101
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Abstract
Bacterial natural products display astounding structural diversity, which, in turn, endows them with a remarkable range of biological activities that are of significant value to modern society. Such structural features are generated by biosynthetic enzymes that construct core scaffolds or perform peripheral modifications, and can thus define natural product families, introduce pharmacophores and permit metabolic diversification. Modern genomics approaches have greatly enhanced our ability to access and characterize natural product pathways via sequence-similarity-based bioinformatics discovery strategies. However, many biosynthetic enzymes catalyse exceptional, unprecedented transformations that continue to defy functional prediction and remain hidden from us in bacterial (meta)genomic sequence data. In this Review, we highlight exciting examples of unusual enzymology that have been uncovered recently in the context of natural product biosynthesis. These suggest that much of the natural product diversity, including entire substance classes, awaits discovery. New approaches to lift the veil on the cryptic chemistries of the natural product universe are also discussed.
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102
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Dong SH, Liu A, Mahanta N, Mitchell DA, Nair SK. Mechanistic Basis for Ribosomal Peptide Backbone Modifications. ACS CENTRAL SCIENCE 2019; 5:842-851. [PMID: 31139720 PMCID: PMC6535971 DOI: 10.1021/acscentsci.9b00124] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Indexed: 05/16/2023]
Abstract
YcaO enzymes are known to catalyze the ATP-dependent formation of azoline heterocycles, thioamides, and (macro)lactamidines on peptide substrates. These enzymes are found in multiple biosynthetic pathways, including those for several different classes of ribosomally synthesized and post-translationally modified peptides (RiPPs). However, there are major knowledge gaps in the mechanistic and structural underpinnings that govern each of the known YcaO-mediated modifications. Here, we present the first structure of any YcaO enzyme bound to its peptide substrate in the active site, specifically that from Methanocaldococcus jannaschii which is involved in the thioamidation of the α-subunit of methyl-coenzyme M reductase (McrA). The structural data are leveraged to identify and test the residues involved in substrate binding and catalysis by site-directed mutagenesis. We also show that thioamide-forming YcaOs can carry out the cyclodehydration of a related peptide substrate, which underscores the mechanistic conservation across the YcaO family and allows for the extrapolation of mechanistic details to azoline-forming YcaOs involved in RiPP biosynthesis. A bioinformatic survey of all YcaOs highlights the diverse sequence space in azoline-forming YcaOs and suggests their early divergence from a common ancestor. The data presented within provide a detailed molecular framework for understanding this family of enzymes, which reconcile several decades of prior data on RiPP cyclodehydratases. These studies also provide the foundational knowledge to impact our mechanistic understanding of additional RiPP biosynthetic classes.
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Affiliation(s)
- Shi-Hui Dong
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Andi Liu
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Nilkamal Mahanta
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Douglas A. Mitchell
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Satish K. Nair
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
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103
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Ge Y, Czekster CM, Miller OK, Botting CH, Schwarz-Linek U, Naismith JH. Insights into the Mechanism of the Cyanobactin Heterocyclase Enzyme. Biochemistry 2019; 58:2125-2132. [PMID: 30912640 PMCID: PMC6497369 DOI: 10.1021/acs.biochem.9b00084] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Cyanobactin
heterocyclases share the same catalytic domain (YcaO)
as heterocyclases/cyclodehydratases from other ribosomal peptide (RiPPs)
biosynthetic pathways. These enzymes process multiple residues (Cys/Thr/Ser)
within the same substrate. The processing of cysteine residues proceeds
with a known order. We show the order of reaction for threonines is
different and depends in part on a leader peptide within the substrate.
In contrast to other YcaO domains, which have been reported to exclusively
break down ATP into ADP and inorganic phosphate, cyanobactin heterocyclases
have been observed to produce AMP and inorganic pyrophosphate during
catalysis. We dissect the nucleotide profiles associated with heterocyclization
and propose a unifying mechanism, where the γ-phosphate of ATP
is transferred in a kinase mechanism to the substrate to yield a phosphorylated
intermediate common to all YcaO domains. In cyanobactin heterocyclases,
this phosphorylated intermediate, in a proportion of turnovers, reacts
with ADP to yield AMP and pyrophosphate.
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Affiliation(s)
- Ying Ge
- Biomedical Sciences Research Complex , University of St Andrews , St Andrews, Fife KY16 9ST , United Kingdom
| | - Clarissa Melo Czekster
- Biomedical Sciences Research Complex , University of St Andrews , St Andrews, Fife KY16 9ST , United Kingdom
| | - Ona K Miller
- Biomedical Sciences Research Complex , University of St Andrews , St Andrews, Fife KY16 9ST , United Kingdom
| | - Catherine H Botting
- Biomedical Sciences Research Complex , University of St Andrews , St Andrews, Fife KY16 9ST , United Kingdom
| | - Ulrich Schwarz-Linek
- Biomedical Sciences Research Complex , University of St Andrews , St Andrews, Fife KY16 9ST , United Kingdom
| | - James H Naismith
- Research Complex at Harwell , Didcot, Oxon OX11 0FA , United Kingdom.,Division of Structural Biology , University of Oxford , Oxford OX3 7BN , United Kingdom.,Rosalind Franklin Institute , Harwell, Didcot, Oxon OX11 0FA , United Kingdom
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104
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Vinogradov AA, Yin Y, Suga H. Macrocyclic Peptides as Drug Candidates: Recent Progress and Remaining Challenges. J Am Chem Soc 2019; 141:4167-4181. [PMID: 30768253 DOI: 10.1021/jacs.8b13178] [Citation(s) in RCA: 433] [Impact Index Per Article: 86.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Peptides as a therapeutic modality attract much attention due to their synthetic accessibility, high degree of specific binding, and the ability to target protein surfaces traditionally considered "undruggable". Unfortunately, at the same time, other pharmacological properties of a generic peptide, such as metabolic stability and cell permeability, are quite poor, which limits the success of de novo discovered biologically active peptides as drug candidates. Here, we review how macrocyclization as well as the incorporation of nonproteogenic amino acids and various conjugation strategies may be utilized to improve on these characteristics to create better drug candidates. We analyze recent progress and remaining challenges in improving individual pharmacological properties of bioactive peptides, and offer our opinion on interfacing these, often conflicting, considerations, to create balanced drug candidates as a potential way to make further progress in this area.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Yizhen Yin
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
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105
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Qiu Y, Du Y, Wang S, Zhou S, Guo Y, Liu W. Radical S-Adenosylmethionine Protein NosN Forms the Side Ring System of Nosiheptide by Functionalizing the Polythiazolyl Peptide S-Conjugated Indolic Moiety. Org Lett 2019; 21:1502-1505. [DOI: 10.1021/acs.orglett.9b00293] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yanping Qiu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yanan Du
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Shoufeng Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Shuaixiang Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yinlong Guo
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
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106
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Mahanta N, Szantai-Kis DM, Petersson EJ, Mitchell DA. Biosynthesis and Chemical Applications of Thioamides. ACS Chem Biol 2019; 14:142-163. [PMID: 30698414 PMCID: PMC6404778 DOI: 10.1021/acschembio.8b01022] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Thioamidation as a posttranslational modification is exceptionally rare, with only a few reported natural products and exactly one known protein example (methyl-coenzyme M reductase from methane-metabolizing archaea). Recently, there has been significant progress in elucidating the biosynthesis and function of several thioamide-containing natural compounds. Separate developments in the chemical installation of thioamides into peptides and proteins have enabled cell biology and biophysical studies to advance the current understanding of natural thioamides. This review highlights the various strategies used by Nature to install thioamides in peptidic scaffolds and the potential functions of this rare but important modification. We also discuss synthetic methods used for the site-selective incorporation of thioamides into polypeptides with a brief discussion of the physicochemical implications. This account will serve as a foundation for the further study of thioamides in natural products and their various applications.
