1
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Guo L, Kuipers OP, Broos J. Facile Halogenation of Antimicrobial Peptides As Demonstrated by Producing Bromotryptophan-Labeled Nisin Variants with Enhanced Antimicrobial Activity. JOURNAL OF NATURAL PRODUCTS 2024; 87:1548-1555. [PMID: 38888620 PMCID: PMC11217935 DOI: 10.1021/acs.jnatprod.4c00118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 05/07/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024]
Abstract
Antimicrobial peptides (AMPs) have raised significant interest, forming a potential new class of antibiotics in the fight against multi-drug-resistant bacteria. Various AMPs are ribosomally synthesized and post-translationally modified peptides (RiPPs). One post-translational modification found in AMPs is the halogenation of Trp residues. This modification has, for example, been shown to be critical for the activity of the potent AMP NAI-107 from Actinoallomurus. Due to the importance of organohalogens, establishing methods for facile and selective halogen atom installation into AMPs is highly desirable. In this study, we introduce an expression system utilizing the food-grade strain Lactococcus lactis, facilitating the efficient incorporation of bromo-Trp (BrTrp) into (modified) peptides, exemplified by the lantibiotic nisin with a single Trp residue or analogue incorporated at position 1. This provides an alternative to the challenges posed by halogenase enzymes, such as poor substrate selectivity. Our method yields expression levels comparable to that of wild-type nisin, while BrTrp incorporation does not interfere with the post-translational modifications of nisin (dehydration and cyclization). One brominated nisin variant exhibits a 2-fold improvement in antimicrobial activity against two tested pathogens, including a WHO priority pathogen, while maintaining the same lipid II binding and bactericidal activity as wild-type nisin. The work presented here demonstrates the potential of this methodology for peptide halogenation, offering a new avenue for the development of diverse antimicrobial products labeled with BrTrp.
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Affiliation(s)
- Longcheng Guo
- Department of Molecular Genetics,
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747, AG, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics,
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747, AG, The Netherlands
| | - Jaap Broos
- Department of Molecular Genetics,
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747, AG, The Netherlands
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2
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Ancajas CMF, Oyedele AS, Butt CM, Walker AS. Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products. Nat Prod Rep 2024. [PMID: 38912779 DOI: 10.1039/d4np00009a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Time span in literature: 1985-early 2024Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties. Choosing what modifications to make requires an understanding of the compound's structure-activity relationships. Use of structure-activity relationships is commonplace and essential in medicinal chemistry campaigns applied to human-designed synthetic compounds. Structure-activity relationships have also been used to improve the properties of natural products, but several challenges still limit these efforts. Here, we review methods for studying the structure-activity relationships of natural products and their limitations. Specifically, we will discuss how synthesis, including total synthesis, late-stage derivatization, chemoenzymatic synthetic pathways, and engineering and genome mining of biosynthetic pathways can be used to produce natural product analogs and discuss the challenges of each of these approaches. Finally, we will discuss computational methods including machine learning methods for analyzing the relationship between biosynthetic genes and product activity, computer aided drug design techniques, and interpretable artificial intelligence approaches towards elucidating structure-activity relationships from models trained to predict bioactivity from chemical structure. Our focus will be on these latter topics as their applications for natural products have not been extensively reviewed. We suggest that these methods are all complementary to each other, and that only collaborative efforts using a combination of these techniques will result in a full understanding of the structure-activity relationships of natural products.
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Affiliation(s)
| | | | - Caitlin M Butt
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
| | - Allison S Walker
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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3
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Le T, Zhang D, Martini RM, Biswas S, van der Donk WA. Use of a head-to-tail peptide cyclase to prepare hybrid RiPPs. Chem Commun (Camb) 2024; 60:6508-6511. [PMID: 38833296 PMCID: PMC11189026 DOI: 10.1039/d3cc04919a] [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: 10/04/2023] [Accepted: 04/25/2024] [Indexed: 06/06/2024]
Abstract
Cyclotides and lanthipeptides are cyclic peptide natural products with promising bioengineering potential. No peptides have been isolated that contain both structural motifs defining these two families, an N-to-C cyclised backbone and lanthionine linkages. We combined their biosynthetic machineries to produce hybrid structures that possess improved activity or stability, demonstrate how the AEP-1 plant cyclase can be utilised to complete the maturation of the sactipeptide subtilosin A, and present head-to-tail cyclisation of the glycocin sublancin. These studies show the plasticity of AEP-1 and its utilisation alongside other post-translational modifications.
