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Baquero F, Beis K, Craik DJ, Li Y, Link AJ, Rebuffat S, Salomón R, Severinov K, Zirah S, Hegemann JD. The pearl jubilee of microcin J25: thirty years of research on an exceptional lasso peptide. Nat Prod Rep 2024; 41:469-511. [PMID: 38164764 DOI: 10.1039/d3np00046j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Covering: 1992 up to 2023Since their discovery, lasso peptides went from peculiarities to be recognized as a major family of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products that were shown to be spread throughout the bacterial kingdom. Microcin J25 was first described in 1992, making it one of the earliest known lasso peptides. No other lasso peptide has since then been studied to such an extent as microcin J25, yet, previous review articles merely skimmed over all the research done on this exceptional lasso peptide. Therefore, to commemorate the 30th anniversary of its first report, we give a comprehensive overview of all literature related to microcin J25. This review article spans the early work towards the discovery of microcin J25, its biosynthetic gene cluster, and the elucidation of its three-dimensional, threaded lasso structure. Furthermore, the current knowledge about the biosynthesis of microcin J25 and lasso peptides in general is summarized and a detailed overview is given on the biological activities associated with microcin J25, including means of self-immunity, uptake into target bacteria, inhibition of the Gram-negative RNA polymerase, and the effects of microcin J25 on mitochondria. The in vitro and in vivo models used to study the potential utility of microcin J25 in a (veterinary) medicine context are discussed and the efforts that went into employing the microcin J25 scaffold in bioengineering contexts are summed up.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- Network Center for Research in Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire OX11 0FA, UK
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, 4072 Brisbane, Queensland, Australia
| | - Yanyan Li
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - A James Link
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Raúl Salomón
- Instituto de Química Biológica "Dr Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán, Argentina
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany.
- Department of Pharmacy, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
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2
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Zhang S, De Leon Rodriguez LM, Li FF, Brimble MA. Recent developments in the cleavage, functionalization, and conjugation of proteins and peptides at tyrosine residues. Chem Sci 2023; 14:7782-7817. [PMID: 37502317 PMCID: PMC10370606 DOI: 10.1039/d3sc02543h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Peptide and protein selective modification at tyrosine residues has become an exploding field of research as tyrosine constitutes a robust alternative to lysine and cysteine-targeted traditional peptide/protein modification protocols. This review offers a comprehensive summary of the latest advances in tyrosine-selective cleavage, functionalization, and conjugation of peptides and proteins from the past three years. This updated overview complements the extensive body of work on site-selective modification of peptides and proteins, which holds significant relevance across various disciplines, including chemical, biological, medical, and material sciences.
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Affiliation(s)
- Shengping Zhang
- Center for Translational Medicine, Shenzhen Bay Laboratory New Zealand
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand
| | | | - Freda F Li
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
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3
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Kretsch AM, Gadgil MG, DiCaprio AJ, Barrett SE, Kille BL, Si Y, Zhu L, Mitchell DA. Peptidase Activation by a Leader Peptide-Bound RiPP Recognition Element. Biochemistry 2023; 62:956-967. [PMID: 36734655 PMCID: PMC10126823 DOI: 10.1021/acs.biochem.2c00700] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The RiPP precursor recognition element (RRE) is a conserved domain found in many prokaryotic ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic gene clusters (BGCs). RREs bind with high specificity and affinity to a recognition sequence within the N-terminal leader region of RiPP precursor peptides. Lasso peptide biosynthesis involves an RRE-dependent leader peptidase, which is discretely encoded or fused to the RRE as a di-domain protein. Here we leveraged thousands of predicted BGCs to define the RRE:leader peptidase interaction through evolutionary covariance analysis. Each interacting domain contributes a three-stranded β-sheet to form a hydrophobic β-sandwich-like interface. The bioinformatics-guided predictions were experimentally confirmed using proteins from discrete and fused lasso peptide BGC architectures. Support for the domain-domain interface derived from chemical shift perturbation, paramagnetic relaxation enhancement experiments, and rapid variant activity screening using cell-free biosynthesis. Further validation of selected variants was performed with purified proteins. We developed a p-nitroanilide-based leader peptidase assay to illuminate the role of RRE domains. Our data show that RRE domains play a dual function. RRE domains deliver the precursor peptide to the leader peptidase, and the rate is saturable as expected for a substrate. RRE domains also partially compose the elusive S2 proteolytic pocket that binds the penultimate threonine of lasso leader peptides. Because the RRE domain is required to form the active site, leader peptidase activity is greatly diminished when the RRE domain is supplied at substoichiometric levels. Full proteolytic activation requires RRE engagement with the recognition sequence-containing portion of the leader peptide. Together, our observations define a new mechanism for protease activity regulation.
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Affiliation(s)
- Ashley M. Kretsch
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Mayuresh G. Gadgil
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Adam J. DiCaprio
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Susanna E. Barrett
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Bryce L. Kille
- Department of Computer Science, Rice University, Houston, Texas, United States of America
| | - Yuanyuan Si
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Lingyang Zhu
- School of Chemical Sciences, NMR Laboratory, University of Illinois, Urbana, Illinois, United States of America
| | - Douglas A. Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
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4
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Glassey E, King AM, Anderson DA, Zhang Z, Voigt CA. Functional expression of diverse post-translational peptide-modifying enzymes in Escherichia coli under uniform expression and purification conditions. PLoS One 2022; 17:e0266488. [PMID: 36121811 PMCID: PMC9484694 DOI: 10.1371/journal.pone.0266488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/22/2022] [Indexed: 11/18/2022] Open
Abstract
RiPPs (ribosomally-synthesized and post-translationally modified peptides) are a class of pharmaceutically-relevant natural products expressed as precursor peptides before being enzymatically processed into their final functional forms. Bioinformatic methods have illuminated hundreds of thousands of RiPP enzymes in sequence databases and the number of characterized chemical modifications is growing rapidly; however, it remains difficult to functionally express them in a heterologous host. One challenge is peptide stability, which we addressed by designing a RiPP stabilization tag (RST) based on a small ubiquitin-like modifier (SUMO) domain that can be fused to the N- or C-terminus of the precursor peptide and proteolytically removed after modification. This is demonstrated to stabilize expression of eight RiPPs representative of diverse phyla. Further, using Escherichia coli for heterologous expression, we identify a common set of media and growth conditions where 24 modifying enzymes, representative of diverse chemistries, are functional. The high success rate and broad applicability of this system facilitates: (i) RiPP discovery through high-throughput “mining” and (ii) artificial combination of enzymes from different pathways to create a desired peptide.