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Affiliation(s)
| | - D Miklos Szantai-Kis
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine , University of Pennsylvania , 3700 Hamilton Walk , Philadelphia , Pennsylvania 19104 , United States
| | - E James Petersson
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine , University of Pennsylvania , 3700 Hamilton Walk , Philadelphia , Pennsylvania 19104 , United States
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104 , United States
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107
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Ghilarov D, Stevenson CEM, Travin DY, Piskunova J, Serebryakova M, Maxwell A, Lawson DM, Severinov K. Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison. Mol Cell 2019; 73:749-762.e5. [PMID: 30661981 PMCID: PMC6395948 DOI: 10.1016/j.molcel.2018.11.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/24/2018] [Accepted: 11/27/2018] [Indexed: 11/29/2022]
Abstract
The introduction of azole heterocycles into a peptide backbone is the principal step in the biosynthesis of numerous compounds with therapeutic potential. One of them is microcin B17, a bacterial topoisomerase inhibitor whose activity depends on the conversion of selected serine and cysteine residues of the precursor peptide to oxazoles and thiazoles by the McbBCD synthetase complex. Crystal structures of McbBCD reveal an octameric B4C2D2 complex with two bound substrate peptides. Each McbB dimer clamps the N-terminal recognition sequence, while the C-terminal heterocycle of the modified peptide is trapped in the active site of McbC. The McbD and McbC active sites are distant from each other, which necessitates alternate shuttling of the peptide substrate between them, while remaining tethered to the McbB dimer. An atomic-level view of the azole synthetase is a starting point for deeper understanding and control of biosynthesis of a large group of ribosomally synthesized natural products. Azole synthetase McbBCD is co-crystallized with its product, microcin B17 Crystal structure of McbBCD reveals an octameric assembly of B4C2D2 Two McbB subunits within each asymmetric unit interact to recognize a peptide Formation of each azole ring requires shuttling of peptide between two active centers
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Affiliation(s)
- Dmitry Ghilarov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Cracow, Poland
| | | | - Dmitrii Y Travin
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Julia Piskunova
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia
| | - Marina Serebryakova
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, NR4 7UH Norwich, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, NR4 7UH Norwich, UK.
| | - Konstantin Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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108
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Sikandar A, Koehnke J. The role of protein–protein interactions in the biosynthesis of ribosomally synthesized and post-translationally modified peptides. Nat Prod Rep 2019; 36:1576-1588. [DOI: 10.1039/c8np00064f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This review covers the role of protein–protein complexes in the biosynthesis of selected ribosomally synthesized and post-translationally modified peptide (RiPP) classes.
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Affiliation(s)
- Asfandyar Sikandar
- Workgroup Structural Biology of Biosynthetic Enzymes
- Helmholtz Institute for Pharmaceutical Research Saarland
- Helmholtz Centre for Infection Research
- Saarland University
- 66123 Saarbrücken
| | - Jesko Koehnke
- Workgroup Structural Biology of Biosynthetic Enzymes
- Helmholtz Institute for Pharmaceutical Research Saarland
- Helmholtz Centre for Infection Research
- Saarland University
- 66123 Saarbrücken
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109
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Schneider O, Simic N, Aachmann FL, Rückert C, Kristiansen KA, Kalinowski J, Jiang Y, Wang L, Jiang CL, Lale R, Zotchev SB. Genome Mining of Streptomyces sp. YIM 130001 Isolated From Lichen Affords New Thiopeptide Antibiotic. Front Microbiol 2018; 9:3139. [PMID: 30619207 PMCID: PMC6306032 DOI: 10.3389/fmicb.2018.03139] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/04/2018] [Indexed: 12/01/2022] Open
Abstract
Streptomyces bacteria are recognized as an important source for antibiotics with broad applications in human medicine and animal health. Here, we report the isolation of a new lichen-associating Streptomyces sp. YIM 130001 from the tropical rainforest in Xishuangbanna (Yunnan, China), which displayed antibacterial activity against Bacillus subtilis. The draft genome sequence of this isolate strain revealed 18 putative biosynthetic gene clusters (BGCs) for secondary metabolites, which is an unusually low number compared to a typical streptomycete. Inactivation of a lantibiotic dehydrogenase-encoding gene from the BGC presumed to govern biosynthesis of a thiopeptide resulted in the loss of bioactivity. Using comparative HPLC analysis, two peaks in the chromatogram were identified in the extract from the wild-type strain, which were missing in the extract from the mutant. The compounds corresponding to the identified peaks were purified, and structure of one compound was elucidated using NMR. The compound, designated geninthiocin B, showed high similarity to several 35-membered macrocyclic thiopeptides geninthiocin, Val-geninthiocin and berninamycin A. Bioinformatics analysis of the geninthiocin B BGC revealed its close homology to that of berninamycins.