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Affiliation(s)
- Tung Le
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Dongtianyu Zhang
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Rachel M Martini
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Subhanip Biswas
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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4
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Guo L, Stoffels K, Broos J, Kuipers OP. Engineering hybrid lantibiotics yields the highly stable and bacteriocidal peptide cerocin V. Microbiol Res 2024; 282:127640. [PMID: 38350171 DOI: 10.1016/j.micres.2024.127640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
Antimicrobial peptides (AMPs) show promise as alternatives to traditional antibiotics for treating drug-resistant infections. Their adaptability and diverse sequence possibilities allow for rational design by modulating physicochemical determinants to achieve desired biological properties, transforming them into peptides for potential new therapies. Nisin, one of the best-studied AMPs, is believed to have potential to be used as a therapeutic, particularly against antibiotic-resistant bacteria. However, its instability in physiological conditions limits its use in clinical applications and pharmaceutical development. Exploration of new natural variants of nisin has uncovered diverse properties using different domains. Shuffling peptide modules can fine-tune the chemical properties of these molecules, potentially enhancing stability while maintaining or improving antimicrobial activity. In this study, hybrid AMPs were created by combining domains from three unique nisin variants, i.e. nisin A, cesin and rombocin, leading to the identification of a promising variant, named cerocin A, which harbours only 25 amino acids compared to the typical 31-35 amino acid length of nisin. Cerocin A demonstrates potent antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA), approaching that of nisin itself. Cerocin A's mode of action involves a dual mechanism through the combination of two domains, consisting of a small ring/domain (6 amino acids) from the C-terminal end of rombocin attached to the preceding peptide of cesin, changing it from a bacteriostatic to a bactericidal peptide. Further mutation studies identified a new variant, cerocin V, with significantly improved resistance against trypsin degradation, while maintaining high potency. Importantly, cerocin V showed no undesired toxic effects on human red blood cells and remained stable in human plasma. In conclusion, we demonstrate that peptide construction using domain engineering is an effective strategy for manipulating both biological and physicochemical aspects, leading to the creation of novel bioactive molecules with desired properties. These constructs are appealing candidates for further optimization and development as novel antibiotics.
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Affiliation(s)
- Longcheng Guo
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Konstantin Stoffels
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Jaap Broos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
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5
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Han SW, Won HS. Advancements in the Application of Ribosomally Synthesized and Post-Translationally Modified Peptides (RiPPs). Biomolecules 2024; 14:479. [PMID: 38672495 PMCID: PMC11048544 DOI: 10.3390/biom14040479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent a significant potential for novel therapeutic applications because of their bioactive properties, stability, and specificity. RiPPs are synthesized on ribosomes, followed by intricate post-translational modifications (PTMs), crucial for their diverse structures and functions. PTMs, such as cyclization, methylation, and proteolysis, play crucial roles in enhancing RiPP stability and bioactivity. Advances in synthetic biology and bioinformatics have significantly advanced the field, introducing new methods for RiPP production and engineering. These methods encompass strategies for heterologous expression, genetic refactoring, and exploiting the substrate tolerance of tailoring enzymes to create novel RiPP analogs with improved or entirely new functions. Furthermore, the introduction and implementation of cutting-edge screening methods, including mRNA display, surface display, and two-hybrid systems, have expedited the identification of RiPPs with significant pharmaceutical potential. This comprehensive review not only discusses the current advancements in RiPP research but also the promising opportunities that leveraging these bioactive peptides for therapeutic applications presents, illustrating the synergy between traditional biochemistry and contemporary synthetic biology and genetic engineering approaches.
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Affiliation(s)
- Sang-Woo Han
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical & Health Science, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea;
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical & Health Science, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea;
- BK21 Project Team, Department of Applied Life Science, Graduate School, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea
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6
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Nguyen DT, Mitchell DA, van der Donk WA. Genome Mining for New Enzyme Chemistry. ACS Catal 2024; 14:4536-4553. [PMID: 38601780 PMCID: PMC11002830 DOI: 10.1021/acscatal.3c06322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 04/12/2024]
Abstract
A revolution in the field of biocatalysis has enabled scalable access to compounds of high societal values using enzymes. The construction of biocatalytic routes relies on the reservoir of available enzymatic transformations. A review of uncharacterized proteins predicted from genomic sequencing projects shows that a treasure trove of enzyme chemistry awaits to be uncovered. This Review highlights enzymatic transformations discovered through various genome mining methods and showcases their potential future applications in biocatalysis.
