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NMR structure determination of protein-RNA complexes involved in pre-mRNA editing and translation regulation

English title NMR structure determination of protein-RNA complexes involved in pre-mRNA editing and translation regulation
Applicant Allain Frédéric
Number 133134
Funding scheme Project funding (Div. I-III)
Research institution Institut für Molekularbiologie und Biophysik ETH Zürich
Institution of higher education ETH Zurich - ETHZ
Main discipline Structural Research
Start/End 01.10.2010 - 30.09.2013
Approved amount 600'000.00
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Keywords (8)

hnRNP; protein-RNA complexes; NMR spectroscopy; RNA binding domains; RNA editing; Translation regulation; Non coding RNA; IRES

Lay Summary (English)

Lead
Understanding the molecular mechanisms regulating gene expression at the posttranscriptional level is a major question in molecular biology, defects in these mechanisms being at the origin of many genetic diseases. This proposal focuses on two of these processes: RNA editing and translation regulation.
Lay summary
Understanding the molecular mechanisms regulating gene expression at the posttranscriptional level is a major question in molecular biology, defects in these mechanisms being at the origin of many genetic diseases. This proposal focuses on two of these processes: RNA editing and translation regulation. RNA editing occurs in human by single base deamination, C to U or A to I. These changes create codons for different amino acids, stop codons or even new splice-sites allowing larger protein diversity. A to I editing is catalysed at specific sites by ADARs whose substrate recognition mechanisms are still unclear. Translation regulation plays a major role in many diverse cellular processes such as carbon metabolism, viral replication, apoptosis, embryonic development, cell differentiation and synapse activation. We focus here on aspects of translational regulation under the control of protein binding the mRNA 5'or 3'UTRs. At the 5'UTR, we are interested in how RsmA/CsrA proteins control bacterial translation initiation and how hnRNP proteins (PTB and hnRNP C) and UNR help IRES-mediated translation initiation of viral and cellular mRNAs. At the 3'UTR, we are interested in how RNA binding proteins like the human CPEBs, hnRNP L and EPRS stabilize mRNAs to regulate translation.We are proposing here to determine the NMR structures of several key protein-RNA complexes involved in RNA editing and translation regulation. First, we aim at understanding how ADAR2 recognizes two of its substrates, second, how the bacterial translation repressor RsmE recognizes certain 5'UTR mRNA and also several non-coding RNA like RsmZ, third, how PTB, hnRNP C and Unr binds IRESes to facilitate or repress translation initiation, fourth, how CPEB and CPEB3 both bind dormant mRNA to regulate their translation and fifth how hnRNP L and EPRS control a riboswitch in VEGFA mRNA.
Direct link to Lay Summary Last update: 23.12.2012

Responsible applicant and co-applicants

Employees

Publications

Publication
Isotope Labeling and Segmental Labeling of Larger RNAs for NMR Structural Studies.
Duss Olivier, Lukavsky Peter J, Allain Frédéric H-T (2012), Isotope Labeling and Segmental Labeling of Larger RNAs for NMR Structural Studies., in Advances in experimental medicine and biology, 992, 121-44.
NMR spectroscopy: an excellent tool to understand RNA and carbohydrate recognition by proteins.
Cléry Antoine, Schubert Mario, Allain Frédéric H-T (2012), NMR spectroscopy: an excellent tool to understand RNA and carbohydrate recognition by proteins., in Chimia, 66(10), 741-6.
Solution structure of the N-terminal dsRBD of Drosophila ADAR and interaction studies with RNA.
Barraud Pierre, Heale Bret S E, O'Connell Mary A, Allain Frédéric H-T (2012), Solution structure of the N-terminal dsRBD of Drosophila ADAR and interaction studies with RNA., in Biochimie, 94(7), 1499-509.
ADAR Proteins: Double-stranded RNA and Z-DNA Binding Domains.
Barraud Pierre, Allain Frédéric H-T (2011), ADAR Proteins: Double-stranded RNA and Z-DNA Binding Domains., in Current topics in microbiology and immunology, 353, 35-60.
RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence.
Masliah Grégoire, Barraud Pierre, Allain Frédéric H-T, RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence., in Cellular and molecular life sciences : CMLS.

