{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/130026"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/130026","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Discovery and characterization of a set of peptide-modifying heme oxygenase-like domain-containing oxidases","abstract":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2027-08-01","abstract_html":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2027-08-01","abstract_has_math":false,"creators":["Battiste, Alexander Jason"],"institution":"University of Illinois Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Chemistry","degree_department":null,"school":null,"contributors":["Mitchell, Douglas A.","Mitchell, Douglas A","Metcalf, William W","Hergenrother, Paul J","Zhao, Huimin"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-07-17","date_published":"2025-07-17","updated_at":"2026-07-22T22:25:06Z","subjects":["Ribosomally Synthesized And Post-translationally Modified Peptides (ripps)","Heme Oxygenase-like Domain-containing Oxidase (hdo)","Genome Mining"],"languages":["en","eng"],"rights":["Copyright 2025 Alex Battiste"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/130026","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Mitchell, Douglas A.","Mitchell, Douglas A","Metcalf, William W","Hergenrother, Paul J","Zhao, Huimin"]},{"key":"dc:creator","label":"Author","values":["Battiste, Alexander Jason"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2025-07-17","2025-08"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Chemistry"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Ribosomally Synthesized And Post-translationally Modified Peptides (ripps)","Heme Oxygenase-like Domain-containing Oxidase (hdo)","Genome Mining"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2025 Alex Battiste"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/130026"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2027-08-01","The student, Alexander Battiste, accepted the attached license on 2025-07-09 at 10:11.","The student, Alexander Battiste, submitted this Dissertation for approval on 2025-07-09 at 15:54.","This Dissertation was approved for publication on 2025-07-17 at 11:10.","DSpace SAF Submission Ingestion Package generated from Vireo submission #22456 on 2025-10-21 at 10:05:41","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."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Discovery and characterization of a set of peptide-modifying heme oxygenase-like domain-containing oxidases"]}]}],"canonical_facts":{"dc:contributor":["Mitchell, Douglas A.","Mitchell, Douglas A","Metcalf, William W","Hergenrother, Paul J","Zhao, Huimin"],"dc:creator":["Battiste, Alexander Jason"],"dc:date":["2025-07-17","2025-08"],"dc:description":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2027-08-01","The student, Alexander Battiste, accepted the attached license on 2025-07-09 at 10:11.","The student, Alexander Battiste, submitted this Dissertation for approval on 2025-07-09 at 15:54.","This Dissertation was approved for publication on 2025-07-17 at 11:10.","DSpace SAF Submission Ingestion Package generated from Vireo submission #22456 on 2025-10-21 at 10:05:41","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."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/130026"],"dc:language":["en","eng"],"dc:rights":["Copyright 2025 Alex Battiste"],"dc:subject":["Ribosomally Synthesized And Post-translationally Modified Peptides (ripps)","Heme Oxygenase-like Domain-containing Oxidase (hdo)","Genome Mining"],"dc:title":["Discovery and characterization of a set of peptide-modifying heme oxygenase-like domain-containing oxidases"],"dc:type":["text"],"thesis:degree_discipline":["Chemistry"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:06Z"}