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A prevalent peptide-binding domain guides ribosomal natural product biosynthesis

Nature Chemical Biology volume 11, pages 564–570 (2015)Cite this article

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Abstract

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a rapidly growing class of natural products. RiPP precursor peptides can undergo extensive enzymatic tailoring to yield structurally and functionally diverse products, and their biosynthetic logic makes them attractive bioengineering targets. Recent work suggests that unrelated RiPP-modifying enzymes contain structurally similar precursor peptide–binding domains. Using profile hidden Markov model comparisons, we discovered related and previously unrecognized peptide-binding domains in proteins spanning the majority of known prokaryotic RiPP classes, and we named this conserved domain the RiPP precursor peptide recognition element (RRE). Through binding studies we verified RRE's roles for three distinct RiPP classes: linear azole-containing peptides, thiopeptides and lasso peptides. Because numerous RiPP biosynthetic enzymes act on peptide substrates, our findings have powerful predictive value as to which protein(s) drive substrate binding, thereby laying a foundation for further characterization of RiPP biosynthetic pathways and the rational engineering of new peptide-binding activities.

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Figure 1: Overview of RiPP biosynthesis and the TOMM subclass.
Figure 2: Structural comparison of four RiPP-modifying enzymes.
Figure 3: RREs are present in diverse RiPP biosynthetic proteins.

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Acknowledgements

We are grateful to A. Maniak and R. Dowen for cloning several of the TOMM biosynthetic proteins and to C. Cox for bioinformatics consultation. We also thank C. Deane for critical review of this manuscript. This work was supported by the US National Institutes of Health (NIH) (1R01 GM097142 to D.A.M. and 2T32 GM070421 to B.J.B. and K.L.D.). Additional financial support came from the University of Illinois at Urbana-Champaign Department of Chemistry (Robert C. and Carolyn J. Springborn Endowment to B.J.B. and Harold R. Snyder Fellowship to K.L.D. and G.A.H.). B.J.B. was also funded by a National Science Foundation Graduate Research Fellowship (DGE-1144245).

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Authors and Affiliations

  1. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA

    Brandon J Burkhart, Graham A Hudson, Kyle L Dunbar & Douglas A Mitchell

  2. Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA

    Brandon J Burkhart, Graham A Hudson, Kyle L Dunbar & Douglas A Mitchell

  3. Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA

    Douglas A Mitchell

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  1. Brandon J Burkhart
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  2. Graham A Hudson
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Contributions

Experiments were designed by D.A.M. and B.J.B. and performed by B.J.B. Critical reagents were provided by K.L.D. and G.A.H. The manuscript was written by D.A.M. and B.J.B. The overall study was conceived and managed by D.A.M.

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Correspondence to Douglas A Mitchell.

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Burkhart, B., Hudson, G., Dunbar, K. et al. A prevalent peptide-binding domain guides ribosomal natural product biosynthesis. Nat Chem Biol 11, 564–570 (2015). https://doi.org/10.1038/nchembio.1856

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