Unravelling the modular architecture of the Ccr4Not-complex
Lead Research Organisation:
University of Edinburgh
Department Name: Sch of Biological Sciences
Abstract
The development of systems biology has revealed that cells use complex functional networks, to control all aspects of life, including responses to the external environment. Perturbation of these networks can leads to too little or too much growth of the cells or even to cell death. Control and fine-tuning of the diverse networks in response to environmental changes is accomplished by adjusting the abundance of the individual proteins according to the actual needs of the cell.
One obvious way to do this is to change the levels of their corresponding mRNAs. The Ccr4Not complex, global player in the regulation of the mRNA levels acts at both ends of the spectrum of mRNA life. On the one hand, it can target the RNA polymerase II to genes to produce new copies of mRNAs. On the other, it can prepare selected mRNAs for degradation. In order to ensure that appropriate adjustments are made, the Ccr4Not-complex senses the state of the cell by communicating with reporter proteins. According to the reports received, the complex switches its functionality and regulates mRNA levels either positively or negatively.
Today, we understand very little about how the Ccr4Not complex accomplishes this fascinating role as master control complex. Some evidence suggests that it has different modules, which it can activate, deactivate, add or delete. Yeast has at least two Ccr4Not complexes: a smaller core complex and a larger complex whose various attachments provide additional functionalities.
I propose to explore where the modules and the attachments are placed and how they switch the functionality of the complex. We will use electron microscopy to visualize the different variants of the complex followed by computational analysis to reconstruct their three-dimensional shapes. The resulting structures will tell us how the different modules are arranged in respect to each other and may provide insight into the mechanisms underlying their regulation of mRNA levels.
The different variants of the Ccr4Not complex can either promote degradation of mRNA or promote generation of mRNA. These different processes occur at different places in the cell. We will use advanced light microscopy to map the distribution of the different variants of the Ccr4Not complex in cells and determine how this changes under different growth conditions.
As a master controller, the Ccr4Not complex is vital for the health of cells and organisms. This is especially evident in stress situations, where cells with impaired Ccr4Not complexes fail to grow properly. At the organismal level, defects in the Ccr4Not complex can lead to heart disease or influence the outcome of certain types of cancer. Indeed the links between function of the Ccr4Not-complex and human health are only now beginning to emerge. Therefore, a mechanistic understanding of structure/function relationships in the Ccr4Not complex will yield important insights, both for a basic understanding of how cells interact with their environment, but also for human health.
One obvious way to do this is to change the levels of their corresponding mRNAs. The Ccr4Not complex, global player in the regulation of the mRNA levels acts at both ends of the spectrum of mRNA life. On the one hand, it can target the RNA polymerase II to genes to produce new copies of mRNAs. On the other, it can prepare selected mRNAs for degradation. In order to ensure that appropriate adjustments are made, the Ccr4Not-complex senses the state of the cell by communicating with reporter proteins. According to the reports received, the complex switches its functionality and regulates mRNA levels either positively or negatively.
Today, we understand very little about how the Ccr4Not complex accomplishes this fascinating role as master control complex. Some evidence suggests that it has different modules, which it can activate, deactivate, add or delete. Yeast has at least two Ccr4Not complexes: a smaller core complex and a larger complex whose various attachments provide additional functionalities.
I propose to explore where the modules and the attachments are placed and how they switch the functionality of the complex. We will use electron microscopy to visualize the different variants of the complex followed by computational analysis to reconstruct their three-dimensional shapes. The resulting structures will tell us how the different modules are arranged in respect to each other and may provide insight into the mechanisms underlying their regulation of mRNA levels.
The different variants of the Ccr4Not complex can either promote degradation of mRNA or promote generation of mRNA. These different processes occur at different places in the cell. We will use advanced light microscopy to map the distribution of the different variants of the Ccr4Not complex in cells and determine how this changes under different growth conditions.