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Affiliation(s)
- Dinh T. Nguyen
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute at the University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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7
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Guo L, Stoffels K, Broos J, Kuipers OP. Altering Specificity and Enhancing Stability of the Antimicrobial Peptides Nisin and Rombocin through Dehydrated Amino Acid Residue Engineering. Peptides 2024; 174:171152. [PMID: 38220092 DOI: 10.1016/j.peptides.2024.171152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/16/2024]
Abstract
Nisin serves as the prototype within the lantibiotic group of antimicrobial peptides, exhibiting a broad-spectrum inhibition against Gram-positive bacteria, including important food-borne pathogens and clinically relevant antibiotic-resistant strains. The gene-encoded nature of nisin allows for gene-based bioengineering, enabling the generation of novel derivatives. It has been demonstrated that nisin mutants can be produced with improved functional properties. Here, we particularly focus on the uncommon amino acid residues dehydroalanine (Dha) and dehydrobutyrin (Dhb), whose functions are not yet fully elucidated. Prior to this study, we developed a new expression system that utilizes the nisin modification machinery NisBTC to advance expression, resulting in enhanced peptide dehydration efficiency. Through this approach, we discovered that the dehydrated amino acid Dhb at position 18 in the peptide rombocin, a short variant of nisin, displayed four times higher activity compared to the non-dehydrated peptide against the strain Lactococcus lactis. Furthermore, we observed that in the peptides nisin and rombocin, the dehydrated amino acid Dha at residue positon 18 exhibited superior activity compared to the dehydrated amino acid Dhb. Upon purifying the wild-type nisin and its variant nisinG18/Dha to homogeneity, the minimum inhibitory concentration (MIC) indicated that the variant exhibited activity similar to that of wild-type nisin in inhibiting the growth of Bacillus cereus but showed twice the MIC values against the other four tested Gram-positive strains. Further stability tests demonstrated that the dehydrated peptide exhibited properties similar to wild-type nisin under different temperatures but displayed higher resistance to proteolytic enzymes compared to wild-type nisin.
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Affiliation(s)
- Longcheng Guo
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Konstantin Stoffels
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Jaap Broos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
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8
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Guo L, Wambui J, Wang C, Broos J, Stephan R, Kuipers OP. Rombocin, a Short Stable Natural Nisin Variant, Displays Selective Antimicrobial Activity against Listeria monocytogenes and Employs a Dual Mode of Action to Kill Target Bacterial Strains. ACS Synth Biol 2024; 13:370-383. [PMID: 38194633 PMCID: PMC10804407 DOI: 10.1021/acssynbio.3c00612] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Nisin, with its unique mode of action and potent antimicrobial activity, serves as a remarkable inspiration for the design of novel antibiotics. However, peptides possess inherent weaknesses, particularly their susceptibility to proteolytic degradation, such as by trypsin, which limits their broader applications. This led us to speculate that natural variants of nisin produced by underexplored bacterial species can potentially overcome these limitations. We carried out genome mining of two Romboutsia sedimentorum strains, RC001 and RC002, leading to the discovery of rombocin A, which is a 25 amino acid residue short nisin variant that is predicted to have only four macrocycles compared to the known 31-35 amino acids long nisin variants with five macrocycles. Using the nisin-controlled expression system, we heterologously expressed fully modified and functional rombocin A in Lactococcus lactis and demonstrated its selective antimicrobial activity against Listeria monocytogenes. Rombocin A uses a dual mode of action involving lipid II binding activity and dissipation of the membrane potential to kill target bacteria. Stability tests confirmed its high stability at different pH values, temperatures, and in particular, against enzymatic degradation. With its gene-encoded characteristic, rombocin A is amenable to bioengineering to generate novel derivatives. Further mutation studies led to the identification of rombocin K, a mutant with enhanced bioactivity against L. monocytogenes. Our findings suggest that rombocin A and its bioengineered variant, rombocin K, are promising candidates for development as food preservatives or antibiotics against L. monocytogenes.
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Affiliation(s)
- Longcheng Guo
- Department
of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Joseph Wambui
- Institute
for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Chenhui Wang
- Department
of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Jaap Broos
- Department
of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Roger Stephan
- Institute
for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Oscar P. Kuipers
- Department
of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Groningen 9747 AG, The Netherlands
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9
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Pourmasoumi F, Hengoju S, Beck K, Stephan P, Klopfleisch L, Hoernke M, Rosenbaum MA, Kries H. Analysing Megasynthetase Mutants at High Throughput Using Droplet Microfluidics. Chembiochem 2023; 24:e202300680. [PMID: 37804133 DOI: 10.1002/cbic.202300680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/08/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are giant enzymatic assembly lines that deliver many pharmaceutically valuable natural products, including antibiotics. As the search for new antibiotics motivates attempts to redesign nonribosomal metabolic pathways, more robust and rapid sorting and screening platforms are needed. Here, we establish a microfluidic platform that reliably detects production of the model nonribosomal peptide gramicidin S. The detection is based on calcein-filled sensor liposomes yielding increased fluorescence upon permeabilization. From a library of NRPS mutants, the sorting platform enriches the gramicidin S producer 14.5-fold, decreases internal stop codons 250-fold, and generates enrichment factors correlating with enzyme activity. Screening for NRPS activity with a reliable non-binary sensor will enable more sophisticated structure-activity studies and new engineering applications in the future.
