[14-ERA IB] MetaCat: A metagenomic collection of novel and highly efficient biocatalysts for industrial biotechnology
Lead Research Organisation:
Bangor University
Department Name: Sch of Biological Sciences
Abstract
Chemical and bio-industries have a steadily growing demand for enzyme biocatalysts, which can catalyze a huge variety of different chemical reactions with high activity, substrate specificity and enantioselectivity. However, enzymes have been evolved by nature to work in living cells and under mild reaction conditions; consequently, most enzymes cannot be applied in industrial processes directly. Although it is known that few enzymes exist, which are well suited for biotechnological applications, the molecular basis is unknown. The MetaCat project will deliver innovative tools
and knowledge for the identification of such robust "all-round frequent hit" enzymes (AFHs).
Metagenomic resources will be exploited by novel function- and sequence-based screenings to identify nitrilases, transaminases, ketoreductases, glycosyl hydrolases and lipases/esterases. A combination of metagenomics and metacatalysis will be used together with structure-based and
high-throughput technologies, generic model substrates mimicking challenging chemical synthesis steps, next generation sequencing technologies as well as in silico data mining. New genetic tools using synthetic biology approaches will be developed to construct a cell-free function-based
screening platform for faster and improved screening. An innovative single-cell laser trapping technology will be established to give access to a new previously unknown enzyme diversity. The identified enzymes will form a marketable versatile biocatalyst collection together with a comprehensive database and can be used as starting points for modeling and in vitro evolution experiments. They will be applied to improve chemical production processes regarding e.g. timelines, purity of the products, environmental sustainability and will lead to value-added products.
Thus, MetaCat will contribute to shorten timelines for development of biotechnological processes and thus to make industrial biocatalysis more attractive and profitable.
and knowledge for the identification of such robust "all-round frequent hit" enzymes (AFHs).
Metagenomic resources will be exploited by novel function- and sequence-based screenings to identify nitrilases, transaminases, ketoreductases, glycosyl hydrolases and lipases/esterases. A combination of metagenomics and metacatalysis will be used together with structure-based and
high-throughput technologies, generic model substrates mimicking challenging chemical synthesis steps, next generation sequencing technologies as well as in silico data mining. New genetic tools using synthetic biology approaches will be developed to construct a cell-free function-based
screening platform for faster and improved screening. An innovative single-cell laser trapping technology will be established to give access to a new previously unknown enzyme diversity. The identified enzymes will form a marketable versatile biocatalyst collection together with a comprehensive database and can be used as starting points for modeling and in vitro evolution experiments. They will be applied to improve chemical production processes regarding e.g. timelines, purity of the products, environmental sustainability and will lead to value-added products.
Thus, MetaCat will contribute to shorten timelines for development of biotechnological processes and thus to make industrial biocatalysis more attractive and profitable.
Technical Summary
Main Project Objectives
-Functional and highly diverse collections of most wanted AFHs serving as novel and improved biocatalysts for direct application in industrial processes.
-An innovation pool for the detection of enzymes: innovative cell-free and single-cell tools for functional metagenome and genome mining.
-Biochemical and bioinformatic tools to identify AFH enzymes.
-Understanding of structures and mechanisms underlying enzyme promiscuity.
-Optimized and efficient chemical production processes
-High value-added products, i. e. platform and fine chemicals and pure enantiomers.
The objectives will be achieved by the following Work Packages
WP 1. Functional metagenomics and screenings (Golyshin)
WP 2. NGS metagenome analyses, sequence-based enzyme identification (Ferrer)
WP 3. Data integration, advanced bioinformatics and software development (Vallenet/Zaparucha)
WP 4. Novel and advanced screening hosts and cell-free metagenomics (Streit/Chow)
WP 5. Enzyme expression, biochemical and structural characterization (Jaeger)
WP 6. Biocatalytic process implementation (Koch)
WP 7. Project management and coordination (Streit/Chow)
The Bangor University-lead WP 1 is broken down in following tasks:
T1. Sample collection
Our resources comprise a wide range of terrestrial, marine, plant- and animal-derived samples containing all forms of microbial life and extremely high diversity. The consortium has access to a wide range of biodiversity that is unique and can in part not be sampled by other groups or companies.
