The Cold Shock Domain of YB-1 Segregates RNA from DNA by Non-Bonded Interactions.

Vladislav Kljashtorny,Lev Ovchinnikov,Dmitry Lyabin,Stanislav Nikonov,Patrick Curmi,Philippe Manivet,Nicolas Vodovar,Jean-Luc Eph Darlix

doi:10.1371/journal.pone.0130318

Abstract

The human YB-1 protein plays multiple cellular roles, of which many are dictated by its binding to RNA and DNA through its Cold Shock Domain (CSD). Using molecular dynamics simulation approaches validated by experimental assays, the YB1 CSD was found to interact with nucleic acids in a sequence-dependent manner and with a higher affinity for RNA than DNA. The binding properties of the YB1 CSD were close to those observed for the related bacterial Cold Shock Proteins (CSP), albeit some differences in sequence specificity. The results provide insights in the molecular mechanisms whereby YB-1 interacts with nucleic acids.

Highlights

The eukaryotic Y-box binding protein 1 (YB-1) is a multifunctional DNA/RNA binding protein that participates in many cellular events through its binding to nucleic acids (NA) and other proteins.YB-1 is involved in different aspect of DNA biology
The CSDYB-1 and bacterial Cold Shock Proteins (CSP) belong to the family of the cold shock proteins that exhibit a beta barrel fold that includes two highly conserved RNA-binding motifs, RNP-1 and RNP-2 (Fig 1A), which include most of the residues involved in the interactions with nucleic acids
Given the close structural relationship between the CSDYB-1 and Bs-CspB, their superposition was used to assign the nucleotide binding sites in the CSDYB-1. This analysis showed that the nucleotide binding site of the CSDYB-1 resembles to that of the CSPs, albeit some notable differences: i) the Phe30 residue of the Bs-CspB that is involved in nucleotide stacking is substituted by the non-aromatic Gln38 in CSDYB-1, ii) the Gln59 of Bs-CspB that is involved in H-bond with an oligonucleotide base is substituted by Glu71 in CSDYB-1; and, iii) most of the bacterial CSPs contain an Phe residue at location 38 which is stacked to a nucleotide bases, while it is replaced by a Gln in the CSDYB-1 (Figs 1 and 2; of note, in the crystal structure of the BsCspB, this residue interacts with symmetrically related molecule shown in magenta)

Summary

Introduction

The eukaryotic Y-box binding protein 1 (YB-1) is a multifunctional DNA/RNA binding protein that participates in many cellular events through its binding to nucleic acids (NA) and other proteins (reviewed in [1,2,3]).YB-1 is involved in different aspect of DNA biology. The eukaryotic Y-box binding protein 1 (YB-1) is a multifunctional DNA/RNA binding protein that participates in many cellular events through its binding to nucleic acids (NA) and other proteins (reviewed in [1,2,3]). YB-1 binds to the so-called Y-box that is present in the promoter regions of a large number of genes that are involved in cell division, differentiation, apoptosis, and immune and stress responses, and regulates their transcription in a positive or negative fashion (reviewed in [1,3]). YB-1 displays a high affinity for single-stranded (ss) DNA, DNA damaged regions [4,5], and possesses a RNA and DNA melting and annealing activity [6,7], its involvement in DNA repair [8,9]. YB-1 binds to RNA both in the nucleus and the cytoplasm. In the PLOS ONE | DOI:10.1371/journal.pone.0130318 July 6, 2015

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Conclusion