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Non-optimal codon usage affects expression, structure and function of clock protein FRQ

Nature volume 495, pages 111–115 (2013)Cite this article

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Abstract

Codon-usage bias has been observed in almost all genomes and is thought to result from selection for efficient and accurate translation of highly expressed genes1,2,3. Codon usage is also implicated in the control of transcription, splicing and RNA structure4,5,6. Many genes exhibit little codon-usage bias, which is thought to reflect a lack of selection for messenger RNA translation. Alternatively, however, non-optimal codon usage may be of biological importance. The rhythmic expression and the proper function of the Neurospora FREQUENCY (FRQ) protein are essential for circadian clock function. Here we show that, unlike most genes in Neurospora, frq exhibits non-optimal codon usage across its entire open reading frame. Optimization of frq codon usage abolishes both overt and molecular circadian rhythms. Codon optimization not only increases FRQ levels but, unexpectedly, also results in conformational changes in FRQ protein, altered FRQ phosphorylation profile and stability, and impaired functions in the circadian feedback loops. These results indicate that non-optimal codon usage of frq is essential for its circadian clock function. Our study provides an example of how non-optimal codon usage functions to regulate protein expression and to achieve optimal protein structure and function.

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Figure 1: Codon optimization of frq results in high FRQ expression levels and loss of circadian rhythmicities.
Figure 2: FRQ activities in circadian feedback loops are impaired in the frq codon-optimized strains.
Figure 3: FRQ protein in the codon-optimized strains is less stable and more sensitive to trypsin digestion.
Figure 4: Codon optimization of the middle region of FRQ impairs FRQ phosphorylation and stabilizes FRQ.

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Acknowledgements

We thank H. Yuan and Q. Ye for technical assistance, J. Dunlap for providing the pfrq-luc-I construct and M. Rosbash for suggesting the temperature experiments. We apologize to those colleagues whose studies we could not cite owing to space limitations. This work was supported by grants from the National Institutes of Health to Y.L. (GM068496 & GM062591) and M.S.S. (GM47498), and from the Welch Foundation (I-1560) to Y.L.

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  1. Jinhu Guo

    Present address: Present address: State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,

Authors and Affiliations

  1. Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA,

    Mian Zhou, Jinhu Guo, Joonseok Cha, Michael Chae & Yi Liu

  2. National Institute of Biological Sciences, 7 Life Science Park Road, Changping District, Beijing 102206, China,

    She Chen

  3. Departments of Neuroscience and Cell Biology and Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, 77555-0620, Texas, USA

    Jose M. Barral

  4. Department of Biology, Texas A&M University, College Station, 77843-3258, Texas, USA

    Matthew S. Sachs

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Contributions

Y.L., M.Z. and J.G. designed the research. M.Z., J.G., J.C., M.C., S.C. and J.M.B. performed experiments. M.Z., J.G., J.M.B., M.S.S. and Y.L. analysed the results. Y.L. and M.Z. wrote the paper; J.G., J.M.B. and M.S.S. edited and commented on the manuscript.

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Correspondence to Yi Liu.

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Zhou, M., Guo, J., Cha, J. et al. Non-optimal codon usage affects expression, structure and function of clock protein FRQ. Nature 495, 111–115 (2013). https://doi.org/10.1038/nature11833

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