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Affiliation(s)
- Olha Schneider
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Nebojsa Simic
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | - Finn Lillelund Aachmann
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Kåre Andre Kristiansen
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Yi Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Lisong Wang
- Key Lab for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Cheng-Lin Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Rahmi Lale
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sergey B Zotchev
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
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110
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Gu W, Sardar D, Pierce E, Schmidt EW. Roads to Rome: Role of Multiple Cassettes in Cyanobactin RiPP Biosynthesis. J Am Chem Soc 2018; 140:16213-16221. [PMID: 30387998 DOI: 10.1021/jacs.8b09328] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are ubiquitous natural products. Bioactive RiPPs are produced from a precursor peptide, which is modified by enzymes. Usually, a single product is encoded in a precursor peptide. However, in cyanobactins and several other RiPP pathways, a single precursor peptide encodes multiple bioactive products flanking with recognition sequences known as "cassettes". The role of multiple cassettes in one peptide is mysterious, but in general their presence is a marker of biosynthetic plasticity. Here, we show that in cyanobactin biosynthesis the presence of multiple cassettes confers distributive enzyme processing to multiple steps of the pathway, a feature we propose to be a hallmark of multicassette RiPPs. TruD heterocyclase is stochastic and distributive. Although a canonical biosynthetic route is favored with certain substrates, every conceivable biosynthetic route is accepted. Together, these factors afford greater plasticity to the biosynthetic pathway by equalizing the processing of each cassette, enabling access to chemical diversity.
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Affiliation(s)
- Wenjia Gu
- Department of Medicinal Chemistry , University of Utah , Salt Lake City , Utah 84112 , United States
| | - Debosmita Sardar
- Department of Medicinal Chemistry , University of Utah , Salt Lake City , Utah 84112 , United States
| | - Elizabeth Pierce
- Department of Medicinal Chemistry , University of Utah , Salt Lake City , Utah 84112 , United States
| | - Eric W Schmidt
- Department of Medicinal Chemistry , University of Utah , Salt Lake City , Utah 84112 , United States
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111
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Dunbar KL, Büttner H, Molloy EM, Dell M, Kumpfmüller J, Hertweck C. Genome Editing Reveals Novel Thiotemplated Assembly of Polythioamide Antibiotics in Anaerobic Bacteria. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807970] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kyle L. Dunbar
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Hannah Büttner
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Evelyn M. Molloy
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
- Natural Product Chemistry; Friedrich Schiller University; 07743 Jena Germany
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112
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Dunbar KL, Büttner H, Molloy EM, Dell M, Kumpfmüller J, Hertweck C. Genome Editing Reveals Novel Thiotemplated Assembly of Polythioamide Antibiotics in Anaerobic Bacteria. Angew Chem Int Ed Engl 2018; 57:14080-14084. [PMID: 30193003 DOI: 10.1002/anie.201807970] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/23/2018] [Indexed: 12/18/2022]
Abstract
Closthioamide (CTA) is a unique symmetric nonribosomal peptide with six thioamide moieties that is produced by the Gram-positive obligate anaerobe Ruminiclostridium cellulolyticum. CTA displays potent inhibitory activity against important clinical pathogens, making it a promising drug candidate. Yet, the biosynthesis of this DNA gyrase-targeting antibiotic has remained enigmatic. Using a combination of genome mining, genome editing (targeted group II intron, CRISPR/Cas9), and heterologous expression, we show that CTA biosynthesis involves specialized enzymes for starter unit biosynthesis, amide bond formation, thionation, and dimerization. Surprisingly, CTA biosynthesis involves a novel thiotemplated peptide assembly line that markedly differs from known nonribosomal peptide synthetases. These findings provide the first insights into the biosynthesis of thioamide-containing nonribosomal peptides and offer a starting point for the discovery of related natural products.
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Affiliation(s)
- Kyle L Dunbar
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Hannah Büttner
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Evelyn M Molloy
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Natural Product Chemistry, Friedrich Schiller University, 07743, Jena, Germany
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113
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Hudson GA, Mitchell DA. RiPP antibiotics: biosynthesis and engineering potential. Curr Opin Microbiol 2018; 45:61-69. [PMID: 29533845 PMCID: PMC6131089 DOI: 10.1016/j.mib.2018.02.010] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 02/23/2018] [Indexed: 01/14/2023]
Abstract
The threat of antibiotic resistant bacterial infections continues to underscore the need for new treatment options. Historically, small molecule metabolites from microbes have provided a rich source of antibiotic compounds, and as a result, significant effort has been invested in engineering the responsible biosynthetic pathways to generate novel analogs with attractive pharmacological properties. Unfortunately, biosynthetic stringency has limited the capacity of non-ribosomal peptide synthetases and polyketide synthases from producing substantially different analogs in large numbers. Another class of natural products, the ribosomally synthesized and post-translationally modified peptides (RiPPs), have rapidly expanded in recent years with many natively displaying potent antibiotic activity. RiPP biosynthetic pathways are modular and intrinsically tolerant to alternative substrates. Several prominent RiPPs with antibiotic activity will be covered in this review with a focus on their biosynthetic plasticity. While only a few RiPP enzymes have been thoroughly investigated mechanistically, this knowledge has already been harnessed to generate new-to-nature compounds. Through the use of synthetic biology approaches, on-going efforts in RiPP engineering hold great promise in unlocking the potential of this natural product class.
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Affiliation(s)
- Graham A Hudson
- Department of Chemistry, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States; Department of Microbiology, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States.
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114
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de Crécy-Lagard V, Haas D, Hanson AD. Newly-discovered enzymes that function in metabolite damage-control. Curr Opin Chem Biol 2018; 47:101-108. [PMID: 30268903 DOI: 10.1016/j.cbpa.2018.09.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/19/2018] [Accepted: 09/11/2018] [Indexed: 01/26/2023]
Abstract
Enzymes of unknown function are estimated to make up around 25% of the sequenced proteome. In the past decade, over 20 conserved families have been shown to function in the metabolism of 'damaged' or abnormal metabolites that are wasteful and often toxic. These newly discovered damage-control enzymes either repair or inactivate the offending metabolites, or pre-empt their formation in the first place. Comparative genomics has been of prime importance in predicting the functions of damage-control enzymes and in guiding the biochemical and genetic tests required to validate these functions.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA; Genetics Institute, University of Florida, Gainesville, FL, USA.
| | - Drago Haas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
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115
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Walsh CT. Nature Builds Macrocycles and Heterocycles into Its Antimicrobial Frameworks: Deciphering Biosynthetic Strategy. ACS Infect Dis 2018; 4:1283-1299. [PMID: 29993235 DOI: 10.1021/acsinfecdis.8b00101] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Natural products with anti-infective activity are largely of polyketide or peptide origin. The nascent scaffolds typically undergo further enzymatic morphing to produce mature active structures. Two kinds of common constraints during maturation of immature scaffolds to active end point metabolites are macrocyclizations and hetrocyclizations. Each builds compact architectures characteristic of many high affinity, specific ligands for therapeutic targets. The chemical logic and enzymatic machinery for macrolactone and macrolactam formations are analyzed for antibiotics such as erythromycins, daptomycin, polymyxins, and vancomycin. In parallel, biosynthetic enzymes build small ring heterocycles, including epoxides, β-lactams, and β-lactones, cyclic ethers such as tetrahydrofurans and tetrahydropyrans, thiazoles, and oxazoles, as well as some seven- and eight-member heterocyclic rings. Combinations of fused heterocyclic scaffolds and heterocycles embedded in macrocycles reveal nature's chemical logic for building active molecular frameworks in short efficient pathways.