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Affiliation(s)
- Emerson Glassey
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Andrew M. King
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Daniel A. Anderson
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Zhengan Zhang
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Christopher A. Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- * E-mail:
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5
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Hegemann JD. Combined thermal and carboxypeptidase Y stability assays for probing the threaded fold of lasso peptides. Methods Enzymol 2022; 663:177-204. [PMID: 35168788 DOI: 10.1016/bs.mie.2021.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Lasso peptides are natural products belonging to the superfamily of ribosomally synthesized and post-translationally modified peptides (RiPPs). The defining characteristic of lasso peptides is their threaded structure, which is reminiscent of a lariat knot. When working with lasso peptides, it is therefore of major importance to understand and evidence their threaded folds. While the full elucidation of their three-dimensional structures via NMR spectroscopy or crystallization remains the gold standard, these methods are time-consuming, require large quantities of highly pure lasso peptides, and therefore might not always be applicable. Instead, the unique properties of lasso peptides in context of their behavior at elevated temperatures and toward carboxypeptidase Y treatment can be leveraged as a tool to investigate and evidence the threaded lasso fold using only minute amounts of compound that does not need to be purified first. This chapter will provide insights into the thermal stability properties of lasso peptides and their behavior when treated with carboxypeptidase Y in comparison to a branched-cyclic peptide with the same amino acid sequence. Furthermore, it will be described in detail how to set up a combined thermal and carboxypeptidase Y stability assay and how to analyze its outcomes.
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Affiliation(s)
- Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany.
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6
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Liu T, Ma X, Yu J, Yang W, Wang G, Wang Z, Ge Y, Song J, Han H, Zhang W, Yang D, Liu X, Ma M. Rational generation of lasso peptides based on biosynthetic gene mutations and site-selective chemical modifications. Chem Sci 2021; 12:12353-12364. [PMID: 34603665 PMCID: PMC8480316 DOI: 10.1039/d1sc02695j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/10/2021] [Indexed: 12/14/2022] Open
Abstract
Lasso peptides are a unique family of natural products whose structures feature a specific threaded fold, which confers these peptides the resistance to thermal and proteolytic degradation. This stability gives lasso peptides excellent pharmacokinetic properties, which together with their diverse reported bioactivities have garnered extensive attention because of their drug development potential. Notably, the threaded fold has proven quite inaccessible by chemical synthesis, which has hindered efficient generation of structurally diverse lasso peptides. We herein report the discovery of a new lasso peptide stlassin (1) by gene activation based on a Streptomyces heterologous expression system. Site-directed mutagenesis on the precursor peptide-encoding gene is carried out systematically, generating 17 stlassin derivatives (2–17 and 21) with residue-replacements at specific positions of 1. The solution NMR structures of 1, 3, 4, 14 and 16 are determined, supporting structural comparisons that ultimately enabled the rational production of disulfide bond-containing derivatives 18 and 19, whose structures do not belong to any of the four classes currently used to classify lasso peptides. Several site-selective chemical modifications are first applied on 16 and 21, efficiently generating new derivatives (20, 22–27) whose structures bear various decorations beyond the peptidyl monotonicity. The high production yields of these stlassin derivatives facilitate biological assays, which show that 1, 4, 16, 20, 21 and 24 possess antagonistic activities against the binding of lipopolysaccharides to toll-like receptor 4 (TLR4). These results demonstrate proof-of-concept for the combined mutational/chemical generation of lasso peptide libraries to support drug lead development. A new class II lasso peptide stlassin (1) was discovered and stlassin derivatives (2–27) were rationally generated by biosynthetic gene mutations and site-selective chemical modifications, expanding the structural diversity of lasso peptides.![]()
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Affiliation(s)
- Tan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xiaojie Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Jiahui Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Wensheng Yang
- School of Medicine, Tongji University 1239 Siping Road Shanghai 200092 China
| | - Guiyang Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Zhengdong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Yuanjie Ge
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Juan Song
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Hua Han
- School of Medicine, Tongji University 1239 Siping Road Shanghai 200092 China
| | - Wen Zhang
- School of Medicine, Tongji University 1239 Siping Road Shanghai 200092 China
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xuehui Liu
- CAS Research Platform for Protein Sciences, Institute of Biophysics, Chinese Academy of Sciences 15 Datun Road, Chao-yang District Beijing 100101 China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
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7
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Long T, Liu L, Tao Y, Zhang W, Quan J, Zheng J, Hegemann JD, Uesugi M, Yao W, Tian H, Wang H. Light‐Controlled Tyrosine Nitration of Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Tengfang Long
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Lei Liu
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Youqi Tao
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Wanli Zhang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals School of Life Science and Technology China Pharmaceutical University Nanjing 211198 China
| | - Jiale Quan
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals School of Life Science and Technology China Pharmaceutical University Nanjing 211198 China
| | - Jie Zheng
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Julian D. Hegemann
- Institute of Chemistry Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Motonari Uesugi
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Uji Kyoto 611-0011 Japan
- School of Pharmacy Fudan University Shanghai 201203 China
| | - Wenbing Yao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals School of Life Science and Technology China Pharmaceutical University Nanjing 211198 China
| | - Hong Tian
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals School of Life Science and Technology China Pharmaceutical University Nanjing 211198 China
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
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Long T, Liu L, Tao Y, Zhang W, Quan J, Zheng J, Hegemann JD, Uesugi M, Yao W, Tian H, Wang H. Light-Controlled Tyrosine Nitration of Proteins. Angew Chem Int Ed Engl 2021; 60:13414-13422. [PMID: 33847040 DOI: 10.1002/anie.202102287] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/31/2021] [Indexed: 12/30/2022]
Abstract
Tyrosine nitration of proteins is one of the most important oxidative post-translational modifications in vivo. A major obstacle for its biochemical and physiological studies is the lack of efficient and chemoselective protein tyrosine nitration reagents. Herein, we report a generalizable strategy for light-controlled protein tyrosine nitration by employing biocompatible dinitroimidazole reagents. Upon 390 nm irradiation, dinitroimidazoles efficiently convert tyrosine residues into 3-nitrotyrosine residues in peptides and proteins with fast kinetics and high chemoselectivity under neutral aqueous buffer conditions. The incorporation of 3-nitrotyrosine residues enhances the thermostability of lasso peptide natural products and endows murine tumor necrosis factor-α with strong immunogenicity to break self-tolerance. The light-controlled time resolution of this method allows the investigation of the impact of tyrosine nitration on the self-assembly behavior of α-synuclein.
