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Schiefelbein K, Lang J, Schuster M, Grigglestone CE, Striga R, Bigler L, Schuman MC, Zerbe O, Li Y, Hartrampf N. Merging Flow Synthesis and Enzymatic Maturation to Expand the Chemical Space of Lasso Peptides. J Am Chem Soc 2024; 146:17261-17269. [PMID: 38759637 PMCID: PMC11212047 DOI: 10.1021/jacs.4c03898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
Many peptidic natural products, such as lasso peptides, cyclic peptides, and cyclotides, are conformationally constrained and show biological stability, making them attractive scaffolds for drug development. Although many peptides can be synthesized and modified through chemical methods, knot-like lasso peptides such as microcin J25 (MccJ25) and their analogues remain elusive. As the chemical space of MccJ25 analogues accessible through purely biological methods is also limited, we proposed a hybrid approach: flow-based chemical synthesis of non-natural precursor peptides, followed by in vitro transformation with recombinant maturation enzymes, to yield a more diverse array of lasso peptides. Herein, we established the rapid, flow-based synthesis of chemically modified MccJ25 precursor peptides (57 amino acids). Heterologous expression of enzymes McjB and McjC was extensively optimized to improve yields and facilitate the synthesis of multiple analogues of MccJ25, including the incorporation of non-canonical tyrosine and histidine derivatives into the lasso scaffold. Finally, using our chemoenzymatic strategy, we produced a biologically active analogue containing three d-amino acids in the loop region and incorporated backbone N-methylations. Our method provides rapid access to chemically modified lasso peptides that could be used to investigate structure-activity relationships, epitope grafting, and the improvement of therapeutic properties.
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Affiliation(s)
- Kevin Schiefelbein
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jakob Lang
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department
of Geography, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Matthias Schuster
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Claire E. Grigglestone
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Robin Striga
- Laboratory
Molecules of Communication and Adaptation of Microorganisms (MCAM).
UMR7245, CNRS-Muséum National d’Histoire
Naturelle (MNHN), Alliance Sorbonne Université, 57 rue Cuvier, 75005 Paris, France
| | - Laurent Bigler
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Meredith C. Schuman
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department
of Geography, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Oliver Zerbe
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Yanyan Li
- Laboratory
Molecules of Communication and Adaptation of Microorganisms (MCAM).
UMR7245, CNRS-Muséum National d’Histoire
Naturelle (MNHN), Alliance Sorbonne Université, 57 rue Cuvier, 75005 Paris, France
| | - Nina Hartrampf
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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2
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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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3
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Cha Y, Kim W, Park Y, Kim M, Son Y, Park W. Antagonistic actions of Paucibacter aquatile B51 and its lasso peptide paucinodin toward cyanobacterial bloom-forming Microcystis aeruginosa PCC7806. JOURNAL OF PHYCOLOGY 2024; 60:152-169. [PMID: 38073162 DOI: 10.1111/jpy.13412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/04/2023] [Accepted: 11/08/2023] [Indexed: 02/17/2024]
Abstract
Superior antagonistic activity against axenic Microcystis aeruginosa PCC7806 was observed with Paucibacter sp. B51 isolated from cyanobacterial bloom samples among 43 tested freshwater bacterial species. Complete genome sequencing, analyzing average nucleotide identity and digital DNA-DNA hybridization, designated the B51 strain as Paucibacter aquatile. Electron and fluorescence microscopic image analyses revealed the presence of the B51 strain in the vicinity of M. aeruginosa cells, which might provoke direct inhibition of the photosynthetic activity of the PCC7806 cells, leading to perturbation of cellular metabolisms and consequent cell death. Our speculation was supported by the findings that growth failure of the PCC7806 cells led to low pH conditions with fewer chlorophylls and down-regulation of photosystem genes (e.g., psbD and psaB) during their 48-h co-culture condition. Interestingly, the concentrated ethyl acetate extracts obtained from B51-grown supernatant exhibited a growth-inhibitory effect on PCC7806. The physical separation of both strains by a filter system led to no inhibitory activity of the B51 cells, suggesting that contact-mediated anti-cyanobacterial compounds might also be responsible for hampering the growth of the PCC7806 cells. Bioinformatic tools identified 12 gene clusters that possibly produce secondary metabolites, including a class II lasso peptide in the B51 genome. Further chemical analysis demonstrated anti-cyanobacterial activity from fractionated samples having a rubrivinodin-like lasso peptide, named paucinodin. Taken together, both contact-mediated inhibition of photosynthesis and the lasso peptide secretion of the B51 strain are responsible for the anti-cyanobacterial activity of P. aquatile B51.
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Affiliation(s)
- Yeji Cha
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Yerim Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Yongjun Son
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
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4
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Yang ZJ, Shao Q, Jiang Y, Jurich C, Ran X, Juarez RJ, Yan B, Stull SL, Gollu A, Ding N. Mutexa: A Computational Ecosystem for Intelligent Protein Engineering. J Chem Theory Comput 2023; 19:7459-7477. [PMID: 37828731 PMCID: PMC10653112 DOI: 10.1021/acs.jctc.3c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Indexed: 10/14/2023]
Abstract
Protein engineering holds immense promise in shaping the future of biomedicine and biotechnology. This Review focuses on our ongoing development of Mutexa, a computational ecosystem designed to enable "intelligent protein engineering". In this vision, researchers will seamlessly acquire sequences of protein variants with desired functions as biocatalysts, therapeutic peptides, and diagnostic proteins through a finely-tuned computational machine, akin to Amazon Alexa's role as a versatile virtual assistant. The technical foundation of Mutexa has been established through the development of a database that combines and relates enzyme structures and their respective functions (e.g., IntEnzyDB), workflow software packages that enable high-throughput protein modeling (e.g., EnzyHTP and LassoHTP), and scoring functions that map the sequence-structure-function relationship of proteins (e.g., EnzyKR and DeepLasso). We will showcase the applications of these tools in benchmarking the convergence conditions of enzyme functional descriptors across mutants, investigating protein electrostatics and cavity distributions in SAM-dependent methyltransferases, and understanding the role of nonelectrostatic dynamic effects in enzyme catalysis. Finally, we will conclude by addressing the future steps and fundamental challenges in our endeavor to develop new Mutexa applications that assist the identification of beneficial mutants in protein engineering.