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Affiliation(s)
- Christopher T. Walsh
- ChEM-H Institute, Stanford University, Shriram 279, 443 Via Ortega, Stanford, California 94305, United States
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116
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Litomska A, Ishida K, Dunbar KL, Boettger M, Coyne S, Hertweck C. Enzymatic Thioamide Formation in a Bacterial Antimetabolite Pathway. Angew Chem Int Ed Engl 2018; 57:11574-11578. [DOI: 10.1002/anie.201804158] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 06/13/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Agnieszka Litomska
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Keishi Ishida
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Kyle L. Dunbar
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Marco Boettger
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Sébastien Coyne
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Christian Hertweck
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
- Faculty of Biological SciencesFriedrich Schiller University Jena 07743 Jena Germany
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117
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Litomska A, Ishida K, Dunbar KL, Boettger M, Coyne S, Hertweck C. Enzymatic Thioamide Formation in a Bacterial Antimetabolite Pathway. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Agnieszka Litomska
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
| | - Kyle L. Dunbar
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
| | - Marco Boettger
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
| | - Sébastien Coyne
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
- Faculty of Biological Sciences; Friedrich Schiller University Jena; 07743 Jena Germany
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118
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Schwalen CJ, Hudson GA, Kille B, Mitchell DA. Bioinformatic Expansion and Discovery of Thiopeptide Antibiotics. J Am Chem Soc 2018; 140:9494-9501. [PMID: 29983054 PMCID: PMC6070396 DOI: 10.1021/jacs.8b03896] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Thiopeptides are members of the ribosomally synthesized and post-translationally modified peptide family of natural products. Most characterized thiopeptides display nanomolar potency toward Gram-positive bacteria by blocking protein translation with several being produced at the industrial scale for veterinary and livestock applications. Employing our custom bioinformatics program, RODEO, we expand the thiopeptide family of natural products by a factor of four. This effort revealed many new thiopeptide biosynthetic gene clusters with products predicted to be distinct from characterized thiopeptides and identified gene clusters for previously characterized molecules of unknown biosynthetic origin. To further validate our data set of predicted thiopeptide biosynthetic gene clusters, we isolated and characterized a structurally unique thiopeptide featuring a central piperidine and rare thioamide moiety. Termed saalfelduracin, this thiopeptide displayed potent antibiotic activity toward several drug-resistant Gram-positive pathogens. A combination of whole-genome sequencing, comparative genomics, and heterologous expression experiments confirmed that the thioamide moiety of saalfelduracin is installed post-translationally by the joint action of two proteins, TfuA and YcaO. These results reconcile the previously unknown origin of the thioamide in two long-known thiopeptides, thiopeptin and Sch 18640. Armed with these new insights into thiopeptide chemical-genomic space, we provide a roadmap for the discovery of additional members of this natural product family.
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Affiliation(s)
- Christopher J. Schwalen
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Graham A. Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Bryce Kille
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
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119
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Tang J, Lu J, Luo Q, Wang H. Discovery and biosynthesis of thioviridamide-like compounds. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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120
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Gu W, Dong SH, Sarkar S, Nair SK, Schmidt EW. The Biochemistry and Structural Biology of Cyanobactin Pathways: Enabling Combinatorial Biosynthesis. Methods Enzymol 2018; 604:113-163. [PMID: 29779651 DOI: 10.1016/bs.mie.2018.03.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyanobactin biosynthetic enzymes have exceptional versatility in the synthesis of natural and unnatural products. Cyanobactins are ribosomally synthesized and posttranslationally modified peptides synthesized by multistep pathways involving a broad suite of enzymes, including heterocyclases/cyclodehydratases, macrocyclases, proteases, prenyltransferases, methyltransferases, and others. Here, we describe the enzymology and structural biology of cyanobactin biosynthetic enzymes, aiming at the twin goals of understanding biochemical mechanisms and biosynthetic plasticity. We highlight how this common suite of enzymes may be utilized to generate a large array or structurally and chemically diverse compounds.
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Affiliation(s)
- Wenjia Gu
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Shi-Hui Dong
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Snigdha Sarkar
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, United States.
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121
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Hegemann JD, van der Donk WA. Investigation of Substrate Recognition and Biosynthesis in Class IV Lanthipeptide Systems. J Am Chem Soc 2018; 140:5743-5754. [PMID: 29633842 PMCID: PMC5932250 DOI: 10.1021/jacs.8b01323] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lanthipeptides belong to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs) and are subdivided into four classes. The first two classes have been heavily studied, but less is known about classes III and IV. The lanthipeptide synthetases of classes III and IV share a similar organization of protein domains: A lyase domain at the N-terminus, a central kinase domain, and a C-terminal cyclase domain. Here, we provide deeper insight into class IV enzymes (LanLs). A series of putative producer strains was screened to identify production conditions of four new venezuelin-like lanthipeptides, and an Escherichia coli based heterologous production system was established for a fifth. The latter not only allowed production of fully modified core peptide but was also employed as the basis for mutational analysis of the precursor peptide to identify regions important for enzyme recognition. These experiments were complemented by in vitro binding studies aimed at identifying the region of the leader peptide recognized by the LanL enzymes as well as determining which domain of the enzyme is recognizing the substrate peptide. Combined, these studies revealed that the kinase domain is mediating the interaction with the precursor peptide and that a putatively α-helical stretch of residues at the center to N-terminal region of the leader peptide is important for enzyme recognition. In addition, a combination of in vitro assays and tandem mass spectrometry was used to elucidate the order of dehydration events in these systems.