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Affiliation(s)
- Tengfang Long
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, No. 163 Xianlin Ave, Nanjing, 210093, China
| | - Lei Liu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, No. 163 Xianlin Ave, Nanjing, 210093, China
| | - Youqi Tao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, No. 163 Xianlin Ave, Nanjing, 210093, China
| | - Wanli Zhang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Jiale Quan
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Jie Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, No. 163 Xianlin Ave, Nanjing, 210093, China
| | - Julian D Hegemann
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Motonari Uesugi
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Uji, Kyoto, 611-0011, Japan.,School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Wenbing Yao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Hong Tian
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, No. 163 Xianlin Ave, Nanjing, 210093, China
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 393] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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10
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How to harness biosynthetic gene clusters of lasso peptides. ACTA ACUST UNITED AC 2020; 47:703-714. [DOI: 10.1007/s10295-020-02292-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023]
Abstract
Abstract
Lasso peptides produced by bacteria have a very unique cyclic structure (“lasso” structure) and are resistant to protease. To date, a number of lasso peptides have been isolated from proteobacteria and actinobacteria. Many lasso peptides exhibit various biological activities, such as antibacterial activity, and are expected to have various applications. Based on study of genome mining, large numbers of biosynthetic gene cluster of lasso peptides are revealed to distribute over genomes of proteobacteria and actinobacteria. However, the biosynthetic gene clusters are cryptic in most cases. Therefore, the combination of genome mining and heterologous production is efficient method for the production of lasso peptides. To utilize lasso peptide as fine chemical, there have been several attempts to add new function to lasso peptide by genetic engineering. Currently, a more efficient lasso peptide production system is being developed to harness cryptic biosynthetic gene clusters of lasso peptide. In this review, the overview of lasso peptide study is discussed.
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11
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Cheng C, Hua ZC. Lasso Peptides: Heterologous Production and Potential Medical Application. Front Bioeng Biotechnol 2020; 8:571165. [PMID: 33117783 PMCID: PMC7549694 DOI: 10.3389/fbioe.2020.571165] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/04/2020] [Indexed: 12/15/2022] Open
Abstract
Lasso peptides are natural products found in bacteria. They belong to a specific family of ribosomally-synthesized and posttranslationally-modified peptides with an unusual lasso structure. Lasso peptides possess remarkable thermal and proteolytic stability and various biological activities, such as antimicrobial activity, enzyme inhibition, receptor blocking, anticancer properties and HIV antagonism. They have promising potential therapeutic effects on gastrointestinal diseases, tuberculosis, Alzheimer’s disease, cardiovascular disease, fungal infections and cancer. Lasso peptides with high stability have been shown to be good carriers for other bioactive peptides. These make them attractive candidates for pharmaceutical research. This review aimed to describe the strategies used for the heterologous production of lasso peptides. Also, it indicated their therapeutical potential and their capacity to use as an efficient scaffold for epitope grafting.
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Affiliation(s)
- Cheng Cheng
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zi-Chun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.,School of Biopharmacy, China Pharmaceutical University, Nanjing, China.,Changzhou High-Tech Research Institute of Nanjing University, Changzhou, China.,Jiangsu Target Pharma Laboratories Inc., Changzhou, China
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12
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Steric complementarity directs sequence promiscuous leader binding in RiPP biosynthesis. Proc Natl Acad Sci U S A 2019; 116:24049-24055. [PMID: 31719203 DOI: 10.1073/pnas.1908364116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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.
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13
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Hegemann JD. Factors Governing the Thermal Stability of Lasso Peptides. Chembiochem 2019; 21:7-18. [DOI: 10.1002/cbic.201900364] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Julian D. Hegemann
- Technische Universität BerlinInstitute of Chemistry Strasse des 17. Juni 124/TC2 10623 Berlin Germany
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14
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Cheung-Lee WL, Link AJ. Genome mining for lasso peptides: past, present, and future. J Ind Microbiol Biotechnol 2019; 46:1371-1379. [PMID: 31165971 DOI: 10.1007/s10295-019-02197-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/23/2019] [Indexed: 01/05/2023]
Abstract
Over the course of roughly a decade, the lasso peptide field has been transformed. Whereas new compounds were discovered infrequently via activity-driven approaches, now, the vast majority of lasso peptide discovery is driven by genome-mining approaches. This paper starts with a historical overview of the first genome-mining approaches for lasso peptide discovery, and then covers new tools that have emerged. Several examples of novel lasso peptides that have been discovered via genome mining are presented as are examples of new enzymes found associated with lasso peptide gene clusters. Finally, this paper concludes with future directions and unsolved challenges in lasso peptide genome mining.
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Affiliation(s)
- Wai Ling Cheung-Lee
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - A James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA. .,Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA. .,Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
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15
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Koos JD, Link AJ. Heterologous and in Vitro Reconstitution of Fuscanodin, a Lasso Peptide from Thermobifida fusca. J Am Chem Soc 2018; 141:928-935. [PMID: 30532970 DOI: 10.1021/jacs.8b10724] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Lasso peptides are a class of ribosomally derived natural products typified by their threaded rotaxane structure. The conversion of a linear precursor peptide into a lasso peptide structure requires two enzymatic activities: cleavage of the precursor via a cysteine protease and cyclization via isopeptide bond formation. In vitro studies of lasso peptide enzymology have been hampered by difficulties in obtaining pure, soluble enzymes. We reasoned that thermophilic bacteria would be a good source for well-behaved lasso peptide biosynthetic enzymes. The genome of the thermophilic actinobacterium Thermobifida fusca encodes for a lasso peptide with an unprecedented Trp residue at its N-terminus, a peptide we have named fuscanodin. Here we reconstitute fuscanodin biosynthesis in vitro with purified components, establishing a minimal fuscanodin synthetase. These experiments have allowed us to probe the kinetics of lasso peptide biosynthesis for the first time, and we report initial rates of fuscanodin biosynthesis. The fuscanodin biosynthetic enzymes are insensitive to substrate concentration and operate in a near single-turnover regime in vitro. While lasso peptides are often touted for their stability to both chaotropic and thermal challenges, fuscanodin is found to undergo a conformational change consistent with lasso peptide unthreading in organic solvents at room temperature.
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16
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Martin-Gómez H, Albericio F, Tulla-Puche J. A Lasso-Inspired Bicyclic Peptide: Synthesis, Structure and Properties. Chemistry 2018; 24:19250-19257. [PMID: 30255960 DOI: 10.1002/chem.201803899] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/25/2018] [Indexed: 11/05/2022]
Abstract
The chemical synthesis of a bicycle inspired by the natural lasso peptide sungsanpin using a combination of solid-phase and in-solution chemistries is described. The bicyclic-derived topoisomer was designed by introducing a covalent linkage between the ring and the loop, which allowed the tying of these two parts of the peptide, rendering the bicyclic structure. Several structural techniques, such as MS fragmentation, ion-mobility and NMR spectroscopic analysis were used to characterize the bicycle. Ion-mobility spectroscopy studies revealed that it showed lasso-like behavior. Its 3D structure was predicted on the basis of the NMR restraints. In addition, the high proteolytic and thermal stability of the bicycle potentially make it a suitable scaffold for epitope grafting.
