Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome

Benjamin Lau; Jingdong Cheng; Dirk Flemming; Giuseppe La Venuta; Otto Berninghausen; Roland Beckmann; Ed Hurt

doi:10.1016/j.molcel.2020.11.009

Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome

Mol Cell. 2021 Jan 21;81(2):293-303.e4. doi: 10.1016/j.molcel.2020.11.009. Epub 2020 Dec 15.

Authors

Benjamin Lau¹, Jingdong Cheng², Dirk Flemming¹, Giuseppe La Venuta¹, Otto Berninghausen², Roland Beckmann³, Ed Hurt⁴

Affiliations

¹ Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
² Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany.
³ Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany. Electronic address: [email protected].
⁴ Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany. Electronic address: [email protected].

PMID: 33326748
DOI: 10.1016/j.molcel.2020.11.009

Abstract

Ribosome assembly is catalyzed by numerous trans-acting factors and coupled with irreversible pre-rRNA processing, driving the pathway toward mature ribosomal subunits. One decisive step early in this progression is removal of the 5' external transcribed spacer (5'-ETS), an RNA extension at the 18S rRNA that is integrated into the huge 90S pre-ribosome structure. Upon endo-nucleolytic cleavage at an internal site, A₁, the 5'-ETS is separated from the 18S rRNA and degraded. Here we present biochemical and cryo-electron microscopy analyses that depict the RNA exosome, a major 3'-5' exoribonuclease complex, in a super-complex with the 90S pre-ribosome. The exosome is docked to the 90S through its co-factor Mtr4 helicase, a processive RNA duplex-dismantling helicase, which strategically positions the exosome at the base of 5'-ETS helices H9-H9', which are dislodged in our 90S-exosome structures. These findings suggest a direct role of the exosome in structural remodeling of the 90S pre-ribosome to drive eukaryotic ribosome synthesis.

Keywords: 5’ ETS; 90S pre-ribosome; MTR4; exosome; ribosome biogenesis.

Publication types

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

MeSH terms

Binding Sites
Cryoelectron Microscopy
DEAD-box RNA Helicases / chemistry*
DEAD-box RNA Helicases / genetics
DEAD-box RNA Helicases / metabolism
Endoribonucleases / chemistry*
Endoribonucleases / genetics
Endoribonucleases / metabolism
Exonucleases / chemistry*
Exonucleases / genetics
Exonucleases / metabolism
Exosome Multienzyme Ribonuclease Complex / genetics
Exosome Multienzyme Ribonuclease Complex / metabolism
Exosome Multienzyme Ribonuclease Complex / ultrastructure*
Models, Molecular
Protein Binding
Protein Biosynthesis
Protein Conformation, alpha-Helical
Protein Conformation, beta-Strand
Protein Interaction Domains and Motifs
RNA Stability
RNA, Ribosomal, 18S / chemistry*
RNA, Ribosomal, 18S / genetics
RNA, Ribosomal, 18S / metabolism
Ribosomes / genetics
Ribosomes / metabolism
Ribosomes / ultrastructure*
Saccharomyces cerevisiae / genetics*
Saccharomyces cerevisiae / metabolism
Saccharomyces cerevisiae Proteins / chemistry*
Saccharomyces cerevisiae Proteins / genetics
Saccharomyces cerevisiae Proteins / metabolism

Substances

RNA, Ribosomal, 18S
Saccharomyces cerevisiae Proteins
Endoribonucleases
Exonucleases
Exosome Multienzyme Ribonuclease Complex
pre-ribosomal RNA endoribonuclease
MTR4 protein, S cerevisiae
DEAD-box RNA Helicases