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Affiliation(s)
- Julian D Hegemann
- Howard Hughes Medical Institute and Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana, Illinois 61801 , United States
| | - Wilfred A van der Donk
- Howard Hughes Medical Institute and Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana, Illinois 61801 , United States
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122
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Travin DY, Metelev M, Serebryakova M, Komarova ES, Osterman IA, Ghilarov D, Severinov K. Biosynthesis of Translation Inhibitor Klebsazolicin Proceeds through Heterocyclization and N-Terminal Amidine Formation Catalyzed by a Single YcaO Enzyme. J Am Chem Soc 2018; 140:5625-5633. [PMID: 29601195 DOI: 10.1021/jacs.8b02277] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Klebsazolicin (KLB) is a recently discovered Klebsiella pneumonia peptide antibiotic targeting the exit tunnel of bacterial ribosome. KLB contains an N-terminal amidine ring and four azole heterocycles installed into a ribosomally synthesized precursor by dedicated maturation machinery. Using an in vitro system for KLB production, we show that the YcaO-domain KlpD maturation enzyme is a bifunctional cyclodehydratase required for the formation of both the core heterocycles and the N-terminal amidine ring. We further demonstrate that the amidine ring is formed concomitantly with proteolytic cleavage of azole-containing pro-KLB by a cellular protease TldD/E. Members of the YcaO family are diverse enzymes known to activate peptide carbonyls during natural product biosynthesis leading to the formation of azoline, macroamidine, and thioamide moieties. The ability of KlpD to simultaneously perform two distinct types of modifications is unprecedented for known YcaO proteins. The versatility of KlpD opens up possibilities for rational introduction of modifications into various peptide backbones.
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Affiliation(s)
- Dmitrii Y Travin
- Department of Bioengineering and Bioinformatics , Lomonosov Moscow State University , Moscow , 119992 , Russia.,Center for Data-Intensive Biomedicine and Biotechnology , Skolkovo Institute of Science and Technology , Skolkovo , 143025 , Russia
| | - Mikhail Metelev
- Center for Data-Intensive Biomedicine and Biotechnology , Skolkovo Institute of Science and Technology , Skolkovo , 143025 , Russia.,Institute of Gene Biology of the Russian Academy of Sciences , Moscow , 119334 , Russia
| | - Marina Serebryakova
- Center for Data-Intensive Biomedicine and Biotechnology , Skolkovo Institute of Science and Technology , Skolkovo , 143025 , Russia.,Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University , Moscow , 119992 , Russia
| | - Ekaterina S Komarova
- Department of Bioengineering and Bioinformatics , Lomonosov Moscow State University , Moscow , 119992 , Russia.,Center for Data-Intensive Biomedicine and Biotechnology , Skolkovo Institute of Science and Technology , Skolkovo , 143025 , Russia
| | - Ilya A Osterman
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University , Moscow , 119992 , Russia.,Center for Translational Biomedicine , Skolkovo Institute of Science and Technology , Skolkovo , 143025 , Russia
| | - Dmitry Ghilarov
- Center for Data-Intensive Biomedicine and Biotechnology , Skolkovo Institute of Science and Technology , Skolkovo , 143025 , Russia.,Institute of Gene Biology of the Russian Academy of Sciences , Moscow , 119334 , Russia
| | - Konstantin Severinov
- Center for Data-Intensive Biomedicine and Biotechnology , Skolkovo Institute of Science and Technology , Skolkovo , 143025 , Russia.,Institute of Gene Biology of the Russian Academy of Sciences , Moscow , 119334 , Russia.,Waksman Institute for Microbiology , Rutgers, The State University of New Jersey , Piscataway , New Jersey 08854 , United States
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123
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Goto Y, Suga H. ArtificialIn VitroBiosynthesis Systems for the Development of Pseudo-Natural Products. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20170379] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
- JST-PRESTO, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
- JST-CREST, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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124
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Abstract
Methyl-coenzyme M reductase (MCR) is an essential enzyme found strictly in methanogenic and methanotrophic archaea. MCR catalyzes a reversible reaction involved in the production and consumption of the potent greenhouse gas methane. The α-subunit of this enzyme (McrA) contains several unusual posttranslational modifications, including the only known naturally occurring example of protein thioamidation. We have recently demonstrated by genetic deletion and mass spectrometry that the tfuA and ycaO genes of Methanosarcina acetivorans are involved in thioamidation of Gly465 in the MCR active site. Modification to thioGly has been postulated to stabilize the active site structure of MCR. Herein, we report the in vitro reconstitution of ribosomal peptide thioamidation using heterologously expressed and purified YcaO and TfuA proteins from M. acetivorans Like other reported YcaO proteins, this reaction is ATP-dependent but requires an external sulfide source. We also reconstitute the thioamidation activity of two TfuA-independent YcaOs from the hyperthermophilic methanogenic archaea Methanopyrus kandleri and Methanocaldococcus jannaschii Using these proteins, we demonstrate the basis for substrate recognition and regioselectivity of thioamide formation based on extensive mutagenesis, biochemical, and binding studies. Finally, we report nucleotide-free and nucleotide-bound crystal structures for the YcaO proteins from M. kandleri Sequence and structure-guided mutagenesis with subsequent biochemical evaluation have allowed us to assign roles for residues involved in thioamidation and confirm that the reaction proceeds via backbone O-phosphorylation. These data assign a new biochemical reaction to the YcaO superfamily and paves the way for further characterization of additional peptide backbone posttranslational modifications.
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125
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Jiang YY, Liu TT, Zhang RX, Xu ZY, Sun X, Bi S. Mechanism and Rate-Determining Factors of Amide Bond Formation through Acyl Transfer of Mixed Carboxylic–Carbamic Anhydrides: A Computational Study. J Org Chem 2018; 83:2676-2685. [DOI: 10.1021/acs.joc.7b03107] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yuan-Ye Jiang
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| | - Tian-Tian Liu
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| | - Rui-Xue Zhang
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| | - Zhong-Yan Xu
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| | - Xue Sun
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| | - Siwei Bi
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
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126
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Schwalen CJ, Hudson GA, Kosol S, Mahanta N, Challis GL, Mitchell DA. In Vitro Biosynthetic Studies of Bottromycin Expand the Enzymatic Capabilities of the YcaO Superfamily. J Am Chem Soc 2017; 139:18154-18157. [PMID: 29200283 PMCID: PMC5915351 DOI: 10.1021/jacs.7b09899] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The bottromycins belong to the ribosomally synthesized and posttranslationally modified peptide (RiPP) family of natural products. Bottromycins exhibit unique structural features, including a hallmark macrolactamidine ring and thiazole heterocycle for which divergent members of the YcaO superfamily have been biosynthetically implicated. Here we report the in vitro reconstitution of two YcaO proteins, BmbD and BmbE, responsible for the ATP-dependent cyclodehydration reactions that yield thiazoline- and macrolactamidine-functionalized products, respectively. We also establish the substrate tolerance for BmbD and BmbE and systematically dissect the role of the follower peptide, which we show serves a purpose similar to canonical leader peptides in directing the biosynthetic enzymes to the substrate. Lastly, we leverage the expanded capabilities of YcaO proteins to conduct an extensive bioinformatic survey to classify known YcaO chemistry. This analysis predicts new functions remain to be uncovered within the superfamily.
