The Hierarchy of Exon-junction Complex Assembly by the Spliceosome Explains Key Features of Mammalian Nonsense-mediated MRNA Decay

Overview

Journal PLoS Biol

Specialty Biology

Date 2009 May 30

PMID 19478851

Citations 74

Authors

Niels H Gehring

Styliani Lamprinaki

Matthias W Hentze

Andreas E Kulozik

Affiliations

Soon will be listed here.

Abstract

Exon junction complexes (EJCs) link nuclear splicing to key features of mRNA function including mRNA stability, translation, and localization. We analyzed the formation of EJCs by the spliceosome, the physiological EJC assembly machinery. We studied a comprehensive set of eIF4A3, MAGOH, and BTZ mutants in complete or C-complex-arrested splicing reactions and identified essential interactions of EJC proteins during and after EJC assembly. These data establish that EJC deposition proceeds through a defined intermediate, the pre-EJC, as an ordered, sequential process that is coordinated by splicing. The pre-EJC consists of eIF4A3 and MAGOH-Y14, is formed before exon ligation, and provides a binding platform for peripheral EJC components that join after release from the spliceosome and connect the core structure with function. Specifically, we identified BTZ to bridge the EJC to the nonsense-mediated messenger RNA (mRNA) decay protein UPF1, uncovering a critical link between mRNP architecture and mRNA stability. Based on this systematic analysis of EJC assembly by the spliceosome, we propose a model of how a functional EJC is assembled in a strictly sequential and hierarchical fashion, including nuclear splicing-dependent and cytoplasmic steps.

Citing Articles

Trypanosomes lack a canonical EJC but possess an UPF1 dependent NMD-like pathway.

Gabiatti B, Freire E, Odenwald J, de Freitas Nascimento J, Holetz F, Carrington M PLoS One. 2025; 20(3):e0315659.

PMID: 40053537 PMC: 11888146. DOI: 10.1371/journal.pone.0315659.

The crosstalk between alternative splicing and circular RNA in cancer: pathogenic insights and therapeutic implications.

Hu H, Tang J, Wang H, Guo X, Tu C, Li Z Cell Mol Biol Lett. 2024; 29(1):142.

PMID: 39550559 PMC: 11568689. DOI: 10.1186/s11658-024-00662-x.

Nonsense-Mediated mRNA Decay in Human Health and Diseases: Current Understanding, Regulatory Mechanisms and Future Perspectives.

Behera A, Panigrahi G, Sahoo A Mol Biotechnol. 2024; .

PMID: 39264527 DOI: 10.1007/s12033-024-01267-7.

The RNA-binding protein EIF4A3 promotes axon development by direct control of the cytoskeleton.

Alsina F, Lupan B, Lin L, Musso C, Mosti F, Newman C Cell Rep. 2024; 43(9):114666.

PMID: 39182224 PMC: 11488691. DOI: 10.1016/j.celrep.2024.114666.

Exon-junction complex association with stalled ribosomes and slow translation-independent disassembly.

Bensaude O, Barbosa I, Morillo L, Dikstein R, Le Hir H Nat Commun. 2024; 15(1):4209.

PMID: 38760352 PMC: 11101648. DOI: 10.1038/s41467-024-48371-5.

References

Gehring N, Neu-Yilik G, Schell T, Hentze M, Kulozik A . Y14 and hUpf3b form an NMD-activating complex. Mol Cell. 2003; 11(4):939-49. DOI: 10.1016/s1097-2765(03)00142-4. View

Palacios I, Gatfield D, St Johnston D, Izaurralde E . An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay. Nature. 2004; 427(6976):753-7. DOI: 10.1038/nature02351. View

Shu M, Steitz J . Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1. Science. 2001; 293(5536):1836-9. DOI: 10.1126/science.1062786. View

Le Hir H, Moore M, Maquat L . Pre-mRNA splicing alters mRNP composition: evidence for stable association of proteins at exon-exon junctions. Genes Dev. 2000; 14(9):1098-108. PMC: 316578. View

