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YcaO-mediated ATP-dependent peptidase activity in ribosomal peptide biosynthesis

Nature Chemical Biology volume 19, pages 111–119 (2023)Cite this article

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Abstract

YcaO enzymes catalyze ATP-dependent post-translation modifications on peptides, including the installation of (ox/thi)azoline, thioamide and/or amidine moieties. Here we demonstrate that, in the biosynthesis of the bis-methyloxazolic alkaloid muscoride A, the YcaO enzyme MusD carries out both ATP-dependent cyclodehydration and peptide bond cleavage, which is a mechanism unprecedented for such a reaction. YcaO-catalyzed modifications are proposed to occur through a backbone O-phosphorylated intermediate, but this mechanism remains speculative. We report, to our knowedge, the first characterization of an acyl-phosphate species consistent with the proposed mechanism for backbone amide activation. The 3.1-Å-resolution cryogenic electron microscopy structure of MusD along with biochemical analysis allow identification of residues that enable peptide cleavage reaction. Bioinformatics analysis identifies other cyanobactin pathways that may deploy bifunctional YcaO enzymes. Our structural, mutational and mechanistic studies expand the scope of modifications catalyzed by YcaO proteins to include peptide hydrolysis and provide evidence for a unifying mechanism for the catalytically diverse outcomes.

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Fig. 1: Canonical YcaO-catalyzed enzymatic reactions.
Fig. 2: Characterization of cyanobactin biosynthesis.
Fig. 3: MusD cleaves the C-terminal peptide of the bis-methyloxazole precusor.
Fig. 4: Identification of an O-phosphorylated intermediate.
Fig. 5: Cryo-EM structure of the MusD YcaO.
Fig. 6: Compairson of YcaO active site structures.

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Data availability

All the data supporting the findings of this study are available within the manuscript, the Supplementary Dataset or the Supplementary Information. Cryo-EM density map of MusD has been deposited in the Electron Microscopy Data Bank (accession no. EMD-26344). The atomic coordinate has been deposited in the Protein Data Bank (ID: 7U58). Source data are provided for Figs. 2–4 and Extended Data Figs. 1, 2, 5, 6, 7 and 10. Source data are provided with this paper.

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Acknowledgements

This work was supported by the National Institutes of Health (NIH) (GM079038 to S.K.N.). The Bruker UltrafleXtreme MALDI TOF/TOF mass spectrometer was purchased, in part, with a grant from the NIH (S10RR027109A). The Titan Glacios was purchased, in part, with a grant from the NIH (S10OD028700). We thank K. M. Flatt, X. Chen and J. Sun (Purdue University) for help with cryo-EM experiments and data processing. We also thank J. Gerlt and D. Mitchell for fruitful discussions.

Author information

Authors and Affiliations

  1. Department of Biochemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, Urbana, IL, USA

    Yiwu Zheng & Satish K. Nair

  2. Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, Urbana, IL, USA

    Satish K. Nair

  3. Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA

    Satish K. Nair

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Contributions

Y.Z. and S.K.N. designed and performed the experiments. Both authors analyzed data and assisted in the writing and editorial process. S.K.N. conceived of and supervised the project.

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Correspondence to Satish K. Nair.

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Extended data

Extended Data Fig. 1 MALDI-TOF-MS analysis of spontaneous hydrolysis of 2c.

1d was incubated with MusD for 15 min. The reaction was then quenched by Ziptip to extract peptides to remove the ATP/enzyme. Peptides were eluted from Ziptip using elution buffer (75% ACN and 25% H2O containing 0.1 TFA%) and mixed with Tris-buffer (20 mM, pH 7.5). We specify this time as the initial point (0 h) for the hydrolysis reaction. The spontaneous hydrolysis of 2c was then determined by MALDI-TOF-MS analysis of the sample over the designated time periods.

Source data

Extended Data Fig. 2 MALDI-TOF-MS analysis of hydroxamate product.

a. 1d (50 µM) was incubated with MusD (10 µM) in the presence of ATP/Mg2+ at 22 °C for 15 min (Blue line). Then NH2OH was added to the reaction to a final concentration of 1 M and the mixture was incubated at 22 °C for another 20 min (red line), resulting in the identification of a new product 1h. b. The propose chemical structure of 1h.

Source data

Extended Data Fig. 3 Single-particle cryo-EM analysis of MusD.

a. Flowchart for cryo-EM data processing. The final average resolution for the entire MusD is estimated to be 3.1 Å. b. Representative 2D classes (box size 256 Å). c. Local resolution map of the final 3D reconstruction. d. The gold-standard Fourier shell correlation (FSC) curve for the 3D reconstruction calculated in cryoSPARC. FSC = 0.143 is indicated.