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Affiliation(s)
- Christopher J. Schwalen
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Graham A. Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Simone Kosol
- Department of Chemistry and Warwick Integrative Synthetic Biology Center, University of Warwick, Coventry CV4 7AL, UK
| | - Nilkamal Mahanta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
| | - Gregory L. Challis
- Department of Chemistry and Warwick Integrative Synthetic Biology Center, University of Warwick, Coventry CV4 7AL, UK
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
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127
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Qiu Y, Du Y, Zhang F, Liao R, Zhou S, Peng C, Guo Y, Liu W. Thiolation Protein-Based Transfer of Indolyl to a Ribosomally Synthesized Polythiazolyl Peptide Intermediate during the Biosynthesis of the Side-Ring System of Nosiheptide. J Am Chem Soc 2017; 139:18186-18189. [DOI: 10.1021/jacs.7b11367] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - Rijing Liao
- Xuhui
Central Hospital, Shanghai Clinical Center, Chinese Academy of Sciences, Shanghai 200031, China
| | | | - Chao Peng
- National
Center for Protein Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai 201210, China
| | | | - Wen Liu
- State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
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128
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Franz L, Adam S, Santos-Aberturas J, Truman AW, Koehnke J. Macroamidine Formation in Bottromycins Is Catalyzed by a Divergent YcaO Enzyme. J Am Chem Soc 2017; 139:18158-18161. [DOI: 10.1021/jacs.7b09898] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laura Franz
- Workgroup
Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for
Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarland University, Campus Geb. E8.1, 66123 Saarbrücken, Germany
| | - Sebastian Adam
- Workgroup
Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for
Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarland University, Campus Geb. E8.1, 66123 Saarbrücken, Germany
| | - Javier Santos-Aberturas
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich NR4 7UH, United Kingdom
| | - Andrew W. Truman
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich NR4 7UH, United Kingdom
| | - Jesko Koehnke
- Workgroup
Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for
Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarland University, Campus Geb. E8.1, 66123 Saarbrücken, Germany
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129
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Cheng Y, Xiang JC, Wang ZX, Ma JT, Wang M, Tang BC, Wu YD, Zhu YP, Wu AX. Dimerization of Phenylalanine: An Approach to Thiazoles and Oxazoles Involved S/O-Insertion. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201701130] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yan Cheng
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry; Central China Normal University; Hubei, Wuhan 430079 People's Republic of China
| | - Jia-Chen Xiang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry; Central China Normal University; Hubei, Wuhan 430079 People's Republic of China
| | - Zi-Xuan Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry; Central China Normal University; Hubei, Wuhan 430079 People's Republic of China
| | - Jin-Tian Ma
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry; Central China Normal University; Hubei, Wuhan 430079 People's Republic of China
| | - Miao Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry; Central China Normal University; Hubei, Wuhan 430079 People's Republic of China
| | - Bo-Cheng Tang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry; Central China Normal University; Hubei, Wuhan 430079 People's Republic of China
| | - Yan-Dong Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry; Central China Normal University; Hubei, Wuhan 430079 People's Republic of China
| | - Yan-Ping Zhu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong; Yantai University; Shandong, Yantai 264005 People's Republic of China
| | - An-Xin Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry; Central China Normal University; Hubei, Wuhan 430079 People's Republic of China
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130
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Structural insights into enzymatic [4+2] aza-cycloaddition in thiopeptide antibiotic biosynthesis. Proc Natl Acad Sci U S A 2017; 114:12928-12933. [PMID: 29158402 DOI: 10.1073/pnas.1716035114] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The [4+2] cycloaddition reaction is an enabling transformation in modern synthetic organic chemistry, but there are only limited examples of dedicated natural enzymes that can catalyze this transformation. Thiopeptides (or more formally thiazolyl peptides) are a class of thiazole-containing, highly modified, macrocyclic secondary metabolites made from ribosomally synthesized precursor peptides. The characteristic feature of these natural products is a six-membered nitrogenous heterocycle that is assembled via a formal [4+2] cycloaddition between two dehydroalanine (Dha) residues. This heteroannulation is entirely contingent on enzyme activity, although the mechanism of the requisite pyridine/dehydropiperidine synthase remains to be elucidated. The unusual aza-cylic product is distinct from the more common carbocyclic products of synthetic and biosynthetic [4+2] cycloaddition reactions. To elucidate the mechanism of cycloaddition, we have determined atomic resolution structures of the pyridine synthases involved in the biosynthesis of the thiopeptides thiomuracin (TbtD) and GE2270A (PbtD), in complex with substrates and product analogs. Structure-guided biochemical, mutational, computational, and binding studies elucidate active-site features that explain how orthologs can generate rigid macrocyclic scaffolds of different sizes. Notably, the pyridine synthases show structural similarity to the elimination domain of lanthipeptide dehydratases, wherein insertions of secondary structural elements result in the formation of a distinct active site that catalyzes different chemistry. Comparative analysis identifies other catalysts that contain a shared core protein fold but whose active sites are located in entirely different regions, illustrating a principle predicted from efforts in de novo protein design.
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131
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Frattaruolo L, Lacret R, Cappello AR, Truman AW. A Genomics-Based Approach Identifies a Thioviridamide-Like Compound with Selective Anticancer Activity. ACS Chem Biol 2017; 12:2815-2822. [PMID: 28968491 DOI: 10.1021/acschembio.7b00677] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Thioviridamide is a structurally novel ribosomally synthesized and post-translational modified peptide (RiPP) produced by Streptomyces olivoviridis NA005001. It is characterized by a structure that features a series of thioamide groups and possesses potent antiproliferative activity in cancer cell lines. Its unusual structure allied to its promise as an anticancer compound led us to investigate the diversity of thioviridamide-like pathways across sequenced bacterial genomes. We have isolated and characterized three diverse members of this family of natural products. This characterization is supported by transformation-associated recombination cloning and heterologous expression of one of these compounds, thiostreptamide S4. Our work provides an insight into the diversity of this rare class of compound and indicates that the unusual N-terminus of thioviridamide is not introduced biosynthetically but is instead introduced during acetone extraction. A detailed analysis of the biological activity of one of the newly discovered compounds, thioalbamide, indicates that it is highly cytotoxic to cancer cells, while exhibiting significantly less activity toward a noncancerous epithelial cell line.
