The nonsense-mediated mRNA decay SMG-1 kinase is regulated by large-scale conformational changes controlled by SMG-8.
Nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance pathway that regulates the degradation of mRNAs harboring premature translation termination codons. NMD also influences the expression of many physiological transcripts. SMG-1 is a large kinase essential to NMD that phosphorylates Upf1, which seems to be the definitive signal triggering mRNA decay. However, the regulation of the kinase activity of SMG-1 remains poorly understood. Here, we reveal the three-dimensional architecture of SMG-1 in complex with SMG-8 and SMG-9, and the structural mechanisms regulating SMG-1 kinase. A bent arm comprising a long region of HEAT (huntington, elongation factor 3, a subunit of PP2A and TOR1) repeats at the N terminus of SMG-1 functions as a scaffold for SMG-8 and SMG-9, and projects from the C-terminal core containing the phosphatidylinositol 3-kinase domain. SMG-9 seems to control the activity of SMG-1 indirectly through the recruitment of SMG-8 to the N-terminal HEAT repeat region of SMG-1. Notably, SMG-8 binding to the SMG-1:SMG-9 complex specifically down-regulates the kinase activity of SMG-1 on Upf1 without contacting the catalytic domain. Assembly of the SMG-1:SMG-8:SMG-9 complex induces a significant motion of the HEAT repeats that is signaled to the kinase domain. Thus, large-scale conformational changes induced by SMG-8 after SMG-9-mediated recruitment tune SMG-1 kinase activity to modulate NMD.
Centro de Investigaciones Biológicas (CIB), Spanish National Research Council (Consejo Superior de Investigaciones Científicas, CSIC), 28040 Madrid, Spain.
Ernesto
E
Arias-Palomo
Akio
A
Yamashita
Israel S
IS
Fernández
Rafael
R
Núñez-Ramírez
Yumi
Y
Bamba
Natsuko
N
Izumi
Shigeo
S
Ohno
Oscar
O
Llorca
D057809:HEK293 Cells; D006367:HeLa Cells; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins; D008958:Models, Molecular; D019869:Phosphatidylinositol 3-Kinases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D011494:Protein Kinases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D055503:Protein Multimerization / Q000502:physiology; D017346:Protein Serine-Threonine Kinases; D020836:Protein Structure, Quaternary; D020365:RNA Helicases; D011994:Recombinant Proteins / Q000378:metabolism; D015534:Trans-Activators / Q000378:metabolism
D047908:Intracellular Signaling Peptides and Proteins; D019869:Phosphatidylinositol 3-Kinases; D011494:Protein Kinases; D017346:Protein Serine-Threonine Kinases; D020365:RNA Helicases; D011994:Recombinant Proteins; D015534:Trans-Activators; C555938:SMG8 protein, human; C514704:SMG1 protein, human; C101828:UPF1 protein, human
Nucleic Acids Res. 2011 Jan;39(1):347-58
20817927
Mol Cell. 2010 Jan 29;37(2):211-22
20122403
Curr Opin Cell Biol. 2009 Jun;21(3):394-402
19359157
Biochim Biophys Acta. 2005 Dec 30;1754(1-2):305-15
16289965
Nat Protoc. 2008;3(6):977-90
18536645
Sci Signal. 2010 Apr 06;3(116):ra27
20371770
J Biol Chem. 2007 Mar 16;282(11):7799-808
17229728
EMBO J. 2008 Feb 6;27(3):471-81
18256698
Structure. 2005 Feb;13(2):243-55
15698568
Nat Rev Genet. 2008 Sep;9(9):699-712
18679436
Structure. 2008 Mar;16(3):468-77
18334221
J Mol Biol. 2005 Apr 22;348(1):139-49
15808859
J Struct Biol. 1999 Dec 1;128(1):82-97
10600563
Genes Dev. 2009 May 1;23(9):1091-105
19417104
DNA Repair (Amst). 2004 Aug-Sep;3(8-9):883-7
15279773
J Biol Chem. 2010 Jan 8;285(2):1414-23
19893054
EMBO J. 2009 Oct 21;28(20):3067-73
19779456
Cell. 2003 Jan 24;112(2):151-5
12553904
Genes Dev. 2001 Sep 1;15(17):2215-28
11544179
Trends Cell Biol. 2008 Jul;18(7):315-21
18524595
Mol Cell. 2010 Aug 13;39(3):396-409
20691628
Mol Cell. 2006 May 19;22(4):511-9
16713581
Genes Dev. 2006 Feb 1;20(3):355-67
16452507
Nat Protoc. 2008;3(12):1941-74
19180078
Cell Mol Life Sci. 2010 Mar;67(5):677-700
19859661
Nature. 2010 Jan 7;463(7277):118-21
20023628
Nat Genet. 2004 Oct;36(10):1073-8
15448691