Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Non-optimal codon usage is a mechanism to achieve circadian clock conditionality

Nature volume 495, pages 116–120 (2013)Cite this article

Subjects

Abstract

Circadian rhythms are oscillations in biological processes that function as a key adaptation to the daily rhythms of most environments. In the model cyanobacterial circadian clock system, the core oscillator proteins are encoded by the gene cluster kaiABC1. Genes with high expression and functional importance, such as the kai genes, are usually encoded by optimal codons, yet the codon-usage bias of the kaiBC genes is not optimized for translational efficiency. We discovered a relationship between codon usage and a general property of circadian rhythms called conditionality; namely, that endogenous rhythmicity is robustly expressed under some environmental conditions but not others2. Despite the generality of circadian conditionality, however, its molecular basis is unknown for any system. Here we show that in the cyanobacterium Synechococcus elongate, non-optimal codon usage was selected as a post-transcriptional mechanism to switch between circadian and non-circadian regulation of gene expression as an adaptive response to environmental conditions. When the kaiBC sequence was experimentally optimized to enhance expression of the KaiB and KaiC proteins, intrinsic rhythmicity was enhanced at cool temperatures that are experienced by this organism in its natural habitat. However, fitness at those temperatures was highest in cells in which the endogenous rhythms were suppressed at cool temperatures as compared with cells exhibiting high-amplitude rhythmicity. These results indicate natural selection against circadian systems in cyanobacteria that are intrinsically robust at cool temperatures. Modulation of circadian amplitude is therefore crucial to its adaptive significance3. Moreover, these results show the direct effects of codon usage on a complex phenotype and organismal fitness. Our work also challenges the long-standing view of directional selection towards optimal codons4,5,6,7, and provides a key example of natural selection against optimal codons to achieve adaptive responses to environmental changes.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Non-optimal codon usage of cyanobacterial clock genes.
Figure 2: Conditional circadian phenotypes of the kai -optimized strains.
Figure 3: Kai protein expression and circadian regulation of cells expressing wild-type or optimized versions of kaiBC.
Figure 4: Optimizing the kaiBC sequence causes slower growth rate at cool temperatures.

Similar content being viewed by others

References

  1. Ishiura, M. et al. Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria. Science 281, 1519–1523 (1998)

    Article  CAS  ADS  Google Scholar 

  2. Njus, D., McMurry, L. & Hastings, J. W. Conditionality of circadian rhythmicity: synergistic action of light and temperature. J. Comp. Physiol. 117, 335–344 (1977)

    Article  Google Scholar 

  3. Woelfle, M. A., Ouyang, Y., Phanvijhitsiri, K. & Johnson, C. H. The adaptive value of circadian clocks: an experimental assessment in cyanobacteria. Curr. Biol. 14, 1481–1486 (2004)

    Article  CAS  Google Scholar 

  4. Drummond, D. A. & Wilke, C. O. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134, 341–352 (2008)

    Article  CAS  Google Scholar 

  5. Bulmer, M. The selection-mutation-drift theory of synonymous codon usage. Genetics 129, 897–907 (1991)

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Plotkin, J. B. & Kudla, G. Synonymous but not the same: the causes and consequences of codon bias. Nature Rev. Genet. 12, 32–42 (2011)

    Article  CAS  Google Scholar 

  7. Shah, P. & Gilchrist, M. A. Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift. Proc. Natl Acad. Sci. USA 108, 10231–10236 (2011)

    Article  CAS  ADS  Google Scholar 

  8. Eyre-Walker, A. & Bulmer, M. Reduced synonymous substitution rate at the start of enterobacterial genes. Nucleic Acids Res. 21, 4599–4603 (1993)

    Article  CAS  Google Scholar 

  9. Akashi, H. Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136, 927–935 (1994)

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Shah, P. & Gilchrist, M. A. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias. PLoS Genet. 6, e1001128 (2010)

    Article  Google Scholar 

  11. Zhou, T., Weems, M. & Wilke, C. O. Translationally optimal codons associate with structurally sensitive sites in proteins. Mol. Biol. Evol. 26, 1571–1580 (2009)