As a master controller, the Ccr4Not complex is vital for the health of cells and organisms. This is especially evident in stress situations, where cells with impaired Ccr4Not complexes fail to grow properly. At the organismal level, defects in the Ccr4Not complex can lead to heart disease or influence the outcome of certain types of cancer. Indeed the links between function of the Ccr4Not-complex and human health are only now beginning to emerge. Therefore, a mechanistic understanding of structure/function relationships in the Ccr4Not complex will yield important insights, both for a basic understanding of how cells interact with their environment, but also for human health.
Technical Summary
The Ccr4Not complex regulates gene expression by mechanisms conserved from yeast to humans. Some of the regulatory functions of the Ccr4Not-complex are at the transcriptional level and probably linked to the core promoter binding whereas others involve the deadenylation of the poly(A)-tail of mRNA, which is a signal for mRNA-degradation. Current evidence suggests that the Ccr4Not-complex has a modular architecture, which enables it to change its function. In yeast the Ccr4Not complex exists in two variants, with approximately 1 MDa and 1.9 MDa, respectively. Despite the important regulatory role of the Ccr4Not complex, structural insights into the organization of this complex regulator are few, and further study is imperative. I hypothesize that changes in the modular organisation of the complex may help cells to adapt to different growth conditions. I therefore propose to use electron microscopy and image processing to study the architecture of the core complex and its larger variant. These investigations will reveal how the two variants are organized, where the subunits and modules in the complexes are located and how the core-complex changes its conformation upon substrate binding. These structural studies will be complemented by biochemical and biophysical characterization of the binary protein-protein and protein-substrate interactions using surface plasmon resonance measurements and state-of-the-art mapping of crosslinks between members of the isolated complexes by mass spectrometry. Characterization of the binary interactions will reveal the network of interactions between subunits in the Ccr4Not complex, their contribution to the stability of the complex and identify subunits that contribute to substrate binding. Finally, live cell imaging will map the distribution of the large and small variants of the Ccr4Not-complex in cells and reveal how it changes during the cell cycle and in response to the nutritional state of the cell.
Planned Impact
Who will benefit from the research?
The immediate beneficiaries are in the academic sector, and include students in Biology and Molecular Medicine, researchers in Cell-Biology, RNA-Biology and molecular Electron Microscopy. In longer terms, the research might become important for pharmacologists, who want to exploit the regulatory role of the Ccr4Not-complex in controlling heart disease and certain cancers. Further indirect beneficiaries are members of the School of Biological Sciences at the University of Edinburgh (UoE) and SULSA (Scottish University Alliance for Live Science).
How will they benefit from this research?
The outcome of the research will increase the general understanding on how levels of mRNA are controlled in the cell. This is a fundamental question in Biology, which is vital to health and disease. Therefore, research in this area will update the text book knowledge, which is taught to students in Cell Biology, Molecular Biology and molecular Medicine.
Researchers in Cell Biology and RNA-Biology will benefit from a structural model of the Ccr4Not complex, which will be important for informing experiments to probe the function of the complex in a rational way.
A link between heart disease and the malfunction of a component of the Ccr4Not complex was established in 2010. This demonstrates the global impact that the disturbance of the Ccr4Not complex has on the whole organism. Other studies suggest links between other components of the Ccr4Not-complex and colorectal cancer. Due to this involvement in different types of diseases, it appears likely that the Ccr4Not complex will emerge as an important drug target in future. The exploitation of this drug target would greatly benefit from detailed structural insights into the organization of the complex.
Members at the School of Biological Sciences at the UoE will benefit from the local implementation and improvement of baculovirus expression. The proposed project will increase the local critical mass of expertise and thus will help to start further projects using similar methods quicker and more cost-effective.
Users of the High-Resolution Cryo Electron microscopy Facility at the UoE from across Scotland will gain from the project-based implementation and enhancement of high-resolution data acquisition and single particle image analysis.
The project is divided in several smaller sub-projects, which offer potential for the training of research students at the cutting edge of technology in electron microscopy, complex expression and protein-protein interaction studies. In the long-term, this will produce highly trained individuals, with a good portfolio of experimental methods that will enable them to tackle new projects from different methodological angles.