T2. Enrichments with industry-relevant substrates
Enrichments will be set up with samples from some of the sites. The samples will be enriched with model substrates provided by industry partners. Further, aerobic but also micro-aerobic and anaerobic conditions for the enrichments will be established. Especially the anaerobic technologies will allow unraveling novel communities and microbes that have not been addressed so far.
-Functional and highly diverse collections of most wanted AFHs serving as novel and improved biocatalysts for direct application in industrial processes.
-An innovation pool for the detection of enzymes: innovative cell-free and single-cell tools for functional metagenome and genome mining.
-Biochemical and bioinformatic tools to identify AFH enzymes.
-Understanding of structures and mechanisms underlying enzyme promiscuity.
-Optimized and efficient chemical production processes
-High value-added products, i. e. platform and fine chemicals and pure enantiomers.
The objectives will be achieved by the following Work Packages
WP 1. Functional metagenomics and screenings (Golyshin)
WP 2. NGS metagenome analyses, sequence-based enzyme identification (Ferrer)
WP 3. Data integration, advanced bioinformatics and software development (Vallenet/Zaparucha)
WP 4. Novel and advanced screening hosts and cell-free metagenomics (Streit/Chow)
WP 5. Enzyme expression, biochemical and structural characterization (Jaeger)
WP 6. Biocatalytic process implementation (Koch)
WP 7. Project management and coordination (Streit/Chow)
The Bangor University-lead WP 1 is broken down in following tasks:
T1. Sample collection
Our resources comprise a wide range of terrestrial, marine, plant- and animal-derived samples containing all forms of microbial life and extremely high diversity. The consortium has access to a wide range of biodiversity that is unique and can in part not be sampled by other groups or companies.
T2. Enrichments with industry-relevant substrates
Enrichments will be set up with samples from some of the sites. The samples will be enriched with model substrates provided by industry partners. Further, aerobic but also micro-aerobic and anaerobic conditions for the enrichments will be established. Especially the anaerobic technologies will allow unraveling novel communities and microbes that have not been addressed so far.
Planned Impact
Potential of the expected results
The potential for industrial applications of the MetaCat enzyme collection is extremely high as they enable efficient production of high-value chemical compounds. The MetaCat participating companies will promote the newly established screening methods and will distribute knowledge and understanding about structural features of enzymes. They put strong emphasis on direct implementation of the identified biocatalysts in industrial production processes and evaluate the whole approach at an early stage, e.g. concerning challenging synthesis steps. Further, the novel technologies developed (esp. the cell-free systems) will ultimately result in a strong leadership.
Environmental benefit
Enzyme application significantly lowers the use of often highly toxic conventional catalysts and reduces environmental burden. Biocatalytic processes decrease energy consumption and costs as they can usually be carried out at lower temperatures and with fewer reaction steps, i.e. milder process conditions. Thus, the use of organic solvents can be reduced; unwanted by- and waste-products can be circumvented or converted. Renewable resources can be used more efficiently leading to a higher sustainability. A bio-efficiency study can be commissioned to evaluate benefits of novel enzymatic reactions and improved or novel industrial processes.
Integration of the whole value-added chain
The MetaCat consortium members cover the whole value chain. Novozymes is world leader in finding bio-industrial solutions and evocatal is expert in the production of enzymes and fine chemicals. Bayer is one of the most important chemical and pharmaceutical companies and will distribute the enzymatically produced value-added products worldwide. All companies are highly interested to implement and further commercialize the developed screenings and the resulting enzymes.
The potential for industrial applications of the MetaCat enzyme collection is extremely high as they enable efficient production of high-value chemical compounds. The MetaCat participating companies will promote the newly established screening methods and will distribute knowledge and understanding about structural features of enzymes. They put strong emphasis on direct implementation of the identified biocatalysts in industrial production processes and evaluate the whole approach at an early stage, e.g. concerning challenging synthesis steps. Further, the novel technologies developed (esp. the cell-free systems) will ultimately result in a strong leadership.
