Bioinformatic discovery of new ribosomally synthesized and post-translationally modified peptides in plants and fungi
- UNCG Author/Contributor (non-UNCG co-authors, if there are any, appear on document)
- Brigitte G. Ampolini (Creator)
- Institution
- The University of North Carolina at Greensboro (UNCG )
- Web Site: http://library.uncg.edu/
- Advisor
- Jonathan Chekan
Abstract: Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a chemically diverse class of natural products with exciting potential. The genomic basis of RiPPs creates a unique opportunity to discover new natural products bioinformatically using genome and transcriptome mining. Class specific features of RiPP gene clusters can be used to guide the bioinformatic analysis to discover new molecules and enzymes. Here, we searched for new fungal dikaritins by genome mining with a diagnostic biosynthetic enzyme, leading to the discovery of 77 putative new dikaritins. Applying a similar genome mining strategy to plants, we created a custom hidden Markov model to define a new class of plant cyclopeptides called burptides and to search through all Viridiplantae genomes for the potential to make new burptides. Ultimately, this bioinformatic analysis led to the discovery of a new molecule from Coffea arabica: arabipeptin A. To continue looking for new burptides, we used our custom hidden Markov model to search publicly available raw transcriptomic data. This process involved the creation of a pipeline that automates the process of downloading, assembling, and analyzing transcriptomic data with the custom burptide HMM. The results of the transcriptome search yielded 67 potential producers of novel burptides. RiPP cores bioinformatically seen in potential producer Gardenia jasminoides, were later verified by mass spectrometry, validating our transcriptome mining approach. This approach to bioinformatic mining has led to the identification of numerous potential molecules in both plants and fungi that will aid in the search for new RiPP natural products.
Bioinformatic discovery of new ribosomally synthesized and post-translationally modified peptides in plants and fungi
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Created on 8/1/2023
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Additional Information
- Publication
- Thesis
- Language: English
- Date: 2023
- Keywords
- BURP, Burptide, Cyclopeptide alkaloids, Dikaritin, Genome mining, RiPP
- Subjects
- Natural products $x Biotechnology
- Peptides $x Biotechnology
- Bioinformatics
- Biosynthesis