Liang Meng Wee, PhD
My graduate work with Phil investigated the molecular mechanism of Argonaute proteins to silence gene expression using quantitative kinetics. We demonstrate that Argonaute protein partitions small RNA guide into biochemically distinct domains, which contributes to the differences in targeting by microRNA (miRNA) and small interfering RNA (siRNA). Fly Argonaute 2 (Ago2) uses siRNA that binds extensively to its target with slow association and dissociation kinetics. Presumably, a slow off-rate ensures that most bound targets are cleaved, an attribute of Ago2 critical to its function in antiviral defense. By contrast, mouse AGO2 that operate using miRNA mediated target repression binds and dissociates from its targets rapidly. Our results present quantitative molecular choreographies of Argonaute proteins in locating, securing and regulating target mRNAs.
My current postdoctoral research examines the mechanism underlying the unique phenomenon of translation-transcription coupling in bacteria. By monitoring the activity of RNA polymerase (RNAP) using a combination of single molecule optical trap and bulk measurements, we are able to show that an abutting ribosome increases the rate of transcription by reducing pause probability and pause duration. Moreover, the ribosome unwinds RNA terminator hairpin in the wake of transcription abrogating premature transcription termination. When challenged with limiting ribonucleotide, the ribosome improved transcription rate at the expense of increased misincorporation by RNAP suggesting a balance between speed and fidelity. Given that a stationary RNAP can hinder DNA replication, we propose that by minimizing transcription pauses, the ribosome tips the scale in favor of transient errors in mRNA over permanent alterations to the genome when bacteria is starved.