Collaboration

Group / person Country
Types of collaboration
ETH Zurich/ Prof. G. Jeschke Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
University of Barcelona/ Dr Raul Mendez Spain (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
RNA-Methods workshop Talk given at a conference 13.12.2013 Frankfurt , Germany Allain Frédéric;
RNA Club Zürich Talk given at a conference 25.11.2013 Zürich, Switzerland Duss Olivier;
Swiss-Kyoto symposium Talk given at a conference 21.11.2013 Züirch, Switzerland Allain Frédéric;
Faculté de Pharmacie, Institute Seminar Talk given at a conference 14.10.2013 Paris, France Allain Frédéric;
Structure and dynamics of biological macromolecules. A biophysical worshop Talk given at a conference 26.09.2013 Nove Hrady, Czech Republic Allain Frédéric;
EBSA Talk given at a conference 16.07.2013 Lisbon, Portugal Allain Frédéric;
RNA Society Meeting 2013 Talk given at a conference 13.06.2013 Davos, Switzerland Duss Olivier;
regulating with RNA in Bacteria Talk given at a conference 05.06.2013 Würzburg , Germany Allain Frédéric;
CEA Institute Seminar Talk given at a conference 17.05.2013 Saclay, France Allain Frédéric;
IGBMC Institute seminar Talk given at a conference 02.05.2013 Strasbourg, France Allain Frédéric;
Symposium "Molecular machines in RNA processing, translation and transport Talk given at a conference 14.02.2013 Göttingen, Germany Allain Frédéric;
RNA lecture Series Talk given at a conference 21.01.2013 Vienna, Austria Allain Frédéric;
Cell symposia “functional RNA” Talk given at a conference 03.12.2012 Sitges, Spain, Spain Allain Frédéric;
RNA Club Zürich Talk given at a conference 15.10.2012 Zürich, Switzerland Afroz Tariq;
Lecture at University of Barcelona Talk given at a conference 05.10.2012 Barcelona, Spain, Spain Allain Frédéric;
Summer Seminar Talk given at a conference 04.10.2012 Hirschegg , Austria Dorn Georg;
FEBS meeting 2012 Talk given at a conference 05.09.2012 Seville, Spain, Spain Allain Frédéric;
NCCR Symposium Talk given at a conference 30.08.2012 Zurich, Switzerland, Switzerland Allain Frédéric;
XXVth ICMRBS Talk given at a conference 19.08.2012 Lyon, France Maris Christophe;
XXVth ICMRBS Talk given at a conference 19.08.2012 Lyon, France , France Allain Frédéric;
RNA Society Meeting Talk given at a conference 03.06.2012 Ann Arbor, Michigan, USA, United States of America Afroz Tariq;
Interdisciplinary research in molecular biology and biomedecin Talk given at a conference 29.03.2012 Varsaw, Poland , Poland Allain Frédéric;
6th NMR Winter retreat for protein-RNA interactions Talk given at a conference 13.03.2012 Parpan, Switzerland Afroz Tariq;
6th NMR Winter retreat for protein-RNA interactions Talk given at a conference 13.03.2012 Parpan, Switzerland, Switzerland Allain Frédéric;
6th NMR Winter retreat for protein-RNA interactions Talk given at a conference 13.03.2012 Parpan, Switzerland Duss Olivier;
lecture at the Medical Research Council Talk given at a conference 27.02.2012 Edinburgh, UK , Great Britain and Northern Ireland Allain Frédéric;
lectures at Karolinska Institutet Talk given at a conference 20.02.2012 Stockholm, Sweden , Sweden Allain Frédéric;
Indo-Swiss Symposium on recent trends in NMR of Biomolecules Talk given at a conference 24.01.2012 Pune, India , India Allain Frédéric;
Indo-Swiss Symposium on recent trends in NMR of Biomolecules Talk given at a conference 23.01.2012 Pune, India Afroz Tariq;
Seminar at the Biozentrum Talk given at a conference 06.12.2011 Basel, Switzerland, Switzerland Allain Frédéric;
CECAM Meeting on DNA/RNA dynamics Talk given at a conference 15.09.2011 Zurich, Switzerland, Switzerland Allain Frédéric;
Summer School of Magnetic Resonance for Biological Macromolecules, 2011 Talk given at a conference 21.06.2011 Heifei, China, China Allain Frédéric;
RNA society meeting 2011 Talk given at a conference 16.06.2011 Kyoto, Japan Duss Olivier;
Seminar at FMI Talk given at a conference 25.03.2011 Basel, Switzerland, Switzerland Allain Frédéric;
Parpan Winter retreat Talk given at a conference 06.03.2011 Parpan, Switzerland, Switzerland Allain Frédéric;
Eurasnet meeting Talk given at a conference 04.03.2011 Granada, Spain, Spain Allain Frédéric;
Bio-NMR and EAST-NMR Annual User Meeting Talk given at a conference 26.01.2011 Brno, Czech Republic, Czech Republic Allain Frédéric;
Seminar University of Colorado School of Medicine Talk given at a conference 14.01.2011 Denver, Colorado, USA , United States of America Allain Frédéric;
Keystone meeting Frontiers of NMR in Biology Talk given at a conference 10.01.2011 Big Sky, Montana, USA , United States of America Allain Frédéric;
Czech RNA club 2010 Talk given at a conference 05.11.2010 Ceske Budejovice, Czech Republic , Czech Republic Allain Frédéric;
CSHL Asia “RNA Biology” Talk given at a conference 03.11.2010 Suzhou, China, China Allain Frédéric;
EMBO Workshop of the newly elected EMBO members Talk given at a conference 26.10.2010 Heidelberg, Germany, Germany Allain Frédéric;


