India-UK Development of Metabolic Models to Support Systems Biology Approaches to Bioenergy Research

Lead Research Organisation: Oxford Brookes University
Department Name: Faculty of Health and Life Sciences

Abstract

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Description Metabolic modelling can be used to design metabolic engineering strategies for biotechnological production. We designed genetic modifications to increase the production of alkanes suitable for biofuel in the organism E. coli. (This work has been published in Metabolic Engineering and the model made available for others to use.) We have devised strategies to produce platform chemicals from carbohydrates in Geobacillus thermoglucosidasius using our genome scale metabolic model. This work was continued as part of the RiceFuel follow-on award, These results have also been published and the model made available.
Exploitation Route The metabolic engineering strategy can equally be applied to other potential products from G. thermoglucosidasius and E. coli.
Sectors Chemicals,Energy,Manufacturing, including Industrial Biotechology

URL https://wwwdev.ebi.ac.uk/biomodels/MODEL1703060000
 
Description BBSRC - India DBT Sustainable Bioenergy and Biofuels
Amount £1,393,966 (GBP)
Funding ID BB/K020358/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2013 
End 11/2017
 
Title E coli central carbon metabolism model for alkane synthesis 
Description Currently available from our web server at http://mudshark.brookes.ac.uk/Models/EcoliCCM. Submitted to https://wwwdev.ebi.ac.uk/biomodels/ as MODEL1802080001; awaiting validation. 
Type Of Material Computer model/algorithm 
Year Produced 2018 
Provided To Others? Yes  
Impact Currently the highest yield of alkane from fermentation by E coli, after genetic manipulations designed by analysis of the model. 
URL http://mudshark.brookes.ac.uk/Models/EcoliCCM
 
Title GSM of Geobacillus 
Description Genome scale metabolic model of Geobacillus thermoglucosidasius - thermophile of interest for development as a biotechnological chassis. 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact None to date. 
 
Description Indian partners 
Organisation International Centre for Genetic Engineering and Biotechnology
Country Italy 
Sector Charity/Non Profit 
PI Contribution Training of visiting students from the partners in metabolic modelling techniques to assist in their metabolic engineering projects. Running two one week modelling workshops in ICGEB, New Delhi, to train staff and students from the collaborators in techniques of metabolic modelling and their application to biotechnology.
Collaborator Contribution Provision of visiting PhD students to work in our group (4 visits by 3 PhD students), and one to work at University of Aberdeen with partner Oliver Ebenhoeh.
Impact Three articles in biotechnology journals. Two metabolic models submitted to BioModels database. Follow-on funding through BBSRC/India RiceFuel award to Nigel Minton. (PI, University of Nottingham).
Start Year 2012
 
Description Indian partners 
Organisation Jawaharlal Nehru University, India
Country India 
Sector Academic/University 
PI Contribution Training of visiting students from the partners in metabolic modelling techniques to assist in their metabolic engineering projects. Running two one week modelling workshops in ICGEB, New Delhi, to train staff and students from the collaborators in techniques of metabolic modelling and their application to biotechnology.
Collaborator Contribution Provision of visiting PhD students to work in our group (4 visits by 3 PhD students), and one to work at University of Aberdeen with partner Oliver Ebenhoeh.
Impact Three articles in biotechnology journals. Two metabolic models submitted to BioModels database. Follow-on funding through BBSRC/India RiceFuel award to Nigel Minton. (PI, University of Nottingham).
Start Year 2012
 
Title ScrumPy 
Description Integrated set of Python modules for metabolic modelling, encompassing kinetic models, metabolic control analysis, elementary modes analysis and flux balance analysis. It has been continually updated and extended since its initial public release in 2009. 
Type Of Technology Software 
Open Source License? Yes  
Impact It has been the major modelling tool used to generate all outputs from my research group since 2003. It has been adopted as a modelling tool in a number of other research groups, including the Ebenhoeh group (Aberdeen and Dortmund), the University of Nottingham Synthetic Biology Centre (Minton et al), Yazdani group (International Centre for genetic Engineering and Biotechnology, Delhi) and Kundu group (University of Calcutta). It has been used as a teaching tool in metabolic modelling workshops run as part of a UK-India Partnering award and for the NIBB C1 net. 
URL http://mudshark.brookes.ac.uk/ScrumPy