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Title: Steric complementarity directs sequence promiscuous leader binding in RiPP biosynthesis

Abstract

Enzymes that generate ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products have garnered significant interest, given their ability to produce large libraries of chemically diverse scaffolds. Such RiPP biosynthetic enzymes are predicted to bind their corresponding peptide substrates through sequence-specific recognition of the leader sequence, which is removed after the installation of posttranslational modifications on the core sequence. The conservation of the leader sequence within a given RiPP class, in otherwise disparate precursor peptides, further supports the notion that strict sequence specificity is necessary for leader peptide engagement. Here, we demonstrate that leader binding by a biosynthetic enzyme in the lasso peptide class of RiPPs is directed by a minimal number of hydrophobic interactions. Biochemical and structural data illustrate how a single leader-binding domain can engage sequence-divergent leader peptides using a conserved motif that facilitates hydrophobic packing. The presence of this simple motif in noncognate peptides results in low micromolar affinity binding by binding domains from several different lasso biosynthetic systems. We also demonstrate that these observations likely extend to other RiPP biosynthetic classes. The portability of the binding motif opens avenues for the engineering of semisynthetic hybrid RiPP products.

Authors:
; ; ORCiD logo
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH)
OSTI Identifier:
1578220
Resource Type:
Journal Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 116; Journal Issue: 48; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences
Country of Publication:
United States
Language:
ENGLISH

Citation Formats

Chekan, Jonathan R., Ongpipattanakul, Chayanid, and Nair, Satish K. Steric complementarity directs sequence promiscuous leader binding in RiPP biosynthesis. United States: N. p., 2019. Web. doi:10.1073/pnas.1908364116.
Chekan, Jonathan R., Ongpipattanakul, Chayanid, & Nair, Satish K. Steric complementarity directs sequence promiscuous leader binding in RiPP biosynthesis. United States. doi:10.1073/pnas.1908364116.
Chekan, Jonathan R., Ongpipattanakul, Chayanid, and Nair, Satish K. Tue . "Steric complementarity directs sequence promiscuous leader binding in RiPP biosynthesis". United States. doi:10.1073/pnas.1908364116.
@article{osti_1578220,
title = {Steric complementarity directs sequence promiscuous leader binding in RiPP biosynthesis},
author = {Chekan, Jonathan R. and Ongpipattanakul, Chayanid and Nair, Satish K.},
abstractNote = {Enzymes that generate ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products have garnered significant interest, given their ability to produce large libraries of chemically diverse scaffolds. Such RiPP biosynthetic enzymes are predicted to bind their corresponding peptide substrates through sequence-specific recognition of the leader sequence, which is removed after the installation of posttranslational modifications on the core sequence. The conservation of the leader sequence within a given RiPP class, in otherwise disparate precursor peptides, further supports the notion that strict sequence specificity is necessary for leader peptide engagement. Here, we demonstrate that leader binding by a biosynthetic enzyme in the lasso peptide class of RiPPs is directed by a minimal number of hydrophobic interactions. Biochemical and structural data illustrate how a single leader-binding domain can engage sequence-divergent leader peptides using a conserved motif that facilitates hydrophobic packing. The presence of this simple motif in noncognate peptides results in low micromolar affinity binding by binding domains from several different lasso biosynthetic systems. We also demonstrate that these observations likely extend to other RiPP biosynthetic classes. The portability of the binding motif opens avenues for the engineering of semisynthetic hybrid RiPP products.},
doi = {10.1073/pnas.1908364116},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
issn = {0027-8424},
number = 48,
volume = 116,
place = {United States},
year = {2019},
month = {11}
}

Works referenced in this record:

Natural combinatorial peptide libraries in cyanobacterial symbionts of marine ascidians
journal, November 2006

  • Donia, Mohamed S.; Hathaway, Brian J.; Sudek, Sebastian
  • Nature Chemical Biology, Vol. 2, Issue 12
  • DOI: 10.1038/nchembio829

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks
journal, August 2015

  • Gerlt, John A.; Bouvier, Jason T.; Davidson, Daniel B.
  • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1854, Issue 8
  • DOI: 10.1016/j.bbapap.2015.04.015

The Cyanobactin Heterocyclase Enzyme: A Processive Adenylase That Operates with a Defined Order of Reaction
journal, November 2013

  • Koehnke, Jesko; Bent, Andrew F.; Zollman, David
  • Angewandte Chemie International Edition, Vol. 52, Issue 52
  • DOI: 10.1002/anie.201306302

Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB
journal, October 2014


Acinetodin and Klebsidin, RNA Polymerase Targeting Lasso Peptides Produced by Human Isolates of Acinetobacter gyllenbergii and Klebsiella pneumoniae
journal, February 2017


