Label-Free Protein-RNA Interactome Analysis Identifies Khsrp Signaling Downstream of the p38/Mk2 Kinase Complex as a Critical Modulator of Cell Cycle Progression

Jorge Boucas; Christian Fritz; Anna Schmitt; Arina Riabinska; Lisa Thelen; Martin Peifer; Uschi Leeser; Peter Nuernberg; Janine Altmueller; Matthias Gaestel; Christoph Dieterich; H Christian Reinhardt

doi:10.1371/journal.pone.0125745

Label-Free Protein-RNA Interactome Analysis Identifies Khsrp Signaling Downstream of the p38/Mk2 Kinase Complex as a Critical Modulator of Cell Cycle Progression

PLoS One. 2015 May 20;10(5):e0125745. doi: 10.1371/journal.pone.0125745. eCollection 2015.

Affiliations

¹ Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany.
² Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Department of Translational Genomics, University of Cologne, Cologne, Germany.
³ Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany.
⁴ Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany.
⁵ Institute of Biochemistry, Hannover Medical School, Hannover, Germany.
⁶ Computational RNA Biology and Ageing, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann Straße 9b, 50913, Cologne, Germany.

Abstract

Growing evidence suggests a key role for RNA binding proteins (RBPs) in genome stability programs. Additionally, recent developments in RNA sequencing technologies, as well as mass-spectrometry techniques, have greatly expanded our knowledge on protein-RNA interactions. We here use full transcriptome sequencing and label-free LC/MS/MS to identify global changes in protein-RNA interactions in response to etoposide-induced genotoxic stress. We show that RBPs have distinct binding patterns in response to genotoxic stress and that inactivation of the RBP regulator module, p38/MK2, can affect the entire spectrum of protein-RNA interactions that take place in response to stress. In addition to validating the role of known RBPs like Srsf1, Srsf2, Elavl1 in the genotoxic stress response, we add a new collection of RBPs to the DNA damage response. We identify Khsrp as a highly regulated RBP in response to genotoxic stress and further validate its role as a driver of the G(1/)S transition through the suppression of Cdkn1a(P21) transcripts. Finally, we identify KHSRP as an indicator of overall survival, as well as disease free survival in glioblastoma multiforme.

Publication types

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

MeSH terms

Animals
Cells, Cultured
Cyclin-Dependent Kinase Inhibitor p21 / genetics
DNA Damage / genetics
Disease-Free Survival
ELAV-Like Protein 1 / genetics
G1 Phase Cell Cycle Checkpoints / genetics*
Gene Expression Profiling / methods*
Glioblastoma / genetics
Humans
Intracellular Signaling Peptides and Proteins / genetics*
Mice
Nuclear Proteins / genetics
Protein Serine-Threonine Kinases / genetics*
RNA / genetics*
RNA-Binding Proteins / genetics*
Ribonucleoproteins / genetics
Serine-Arginine Splicing Factors
Signal Transduction / genetics
Trans-Activators / genetics*
p38 Mitogen-Activated Protein Kinases / genetics*

Substances

Cyclin-Dependent Kinase Inhibitor p21
ELAV-Like Protein 1
Elavl1 protein, mouse
Intracellular Signaling Peptides and Proteins
KHSRP protein, human
Nuclear Proteins
RNA-Binding Proteins
Ribonucleoproteins
SRSF2 protein, mouse
Trans-Activators
Serine-Arginine Splicing Factors
RNA
MAP-kinase-activated kinase 2
Protein Serine-Threonine Kinases
p38 Mitogen-Activated Protein Kinases

Grants and funding

This work was supported by the Volkswagenstiftung (Lichtenberg Program H.C.R.), the Deutsche Forschungsgemeinschaft (KFO-286, RE2246/2-1 to H.C.R.), the Helmholtz-Gemeinschaft (Preclinical Comprehensive Cancer Center to H.C.R.), Federal Ministry for Research and Education (BMBF, 01ZX1303A to H.C.R.), the Else Kröner-Fresenius Stiftung (EKFS-2014-A06 to H.C.R.), the Deutsche Krebshilfe (DKH-111112 to H.C.R.) and Deutsche Jose Carreras Stiftung (DJCLS-R12/26 to H.C.R.).