Mapping combinatorial stress responses in bacteria using chimeric proteins and probabilistic modelling
Lead Research Organisation:
Imperial College London
Department Name: Life Sciences
Abstract
Living systems adapt to changing environments in order to survive and to grow and reproduce. Features of an adaptive response have to date been studied in a fairly one dimensional way, yet we know that the cell operates using networks of interactions between the key players that are responsible for the cells growth and viability. These players can sense stress, some will cause new players to appear in the cell, and some of these will work to overcome the stress in different ways. However the relationships between these different players and the levels at which they operate are largely unknown. In particular whether or not a single unique solution to a set of imposed conditions is all that can reasonably operate in the cell is a major unknown. Knowledge of the boundary conditions acceptable to a cell will greatly help advance work where special properties of a cell are desirable, as for example in many biotechnological and synthetic biology settings. By studying two important but relatively experimentally amenable single cell bacteria we will study what cell components change when the cells respond to stress and how their patterns of response amount to an integrated response to stress. To do so we will collect data across several different areas of cell activity, and will perturb cells using novel control proteins to redirect responses away from particular imposed stresses. Data analysis coupled to mathematical modelling will be conducted in order to integrate and describe the observed cellular behaviour, and to help explain how the processes contributing to the cell's responses work as a whole. The collection of data is targeted directly at informing the development and evaluation of mechanistic models of cell response. We have chosen to conduct the same experimental programme in two different bacterial organisms. This comparative dimension to the proposed research project allows us to explore the evolutionary aspects underlying the response to stresses that are intimately linked to bacterial pathogenesis. This also has the potential to inform future analyses in synthetic biology or attempts to direct microorganismal evolution. At the end of the research program we expect to able to better predict how cells cope with large changes in their environments, through a knowledge of which activities within the cell are key to achieving adaptation to stress. Outcomes of the work should provide insights into how cells might be forward evolved for particular purposes, and identify where particular vulnerabilities might exist that may suggest new targets for remedial therapies such as new antibiotic targets.
Technical Summary
Bacteria respond to changing environments by redirecting gene expression to cope with the applied stress, during infection and in the environment as nutrient and abiotic conditions vary. How the complex signal transduction pathways, the associated metabolic factors and protein factors inter-relate to achieve the necessary adaptive changes in the cell has not been well studied at an integrated level. In particular how combinatorial stresses cause adaptive change in the cell is unknown. We plan to use non-native bio-synthetic regulatory proteins to rewire signal transduction pathways to reprogram E. coli and M. tuberculosis to elicit specific gene expression changes, uncoupled from the cognate native cues of gene expression. The main strength of synthetic proteins to study complex biological systems is that they can be made to function independent from the native physiological context. Hence the complex control feedback mechanisms that regulatory systems usually employ to regulate genetic and metabolic flow can be separated out. We plan to produce and characterise bio-synthetic domain exchanged (chimeric) transcription activators of the bacterial RNA polymerase to control genetic flow under defined sets of stress conditions. These chimera will be used to dissect genetic and metabolic control of nitrogen regulation and other stresses and to gauge the relative contributions of genetic and metabolic factors to cell adaptation. Methodologies include quantitative proteomics of key players, metabolic profiling and array technologies to measure protein-DNA interactions and transcript responses linked to advanced modelling approaches. Results of the project are anticipated to contribute significantly to biotechnology, infection research and emerging fields of synthetic and systems biology. Synthetic biology can be applied to uncover design principles of complex genetic networks through dissecting the functional performance of modular system components of the cell.
Organisations
Publications
Adrian Bartos (Author)
(2011)
Toxic metal detection in foodstuff.Synthetic biology approach used to create biosensors
Ale A
(2013)
A general moment expansion method for stochastic kinetic models.
in The Journal of chemical physics
Barnes CP
(2011)
Bayesian design of synthetic biological systems.
in Proceedings of the National Academy of Sciences of the United States of America
Beguerisse-Diaz M
(2012)
Compound stress response in stomatal closure: a mathematical model of ABA and ethylene interaction in guard cells
in BMC Systems Biology
Beguerisse-Díaz M
(2016)
Linear models of activation cascades: analytical solutions and coarse-graining of delayed signal transduction.
in Journal of the Royal Society, Interface
Beguerisse-Díaz M
(2012)
Squeeze-and-breathe evolutionary Monte Carlo optimization with local search acceleration and its application to parameter fitting.
in Journal of the Royal Society, Interface
Behrends V
(2012)
Free glucosylglycerate is a novel marker of nitrogen stress in Mycobacterium smegmatis.
in Journal of proteome research
Behrends V
(2011)
A software complement to AMDIS for processing GC-MS metabolomic data.