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Affiliation(s)
- Zhongyue J. Yang
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data
Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Qianzhen Shao
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Yaoyukun Jiang
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Christopher Jurich
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Xinchun Ran
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Reecan J. Juarez
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Bailu Yan
- Department
of Biostatistics, Vanderbilt University, Nashville, Tennessee 37205, United States
| | - Sebastian L. Stull
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Anvita Gollu
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ning Ding
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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5
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Duan Y, Niu W, Pang L, Mu DS, Du ZJ, Zhang Y, Bian X, Zhong G. Leader peptide removal in lasso peptide biosynthesis based on penultimate isoleucine residue. Front Microbiol 2023; 14:1181125. [PMID: 37497541 PMCID: PMC10368454 DOI: 10.3389/fmicb.2023.1181125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023] Open
Abstract
Lasso peptides are ribosomally synthesized peptides that undergo post-translational modifications including leader peptide removal by B (or the segregated B1 and B2) proteins and core peptide macrolactamization by C proteins to form a unique lariat topology. A conserved threonine residue at the penultimate position of leader peptide is hitherto found in lasso peptide precursors and shown to be a critical recognition element for effective enzymatic processing. We identified a lasso peptide biosynthetic gene cluster (bsf) from Bradymonas sediminis FA350, a Gram-negative and facultatively prey-dependent bacterium that belongs to a novel bacterial order Bradymonadales in the class Deltaproteobacteria. The kinase BsfK specifically catalyzes the phosphorylation of the precursor peptide BsfA on the Ser3 residue. BsfB1 performs dual functions to accelerate the post-translational phosphorylation and assist BsfB2 in leader peptide removal. Most importantly, the penultimate residue of leader peptide is an isoleucine rather than the conserved threonine and this isoleucine has a marked impact on the phosphorylation of Ser3 as well as leader peptide removal, implying that BsfB1 and BsfB2 exhibit a new substrate selectivity for leader peptide binding and excision. This is the first experimentally validated penultimate isoleucine residue in a lasso peptide precursor to our knowledge. In silico analysis reveals that the leader peptide Ile/Val(-2) residue is rare but not uncommon in phosphorylated lasso peptides, as this residue is also discovered in Acidobacteriaceae and Sphingomonadales in addition to Bradymonadales.
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Affiliation(s)
- Yuwei Duan
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Weijing Niu
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Linlin Pang
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Da-Shuai Mu
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Marine College, Shandong University, Weihai, China
| | - Zong-Jun Du
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Marine College, Shandong University, Weihai, China
| | - Youming Zhang
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology and Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoying Bian
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Guannan Zhong
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Suzhou Research Institute of Shandong University, Suzhou, China
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6
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Juarez RJ, Jiang Y, Tremblay M, Shao Q, Link AJ, Yang ZJ. LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling. J Chem Inf Model 2023; 63:522-530. [PMID: 36594886 PMCID: PMC10117200 DOI: 10.1021/acs.jcim.2c00945] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Lasso peptides are a subclass of ribosomally synthesized and post-translationally modified peptides with a slipknot conformation. With superior thermal stability, protease resistance, and antimicrobial activity, lasso peptides are promising candidates for bioengineering and pharmaceutical applications. To enable high-throughput computational prediction and design of lasso peptides, we developed a software, LassoHTP, for automatic lasso peptide structure construction and modeling. LassoHTP consists of three modules, including the scaffold constructor, mutant generator, and molecular dynamics (MD) simulator. With a user-provided sequence and conformational annotation, LassoHTP can either generate the structure and conformational ensemble as is or conduct random mutagenesis. We used LassoHTP to construct eight known lasso peptide structures de novo and to simulate their conformational ensembles for 100 ns MD simulations. For benchmarking, we calculated the root mean square deviation (RMSD) of these ensembles with reference to their experimental crystal or NMR PDB structures; we also compared these RMSD values against those of the MD ensembles that are initiated from the PDB structures. Dihedral principal component analysis was also conducted. The results show that the LassoHTP-initiated ensembles are similar to those of the PDB-initiated ensembles. LassoHTP offers a computational platform to develop strategies for lasso peptide prediction and design.
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Affiliation(s)
- Reecan J. Juarez
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Matthew Tremblay
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Chemistry and Molecular Biology, Princeton University, 207 Hoyt Laboratory, Princeton, New Jersey 08544, United States
| | - Zhongyue J. Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
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7
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Carson DV, Patiño M, Elashal HE, Cartagena AJ, Zhang Y, Whitley ME, So L, Kayser-Browne AK, Earl AM, Bhattacharyya RP, Link AJ. Cloacaenodin, an Antimicrobial Lasso Peptide with Activity against Enterobacter. ACS Infect Dis 2023; 9:111-121. [PMID: 36519726 PMCID: PMC10038104 DOI: 10.1021/acsinfecdis.2c00446] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Using genome mining and heterologous expression, we report the discovery and production of a new antimicrobial lasso peptide from species related to the Enterobacter cloacae complex. Using NMR and mass spectrometric analysis, we show that this lasso peptide, named cloacaenodin, employs a threaded lasso fold which imparts proteolytic resistance that its unthreaded counterpart lacks. Cloacaenodin has selective, low micromolar, antimicrobial activity against species related to the E. cloacae complex, including species implicated in nosocomial infections and against clinical isolates of carbapenem-resistant Enterobacterales. We further used site-directed mutagenesis to probe the importance of specific residues to the peptide's biosynthesis, stability, and bioactivity.
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Affiliation(s)
- Drew V. Carson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Monica Patiño
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Hader E. Elashal
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Alexis Jaramillo Cartagena
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Yi Zhang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Megan E. Whitley
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Larry So
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Angelo K. Kayser-Browne
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Roby P. Bhattacharyya
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Infectious Diseases Division, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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8
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Hills E, Woodward TJ, Fields S, Brandsen BM. Comprehensive Mutational Analysis of the Lasso Peptide Klebsidin. ACS Chem Biol 2022; 17:998-1010. [PMID: 35315272 PMCID: PMC9976627 DOI: 10.1021/acschembio.2c00148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Antibiotic resistance is a growing threat to public health, making the development of antibiotics of critical importance. One promising class of potential new antibiotics are ribosomally synthesized and post-translationally modified peptides (RiPPs), which include klebsidin, a lasso peptide from Klebsiella pneumoniae that inhibits certain bacterial RNA polymerases. We develop a high-throughput assay based on growth inhibition of Escherichia coli to analyze the mutational tolerance of klebsidin. We transform a library of klebsidin variants into E. coli and use next-generation DNA sequencing to count the frequency of each variant before and after its expression, thereby generating functional scores for 320 of 361 single amino acid changes. We identify multiple positions in the macrocyclic ring and the C-terminal tail region of klebsidin that are intolerant to mutation, as well as positions in the loop region that are highly tolerant to mutation. Characterization of selected peptide variants scored as active reveals that each adopts a threaded lasso conformation; active loop variants applied extracellularly as peptides slow the growth of E. coli and K. pneumoniae. We generate an E. coli strain with a mutation in RNA polymerase that confers resistance to klebsidin and similarly carry out a selection with the klebsidin library. We identify a single variant, klebsidin F9Y, that maintains activity against the resistant E. coli when expressed intracellularly. This finding supports the utility of this method and suggests that comprehensive mutational analysis of lasso peptides can identify unique and potentially improved variants.