Associated projects

Number Title Start Funding scheme
127454 Post-transcriptional regulation of germ cell apoptosis in C. elegans 01.11.2009 Sinergia
127333 Glycocode: towards the structure and function of glycans 01.11.2009 Sinergia
139221 New electronics for 900MHz NMR spectrometer 01.12.2011 R'EQUIP
118118 NMR structure determination of protein-RNA complexes involved in pre-mRNA editing and translation regulation 01.10.2007 Project funding (Div. I-III)
131031 Nuclear import and substrate recognition by double stranded RNA binding domains (D-A-CH/LAE) 01.05.2010 Project funding (Div. I-III)
149921 NMR structure determination of protein-RNA complexes involved in pre-mRNA splicing and translation regulation 01.10.2013 Project funding (Div. I-III)

Abstract

Understanding the molecular mechanisms regulating gene expression at the posttranscriptional level is a major question in molecular biology, defects in these mechanisms being at the origin of many genetic diseases. This proposal focuses on two of these processes: RNA editing and translation regulation. RNA editing occurs in human by single base deamination, C to U or A to I. These changes create codons for different amino acids, stop codons or even new splice-sites allowing larger protein diversity. A to I editing is catalysed at specific sites by ADARs whose substrate recognition mechanisms are still unclear. Translation regulation plays a major role in many diverse cellular processes such as carbon metabolism, viral replication, apoptosis, embryonic development, cell differentiation and synapse activation. We focus here on aspects of translational regulation under the control of protein binding the mRNA 5’or 3’UTRs. At the 5’UTR, we are interested in how RsmA/CsrA proteins control bacterial translation initiation and how hnRNP proteins (PTB and hnRNP C) and UNR help IRES-mediated translation initiation of viral and cellular mRNAs. At the 3’UTR, we are interested in how RNA binding proteins like the human CPEBs, hnRNP L and EPRS stabilize mRNAs to regulate translation.We are proposing here to determine the NMR structures of several key protein-RNA complexes involved in RNA editing and translation regulation. First, we aim at understanding how ADAR2 recognizes two of its substrates,, second, how the bacterial translation repressor RsmE recognizes certain 5’UTR mRNA and also several non-coding RNA like RsmZ, third, how PTB, hnRNP C and Unr binds IRESes to facilitate or repress translation initiation, fourth, how CPEB and CPEB3 both bind dormant mRNA to regulate their translation and fifth how hnRNP L and EPRS control a riboswitch in VEGFA mRNA.
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