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Affiliation(s)
- Helena Martin-Gómez
- Institute for Research in Biomedicine, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Fernando Albericio
- Department of Inorganic and Organic Chemistry, Organic Chemistry Section, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain.,CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 10, 08028, Barcelona, Spain.,School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Judit Tulla-Puche
- Department of Inorganic and Organic Chemistry, Organic Chemistry Section, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain.,CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 10, 08028, Barcelona, Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028, Barcelona, Spain
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17
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Martin-Gómez H, Linne U, Albericio F, Tulla-Puche J, Hegemann JD. Investigation of the Biosynthesis of the Lasso Peptide Chaxapeptin Using an E. coli-Based Production System. JOURNAL OF NATURAL PRODUCTS 2018; 81:2050-2056. [PMID: 30178995 DOI: 10.1021/acs.jnatprod.8b00392] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Lasso peptides are natural products belonging to the family of ribosomally synthesized and posttranslationally modified peptides (RiPPs) and are defined by their unique topology. Even though lasso peptide biosynthetic gene clusters are found in many different kinds of bacteria, most of the hitherto studied lasso peptides were of proteobacterial or actinobacterial origin. Despite this, no E. coli-based production system has been reported for actinobacterial lasso peptides, while there are numerous examples of this for proteobacterial lasso peptides. Here, a heterologous production system of the lasso peptide chaxapeptin was established in E. coli. Chaxapeptin, originally isolated from Streptomyces leeuwenhoekii strain C58, is closely related to the lasso peptide sungsanpin (produced by a marine Streptomyces sp.) and shares its inhibitory activity against cell invasion by the human lung cancer cell line A549. Our production system not only allowed isolation of the mature lasso peptide outside of the native producer with a yield of 0.1 mg/L (compared to 0.7 mg/L from S. leeuwenhoekii) but also was used for a mutational study to identify residues in the precursor peptide that are important for biosynthesis. In addition to these experiments, the stability of chaxapeptin against thermal denaturation and proteases was assessed.
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Affiliation(s)
- Helena Martin-Gómez
- Institute for Research in Biomedicine , Baldiri Reixac 10 , 08028 Barcelona , Spain
- Department of Chemistry , Philipps-University Marburg , Hans-Meerwein-Strasse 4 , 35032 Marburg , Germany
| | - Uwe Linne
- Department of Chemistry , Philipps-University Marburg , Hans-Meerwein-Strasse 4 , 35032 Marburg , Germany
| | - Fernando Albericio
- Department of Inorganic and Organic Chemistry-Organic Chemistry Section , University of Barcelona , Martí i Franquès 1-11 , 08028 Barcelona , Spain
- CIBER-BBN, Networking Centre on Bioengineering , Biomaterials and Nanomedicine , Baldiri Reixac 10 , 08028 Barcelona , Spain
- School of Chemistry and Physics , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Judit Tulla-Puche
- Department of Inorganic and Organic Chemistry-Organic Chemistry Section , University of Barcelona , Martí i Franquès 1-11 , 08028 Barcelona , Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB) , 08028 Barcelona , Spain
| | - Julian D Hegemann
- Department of Chemistry , Philipps-University Marburg , Hans-Meerwein-Strasse 4 , 35032 Marburg , Germany
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 S. Mathews Avenue , Urbana , Illinois 61801 , United States
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18
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Zhang Y, Chen M, Bruner SD, Ding Y. Heterologous Production of Microbial Ribosomally Synthesized and Post-translationally Modified Peptides. Front Microbiol 2018; 9:1801. [PMID: 30135682 PMCID: PMC6092494 DOI: 10.3389/fmicb.2018.01801] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/17/2018] [Indexed: 12/30/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides, or RiPPs, which have mainly isolated from microbes as well as plants and animals, are an ever-expanding group of peptidic natural products with diverse chemical structures and biological activities. They have emerged as a major category of secondary metabolites partly due to a myriad of microbial genome sequencing endeavors and the availability of genome mining software in the past two decades. Heterologous expression of RiPP gene clusters mined from microbial genomes, which are often silent in native producers, in surrogate hosts such as Escherichia coli and Streptomyces strains can be an effective way to elucidate encoded peptides and produce novel derivatives. Emerging strategies have been developed to facilitate the success of the heterologous expression by targeting multiple synthetic biology levels, including individual proteins, pathways, metabolic flux and hosts. This review describes recent advances in heterologous production of RiPPs, mainly from microbes, with a focus on E. coli and Streptomyces strains as the surrogate hosts.
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Affiliation(s)
- Yi Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, FL, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
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19
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Hegemann JD, Schwalen CJ, Mitchell DA, van der Donk WA. Elucidation of the roles of conserved residues in the biosynthesis of the lasso peptide paeninodin. Chem Commun (Camb) 2018; 54:9007-9010. [PMID: 30046789 DOI: 10.1039/c8cc04411b] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Substrate binding assays, in vitro proteolytic processing assays, and heterologous lasso peptide production were used to investigate the roles of conserved precursor peptide residues during paeninodin maturation. Specifically, we delineate which residues are important for substrate recognition, proteolysis, and lasso peptide macrocyclization.
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Affiliation(s)
- Julian D Hegemann
- Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, USA. and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, USA.
| | - Christopher J Schwalen
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, USA. and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, USA. and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Wilfred A van der Donk
- Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, USA. and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, USA. and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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20
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Natural product diversity of actinobacteria in the Atacama Desert. Antonie van Leeuwenhoek 2018; 111:1467-1477. [DOI: 10.1007/s10482-018-1030-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/25/2018] [Indexed: 11/26/2022]
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21
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Martin-Gómez H, Tulla-Puche J. Lasso peptides: chemical approaches and structural elucidation. Org Biomol Chem 2018; 16:5065-5080. [DOI: 10.1039/c8ob01304g] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The diverse functionality and the extraordinary stability of lasso peptides make these molecules attractive scaffolds for drug discovery. The ability to generate lasso peptides chemically remains a challenging endeavor.