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Affiliation(s)
- Ethan Hills
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Tyler J. Woodward
- Department of Chemistry and Biochemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States,Department of Medicine, University of Washington, Seattle, Washington 98195, United States
| | - Benjamin M. Brandsen
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States,Department of Chemistry and Biochemistry, Creighton University, Omaha, Nebraska 68178, United States,Correspondence: Benjamin M. Brandsen, , ph. 402 280-2153
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9
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Xiu H, Wang M, Fage CD, He Y, Niu X, Han M, Li F, An X, Fan H, Song L, Zheng G, Zhu S, Tong Y. Discovery and Characterization of Rubrinodin Provide Clues into the Evolution of Lasso Peptides. Biochemistry 2022; 61:595-607. [PMID: 35298141 DOI: 10.1021/acs.biochem.2c00029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lasso peptides are unique natural products that comprise a class of ribosomally synthesized and post-translationally modified peptides. Their defining three-dimensional structure is a lariat knot, in which the C-terminal tail is threaded through a macrolactam ring formed between the N-terminal amino group and an Asp or Glu side chain (i.e., an isopeptide bond). Recent genome mining strategies have revealed various types of lasso peptide biosynthetic gene clusters and have thus redefined the known chemical space of lasso peptides. To date, over 20 different types of these gene clusters have been discovered, including several different clades from Proteobacteria. Despite the diverse architectures of these gene clusters, which may or may not encode various tailoring enzymes, most currently known lasso peptides are synthesized by two discrete clades defined by the presence of an ATP-binding cassette transporter or its absence and (sometimes) concurrent appearance of an isopeptidase, raising questions about their evolutionary history. Herein, we discovered and characterized the lasso peptide rubrinodin, which is assembled by a gene cluster encoding both an ATP-binding cassette transporter and an isopeptidase. Our bioinformatics analyses of this and other representative cluster types provided new clues into the evolutionary history of lasso peptides. Furthermore, our structural and biochemical investigations of rubrinodin permitted the conversion of this thermolabile lasso peptide into a more thermostable scaffold.
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Affiliation(s)
- Huanhuan Xiu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Mengjiao Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | | | - Yile He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meng Han
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Fei Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Guojun Zheng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Shaozhou Zhu
- National Institutes for Food and Drug Control, Beijing 102629, People's Republic of China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
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10
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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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11
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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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12
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Dit Fouque KJ, Scutelnic V, Hegemann JD, Rebuffat S, Maître P, Rizzo TR, Fernandez-Lima F. Structural Insights from Tandem Mass Spectrometry, Ion Mobility-Mass Spectrometry, and Infrared/Ultraviolet Spectroscopy on Sphingonodin I: Lasso vs Branched-Cyclic Topoisomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1096-1104. [PMID: 33765377 DOI: 10.1021/jasms.1c00041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lasso peptides form a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by a mechanically interlocked topology, where the C-terminal tail of the peptide is threaded and trapped within an N-terminal macrolactam ring. Sphingonodin I is a lasso peptide that has not yet been structurally characterized using the traditional structural biology tools (e.g., NMR and X-ray crystallography), and its biological function has not yet been elucidated. In the present work, we describe structural signatures characteristic of the class II lasso peptide sphingonodin I and its branched-cyclic analogue using a combination of gas-phase ion tools (e.g., tandem mass spectrometry, MS/MS, trapped ion mobility spectrometry, TIMS, and infrared, IR, and ultraviolet, UV, spectroscopies). Tandem MS/MS CID experiments on sphingonodin I yielded mechanically interlocked species with associated bi and yj fragments demonstrating the presence of a lasso topology, while tandem MS/MS ECD experiments on sphingonodin I showed a significant increase in hydrogen migration in the loop region when compared to the branched-cyclic analogue. The high-mobility resolving power of TIMS permitted the separation of both topoisomers, where sphingonodin I adopted a more compact structure than its branched-cyclic analogue. Cryogenic and room-temperature IR spectroscopy experiments evidenced a different hydrogen bond network between the two topologies, while cryogenic UV spectroscopy experiments clearly demonstrated a distinct phenylalanine environment for the lasso peptide.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, AHC4-233, Miami, Florida 33199, United States
| | - Valeriu Scutelnic
- Laboratory of Molecular Physical Chemistry, Ecole Polytechnique Fedérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
| | - Julian D Hegemann
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms, National Museum of Natural History, CNRS, 57 rue Cuvier, CP-54, 75005 Paris, France
| | - Philippe Maître
- Laboratoire de Chimie Physique, Université Paris Sud, UMR 8000 CNRS, Faculté des Sciences, Bât. 349, 91405 Orsay Cedex France
| | - Thomas R Rizzo
- Laboratory of Molecular Physical Chemistry, Ecole Polytechnique Fedérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, AHC4-233, Miami, Florida 33199, United States
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13
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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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14
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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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15
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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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16
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Sabino YNV, de Araújo KC, de Assis FGDV, Moreira SM, Lopes TDS, Mendes TADO, Huws SA, Mantovani HC. In silico Screening Unveil the Great Potential of Ruminal Bacteria Synthesizing Lasso Peptides. Front Microbiol 2020; 11:576738. [PMID: 33072042 PMCID: PMC7533575 DOI: 10.3389/fmicb.2020.576738] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022] Open
Abstract
Studies of rumen microbial ecology suggest that the capacity to produce antimicrobial peptides could be a useful trait in species competing for ecological niches in the ruminal ecosystem. However, little is known about the synthesis of lasso peptides by ruminal microorganisms. Here we analyzed the distribution and diversity of lasso peptide gene clusters in 425 bacterial genomes from the rumen ecosystem. Genome mining was performed using antiSMASH 5, BAGEL4, and a database of well-known precursor sequences. The genomic context of the biosynthetic clusters was investigated to identify putative lasA genes and protein sequences from enzymes of the biosynthetic machinery were evaluated to identify conserved motifs. Metatranscriptome analysis evaluated the expression of the biosynthetic genes in the rumen microbiome. Several incomplete (n = 23) and complete (n = 11) putative lasso peptide clusters were detected in the genomes of ruminal bacteria. The complete gene clusters were exclusively found within the phylum Firmicutes, mainly (48%) in strains of the genus Butyrivibrio. The analysis of the genetic organization of complete putative lasso peptide clusters revealed the presence of co-occurring genes, including kinases (85%), transcriptional regulators (49%), and glycosyltransferases (36%). Moreover, a conserved pattern of cluster organization was detected between strains of the same genus/species. The maturation enzymes LasB, LasC, and LasD showed regions highly conserved, including the presence of a transglutaminase core in LasB, an asparagine synthetase domain in LasC, and an ABC-type transporter system in LasD. Phylogenetic trees of the essential biosynthetic proteins revealed that sequences split into monophyletic groups according to their shared single common ancestor. Metatranscriptome analyses indicated the expression of the lasso peptides biosynthetic genes within the active rumen microbiota. Overall, our in silico screening allowed the discovery of novel biosynthetic gene clusters in the genomes of ruminal bacteria and revealed several strains with the genetic potential to synthesize lasso peptides, suggesting that the ruminal microbiota represents a potential source of these promising peptides.