Chamieh H, Ballut L, Bonneau F, Le Hir H . NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity. Nat Struct Mol Biol. 2007; 15(1):85-93. DOI: 10.1038/nsmb1330. View

Conti E, Izaurralde E . Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. Curr Opin Cell Biol. 2005; 17(3):316-25. DOI: 10.1016/j.ceb.2005.04.005. View

Chang Y, Imam J, Wilkinson M . The nonsense-mediated decay RNA surveillance pathway. Annu Rev Biochem. 2007; 76:51-74. DOI: 10.1146/annurev.biochem.76.050106.093909. View

Gozani O, Patton J, REED R . A novel set of spliceosome-associated proteins and the essential splicing factor PSF bind stably to pre-mRNA prior to catalytic step II of the splicing reaction. EMBO J. 1994; 13(14):3356-67. PMC: 395233. DOI: 10.1002/j.1460-2075.1994.tb06638.x. View

Le Hir H, Gatfield D, Izaurralde E, Moore M . The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. EMBO J. 2001; 20(17):4987-97. PMC: 125616. DOI: 10.1093/emboj/20.17.4987. View

10.

Andersen C, Ballut L, Johansen J, Chamieh H, Nielsen K, Oliveira C . Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Science. 2006; 313(5795):1968-72. DOI: 10.1126/science.1131981. View

11.

Zhang Z, Krainer A . Splicing remodels messenger ribonucleoprotein architecture via eIF4A3-dependent and -independent recruitment of exon junction complex components. Proc Natl Acad Sci U S A. 2007; 104(28):11574-9. PMC: 1913901. DOI: 10.1073/pnas.0704946104. View

12.

Shi H, Xu R . Crystal structure of the Drosophila Mago nashi-Y14 complex. Genes Dev. 2003; 17(8):971-6. PMC: 196043. DOI: 10.1101/gad.260403. View

13.

Fribourg S, Gatfield D, Izaurralde E, Conti E . A novel mode of RBD-protein recognition in the Y14-Mago complex. Nat Struct Biol. 2003; 10(6):433-9. DOI: 10.1038/nsb926. View

14.

Ideue T, Sasaki Y, Hagiwara M, Hirose T . Introns play an essential role in splicing-dependent formation of the exon junction complex. Genes Dev. 2007; 21(16):1993-8. PMC: 1948854. DOI: 10.1101/gad.1557907. View

15.

Degot S, Regnier C, Wendling C, Chenard M, Rio M, Tomasetto C . Metastatic Lymph Node 51, a novel nucleo-cytoplasmic protein overexpressed in breast cancer. Oncogene. 2002; 21(28):4422-34. DOI: 10.1038/sj.onc.1205611. View

16.

REED R . The organization of 3' splice-site sequences in mammalian introns. Genes Dev. 1989; 3(12B):2113-23. DOI: 10.1101/gad.3.12b.2113. View

17.

Le Hir H, Nott A, Moore M . How introns influence and enhance eukaryotic gene expression. Trends Biochem Sci. 2003; 28(4):215-20. DOI: 10.1016/S0968-0004(03)00052-5. View

18.

Bono F, Ebert J, Unterholzner L, Guttler T, Izaurralde E, Conti E . Molecular insights into the interaction of PYM with the Mago-Y14 core of the exon junction complex. EMBO Rep. 2004; 5(3):304-10. PMC: 1299003. DOI: 10.1038/sj.embor.7400091. View

19.

Gehring N, Lamprinaki S, Kulozik A, Hentze M . Disassembly of exon junction complexes by PYM. Cell. 2009; 137(3):536-48. DOI: 10.1016/j.cell.2009.02.042. View

20.

Moore M . From birth to death: the complex lives of eukaryotic mRNAs. Science. 2005; 309(5740):1514-8. DOI: 10.1126/science.1111443. View