Molecular recognition in post-transcriptional regulation 2
Lead Research Organisation:
University College London
Department Name: UNLISTED
Abstract
The functioning of the human body and of complex organisms in general requires different proteins to be produced in different types of cells. This cell-type-specific protein production is achieved by precisely regulating the translation of the genetic code into proteins. The two steps in this process of translation are, first, the translation of the DNA-encoded information into RNA and, then, the translation of the RNA code into a protein molecule. Both processes are regulated by biological machines, which are composed of proteins and, in some cases, RNA molecules. We focus on the regulation of the RNA-to-protein step (or post-transcriptional regulation) and investigate how the protein RNA machines assemble in a solution environment and regulate gene expression. Our structural studies complement other techniques such as X-ray crystallography, which can be used to study molecules in a static crystalline state. Analysing the structures of the molecules that govern regulation of protein synthesis has a direct medical relevance, as this process lies at the basis of common genetic diseases, cancer and viral infections. We work on an important regulatory mechanism, called ARE mediated mRNA decay (AMD), that increase the synthesis of specific proteins in inflammation and healing processes. This mechanism, if permanently switched on, can lead to inflammatory arthritis and cancer. We want to understand how the switch works at the molecular level and design specific therapies to switch in off when required.||Using a similar technical approach we are also investigating a key regulatory protein from herpes virus. This project wants to facilitate the design of anti-herpes drugs to treat people infected with this virus, which forms a major threat to immunodepressed patients, increases the risk of organ transplantation and chemotherapy and reduces the life expectancy of AIDS sufferers. Molecular insight into the interaction of ICP27 with its functional binding partners needs to be obtained if we are, for example, to design or optimise compounds to lock protein and RNA in a non-functional conformation or to (de)stabilise protein RNA complexes.
Technical Summary
Multifunctional eukaryotic regulatory proteins and their viral functional equivalents control gene expression by interacting with mRNAs in large macromolecular aggregates. Dissection of the molecular basis of post-transcriptional regulatory mechanisms has a direct medical relevance, as changes in the regulation of mRNA metabolism lie at the basis of common genetic diseases, cancer and viral infection. Current therapies for these diseases do not focus on the post-transcriptional steps of regulation but rather on the transcriptional ones, that are better understood. Our aim is to clarify the structure-function relation that is at the basis of mRNA recognition by post-transcriptional regulatory proteins and to suggest strategies to control this recognition. Adenine-uracil-rich element (ARE)-mediated mRNA decay (AMD) regulates the concentration of mRNAs that contain AREs within their 3 untranslated regions (3 UTRs) by promoting their degradation. Transient AMD shut-off up-regulates the stability of these mRNAs and is important for processes that require a fast response of the organism such as cellular growth, immune response, cardiovascular toning and external stress-mediated pathways. However, impaired AMD and the consequent pathological long-term increase in the stability of a subset of mRNAs have been related to several types of cancer (skin tumours, colorectal cancer, Hodgkins lymphoma, lung carcinoma and leukaemia) and auto-inflammatory diseases (Crohn-like inflammatory bowel disease and inflammatory arthritis). K-homology splicing regulator protein (KSRP) is an important player in AMD that interacts with several different AREs mediating the degradation of the corresponding mRNAs. Our work centers on the analysis of the structural and functional elements that contribute to KSRP-RNA interactions and to mRNA degradation. We are studying the structure and dynamics of the different domains of the protein and investigated their relationship to mRNA degradation. Using structural and functional information, we plan to dissect the details of the interaction with the RNA and help the design of a strategy for the tuning of KSRP activity. Herpes viridae induced infections are a major threat to immunodepressed patients, increasing the risk of transplants and chemotherapy and reducing the life expectancy of AIDS sufferers. Current herpes virus therapies (e.g. Acyclovir) aim to block the synthesis of new DNA, but resistance to these treatments is increasing. Successful viral replication is achieved through the tightly regulated expression of viral genes. A key component of the regulatory mechanism is ICP27, an essential HSV-1 RNA binding protein that regulates protein expression, both at the transcriptional and post-transcriptional level. We will study both ICP27 and the mechanism of post-transcriptional regulation acted upon by this protein, in particular 3 mRNA editing. Using the same strategy described above for the protein KSRP, we will obtain a better understanding of the regulatory cycle of the virus and define specific structural features amenable to structure-aided drug design.