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Affiliation(s)
| | - Judit Tulla-Puche
- Department of Inorganic and Organic Chemistry – Organic Chemistry Section
- University of Barcelona
- Barcelona
- Spain
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22
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Hetrick KJ, van der Donk WA. Ribosomally synthesized and post-translationally modified peptide natural product discovery in the genomic era. Curr Opin Chem Biol 2017; 38:36-44. [PMID: 28260651 DOI: 10.1016/j.cbpa.2017.02.005] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 01/08/2023]
Abstract
In the past 15 years, the cost of sequencing a genome has plummeted. Consequently, the number of sequenced bacterial genomes has exponentially increased, and methods for natural product discovery have evolved rapidly to take advantage of the wealth of genomic data. This review highlights applications of genome mining software to compare and organize large-scale data sets and methods for identifying unique biosynthetic pathways amongst the thousands of ribosomally synthesized and post-translationally modified peptide (RiPP) gene clusters. We also discuss a small number of the many RiPPs discovered in the years 2014-2016.
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Affiliation(s)
- Kenton J Hetrick
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61822, USA
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61822, USA.
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23
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Tietz JI, Schwalen CJ, Patel PS, Maxson T, Blair PM, Tai HC, Zakai UI, Mitchell DA. A new genome-mining tool redefines the lasso peptide biosynthetic landscape. Nat Chem Biol 2017; 13:470-478. [PMID: 28244986 PMCID: PMC5391289 DOI: 10.1038/nchembio.2319] [Citation(s) in RCA: 289] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/06/2016] [Indexed: 12/14/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptide (RiPP) natural products are attractive for genome-driven discovery and re-engineering, but limitations in bioinformatic methods and exponentially increasing genomic data make large-scale mining of RiPP data difficult. We report RODEO (Rapid ORF Description and Evaluation Online), which combines hidden-Markov-model-based analysis, heuristic scoring, and machine learning to identify biosynthetic gene clusters and predict RiPP precursor peptides. We initially focused on lasso peptides, which display intriguing physicochemical properties and bioactivities, but their hypervariability renders them challenging prospects for automated mining. Our approach yielded the most comprehensive mapping to date of lasso peptide space, revealing >1,300 compounds. We characterized the structures and bioactivities of six lasso peptides, prioritized based on predicted structural novelty, including one with an unprecedented handcuff-like topology and another with a citrulline modification exceptionally rare among bacteria. These combined insights significantly expand the knowledge of lasso peptides and, more broadly, provide a framework for future genome-mining efforts.
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Affiliation(s)
- Jonathan I Tietz
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher J Schwalen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Parth S Patel
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Tucker Maxson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Patricia M Blair
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Hua-Chia Tai
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Uzma I Zakai
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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24
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Allen CD, Chen MY, Trick AY, Le DT, Ferguson AL, Link AJ. Thermal Unthreading of the Lasso Peptides Astexin-2 and Astexin-3. ACS Chem Biol 2016; 11:3043-3051. [PMID: 27588549 DOI: 10.1021/acschembio.6b00588] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lasso peptides are a class of knot-like polypeptides in which the C-terminal tail of the peptide threads through a ring formed by an isopeptide bond between the N-terminal amine group and a side chain carboxylic acid. The small size (∼20 amino acids) and simple topology of lasso peptides make them a good model system for studying the unthreading of entangled polypeptides, both with experiments and atomistic simulation. Here, we present an in-depth study of the thermal unthreading behavior of two lasso peptides astexin-2 and astexin-3. Quantitative kinetics and energetics of the unthreading process were determined for variants of these peptides using a series of chromatography and mass spectrometry experiments and biased molecular dynamics (MD) simulations. In addition, we show that the Tyr15Phe variant of astexin-3 unthreads via an unprecedented "tail pulling" mechanism. MD simulations on a model ring-thread system coupled with machine learning approaches also led to the discovery of physicochemical descriptors most important for peptide unthreading.
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Affiliation(s)
- Caitlin D. Allen
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Maria Y. Chen
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Alexander Y. Trick
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Dan Thanh Le
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Andrew L. Ferguson
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - A. James Link
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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25
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The B1 Protein Guides the Biosynthesis of a Lasso Peptide. Sci Rep 2016; 6:35604. [PMID: 27752134 PMCID: PMC5067487 DOI: 10.1038/srep35604] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/03/2016] [Indexed: 02/02/2023] Open
Abstract
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) with a unique lariat knot-like fold that endows them with extraordinary stability and biologically relevant activity. However, the biosynthetic mechanism of these fascinating molecules remains largely speculative. Generally, two enzymes (B for processing and C for cyclization) are required to assemble the unusual knot-like structure. Several subsets of lasso peptide gene clusters feature a "split" B protein on separate open reading frames (B1 and B2), suggesting distinct functions for the B protein in lasso peptide biosynthesis. Herein, we provide new insights into the role of the RiPP recognition element (RRE) PadeB1, characterizing its capacity to bind the paeninodin leader peptide and deliver its peptide substrate to PadeB2 for processing.
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26
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Zhu S, Fage CD, Hegemann JD, Yan D, Marahiel MA. Dual substrate-controlled kinase activity leads to polyphosphorylated lasso peptides. FEBS Lett 2016; 590:3323-3334. [DOI: 10.1002/1873-3468.12386] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/10/2016] [Accepted: 08/30/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Shaozhou Zhu
- Department of Chemistry and Biochemistry; Philipps-Universität Marburg; Germany
- State Key Laboratory of Chemical Resources Engineering; Beijing University of Chemical Technology; China
| | - Christopher D. Fage
- Department of Chemistry and Biochemistry; Philipps-Universität Marburg; Germany
| | - Julian D. Hegemann
- Department of Chemistry and Biochemistry; Philipps-Universität Marburg; Germany
| | - Dushan Yan
- Department of Chemistry and Biochemistry; Philipps-Universität Marburg; Germany
| | - Mohamed A. Marahiel
- Department of Chemistry and Biochemistry; Philipps-Universität Marburg; Germany
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27
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Fage CD, Hegemann JD, Nebel AJ, Steinbach RM, Zhu S, Linne U, Harms K, Bange G, Marahiel MA. Structure and Mechanism of the Sphingopyxin I Lasso Peptide Isopeptidase. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Christopher D. Fage
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Julian D. Hegemann
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Annika J. Nebel
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Roman M. Steinbach
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Shaozhou Zhu
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Uwe Linne
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Klaus Harms
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Gert Bange
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Mohamed A. Marahiel
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
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28
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Fage CD, Hegemann JD, Nebel AJ, Steinbach RM, Zhu S, Linne U, Harms K, Bange G, Marahiel MA. Structure and Mechanism of the Sphingopyxin I Lasso Peptide Isopeptidase. Angew Chem Int Ed Engl 2016; 55:12717-21. [DOI: 10.1002/anie.201605232] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/21/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Christopher D. Fage
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Julian D. Hegemann
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Annika J. Nebel
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Roman M. Steinbach
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Shaozhou Zhu
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Uwe Linne
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Klaus Harms
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Gert Bange
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Mohamed A. Marahiel
- Fachbereich Chemie; Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
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29
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Structure-Activity Analysis of Gram-positive Bacterium-producing Lasso Peptides with Anti-mycobacterial Activity. Sci Rep 2016; 6:30375. [PMID: 27457620 PMCID: PMC4960549 DOI: 10.1038/srep30375] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/30/2016] [Indexed: 01/07/2023] Open
Abstract
Lariatin A, an 18-residue lasso peptide encoded by the five-gene cluster larABCDE, displays potent and selective anti-mycobacterial activity. The structural feature is an N-terminal macrolactam ring, through which the C-terminal passed to form the rigid lariat-protoknot structure. In the present study, we established a convergent expression system by the strategy in which larA mutant gene-carrying plasmids were transformed into larA-deficient Rhodococcus jostii, and generated 36 lariatin variants of the precursor protein LarA to investigate the biosynthesis and the structure-activity relationships. The mutational analysis revealed that four amino acid residues (Gly1, Arg7, Glu8, and Trp9) in lariatin A are essential for the maturation and production in the biosynthetic machinery. Furthermore, the study on structure-activity relationships demonstrated that Tyr6, Gly11, and Asn14 are responsible for the anti-mycobacterial activity, and the residues at positions 15, 16 and 18 in lariatin A are critical for enhancing the activity. This study will not only provide a useful platform for genetically engineering Gram-positive bacterium-producing lasso peptides, but also an important foundation to rationally design more promising drug candidates for combatting tuberculosis.
