Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14A in ribosome biogenesis

Franziska M Boneberg; Tobias Brandmann; Lena Kobel; Jasmin van den Heuvel; Katja Bargsten; Lukas Bammert; Ulrike Kutay; Martin Jinek

doi:10.1261/rna.069609.118

Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14A in ribosome biogenesis

RNA. 2019 Jun;25(6):685-701. doi: 10.1261/rna.069609.118. Epub 2019 Mar 25.

Authors

Franziska M Boneberg¹, Tobias Brandmann^#¹, Lena Kobel^#¹, Jasmin van den Heuvel^#², Katja Bargsten¹, Lukas Bammert², Ulrike Kutay², Martin Jinek¹

Affiliations

¹ Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland.
² Department of Biology, Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland.

^# Contributed equally.

Abstract

Eukaryotic ribosome biogenesis is a highly orchestrated process involving numerous assembly factors including ATP-dependent RNA helicases. The DEAH helicase DHX37 (Dhr1 in yeast) is activated by the ribosome biogenesis factor UTP14A to facilitate maturation of the small ribosomal subunit. We report the crystal structure of DHX37 in complex with single-stranded RNA, revealing a canonical DEAH ATPase/helicase architecture complemented by a structurally unique carboxy-terminal domain (CTD). Structural comparisons of the nucleotide-free DHX37-RNA complex with DEAH helicases bound to RNA and ATP analogs reveal conformational changes resulting in a register shift in the bound RNA, suggesting a mechanism for ATP-dependent 3'-5' RNA translocation. We further show that a conserved sequence motif in UTP14A interacts with and activates DHX37 by stimulating its ATPase activity and enhancing RNA binding. In turn, the CTD of DHX37 is required, but not sufficient, for interaction with UTP14A in vitro and is essential for ribosome biogenesis in vivo. Together, these results shed light on the mechanism of DHX37 and the function of UTP14A in controlling its recruitment and activity during ribosome biogenesis.

Keywords: RNA helicase; X-ray crystallography; ribosome biogenesis.

Publication types

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

MeSH terms

Adenosine Triphosphatases / chemistry*
Adenosine Triphosphatases / genetics
Adenosine Triphosphatases / metabolism
Adenosine Triphosphate / analogs & derivatives*
Adenosine Triphosphate / metabolism
Animals
Binding Sites
Cloning, Molecular
Crystallography, X-Ray
DEAD-box RNA Helicases / chemistry*
DEAD-box RNA Helicases / genetics
DEAD-box RNA Helicases / metabolism
Escherichia coli / genetics
Escherichia coli / metabolism
Gene Expression
Genetic Vectors / chemistry
Genetic Vectors / metabolism
Humans
Kinetics
Mice
Models, Molecular
Organelle Biogenesis*
Protein Binding
Protein Biosynthesis
Protein Conformation, alpha-Helical
Protein Conformation, beta-Strand
Protein Interaction Domains and Motifs
RNA / chemistry*
RNA / metabolism
RNA Helicases / chemistry*
RNA Helicases / genetics
RNA Helicases / metabolism
Recombinant Fusion Proteins / chemistry
Recombinant Fusion Proteins / genetics
Recombinant Fusion Proteins / metabolism
Ribonucleoproteins, Small Nucleolar / chemistry*
Ribonucleoproteins, Small Nucleolar / genetics
Ribonucleoproteins, Small Nucleolar / metabolism
Ribosomes / genetics
Ribosomes / metabolism
Substrate Specificity

Substances

Recombinant Fusion Proteins
Ribonucleoproteins, Small Nucleolar
UTP14A protein, human
RNA
Adenosine Triphosphate
Adenosine Triphosphatases
DEAD-box RNA Helicases
Dhx37 protein, mouse
RNA Helicases