Organisations
- University College London (Lead Research Organisation)
- UNIVERSITY OF OXFORD (Collaboration)
- Francis Crick Institute (Collaboration)
- University College London (Collaboration)
- Sapienza University of Rome (Collaboration)
- University of Toronto (Collaboration)
- Albert Ludwig University of Freiburg (Collaboration)
- Medical Research Council (MRC) (Collaboration)
- KING'S COLLEGE LONDON (Collaboration)
People |
ORCID iD |
Andres Ramos (Principal Investigator) |
Publications
Castilla-Llorente V
(2014)
PolyQ-mediated regulation of mRNA granules assembly.
in Biochemical Society transactions
Castilla-Llorente V
(2013)
Terminal loop-mediated regulation of miRNA biogenesis: selectivity and mechanisms.
in Biochemical Society transactions
Briata P
(2013)
Functional and molecular insights into KSRP function in mRNA decay.
in Biochimica et biophysica acta
Nicastro G
(2017)
Mechanism of ß-actin mRNA Recognition by ZBP1.
in Cell reports
Chaves-Arquero B
(2023)
Affinity-enhanced RNA-binding domains as tools to understand RNA recognition
in Cell Reports Methods
Nicastro G
(2015)
KH-RNA interactions: back in the groove.
in Current opinion in structural biology
Gallagher C
(2018)
Joining the dots - protein-RNA interactions mediating local mRNA translation in neurons.
in FEBS letters
Hobor F
(2018)
A cryptic RNA-binding domain mediates Syncrip recognition and exosomal partitioning of miRNA targets.
in Nature communications
Acton O
(2019)
Structural basis for Fullerene geometry in a human endogenous retrovirus capsid.
in Nature communications
Mittal A
(2018)
The structure of the RbBP5 ß-propeller domain reveals a surface with potential nucleic acid binding sites.
in Nucleic acids research
Description | Marie Curie FP7 |
Amount | € 221,606 (EUR) |
Funding ID | 626920 |
Organisation | European Commission |
Department | Research Executive Agency (REA) |
Sector | Public |
Country | Belgium |
Start | 09/2014 |
End | 09/2016 |
Description | Wellcome Trust Institutional Strategic Support Fund UCL |
Amount | £1,500,000 (GBP) |
Funding ID | 097815/Z/11/B |
Organisation | Wellcome Trust |
Department | Wellcome Trust Institutional Strategic Support Fund |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 04/2014 |
End | 06/2015 |
Title | 2D NMR lineshape analysis |
Description | A tool to extract kinetics and affinity information from 2D NMR lineshape analysis during a titration. This work is a collaboration with John Christodoulou's group. |
Type Of Material | Technology assay or reagent |
Year Produced | 2016 |
Provided To Others? | Yes |
Impact | More than 100 users have visited the site. |
Title | High-throughput analysis of protein-RNA interactions |
Description | High-throughput analysis of protein-RNA interactions using Scaffold Independent Analysis and Principal Component Analysis |
Type Of Material | Technology assay or reagent |
Provided To Others? | No |
Impact | This is a new tool. In the group has allowed to analyze a large number of protein-RNA binding domains |
Description | Development and application of NMR methods for the study of macromolecular complexes |
Organisation | Medical Research Council (MRC) |
Department | MRC Biomedical NMR Centre |
Country | United Kingdom |
Sector | Public |
PI Contribution | Framework, samples, intellectual input, recording and processing of experiments, data analysis |
Collaborator Contribution | intellectual input, recording and processing of experiments, data analysis. Recent we started a collaboration on a related problem with the group of John Christodoulou in UCL, SMB where we provided data and intellectual input and the Chrristodoulou group provided the framework of analysis. |
Impact | PMID: 25586222; PMID: 23142982; PMID: 20711187; PMID: 20385598; PMID: 19198587; PMID: 17437720; PMID: 16407062; PMID: 15929005; PMID: 15665873; PMID: 27109776 |
Description | Development and application of NMR methods for the study of macromolecular complexes |
Organisation | University College London |
Department | Institute of Structural and Molecular Biology |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Framework, samples, intellectual input, recording and processing of experiments, data analysis |
Collaborator Contribution | intellectual input, recording and processing of experiments, data analysis. Recent we started a collaboration on a related problem with the group of John Christodoulou in UCL, SMB where we provided data and intellectual input and the Chrristodoulou group provided the framework of analysis. |
Impact | PMID: 25586222; PMID: 23142982; PMID: 20711187; PMID: 20385598; PMID: 19198587; PMID: 17437720; PMID: 16407062; PMID: 15929005; PMID: 15665873; PMID: 27109776 |
Description | IMP1 structure and function |
Organisation | Albert Ludwig University of Freiburg |
Country | Germany |
Sector | Academic/University |
PI Contribution | structural and functional analysis of IMP1 interactions with the protein and RNA partners |
Collaborator Contribution | University of Freiburg - genomic analysis UCL - functional analysis Crick - biophysical modelling and use of facilities |
Impact | PMID: 28147274 This is a a multi-disciplinary collaboration. |
Start Year | 2015 |
