Physics Colloquium - Biophysics from biologist’s perspective

Understanding cellular processes at molecular level have revolutionized our view of biology. The biophysical methods and approaches were instrumental in defining biomolecule structures and their spatial organization, which ultimately revealed how biomolecules function. The complexity and dynamics of the biological systems still challenge conventional methods. The recent advances in imaging techniques circumvented this by allowing tracking of individual proteins and nucleic acid molecules. These approaches were instrumental in defining mechanism of protein synthesis (translation). Internal Ribosome Entry Sites (IRESs) are RNA structures employed by viruses to hijack host translation apparatus. IRESes require a reduced compliment of translation factors and thus serve as a great model due to their apparent simplicity. The Inter Genomic Region IRES of Dicistroviridae viruses is able to promote translation in the absence of all initiation factors. We used the Cricket Paralysis Virus (CrPV) IRES to reveal the rich underlying complexity of this deceivingly simple system. Using single-molecule fluorescence methods we demonstrated that initiation on CrPV IRES occurs via multiple parallel pathways, and includes a number of unstable intermediates where the initiation outcome is defined by the rates of parallel pathways. This work highlighted the complexity of initiation and hinted that parallel pathways are a general characteristic of translation initiation.