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Affiliation(s)
- Farzaneh Pourmasoumi
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sundar Hengoju
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Katharina Beck
- Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität, Hermann-Herder-Str. 9, 79104, Freiburg i. Br., Germany
| | - Philipp Stephan
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Lukas Klopfleisch
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Maria Hoernke
- Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität, Hermann-Herder-Str. 9, 79104, Freiburg i. Br., Germany
- Faculty of Chemistry, Martin-Luther-Universität, Von-Danckelmann-Platz 4, 06108, Halle (S.), Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Department of Chemistry, University of Bayreuth, Universitätsstrasse 30, 95440, Bayreuth, Germany
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10
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Chang JS, Vinogradov AA, Zhang Y, Goto Y, Suga H. Deep Learning-Driven Library Design for the De Novo Discovery of Bioactive Thiopeptides. ACS CENTRAL SCIENCE 2023; 9:2150-2160. [PMID: 38033794 PMCID: PMC10683472 DOI: 10.1021/acscentsci.3c00957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/27/2023] [Accepted: 10/19/2023] [Indexed: 12/02/2023]
Abstract
Broad substrate tolerance of ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic enzymes has allowed numerous strategies for RiPP engineering. However, despite relaxed specificities, exact substrate preferences of RiPP enzymes are often difficult to pinpoint. Thus, when designing combinatorial libraries of RiPP precursors, balancing the compound diversity with the substrate fitness can be challenging. Here, we employed a deep learning model to streamline the design of mRNA display libraries. Using an in vitro reconstituted thiopeptide biosynthesis platform, we performed mRNA display-based profiling of substrate fitness for the biosynthetic pathway involving five enzymes to train an accurate deep learning model. We then utilized the model to design optimal mRNA libraries and demonstrated their utility in affinity selections against IRAK4 kinase and the TLR10 cell surface receptor. The selections led to the discovery of potent thiopeptide ligands against both target proteins (KD up to 1.3 nM for the best compound against IRAK4 and 300 nM for TLR10). The IRAK4-targeting compounds also inhibited the kinase at single-digit μM concentrations in vitro, exhibited efficient internalization into HEK293H cells, and suppressed NF-kB-mediated signaling in cells. Altogether, the developed approach streamlines the discovery of pseudonatural RiPPs with de novo designed biological activities and favorable pharmacological properties.
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Affiliation(s)
- Jun Shi Chang
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Alexander A. Vinogradov
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yue Zhang
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuki Goto
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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11
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Guo L, Wang C, Broos J, Kuipers OP. Lipidated variants of the antimicrobial peptide nisin produced via incorporation of methionine analogs for click chemistry show improved bioactivity. J Biol Chem 2023; 299:104845. [PMID: 37209826 PMCID: PMC10404616 DOI: 10.1016/j.jbc.2023.104845] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/10/2023] [Accepted: 05/14/2023] [Indexed: 05/22/2023] Open
Abstract
The increase in antibiotic resistance calls for accelerated molecular engineering strategies to diversify natural products for drug discovery. The incorporation of non-canonical amino acids (ncAAs) is an elegant strategy for this purpose, offering a diverse pool of building blocks to introduce desired properties into antimicrobial lanthipeptides. We here report an expression system using Lactococcus lactis as a host for non-canonical amino acid incorporation with high efficiency and yield. We show that incorporating the more hydrophobic analog ethionine (instead of methionine) into nisin improves its bioactivity against several Gram-positive strains we tested. New-to-nature variants were further created by click chemistry. By azidohomoalanine (Aha) incorporation and subsequent click chemistry, we obtained lipidated variants at different positions in nisin or in truncated nisin variants. Some of them show improved bioactivity and specificity against several pathogenic bacterial strains. These results highlight the ability of this methodology for lanthipeptide multi-site lipidation, to create new-to-nature antimicrobial products with diverse features, and extend the toolbox for (lanthi)peptide drug improvement and discovery.