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Affiliation(s)
| | | | | | | | | | | | - Sharon Ann Huws
- Institute for Global Food Security, School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, United Kingdom
| | - Hilário C Mantovani
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Brazil
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17
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Zhong Z, He B, Li J, Li YX. Challenges and advances in genome mining of ribosomally synthesized and post-translationally modified peptides (RiPPs). Synth Syst Biotechnol 2020; 5:155-172. [PMID: 32637669 PMCID: PMC7327761 DOI: 10.1016/j.synbio.2020.06.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 01/05/2023] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a class of cyclic or linear peptidic natural products with remarkable structural and functional diversity. Recent advances in genomics and synthetic biology, are facilitating us to discover a large number of new ribosomal natural products, including lanthipeptides, lasso peptides, sactipeptides, thiopeptides, microviridins, cyanobactins, linear thiazole/oxazole-containing peptides and so on. In this review, we summarize bioinformatic strategies that have been developed to identify and prioritize biosynthetic gene clusters (BGCs) encoding RiPPs, and the genome mining-guided discovery of novel RiPPs. We also prospectively provide a vision of what genomics-guided discovery of RiPPs may look like in the future, especially the discovery of RiPPs from dominant but uncultivated microbes, which will be promoted by the combinational use of synthetic biology and metagenome mining strategies.
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Affiliation(s)
- Zheng Zhong
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong SAR, China
| | - Beibei He
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong SAR, China
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, USA
| | - Yong-Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong SAR, China
- The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China
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18
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Fuwa H, Hemmi H, Kaweewan I, Kozaki I, Honda H, Kodani S. Heterologous production of new lasso peptide koreensin based on genome mining. J Antibiot (Tokyo) 2020; 74:42-50. [PMID: 32855516 DOI: 10.1038/s41429-020-00363-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 11/09/2022]
Abstract
Lasso peptides are a class of ribosomally biosynthesized and posttranslationally modified peptides with a knot structure as a common motif. Based on a genome search, a new biosynthetic gene cluster of lasso peptide was found in the genome of the proteobacterium Sphingomonas koreensis. Interestingly, the amino acid sequence of the precursor peptide gene includes two cell adhesion motif sequences (KGD and DGR). Heterologous production of the new lasso peptide was performed using the cryptic biosynthetic gene cluster of S. koreensis. As a result, a new lasso peptide named koreensin was produced by the gene expression system in the host strain Sphingomonas subterranea. The structure of koreensin was determined by NMR and ESI-MS analysis. The three-dimensional structure of koreensin was obtained based on an NOE experiment and the coupling constants. A variant peptide (koreensin-RGD), which had RGD instead of KGD, was produced by heterologous production with site-directed mutagenesis experiment. Koreensin and koreensin-RGD did not show cell adhesion inhibitory activity, although the molecules possessed cell adhesion motifs. The possible presence of a salt bridge between the motifs in koreensin was indicated, and it may prevent the cell adhesion motif from functioning.
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Affiliation(s)
- Hiroki Fuwa
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hikaru Hemmi
- Food Research Institute, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Issara Kaweewan
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Ikko Kozaki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Hiroyuki Honda
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan. .,Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan. .,Academic Institute, Shizuoka University, Shizuoka, Japan.
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19
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Acevedo-Jake A, Ball AT, Galli M, Kukwikila M, Denis M, Singleton DG, Tavassoli A, Goldup SM. AT-CuAAC Synthesis of Mechanically Interlocked Oligonucleotides. J Am Chem Soc 2020; 142:5985-5990. [PMID: 32155338 PMCID: PMC8016193 DOI: 10.1021/jacs.0c01670] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Indexed: 12/22/2022]
Abstract
We present a simple strategy for the synthesis of main chain oligonucleotide rotaxanes with precise control over the position of the macrocycle. The novel DNA-based rotaxanes were analyzed to assess the effect of the mechanical bond on their properties.
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Affiliation(s)
- Amanda Acevedo-Jake
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Andrew T. Ball
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Marzia Galli
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Mikiembo Kukwikila
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Mathieu Denis
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Daniel G. Singleton
- ATDBio
Ltd, School of Chemistry, University of
Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Ali Tavassoli
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Stephen M. Goldup
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
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20
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Li G, Delafield DG, Li L. Improved structural elucidation of peptide isomers and their receptors using advanced ion mobility-mass spectrometry. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.05.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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21
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Cortés-Albayay C, Jarmusch SA, Trusch F, Ebel R, Andrews BA, Jaspars M, Asenjo JA. Downsizing Class II Lasso Peptides: Genome Mining-Guided Isolation of Huascopeptin Containing the First Gly1-Asp7 Macrocycle. J Org Chem 2020; 85:1661-1667. [DOI: 10.1021/acs.joc.9b02231] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Carlos Cortés-Albayay
- Centre for Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago 8370450, Chile
| | - Scott A. Jarmusch
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, U.K
| | - Franziska Trusch
- Institute of Medical Sciences, University of Aberdeen, Foresterhill AB25 2ZD, Scotland, U.K
- Division of Plant Sciences, College of Life Science, University of Dundee (at JHI), Errol Road, Invergowrie, Dundee DD2 5DA, U.K
| | - Rainer Ebel
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, U.K
| | - Barbara A. Andrews
- Centre for Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago 8370450, Chile
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, U.K
| | - Juan A. Asenjo
- Centre for Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago 8370450, Chile
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22
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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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23
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Tan S, Moore G, Nodwell J. Put a Bow on It: Knotted Antibiotics Take Center Stage. Antibiotics (Basel) 2019; 8:antibiotics8030117. [PMID: 31405236 PMCID: PMC6784204 DOI: 10.3390/antibiotics8030117] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/06/2019] [Accepted: 08/09/2019] [Indexed: 01/15/2023] Open
Abstract
Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large class of natural products produced across all domains of life. The lasso peptides, a subclass of RiPPs with a lasso-like structure, are structurally and functionally unique compared to other known peptide antibiotics in that the linear peptide is literally "tied in a knot" during its post-translational maturation. This underexplored class of peptides brings chemical diversity and unique modes of action to the antibiotic space. To date, eight different lasso peptides have been shown to target three known molecular machines: RNA polymerase, the lipid II precursor in peptidoglycan biosynthesis, and the ClpC1 subunit of the Clp protease involved in protein homeostasis. Here, we discuss the current knowledge on lasso peptide biosynthesis as well as their antibiotic activity, molecular targets, and mechanisms of action.
