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Co-occurrence of enzyme domains guides the discovery of an oxazolone synthetase

Abstract

Multidomain enzymes orchestrate two or more catalytic activities to carry out metabolic transformations with increased control and speed. Here, we report the design and development of a genome-mining approach for targeted discovery of biochemical transformations through the analysis of co-occurring enzyme domains (CO-ED) in a single protein. CO-ED was designed to identify unannotated multifunctional enzymes for functional characterization and discovery based on the premise that linked enzyme domains have evolved to function collaboratively. Guided by CO-ED, we targeted an unannotated predicted ThiF–nitroreductase di-domain enzyme found in more than 50 proteobacteria. Through heterologous expression and biochemical reconstitution, we discovered a series of natural products containing the rare oxazolone heterocycle and characterized their biosynthesis. Notably, we identified the di-domain enzyme as an oxazolone synthetase, validating CO-ED-guided genome mining as a methodology with potential broad utility for both the discovery of unusual enzymatic transformations and the functional annotation of multidomain enzymes.

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Fig. 1: Outline of the CO-ED workflow.
Fig. 2: CO-ED networks can help guide enzyme discovery.
Fig. 3: Heterologous expression of oxzAB results in the production of a series of oxazolones.
Fig. 4: In vitro characterization of oxazolone biosynthesis by P. rubra OxzA and OxzB.

Data availability

All data generated during this study are included in this article and its Supplementary Information. CO-ED networks used to generate Fig. 2 and several Supplementary Figs. showing CO-ED networks are available in Supplementary Data 1. The curated set of enzyme domains for CO-ED can be found as the node table of the ‘all_of_uniprot’ network in Supplementary Data 1, as well as at https://github.com/tderond/CO-ED/blob/master/pfamID_to_name_desc_longdesc.tsv. This same set of domains is also the default setting for the web tool. NMR spectra of newly reported structures are available in the Supplementary Note. Tandem MS spectra of newly reported structures are available in the Supplementary Note and were also deposited to the GNPS spectral library at the URLs shown in the Supplementary Note. The following bioinformatic databases were employed in this study: BRENDA (https://www.brenda-enzymes.org/), MIBiG (https://mibig.secondarymetabolites.org/), UniProt (https://www.uniprot.org/) and Pfam-A (http://pfam.xfam.org). Source data are provided with this paper.

Code availability

Jupyter notebooks containing Python code for CO-ED analysis and for generating the statistics shown in Supplementary Figs. 1 and 18 are publicly available at https://github.com/tderond/CO-ED.

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Acknowledgements

We thank our UCSD colleagues J. Li, V. Shende, T. Fallon and B. Duggan for helpful discussions. This work was supported by National Institutes of Health awards F32GM129960 to T.d.R. and R01GM085770 to B.S.M., as well as an American Society for Pharmacognosy Undergraduate Research Award and a UC San Diego ‘Eureka’ Undergraduate Research Scholarship to J.E.A.

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T.d.R. and B.S.M. designed research; T.d.R. and J.E.A. performed research; T.d.R. analyzed data; T.d.R. and B.S.M. wrote the paper.

Corresponding authors

Correspondence to Tristan de Rond or Bradley S. Moore.

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The authors declare no competing interests.

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Peer review information Nature Chemical Biology thanks A. James Link, Maude Pupin and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Survey of transformations known to be catalyzed by the ThiF and nitroreductase domains, and properties of organisms harboring a ThiF-nitroreductase di-domain enzyme identified by CO-ED.

a, OxzB exhibits homology to both the ThiF and nitroreductase enzyme families. Shown is a selection of characterized members of these enzyme families along with the transformations they catalyze, along with midpoint-rooted gene trees showing the relationships between each other and OxzB. ThiF family enzymes are known to catalyze ATP-dependent carboxylate activating reactions, while nitroreductase family enzymes catalyze a variety of redox reactions. Inferred phylogenies were generated from protein sequences using neighbor joining on the MAFFT web server51 and midpoint-rooted. Scale bars designate 1 substitution per site. b,c, Phylogenetic distribution (b) and habitat (c) of the host organisms harboring genes encoding OxzB proteins represented in the Uniprot database. Organisms with unknown habitats are not included. d, Genomic context of oxzB genes as determined using the Enzyme Function Initiative Genome Neighborhood Tool42. Most oxzB homologs are accompanied by oxzA, which codes for an N-acyltransferase. The arrow labeled ‘?’ represents genes unrelated to oxzA or oxzB. Organisms with unknown oxzB genomic context (for example, at the edge of a contig) are not included.

Source data

Extended Data Fig. 2 Induction of oxazolone production in P. rubra and C. chukchiensis by various antibiotics.

Bacteria were grown as a lawn on Marine Agar 2216 with a drop of antibiotic. A consistent amount of biomass adjacent to the zone of inhibition was harvested, extracted and analyzed by HPLC. Dots indicate summed peak areas between wavelengths of 300 nm and 400 nm. Three biological replicates were analyzed for each condition.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–19, Tables 1 and 2 and Note

Reporting Summary

Supplementary Data 1

Source data

Source Data Extended Data Fig. 1

Statistical source data for Extended Data Fig. 1b–d.

Source Data Extended Data Fig. 2

Statistical source data.

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de Rond, T., Asay, J.E. & Moore, B.S. Co-occurrence of enzyme domains guides the discovery of an oxazolone synthetase. Nat Chem Biol 17, 794–799 (2021). https://doi.org/10.1038/s41589-021-00808-4

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