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Affiliation(s)
- Longcheng Guo
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Chenhui Wang
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Jaap Broos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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12
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Mi X, Desormeaux EK, Le TT, van der Donk WA, Shukla D. Sequence controlled secondary structure is important for the site-selectivity of lanthipeptide cyclization. Chem Sci 2023; 14:6904-6914. [PMID: 37389248 PMCID: PMC10306099 DOI: 10.1039/d2sc06546k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/08/2023] [Indexed: 07/01/2023] Open
Abstract
Lanthipeptides are ribosomally synthesized and post-translationally modified peptides that are generated from precursor peptides through a dehydration and cyclization process. ProcM, a class II lanthipeptide synthetase, demonstrates high substrate tolerance. It is enigmatic that a single enzyme can catalyze the cyclization process of many substrates with high fidelity. Previous studies suggested that the site-selectivity of lanthionine formation is determined by substrate sequence rather than by the enzyme. However, exactly how substrate sequence contributes to site-selective lanthipeptide biosynthesis is not clear. In this study, we performed molecular dynamic simulations for ProcA3.3 variants to explore how the predicted solution structure of the substrate without enzyme correlates to the final product formation. Our simulation results support a model in which the secondary structure of the core peptide is important for the final product's ring pattern for the substrates investigated. We also demonstrate that the dehydration step in the biosynthesis pathway does not influence the site-selectivity of ring formation. In addition, we performed simulation for ProcA1.1 and 2.8, which are well-suited candidates to investigate the connection between order of ring formation and solution structure. Simulation results indicate that in both cases, C-terminal ring formation is more likely which was supported by experimental results. Our findings indicate that the substrate sequence and its solution structure can be used to predict the site-selectivity and order of ring formation, and that secondary structure is a crucial factor influencing the site-selectivity. Taken together, these findings will facilitate our understanding of the lanthipeptide biosynthetic mechanism and accelerate bioengineering efforts for lanthipeptide-derived products.
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Affiliation(s)
- Xuenan Mi
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Emily K Desormeaux
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Tung T Le
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Diwakar Shukla
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
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13
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Field D, Fernandez de Ullivarri M, Ross RP, Hill C. After a century of nisin research - where are we now? FEMS Microbiol Rev 2023; 47:fuad023. [PMID: 37300874 PMCID: PMC10257480 DOI: 10.1093/femsre/fuad023] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/13/2023] Open
Abstract
It is almost a century since nisin was discovered in fermented milk cultures, coincidentally in the same year that penicillin was first described. Over the last 100 years this small, highly modified pentacyclic peptide has not only found success in the food industry as a preservative but has also served as the paradigm for our understanding of the genetic organization, expression, and regulation of genes involved in lantibiotic biosynthesis-one of the few cases of extensive post-translation modification in prokaryotes. Recent developments in understanding the complex biosynthesis of nisin have shed light on the cellular location of the modification and transport machinery and the co-ordinated series of spatio-temporal events required to produce active nisin and provide resistance and immunity. The continued unearthing of new natural variants from within human and animal gastrointestinal tracts has sparked interest in the potential application of nisin to influence the microbiome, given the growing recognition of the role the gastrointestinal microbiota plays in health and disease. Moreover, interdisciplinary approaches have taken advantage of biotechnological advancements to bioengineer nisin to produce novel variants and expand nisin functionality for applications in the biomedical field. This review will discuss the latest progress in these aspects of nisin research.
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Affiliation(s)
- Des Field
- APC Microbiome Ireland, University College Cork,Western Road, Cork T12 YN60, Ireland
- School of Microbiology, University College Cork, College Road, Cork T12 YT20, Ireland
| | | | - R Paul Ross
- APC Microbiome Ireland, University College Cork,Western Road, Cork T12 YN60, Ireland
- School of Microbiology, University College Cork, College Road, Cork T12 YT20, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork,Western Road, Cork T12 YN60, Ireland
- School of Microbiology, University College Cork, College Road, Cork T12 YT20, Ireland
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14
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Vagstad AL. Engineering ribosomally synthesized and posttranslationally modified peptides as new antibiotics. Curr Opin Biotechnol 2023; 80:102891. [PMID: 36702077 DOI: 10.1016/j.copbio.2023.102891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 01/25/2023]
Abstract
The rise of antimicrobial resistance is an urgent public health threat demanding the invention of new drugs to combat infections. Naturally sourced nonribosomal peptides (NRPs) have a long history as antimicrobial drugs. Through recent advances in genome mining and engineering technologies, their ribosomally synthesized and posttranslationally modified peptide (RiPP) counterparts are poised to further contribute to the arsenal of anti-infectives. As natural products from diverse organisms involved in interspecies competition, many RiPPs already possess antimicrobial activities that can be further optimized as drug candidates. Owing to the mutability of precursor protein genes that encode their core structures and the availability of diverse posttranslational modification (PTM) enzymes with broad substrate tolerances, RiPP systems are well suited to engineer complex peptides with desired functions.