Environmental benefit
Enzyme application significantly lowers the use of often highly toxic conventional catalysts and reduces environmental burden. Biocatalytic processes decrease energy consumption and costs as they can usually be carried out at lower temperatures and with fewer reaction steps, i.e. milder process conditions. Thus, the use of organic solvents can be reduced; unwanted by- and waste-products can be circumvented or converted. Renewable resources can be used more efficiently leading to a higher sustainability. A bio-efficiency study can be commissioned to evaluate benefits of novel enzymatic reactions and improved or novel industrial processes.
Integration of the whole value-added chain
The MetaCat consortium members cover the whole value chain. Novozymes is world leader in finding bio-industrial solutions and evocatal is expert in the production of enzymes and fine chemicals. Bayer is one of the most important chemical and pharmaceutical companies and will distribute the enzymatically produced value-added products worldwide. All companies are highly interested to implement and further commercialize the developed screenings and the resulting enzymes.
Organisations
Publications
Alonso S
(2019)
Genetically engineered proteins with two active sites for enhanced biocatalysis and synergistic chemo- and biocatalysis
in Nature Catalysis
Bargiela R
(2015)
Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data.
in Frontiers in microbiology
Cea-Rama I
(2021)
Structure and evolutionary trace-assisted screening of a residue swapping the substrate ambiguity and chiral specificity in an esterase.
in Computational and structural biotechnology journal
Chernyh NA
(2020)
Dissimilatory sulfate reduction in the archaeon 'Candidatus Vulcanisaeta moutnovskia' sheds light on the evolution of sulfur metabolism.
in Nature microbiology
Coscolín C
(2019)
Bioprospecting Reveals Class III ?-Transaminases Converting Bulky Ketones and Environmentally Relevant Polyamines.
in Applied and environmental microbiology
Distaso MA
(2020)
High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream.
in Frontiers in microbiology
Ferrer M
(2016)
Biodiversity for biocatalysis: A review of the a/ß-hydrolase fold superfamily of esterases-lipases discovered in metagenomes
in Biocatalysis and Biotransformation
Ferrer M
(2016)
Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends.
in Microbial biotechnology
Gavrilov SN
(2019)
Microbial Communities of Polymetallic Deposits' Acidic Ecosystems of Continental Climatic Zone With High Temperature Contrasts.
in Frontiers in microbiology
Description | Based on the data published since the emergency of the field of metagenomics (some 20 years ago), a thorough analysis of the potential of various environments to deliver enzyme candidates for important industrial bioconversions has been done and published. Apparently, only 10-12 % of metagenomic studies dealt to some extent with enzyme discovery, with marine environments being largely undersampled despite delivering a high proportion of positive hits per Mbp of screened DNA. The study suggested that more emphasis should be put on the activity-based screens of marine-based microbes and their communities and proposed some solutions to streamline the activity-based pipeline of enzyme discovery for industrial biocatalysis. Another analysis was related with a specific group of a/ß-hydrolase fold superfamily of lipases-esterases (Lip-Est), which is a group of enzymes with a wide range of industrial applications) discovered from metagenomes. Interestingly, these enzymes demonstrate a great structural variability (suggesting the Lip-Est biodiversity is undersampled) and a great potential for industrial applications (some 60 % exhibited features useful for industrial catalysis). Metagenomic expression libraries from more than 10 samples representing extremophilic and high-diversity environments have been established and used. These were assessed as a new resource for mining new enzymatic activities in frames of this project. Analysis of >1M clones from libraries has revealed >700 enzyme hits representing with validated carboxylesterase activities in 80 proteins representing 17 families of carboxylesterases. Seven proteins exhibited activities to depolymerise polylactic acid and polycaprolactonepolymers. The study has produced four new crystal structures of proteins and, interestingly, has revealed two novel conserved protein families with esterase activities. The study conducted at Bangor University has further expanded the enzymatic toolbox for important industrial conversions through identification and characterisation of novel nitrilases (35), glycosyde hydrolases (17), ketoreductases (29), lipases/esterases (9) and transaminases (10). These enzymes have been assessed for applicability in biocatalysis at the industrial partner, Bayer AG. |