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30
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Zhu S, Hegemann JD, Fage CD, Zimmermann M, Xie X, Linne U, Marahiel MA. Insights into the Unique Phosphorylation of the Lasso Peptide Paeninodin. J Biol Chem 2016; 291:13662-78. [PMID: 27151214 DOI: 10.1074/jbc.m116.722108] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Indexed: 11/06/2022] Open
Abstract
Lasso peptides are a new class of ribosomally synthesized and post-translationally modified peptides and thus far are only isolated from proteo- and actinobacterial sources. Typically, lasso peptide biosynthetic gene clusters encode enzymes for biosynthesis and export but not for tailoring. Here, we describe the isolation of the novel lasso peptide paeninodin from the firmicute Paenibacillus dendritiformis C454 and reveal within its biosynthetic cluster a gene encoding a kinase, which we have characterized as a member of a new class of lasso peptide-tailoring kinases. By employing a wide variety of peptide substrates, it was shown that this novel type of kinase specifically phosphorylates the C-terminal serine residue while ignoring those located elsewhere. These experiments also reveal that no other recognition motif is needed for efficient enzymatic phosphorylation of the C-terminal serine. Furthermore, through comparison with homologous HPr kinases and subsequent mutational analysis, we confirmed the essential catalytic residues. Our study reveals how lasso peptides are chemically diversified and sets the foundation for rational engineering of these intriguing natural products.
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Affiliation(s)
- Shaozhou Zhu
- From the Department of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Julian D Hegemann
- From the Department of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Christopher D Fage
- From the Department of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Marcel Zimmermann
- From the Department of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Xiulan Xie
- From the Department of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Uwe Linne
- From the Department of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Mohamed A Marahiel
- From the Department of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, 35032 Marburg, Germany
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31
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Zhao N, Pan Y, Cheng Z, Liu H. Lasso peptide, a highly stable structure and designable multifunctional backbone. Amino Acids 2016; 48:1347-56. [PMID: 27074719 DOI: 10.1007/s00726-016-2228-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/01/2016] [Indexed: 12/18/2022]
Abstract
Lasso peptide belongs to a new class of natural product with highly compact and stable structure. It has varieties of biological activities, among which the most important one is its antibacterial efficacy. Novel lasso peptides have been constantly discovered and analyzed by advanced techniques, and the biosynthesis or even chemical synthesis of lasso peptide has been studied after learning its constituent amino acids and maturation process. Structural identification of lasso peptide provides information for elucidating the mechanisms of its antibacterial activity and basis for further modifications. Ring of lasso peptide is the key to both its highly compact and stable structure and its intrinsic antibacterial property. The loop has been considered as suitable modification region of lasso peptide, such as V11-S18 of MccJ25 being modifiable without disrupting the lasso structure in biosynthesis. The tail is the immunity protein that can export lasso peptide out of its produced strain and serve as a self-protection mechanism at the same time. Most of currently known lasso peptides are non-pathogenic, which implies that the modified lasso peptides are promising candidates for medical applications. Arginine, glycine, and aspartic acid as a ligands of cancer-specific receptor have been grafted to the loop of lasso peptide without losing its bioactivity, and many other targets are expected to be used for lasso peptide modification. Multi-molecular modification and large-scale production need to be studied and solved in future for designing and using multifunctional lasso peptide based on its extraordinary stable structure.
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Affiliation(s)
- Ning Zhao
- Institute of Molecular Medicine, College of Life and Health Sciences, Northeastern University, Shenyang, 110000, China
| | - Yongxu Pan
- Institute of Molecular Medicine, College of Life and Health Sciences, Northeastern University, Shenyang, 110000, China
| | - Zhen Cheng
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Bio-X Program and Stanford Cancer Center, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Hongguang Liu
- Institute of Molecular Medicine, College of Life and Health Sciences, Northeastern University, Shenyang, 110000, China.
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32
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Hegemann JD, Fage CD, Zhu S, Harms K, Di Leva FS, Novellino E, Marinelli L, Marahiel MA. The ring residue proline 8 is crucial for the thermal stability of the lasso peptide caulosegnin II. MOLECULAR BIOSYSTEMS 2016; 12:1106-9. [DOI: 10.1039/c6mb00081a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lasso peptides are fascinating natural products with a unique structural fold that can exhibit tremendous thermal stability.