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Affiliation(s)
- Anna L Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
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15
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Ren H, Dommaraju SR, Huang C, Cui H, Pan Y, Nesic M, Zhu L, Sarlah D, Mitchell DA, Zhao H. Genome mining unveils a class of ribosomal peptides with two amino termini. Nat Commun 2023; 14:1624. [PMID: 36959188 PMCID: PMC10036551 DOI: 10.1038/s41467-023-37287-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 03/09/2023] [Indexed: 03/25/2023] Open
Abstract
The era of inexpensive genome sequencing and improved bioinformatics tools has reenergized the study of natural products, including the ribosomally synthesized and post-translationally modified peptides (RiPPs). In recent years, RiPP discovery has challenged preconceptions about the scope of post-translational modification chemistry, but genome mining of new RiPP classes remains an unsolved challenge. Here, we report a RiPP class defined by an unusual (S)-N2,N2-dimethyl-1,2-propanediamine (Dmp)-modified C-terminus, which we term the daptides. Nearly 500 daptide biosynthetic gene clusters (BGCs) were identified by analyzing the RiPP Recognition Element (RRE), a common substrate-binding domain found in half of prokaryotic RiPP classes. A representative daptide BGC from Microbacterium paraoxydans DSM 15019 was selected for experimental characterization. Derived from a C-terminal threonine residue, the class-defining Dmp is installed over three steps by an oxidative decarboxylase, aminotransferase, and methyltransferase. Daptides uniquely harbor two positively charged termini, and thus we suspect this modification could aid in membrane targeting, as corroborated by hemolysis assays. Our studies further show that the oxidative decarboxylation step requires a functionally unannotated accessory protein. Fused to the C-terminus of the accessory protein is an RRE domain, which delivers the unmodified substrate peptide to the oxidative decarboxylase. This discovery of a class-defining post-translational modification in RiPPs may serve as a prototype for unveiling additional RiPP classes through genome mining.
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Affiliation(s)
- Hengqian Ren
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shravan R Dommaraju
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chunshuai Huang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Haiyang Cui
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yuwei Pan
- Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Marko Nesic
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lingyang Zhu
- School of Chemical Sciences, NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - David Sarlah
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Douglas A Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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16
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Thokkadam A, Do T, Ran X, Brynildsen MP, Yang ZJ, Link AJ. High-Throughput Screen Reveals the Structure-Activity Relationship of the Antimicrobial Lasso Peptide Ubonodin. ACS CENTRAL SCIENCE 2023; 9:540-550. [PMID: 36968541 PMCID: PMC10037499 DOI: 10.1021/acscentsci.2c01487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Indexed: 06/16/2023]
Abstract
The Burkholderia cepacia complex (Bcc) is a group of bacteria including opportunistic human pathogens. Immunocompromised individuals and cystic fibrosis patients are especially vulnerable to serious infections by these bacteria, motivating the search for compounds with antimicrobial activity against the Bcc. Ubonodin is a lasso peptide with promising activity against Bcc species, working by inhibiting RNA polymerase in susceptible bacteria. We constructed a library of over 90 000 ubonodin variants with 2 amino acid substitutions and used a high-throughput screen and next-generation sequencing to examine the fitness of the entire library, generating the most comprehensive data set on lasso peptide activity so far. This screen revealed information regarding the structure-activity relationship of ubonodin over a large sequence space. Remarkably, the screen identified one variant with not only improved activity compared to wild-type ubonodin but also a submicromolar minimum inhibitory concentration (MIC) against a clinical isolate of the Bcc member Burkholderia cenocepacia. Ubonodin and several of the variants identified in this study had lower MICs against certain Bcc strains than those of many clinically approved antibiotics. Finally, the large library size enabled us to develop DeepLasso, a deep learning model that can predict the RNAP inhibitory activity of an ubonodin variant.
