Revealing the molecular details of azoline formation in ribosomal natural product biosynthesis

Dunbar, Kyle

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https://hdl.handle.net/2142/73109 Copy

Description

Title

Revealing the molecular details of azoline formation in ribosomal natural product biosynthesis

Author(s)

Dunbar, Kyle

Issue Date

2015-01-21

Director of Research (if dissertation) or Advisor (if thesis)

Mitchell, Douglas A.

Doctoral Committee Chair(s)

Mitchell, Douglas A

Committee Member(s)

• van der Donk, Wilfred A.
• Nair, Satish K.
• Gerlt, John A.

Department of Study

Chemistry

Discipline

Chemistry

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• Azoline Biosynthesis
• ribosomally synthesized and post-translationally modified peptide (RiPP) Biosynthesis
• thiazole/oxazole-modified microcin (TOMM) Biosynthesis
• Cyclodehydratase
• YcaO

Abstract

The thiazole/oxazole-modified microcins (TOMMs) are a recently grouped class of ribosomally synthesized and posttranslationally modified peptides. Encoded by many bacteria and archaea, these natural products occupy a large chemical and functional space and are linked by the presence of the eponymous azole moieties. Previous work has demonstrated that an evolutionarily conserved, heterotrimeric enzyme complex (TOMM synthetase) is responsible for azole biogenesis. The TOMM synthetase transforms select serine, threonine and cysteine residues in the core peptide into azole heterocycles via a two-step cyclodehydration-dehydrogenation reaction. The installation of the azol(in)e heterocycles endows the peptide with rigidity and, in all characterized TOMM natural products, is required for biological activity. Despite being reconstituted nearly two decades ago, many questions remain regarding the role of each protein in the TOMM synthetase and the mechanism of cyclodehydration. Previous attempts to elucidate the molecular details of azole formation were impeded by the poor stability/solubility of reconstituted TOMM synthetases. In this thesis I report the characterization of the biosynthetic machinery from two novel TOMM cluster from Bacillus sp. Al Hakam that do not suffer from these issues. Using these robust synthetase complexes, I demonstrate that the cyclodehydration reaction proceeds via a phosphorylated hemi-orthoamide intermediate (chapter 2) and provide definitive roles from each of the proteins in the cyclodehydratase complex (chapter 4 and 5). My findings identify an unprecedented role for ATP and provide the first function to the previously uncharacterized YcaO superfamily of proteins. Furthermore, in order to complete my mechanistic investigations of the TOMM synthetase, I developed a novel strategy for generating peptides with site-specific carbonyl oxygen isotope labels (chapter 3). I also demonstrate that this strategy can be expanded to the site-specific installation of thioamides.

Graduation Semester

2014-12

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http://hdl.handle.net/2142/73109

Copyright and License Information

Copyright 2014 Kyle L. Dunbar

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