    Article  CAS  Google Scholar 

  12. Ikemura, T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 151, 389–409 (1981)

    Article  CAS  Google Scholar 

  13. Sharp, P. M. & Li, W. H. The codon adaptation index—a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15, 1281–1295 (1987)

    Article  CAS  ADS  Google Scholar 

  14. Lynn, D. J., Singer, G. A. & Hickey, D. A. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res. 30, 4272–4277 (2002)

    Article  CAS  Google Scholar 

  15. Paul, S., Bag, S. K., Das, S., Harvill, E. T. & Dutta, C. Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes. Genome Biol. 9, R70 (2008)

    Article  Google Scholar 

  16. Ouyang, Y., Andersson, C. R., Kondo, T., Golden, S. S. & Johnson, C. H. Resonating circadian clocks enhance fitness in cyanobacteria. Proc. Natl Acad. Sci. USA 95, 8660–8664 (1998)

    Article  CAS  ADS  Google Scholar 

  17. Liu, Y. et al. Circadian orchestration of gene expression in cyanobacteria. Genes Dev. 9, 1469–1478 (1995)

    Article  CAS  Google Scholar 

  18. Ito, H. et al. Cyanobacterial daily life with Kai-based circadian and diurnal genome-wide transcriptional control in Synechococcus elongatus. Proc. Natl Acad. Sci. USA 106, 14168–14173 (2009)

    Article  CAS  ADS  Google Scholar 

  19. Vijayan, V., Zuzow, R. & O’Shea, E. K. Oscillations in supercoiling drive circadian gene expression in cyanobacteria. Proc. Natl Acad. Sci. USA 106, 22564–22568 (2009)

    Article  CAS  ADS  Google Scholar 

  20. Vijayan, V., Jain, I. H. & O’Shea, E. K. A high resolution map of a cyanobacterial transcriptome. Genome Biol. 12, R47 (2011)

    Article  Google Scholar 

  21. Woelfle, M. A., Xu, Y., Qin, X. & Johnson, C. H. Circadian rhythms of superhelical status of DNA in cyanobacteria. Proc. Natl Acad. Sci. USA 104, 18819–18824 (2007)

    Article  CAS  ADS  Google Scholar 

  22. Kudla, G., Murray, A. W., Tollervey, D. & Plotkin, J. B. Coding-sequence determinants of gene expression in Escherichia coli. Science 324, 255–258 (2009)

    Article  CAS  ADS  Google Scholar 

  23. Tuller, T., Waldman, Y. Y., Kupiec, M. & Ruppin, E. Translation efficiency is determined by both codon bias and folding energy. Proc. Natl Acad. Sci. USA 107, 3645–3650 (2010)

    Article  CAS  ADS  Google Scholar 

  24. Gu, W., Zhou, T. & Wilke, C. O. A universal trend of reduced mRNA stability near translation-initiation site in prokaryotes and eukaryotes. PLOS Comput. Biol. 6, e1000664 (2010)

    Article  ADS  Google Scholar 

  25. Zhou, M. et al. Non-optimal codon usage affects expression, structure and function of clock protein FRQ. Naturehttp://dx.doi.org/10.1038/nature11833 (this issue)

  26. Pittendrigh, C. S. On temperature independence in the clock system controlling emergence time in Drosophila. Proc. Natl Acad. Sci. USA 40, 1018–1029 (1954)

    Article  CAS  ADS  Google Scholar 

  27. Kondo, T. et al. Circadian rhythms in prokaryotes: luciferase as a reporter of circadian gene expression in cyanobacteria. Proc. Natl Acad. Sci. USA 90, 5672–5676 (1993)

    Article  CAS  ADS  Google Scholar 

  28. Xu, Y., Mori, T. & Johnson, C. H. Cyanobacterial circadian clockwork: roles of KaiA, KaiB and the kaiBC promoter in regulating KaiC. EMBO J. 22, 2117–2126 (2003)

    Article  CAS  Google Scholar 

  29. Nakajima, M., Ito, H. & Kondo, T. In vitro regulation of circadian phosphorylation rhythm of cyanobacterial clock protein KaiC by KaiA and KaiB. FEBS Lett. 584, 898–902 (2010)