Xanthomonas campestris PqqD in the pyrroloquinoline quinone biosynthesis operon adopts a novel saddle-like fold that possibly serves as a PQQ carrier
journal, September 2009

  • Tsai, Tung-Yi; Yang, Chao-Yu; Shih, Hui-Ling
  • Proteins: Structure, Function, and Bioinformatics, Vol. 76, Issue 4
  • DOI: 10.1002/prot.22461

Cyanobactins—ribosomal cyclic peptides produced by cyanobacteria
journal, February 2010

  • Sivonen, Kaarina; Leikoski, Niina; Fewer, David P.
  • Applied Microbiology and Biotechnology, Vol. 86, Issue 5
  • DOI: 10.1007/s00253-010-2482-x

Caulosegnins I–III: A Highly Diverse Group of Lasso Peptides Derived from a Single Biosynthetic Gene Cluster
journal, December 2012

  • Hegemann, Julian D.; Zimmermann, Marcel; Xie, Xiulan
  • Journal of the American Chemical Society, Vol. 135, Issue 1
  • DOI: 10.1021/ja308173b

Chimeric Leader Peptides for the Generation of Non-Natural Hybrid RiPP Products
journal, June 2017


The PqqD homologous domain of the radical SAM enzyme ThnB is required for thioether bond formation during thurincin H maturation
journal, May 2015


Two Enzymes Catalyze the Maturation of a Lasso Peptide in Escherichia coli
journal, July 2007

  • Duquesne, Sophie; Destoumieux-Garzon, Delphine; Zirah, Severine
  • Chemistry & Biology, Vol. 14, Issue 7, p. 793-803
  • DOI: 10.1016/j.chembiol.2007.06.004

Characterization of caulonodin lasso peptides revealed unprecedented N-terminal residues and a precursor motif essential for peptide maturation
journal, January 2014

  • Zimmermann, Marcel; Hegemann, Julian D.; Xie, Xiulan
  • Chem. Sci., Vol. 5, Issue 10
  • DOI: 10.1039/C4SC01428F

A new genome-mining tool redefines the lasso peptide biosynthetic landscape
journal, February 2017

  • Tietz, Jonathan I.; Schwalen, Christopher J.; Patel, Parth S.
  • Nature Chemical Biology, Vol. 13, Issue 5
  • DOI: 10.1038/nchembio.2319

Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides
journal, August 2017

  • Grove, Tyler L.; Himes, Paul M.; Hwang, Sungwon
  • Journal of the American Chemical Society, Vol. 139, Issue 34
  • DOI: 10.1021/jacs.7b01283

Enzymatic Reconstitution and Biosynthetic Investigation of the Lasso Peptide Fusilassin
journal, November 2018

  • DiCaprio, Adam J.; Firouzbakht, Arash; Hudson, Graham A.
  • Journal of the American Chemical Society, Vol. 141, Issue 1
  • DOI: 10.1021/jacs.8b09928

Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria
journal, May 2010

  • Li, B.; Sher, D.; Kelly, L.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 23
  • DOI: 10.1073/pnas.0913677107

‘Democratized’ genomic enzymology web tools for functional assignment
journal, December 2018


Analysis of modular bioengineered antimicrobial lanthipeptides at nanoliter scale
journal, April 2019

  • Schmitt, Steven; Montalbán-López, Manuel; Peterhoff, David
  • Nature Chemical Biology, Vol. 15, Issue 5
  • DOI: 10.1038/s41589-019-0250-5

How the MccB bacterial ancestor of ubiquitin E1 initiates biosynthesis of the microcin C7 antibiotic
journal, June 2009

  • Regni, Catherine A.; Roush, Rebecca F.; Miller, Darcie J.
  • The EMBO Journal, Vol. 28, Issue 13
  • DOI: 10.1038/emboj.2009.146

Aestuaramides, a Natural Library of Cyanobactin Cyclic Peptides Resulting from Isoprene-Derived Claisen Rearrangements
journal, February 2013

  • McIntosh, John A.; Lin, Zhenjian; Tianero, Ma. Diarey B.
  • ACS Chemical Biology, Vol. 8, Issue 5
  • DOI: 10.1021/cb300614c

A lanthipeptide library used to identify a protein–protein interaction inhibitor
journal, March 2018


Insights into the Unique Phosphorylation of the Lasso Peptide Paeninodin
journal, May 2016

  • Zhu, Shaozhou; Hegemann, Julian D.; Fage, Christopher D.
  • Journal of Biological Chemistry, Vol. 291, Issue 26
  • DOI: 10.1074/jbc.M116.722108

Dissecting the Maturation Steps of the Lasso Peptide Microcin J25 in vitro
journal, April 2012


Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition
journal, September 2017

  • Davis, Katherine M.; Schramma, Kelsey R.; Hansen, William A.
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 39
  • DOI: 10.1073/pnas.1703663114

Elucidation of the roles of conserved residues in the biosynthesis of the lasso peptide paeninodin
journal, January 2018

  • Hegemann, Julian D.; Schwalen, Christopher J.; Mitchell, Douglas A.
  • Chemical Communications, Vol. 54, Issue 65
  • DOI: 10.1039/C8CC04411B

Linking Chemistry and Genetics in the Growing Cyanobactin Natural Products Family
journal, April 2011


Structural analysis of leader peptide binding enables leader-free cyanobactin processing
journal, June 2015

  • Koehnke, Jesko; Mann, Greg; Bent, Andrew F.
  • Nature Chemical Biology, Vol. 11, Issue 8
  • DOI: 10.1038/nchembio.1841

Molecular cloning of the gene cluster for lariatin biosynthesis of Rhodococcus jostii K01-B0171
journal, March 2012

  • Inokoshi, Junji; Matsuhama, Maki; Miyake, Midori
  • Applied Microbiology and Biotechnology, Vol. 95, Issue 2
  • DOI: 10.1007/s00253-012-3973-8

High Divergence of the Precursor Peptides in Combinatorial Lanthipeptide Biosynthesis
journal, September 2014

  • Zhang, Qi; Yang, Xiao; Wang, Huan
  • ACS Chemical Biology, Vol. 9, Issue 11
  • DOI: 10.1021/cb500622c

Lassomycin, a Ribosomally Synthesized Cyclic Peptide, Kills Mycobacterium tuberculosis by Targeting the ATP-Dependent Protease ClpC1P1P2
journal, April 2014


Heterologous and in Vitro Reconstitution of Fuscanodin, a Lasso Peptide from Thermobifida fusca
journal, December 2018

  • Koos, Joseph D.; Link, A. James
  • Journal of the American Chemical Society, Vol. 141, Issue 2
  • DOI: 10.1021/jacs.8b10724

Requirements of the Engineered Leader Peptide of Nisin for Inducing Modification, Export, and Cleavage
journal, November 2010

  • Plat, Annechien; Kluskens, Leon D.; Kuipers, Anneke
  • Applied and Environmental Microbiology, Vol. 77, Issue 2
  • DOI: 10.1128/AEM.01503-10

PqqD Is a Novel Peptide Chaperone That Forms a Ternary Complex with the Radical S -Adenosylmethionine Protein PqqE in the Pyrroloquinoline Quinone Biosynthetic Pathway
journal, March 2015

  • Latham, John A.; Iavarone, Anthony T.; Barr, Ian
  • Journal of Biological Chemistry, Vol. 290, Issue 20
  • DOI: 10.1074/jbc.M115.646521

Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature
journal, January 2013

  • Arnison, Paul G.; Bibb, Mervyn J.; Bierbaum, Gabriele
  • Nat. Prod. Rep., Vol. 30, Issue 1
  • DOI: 10.1039/c2np20085f

A prevalent peptide-binding domain guides ribosomal natural product biosynthesis
journal, July 2015

  • Burkhart, Brandon J.; Hudson, Graham A.; Dunbar, Kyle L.
  • Nature Chemical Biology, Vol. 11, Issue 8
  • DOI: 10.1038/nchembio.1856

The B1 Protein Guides the Biosynthesis of a Lasso Peptide
journal, October 2016

  • Zhu, Shaozhou; Fage, Christopher D.; Hegemann, Julian D.
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep35604

A global assembly line for cyanobactins
journal, April 2008

  • Donia, Mohamed S.; Ravel, Jacques; Schmidt, Eric W.
  • Nature Chemical Biology, Vol. 4, Issue 6
  • DOI: 10.1038/nchembio.84

Identification of distinct nisin leader peptide regions that determine interactions with the modification enzymes NisB and NisC
journal, January 2013


WebLogo: A Sequence Logo Generator
journal, May 2004

  • Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc
  • Genome Research, Vol. 14, Issue 6, p. 1188-1190
  • DOI: 10.1101/gr.849004

Precursor-centric genome-mining approach for lasso peptide discovery
journal, September 2012

  • Maksimov, M. O.; Pelczer, I.; Link, A. J.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 38
  • DOI: 10.1073/pnas.1208978109

Recognition Sequences and Substrate Evolution in Cyanobactin Biosynthesis
journal, March 2014

  • Sardar, Debosmita; Pierce, Elizabeth; McIntosh, John A.
  • ACS Synthetic Biology, Vol. 4, Issue 2
  • DOI: 10.1021/sb500019b