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Gene regulation by translational inhibition is determined by Dicer partnering proteins

Nature Plants volume 1, Article number: 14027 (2015) Cite this article

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Abstract

MicroRNAs (miRNAs) are small regulatory RNAs produced by Dicer proteins that regulate gene expression in development and adaptive responses to the environment1–4. In animals, the degree of base pairing between a miRNA and its target messenger RNA seems to determine whether the regulation occurs through cleavage or translation inhibition1. In contrast, the selection of regulatory mechanisms is independent of the degree of mismatch between a plant miRNA and its target transcript5. However, the components and mechanism(s) that determine whether a plant miRNA ultimately regulates its targets by guiding cleavage or translational inhibition are unknown6. Here we show that the form of regulatory action directed by a plant miRNA is determined by DRB2, a DICER-LIKE1 (DCL1) partnering protein. The dependence of DCL1 on DRB1 for miRNA biogenesis is well characterized7–9, but we show that it is only required for miRNA-guided transcript cleavage. We found that DRB2 determines miRNA-guided translational inhibition and represses DRB1 expression, thereby allowing the active selection of miRNA regulatory action. Furthermore, our results reveal that the core silencing proteins ARGONAUTE1 (AGO1) and SERRATE (SE) are highly regulated by miRNA-guided translational inhibition. DRB2 has been remarkably conserved throughout plant evolution, raising the possibility that translational repression is the ancient form of miRNA-directed gene regulation in plants, and that Dicer partnering proteins, such as human TRBP, might play a similar role in other eukaryotic systems.

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Figure 1: Expression patterns of DRB1 and DRB2 in wild-type plants, and miRNA target expression in drb1 and drb2.
Figure 2: Accumulation of miRNA target mRNAs and proteins in the shoot apex of drb1 and drb2.
Figure 3: Regulation of miRNA targets in floral tissue of drb1 and drb2.
Figure 4: Translational and post-translational regulation of DRB1 and DCL1, and evolutionary conservation of DRB1 and DRB2 proteins.

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Acknowledgements

We thank K. Nakasugi for deep sequencing data analysis and D. Barton for GUS imaging, A. Tay for statistical analysis of proteomics data, A.V.R. Ribeiro for graphical assistance and T. Roberts and R. Hellens for critical reading of our manuscript. We acknowledge M. Raftery, L. Zhong and S. Liu Lau for their maintenance of the orbitrap mass spectrometers at the UNSW Bioanalytical Mass Spectrometry Facility. PMW acknowledges support as a Federation Fellow from the Australian Research Council and contributions from the University of Sydney, CSIRO and QUT. M.R.W. acknowledges support from the Australian Research Council, the Australian Federal Government EIF Super Science Scheme and the University of New South Wales. G.H-S. was the recipient of an Australian Research Council Australian Postdoctoral Research Fellowship and funds from the University of New South Wales ECR Scheme. R.S.R. was the recipient of an Australian Postgraduate Award.

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Authors and Affiliations

  1. School of Biological Sciences, University of Sydney, Macleay Building A12, Sydney, 2006, New South Wales, Australia

    Rodrigo S. Reis & Peter M. Waterhouse

  2. Faculty of Agriculture and Environment, University of Sydney, Eveleigh, New South Wales, Australia

    Rodrigo S. Reis

  3. Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, New South Wales, Australia

    Gene Hart-Smith & Marc R. Wilkins

  4. School of Environmental and Life Sciences, University of Newcastle, Callaghan, 2308, New South Wales, Australia

    Andrew L. Eamens

  5. Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, 4001, Queensland, Australia

    Peter M. Waterhouse

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  1. Rodrigo S. Reis
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Contributions

G.H-S., R.S.R. and M.R.W. conceived and designed the proteomics experiments; G.H-S. performed the mass spectrometry experiments and data analysis; R.S.R., A.L.E. and P.M.W. conceived all other experiments; A.L.E. performed miR863 northern blots; R.S.R. designed and performed all other experiments; R.S.R. and P.M.W. interpreted the data; R.S.R., A.L.E. and P.M.W. wrote the manuscript.

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Correspondence to Rodrigo S. Reis or Peter M. Waterhouse.

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Reis, R., Hart-Smith, G., Eamens, A. et al. Gene regulation by translational inhibition is determined by Dicer partnering proteins. Nature Plants 1, 14027 (2015). https://doi.org/10.1038/nplants.2014.27

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