Advancing the Prediction of Unexpected Cellular Behavior Due to Enzyme Promiscuity and Enzyme Solubility
Amin, Sara.
2019
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The introduction of
non-native synthesis pathways into microbial hosts has been instrumental in transforming
cellular organisms into microbial factories that produce commercially useful
biomolecules. While experimental efforts have achieved significant success, they are
costly and time consuming. The development of computational methods that analyze the
feasible design space promise to guide ... read moreexperimentation and expedite novel discoveries.
This thesis introduces computational workflows that advance the design of biological
systems through the consideration of promiscuous actions of enzymes. While enzymes are
recognized to be promiscuous in many biological engineering applications, the effects of
promiscuity on cellular physiology is understudied and not well documented. We show that
predicting derivative products due to enzyme promiscuity explains metabolomics
measurements for Escherichia coli in ECMDB, the E. coli Metabolome Database. Further,
predicted products and their catalyzing reactions are suggested to extend iML1515, the
most comprehensive genome-scale model of Escherichia coli MG1655. We also show that,
after the introduction of heterologous enzymes, cellular hosts have unexpected cellular
activity due to two disruption scenarios: the cellular host enzymes are promiscuous
towards the synthesis pathway metabolites, and the synthesis pathways enzymes are
promiscuous towards host metabolites. The latter may explain unexpected results in the
experimental literature. This thesis also introduces a workflow for bridging the gap
between synthesis pathway construction in a cellular host and the identification of
their genetic implementation. Genes can be sourced from various organisms; however, not
all genes are soluble in the host. Our technique, Probabilistic Pathway Assembly with
Solubility Confidence Scores (ProPASS), links synthesis pathway construction with the
exploration of soluble enzymes within the host. Predicted protein solubility scores are
used as a confidence level to quantify the compatibility of each pathway enzyme with the
host (E. coli). ProPASS offers experimental guidance to avoid trial-and-error approaches
to enzyme selection.
Thesis (Ph.D.)--Tufts University, 2019.
Submitted to the Dept. of Computer Science.
Advisors: Soha Hassoun, and Nikhil Nair.
Committee: Sam Guyer, Remco Chang, and Rudiyanto Gunawan.
Keywords: Computer science, and Bioengineering.read less - ID:
- 6395wm66b
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