13TSB_SynBio Ligniflex: A synthetic biology platform to optimise the process and products of enzymatic lignin disruption

Lead Research Organisation: University of Edinburgh
Department Name: Sch of Biological Sciences

Abstract

Increasing global energy consumption is accelerating the rate of fossil fuel depletion. When oil reserves are eventually exhausted the essential by-products produced in refining will no longer be available. Since these aromatic chemicals are used in many processes including the manufacture of plastics, detergents, fertilizers, pharmaceuticals, paints and synthetic fibres it is vital that alternative sources become available.

Lignin is the 'woody' part of plants and therefore it can be produced sustainably, it is renewable and a natural form of carbon storage. Importantly for this proposal, it is a complex polymer made of aromatic chemical building blocks, potential replacements for the aforementioned non-renewable aromatic oil-refining by-products.

Our goal is to test the feasibility of producing low molecular weight aromatic chemical feedstocks from the lignin that is currently a waste product from wood processing and paper manufacturing, so that it may be used to manufacture useful products. We propose to develop a "front-end" to optimise the conversion of lignin into its constitutive aromatic chemical building blocks. This technology may be bolted to any "back-end" in a biorefinery to produce bioplastics, biosurfactants, biomaterials and so on. By exploring and optimising a technology which allows for the rapid tuning of bacteria or fungi for exploiting the conversion of lignin, we stand to limit waste by being able to optimise the degradation products being used as chemical feedstocks and diversify the range of end-bioproducts possible.

The proposed work uses a novel synthetic biology platform to create gene combinations which give the optimal degradation (with regards to efficiency and products produced) of waste lignin. These combinations may then be used as a starting point to generate further combinations in an iterative design-make-test process. This will create value for the user in terms of improvements in the yield of lignin conversion to useable feedstock. In addition to enabling the optimisation of enzyme blends for any given application, analysis of the results will allow the team to develop heuristics which will facilitate the rational design of whole biomass processing systems in the future, and will lead to a deeper understanding of biomass degradation processes.

Therefore, in brief, we are proposing to use synthetic biology to engineer microorganisms capable of enzymatically degrading waste from the paper manufacturing industry to provide a new source of aromatic feedstock molecules, securing the supply of these molecules to industry and ensuring society can continue to use the everyday items we all take for granted. An integral phase of the project will involve applying state of the art analytical techniques to positively identify discrete low molecular weight aromatic chemicals to produce viable commercial leads derived from novel engineered lignolytic activity.

The technology developed will be offered to the marketplace by Ingenza Ltd. There are a number of possible routes for commercialisation including:
i.) Biomanufacture of bulk quantities of the enzyme blend for sale direct to biorefinery operators as cell lysate or extract. ii.) Alternatively, the specific cell line itself could be made available under license to a customer, as a lignolytic processing tool. iii.) Provision of a contract service to customers wishing to have a bespoke digestion chassis implemented for the particular biomass of interest to them; probably involving some form of strain maintenance and further modification as required.

Technical Summary

Our goal is to test the feasibility of producing low molecular weight aromatic chemical feedstocks from the lignin that is currently a waste product from wood processing and paper manufacturing, so that it may be used to manufacture useful products. We propose to develop a "front-end" to optimise the conversion of lignin into its constitutive aromatic chemical building blocks. This technology may be bolted to any "back-end" in a biorefinery to produce bioplastics, biosurfactants, biomaterials and so on. By exploring and optimising a technology which allows for the rapid tuning of bacteria or fungi for exploiting the conversion of lignin, we stand to limit waste by being able to optimise the degradation products being used as chemical feedstocks and diversify the range of end-bioproducts possible.

The proposed work uses a novel synthetic biology platform to create gene combinations which give the optimal degradation (with regards to efficiency and products produced) of waste lignin. These combinations may then be used as a starting point to generate further combinations in an iterative design-make-test process. This will create value for the user in terms of improvements in the yield of lignin conversion to useable feedstock. In addition to enabling the optimisation of enzyme blends for any given application, analysis of the results will allow the team to develop heuristics which will facilitate the rational design of whole biomass processing systems in the future, and will lead to a deeper understanding of biomass degradation processes.

The technology developed will be offered to the marketplace by Ingenza Ltd. There are a number of possible routes for commercialisation including:
i.) Biomanufacture of bulk quantities of the enzyme blend for sale direct to biorefinery operators. ii.) Licensing of the specific cell line as a lignolytic processing tool. iii.) Provision of a contract service to customers wishing to have a bespoke digestion chassis.

Planned Impact

"The Technology Strategy Board does not require this section to be completed for this call".
 
Description In this project we screened the genomes of biomass-degrading microorganisms for sequences encoding candidate genes for lignin degrading enzymes. These genes were codon optimized for yeast, synthesised in a standardised modular format and expression levels were engineered to optimize inducible expression. Our industrial partner, Ingenza, performed large-scale combinatorial assembly in order to produce a large number of combinations of genes and expression control systems. Together, we characterised the performance of these putative lignin degrading enzymes and combinations of enzymes, demonstrating feasibility using novel high-throughput solid phase screens. We also assessed the performance of our degradation cassettes on industrial waste lignin and analysed the reaction products.
Exploitation Route The novel enzymes identified are being further characterised in our laboratory through the work of PhD students.
We were successful in our application to the Scottish IBioIC for a studentship, with a cash contribution from the Forestry Commission Scotland of £28k and an offer of in kind support from the SME Bio-Sep Ltd.
We also intend to investigate the impact of pretreatments prior to enzyme degradation with the input of Ingenza and other SMEs.
Developments will be communicated, through conferences and the BBSRC NIBB phase 2, to academia and industry (bioenergy and IB sector).
Sectors Agriculture, Food and Drink,Energy,Manufacturing, including Industrial Biotechology