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Affiliation(s)
- Julian D. Hegemann
- Department of Chemistry/Biochemistry
- LOEWE Center for Synthetic Microbiology
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Christopher D. Fage
- Department of Chemistry/Biochemistry
- LOEWE Center for Synthetic Microbiology
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Shaozhou Zhu
- Department of Chemistry/Biochemistry
- LOEWE Center for Synthetic Microbiology
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Klaus Harms
- Department of Chemistry/Biochemistry
- LOEWE Center for Synthetic Microbiology
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | | | - Ettore Novellino
- Department of Pharmacy
- Università di Napoli “Federico II”
- 80131 Napoli
- Italy
| | - Luciana Marinelli
- Department of Pharmacy
- Università di Napoli “Federico II”
- 80131 Napoli
- Italy
| | - Mohamed A. Marahiel
- Department of Chemistry/Biochemistry
- LOEWE Center for Synthetic Microbiology
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
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33
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Li Y, Ducasse R, Zirah S, Blond A, Goulard C, Lescop E, Giraud C, Hartke A, Guittet E, Pernodet JL, Rebuffat S. Characterization of Sviceucin from Streptomyces Provides Insight into Enzyme Exchangeability and Disulfide Bond Formation in Lasso Peptides. ACS Chem Biol 2015; 10:2641-9. [PMID: 26343290 DOI: 10.1021/acschembio.5b00584] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lasso peptides are bacterial ribosomally synthesized and post-translationally modified peptides. They have sparked increasing interest in peptide-based drug development because of their compact, interlocked structure, which offers superior stability and protein-binding capacity. Disulfide bond-containing lasso peptides are rare and exhibit highly sought-after activities. In an effort to expand the repertoire of such molecules, we heterologously expressed, in Streptomyces coelicolor, the gene cluster encoding sviceucin, a type I lasso peptide with two disulfide bridges originating from Streptomyces sviceus, which allowed it to be fully characterized. Sviceucin and its reduced forms were characterized by mass spectrometry and peptidase digestion. The three-dimensional structure of sviceucin was determined using NMR. Sviceucin displayed antimicrobial activity selectively against Gram-positive bacteria and inhibition of fsr quorum sensing in Enterococcus faecalis. This study adds sviceucin to the type I lasso peptide family as a new representative. Moreover, new clusters encoding disulfide-bond containing lasso peptides from Actinobacteria were identified by genome mining. Genetic and functional analyses revealed that the formation of disulfide bonds in sviceucin does not require a pathway-encoded thiol-disulfide oxidoreductase. Most importantly, we demonstrated the functional exchangeability of the sviceucin and microcin J25 (a non-disulfide-bridged lasso peptide) macrolactam synthetases in vitro, highlighting the potential of hybrid lasso synthetases in lasso peptide engineering.
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Affiliation(s)
- Yanyan Li
- Laboratory Molecules
of Communication and Adaptation of Microorganisms (MCAM, UMR 7245
CNRS-MNHN), Sorbonne Universités, Muséum National d’Histoire
Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, F-75005, Paris, France
| | - Rémi Ducasse
- Laboratory Molecules
of Communication and Adaptation of Microorganisms (MCAM, UMR 7245
CNRS-MNHN), Sorbonne Universités, Muséum National d’Histoire
Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, F-75005, Paris, France
| | - Séverine Zirah
- Laboratory Molecules
of Communication and Adaptation of Microorganisms (MCAM, UMR 7245
CNRS-MNHN), Sorbonne Universités, Muséum National d’Histoire
Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, F-75005, Paris, France
| | - Alain Blond
- Laboratory Molecules
of Communication and Adaptation of Microorganisms (MCAM, UMR 7245
CNRS-MNHN), Sorbonne Universités, Muséum National d’Histoire
Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, F-75005, Paris, France
| | - Christophe Goulard
- Laboratory Molecules
of Communication and Adaptation of Microorganisms (MCAM, UMR 7245
CNRS-MNHN), Sorbonne Universités, Muséum National d’Histoire
Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, F-75005, Paris, France
| | - Ewen Lescop
- Institut
de Chimie
des Substances Naturelles, Centre de Recherche de Gif, UPR 2301 CNRS
Université Paris-Sud, 1 avenue
de la Terrasse, F-91198 Gif-sur-Yvette, France
| | - Caroline Giraud
- Unité de
Recherche Risques Microbiens (U2RM)-Stress et Virulence (EA 4655),
Université de Caen-Basse Normandie, F-14032 Caen, France
| | - Axel Hartke
- Unité de
Recherche Risques Microbiens (U2RM)-Stress et Virulence (EA 4655),
Université de Caen-Basse Normandie, F-14032 Caen, France
| | - Eric Guittet
- Institut
de Chimie
des Substances Naturelles, Centre de Recherche de Gif, UPR 2301 CNRS
Université Paris-Sud, 1 avenue
de la Terrasse, F-91198 Gif-sur-Yvette, France
| | - Jean-Luc Pernodet
- Institute
for
Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris-Sud, Bât. 400, Université
Paris-Sud, F-91405 Orsay, France
| | - Sylvie Rebuffat
- Laboratory Molecules
of Communication and Adaptation of Microorganisms (MCAM, UMR 7245
CNRS-MNHN), Sorbonne Universités, Muséum National d’Histoire
Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, F-75005, Paris, France
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34
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Maksimov MO, Koos JD, Zong C, Lisko B, Link AJ. Elucidating the Specificity Determinants of the AtxE2 Lasso Peptide Isopeptidase. J Biol Chem 2015; 290:30806-12. [PMID: 26534965 DOI: 10.1074/jbc.m115.694083] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Indexed: 11/06/2022] Open
Abstract
Lasso peptide isopeptidase is an enzyme that specifically hydrolyzes the isopeptide bond of lasso peptides, rendering these peptides linear. To carry out a detailed structure-activity analysis of the lasso peptide isopeptidase AtxE2 from Asticcacaulis excentricus, we solved NMR structures of its substrates astexin-2 and astexin-3. Using in vitro enzyme assays, we show that the C-terminal tail portion of these peptides is dispensable with regards to isopeptidase activity. A collection of astexin-2 and astexin-3 variants with alanine substitutions at each position within the ring and the loop was constructed, and we showed that all of these peptides except for one were cleaved by the isopeptidase. Thus, much like the lasso peptide biosynthetic enzymes, lasso peptide isopeptidase has broad substrate specificity. Quantitative analysis of the cleavage reactions indicated that alanine substitutions in loop positions of these peptides led to reduced cleavage, suggesting that the loop is serving as a recognition element for the isopeptidase.