Exploitation Route | This project has produced resources useful to the researchers from academia and industry: de novo sequencing data are publically available, readily screeanable libraries from a range of unique environments that may be shared to be subjected to other screens; most of the in silico and wet-lab enzyme analysis data are published in the open access journals or are in preparation. The analysis already performed in this study may be useful for establishing new enzyme biocatalysts from the scratch and to help narrowing down the screening efforts by focussing on most appropriate strategies. One of the most significant outcomes of this project was the publication of a paper (DOI: 10.1021/acschembio.7b00996) on determinants of enzyme promiscuity in carboxylesterases, which allows a precise prediction of the ability of an enzyme to use a great number of substrates, which is an important feature for engineering biocatalysts for unusual conversions. |
Sectors | Chemicals Education Environment Healthcare Pharmaceuticals and Medical Biotechnology |
Description | CEB-The Centre for Environmental Biotechnology, co-funded by ERDF (Welsh European Funding Organisation, Welsh Assembly Government) and Bangor University |
Amount | £7,600,000 (GBP) |
Funding ID | 81280 |
Organisation | European Commission |
Department | European Regional Development Fund (ERDF) |
Sector | Public |
Country | Belgium |
Start | 11/2017 |
End | 11/2022 |
Description | FuturEnzyme: Enzymes for more environment-friendly consumer products |
Amount | € 6,000,000 (EUR) |
Funding ID | 101000327 |
Organisation | European Commission H2020 |
Sector | Public |
Country | Belgium |
Start | 05/2021 |
End | 05/2025 |
Description | "Activity-Based Bioprospecting for Hydrolases In Enrichment Cultures from Thermal Vents of Ischia Island (Italy)" Oral presentation 15th International Congress on Thermophiles, "Thermophiles-2019" Fukuoka, Japan, September 2-6, 2019. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Oral presentation at a very important International Congress, attended by approx 300 researchers from across the world. Few important links established (e.g. with researchers from Institute Pasteur and Unis of Fukuoka, Naples and Tokyo), existing collaborations fostered (e.g. NCBI/NLM/NIH, Universities of Bergen, Vienna and Copenhagen). |
Year(s) Of Engagement Activity | 2019 |
URL | http://www.acplan.jp/thermophiles2019/ |
Description | "Bioprospecting for new enzymes in petroleum-degrading microorganisms", Oral presentation at the Environmental Biotechnology Network (EBNet) Research Colloquium Edinburgh, January 22-23, 2020 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Oral presentation at the event organised by Environmental Biotechnology Network (EBNet, BBSRC-funded) Colloquium Edinburgh, attended by >60 academics, industry and science-funding bodies. Important discussions on harnessing microbial processes to mitigate petroleum and plastics pollution in marine environment |
Year(s) Of Engagement Activity | 2020 |
URL | https://ebnet.ac.uk/ebnetrc2020/ |
Description | "Marine petroleum-degrading microorganisms, their ecology and applications", Keynote presentation at the Seminar, Biodiversity and applications of marine microorganisms and their enzymes, Catholic University of Valencia, March 5, 2019 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Keynote presentation at the Seminar, Biodiversity and applications of marine microorganisms and their enzymes, Catholic University of Valencia, attended by approx 90 masters and teaching staff, students, promoted lively discussion on various applications of enzymes from petroleum-degraading microorganisms, including plastics conversion |
Year(s) Of Engagement Activity | 2019 |
Description | Bangor University Open Days |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | Prof Golyshin and his team members present on their research show lab facilities to prospective students and their family members. event is organised on a regular basis, 3 times a year |
Year(s) Of Engagement Activity | 2015,2016 |
Description | Gene Park event |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | Prof P Golyshin did a presentation on his past and ongoing research activities for a general public, organised by Wales Gene Park on March 3, 2016 and discussed currnet and furure trends in biotechnology-related resaerch |
Year(s) Of Engagement Activity | 2016 |
Description | Invited presentation at the Department of Biological Sciences, University of Essex, Dec 8, 2016 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | The presentation by Prof P Golyshin at the Biological Sciences Dept, University of Essex titled 'Discovery of new enzymes from microbial biodiversity hotspots' has stimulated lively discussions with colleagues, which has resulted in drafting plans for potential RCUK grant applications |
Year(s) Of Engagement Activity | 2016 |