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Affiliation(s)
- Stephanie Tan
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Gaelen Moore
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Justin Nodwell
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
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24
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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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25
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Hegemann JD, Bobeica SC, Walker MC, Bothwell IR, van der Donk WA. Assessing the Flexibility of the Prochlorosin 2.8 Scaffold for Bioengineering Applications. ACS Synth Biol 2019; 8:1204-1214. [PMID: 31042373 PMCID: PMC6525029 DOI: 10.1021/acssynbio.9b00080] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyclization is a common strategy to confer proteolytic resistance to peptide scaffolds. Thus, cyclic peptides have been the focus of extensive bioengineering efforts. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a superfamily of peptidic natural products that often contain macrocycles. In the RiPP family of lanthipeptides, macrocyclization is accomplished through formation of thioether cross-links between cysteines and dehydrated serines/threonines. The recent production of lanthipeptide libraries and development of methods to display lanthipeptides on yeast or phage highlights their potential for bioengineering and synthetic biology. In this regard, the prochlorosins are especially promising as the corresponding class II lanthipeptide synthetase ProcM matures numerous precursor peptides with diverse core peptide sequences. To facilitate future bioengineering projects, one of its native substrates, ProcA2.8, was subjected in this study to in-depth mutational analysis to test the limitations of ProcM-mediated cyclization. Alanine scan mutagenesis was performed on all residues within the two rings, and multiple prolines were introduced at various positions. Moreover, mutation, deletion, and insertion of residues in the region linking the two lanthionine rings was tested. Additional residues were also introduced or deleted from either ring, and inversion of ring forming residues was attempted to generate diastereomers. The findings were used for epitope grafting of the RGD integrin binding epitope within prochlorosin 2.8, resulting in a low nanomolar affinity binder of the αvβ3 integrin that was more stable toward proteolysis and displayed higher affinity than the linear counterpart.
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Affiliation(s)
- Julian D. Hegemann
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Silvia C. Bobeica
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Mark C. Walker
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Ian R. Bothwell
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
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26
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Núñez-Montero K, Lamilla C, Abanto M, Maruyama F, Jorquera MA, Santos A, Martinez-Urtaza J, Barrientos L. Antarctic Streptomyces fildesensis So13.3 strain as a promising source for antimicrobials discovery. Sci Rep 2019; 9:7488. [PMID: 31097761 PMCID: PMC6522549 DOI: 10.1038/s41598-019-43960-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/01/2019] [Indexed: 12/29/2022] Open
Abstract
Antarctic have been suggested as an attractive source for antibiotics discovery and members of Streptomyces genus have historically been studied as natural producers of antimicrobial metabolites. Nonetheless, our knowledge on antibiotic-producing Streptomyces from Antarctic is very limited. In this study, the antimicrobial activity of organic extracts from Antarctic Streptomyces strains was evaluated by disk diffusion assays and minimum inhibitory concentration. The strain Streptomyces sp. So13.3 showed the greatest antibiotic activity (MIC = 15.6 μg/mL) against Gram-positive bacteria and growth reduction of Gram‒negative pathogens. The bioactive fraction in the crude extract was revealed by TLC‒bioautography at Rf = 0.78 with molecular weight between 148 and 624 m/z detected by LC-ESI-MS/MS. The strain So13.3 was taxonomically affiliated as Streptomyces fildesensis. Whole genome sequencing and analysis suggested a 9.47 Mb genome size with 42 predicted biosynthetic gene clusters (BGCs) and 56 putative clusters representing a 22% of total genome content. Interestingly, a large number of them (11 of 42 BGCs and 40 of 56 putative BGCs), did not show similarities with other known BGCs. Our results highlight the potential of the Antarctic Streptomyces strains as a promising source of novel antimicrobials, particularly the strain Streptomyces fildesensis So13.3, which first draft genome is reported in this work.
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Affiliation(s)
- Kattia Núñez-Montero
- Laboratorio de Biología Molecular Aplicada, Centro de Excelencia en Medicina Traslacional, Universidad de La Frontera, Temuco, Chile.,Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile.,Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Claudio Lamilla
- Laboratorio de Biología Molecular Aplicada, Centro de Excelencia en Medicina Traslacional, Universidad de La Frontera, Temuco, Chile.,Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Michel Abanto
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Fumito Maruyama
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile.,Department of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida‒Konoe‒cho, Sakyo‒ku, Kyoto, Japan
| | - Milko A Jorquera
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile.,Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Andrés Santos
- Laboratorio de Biología Molecular Aplicada, Centro de Excelencia en Medicina Traslacional, Universidad de La Frontera, Temuco, Chile.,Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile.,Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, Weymouth, Dorset, DT4 8UB, UK
| | - Jaime Martinez-Urtaza
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, Weymouth, Dorset, DT4 8UB, UK
| | - Leticia Barrientos
- Laboratorio de Biología Molecular Aplicada, Centro de Excelencia en Medicina Traslacional, Universidad de La Frontera, Temuco, Chile. .,Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Temuco, Chile.
