Award details

Development and application of an in silico metabolic model of Geobacillus thermoglucosidasius

Reference	BB/I015841/2
Principal Investigator / Supervisor	Emeritus Professor David Jonathan Leak
Co-Investigators / Co-Supervisors
Institution	University of Bath
Department	Biology and Biochemistry
Funding type	Skills
Value (£)	71,416
Status	Completed
Type	Training Grants
Start date	01/02/2013
End date	30/09/2015
Duration	32 months

Abstract

unavailable

Summary

TMO Renewables Ltd, the CASE collaborating company, has developed an ethanol fermentation process capable of using sugars derived from lignocellulosic substrates, based on engineering the fermentation pathways of Geobacillus thermoglucosidasius. As part of the work they have contracted to obtain the genome sequence of this organism, which is almost complete. In the initial stages, the annotation of a genome sequence is usually done automatically, based on the search for open reading frames (orfs) and bio-informatic homology searches. This means that initial annotations often contain errors and unclassified orfs. In this project the student will start to build a genomic scale metabolic model of this organism, using the initial genome sequence as a starting point. The ultimate goal is to build an in silico model of the metabolic capabilities of this organism based on Palsson's flux balance analysis approach (Palsson BO (2006) Systems Biology. Properties of Reconstructed Networks. Cambridge University Press, New York, USA). However, because Geobacillus spp are not extensively described at a biochemical and physiological level, this will require a considerable amount of experimental validation to eg confirm the gene assignments and fill in missing metabolic links. Once constructed, an in silico metabolic model can have predictive capabilities. Initially, these can be used to authenticate the quality of the model, which invariably includes an number of assumptions/estimates. However, in the long term, these may be used to predict the optimal route for metabolic engineering for a defined objective, which is one of the future aims of the company. In the interim, however, the logical iterative experimental and in silico construction of the model should generate new insights into the physiology and biochemistry of this increasingly important group of thermophiles. The combined experimental and modelling aspects of this programme will form an excellent training programme fora postgraduate student with a biological background, exposing them to one of the more accessible avenues of systems biology.

Committee	Not funded via Committee
Research Topics	X – not assigned to a current Research Topic
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	Training Grant - Industrial Case

Associated awards:

BB/I015841/1 Development and application of an in silico metabolic model of Geobacillus thermoglucosidasius

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