Logic-directed evolution of new biosensor molecules in vivo

Lead Research Organisation: Imperial College London
Department Name: Life Sciences

Abstract

The ability to rapidly and accurately detect small molecules has widespread use within security and defence contexts such as detection of explosives, biological agents or pathogens. This project will develop a new platform for the development of novel sensors. Sensors require highly specific detection of molecules in very low concentrations. The use of biological approaches for this purpose is attractive since many biological systems have evolved for precisely this purpose. While biological diversity offers a rich source of variety, it is ultimately limited to what can be isolated and characterised. In vitro methods for evolving new biological functionality and diversity have proven useful but are ultimately limited in the range of biological diversity that can be sampled. This project will develop a prototype for the evolution of new biological specificity in vivo, with feedback bio-'logic' circuitry that will enable end-point evolution of biological systems to new specificities. The isolation of new proteins with altered specificity will be essential for the creation of a new generation of biosensors.

Technical Summary

This proposal seeks to develop a new platform for the development of new-to-nature protein specificities suitable for use in biosensor devices. We will develop a novel method for the directed evolution of new specificities in signal transduction systems. We have developed an in vivo system in bacteria that is able to direct mutation to specific target genes, thus providing the basis for a mechanism of targeted directed evolution in vivo. This project will create a biological logic circuit that will self-limit the evolution to the point when a new specificity has been created, at this point the evolution will stop and a selectable output will be switched on. We have termed this end-point evolution.

The key problem in creating new biological specificity is identifying it. The sequence space in biological diversity is so vast, that identifying the one mutant that has the desired specificity is difficult. This project aims to tackle this directly by the design, modelling and implementation of genetic control circuits: 'Bio-Logic'. This will be programmed for end-point evolution so that the desired phenotype will switch off further mutation and switch on an output and selectable marker. The ability to threshold the response and increase stringency of selection is important and will come from lowering the concentration of the response molecule for which specificity is being engineered, and/or increasing the stringency of selection.

Planned Impact

The heightened terrorist threat has lead to the requirement for rapid and accurate detection of chemical and biological agents, as well as explosives. It must be considered that although the perceived threat from biological agents is low, recent enhancements in technologies such as gene synthesis, means that threat levels should not be treated as non-existent, nor indeed unchanging. The ability to detect biologically infectious agents is a strategic security requirement as well as a medical challenge. The development of cheap and easy to deploy explosives sensors in the environment could have a great impact on reducing the combat threat of expolsive devices, such as landmines and improvised explosive devices, as well as reducing the civilian impact from the millions of landmines that have been left in the ground. We therefore consider that the development of sensors for infectious agents and/or explosives may have the greatest potential for a step-change in technological driven approaches to these key problems.

Imagine a real-time explosives detector that can 'smell' the presence of an IED before it is reached, or identify airline passengers who have been in contact with restricted chemicals. Imagine a pathogen detection system that can easily detect water borne pathogens in remote and inaccessible locations, or identify an infection before it poses a clinical threat.

There is an increasing demand for new fast and accurate sensor technology and these futuristic scenarios are not necessarily far off. Both of the targets identified above require the detection of small molecules at very low concentrations. The exquisite molecular recognition that proteins are capable of provides an ideal platform for the basis of recognition. However, its key limitation is the ability to develop new specificities for molecular recognition. This proposal seeks to tackle this issue directly in a format that is readily adaptable for new molecular targets. This can therefore provide a technological platform that can be applied to the rapid development of new sensors. This has the potential to transform the pathway to the development of new biosensors.

Publications

10 25 50
 
Description We have developed our DNA assembly technology, which was necessary for the design and build aspect of this proposal.
We have built and tested individual components of the design that we specified
Exploitation Route The development of our DNA assembly methodology, although not a primary objective of this proposal has led to considerable other benefits, collaborations and further funding.
Sectors Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description Our DNA Assembly technology has been used by Industry
First Year Of Impact 2014
Sector Manufacturing, including Industrial Biotechology
Impact Types Economic

 
Description A semi-autonomous robot synthetic biologist for industrial biodesign and manufacturing
Amount £884,199 (GBP)
Funding ID EP/R034915/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 08/2018 
End 08/2021
 
Description BBSRC Network in Biotechnology
Amount £99,000 (GBP)
Funding ID Sub project from University of Manchester who hold the main Network award 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2015 
End 05/2016
 
Description EPSRC Innovation and Knowledge Centre in Synthetic Biology - 24 month review
Amount £2,010,000 (GBP)
Funding ID (EP/N023854/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 12/2015 
End 11/2018
 
