Translational control and regulation

Protein synthesis is a complex and highly regulated process coordinated by the large macromolecular machine, the ribosome. The ribosome is a one of the most conserved and critical macromolecular complexes and over four decades of biochemical, genetic and structural analyses have provided immense insights into its function. The Dunham laboratory is interested in determining a molecular framework for how dysregulation of the bacterial ribosome results from different cellular environments that control bacterial proliferation and persistence.

Specific projects in the lab include: 1) determination of the molecular mechanisms for mRNA frameshifting that cause the ribosome to read an alternative genetic code resulting in different gene expression patterns; 2) the structural and functional basis of negative regulation of their own expression by toxin-antitoxin complexes during steady state growth, and the rapid translation of specific mRNAs to change the cellular proteome during stress conditions; 3) the role of ribosomal RNA modification enzymes that confer antibiotic resistance.

Regulation of protein synthesis

Biological fitness is critically dependent upon the accurate flow of genetic information from DNA to RNA to protein. Breakdown in translational fidelity of the ribosome is detrimental to cells due its central role in the production of all proteins in every living organism. Major types of errors resulting from ribosome dysregulation include mRNA frame reading and tRNA selection errors. When the ribosome reads a non-three nucleotide codon, this causes expression of aberrant or nonsense proteins, which are then targeted for degradation. Recently, my laboratory has made exciting discoveries regarding the molecular basis for both these types of errors (Fagan et al., PNAS 2013; Fagan et al., RNA 2014; Maehigashi et al., PNAS 2014).
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Toxin-mediated degradation of mRNA during the bacterial stringent response

Bacteria adapt to stressful conditions by rapidly adjusting their metabolic rates via global regulatory responses. General mechanisms for adaption include the SOS response, general stress response, the heat-shock response and the stringent response. Factors involved in the stringent response have been identified across diverse microorganisms but their detailed molecular mechanisms of target recognition and action are still unknown. One major focus of my lab is to study how specific proteins involved in the stringent response repress translation, allowing bacteria to enter a nonreplicative latent state known as persistence.
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RNA modification and antibiotic resistance

Increasing global spread of antibiotic resistance among pathogenic bacteria threatens a post-antibiotic era in healthcare. Detailed studies of resistance mechanisms are therefore urgently required. The ribosome is a major antibiotic target, but bacteria can acquire resistance by modification of drug-binding sites. In collaboration with Prof. Graeme Conn’s lab at Emory University, we have been studying the molecular basis for antibiotic-resistance arising via enzymatic modification of the small ribosomal subunit. We solved the X-ray structure of the first molecular ‘snapshot’ of 30S recognition by a human pathogen-derived, aminoglycoside-resistance rRNA methyltransferase, NpmA (Dunkle et al., PNAS 2014).
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