Description | IMP1 structure and function |
Organisation | Francis Crick Institute |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | structural and functional analysis of IMP1 interactions with the protein and RNA partners |
Collaborator Contribution | University of Freiburg - genomic analysis UCL - functional analysis Crick - biophysical modelling and use of facilities |
Impact | PMID: 28147274 This is a a multi-disciplinary collaboration. |
Start Year | 2015 |
Description | IMP1 structure and function |
Organisation | University College London |
Department | Institute of Neurology |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | structural and functional analysis of IMP1 interactions with the protein and RNA partners |
Collaborator Contribution | University of Freiburg - genomic analysis UCL - functional analysis Crick - biophysical modelling and use of facilities |
Impact | PMID: 28147274 This is a a multi-disciplinary collaboration. |
Start Year | 2015 |
Description | IMP1 structure and function |
Organisation | University College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | structural and functional analysis of IMP1 interactions with the protein and RNA partners |
Collaborator Contribution | University of Freiburg - genomic analysis UCL - functional analysis Crick - biophysical modelling and use of facilities |
Impact | PMID: 28147274 This is a a multi-disciplinary collaboration. |
Start Year | 2015 |
Description | Molecular basis of syncrip-RNA recognition |
Organisation | Sapienza University of Rome |
Department | Department of Classics |
Country | Italy |
Sector | Academic/University |
PI Contribution | All the molecular and structural biology work |
Collaborator Contribution | provided information on the interaction between the Syncrip protein and cellular mRNA, provided some original clones |
Impact | This is a multi-disciplinary collaboration. A paper has been published this year. |
Start Year | 2014 |
Description | Molecular basis of syncrip-RNA recognition |
Organisation | University of Oxford |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | All the molecular and structural biology work |
Collaborator Contribution | provided information on the interaction between the Syncrip protein and cellular mRNA, provided some original clones |
Impact | This is a multi-disciplinary collaboration. A paper has been published this year. |
Start Year | 2014 |
Description | RBM10 RNA recognition and mRNA metabolism |
Organisation | Francis Crick Institute |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Molecular and structural work on RBM10 structure and RBM10-RNA recognition |
Collaborator Contribution | Bioinformatic work, functional splicing assays - Kings College Support with X-ray crystallography work - Crick Institute University of Toronto - RNAcompete assays |
Impact | This is a multi-disciplinary collaboration. the paper is under review |
Start Year | 2015 |
Description | RBM10 RNA recognition and mRNA metabolism |
Organisation | King's College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Molecular and structural work on RBM10 structure and RBM10-RNA recognition |
Collaborator Contribution | Bioinformatic work, functional splicing assays - Kings College Support with X-ray crystallography work - Crick Institute University of Toronto - RNAcompete assays |
Impact | This is a multi-disciplinary collaboration. the paper is under review |
Start Year | 2015 |
Description | RBM10 RNA recognition and mRNA metabolism |
Organisation | University of Toronto |
Country | Canada |
Sector | Academic/University |
PI Contribution | Molecular and structural work on RBM10 structure and RBM10-RNA recognition |
Collaborator Contribution | Bioinformatic work, functional splicing assays - Kings College Support with X-ray crystallography work - Crick Institute University of Toronto - RNAcompete assays |
Impact | This is a multi-disciplinary collaboration. the paper is under review |
Start Year | 2015 |
Description | iCLIP studies of multi-domain protein-RNA recognition |
Organisation | University College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | design of protein mutants, all cell biology studies, performing iCLIP, co-analysing iCLIP data |
Collaborator Contribution | provide expertise for designing iCLIP experiments, sequencing, co-analysing iCLIP the data |
Impact | This is a multi-disciplinary collaboration, the outputs are to come |
Start Year | 2013 |
Title | Macro for the PCA analysis of NMR spectra |
Description | This is a macro within the NMRPipe program to process NMR spectra and implement a PCA analysis. as described in the DOI below. |
Type Of Technology | Software |
Year Produced | 2015 |
Impact | The macro has been requested from groups in the US and Canada |
Description | Established the london RNA club |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Other academic audiences (collaborators, peers etc.) |
Results and Impact | We have set up a London RNA Club as a forum for the London RNA community. No such forum existed previously. We have designed a webpage for the forum: http://londonrnaclub.uk/ This has brought together the London RNA community |
Year(s) Of Engagement Activity | 2014 |