Dissertation
AN INTEGRATED COMPUTATIONAL AND EXPERIMENTAL BIOLOGY APPROACH TO STREAMLINE METABOLIC PATHWAY ENGINEERING IN BACILLUS SUBTILIS
Doctor of Philosophy (PhD), Washington State University
01/2013
Handle:
https://hdl.handle.net/2376/112114
Abstract
Isoprene is an important commodity due to its use as the monomer component of rubber and as a platform chemical for adhesives and synthetic chemistry. Renewable methods for producing isoprene are being investigated to meet product demand and reduce the environmental impact of current production methods. To this end, methods for large scale production of isoprene from a microbial host are being explored as cleaner sources of raw material.
Bacillus subtilis is a spore-forming, rod-shaped soil bacterium, and has been extensively studied as a model organism for both gram-positive bacteria and endospore forming bacteria. B. subtilis uses the 1-deoxy-D-xylulose-5-phosphate (DXP) pathway to produce isoprene; however, the regulatory mechanisms of the isoprene biosynthesis pathway are poorly understood. The focus of the work presented here is to identify and exploit the regulatory mechanisms of the DXP pathway in order to produce a strain of B. subtilis which produces increased levels of isoprene in comparison to the wild type DSM10 strain.
An introduction that describes the DXP Pathway and an assessment of commercial viability for bioisoprene production is presented in the first chapter. The second chapter provides an analysis of the genome sequences of Bacillus subtilis strains 168 and DSM10. These strains have been determined to be greater than 98% identical, enabling the body of knowledge for the 168 strain to be applied to the DSM10 strain.
The third chapter examines genome wide gene expression patterns in comparison to isoprene production from multiple environmental and genetic perturbations and provides a model based on transcriptomics data for predicting isoprene production. Chapter four provides an analysis of proteomics data sets which revealed a connection between the DXP pathway and competence development. Chapter five describes the predictive capacity of current mathematical models for isoprene production, and chapter six is in the format of a NSF grant which proposes to continue the work using an integrated regulatory and metabolic model to improve in silico simulations of metabolism. Conclusions that can be drawn from this work are given in chapter seven.
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Details
- Title
- AN INTEGRATED COMPUTATIONAL AND EXPERIMENTAL BIOLOGY APPROACH TO STREAMLINE METABOLIC PATHWAY ENGINEERING IN BACILLUS SUBTILIS
- Creators
- Becky Michelle Hess
- Contributors
- Birgitte K Ahring (Advisor)Henry S Wiley (Committee Member)Timothy S Straub (Committee Member)Nehal Abu-Lail (Committee Member)Luying Xun (Committee Member)
- Awarding Institution
- Washington State University
- Academic Unit
- Biological Systems Engineering, Department of
- Theses and Dissertations
- Doctor of Philosophy (PhD), Washington State University
- Number of pages
- 202
- Identifiers
- 99900581647301842
- Language
- English
- Resource Type
- Dissertation