Back to Search
Start Over
Crystal structure of a Y-box binding protein 1 (YB-1)–RNA complex reveals key features and residues interacting with RNA
- Source :
- J Biol Chem
- Publication Year :
- 2019
- Publisher :
- Elsevier BV, 2019.
-
Abstract
- The Y-box binding protein 1 (YB-1) is a member of the cold shock domain (CSD) protein family and is recognized as an oncogenic factor in several solid tumors. By binding to RNA, YB-1 participates in several steps of posttranscriptional regulation of gene expression, including mRNA splicing, stability, and translation; microRNA processing; and stress granule assembly. However, the mechanisms in YB-1–mediated regulation of RNAs are unclear. Previously, we used both systematic evolution of ligands by exponential enrichment (SELEX) and individual-nucleotide resolution UV cross-linking and immunoprecipitation coupled RNA-Seq (iCLIP-Seq) analyses, which defined the RNA-binding consensus sequence of YB-1 as CA(U/C)C. We also reported that through binding to its core motif CAUC in primary transcripts, YB-1 regulates the alternative splicing of a CD44 variable exon and the biogenesis of miR-29b-2 during both Drosha and Dicer steps. To elucidate the molecular basis of the YB-1–RNA interactions, we report high-resolution crystal structures of the YB-1 CSD in complex with different RNA oligos at 1.7 Å resolution. The structure revealed that CSD interacts with RNA mainly through π–π stacking interactions assembled by four highly conserved aromatic residues. Interestingly, YB-1 CSD forms a homodimer in solution, and we observed that two residues, Tyr-99 and Asp-105, at the dimer interface are important for YB-1 CSD dimerization. Substituting these two residues with Ala reduced CSD's RNA-binding activity and abrogated the splicing activation of YB-1 targets. The YB-1 CSD–RNA structures presented here at atomic resolution provide mechanistic insights into gene expression regulated by CSD-containing proteins.
- Subjects :
- 0301 basic medicine
Biochemistry
03 medical and health sciences
Exon
Humans
Stress granule assembly
RNA, Messenger
Molecular Biology
Post-transcriptional regulation
030102 biochemistry & molecular biology
biology
Chemistry
Single-stranded RNA binding
Alternative splicing
RNA-Binding Proteins
RNA
Exons
Cell Biology
Cell biology
DNA-Binding Proteins
Alternative Splicing
030104 developmental biology
RNA splicing
biology.protein
Y-Box-Binding Protein 1
Protein Binding
Dicer
Subjects
Details
- ISSN :
- 00219258
- Volume :
- 294
- Database :
- OpenAIRE
- Journal :
- Journal of Biological Chemistry
- Accession number :
- edsair.doi.dedup.....d19837e65caefa6ff282a6ad17da79f3