    Article  CAS  Google Scholar 

  30. Konigsberg, W. & Godson, G. N. Evidence for use of rare codons in the dnaG gene and other regulatory genes of Escherichia coli. Proc. Natl Acad. Sci. USA 80, 687–691 (1983)

    Article  CAS  ADS  Google Scholar 

  31. Liu, Y., Garceau, N. Y., Loros, J. J. & Dunlap, J. C. Thermally regulated translational control of FRQ mediates aspects of temperature responses in the Neurospora circadian clock. Cell 89, 477–486 (1997)

    Article  CAS  Google Scholar 

  32. Sharp, P. M. & Li, W. H. An evolutionary perspective on synonymous codon usage in unicellular organisms. J. Mol. Evol. 24, 28–38 (1986)

    Article  CAS  ADS  Google Scholar 

  33. Schuster, P., Fontana, W., Stadler, P. F. & Hofacker, I. L. From sequences to shapes and back: a case study in RNA secondary structures. Proc. R. Soc. Lond. B 255, 279–284 (1994)

    Article  CAS  ADS  Google Scholar 

  34. Bustos, S. A. & Golden, S. S. Expression of the psbDII gene in Synechococcus sp. strain PCC 7942 requires sequences downstream of the transcription start site. J. Bacteriol. 173, 7525–7533 (1991)

    Article  CAS  Google Scholar 

  35. Xu, Y., Mori, T. & Johnson, C. H. Circadian clock-protein expression in cyanobacteria: rhythms and phase setting. EMBO J. 19, 3349–3357 (2000)

    Article  CAS  Google Scholar 

  36. Xu, Y. et al. Intramolecular regulation of phosphorylation status of the circadian clock protein KaiC. PLoS ONE 4, e7509 (2009)

    Article  ADS  Google Scholar 

  37. Izumo, M., Johnson, C. H. & Yamazaki, S. Circadian gene expression in mammalian fibroblasts revealed by real-time luminescence reporting: temperature compensation and damping. Proc. Natl Acad. Sci. USA 100, 16089–16094 (2003)

    Article  CAS  ADS  Google Scholar 

Download references

Acknowledgements

We are grateful for the suggestions of M. Woelfle and the technical assistance of D. Zelli and C. Chintanaphol. This research was supported by grants from the National Institute of General Medical Science to C.H.J. (R01 GM067152 and R01 GM088595) and to Y.L. (GM068496 and GM062591), the Welch Foundation (I-1560) to Y.L., and the National Science Foundation (DEB-0844968) and the Searle Scholars Program to A.R. P.S. acknowledges support from a Burroughs Wellcome Fund Career Award and a David & Lucille Packard Foundation Fellowship awarded to Joshua B. Plotkin.

Author information

Authors and Affiliations

  1. Department of Biological Sciences, Vanderbilt University, Nashville, 37235, Tennessee, USA

    Yao Xu, Peijun Ma, Antonis Rokas & Carl Hirschie Johnson

  2. Department of Biology, University of Pennsylvania, Philadelphia, 19104, Pennsylvania, USA

    Premal Shah

  3. Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, 75390, Texas, USA

    Yi Liu

Authors
  1. Yao Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Peijun Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Premal Shah
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Antonis Rokas
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yi Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Carl Hirschie Johnson
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Y.X. and P.M. collected data; Y.X., P.M. and Y.L. analysed the experimental data; Y.X., P.S. and A.R. analysed the bioinformatic data; Y.L. and C.H.J. designed the original conceptual basis for the study; Y.X. and C.H.J. designed the experimental bases for the study; Y.X., P.S. and C.H.J. wrote the manuscript. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Carl Hirschie Johnson.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-7 and Supplementary Tables 1-10. (PDF 1629 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Xu, Y., Ma, P., Shah, P. et al. Non-optimal codon usage is a mechanism to achieve circadian clock conditionality. Nature 495, 116–120 (2013). https://doi.org/10.1038/nature11942

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature11942

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing