Functional analysis of the novel upstream ORF in enteroviruses

The genus Enterovirus consists of a large group of viruses, of which over 100 serotypes are known to be human pathogens. Disease phenotype in humans ranges from sub-clinical to acute flaccid paralysis, myocarditis, and meningitis. Until recently, it was thought that enteroviruses encode all their proteins in a single long open reading frame. However, it is now known that in many enteroviruses a small upstream open reading frame (uORF) encodes an additional protein termed UP (Upstream Protein). The mechanism by which the uORF is translated is unknown and thus the regulation of UP expression is undetermined. This work aims to address these questions using reporter systems and ribosome profiling, amongst other techniques. Building on previously published work, we investigate the relationship between the structure of the domain VI stem loop of the echovirus 7 internal ribosome entry site and translation of the uORF. Through profiling initiating ribosomes of echovirus 7 infected cells, we characterise the profile of initiation events during virus infection. Our findings provide mechanistic insights into gene expression mechanism of enterovirus-infected cells.