What will be done to ensure that the beneficiaries benefit from this research?
The scientific results of this research will be communicated to the beneficiaries by publication in peer reviewed journals, by deposition of the data in appropriate data bases and by the presentation of the results in national and international meetings.
Technological advances established in the EM-facility at the UoE will be communicated to other facility-users in local users meetings, Wiki-style protocols and project based experimental advice supported by the SULSA technologist (Chris Kennaway). Chris will also be involved in the project, which will enable an effective transfer of knowledge between different projects in the facility.
The immediate beneficiaries are in the academic sector, and include students in Biology and Molecular Medicine, researchers in Cell-Biology, RNA-Biology and molecular Electron Microscopy. In longer terms, the research might become important for pharmacologists, who want to exploit the regulatory role of the Ccr4Not-complex in controlling heart disease and certain cancers. Further indirect beneficiaries are members of the School of Biological Sciences at the University of Edinburgh (UoE) and SULSA (Scottish University Alliance for Live Science).
How will they benefit from this research?
The outcome of the research will increase the general understanding on how levels of mRNA are controlled in the cell. This is a fundamental question in Biology, which is vital to health and disease. Therefore, research in this area will update the text book knowledge, which is taught to students in Cell Biology, Molecular Biology and molecular Medicine.
Researchers in Cell Biology and RNA-Biology will benefit from a structural model of the Ccr4Not complex, which will be important for informing experiments to probe the function of the complex in a rational way.
A link between heart disease and the malfunction of a component of the Ccr4Not complex was established in 2010. This demonstrates the global impact that the disturbance of the Ccr4Not complex has on the whole organism. Other studies suggest links between other components of the Ccr4Not-complex and colorectal cancer. Due to this involvement in different types of diseases, it appears likely that the Ccr4Not complex will emerge as an important drug target in future. The exploitation of this drug target would greatly benefit from detailed structural insights into the organization of the complex.
Members at the School of Biological Sciences at the UoE will benefit from the local implementation and improvement of baculovirus expression. The proposed project will increase the local critical mass of expertise and thus will help to start further projects using similar methods quicker and more cost-effective.
Users of the High-Resolution Cryo Electron microscopy Facility at the UoE from across Scotland will gain from the project-based implementation and enhancement of high-resolution data acquisition and single particle image analysis.
The project is divided in several smaller sub-projects, which offer potential for the training of research students at the cutting edge of technology in electron microscopy, complex expression and protein-protein interaction studies. In the long-term, this will produce highly trained individuals, with a good portfolio of experimental methods that will enable them to tackle new projects from different methodological angles.
What will be done to ensure that the beneficiaries benefit from this research?
The scientific results of this research will be communicated to the beneficiaries by publication in peer reviewed journals, by deposition of the data in appropriate data bases and by the presentation of the results in national and international meetings.
Technological advances established in the EM-facility at the UoE will be communicated to other facility-users in local users meetings, Wiki-style protocols and project based experimental advice supported by the SULSA technologist (Chris Kennaway). Chris will also be involved in the project, which will enable an effective transfer of knowledge between different projects in the facility.
Organisations
People |
ORCID iD |
Bettina Boettcher (Principal Investigator) |
Publications
Böttcher B
(2015)
Viral Nanotechnology
Böttcher B
(2015)
The Structure of YnaI Implies Structural and Mechanistic Conservation in the MscS Family of Mechanosensitive Channels.
in Structure (London, England : 1993)
Dong H
(2013)
Crystal structure of Schmallenberg orthobunyavirus nucleoprotein-RNA complex reveals a novel RNA sequestration mechanism.
in RNA (New York, N.Y.)