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Affiliation(s)
- Alina Thokkadam
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Truc Do
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Xinchun Ran
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Mark P. Brynildsen
- 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
| | - Zhongyue J. Yang
- Department
of Chemistry, 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
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37235, 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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17
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Ren H, Dommaraju SR, Huang C, Cui H, Pan Y, Nesic M, Zhu L, Sarlah D, Mitchell DA, Zhao H. Genome mining unveils a class of ribosomal peptides with two amino termini. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531785. [PMID: 36945508 PMCID: PMC10028931 DOI: 10.1101/2023.03.08.531785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
The era of inexpensive genome sequencing and improved bioinformatics tools has reenergized the study of natural products, including the ribosomally synthesized and post-translationally modified peptides (RiPPs). In recent years, RiPP discovery has challenged preconceptions about the scope of post-translational modification chemistry, but genome mining of new RiPP classes remains an unsolved challenge. Here, we report a RiPP class defined by an unusual ( S )- N 2 , N 2 -dimethyl-1,2-propanediamine (Dmp)-modified C -terminus, which we term the daptides. Nearly 500 daptide biosynthetic gene clusters (BGCs) were identified by analyzing the RiPP Recognition Element (RRE), a common substrate-binding domain found in half of prokaryotic RiPP classes. A representative daptide BGC from Microbacterium paraoxydans DSM 15019 was selected for experimental characterization. Derived from a C -terminal threonine residue, the class-defining Dmp is installed over three steps by an oxidative decarboxylase, aminotransferase, and methyltransferase. Daptides uniquely harbor two positively charged termini, and thus we suspect this modification could aid in membrane targeting, as corroborated by hemolysis assays. Our studies further show that the oxidative decarboxylation step requires a functionally unannotated accessory protein. Fused to the C -terminus of the accessory protein is an RRE domain, which delivers the unmodified substrate peptide to the oxidative decarboxylase. This discovery of a class-defining post-translational modification in RiPPs may serve as a prototype for unveiling additional RiPP classes through genome mining.
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18
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Zhong G, Wang ZJ, Yan F, Zhang Y, Huo L. Recent Advances in Discovery, Bioengineering, and Bioactivity-Evaluation of Ribosomally Synthesized and Post-translationally Modified Peptides. ACS BIO & MED CHEM AU 2023; 3:1-31. [PMID: 37101606 PMCID: PMC10125368 DOI: 10.1021/acsbiomedchemau.2c00062] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 04/28/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are of increasing interest in natural products as well as drug discovery. This empowers not only the unique chemical structures and topologies in natural products but also the excellent bioactivities such as antibacteria, antifungi, antiviruses, and so on. Advances in genomics, bioinformatics, and chemical analytics have promoted the exponential increase of RiPPs as well as the evaluation of biological activities thereof. Furthermore, benefiting from their relatively simple and conserved biosynthetic logic, RiPPs are prone to be engineered to obtain diverse analogues that exhibit distinct physiological activities and are difficult to synthesize. This Review aims to systematically address the variety of biological activities and/or the mode of mechanisms of novel RiPPs discovered in the past decade, albeit the characteristics of selective structures and biosynthetic mechanisms are briefly covered as well. Almost one-half of the cases are involved in anti-Gram-positive bacteria. Meanwhile, an increasing number of RiPPs related to anti-Gram-negative bacteria, antitumor, antivirus, etc., are also discussed in detail. Last but not least, we sum up some disciplines of the RiPPs' biological activities to guide genome mining as well as drug discovery and optimization in the future.
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Affiliation(s)
- Guannan Zhong
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute, Shandong University, Suzhou, Jiangsu 215123, P. R. China
| | - Zong-Jie Wang
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Fu Yan
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- CAS
Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Liujie Huo
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute, Shandong University, Suzhou, Jiangsu 215123, P. R. China
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19
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Do T, Link AJ. Protein Engineering in Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs). Biochemistry 2023; 62:201-209. [PMID: 35006671 PMCID: PMC9454058 DOI: 10.1021/acs.biochem.1c00714] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) make up a rapidly growing superfamily of natural products. RiPPs exhibit an extraordinary range of structures, but they all begin as gene-encoded precursor peptides that are linear chains of amino acids produced by ribosomes. Given the gene-encoded nature of RiPP precursor peptides, the toolbox of protein engineering can be directly applied to these precursors. This Perspective will discuss examples of site-directed mutagenesis, noncanonical amino acid mutagenesis, and the construction and screening of combinatorial libraries as applied to RiPPs. These studies have led to important insights into the biosynthesis and bioactivity of RiPPs and the reengineering of RiPPs for entirely new functions.