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27
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Zhu S, Su Y, Shams S, Feng Y, Tong Y, Zheng G. Lassomycin and lariatin lasso peptides as suitable antibiotics for combating mycobacterial infections: current state of biosynthesis and perspectives for production. Appl Microbiol Biotechnol 2019; 103:3931-3940. [PMID: 30915503 DOI: 10.1007/s00253-019-09771-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/12/2019] [Accepted: 03/12/2019] [Indexed: 11/30/2022]
Abstract
Lasso peptides are ribosomally synthesized and post-translationally modified natural products with a characteristic slipknot-like structure, which confers these peptides remarkable stability and diverse pharmacologically relevant bioactivities. Among all the reported lasso peptides, lassomycin and lariatins are unique lasso peptides that exhibit noticeable anti-tuberculosis (TB) activity. Due to the unique threaded structure and the unusual bactericidal mechanism toward Mycobacterium tuberculosis, these peptides have drawn considerable interest, not only in the field of total synthesis but also in several other fields including biosynthesis, bioengineering, and structure-activity studies. During the past few years, significant progress has been made in understanding the biosynthetic mechanism of these intriguing compounds, which has provided a solid foundation for future work. This review highlights recent achievements in the discovery, structure elucidation, biological activity, and the unique anti-TB mechanism of lasso peptides. Moreover, the discovery of their biosynthetic pathway has laid the foundation for combinatorial biosynthesis of their analogs, which provides new perspectives for the production of novel anti-TB lasso peptides.
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Affiliation(s)
- Shaozhou Zhu
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
| | - Yu Su
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Saira Shams
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yue Feng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yigang Tong
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Guojun Zheng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
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28
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Structural signatures of the class III lasso peptide BI-32169 and the branched-cyclic topoisomers using trapped ion mobility spectrometry–mass spectrometry and tandem mass spectrometry. Anal Bioanal Chem 2019; 411:6287-6296. [DOI: 10.1007/s00216-019-01613-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 12/14/2018] [Accepted: 01/15/2019] [Indexed: 10/27/2022]
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29
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Discovery and characterization of a novel C-terminal peptide carboxyl methyltransferase in a lassomycin-like lasso peptide biosynthetic pathway. Appl Microbiol Biotechnol 2019; 103:2649-2664. [DOI: 10.1007/s00253-019-09645-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/02/2019] [Accepted: 01/10/2019] [Indexed: 12/28/2022]
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30
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Kaweewan I, Hemmi H, Komaki H, Harada S, Kodani S. Isolation and structure determination of a new lasso peptide specialicin based on genome mining. Bioorg Med Chem 2018; 26:6050-6055. [PMID: 30448257 DOI: 10.1016/j.bmc.2018.11.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/05/2018] [Accepted: 11/06/2018] [Indexed: 10/27/2022]
Abstract
Based on genome mining, a new lasso peptide specialicin was isolated from the extract of Streptomyces specialis. The structure of specialicin was established by ESI-MS and NMR analyses to be a lasso peptide with the length of 21 amino acids, containing an isopeptide bond and two disulfide bonds in the molecule. The stereochemistries of the constituent amino acids except for Trp were determined to be L and the stereochemistry of Trp at C-terminus was determined to be D. Three dimensional structure of specialicin was determined based on NOE experimental data, which indicated that specialicin possessed the similar conformational structure with siamycin I. Specialicin showed the antibacterial activity against Micrococcus luteus and the moderate anti-HIV activity against HIV-1 NL4-3. The biosynthetic gene cluster of specialicin was proposed from the genome sequence data of S. specialis.
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Affiliation(s)
- Issara Kaweewan
- Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, 432-8561 Shizuoka, Japan
| | - Hikaru Hemmi
- Food Research Institute, NARO, 2-1-12 Kan-nondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shigeyoshi Harada
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Shinya Kodani
- Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, 432-8561 Shizuoka, Japan; Academic Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529 Japan.
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31
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Kodani S, Hemmi H, Miyake Y, Kaweewan I, Nakagawa H. Heterologous production of a new lasso peptide brevunsin in Sphingomonas subterranea. ACTA ACUST UNITED AC 2018; 45:983-992. [DOI: 10.1007/s10295-018-2077-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/30/2018] [Indexed: 11/29/2022]
Abstract
Abstract
A shuttle vector pHSG396Sp was constructed to perform gene expression using Sphingomonas subterranea as a host. A new lasso peptide biosynthetic gene cluster, derived from Brevundimonas diminuta, was amplified by PCR and integrated to afford a expression vector pHSG396Sp-12697L. The new lasso peptide brevunsin was successfully produced by S. subterranea, harboring the expression vector, with a high production yield (10.2 mg from 1 L culture). The chemical structure of brevunsin was established by NMR and MS/MS experiments. Based on the information obtained from the NOE experiment, the three-dimensional structure of brevunsin was determined, which indicated that brevunsin possessed a typical lasso structure. This expression vector system provides a new heterologous production method for unexplored lasso peptides that are encoded by bacterial genomes.
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Affiliation(s)
- Shinya Kodani
- College of Agriculture Academic Institute, Shizuoka University 836 Ohya, Suruga-ku 422-8529 Shizuoka Japan
- 0000 0001 0656 4913 grid.263536.7 Graduate School of Integrated Science and Technology Shizuoka University 422-8529 Shizuoka Japan
- 0000 0001 0656 4913 grid.263536.7 Graduate School of Science and Technology Shizuoka University 422-8529 Shizuoka Japan
| | - Hikaru Hemmi
- 0000 0001 2222 0432 grid.416835.d Food Research Institute, National Agriculture and Food Research Organization (NARO) 305-8642 Ibaraki Japan
| | - Yuto Miyake
- 0000 0001 0656 4913 grid.263536.7 Graduate School of Integrated Science and Technology Shizuoka University 422-8529 Shizuoka Japan
| | - Issara Kaweewan
- 0000 0001 0656 4913 grid.263536.7 Graduate School of Science and Technology Shizuoka University 422-8529 Shizuoka Japan
| | - Hiroyuki Nakagawa
- 0000 0001 2222 0432 grid.416835.d Food Research Institute, National Agriculture and Food Research Organization (NARO) 305-8642 Ibaraki Japan
- 0000 0001 2222 0432 grid.416835.d Advanced Analysis Center National Agriculture and Food Research Organization (NARO) 305-8642 Ibaraki Japan
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32
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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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33
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Zong C, Cheung-Lee WL, Elashal HE, Raj M, Link AJ. Albusnodin: an acetylated lasso peptide from Streptomyces albus. Chem Commun (Camb) 2018; 54:1339-1342. [PMID: 29350227 DOI: 10.1039/c7cc08620b] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We describe a lasso peptide, albusnodin, that is post-translationally modified with an acetyl group, the first example of a lasso peptide with this modification. Using heterologous expression, we further show that the acetyltransferase colocalized with the albusnodin gene cluster is required for the biosynthesis of this lasso peptide. This type of lasso peptide is widespread in Actinobacteria with 44 examples found in currently sequenced genomes.
