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Bi-directional ribosome scanning controls the stringency of start codon selection

Author

Listed:
  • Yifei Gu

    (Cornell University)

  • Yuanhui Mao

    (Cornell University)

  • Longfei Jia

    (Cornell University)

  • Leiming Dong

    (Cornell University)

  • Shu-Bing Qian

    (Cornell University)

Abstract

The fidelity of start codon recognition by ribosomes is paramount during protein synthesis. The current knowledge of eukaryotic translation initiation implies unidirectional 5ʹ→3ʹ migration of the pre-initiation complex (PIC) along the 5ʹ UTR. In probing translation initiation from ultra-short 5ʹ UTR, we report that an AUG triplet near the 5ʹ end can be selected via PIC backsliding. Bi-directional ribosome scanning is supported by competitive selection of closely spaced AUG codons and recognition of two initiation sites flanking an internal ribosome entry site. Transcriptome-wide PIC profiling reveals footprints with an oscillation pattern near the 5ʹ end and start codons. Depleting the RNA helicase eIF4A leads to reduced PIC oscillations and impaired selection of 5ʹ end start codons. Enhancing the ATPase activity of eIF4A promotes nonlinear PIC scanning and stimulates upstream translation initiation. The helicase-mediated PIC conformational switch may provide an operational mechanism that unifies ribosome recruitment, scanning, and start codon selection.

Suggested Citation

  • Yifei Gu & Yuanhui Mao & Longfei Jia & Leiming Dong & Shu-Bing Qian, 2021. "Bi-directional ribosome scanning controls the stringency of start codon selection," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26923-3
    DOI: 10.1038/s41467-021-26923-3
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    References listed on IDEAS

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    1. Shintaro Iwasaki & Stephen N. Floor & Nicholas T. Ingolia, 2016. "Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor," Nature, Nature, vol. 534(7608), pages 558-561, June.
    2. Stuart K. Archer & Nikolay E. Shirokikh & Traude H. Beilharz & Thomas Preiss, 2016. "Dynamics of ribosome scanning and recycling revealed by translation complex profiling," Nature, Nature, vol. 535(7613), pages 570-574, July.
    3. Ulf-Peter Guenther & David E. Weinberg & Meghan M. Zubradt & Frank A. Tedeschi & Brittany N. Stawicki & Leah L. Zagore & Gloria A. Brar & Donny D. Licatalosi & David P. Bartel & Jonathan S. Weissman &, 2018. "The helicase Ded1p controls use of near-cognate translation initiation codons in 5′ UTRs," Nature, Nature, vol. 559(7712), pages 130-134, July.
    4. Jun Zhou & Ji Wan & Xiangwei Gao & Xingqian Zhang & Samie R. Jaffrey & Shu-Bing Qian, 2015. "Dynamic m6A mRNA methylation directs translational control of heat shock response," Nature, Nature, vol. 526(7574), pages 591-594, October.
    5. Amedee des Georges & Vidya Dhote & Lauriane Kuhn & Christopher U. T. Hellen & Tatyana V. Pestova & Joachim Frank & Yaser Hashem, 2015. "Structure of mammalian eIF3 in the context of the 43S preinitiation complex," Nature, Nature, vol. 525(7570), pages 491-495, September.
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    1. Fajin Li & Jianhuo Fang & Yifan Yu & Sijia Hao & Qin Zou & Qinglin Zeng & Xuerui Yang, 2023. "Reanalysis of ribosome profiling datasets reveals a function of rocaglamide A in perturbing the dynamics of translation elongation via eIF4A," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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