Description | Invited, Oral presentation "Challenges in Enzyme Discovery in the Postgenomic Era", 5th CONFERENCE "ENZYMES IN THE ENVIRONMENT" Bangor, UK, July 2016 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Prof P Golyshin did the oral presentation "Challenges in Enzyme Discovery in the Postgenomic Era", at the 5th CONFERENCE "ENZYMES IN THE ENVIRONMENT" Bangor, UK, July 2016. The talk was followed by the discussion on the perspectives of enzyme discovery using activity-based metagenomics approaches and helped establishing contacts with scientists in the broad field of enzyme discovery and applications. |
Year(s) Of Engagement Activity | 2016 |
URL | http://enzymes-in-the-environment.org/ |
Description | Keynote presentation, 7th European Conference on Prokaryotic and Fungal Genomes "ProkaGenomics 2017" |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | 7th European Conference on Prokaryotic and Fungal Genomes "ProkaGenomics 2017" (http://www.prokagenomics.org/ ), Invited plenary (keynote) lecture "Activity-based discovery of novel enzymes from marine environments".September 19-22, 2017 |
Year(s) Of Engagement Activity | 2017 |
URL | http://www.prokagenomics.org/ |
Description | Keynote presentation, INMARE symposium |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Keynote presentation, INMARE workshop (April 5, 2017). University of Hamburg (Germany). The lecture addressing new developments in bioprospecting for novel enzymes from biodiversity hotspots was held in frames of the INMARE workshop for academics, undergrad and postgrad students (approx 150 people attended). |
Year(s) Of Engagement Activity | 2017 |
URL | https://lecture2go.uni-hamburg.de/l2go/-/get/v/21251 |
Description | Oral presentation 'Metagenomic Mining of Thermophilic Enzymes from Marine Microbial Communities', 13th International Conference "Thermophiles 2015", Santiago de Chile, September 2015 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Prof Golyshin held the oral presentation titled 'Metagenomic Mining of Thermophilic Enzymes from Marine Microbial Communities' at 13th International Conference "Thermophiles 2015", Santiago de Chile, September 3, 2015. The conference was attended by big-calibre international scientists active in research in extremophiles (>300 attendees). The presentation has facilitated establishing new links with scientists from across the globe. |
Year(s) Of Engagement Activity | 2015 |
URL | http://www.thermophiles2015.cl/ |
Description | Oral presentation at the 4th International Conference on Microbial Diversity 2017 (MD 2017), Bari Italy |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Oral presentation, "Biology of the cosmopolitan hyperacidophilic archaeon Ferroplasma" at the 4th International Conference on Microbial Diversity 2017 (MD 2017), October 26, 2017, Bari Italy |
Year(s) Of Engagement Activity | 2017 |
URL | https://www.md2017.it/ |
Description | Oral presentation at the 12th International Symposium "Extremophiles-2018", Ischia-Naples, September 16-20, 2018 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Prof Golyshin held the oral presentation titled "Enzyme discovery from marine microbial biodiversity hotspots", at the 12th International Conference "Extremophiles-2018", Ischia, September 16-20, 2019. The conference was attended by high-profile international scientists active in research in extremophiles (>400 attendees). The presentation has facilitated establishing new links with scientists from across the globe. |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.extremophiles2018.org/ |
Description | Plenary Lecture, "MINIG METAGENOMES FOR NOVEL ENZYMES", III Conference on Microbial DiversityThe Challenge of Diversity, Perugia, October 2015 |
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 | Plenary Lecture of Prof Peter Golyshin "MINIG METAGENOMES FOR NOVEL ENZYMES" held at the III Conference on Microbial DiversityThe Challenge of Diversity, Perugia, on October 28, 2015 (attended by about 150 participants from academia and industry) was very helpful in promoting new contacts with researchers in the field and has stimulated lively discussions on the perspectives of enzyme discovery for industrial applications. |
Year(s) Of Engagement Activity | 2015 |
URL | http://www.simtrea.org/MD2015/First_Announcement_MD2015.pdf |
Description | School of Natural Sciences, Bangor University Open Days for perspective undergraduate students (three times per semester) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | The Open Days are organised by Bangor University to attract prospective students (and their family members) to enthuse with environmental and biotech research. In our laboratories, we demonstrated research facilities and explain our ongoing projects. Approximately 20 students and their family members (per visit) take part in conversations and express their interest in our science (approx 120 p.a.) |
Year(s) Of Engagement Activity | 2019,2020 |