to specific metal ions.

We have focused our efforts on a superfamily of metal sensor proteins, the ArsR family, that collectively respond to a wide range of essential metal ions and heavy metal pollutants (As, Cd, Pb). Comparative studies of a subset of closely related ArsR-family sensors with distinct metal specificity profiles allows us to identify both key metal specificity determinants and common mechanistic features of these protein-based sensors. We have recently discovered what we propose is the founding member of a large family of Cu-specific sensors, CsoR from M. tuberculosis and work is underway to understand the structure and function of this novel regulator. Finally, we have initiated structural characterization of a tetranuclear Cu-cluster (Cu4S6) in metalloregulatory factor-1 (MTF-1) that mediates Cu-dependent up-regulation of metallothionein gene expression that protects Drosophila from Cu-toxicity.

2) A Tunable Metal Biosensing Device. In an extension of the above project, we are in the process of devising an approach that exploits the intrinsic metal selectivities of a collection of ArsR-family sensors to create a reagentless, multichannel microfluidic chemosensing device that can simultaneously detect and quantify multiple heavy metal analytes in complex mixtures. FRET-based and CdSe quantum dot-based approaches are targeted for development.

3) Ribosomal Frameshifting. In this project, we seek to understand the molecular mechanism of how elongating ribosomes are programmed to shift translational reading frames upon encountering a "frameshift" signal embedded in a messenger RNA. Many infectious RNA virus families, including retroviruses (HIV-1) and coronaviruses (the causative agent of SARS), employ this strategy to properly express their genomes. The frameshift signal is often an RNA folding motif called an RNA pseudoknot, and has become a important antiviral target.

We have used NMR spectroscopy to solve the solution structures of several frameshifting pseudoknots from agriculturally important plant luteoviruses as a model system. These studies have lead to the hypothesis that the mechanical properties of these RNA molecules, not their ground-state structures per se, dictate characteristic frameshifting efficiencies on the ribosome. We have outlined a strategy that employs a mechanical force/FRET-based laser tweezers approach in collaboration with TJ Ha's group in Urbana to measure the kinetics of unfolding/refolding of single RNA molecules in the presence and absence of precisely positioned ribosomes.

4) RNA structure and RNA-protein interactions in mammalian coronaviruses (CoVs). In this new collaborative project with JL Leibowitz's group at Texas A&M, we are using the tools of biophysical chemistry and NMR spectroscopy to understand the structure and biological function of the very "tips" of the coronavirus genome, the 5' and 3' untranslated regions (UTRs) that direct the replication and propagation of SARS-CoV and closely related group 2 CoVs. Although this project is at an early stage, we anticipate using mass spectrometry-based fingerprinting methods to identity cellular or virally encoded proteins that interact with specific RNA targets, drug discovery approaches that could be used to target these specialized regulatory RNA motifs, and NMR spectroscopy to solve their structures.

Selected Publications:

Liu, P., Li, L., Millership, J. J., Leibowitz, J. L., & GIEDROC, D. P. (2007) A U-turn motif-containing stem-loop in the coronavirus 5' untranslated region (UTR) plays a functional role in replication. RNA 13, 763-780.

Liu, T., Ramesh, A., Ma, Z, Ward, S. K., Zhang, L., George, G. N., Talaat, A. M., Sacchettini, J. C., & GIEDROC, D. P. (2007) CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator. Nature Chem. Biol. 3, 60-68.

Cornish, P. V., Stammler, S. N. & GIEDROC, D. P. (2006) The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical. RNA 12, 1959-1969.

Cornish, P. V. & GIEDROC, D. P. (2006) Pairwise coupling analysis of helical junction hydrogen bonding interactions in luteoviral RNA pseudoknots. Biochemistry 45, 11162-11171.

Cornish, P. V. GIEDROC, D. P. & Hennig, M. (2006) Dissecting non-canonical interactions in frameshift-stimulating mRNA pseudoknots. J. Biomol. NMR 35, 209-223.

Lee, S., Arunkumar, A.I., Chen, X., & GIEDROC, D. P. (2006) Structural Insights into Homo- and Heterotropic Allosteric Coupling in the Zinc Sensor S. aureus CzrA from Covalently Fused Dimers. J. Am. Chem. Soc. 128, 1937-1947.

Pennella, M.A., Arunkumar, A.I., & GIEDROC, D. P. (2006) Individual Metal Ligands Play Distinct Functional Roles in the Zinc Sensor Staphylococcus aureus CzrA. J. Mol. Biol. 356, 1124-1136.

Cornish, P.V., Hennig, M., & GIEDROC, D. P. (2005) A Loop 2 Cytidine-Stem 1 Minor Groove Interaction as a Positive Determinant for Pseudoknot-Stimulated -1 Ribosomal Frameshifting. Proc. Natl. Acad. Sci. USA 102, 12694-12699.

Pennella, M. A., & GIEDROC, D. P. (2005) Structural Determinants of Metal Selectivity in Prokaryotic Metal-Responsive Transcriptional Regulators. Biometals 18, 413-428 (invited review).

Apuy, J. A., Busenlehner, L. S., Russell, D. H., & GIEDROC, D. P. (2004) Ratiometric Pulsed Alkylation-Mass Spectrometry as a Probe of Thiolate Reactivity in Different Metalloderivatives of S. aureus pI258 CadC Biochemistry 43, 3824-3834.

Chen, X., Zhang, B., Harmon, P. M., Schaffner, W., Peterson, D. O., & GIEDROC, D. P. (2004) A Novel Cysteine Cluster in Human MTF-1 is Required for Heavy Metal-induced Transcriptional Activation in vivo. J. Biol. Chem. 279, 4515-4522.

Eicken, C., Pennella, M. A., Chen, X., Koshlap, K., VanZile, M. L., Sacchettini, J. C., & GIEDROC, D. P. (2003) A Metal-Ligand mediated Intersubunit Allosteric Switch in Related SmtB/ArsR Zinc Sensor Proteins. J. Mol. Biol. 333, 683-695.

GIEDROC, D. P., Cornish, P. V., & Hennig, M. A. (2003) Detection of Scalar Couplings Involving 2'-Hydroxyl Protons Across Hydrogen Bonds in a Frameshifting RNA Pseudoknot. J. Am. Chem. Soc 125, 4676-4677.

Pennella, M. A., Shokes, J. E., Cosper, N. J., Scott, R. A., & GIEDROC, D. P. (2003) Structural Elements of Metal Selectivity in Metal Sensor Proteins. Proc. Natl. Acad. Sci. USA 100, 3713-3718.