title: Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites.
abstract: Mammalian Quaking (QKI) and its Caenorhabditis elegans homolog, GLD-1 (defective in germ line development), are evolutionarily conserved RNA-binding proteins, which post-transcriptionally regulate target genes essential for developmental processes and myelination. We present X-ray structures of the STAR (signal transduction and activation of RNA) domain, composed of Qua1, K homology (KH), and Qua2 motifs of QKI and GLD-1 bound to high-affinity in vivo RNA targets containing YUAAY RNA recognition elements (RREs). The KH and Qua2 motifs of the STAR domain synergize to specifically interact with bases and sugar-phosphate backbones of the bound RRE. Qua1-mediated homodimerization generates a scaffold that enables concurrent recognition of two RREs, thereby plausibly targeting tandem RREs present in many QKI-targeted transcripts. Structure-guided mutations reduced QKI RNA-binding affinity in vitro and in vivo, and expression of QKI mutants in human embryonic kidney cells (HEK293) significantly decreased the abundance of QKI target mRNAs. Overall, our studies define principles underlying RNA target selection by STAR homodimers and provide insights into the post-transcriptional regulatory function of mammalian QKI proteins.
authors: Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
authors: Marianna
authors: M
authors: Teplova
authors: Markus
authors: M
authors: Hafner
authors: Dmitri
authors: D
authors: Teplov
authors: Katharina
authors: K
authors: Essig
authors: Thomas
authors: T
authors: Tuschl
authors: Dinshaw J
authors: DJ
authors: Patel
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D017173:Caenorhabditis elegans / Q000737:chemistry / Q000235:genetics; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D019281:Dimerization; D004926:Escherichia coli / Q000235:genetics; D005786:Gene Expression Regulation; D057809:HEK293 Cells; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D012313:RNA / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D029742:Caenorhabditis elegans Proteins; C094448:GLD-1 protein, C elegans; C490832:QKI protein, human; D016601:RNA-Binding Proteins; D012313:RNA
references: Science. 1964 Apr 17;144(3616):309-11
references: 14169723
references: Dev Growth Differ. 2003 Oct-Dec;45(5-6):449-62
references: 14706070
references: PLoS Genet. 2011 Jan 06;7(1):e1001269
references: 21253564
references: Cell Cycle. 2010 May 15;9(10):1929-33
references: 20495365
references: Adv Exp Med Biol. 2010;693:106-22
references: 21189689
references: Bioinformatics. 2009 May 1;25(9):1105-11
references: 19289445
references: Cell. 2010 Apr 2;141(1):129-41
references: 20371350
references: J Mol Biol. 2012 Nov 9;423(5):766-81
references: 22982292
references: Trends Genet. 1997 Dec;13(12):479-84
references: 9433137
references: Mol Cell. 2011 Aug 5;43(3):327-39
references: 21723170
references: Mol Cell. 2011 Aug 5;43(3):340-52
references: 21723171
references: Genet Res. 1988 Apr;51(2):95-102
references: 3410318
references: Genetics. 1995 Feb;139(2):579-606
references: 7713419
references: Methods Enzymol. 1997;276:523-30
references: 9048379
references: J Neurosci Res. 2008 Feb 1;86(2):233-42
references: 17787018
references: Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4233-8
references: 11917126
references: Mol Cell Biol. 1998 Aug;18(8):4863-71
references: 9671495
references: Nat Neurosci. 2005 Jan;8(1):27-33
references: 15568022
references: Nat Struct Mol Biol. 2011 Nov 13;18(12):1428-31
references: 22081015
references: Mol Cell Biol. 1997 Oct;17(10):5707-18
references: 9315629
references: EMBO J. 2011 Feb 2;30(3):533-45
references: 21169991
references: Genes Dev. 2012 Jan 1;26(1):43-53
references: 22215810
references: Nat Protoc. 2012 Mar 01;7(3):562-78
references: 22383036
references: J Biol Chem. 2010 Sep 10;285(37):28893-901
references: 20610388
references: Structure. 2010 Mar 10;18(3):377-89
references: 20223220
references: Acta Crystallogr D Biol Crystallogr. 2002 Oct;58(Pt 10 Pt 2):1772-9
references: 12351820
references: Genome Biol. 2011 Aug 18;12(8):R79
references: 21851591
references: Development. 2011 May;138(9):1783-94
references: 21447554
references: Methods Enzymol. 1997;276:307-26
references: 27754618
references: RNA. 2008 Dec;14(12):2580-96
references: 18978028
references: Dev Biol. 1996 Nov 25;180(1):165-83
references: 8948583
references: Nat Struct Mol Biol. 2005 Aug;12(8):691-8
references: 16041388
references: Adv Exp Med Biol. 2010;693:93-105
references: 21189688
references: Structure. 2011 Jul 13;19(7):930-44
references: 21742260
references: Trends Genet. 2008 Feb;24(2):94-101
references: 18192064
references: Biochim Biophys Acta. 2008 Aug;1779(8):486-94
references: 18590840
references: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
references: 20124702
references: Nat Struct Mol Biol. 2004 Jan;11(1):20-8
references: 14718919
references: Neuron. 2002 Dec 5;36(5):815-29
references: 12467586
references: J Biol Chem. 2008 Oct 17;283(42):28757-66
references: 18701464
references: Mol Cell. 2011 Dec 9;44(5):828-40
references: 22152485
references: Mol Cell. 1999 Oct;4(4):573-84
references: 10549289
references: Nat Struct Mol Biol. 2008 Dec;15(12):1343-51
references: 19043415
references: Genes Dev. 1995 Jun 15;9(12):1491-504
references: 7601353
references: Science. 2001 Nov 2;294(5544):1098-102
references: 11691992
references: Science. 2005 Sep 23;309(5743):2054-7
references: 16179478
references: J Mol Biol. 2005 Apr 29;348(2):265-79
references: 15811367
references: Nat Genet. 1996 Mar;12(3):260-5
references: 8589716
references: RNA. 2004 Sep;10(9):1449-58
references: 15273320