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Affiliation(s)
- Chuhan Zong
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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34
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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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35
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Romano M, Fusco G, Choudhury HG, Mehmood S, Robinson CV, Zirah S, Hegemann JD, Lescop E, Marahiel MA, Rebuffat S, De Simone A, Beis K. Structural Basis for Natural Product Selection and Export by Bacterial ABC Transporters. ACS Chem Biol 2018; 13:1598-1609. [PMID: 29757605 DOI: 10.1021/acschembio.8b00226] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacteria under stress produce ribosomally synthesized and post-translationally modified peptides (RiPPs) to target closely related species, such as the lasso peptide microcin J25 (MccJ25). These peptides are also toxic to the producing organisms that utilize dedicated ABC transporters to achieve self-immunity. MccJ25 is exported by the Escherichia coli ABC transporter McjD through a complex mechanism of recognition that has remained elusive. Here, we used biomolecular NMR to study this interaction and identified a region of the toxic peptide that is crucial to its recognition by the ABC transporter. Our study provides evidence that McjD is highly specific to MccJ25 and not to other RiPPs or antibiotics, unlike multidrug ABC transporters. Additionally, we show that MccJ25 is not exported by another natural product ABC transporter. Therefore, we propose that specific interactions between natural product ABC transporters and their substrate provides them with their high degree of specificity. Taken together, these findings suggest that ABC transporters might have acquired structural elements in their binding cavity to recognize and allow promiscuous export of a larger variety of compounds.
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Affiliation(s)
- Maria Romano
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
- Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire OX11 0DE, United Kingdom
| | - Giuliana Fusco
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Hassanul G. Choudhury
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
- Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire OX11 0DE, United Kingdom
| | - Shahid Mehmood
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Séverine Zirah
- Communication Molecules and Adaptation of Microorganisms Laboratory (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier 75005 Paris, France
| | - Julian D. Hegemann
- Department of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Roger Adams Laboratory, Department of Chemistry, University of Illinois at Urbana—Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 1 av. de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Mohamed A. Marahiel
- Department of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Sylvie Rebuffat
- Communication Molecules and Adaptation of Microorganisms Laboratory (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier 75005 Paris, France
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
- Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire OX11 0DE, United Kingdom
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36
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Dit Fouque KJ, Moreno J, Hegemann JD, Zirah S, Rebuffat S, Fernandez-Lima F. Identification of Lasso Peptide Topologies Using Native Nanoelectrospray Ionization-Trapped Ion Mobility Spectrometry–Mass Spectrometry. Anal Chem 2018; 90:5139-5146. [DOI: 10.1021/acs.analchem.7b05230] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Javier Moreno
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Julian D. Hegemann
- Department of Chemistry, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Séverine Zirah
- Muséum National d’Histoire Naturelle, Laboratoire MCAM, Sorbonne Universités, 75005 Paris, France
| | - Sylvie Rebuffat
- Muséum National d’Histoire Naturelle, Laboratoire MCAM, Sorbonne Universités, 75005 Paris, France
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
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37
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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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38
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Jeanne Dit Fouque K, Lavanant H, Zirah S, Hegemann JD, Fage CD, Marahiel MA, Rebuffat S, Afonso C. General rules of fragmentation evidencing lasso structures in CID and ETD. Analyst 2018; 143:1157-1170. [DOI: 10.1039/c7an02052j] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Lasso peptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by a mechanically interlocked structure in which the C-terminal tail of the peptide is threaded and trapped within an N-terminal macrolactam ring.
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Affiliation(s)
| | | | - S. Zirah
- Muséum National d'Histoire Naturelle
- Sorbonne Universités
- Centre national de la Recherche scientifique
- Laboratoire Molécules de Communication et Adaptation des Microorganismes
- UMR 7245 CNRS-MNHN
| | - J. D. Hegemann
- Roger Adams Laboratory
- Department of Chemistry
- University of Illinois at Urbana–Champaign
- Urbana
- USA
| | - C. D. Fage
- Department of Chemistry
- Biochemistry; LOEWE Center for Synthetic Microbiology
- Philipps-University Marburg
- Marburg
- Germany
| | - M. A. Marahiel
- Department of Chemistry
- Biochemistry; LOEWE Center for Synthetic Microbiology
- Philipps-University Marburg
- Marburg
- Germany
| | - S. Rebuffat
- Muséum National d'Histoire Naturelle
- Sorbonne Universités
- Centre national de la Recherche scientifique
- Laboratoire Molécules de Communication et Adaptation des Microorganismes
- UMR 7245 CNRS-MNHN
| | - C. Afonso
- Normandie Univ
- UNIROUEN
- INSA Rouen
- CNRS
- COBRA
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39
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Meyder A, Nittinger E, Lange G, Klein R, Rarey M. Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures. J Chem Inf Model 2017; 57:2437-2447. [PMID: 28981269 DOI: 10.1021/acs.jcim.7b00391] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Macromolecular structures resolved by X-ray crystallography are essential for life science research. While some methods exist to automatically quantify the quality of the electron density fit, none of them is without flaws. Especially the question of how well individual parts like atoms, small fragments, or molecules are supported by electron density is difficult to quantify. While taking experimental uncertainties correctly into account, they do not offer an answer on how reliable an individual atom position is. A rapid quantification of this atomic position reliability would be highly valuable in structure-based molecular design. To overcome this limitation, we introduce the electron density score EDIA for individual atoms and molecular fragments. EDIA assesses rapidly, automatically, and intuitively the fit of individual as well as multiple atoms (EDIAm) into electron density accompanied by an integrated error analysis. The computation is based on the standard 2fo - fc electron density map in combination with the model of the molecular structure. For evaluating partial structures, EDIAm shows significant advantages compared to the real-space R correlation coefficient (RSCC) and the real-space difference density Z score (RSZD) from the molecular modeler's point of view. Thus, EDIA abolishes the time-consuming step of visually inspecting the electron density during structure selection and curation. It supports daily modeling tasks of medicinal and computational chemists and enables a fully automated assembly of large-scale, high-quality structure data sets. Furthermore, EDIA scores can be applied for model validation and method development in computer-aided molecular design. In contrast to measuring the deviation from the structure model by root-mean-squared deviation, EDIA scores allow comparison to the underlying experimental data taking its uncertainty into account.