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Affiliation(s)
- Luca Frattaruolo
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom
- Department
of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Rodney Lacret
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom
| | - Anna Rita Cappello
- Department
of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Andrew W. Truman
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom
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132
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Müller MM. Post-Translational Modifications of Protein Backbones: Unique Functions, Mechanisms, and Challenges. Biochemistry 2017; 57:177-185. [PMID: 29064683 PMCID: PMC5770884 DOI: 10.1021/acs.biochem.7b00861] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Post-translational
modifications (PTMs) dramatically enhance the
capabilities of proteins. They introduce new functionalities and dynamically
control protein activity by modulating intra- and intermolecular interactions.
Traditionally, PTMs have been considered as reversible attachments
to nucleophilic functional groups on amino acid side chains, whereas
the polypeptide backbone is often thought to be inert. This paradigm
is shifting as chemically and functionally diverse alterations of
the protein backbone are discovered. Importantly, backbone PTMs can
control protein structure and function just as side chain modifications
do and operate through unique mechanisms to achieve these features.
In this Perspective, I outline the various types of protein backbone
modifications discovered so far and highlight their contributions
to biology as well as the challenges in studying this versatile yet
poorly characterized class of PTMs.
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Affiliation(s)
- Manuel M Müller
- Department of Chemistry, King's College London , 7 Trinity Street, London SE1 1DB, United Kingdom
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133
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Mahanta N, Hudson GA, Mitchell DA. Radical S-Adenosylmethionine Enzymes Involved in RiPP Biosynthesis. Biochemistry 2017; 56:5229-5244. [PMID: 28895719 DOI: 10.1021/acs.biochem.7b00771] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) display a diverse range of structures and continue to expand as a natural product class. Accordingly, RiPPs exhibit a wide array of bioactivities, acting as broad and narrow spectrum growth suppressors, antidiabetics, and antinociception and anticancer agents. Because of these properties, and the complex repertoire of post-translational modifications (PTMs) that give rise to these molecules, RiPP biosynthesis has been intensely studied. RiPP biosynthesis often involves enzymes that perform unique chemistry with intriguing reaction mechanisms, which attract chemists and biochemists alike to study and re-engineer these pathways. One particular type of RiPP biosynthetic enzyme is the so-called radical S-adenosylmethionine (rSAM) enzyme, which utilizes radical-based chemistry to install several distinct PTMs. Here, we describe the rSAM enzymes characterized over the past decade that catalyze six reaction types from several RiPP biosynthetic pathways. We present the current state of mechanistic understanding and conclude with possible directions for future characterization of this enzyme family.
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Affiliation(s)
- Nilkamal Mahanta
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Graham A Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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134
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Vishwanatha TM, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. Cysteine Isocyanide in Multicomponent Reaction: Synthesis of Peptido-Mimetic 1,3-Azoles. J Org Chem 2017; 82:9585-9594. [PMID: 28817272 PMCID: PMC5603900 DOI: 10.1021/acs.joc.7b01615] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
An alternative approach toward the
simple and robust synthesis
of highly substituted peptidic thiazole derivatives using Ugi-multicomponent
reaction (U-MCR) is described. Thus, we introduced the enantiopure
(R)-2-methyl-2-isocyano-3-(tritylthio)propanoate
as a novel class of isocyanide in MCR. This bifunctional isocyanide
was found to undergo mild cyclodehydration to afford thiazole containing
peptidomimetics in a short synthetic sequence. Several examples of
bis-heterocyclic rings were also synthesized through the proper choice
of the aldehyde component in the U-4CR. The method opens a wide range
of applications toward the synthesis of nonribosomal natural products
and other bioactive compounds.
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Affiliation(s)
- Thimmalapura M Vishwanatha
- University of Groningen , Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Jagiellonian University , Department of Crystal Chemistry and Crystal Physics, Ingardena 3, 30-060 Krakow, Poland
| | - Justyna Kalinowska-Tłuścik
- Jagiellonian University , Department of Crystal Chemistry and Crystal Physics, Ingardena 3, 30-060 Krakow, Poland
| | - Alexander Dömling
- University of Groningen , Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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135
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Nayak DD, Mahanta N, Mitchell DA, Metcalf WW. Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea. eLife 2017; 6. [PMID: 28880150 PMCID: PMC5589413 DOI: 10.7554/elife.29218] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/11/2017] [Indexed: 12/14/2022] Open
Abstract
Methyl-coenzyme M reductase (MCR), found in strictly anaerobic methanogenic and methanotrophic archaea, catalyzes the reversible production and consumption of the potent greenhouse gas methane. The α subunit of MCR (McrA) contains several unusual post-translational modifications, including a rare thioamidation of glycine. Based on the presumed function of homologous genes involved in the biosynthesis of thioviridamide, a thioamide-containing natural product, we hypothesized that the archaeal tfuA and ycaO genes would be responsible for post-translational installation of thioglycine into McrA. Mass spectrometric characterization of McrA from the methanogenic archaeon Methanosarcina acetivorans lacking tfuA and/or ycaO revealed the presence of glycine, rather than thioglycine, supporting this hypothesis. Phenotypic characterization of the ∆ycaO-tfuA mutant revealed a severe growth rate defect on substrates with low free energy yields and at elevated temperatures (39°C - 45°C). Our analyses support a role for thioglycine in stabilizing the protein secondary structure near the active site.
