Reconstitution and analyses of RNA interactions with eukaryotic translation initiation factors and ribosomal preinitiation complexes

• Published in: Methods (San Diego, Calif.) Vol. 162-163; pp. 42 - 53
• Main Authors: Liu, Xiaozhuo, Schuessler, Peter J., Sahoo, Ansuman, Walker, Sarah E.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.06.2019
• Subjects: eIF3; eIF4B; eIF4F; Eukaryotic initiation factors; MRNA translation initiation; Ribosome; MRNA translation initiation; eIF4B; Ribosome; Eukaryotic initiation factors; eIF4F; eIF3
• ISSN: 1046-2023; 1095-9130
• DOI: 10.1016/j.ymeth.2019.03.024

•Eukaryotic translation initiation factors bind RNA and the ribosome to affect changes in translation.•Capped mRNAs display strong dependence on the eIF4 factors for ribosome binding.•Factor dependence of translation initiation can be kinetically determined.•Optimized purification strategies allow larger studies of apparent affinities of translation initiation factors for the preinitiation complex. Control of translation initiation plays a critical role in the regulation of gene expression in all organisms, yet the mechanics of translation initiation in eukaryotic organisms are not well understood. Confounding studies of translation are the large number and overlapping functions of many initiation factors in cells, and a lack of cap-dependence in many in vitro systems. To shed light on intricate mechanisms that are often obscured in vivo, we use a fully reconstituted translation initiation system for analyzing RNA interactions with eukaryotic translation initiation factors and complexes from the model organism Saccharomyces cerevisiae. This system exhibits strong cap dependence, and dependence on translation factors varies with mRNA 5′ UTR sequences as expected from genome-wide studies of translation. Here we provide optimized protocols for purification and analysis of the effects of labeled and unlabeled mRNA recruitment factors on both the rate and factor dependence of mRNA recruitment to the translation preinitiation complex in response to RNA sequence- and structure-changes. In addition to providing streamlined and detailed protocols, we describe a new construct for purification of higher yields of fluorescently labeled and unlabeled full-length eIF4G.