Backbone-independent nucleic acid binding by splicing factor SUP-12 reveals key aspects of molecular recognition

Samir Amrane; Karine Rebora; Ilyass Zniber; Denis Dupuy; Cameron D Mackereth

doi:10.1038/ncomms5595

Backbone-independent nucleic acid binding by splicing factor SUP-12 reveals key aspects of molecular recognition

Nat Commun. 2014 Sep 3:5:4595. doi: 10.1038/ncomms5595.

Authors

Samir Amrane¹, Karine Rebora¹, Ilyass Zniber¹, Denis Dupuy¹, Cameron D Mackereth¹

Affiliation

¹ 1] Institut Européen de Chimie et Biologie, IECB, Univ. Bordeaux, 2 rue Robert Escarpit, F-33607 Pessac, France [2] Inserm, U869, ARNA Laboratory, 146 rue Léo Saignat, F-33076 Bordeaux, France.

PMID: 25183497
DOI: 10.1038/ncomms5595

Abstract

Cellular differentiation is frequently accompanied by alternative splicing, enabled by the expression of tissue-specific factors which bind to pre-mRNAs and regulate exon choice. During Caenorhabditis elegans development, muscle-specific expression of the splicing factor SUP-12, together with a member of the Fox-1 family of splicing proteins, generates a functionally distinct isoform of the fibroblast growth factor receptor EGL-15. Using a combination of NMR spectroscopy and isothermal titration calorimetry, we determined the mode of nucleic acid binding by the RNA recognition motif domain of SUP-12. The calculated structures provide the first atomic details of RNA and DNA binding by the family of proteins that include SUP-12, RBM24, RBM38/RNPC1, SEB-4 and XSeb4R. This information was further used to design strategic mutations to probe the interaction with ASD-1 and to quantitatively perturb splicing in vivo.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alternative Splicing*
Amino Acid Sequence
Animals
Base Sequence
Caenorhabditis elegans / genetics*
Caenorhabditis elegans / growth & development
Caenorhabditis elegans / metabolism
Caenorhabditis elegans Proteins / chemistry*
Caenorhabditis elegans Proteins / genetics
Caenorhabditis elegans Proteins / metabolism
Calorimetry
Cell Differentiation
Crystallography, X-Ray
Escherichia coli / genetics
Escherichia coli / metabolism
Gene Expression
Magnetic Resonance Spectroscopy
Models, Molecular
Molecular Sequence Data
Protein Binding
RNA / chemistry*
RNA / metabolism
RNA-Binding Proteins / chemistry*
RNA-Binding Proteins / genetics
RNA-Binding Proteins / metabolism
Receptors, Fibroblast Growth Factor / chemistry*
Receptors, Fibroblast Growth Factor / genetics
Receptors, Fibroblast Growth Factor / metabolism
Recombinant Proteins

Substances

Asd-1 protein, C elegans
Caenorhabditis elegans Proteins
EGL-15 protein, C elegans
FOX-1 protein, C elegans
RNA-Binding Proteins
Receptors, Fibroblast Growth Factor
Recombinant Proteins
Sup-12 protein, C elegans
RNA

Associated data

PDB/4CH0
PDB/4CH1
PDB/4CIO