Extended Data Fig. 4 Flow chart for cryo-EM data processing to obtain MusD map with N-terminal density.

After ab-initio reconstruction and heterogeneous refinement, two maps were selected for further NU-refinement. Density for the N-terminal RRE can be observed in the low-resolution map (3.75 Å).

Extended Data Fig. 5 Activity of Ala-substituted MusD variants.

Positions in the active site of MusD were targeted for Ala replacement by site-directed mutagenesis based the CryoEM structure of MusD. These MusD variants were assayed for enzymatic activity by co-expression with MusE and MusOX, and analyzed using MALDI-TOF-MS.

Source data

Extended Data Fig. 6 In vitro reconstitution of MusDE665A activity.

MALDI-TOF-MS analysis of incubation of MusE (50 µM) with MusDE665A (10 µM) and MusOX (10 µM) in the presence of 2 mM ATP/Mg2+ and 100 µM FMN. MusDE665A/MusOX can catalyze the formation of 1d, but the hydrolysis of peptide bond was not observed.

Source data

Extended Data Fig. 7 MALDI–TOF analysis of modification of MusE variants by MusD and MusOX through co-expression in E. coli.

The results were summarized in the table. * indicates hydrolysis product. ξ indicates the formation of two a(ox/thia)zoloes, # indicates the formation of one a(ox/thi)azoles & indicates unmodified MusE variants.

Source data

Extended Data Fig. 8 Bioinformatic analyses suggest other bifunctional YcaOs.

a. Colored sequence similarity network (SSN) of the closest 448 homologues of MusD (alignment score 330) found across cyanobacteria clustered based on sequence similarity (MusD is found in cluster 10). b-d. Genome neighborhood network (GNN) analysis of selected clusters identified in the SSN, which likely encode for cyanobactins. The GNNs were generated using default ‘Neighborhood size” (10) and a query-neighbor co-occurrence threshold of 20%. The circles that are critical for the biosynthesis of cyanobactin are colored in yellow. The GNNs are shown for (b) cluster 10, (c) cluster 4, and (d) cluster 2.

Extended Data Fig. 9 Cyanobactin biosynthetic gene cluster lack of enzyme G.

Proposed cyanobactin biosynthetic gene cluster with high similarity to that of muscoride A (cluster 10) as identified in the SSN and GNN analysis.

Extended Data Fig. 10 MALDI–TOF analysis of coexpression of MusD/OX with either MusESTS or MusETSS.

a. Coexpression of MusD/OX with MusESTS led to a mass loss 216 Da, relative to the unmofied peptide, which corresponds to the formation of three heterocycles and the removal of the C-terminal Gly-Val. b. Coexpression of MusD/OX with MusESTS led to the production of three MusETSS derivatives. A mass loss of 216 Da (relative to the unmodified precursor) (m/z = 6983) is the major product, consistent with the formation of three heterocycles and the removal of the C-terminal Gly-Val. A mass loss of 196 (m/z = 6913) corresponds to formation of two heterocycles and removal of the C-terminal Gly-Val. A mass loss of 176 (m/z = 6933) corresponds to one heterocycles and removal of the C-terminal Gly-Val.

Source data

Supplementary information

Supplementary Information

Supplementary Figs. 1–15 and Supplementary Table 1

Reporting Summary

Supplementary Data 1

Accession number of YcaO enzymes

Source data

Source Data Fig. 2

Raw data for Fig. 2c,d

Source Data Fig. 3

Raw data for Fig. 3a

Source Data Fig. 4

Raw data for Fig. 4a–c

Source Data Extended Data Fig. 1

Raw data for Extended Data Fig. 1b

Source Data Extended Data Fig. 2

Raw data for Extended Data Fig. 2a

Source Data Extended Data Fig. 5

Raw data for Extended Data Fig. 5

Source Data Extended Data Fig. 6

Raw data for Extended Data Fig. 6b

Source Data Extended Data Fig. 7

Raw data for Extended Data Fig. 7

Source Data Extended Data Fig. 10

Raw data for Extended Data Fig. 10a,b

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Zheng, Y., Nair, S.K. YcaO-mediated ATP-dependent peptidase activity in ribosomal peptide biosynthesis. Nat Chem Biol 19, 111–119 (2023). https://doi.org/10.1038/s41589-022-01141-0

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