title: A Genome Scale Model of Geobacillus thermoglucosidasius (C56-YS93) reveals its biotechnological potential on rice straw hydrolysate.
abstract: Rice straw is a major crop residue which is burnt in many countries, creating significant air pollution. Thus, alternative routes for disposal of rice straw are needed. Biotechnological treatment of rice straw hydrolysate has potential to convert this agriculture waste into valuable biofuel(s) and platform chemicals. Geobacillus thermoglucosidasius is a thermophile with properties specially suited for use as a biocatalyst in lignocellulosic bioprocesses, such as high optimal temperature and tolerance to high levels of ethanol. However, the capabilities of G. thermoglucosidasius to utilise sugars in rice straw hydrolysate for making bioethanol and other platform chemicals have not been fully explored. In this work, we have created a genome scale metabolic model (denoted iGT736) of the organism containing 736 gene products, 1159 reactions and 1163 metabolites. The model was validated both by purely theoretical approaches and by comparing the behaviour of the model to previously published experimental results. The model was then used to determine the yields of a variety of platform chemicals from glucose and xylose - two primary sugars in rice straw hydrolysate. A comparison with results from a model of Escherichia coli shows that G. thermoglucosidasius is capable of producing a wider range of products, and that for the products also produced by E. coli, the yields are comparable. We also discuss strategies to utilise arabinose, a minor component of rice straw hydrolysate, and propose additional reactions to lead to the synthesis of xylitol, not currently produced by G. thermoglucosidasius. Our results provide additional motivation for the current exploration of the industrial potential of G. thermoglucosidasius and we make our model publicly available to aid the development of metabolic engineering strategies for this organism.
authors.affiliation: DBT-ICGEB Center for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, 110067 New Delhi, India. Electronic address: ahmadbioinfo@gmail.com.
authors.forename: Ahmad
authors.initials: A
authors.lastname: Ahmad
authors.affiliation: Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, OX3 0BP, Oxford, UK. Electronic address: Hassan.Hartman@phe.gov.uk.
authors.forename: Hassan B
authors.initials: HB
authors.lastname: Hartman
authors.affiliation: DBT-ICGEB Center for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, 110067 New Delhi, India. Electronic address: skrishnabio@gmail.com.
authors.forename: S
authors.initials: S
authors.lastname: Krishnakumar
authors.affiliation: Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, OX3 0BP, Oxford, UK. Electronic address: dfell@brookes.ac.uk.
authors.forename: David A
authors.initials: DA
authors.lastname: Fell
authors.affiliation: Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, OX3 0BP, Oxford, UK. Electronic address: mgpoolman@brookes.ac.uk.
authors.forename: Mark G
authors.initials: MG
authors.lastname: Poolman
authors.affiliation: DBT-ICGEB Center for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, 110067 New Delhi, India. Electronic address: shireesh@icgeb.res.in.
authors.forename: Shireesh
authors.initials: S
authors.lastname: Srivastava
mesh_terms: D016680:Genome, Bacterial; D056506:Geobacillus / Q000235:genetics / Q000378:metabolism*; D005947:Glucose / Q000378:metabolism; D008031:Lignin / Q000378:metabolism; D060847:Metabolic Engineering; D008954:Models, Biological; D012275:Oryza; D014866:Waste Products; D014994:Xylose / Q000378:metabolism
chemical_list: D014866:Waste Products; C036909:lignocellulose; D008031:Lignin; D014994:Xylose; D005947:Glucose
keywords: Fermentation; Flux balance analysis; Metabolic modelling; Rice straw; Thermophile