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A UPF3-mediated regulatory switch that maintains RNA surveillance

Nature Structural & Molecular Biology volume 16, pages 747–753 (2009)Cite this article

Abstract

Nonsense-mediated decay (NMD) is an RNA decay pathway that downregulates aberrant mRNAs and a subset of normal mRNAs. The regulation of NMD is poorly understood. Here we identify a regulatory mechanism acting on two related UPF (up-frameshift) factors crucial for NMD: UPF3A and UPF3B. This regulatory mechanism, which reduces the level of UPF3A in response to the presence of UPF3B, is relieved in individuals harboring UPF3B mutations, leading to strongly increased steady-state levels of UPF3A. UPF3A compensates for the loss of UPF3B by regulating several NMD target transcripts, but it can also impair NMD, as it competes with the stronger NMD activator UPF3B for binding to the essential NMD factor UPF2. This deleterious effect of UPF3A protein is prevented by its destabilization using a conserved UPF3B-dependent mechanism. Together, our results suggest that UPF3A levels are tightly regulated by a post-transcriptional switch to maintain appropriate levels of NMD substrates in cells containing different levels of UPF3B.

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Figure 1: Upregulation of UPF3A in response to depletion or loss of UPF3B.
Figure 2: UPF3A protein is destabilized by UPF3B via an NMD-independent mechanism.
Figure 3: UPF3B requires its UPF2 binding domain to destabilize UPF3A.
Figure 4: UPF3A is destabilized because it competes with UPF3B for binding to UPF2.
Figure 5: UPF3A functionally compensates and competes with UPF3B.
Figure 6: A model delineating how UPF3A and UPF3B both compete and functionally compensate for each other.

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Acknowledgements

We thank J. Lykke-Andersen (University of Colorado) for several independent aliquots of antibodies against UPF1, UPF2, UPF3A and UPF3B, as well as the MS2-UPF1 and MS2-UPF2 constructs; L. Maquat (University of Rochester) for the T7-UPF2 constructs; M. Hentze (European Molecular Biology Labortaory, Heidelberg), A. Kulozik (University of Heidelberg,) and N. Gehring (University of Heidelberg) for human UPF3A and UPF3B constructs; M. Moore (University of Massachusetts) and A.-B. Shyu (University of Texas-Houston) for their polysome protocols; C. Shoubridge and L. Vandeleur (University of Adelaide) for culturing Epstein-Barr virus–immortalized B cell lines; and C. Schwartz and A. Srivastava (JC Self Research Institute of Human Genetics) for sharing the lymphoblastoid cell lines from family 1. Finally, we thank the many investigators whose publications inspired this work; we apologize that there is insufficient space to acknowledge them and reference all of their relevant publications. This work was funded by the US National Institutes of Health grant GM058595 (M.F.W.) and an Australian National Health and Medical Research Council grant (J.G.).

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  1. Miles F Wilkinson

    Present address: Present address: Reproductive Medicine Department, University of California, San Diego, California, USA.,

Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA

    Wai-Kin Chan, Angela D Bhalla, Lulu Huang & Miles F Wilkinson

  2. The Genes & Development Graduate Program, The University of Texas Graduate School of Biomedical Sciences at Houston, Texas, USA

    Angela D Bhalla & Lulu Huang

  3. Centre de Génétique Moléculaire, CNRS-UPR2167, Gif-sur-Yvette, France

    Hervé Le Hir

  4. SA Pathology, Women's and Children's Hospital, Adelaide, South Australia, Australia

    Lam Son Nguyen & Jozef Gécz

  5. Department of Pediatrics, University of Adelaide, Adelaide, South Australia, Australia

    Jozef Gécz

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Contributions

W.-K.C. and M.F.W. designed the experiments; L.S.N. and J.G. provided samples for the experiments; H.L.H. produced recombinant proteins and performed in vitro binding assays; W.-K.C. carried out the experiments with the help of A.D.B. and L.H; W.-K.C. and M.F.W. wrote the manuscript with the help of L.S.N., J.G., A.D.B. and L.H.

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Correspondence to Miles F Wilkinson.

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Chan, WK., Bhalla, A., Le Hir, H. et al. A UPF3-mediated regulatory switch that maintains RNA surveillance. Nat Struct Mol Biol 16, 747–753 (2009). https://doi.org/10.1038/nsmb.1612

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