Grimm C
(2019)
Structural Basis of Poxvirus Transcription: Vaccinia RNA Polymerase Complexes.
in Cell
Song B
(2019)
Capabilities of the Falcon III detector for single-particle structure determination.
in Ultramicroscopy
Sundaramoorthy R
(2017)
Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.
in eLife
Description | the production of the different building blocks of the Ccr4Not complex was established; the interaction of the building blocks was quantified; the complex was purified from yeast and characterized by EM |
Exploitation Route | The research is still under way, the methodological findings have been shared at conferences and EMBO courses |
Sectors | Education,Pharmaceuticals and Medical Biotechnology |
Description | Findings and research have been used to train students at a high level |
First Year Of Impact | 2013 |
Sector | Education |
Impact Types | Economic |
Description | Multi User Equipment Grant |
Amount | £389,083 (GBP) |
Organisation | Wellcome Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 01/2015 |
End | 12/2019 |
Description | Research Grant |
Amount | € 356,000 (EUR) |
Funding ID | BO1150/15-1 |
Organisation | German Research Foundation |
Sector | Charity/Non Profit |
Country | Germany |
Start | 05/2017 |
End | 04/2020 |
Description | Sachbeihilfe Interaction of Hepatitis B surface protein fragments with Hepatitis B capsids |
Amount | € 409,950 (EUR) |
Funding ID | bo1150/17-1 |
Organisation | German Research Foundation |
Sector | Charity/Non Profit |
Country | Germany |
Start | 09/2019 |
End | 08/2022 |
Description | Sachbeihilfe: Structure of Lymphostatin |
Amount | € 309,650 (EUR) |
Funding ID | bo1150/18-1 |
Organisation | German Research Foundation |
Sector | Charity/Non Profit |
Country | Germany |
Start | 01/2020 |
End | 12/2022 |
Description | University of Wuerzburg-Graduate School of Life Sciences |
Amount | € 60,000 (EUR) |
Organisation | University of Wurzburg |
Sector | Academic/University |
Country | Germany |
Start | 09/2016 |
End | 08/2019 |
Description | Creation of a project Website |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | A web site for the project was created and linked to the group web site A project specific website was produced to inform on the project, the staff and other relevant resources on the Web Webpage no actual impacts realised to date |
Year(s) Of Engagement Activity | 2013 |
URL | http://boettcher.bio.ed.ac.uk/ccr4not/ccr4not.php |
Description | EMBO practical course on 3D-EM |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Workshop on cryo-EM techniques; Taught students single particle image processing. The postgraduate students gained expert insight into the method, which enabled them to use the method in their home institutes. |
Year(s) Of Engagement Activity | 2016 |
Description | Introducing the project at the University of Wuerzburg |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Postgraduate students |
Results and Impact | Instritute attended to learn about the state of the project. Talk sparked an intense discussion about methods |
Year(s) Of Engagement Activity | 2017 |
Description | Lecture to WT-PhD students |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Postgraduate students |
Results and Impact | The research project was explained to newly arrived Wellcome Trust PhD-students. The aim was to make the students aware of this line of research and to attract them for a possible rotation project Powerpoint presentation no actual impacts realised to date |
Year(s) Of Engagement Activity | 2013 |
Description | Lecture: Studying biological assemblies by electron microscopy and image processing |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | Yes |
Geographic Reach | regional |
Primary Audience | Participants in your research or patient groups |
Results and Impact | A lecture was given in Dundee to make the local community aware of the potential of the method and the developments in methods in Edinburgh Power point presentation no actual impacts realised to date |
Year(s) Of Engagement Activity | 2013 |
Description | Microscopy Conference in London |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | the talk was attended by a multidisciplinary audience that changed their views on the capabilities of the method |
Year(s) Of Engagement Activity | 2015 |
Description | Poster Presentation and Talk by Cihan Makbul at the EMBO workshop on macromolecular complex characteriization |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other academic audiences (collaborators, peers etc.) |
Results and Impact | lively discussion with peers about the project started collaboration with group in Grenoble |
Year(s) Of Engagement Activity | 2014 |
Description | Talk @ Microscopy Conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other academic audiences (collaborators, peers etc.) |
Results and Impact | talk sparked interest in electron cryo microscopy sparked discussions with some companies and oversea colleagues |
Year(s) Of Engagement Activity | 2015 |
Description | Talk Gordon Research Conference on 3DEM |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other academic audiences (collaborators, peers etc.) |
