Plant genome mining for triterpene biosynthetic genes and gene clusters

Owen, Charlotte (2020) Plant genome mining for triterpene biosynthetic genes and gene clusters. Doctoral thesis, University of East Anglia.

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Abstract

Plant specialised metabolites are highly diverse in their functions and chemistries. The discovery of plant biosynthetic gene clusters (BGCs) and the rapidly increasing volume of sequence data available for analysis provides a timely opportunity for wide, comprehensive analyses of BGCs across plants. Triterpenes were chosen as exemplars for this, given the solid foundation of established literature and the existence of powerful characterisation platforms to permit an iterative synthetic biology approach. After an assessment of current BGC mining tools, key limitations were identified regarding accuracy and specificity of putative enzyme and pathway classifiers, as well as in variation of genome quality. Many of these limitations were overcome through the creation of systematic tools for locating, classifying and predicting the function of three key triterpene enzyme families: oxidosqualene cyclases (OSCs), cytochrome P450s and glycosyl-transferases. The generation of these tools represent a step-change in our ability to effectively analyse large volumes of sequence data. In the application of these tools, a wide range of data were generated to explore the evolutionary patterns of these families in the Viridiplantae, across a taxonomic range an order of magnitude greater than previous studies. The dynamic and diverse nature of triterpene biosynthetic enzyme evolution was observed, and the methodologies validated by comparison to known biosynthetic pathways and gene clusters. These data, when combined with comprehensive enrichment analysis of gene families co-located with OSCs, have provided a wealth of options for future study. These include: assessing if variation in repertoires of key enzyme subfamilies between plant clades impacts their biosynthetic potential, designer metabolite synthesis via the use of rigorous synthetic biology approaches, assessing non-biosynthetic genes as potential components of BGCs and exploring the space between entirely clustered and non-clustered biosynthetic pathways to build a cohesive model for plant gene organisation in the context of specialised metabolism.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Biological Sciences
Depositing User: Chris White
Date Deposited: 08 Feb 2021 11:09
Last Modified: 08 Feb 2021 11:09
URI: https://ueaeprints.uea.ac.uk/id/eprint/79183
DOI:

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