 
Description Coordinated a University response to the Convention on Biological Diversity
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a national consultation
 
Description Coordinated responses to the Convention on Biological Diversity on the potential impacts of synthetic biology opinions II and III
Geographic Reach Europe 
Policy Influence Type Participation in a national consultation
 
Description Open-ended Online Forum on Synthetic Biology
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a national consultation
 
Description Public consultation on the preliminary opinion on Synthetic Biology
Geographic Reach Asia 
Policy Influence Type Participation in a national consultation
URL http://ec.europa.eu/health/scientific_committees/emerging/docs/scenihr_o_044.pdf
 
Description SSAC report on SB: opportunities for Scotland
Geographic Reach National 
Policy Influence Type Participation in a national consultation
URL http://www.scottishscience.org.uk/article/opportunities-scotland-synthetic-biology-ssac-report-publi...
 
Description BBSRC: SPARKING IMPACT AWARD
Amount £19,651 (GBP)
Funding ID SI.1 2013-0103 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2014 
End 08/2014
 
Description International Partnering Awards
Amount £25,000 (GBP)
Funding ID BB/L010828/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2013 
End 09/2016
 
Description Lignin-Based Metallic Nanoparticle Composites as Anti-Corrosion Agents
Amount £100,000 (GBP)
Funding ID CDE100662 
Organisation Defence Science & Technology Laboratory (DSTL) 
Sector Public
Country United Kingdom
Start 07/2016 
End 06/2017
 
Description Lignocellulosic Biorefinery Network, BBSRC NIBB 
Organisation University of York
Country United Kingdom 
Sector Academic/University 
PI Contribution I am a member of the Lignocellulosic Biorefinery Network, BBSRC NIBB
Collaborator Contribution Simon McQueen-Mason leads the Lignocellulosic Biorefinery Network, BBSRC NIBB
Impact multidisciplinary network
Start Year 2014
 
Description Article in Infinite magazine 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Article in ERI's annual magazine Infinite featuring the recent Technology Strategy Board funded projects, which includes Ligniflex.

I had 2 industry representatives ask me about TSB funding schemes and my experience.
Photos taken for this feature have appeared in information leaflets from the University and the Edinburgh International Science Festival
Year(s) Of Engagement Activity 2013
 
Description BBC news article 
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 Short interview and follow ups to enable research to be included in a abc news feature article
Year(s) Of Engagement Activity 2016
URL http://www.bbc.co.uk/news/business-35279854
 
Description Bang Goes the Borders activities 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Organised and demonstrated research-related activities for Bang Goes the Borders event in Melrose, Scottish Borders. We discussed our research and its impact with both school pupils and their families.
Year(s) Of Engagement Activity 2017
 
Description Debate Panelist at RI 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Biochemical Society and Royal Society of Biology ran a debate in collaboration as part of Biology Week entitled 'Synthetic Life: How far could it go? How far should it go?'. The debate was hosted by Dr Adam Rutherford, I was one of four panelists.
The debate is now on You Tube through the Royal Institution's website
https://www.rsb.org.uk/biologist-features/158-biologist/features/1405-synthetic-biology-can-we-should-we
http://www.bionews.org.uk/page_580228.asp
https://biochemicalsociety.wordpress.com/2015/10/16/synthetic-biology-defying-definition/
http://www.biochemist.org/bio/03706/0038/037060038.pdf
Year(s) Of Engagement Activity 2015
URL https://www.youtube.com/watch?v=YDbUYiTAMJU
 
Description Debate Panelist at iGEM Giant Jamboree 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Debate Panelist at iGEM Giant Jamboree, the final event held at the end of an international synthetic biology competition that has 2500+ participants. The highlight event was to discuss the gender disparities in iGEM and synthetic biology.
I have since taken part in a diversity advisory committee for the competition which has recommended changes to the competition.
Year(s) Of Engagement Activity 2015
 
Description Highlighting Synthetic Biology at the Edinburgh International Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Highlighting Synthetic Biology at a stand within the Museum while a room-sized balloon sculpture was being created and linking its creation to synthetic biology principles provoked many discussions and drew a lot of attention from visitors.

Asked to participate in the festival and highlight synthetic biology again the following year
Year(s) Of Engagement Activity 2013
 
Description Invited speaker to 'Curious Minds' lecture series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Third sector organisations
Results and Impact Presented my research in an accessible way to the Perthshire Society of Natural Science. A regional learned society.
Year(s) Of Engagement Activity 2018
 
Description Synthetic biology debate panellist 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Invited synthetic biology debate panellist at the Linnean Society of London, hosted by the London Evolutionary Research Network. This was a public debate, organised by a learned society.
Year(s) Of Engagement Activity 2018
 
Description UN Biodiversity Conference 2018 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact The Royal Society, the African Academy of Sciences and the Wellcome Trust organised an event on synthetic biology at the Conference of Parties to the UN Convention on Biological Diversity. This event informed conference delegates about synthetic biology as they debate how these technologies should be regulated. The Convention on Biological Diversity's (CBD) has been in discussions on synthetic biology since the 2016 Conference of Parties (COP) and there was another effort at this year's COP to agree proposals that would serve as a moratorium on gene drive research and possibly have wider implications for synthetic biology.
This event at COP was to provide delegates with an opportunity to hear about synthetic biology research and governance in a range of countries and contexts.
Year(s) Of Engagement Activity 2018