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Affiliation(s)
- Agnes Meyder
- ZBH-Center for Bioinformatics, Universität Hamburg , Hamburg 20146, Germany
| | - Eva Nittinger
- ZBH-Center for Bioinformatics, Universität Hamburg , Hamburg 20146, Germany
| | | | | | - Matthias Rarey
- ZBH-Center for Bioinformatics, Universität Hamburg , Hamburg 20146, Germany
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40
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Isolation and structure determination of a new lasso peptide subterisin from Sphingomonas subterranea. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.07.064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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41
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Zong C, Wu MJ, Qin JZ, Link AJ. Lasso Peptide Benenodin-1 Is a Thermally Actuated [1]Rotaxane Switch. J Am Chem Soc 2017; 139:10403-10409. [PMID: 28696674 DOI: 10.1021/jacs.7b04830] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mechanically interlocked molecules that change their conformation in response to stimuli have been developed by synthetic chemists as building blocks for molecular machines. Here we describe a natural product, the lasso peptide benenodin-1, which exhibits conformational switching between two distinct threaded conformers upon actuation by heat. We have determined the structures of both conformers and have characterized the kinetics and energetics of the conformational switch. Single amino acid substitutions to benenodin-1 generate peptides that are biased to a single conformer, showing that the switching behavior is potentially an evolvable trait in these peptides. Lasso peptides such as benenodin-1 can be recognized and cleaved by enzymes called lasso peptide isopeptidases. We show that only the native conformer of benenodin-1 is cleaved by its cognate isopeptidase. Thus, thermally induced conformational switching of benenodin-1 may also be relevant to the biological function of these molecules.
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Affiliation(s)
- Chuhan Zong
- Department of Chemistry, ‡Department of Molecular Biology, and §Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States
| | - Michelle J Wu
- Department of Chemistry, ‡Department of Molecular Biology, and §Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States
| | - Jason Z Qin
- Department of Chemistry, ‡Department of Molecular Biology, and §Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States
| | - A James Link
- Department of Chemistry, ‡Department of Molecular Biology, and §Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States
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42
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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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43
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Fouque KJD, Lavanant H, Zirah S, Hegemann JD, Zimmermann M, Marahiel MA, Rebuffat S, Afonso C. Signatures of Mechanically Interlocked Topology of Lasso Peptides by Ion Mobility-Mass Spectrometry: Lessons from a Collection of Representatives. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:315-322. [PMID: 27812920 DOI: 10.1007/s13361-016-1524-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/30/2016] [Accepted: 10/07/2016] [Indexed: 06/06/2023]
Abstract
Lasso peptides are characterized by a mechanically interlocked structure, where the C-terminal tail of the peptide is threaded and trapped within an N-terminal macrolactam ring. Their compact and stable structures have a significant impact on their biological and physical properties and make them highly interesting for drug development. Ion mobility - mass spectrometry (IM-MS) has shown to be effective to discriminate the lasso topology from their corresponding branched-cyclic topoisomers in which the C-terminal tail is unthreaded. In fact, previous comparison of the IM-MS data of the two topologies has yielded three trends that allow differentiation of the lasso fold from the branched-cyclic structure: (1) the low abundance of highly charged ions, (2) the low change in collision cross sections (CCS) with increasing charge state and (3) a narrow ion mobility peak width. In this study, a three-dimensional plot was generated using three indicators based on these three trends: (1) mean charge divided by mass (ζ), (2) relative range of CCS covered by all protonated molecules (ΔΩ/Ω) and (3) mean ion mobility peak width (δΩ). The data were first collected on a set of twenty one lasso peptides and eight branched-cyclic peptides. The indicators were obtained also for eight variants of the well-known lasso peptide MccJ25 obtained by site-directed mutagenesis and further extended to five linear peptides, two macrocyclic peptides and one disulfide constrained peptide. In all cases, a clear clustering was observed between constrained and unconstrained structures, thus providing a new strategy to discriminate mechanically interlocked topologies. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Hélène Lavanant
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000, Rouen, France.
| | - Séverine Zirah
- Muséum National d'Histoire Naturelle, Sorbonne Universités, Centre national de la Recherche scientifique, Laboratoire Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Julian D Hegemann
- Department of Chemistry, Biochemistry; LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany
| | - Marcel Zimmermann
- Department of Chemistry, Biochemistry; LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany
| | - Mohamed A Marahiel
- Department of Chemistry, Biochemistry; LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany
| | - Sylvie Rebuffat
- Muséum National d'Histoire Naturelle, Sorbonne Universités, Centre national de la Recherche scientifique, Laboratoire Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Carlos Afonso
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000, Rouen, France
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44
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Kodani S, Inoue Y, Suzuki M, Dohra H, Suzuki T, Hemmi H, Ohnishi-Kameyama M. Sphaericin, a Lasso Peptide from the Rare ActinomycetePlanomonospora sphaerica. European J Org Chem 2017. [DOI: 10.1002/ejoc.201601334] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shinya Kodani
- Academic Institute; Shizuoka University; 836 Ohya, Suruga-ku 422-8529 Shizuoka Japan
- Graduate School of Integrated Science and Technology; Shizuoka University; 836 Ohya, Suruga-ku 422-8529 Shizuoka Japan
| | - Yuto Inoue
- Graduate School of Integrated Science and Technology; Shizuoka University; 836 Ohya, Suruga-ku 422-8529 Shizuoka Japan
| | - Masahiro Suzuki
- Graduate School of Integrated Science and Technology; Shizuoka University; 836 Ohya, Suruga-ku 422-8529 Shizuoka Japan
| | - Hideo Dohra
- Graduate School of Integrated Science and Technology; Shizuoka University; 836 Ohya, Suruga-ku 422-8529 Shizuoka Japan
- Research Institute of Green Science and Technology; Shizuoka University; 836 Ohya, Suruga-ku 422-8529 Shizuoka Japan
| | - Tomohiro Suzuki
- Center for Bioscience Research and Education; Utsunomiya University; Minemachi 350, Utsunomiya 321-8505 Tochigi Japan
| | - Hikaru Hemmi
- Food Research Institute; National Agriculture and Food Research Organization (NARO); 2-1-12 Kannondai, Tsukuba 305-8642 Ibaraki Japan
| | - Mayumi Ohnishi-Kameyama
- Food Research Institute; National Agriculture and Food Research Organization (NARO); 2-1-12 Kannondai, Tsukuba 305-8642 Ibaraki Japan
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45
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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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46
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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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47
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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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48
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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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49
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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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50
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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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