title: The Signature of the Five-Stranded vRRM Fold Defined by Functional, Structural and Computational Analysis of the hnRNP L Protein.
abstract: The RNA recognition motif (RRM) is the far most abundant RNA binding domain. In addition to the typical β1α1β2β3α2β4 fold, various sub-structural elements have been described and reportedly contribute to the high functional versatility of RRMs. The heterogeneous nuclear ribonucleoprotein L (hnRNP L) is a highly abundant protein of 64 kDa comprising four RRM domains. Involved in many aspects of RNA metabolism, hnRNP L specifically binds to RNAs containing CA repeats or CA-rich clusters. However, a comprehensive structural description of hnRNP L including its sub-structural elements is missing. Here, we present the structural characterization of the RRM domains of hnRNP L and demonstrate their function in repressing exon 4 of SLC2A2. By comparison of the sub-structural elements between the two highly similar paralog families of hnRNP L and PTB, we defined signatures underlying interacting C-terminal coils (ICCs), the RRM34 domain interaction and RRMs with a C-terminal fifth β-strand, a variation we denoted vRRMs. Furthermore, computational analysis revealed new putative ICC-containing RRM families and allowed us to propose an evolutionary scenario explaining the origins of the ICC and fifth β-strand sub-structural extensions. Our studies provide insights of domain requirements in alternative splicing mediated by hnRNP L and molecular descriptions for the sub-structural elements. In addition, the analysis presented may help to classify other abundant RRM extensions and to predict structure-function relationships.
authors.affiliation: Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
authors.forename: Markus
authors.initials: M
authors.lastname: Blatter
authors.affiliation: International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland.
authors.forename: Stanislaw
authors.initials: S
authors.lastname: Dunin-Horkawicz
authors.affiliation: Institute of Biochemistry, Justus Liebig University of Giessen, 35392 Giessen, Germany.
authors.forename: Inna
authors.initials: I
authors.lastname: Grishina
authors.affiliation: Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
authors.forename: Christophe
authors.initials: C
authors.lastname: Maris
authors.affiliation: Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
authors.forename: Stephane
authors.initials: S
authors.lastname: Thore
authors.affiliation: Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
authors.forename: Timm
authors.initials: T
authors.lastname: Maier
authors.affiliation: Institute of Biochemistry, Justus Liebig University of Giessen, 35392 Giessen, Germany.
authors.forename: Albrecht
authors.initials: A
authors.lastname: Bindereif
authors.affiliation: International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland; Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland.
authors.forename: Janusz M
authors.initials: JM
authors.lastname: Bujnicki
authors.affiliation: Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland. Electronic address: allain@mol.biol.ethz.ch.
authors.forename: Frédéric H-T
authors.initials: FH
authors.lastname: Allain
mesh_terms: D017398:Alternative Splicing; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D005091:Exons; D051273:Glucose Transporter Type 2 / Q000235:genetics*; D034664:Heterogeneous-Nuclear Ribonucleoprotein L / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012313:RNA / Q000235:genetics / Q000378:metabolism*
chemical_list: D051273:Glucose Transporter Type 2; D034664:Heterogeneous-Nuclear Ribonucleoprotein L; D012313:RNA
keywords: RNA recognition motif; evolutionary analysis; fifth β-strand; hnRNP L; interacting C-terminal coil; repressor function