Dataset Information

Time-series RNA-seq data of Geobacillus thermoglucosidasius DSM2542

ABSTRACT: Time-series RNA-seq data of Geobacillus thermoglucosidasius DSM2542

PROVIDER: PRJNA699432 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13627101_1.fastq.gz	Fastqsanger.gz
	SRR13627101_2.fastq.gz	Fastqsanger.gz
	SRR13627102_1.fastq.gz	Fastqsanger.gz
	SRR13627102_2.fastq.gz	Fastqsanger.gz
	SRR13627103_1.fastq.gz	Fastqsanger.gz

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Project description:Ahmad2017 - Genome-scale metabolic model (iGT736) of Geobacillus thermoglucosidasius (C56-YS93) This model is described in the article: A Genome Scale Model of Geobacillus thermoglucosidasius (C56-YS93) reveals its biotechnological potential on rice straw hydrolysate Ahmad Ahmada, Hassan B. Hartmanb, S. Krishnakumara, David A. Fellb, Mark G. Poolmanb, Shireesh Srivastavaa Journal of Biotechnology 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 Geobacillus thermoglucosidasius to utilize 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 Geobacillus thermoglucosidasius is capable of producing a wider range of products, and that for the products also produced by Escherichia 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 Geobacillus thermoglucosidasius. Our results provide additional motivation for the current exploration of the industrial potential of Geobacillus thermoglucosidasius and we make our model publicly available to aid the development of metabolic engineering strategies for this organism. This model is hosted on BioModels Database and identified by: MODEL1703060000. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Dataset Information

Time-series RNA-seq data of Geobacillus thermoglucosidasius DSM2542

Dataset's files

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