Open AccessQuantifying the dynamics of IRES and cap translation with single-molecule resolution in live cells
Author(s) -
Amanda Koch,
Luis U. Aguilera,
Tatsuya Morisaki,
Timothy J. Stasevich
Publication year - 2020
Publication title -
nature structural and molecular biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.448
H-Index - 270
eISSN - 1545-9993
pISSN - 1545-9985
DOI - 10.1038/s41594-020-0504-7
Subject(s) - internal ribosome entry site , translation (biology) , ribosome , biology , microbiology and biotechnology , orfs , protein biosynthesis , eukaryotic translation , stress granule , open reading frame , rna , computational biology , messenger rna , biophysics , genetics , gene , peptide sequence
Viruses use internal ribosome entry sites (IRES) to hijack host ribosomes and promote cap-independent translation. Although they are well-studied in bulk, the dynamics of IRES-mediated translation remain unexplored at the single-molecule level. Here, we developed a bicistronic biosensor encoding distinct repeat epitopes in two open reading frames (ORFs), one translated from the 5' cap, and the other from the encephalomyocarditis virus IRES. When combined with a pair of complementary probes that bind the epitopes cotranslationally, the biosensor lights up in different colors depending on which ORF is translated. Using the sensor together with single-molecule tracking and computational modeling, we measured the kinetics of cap-dependent versus IRES-mediated translation in living human cells. We show that bursts of IRES translation are shorter and rarer than bursts of cap translation, although the situation reverses upon stress. Collectively, our data support a model for translational regulation primarily driven by transitions between translationally active and inactive RNA states.