Diversity and Evolution of Cyclic Peptides in Flax (Linum usitatissimum L.)
| dc.contributor.advisor | Reaney, Martin | |
| dc.contributor.advisor | Sharbel, Timothy | |
| dc.contributor.committeeMember | Willenborg, Christian | |
| dc.contributor.committeeMember | Kochian, Leon | |
| dc.contributor.committeeMember | Links, Matthew | |
| dc.contributor.committeeMember | Prager, Sean | |
| dc.contributor.committeeMember | Deyholos, Michael | |
| dc.creator | Song, Ziliang | |
| dc.creator.orcid | 0000-0002-6616-1750 | |
| dc.date.accessioned | 2023-08-21T19:41:47Z | |
| dc.date.available | 2023-08-21T19:41:47Z | |
| dc.date.copyright | 2023 | |
| dc.date.created | 2023-08 | |
| dc.date.issued | 2023-08-21 | |
| dc.date.submitted | August 2023 | |
| dc.date.updated | 2023-08-21T19:41:48Z | |
| dc.description.abstract | Plants produce a myriad of compounds in response to various survival challenges. One novel family of natural products are the ribosomally-synthesized cyclic peptides (CPs). They are derived from precursor proteins undergoing post-translational modification (PTM). Potentially acting as defense agents in plants, CPs have various bioactivities for agricultural and pharmaceutical applications. While thousands of CPs have been discovered across multiple plant families over the past decades, limited attention has been paid to their evolution in plants. Here, my thesis begins with a literature review on plant CPs evolution. In brief, plant CPs exhibit 3 types of evolution, namely convergent evolution of the cyclized backbone, parallel evolution of the biosynthetic pathway and divergent evolution of the CP sequences. The increasing application of genome mining to the discovery of new CPs inspired me to explore the diversity of linusorbs, the orbitide class of CPs in cultivated flax (Linum usitatissimum L.). The first chapter reports my genome mining work using a profile-based approach. The previously found linusorb molecules are derived from 11 unique domains in 5 precursor proteins. Each linusorb domain is flanked by conserved residues, and the entire linusorb-embedded unit is repetitive in most precursor proteins. Based on this pattern I developed profiles to search the reannotated flax genome assembly, and identified 25 novel proteins each containing multiple profile-matching repeats embedded with linusorb-like domains (LLDs). This customized, profile-based mining approach has the advantage of finding unrelated proteins containing putative linusorbs, revealing their potential diversity in the flax genome. The second chapter analyzes the duplication patterns of these repeats. The gene sequences extracted from genome assembly were first verified by Sanger sequencing. Misassembly of Illumina reads were widely found in the repeat regions of these genes. Pairwise alignment of the corrected and reannotated gene sequences identified 8 groups of paralogues. Examination of repeats based on pairwise similarity discerned 3 modes of tandem duplication differing in the number of repeats as a unit. The significantly lower similarities of repeats across paralogues than within suggested repeat divergence after ancestral gene duplication. The flanking non-repetitive regions also indicated functional divergence across the paralogues. II The third chapter investigated the evolution of linusorbs. Both linusorbs and LLDs are moderately hydrophobic in contrast with the hydrophilic spacers. The unexpected predominance of conserved flanking signatures among the LLDs indicated their significant role in PTM and parallel evolution of the processing pathway. The LLD-containing repeats across paralogues are less similar than those within paralogues but more similar than those across non-paralogues, suggesting adaptive evolution of the paralogues. Positive selection was detected to episodically act on repeats within and across protein paralogues. Collectively, linusorb evolution in the flax genome is best described as a multifaceted model of adaptation. These findings in the diversity and evolution of CPs in flax lay a foundation for future studies on the functions and applications of these natural products. | |
| dc.format.mimetype | application/pdf | |
| dc.identifier.uri | https://hdl.handle.net/10388/14911 | |
| dc.language.iso | en | |
| dc.subject | cyclic peptide | |
| dc.subject | flax | |
| dc.subject | Linum usitatissimum | |
| dc.subject | diversity | |
| dc.subject | evolution | |
| dc.subject | plant | |
| dc.subject | orbitide | |
| dc.subject | linusorb | |
| dc.subject | genome mining | |
| dc.subject | repeat | |
| dc.subject | duplication | |
| dc.subject | adaptive evolution | |
| dc.title | Diversity and Evolution of Cyclic Peptides in Flax (Linum usitatissimum L.) | |
| dc.type | Thesis | |
| dc.type.material | text | |
| thesis.degree.department | Plant Sciences | |
| thesis.degree.discipline | Plant Sciences | |
| thesis.degree.grantor | University of Saskatchewan | |
| thesis.degree.level | Doctoral | |
| thesis.degree.name | Doctor of Philosophy (Ph.D.) |