in Analytical biochemistry
Description | Large novel data sets and sophisticated and adapted mathematical models have shed unprecedented light into the complexities of how bacterial cells cope with stress . These are detailed in dozens of our publications. |
Exploitation Route | The finding will be taken forward in translational biology by ourselves, thanks to the BBSRC sLoLa funding BB/N003608. Globally, findings have contributed to supporting re-vitalising the field of bacterial nitrogen assimilation and fixation. Bacteria process the bulk of the global nitrogen cycle. Severe global nitrogen imbalances that result from fertiliser production and application has been deemed the second biggest ecological challenge facing human development (Rockström et al. (2009) A safe operating space for humanity. Nature 461: 472-475). Our findings contributed to the knowledge base that could address this challenge. |
Sectors | Agriculture Food and Drink Environment Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
Description | As impetus for RCUK policy recommendations on synthetic biology and educational on microbiology through Royal Society summer exhibition. |
First Year Of Impact | 2013 |
Sector | Education,Environment,Government, Democracy and Justice |
Impact Types | Societal |
Description | A synthetic biology roadmap for the UK |
Geographic Reach | Europe |
Policy Influence Type | Citation in other policy documents |
Impact | The roadmap provided guidance for academics and society on the future directions of the emerging field of synthetic biology |
URL | http://www.rcuk.ac.uk/RCUK-prod/assets/documents/publications/SyntheticBiologyRoadmap.pdf |
Description | Biotechnology options for tackling the global nitrogen crisis |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Contribution to a national consultation/review |
URL | http://www.foodsecurity.ac.uk/blog/2015/11/the-nitrogen-crisis-what-are-the-solutions/ |
Description | BBSRC Oxygen-tolerant nitrogenase |
Amount | £825,000 (GBP) |
Funding ID | BB/L011468/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 12/2013 |
End | 12/2016 |
Description | BBSRC strategic LoLa |
Amount | £4,000,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 01/2016 |
End | 01/2020 |
Description | Divalent metal ions: Bacterial signaling and scope for biosensors |
Amount | £6,000 (GBP) |
Organisation | European Molecular Biology Organisation |
Sector | Charity/Non Profit |
Country | Germany |
Start |
Description | Wellcome Trust 4 year Phd Programme |
Amount | £2,400,000 (GBP) |
Organisation | Wellcome Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 09/2016 |
End | 09/2022 |
Description | Clever Microbes |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Royal Society Summer Exhibition 2013 no actual impacts realised to date |
Year(s) Of Engagement Activity | 2013 |
URL | http://sse.royalsociety.org/2013/ |
Description | How bacteria may power computers |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Article in Financial Times Magazine http://www.ft.com/cms/s/2/25a1f6d4-ff5e-11e0-aa11-00144feabdc0.html#axzz1cjfiNUDt Dissemination Lola outcomes to wider public no actual impacts realised to date |
Year(s) Of Engagement Activity | 2011 |
URL | http://www.ft.com/cms/s/2/25a1f6d4-ff5e-11e0-aa11-00144feabdc0.html#axzz1cjfiNUDt |
Description | Integrating genome-scale metabolic models with -omic data to improve functional annotation in Mycobacterium tuberculosis |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | We intend to integrate several data sources to improve the level of annotation in fully sequenced organisms using M. tuberculosis and M. smegmatis as model subjects. We will take into account: metabolic network properties, protein structure prediction, models of molecular evolution and high quality -omic data to expand and improve gene annotations for these organisms. Data will include transcriptomic, metabolomic, proteomic, phosphoproteomic and ChIP-chip analyses of the two organisms. Through the combination of many data and model types we hope to provide a powerful system for the annotation of genes thus far recalcitrant to functional assignment. Poster no actual impacts realised to date |
Year(s) Of Engagement Activity | 2010 |
Description | Outreach for schoolchildren |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Schools |
Results and Impact | Member of team running outreach activities for schoolchildren visiting the section of Computational and Systems Medicine; regular occurrence, 3 times per year on average. Please NB that start and end dates refer to the total period over which these visits were arranged: 6 school visits took place over this period, 1 day for each. no actual impacts realised to date |
Year(s) Of Engagement Activity | 2012 |
URL | http://www.cambridgeliteraryfestival.com/events/thinking-aloud-1-stem-cells |
Description | Two genes better than one for important plant pest |
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 | Following publication of Jovanovic et al. (2011) in Nature Communications (see publication outputs). BBSRC News and Events, media outlet, see: http://www.bbsrc.ac.uk/news/food-security/2011/110201-pr-two-genes-better-than-one.aspx no actual impacts realised to date |
Year(s) Of Engagement Activity | 2011 |
URL | http://www.bbsrc.ac.uk/news/food-security/2011/110201-pr-two-genes-better-than-one.aspx |