Description EU Marie Curie IEF Fellowship
Amount € 221,606 (EUR)
Funding ID 628019 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 03/2014 
End 03/2016
 
Description Innovate UK
Amount £347,000 (GBP)
Funding ID 101847 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 06/2014 
End 07/2015
 
Description SynbiCITE - Innovation and Knowledge Centre in Synthetic Biology - Collaborative Programme - Tranche 1
Amount £2,907,115 (GBP)
Funding ID EP/M006700/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 06/2014 
End 09/2017
 
Description SynbiCITE - an Imperial College led Innovation and Knowledge Centre (IKC) in Synthetic BiologY
Amount £5,074,187 (GBP)
Funding ID EP/L011573/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 09/2013 
End 09/2018
 
Title BASIC DNA assembly 
Description This method provides for a highly scalable and efficient standardised method for assembling DNA parts to create new biological systems. 
Type Of Material Technology assay or reagent 
Year Produced 2014 
Provided To Others? Yes  
Impact High throughput DNA assembly is currently being implemented on an automated workflow for industrial collaboration. We have collaborations with a number of academic and industrial partners to translate this technology. 
 
Description Collaboration with Dr. Reddys 
Organisation Chirotech Technology
Country United Kingdom 
Sector Private 
PI Contribution We have translated our DNA assembly technology into Chirotech and they are now implementing this throughout their operation and Dr. Reddys. This has led to a BBSRC Biocatnet proof of concept funding to further develop this pipeline for developing optimised workflows and enhanced biological systems.
Collaborator Contribution Chirotech have provided industrial relevance and access to their enzymes.
Impact BBSRC Biocatnet proof of concept fund
Start Year 2013
 
Description Isogenica collaboration 
Organisation Isogenica
Country United Kingdom 
Sector Private 
PI Contribution We have brought our DNA assembly technology to Isogenica
Collaborator Contribution They have provided experience, context and advice.
Impact Innovate UK grant
Start Year 2014
 
Description BioSynSys 2015 Biologie de synthese et des systemes 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The establishment of a French GDR for systems and synthetic biology is intended to bring together the collective efforts of the French nation in this area of research as well as providing a method for further international interaction. I was invited as a plenary speaker to their inaugural conference.
Year(s) Of Engagement Activity 2015
URL http://biosynsys2015.sciencesconf.org/?lang=en
 
Description Invited Seminar at University of Stuttgart 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to give a seminar to the Institut für Bioverfahrenstechnik
Year(s) Of Engagement Activity 2015
 
Description Invited seminar at LMU Munich 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to give a plenary talk at the Institute retreat.
Year(s) Of Engagement Activity 2015
 
Description Research conference - Industrial Biotechnology Dalian, China 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Stimulated discussions and I made a contact with industry who is interested in using our technology

I made a contact with industry who is interested in using our technology
Year(s) Of Engagement Activity 2014
 
Description Visit to CSIC Madrid 
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 This was a 3 day visit to the laboratory of Victor de Lorenzo, to share our ideas and practices and to develop new ideas and projects.

There were many discussions during the 3 days that cross-fertilised a lot of ideas.
Year(s) Of Engagement Activity 2014
 
Description Visit to WITS University, South Africa 
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 generated a lot of interest and increased peoples awareness of synthetic biology.

Created a new collaboration that will facilitate sharing of tools, resources and ideas with a developing nation.
Year(s) Of Engagement Activity 2014
 
Description Workshop: Synthetic biology: containment and release of engineered micro-organisms, Kings College 2013 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact I was extensively involved in the discussions during the workshop

The workshop produced a Scoping Report, which was used as evidence by the Secretariat of the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA) of the Convention on Biological Diversity, for its preparatory work to determine whether synthetic biology should be identified as a 'New & Emerging Issue relating to the conservation and sustainable use of biodiversity" under the Convention.
Year(s) Of Engagement Activity 2013
URL http://www.kcl.ac.uk/sspp/departments/sshm/research/csynbi-PDFs/Scoping-Report.pdf
 
Description Workshop: Worldviews and values in Synthetic Biology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact The presentation was integrated into two days of discussion amongst workshop participants. The outcome of the workshop was a public document that has been widely disseminated.
http://synenergene.eu/resource/summary-report-paris-workshop-worldviews-and-values-synthetic-biology


The outcome of the workshop was a public document that has been widely disseminated.
http://synenergene.eu/resource/summary-report-paris-workshop-worldviews-and-values-synthetic-biology
Year(s) Of Engagement Activity 2014
URL http://synenergene.eu/resource/summary-report-paris-workshop-worldviews-and-values-synthetic-biology