Translocation kinetics and structural dynamics of ribosomes are modulated by the conformational plasticity of downstream pseudoknots

Nucleic Acids Research
Bo WuChunlai Chen

Abstract

Downstream stable mRNA secondary structures can stall elongating ribosomes by impeding the concerted movements of tRNAs and mRNA on the ribosome during translocation. The addition of a downstream mRNA structure, such as a stem-loop or a pseudoknot, is essential to induce -1 programmed ribosomal frameshifting (-1 PRF). Interestingly, previous studies revealed that -1 PRF efficiencies correlate with conformational plasticity of pseudoknots, defined as their propensity to form incompletely folded structures, rather than with the mechanical properties of pseudoknots. To elucidate the detailed molecular mechanisms of translocation and -1 PRF, we applied several smFRET assays to systematically examine how translocation rates and conformational dynamics of ribosomes were affected by different pseudoknots. Our results show that initial pseudoknot-unwinding significantly inhibits late-stage translocation and modulates conformational dynamics of ribosomal post-translocation complexes. The effects of pseudoknots on the structural dynamics of ribosomes strongly correlate with their abilities to induce -1 PRF. Our results lead us to propose a kinetic scheme for translocation which includes an initial power-stroke step and a following therma...Continue Reading

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Citations

Sep 11, 2019·Proceedings of the National Academy of Sciences of the United States of America·Jonathan D Dinman
Jul 1, 2020·Annual Review of Virology·Wesley D PennSuchetana Mukhopadhyay
Aug 15, 2019·Proceedings of the National Academy of Sciences of the United States of America·Matthew T J HalmaMichael T Woodside
Jun 18, 2020·Nature Communications·Martin MiklEran Segal
Aug 21, 2020·Proceedings of the National Academy of Sciences of the United States of America·Sijia PengChunlai Chen
Feb 11, 2021·Bio Systems·Julie D ThompsonChristian J Michel
Jul 15, 2021·Computational and Structural Biotechnology Journal·Kai-Chun Chang, Jin-Der Wen
Aug 14, 2020·Biochemistry·Moye JiaYunfei Hu

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Methods Mentioned

BETA
protein modification
fluorescence resonance
in vitro transcription
electrophoresis
FRET
optical tweezers

Software Mentioned

ImageJ
Cell Vision
POST
smFRET

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