Conformational rearrangements enable iterative backbone N-methylation in RiPP biosynthesis

Fredarla S. Miller, Kathryn K. Crone, Matthew R. Jensen, Sudipta Shaw, William R. Harcombe, Mikael H. Elias, Michael F. Freeman

Research output: Contribution to journalArticlepeer-review

Abstract

Peptide backbone α-N-methylations change the physicochemical properties of amide bonds to provide structural constraints and other favorable characteristics including biological membrane permeability to peptides. Borosin natural product pathways are the only known ribosomally encoded and posttranslationally modified peptides (RiPPs) pathways to incorporate backbone α-N-methylations on translated peptides. Here we report the discovery of type IV borosin natural product pathways (termed ‘split borosins’), featuring an iteratively acting α-N-methyltransferase and separate precursor peptide substrate from the metal-respiring bacterium Shewanella oneidensis. A series of enzyme-precursor complexes reveal multiple conformational states for both α-N-methyltransferase and substrate. Along with mutational and kinetic analyses, our results give rare context into potential strategies for iterative maturation of RiPPs.

Original languageEnglish (US)
Article number5355
JournalNature communications
Volume12
Issue number1
DOIs
StatePublished - Sep 9 2021
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by the National Institutes of Health (R35 GM133475 to M.F.F.) and the University of Minnesota along with the BioTechnology Institute (M.F.F., M.H.E. and W.A.H.). We thank J. Gralnick for the strain S. oneidensis MR-1 and A. Imani for borosin gene expressions from S. sp. NRRL S-118. We are grateful to A. Jenks for help with cryoprotecting crystals and M. Quijano for initial bioinformatics analysis. We thank A. Buller for useful discussions in revising this manuscript. We also thank the Advanced Photon Source (APS, Argonne, Illinois) and beamline staff for access and support and K. Shi for assistance at the University of Minnesota Nanoliter Crystallization Facility.

Publisher Copyright:
© 2021, The Author(s).

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