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Affiliation(s)
- Dipti D Nayak
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, United States
| | - Nilkamal Mahanta
- Department of Chemistry, University of Illinois, Urbana, United States
| | - Douglas A Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, United States.,Department of Chemistry, University of Illinois, Urbana, United States.,Department of Microbiology, University of Illinois, Urbana, United States
| | - William W Metcalf
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, United States.,Department of Microbiology, University of Illinois, Urbana, United States
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136
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Metelev M, Osterman IA, Ghilarov D, Khabibullina NF, Yakimov A, Shabalin K, Utkina I, Travin DY, Komarova ES, Serebryakova M, Artamonova T, Khodorkovskii M, Konevega AL, Sergiev PV, Severinov K, Polikanov YS. Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel. Nat Chem Biol 2017; 13:1129-1136. [PMID: 28846667 PMCID: PMC5701663 DOI: 10.1038/nchembio.2462] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/19/2017] [Indexed: 12/19/2022]
Abstract
While screening of small-molecular metabolites produced by most cultivatable microorganisms often results in rediscovery of known compounds, genome-mining programs allow to harness much greater chemical diversity and result in discovery of new molecular scaffolds. Here we report genome-guided identification of a new antibiotic klebsazolicin (KLB) from Klebsiella pneumoniae that inhibits growth of sensitive cells by targeting ribosome. A member of ribosomally-synthesized post-translationally modified peptides (RiPPs), KLB is characterized by the presence of unique N-terminal amidine ring essential for its activity. Biochemical in vitro studies indicate that KLB inhibits ribosome by interfering with translation elongation. Structural analysis of the ribosome-KLB complex reveals the compound bound in the peptide exit tunnel overlapping with the binding sites of macrolides or streptogramins-B. KLB adopts compact conformation and largely obstructs the tunnel. Engineered KLB fragments retain in vitro activity and can serve as a starting point for the development of new bioactive compounds.
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Affiliation(s)
- Mikhail Metelev
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.,Institute of Antimicrobial Chemotherapy, Smolensk State Medical Academy, Smolensk, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Ilya A Osterman
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry Ghilarov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Nelli F Khabibullina
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Alexander Yakimov
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.,Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia
| | - Konstantin Shabalin
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia
| | - Irina Utkina
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Dmitry Y Travin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina S Komarova
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Marina Serebryakova
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia.,Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatyana Artamonova
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
| | - Mikhail Khodorkovskii
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
| | - Andrey L Konevega
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.,Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia
| | - Petr V Sergiev
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Konstantin Severinov
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia.,Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA.,Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, USA
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137
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Lin Z, Ji J, Zhou S, Zhang F, Wu J, Guo Y, Liu W. Processing 2-Methyl-l-Tryptophan through Tandem Transamination and Selective Oxygenation Initiates Indole Ring Expansion in the Biosynthesis of Thiostrepton. J Am Chem Soc 2017; 139:12105-12108. [DOI: 10.1021/jacs.7b05337] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Zhi Lin
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Jia Ji
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Shuaixiang Zhou
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Fang Zhang
- State
Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Jiequn Wu
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
| | - Yinlong Guo
- State
Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wen Liu
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
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138
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Lin Z, He Q, Liu W. Bio-inspired engineering of thiopeptide antibiotics advances the expansion of molecular diversity and utility. Curr Opin Biotechnol 2017; 48:210-219. [PMID: 28672170 DOI: 10.1016/j.copbio.2017.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/14/2017] [Accepted: 06/14/2017] [Indexed: 02/08/2023]
Abstract
Thiopeptide antibiotics, which are a class of sulfur-rich and highly modified peptide natural products, exhibit a wide variety of important biological properties. These antibiotics are ribosomally synthesized and arise from post-translational modifications, exemplifying a process through which nature develops the structural complexity from Ser/Thr and Cys-rich precursor peptides. Following a brief review of the knowledge gained from nature in terms of the formation of a common thiopeptide scaffold and its specialization to individual members, we highlight the significance of bio-inspired engineering, which has greatly expanded the molecular diversity and utility of thiopeptide antibiotics regarding the search for clinically useful agents, investigation into new mechanisms of action and access to typically 'inaccessible' biosynthetic processes over the past two years.
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Affiliation(s)
- Zhi Lin
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Qingli He
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China.
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139
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Burkhart B, Kakkar N, Hudson GA, van der Donk WA, Mitchell DA. Chimeric Leader Peptides for the Generation of Non-Natural Hybrid RiPP Products. ACS CENTRAL SCIENCE 2017; 3:629-638. [PMID: 28691075 PMCID: PMC5492250 DOI: 10.1021/acscentsci.7b00141] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Indexed: 05/21/2023]
Abstract
Combining biosynthetic enzymes from multiple pathways is an attractive approach for producing molecules with desired structural features; however, progress has been hampered by the incompatibility of enzymes from unrelated pathways and intolerance toward alternative substrates. Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a diverse natural product class that employs a biosynthetic logic that is highly amenable to engineering new compounds. RiPP biosynthetic proteins modify their substrates by binding to a motif typically located in the N-terminal leader region of the precursor peptide. Here, we exploit this feature by designing leader peptides that enable recognition and processing by multiple enzymes from unrelated RiPP pathways. Using this broadly applicable strategy, a thiazoline-forming cyclodehydratase was combined with enzymes from the sactipeptide and lanthipeptide families to create new-to-nature hybrid RiPPs. We also provide insight into design features that enable control over the hybrid biosynthesis to optimize enzyme compatibility and establish a general platform for engineering additional hybrid RiPPs.
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Affiliation(s)
- Brandon
J. Burkhart
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Nidhi Kakkar
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Graham A. Hudson
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Wilfred A. van der Donk
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- (W.A.V.) Phone: 1-217-244-5360. Fax: 1-217-244 8533. E-mail:
| | - Douglas A. Mitchell
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- (D.A.M.) Phone: 1-217-333-1345. Fax: 1-217-333-0508. E-mail:
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140
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141
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Repka LM, Chekan JR, Nair SK, van der Donk WA. Mechanistic Understanding of Lanthipeptide Biosynthetic Enzymes. Chem Rev 2017; 117:5457-5520. [PMID: 28135077 PMCID: PMC5408752 DOI: 10.1021/acs.chemrev.6b00591] [Citation(s) in RCA: 331] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Lanthipeptides
are ribosomally synthesized and post-translationally
modified peptides (RiPPs) that display a wide variety of biological
activities, from antimicrobial to antiallodynic. Lanthipeptides that
display antimicrobial activity are called lantibiotics. The post-translational
modification reactions of lanthipeptides include dehydration of Ser
and Thr residues to dehydroalanine and dehydrobutyrine, a transformation
that is carried out in three unique ways in different classes of lanthipeptides.
In a cyclization process, Cys residues then attack the dehydrated
residues to generate the lanthionine and methyllanthionine thioether
cross-linked amino acids from which lanthipeptides derive their name.
The resulting polycyclic peptides have constrained conformations that
confer their biological activities. After installation of the characteristic
thioether cross-links, tailoring enzymes introduce additional post-translational
modifications that are unique to each lanthipeptide and that fine-tune
their activities and/or stability. This review focuses on studies
published over the past decade that have provided much insight into
the mechanisms of the enzymes that carry out the post-translational
modifications.
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Affiliation(s)
- Lindsay M Repka
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jonathan R Chekan
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Satish K Nair
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wilfred A van der Donk
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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