Discovery and characterization of a set of peptide-modifying heme oxygenase-like domain-containing oxidases

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a class of natural products made through the post-translational modification of genetically encoded and ribosomally synthesized precursor peptides. Because of their wide array of bioactivities, it would be desirable to be able to catalog all RiPPs, both in terms of their structure and their bioactivities. However, while bioinformatic methods for RiPP identification have improved dramatically in the past decade, it is still challenging to identify RiPPs from new classes. This is especially true if the new RiPP class does not rely on enzymes that are homologous to enzymes from known classes of RiPPs. Even if a RiPP biosynthetic gene cluster (BGC) can be identified, there are often multiple residues that could possibly be modified by the enzymes, and it is not clear which of them will get modified. To determine the structure, and to determine the bioactivity of the natural product, the product must be purified, which can be a time consuming process. Two methods are described here, one method for the rapid assembly of RiPP BGCs into expression plasmids to facilitate their isolation from heterologous hosts, and one bioinformatic method for the discovery of new classes of RiPPs. Using these methods, a number of RiPPs from known classes are characterized, including some with bioactivities against known pathogens, and a new class of RiPPs is discovered. These new RiPPs are modified by a set of heme oxygenase domain-containing oxygenases (HDOs), an emerging class of metal dependent enzymes.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Chemistry

Grantor

University of Illinois Urbana-Champaign

Year dc:date

2025

Author dc:creator

• Battiste, Alexander Jason

Contributors dc:contributor

• Mitchell, Douglas A.
• Mitchell, Douglas A
• Metcalf, William W
• Hergenrother, Paul J
• Zhao, Huimin

• Ribosomally Synthesized And Post-translationally Modified Peptides (ripps)
• Heme Oxygenase-like Domain-containing Oxidase (hdo)
• Genome Mining

Statement dc:rights

• Copyright 2025 Alex Battiste

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/130026

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F130026