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Affiliation(s)
| | | | - Chuhan Zong
- Chemistry, Princeton University, Princeton, New Jersey 08544
| | - Bozhena Lisko
- From the Departments of Chemical and Biological Engineering
| | - A James Link
- From the Departments of Chemical and Biological Engineering, Molecular Biology, and
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35
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Elsayed SS, Trusch F, Deng H, Raab A, Prokes I, Busarakam K, Asenjo JA, Andrews BA, van West P, Bull AT, Goodfellow M, Yi Y, Ebel R, Jaspars M, Rateb ME. Chaxapeptin, a Lasso Peptide from Extremotolerant Streptomyces leeuwenhoekii Strain C58 from the Hyperarid Atacama Desert. J Org Chem 2015; 80:10252-60. [DOI: 10.1021/acs.joc.5b01878] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Somayah S. Elsayed
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Franziska Trusch
- Aberdeen
Oomycetes Laboratory, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K
| | - Hai Deng
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Andrea Raab
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Ivan Prokes
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | | | - Juan A. Asenjo
- Centre
for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Barbara A. Andrews
- Centre
for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Pieter van West
- Aberdeen
Oomycetes Laboratory, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K
| | - Alan T. Bull
- School
of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Michael Goodfellow
- School
of Biology, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
| | - Yu Yi
- Key Laboratory
of Combinatory Biosynthesis and Drug Discovery, School of Pharmaceutical
Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, P. R. China
| | - Rainer Ebel
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Marcel Jaspars
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Mostafa E. Rateb
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
- Pharmacognosy
Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 32514, Egypt
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36
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Hegemann JD, Zimmermann M, Xie X, Marahiel MA. Lasso peptides: an intriguing class of bacterial natural products. Acc Chem Res 2015; 48:1909-19. [PMID: 26079760 DOI: 10.1021/acs.accounts.5b00156] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Natural products of peptidic origin often represent a rich source of medically relevant compounds. The synthesis of such polypeptides in nature is either initiated by deciphering the genetic code on the ribosome during the translation process or driven by ribosome-independent processes. In the latter case, highly modified bioactive peptides are assembled by multimodular enzymes designated as nonribosomal peptide synthetases (NRPS) that act as a protein-template to generate chemically diverse peptides. On the other hand, the ribosome-dependent strategy, although relying strictly on the 20-22 proteinogenic amino acids, generates structural diversity by extensive post-translational-modification. This strategy seems to be highly distributed in all kingdoms of life. One example for this is the lasso peptides, which are an emerging class of ribosomally assembled and post-translationally modified peptides (RiPPs) from bacteria that were first described in 1991. A wide range of interesting biological activities are known for these compounds, including antimicrobial, enzyme inhibitory, and receptor antagonistic activities. Since 2008, genome mining approaches allowed the targeted isolation and characterization of such molecules and helped to better understand this compound class and their biosynthesis. Their defining structural feature is a macrolactam ring that is threaded by the C-terminal tail and held in position by sterically demanding residues above and below the ring, resulting in a unique topology that is reminiscent of a lariat knot. The ring closure is achieved by an isopeptide bond formed between the N-terminal α-amino group of a glycine, alanine, serine, or cysteine and the carboxylic acid side chain of an aspartate or glutamate, which can be located at positions 7, 8, or 9 of the amino acid sequence. In this Account, we discuss the newest findings about these compounds, their biosynthesis, and their physicochemical properties. This includes the suggested mechanism through which the precursor peptide is enzymatically processed into a mature lasso peptide and crucial residues for enzymatic recognition. Furthermore, we highlight new insights considering the protease and thermal stability of lasso peptides and discuss why seven amino acid residue rings are likely to be the lower limit feasible for this compound class. To elucidate their fascinating three-dimensional structures, NMR spectroscopy is commonly employed. Therefore, the general methodology to elucidate these structures by NMR will be discussed and pitfalls for these approaches are highlighted. In addition, new tools provided by recent investigations to assess and prove the lasso topology without a complete structure elucidation will be summarized. These include techniques like ion mobility-mass spectrometry and a combined approach of thermal and carboxypeptidase treatment with subsequent LC-MS analysis. Nevertheless, even though much was learned about these compounds in recent years, their true native function and the exact enzymatic mechanism of their maturation remain elusive.
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Affiliation(s)
- Julian D. Hegemann
- Department of Chemistry,
Biochemistry and LOEWE-Center
for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Strasse
4, D-35032, Marburg, Germany
| | - Marcel Zimmermann
- Department of Chemistry,
Biochemistry and LOEWE-Center
for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Strasse
4, D-35032, Marburg, Germany
| | - Xiulan Xie
- Department of Chemistry,
Biochemistry and LOEWE-Center
for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Strasse
4, D-35032, Marburg, Germany
| | - Mohamed A. Marahiel
- Department of Chemistry,
Biochemistry and LOEWE-Center
for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Strasse
4, D-35032, Marburg, Germany
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37
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Metelev M, Tietz JI, Melby JO, Blair PM, Zhu L, Livnat I, Severinov K, Mitchell DA. Structure, bioactivity, and resistance mechanism of streptomonomicin, an unusual lasso Peptide from an understudied halophilic actinomycete. ACTA ACUST UNITED AC 2015; 22:241-50. [PMID: 25601074 DOI: 10.1016/j.chembiol.2014.11.017] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 11/04/2014] [Accepted: 12/10/2014] [Indexed: 10/24/2022]
Abstract
Natural products are the most historically significant source of compounds for drug development. However, unacceptably high rates of compound rediscovery associated with large-scale screening of common microbial producers have resulted in the abandonment of many natural product drug discovery efforts, despite the increasing prevalence of clinically problematic antibiotic resistance. Screening of underexplored taxa represents one strategy to avoid rediscovery. Herein we report the discovery, isolation, and structural elucidation of streptomonomicin (STM), an antibiotic lasso peptide from Streptomonospora alba, and report the genome for its producing organism. STM-resistant clones of Bacillus anthracis harbor mutations to walR, the gene encoding a response regulator for the only known widely distributed and essential two-component signal transduction system in Firmicutes. To the best of our knowledge, Streptomonospora had been hitherto biosynthetically and genetically uncharacterized, with STM being the first reported compound from the genus. Our results demonstrate that understudied microbes remain fruitful reservoirs for the rapid discovery of novel, bioactive natural products.
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Affiliation(s)
- Mikhail Metelev
- Institute for Nanobiotechnologies, Saint Petersburg State Polytechnical University, Saint Petersburg 195251, Russia; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jonathan I Tietz
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Joel O Melby
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Patricia M Blair
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lingyang Zhu
- NMR Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Itamar Livnat
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Konstantin Severinov
- Institute for Nanobiotechnologies, Saint Petersburg State Polytechnical University, Saint Petersburg 195251, Russia; Department of Molecular Biology and Biochemistry, Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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38
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Al Toma RS, Kuthning A, Exner MP, Denisiuk A, Ziegler J, Budisa N, Süssmuth RD. Site-Directed and Global Incorporation of Orthogonal and Isostructural Noncanonical Amino Acids into the Ribosomal Lasso Peptide Capistruin. Chembiochem 2014; 16:503-9. [DOI: 10.1002/cbic.201402558] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Indexed: 02/01/2023]
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