Structure, Dynamics and Oligomerization in Ligand-Mediated Regulation of Gene Expression

Mark Foster
Department of Biochemistry, The Ohio State University

(May 13, 2010 11:30 AM - 12:18 PM)

Structure, Dynamics and Oligomerization in Ligand-Mediated Regulation of Gene Expression

Abstract

Across all domains of life, gene expression is tightly regulated in response to changing cellular and environmental conditions. These signals are often detected by macromolecular sensors which respond through structural rearrangements, effectively "flipping the switch" to initiate or terminate a molecular cascade of events that result in a regulatory outcome. TRAP (trp RNA-binding Attenuation Protein) forms oligomeric protein rings that can bind to cellular tryptophan (Trp). Once bound to Trp, TRAP becomes activated for binding to a conserved RNA sequence in the 5'-leader region of the trp operon, whose genes encodes a number of enzymes involved in the biosynthesis of the amino acid. Binding of TRAP to RNA prevents transcription of the trp operon, lowering Trp production. In the absence of Trp, TRAP cannot bind RNA, and the 5' leader adopts a conformation that allows for transcription of the gene and increased production of Trp. Anti-TRAP is an oligomeric protein that can bind to Trp-activated TRAP and prevent it from binding RNA. Anti-TRAP production in cells is also responsive to cellular levels of Trp. Anti-TRAP is found to equilibrate between different oligomeric states: trimers (AT3) and dodecamers (AT12). It is the trimeric form of the protein, AT3, which can bind and inhibits TRAP. The equilibrium between AT3 and AT12 is determined by concentration and pH. The pH dependence of the equilibrium between "active" AT3 and "inactive" AT12 hints to a new mechanism for responding to environmental changes. Biophysical studies (spectroscopic, thermodynamic, kinetic) of the process and effect of ligand binding to allosteric gene-regulatory macromolecules provide unique as well as universal insights into the role of structure and dynamics in the regulation of gene expression by small molecule ligands. Valbuzzi A, Yanofsky C. Inhibition of the B. subtilis regulatory protein TRAP by the TRAP-inhibitory protein, AT. Science 2001; 293 (5537): 2057-9. PMID: 11557884 | DOI: 10.1126/science.1062187 Gollnick P, Babitzke P, Antson A, Yanofsky C. Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. Annu Rev Genet 2005; 39: 47-68. PMID: 16285852 | DOI: 10.1146/annurev.genet.39.073003.093745 Shevtsov MB, Chen Y, Gollnick P, Antson AA. Crystal structure of Bacillus subtilis anti-TRAP protein, an antagonist of TRAP/RNA interaction. Proc Natl Acad Sci U S A 2005; 102 (49): 17600-5. PMID: 16306262 | DOI: 10.1073/pnas.0508728102 McElroy CA, Manfredo A, Gollnick P, Foster MP. Thermodynamics of tryptophan-mediated activation of the trp RNA-binding attenuation protein. Biochemistry 2006; 45 (25): 7844-53. PMID: 16784236 | DOI: 10.1021/bi0526074