Structural analysis of the yeast exosome Rrp6p-Rrp47p complex by small-angle X-ray scattering

Emil Dedic; Paulina Seweryn; Anette Thyssen Jonstrup; Rasmus Koch Flygaard; Natalya U Fedosova; Søren Vrønning Hoffmann; Thomas Boesen; Ditlev Egeskov Brodersen

doi:10.1016/j.bbrc.2014.06.032

Structural analysis of the yeast exosome Rrp6p-Rrp47p complex by small-angle X-ray scattering

Biochem Biophys Res Commun. 2014 Jul 18;450(1):634-40. doi: 10.1016/j.bbrc.2014.06.032. Epub 2014 Jun 14.

Authors

Emil Dedic¹, Paulina Seweryn¹, Anette Thyssen Jonstrup¹, Rasmus Koch Flygaard¹, Natalya U Fedosova², Søren Vrønning Hoffmann³, Thomas Boesen⁴, Ditlev Egeskov Brodersen⁵

Affiliations

¹ Centre for mRNP Biogenesis and Metabolism, Gustav Wieds Vej 10c, Aarhus University, DK-8000 Aarhus C, Denmark; Department of Molecular Biology and Genetics, Gustav Wieds Vej 10c, Aarhus University, DK-8000 Aarhus C, Denmark.
² Department of Biomedicine, Ole Worms Allé 6, Aarhus University, DK-8000 Aarhus C, Denmark.
³ Institute for Storage Ring Facilities (ISA), Department of Physics and Astronomy, Ny Munkegade 120, Aarhus University, DK-8000 Aarhus C, Denmark.
⁴ Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Gustav Wieds Vej 10c, Aarhus University, DK-8000 Aarhus C, Denmark; Department of Molecular Biology and Genetics, Gustav Wieds Vej 10c, Aarhus University, DK-8000 Aarhus C, Denmark.
⁵ Centre for mRNP Biogenesis and Metabolism, Gustav Wieds Vej 10c, Aarhus University, DK-8000 Aarhus C, Denmark; Department of Molecular Biology and Genetics, Gustav Wieds Vej 10c, Aarhus University, DK-8000 Aarhus C, Denmark. Electronic address: deb@mb.au.dk.

PMID: 24937447
DOI: 10.1016/j.bbrc.2014.06.032

Abstract

The RNase D-type 3'-5' exonuclease Rrp6p from Saccharomyces cerevisiae is a nuclear-specific cofactor of the RNA exosome and associates in vivo with Rrp47p (Lrp1p). Here, we show using biochemistry and small-angle X-ray scattering (SAXS) that Rrp6p and Rrp47p associate into a stable, heterodimeric complex with an elongated shape consistent with binding of Rrp47p to the nuclease domain and opposite of the HRDC domain of Rrp6p. Rrp47p reduces the exonucleolytic activity of Rrp6p on both single-stranded and structured RNA substrates without significantly altering the affinity towards RNA or the ability of Rrp6p to degrade RNA secondary structure.

Keywords: 3′–5′ nuclease; Exosome; RNA processing; RNA turnover; Ribosomal RNA; snoRNA.

Publication types

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

MeSH terms

Amino Acid Sequence
Binding Sites
Computer Simulation
DNA-Binding Proteins / chemistry
DNA-Binding Proteins / metabolism*
DNA-Binding Proteins / ultrastructure*
Exosome Multienzyme Ribonuclease Complex / chemistry
Exosome Multienzyme Ribonuclease Complex / metabolism*
Exosome Multienzyme Ribonuclease Complex / ultrastructure*
Models, Chemical
Models, Molecular
Molecular Sequence Data
Nuclear Proteins / chemistry
Nuclear Proteins / metabolism*
Nuclear Proteins / ultrastructure*
Protein Binding
Protein Conformation
RNA / chemistry
RNA / metabolism*
RNA / ultrastructure*
RNA-Binding Proteins / chemistry
RNA-Binding Proteins / metabolism*
RNA-Binding Proteins / ultrastructure*
Saccharomyces cerevisiae Proteins / chemistry
Saccharomyces cerevisiae Proteins / metabolism*
Saccharomyces cerevisiae Proteins / ultrastructure*
Scattering, Small Angle
X-Ray Diffraction

Substances

DNA-Binding Proteins
LRP1 protein, S cerevisiae
Nuclear Proteins
RNA-Binding Proteins
Saccharomyces cerevisiae Proteins
RNA
Exosome Multienzyme Ribonuclease Complex
RRP6 protein, S cerevisiae