A. Wali Karzai, Ph.D.

Research

Our group is interested in studying RNA-protein interactions and translational control of gene expression. Specific complexes of protein and RNA carry out many essential biological functions, including RNA processing, RNA turnover, RNA folding, as well as the translation of genetic information from mRNA into protein sequences. A major research focus in my lab concerns the SmpB/SsrA quality control system for protein tagging, directed degradation, and ribosome rescue. We are also interested in understanding how sequence and structure in RNA-binding proteins contribute to the formation of RNA-protein complexes and promote specific biological functions. We use a combination of molecular genetics, protein biochemistry, functional genomics, bioinformatics, and X-ray crystallography to determine the biological function and mechanism of action of specific RNA-protein complexes. Current emphasis is on molecular characterization of how the SmpB protein recognizes SsrA RNA and promotes the detection and rescue of stalled ribosomes, in a process known as trans-translation. The relative simplicity of the SmpB-SsrA interaction, the stability of the complex, and recruitment of additional novel factors during trans-translation makes this an ideal system to study the basic principles underlying the assembly of RNA-protein complexes.