Codon Selection Affects Recruitment of Ribosome-Associating Factors during Translation

• Published in: ACS synthetic biology Vol. 9; no. 2; pp. 329 - 342
• Main Authors: Rojano-Nisimura, Alejandra M, Haning, Katie, Janovsky, Justin, Vasquez, Kevin A, Thompson, Jeffrey P, Contreras, Lydia M
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 21.02.2020
• Subjects: Bacterial Proteins - biosynthesis; Bacterial Proteins - genetics; Codon - metabolism; Escherichia coli - metabolism; Luminescent Proteins - biosynthesis; Luminescent Proteins - genetics; Molecular Chaperones - metabolism; Protein Biosynthesis; Ribosomal Proteins - metabolism; Ribosomes - metabolism; RNA, Messenger - metabolism; Signal Recognition Particle - metabolism; translation pausing; translation regulation; protein chaperones; ribosome-associated factors
• ISSN: 2161-5063; 2161-5063
• DOI: 10.1021/acssynbio.9b00344

An intriguing aspect of protein synthesis is how cotranslational events are managed inside the cell. In this study, we developed an in vivo bimolecular fluorescence complementation assay coupled to SecM stalling (BiFC-SecM) to study how codon usage influences the interactions of ribosome-associating factors that occur cotranslationally. We profiled ribosomal associations of a number of proteins, and observed differential association of chaperone proteins TF, DnaK, GroEL, and translocation factor Ffh as a result of introducing synonymous codon substitutions that change the affinity of the translating sequence to the ribosomal anti-Shine–Dalgarno (aSD) sequence. The use of pausing sequences within proteins regulates their transit within the translating ribosome. Our results indicate that the dynamics between cellular factors and the new polypeptide chain are affected by how codon composition is designed. Furthermore, associating factors may play a role in processes including protein quality control (folding and degradation) and cellular respiration.