Results and Impact | 200 colleagues attended talk, which sparked discussion about what is needed to obtain certain results some discussions with colleagues on what is needed in equipment and how feasible it is to have high-end equipment in naional facilities compared to in individual labs |
Year(s) Of Engagement Activity | 2014 |
Description | Talk at Stuttgart University |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Postgraduate students |
Results and Impact | 60 students attended the talk; discussed details of the method with individual Post-Grad students, made them consider electron microscopy for their own research; attracted one PhD-student into electron microscopy and image processing; promoted his attendance of the international EMBO course on electron microscopy and image processing |
Year(s) Of Engagement Activity | 2014 |
Description | Talk at the Cryo EM workshop at LMB-Cambridge |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other academic audiences (collaborators, peers etc.) |
Results and Impact | some 100 researchers and students attended; their was a lively discussion on the topic and exchange of information on all different aspects of the method none |
Year(s) Of Engagement Activity | 2014 |
Description | Talk at the University Frankfurt |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Postgraduate students |
Results and Impact | The talk started a lively discussion about best practise for efficient data acquisition |
Year(s) Of Engagement Activity | 2015 |
Description | Talk at the University Wuerzburg "Studying biological assemblies by electron microscopy and image processing" |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Postgraduate students |
Results and Impact | The talk influenced the views on the potential of electron microscopy. It sparked discussions about setting-up a cryo EM facility locally. |
Year(s) Of Engagement Activity | 2015 |
Description | Talk at the University of Freiburg |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Participants in your research and patient groups |
Results and Impact | Introducing the potential of electron microscopy for investigating biological nano machines talk to the Chemistry department. Discussion of electron microscopy as a method in Biophysics power point presentation no actual impacts realised to date |
Year(s) Of Engagement Activity | 2013 |
Description | Talk to WT-roatation students |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | students attended the talk and similar talks of colleagues; this informed their choice of rotation projects and consequently research topics for the PhD-studies none |
Year(s) Of Engagement Activity | 2014 |
Description | Talk to Wellcome Trust Students |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Postgraduate students |
Results and Impact | students started considering electron microscopy for their research; they became interested in our Research on the Ccr4Not Complex students asked questions, 1 student selected a rotation project in the described topic |
Year(s) Of Engagement Activity | 2015 |
Description | Talk to Wellcome Trust Students 2015 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Postgraduate students |
Results and Impact | I showed the students the potential of electron microscopy. Some changed their views on the topic and selected a rotation practical to extend their knowledge in this area |
Year(s) Of Engagement Activity | 2015 |
Description | Talk: Structure determination of biological complexes by electron microscopy and image processing |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | Yes |
Geographic Reach | International |
Primary Audience | Participants in your research or patient groups |
Results and Impact | Invited seminar at the University of Mainz Talk in a minisymposium in the Biology department of the University of Mainz. power point presentation no actual impacts realised to date |
Year(s) Of Engagement Activity | 2013 |
Description | Teacher in EMBO-Practical Course on electron cryo microscopy and image processing |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | 25 international students were trained in high level electron microscopy and image processing better skills in data analysis in group of students |
Year(s) Of Engagement Activity | 2014 |
Description | Tlk in Birmingham "Recent Technologies in Microbiology" |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Postgraduate students |
Results and Impact | PhD-student organized symposium in Birmingham. The PhD students wanted to learn about new techniques and had invited several experts in their fields. The talk parked questions and discussion afterwards |
Year(s) Of Engagement Activity | 2015 |
Description | eBic sample preparation course |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | participants were intoduced to sample preparation in cryo-EM with hands-on demonstrations. This sparke questions and enabled students to use the method for their own research. |
Year(s) Of Engagement Activity | 2017 |