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Affiliation(s)
- Truc Do
- Department of Chemical and Biological Engineering, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
| | - A. James Link
- Department of Chemical and Biological Engineering, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
- Department of Chemistry, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
- Department of Molecular Biology, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
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20
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Mordhorst S, Ruijne F, Vagstad AL, Kuipers OP, Piel J. Emulating nonribosomal peptides with ribosomal biosynthetic strategies. RSC Chem Biol 2023; 4:7-36. [PMID: 36685251 PMCID: PMC9811515 DOI: 10.1039/d2cb00169a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Peptide natural products are important lead structures for human drugs and many nonribosomal peptides possess antibiotic activity. This makes them interesting targets for engineering approaches to generate peptide analogues with, for example, increased bioactivities. Nonribosomal peptides are produced by huge mega-enzyme complexes in an assembly-line like manner, and hence, these biosynthetic pathways are challenging to engineer. In the past decade, more and more structural features thought to be unique to nonribosomal peptides were found in ribosomally synthesised and posttranslationally modified peptides as well. These streamlined ribosomal pathways with modifying enzymes that are often promiscuous and with gene-encoded precursor proteins that can be modified easily, offer several advantages to produce designer peptides. This review aims to provide an overview of recent progress in this emerging research area by comparing structural features common to both nonribosomal and ribosomally synthesised and posttranslationally modified peptides in the first part and highlighting synthetic biology strategies for emulating nonribosomal peptides by ribosomal pathway engineering in the second part.
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Affiliation(s)
- Silja Mordhorst
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Fleur Ruijne
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, 9747 AG Groningen The Netherlands
| | - Anna L Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, 9747 AG Groningen The Netherlands
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
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21
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Guo E, Fu L, Fang X, Xie W, Li K, Zhang Z, Hong Z, Si T. Robotic Construction and Screening of Lanthipeptide Variant Libraries in Escherichia coli. ACS Synth Biol 2022; 11:3900-3911. [PMID: 36379012 DOI: 10.1021/acssynbio.2c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lanthipeptides are a major class of ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by thioether cross-links called lanthionine (Lan) and methyllanthionine (MeLan). Previously, we developed a method to produce mature lanthipeptides in recombinant Escherichia coli, but manual steps hinder large-scale analogue screening. Here we devised an automated workflow for creating and screening variant libraries of haloduracin, a two-component class II lanthipeptide. An integrated work cell of a synthetic biology foundry was programmed to robotically execute DNA library construction, host transformation, peptide production, mass spectrometry analysis, and activity screening by agar diffusion assay. For recombinantly produced Halα peptides, the sequence-activity relationship of 380 single-residue variants and >1300 triple-residue combinatorial variants were rapidly analyzed in microplates within weeks. The peptide expression levels in E. coli were also visualized via robotic creation and analysis of GFP-lanthipeptide fusions for select peptide mutants. Following shake-flask fermentation and purification, one Halα mutant was confirmed with enhanced specific antimicrobial activity relative to the wild-type peptide. Overall, this approach may be generally applicable for the high-throughput characterization and engineering of RiPP natural products.
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Affiliation(s)
- Erpeng Guo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,BGI-Shenzhen, Shenzhen 518083, China
| | - Lihao Fu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoting Fang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wenhao Xie
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Keyi Li
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhiyu Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhilai Hong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,BGI-Shenzhen, Shenzhen 518083, China
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,BGI-Shenzhen, Shenzhen 518083, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Shenzhen 518055, China
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22
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Arias-Orozco P, Yi Y, Ruijne F, Cebrián R, Kuipers OP. Investigating the Specificity of the Dehydration and Cyclization Reactions in Engineered Lanthipeptides by Synechococcal SyncM. ACS Synth Biol 2022; 12:164-177. [PMID: 36520855 PMCID: PMC9872173 DOI: 10.1021/acssynbio.2c00455] [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] [Indexed: 12/23/2022]
Abstract
ProcM-like enzymes are class II promiscuous lanthipeptide synthetases that are an attractive tool in synthetic biology for producing lanthipeptides with biotechnological or clinically desired properties. SyncM is a recently described modification enzyme from this family used to develop a versatile expression platform for engineering lanthipeptides. Most remarkably, SyncM can modify up to 79 SyncA substrates in a single strain. Six SyncAs were previously characterized from this pool of substrates. They showed particular characteristics, such as the presence of one or two lanthionine rings, different flanking residues influencing ring formation, and different ring directions, demonstrating the relaxed specificity of SyncM toward its precursor peptides. To gain a deeper understanding of the potential of SyncM as a biosynthetic tool, we further explored the enzyme's capabilities and limits in dehydration and ring formation. We used different SyncA scaffolds for peptide engineering, including changes in the ring's directionality (relative position of Ser/Thr to Cys in the peptide) and size. We further aimed to rationally design mimetics of cyclic antimicrobials and introduce macrocycles in prochlorosin-related and nonrelated substrates. This study highlights the largest lanthionine ring with 15 amino acids (ring-forming residues included) described to date. Taking advantage of the amino acid substrate tolerance of SyncM, we designed the first single-SyncA-based antimicrobial. The insights gained from this work will aid future bioengineering studies. Additionally, it broadens SyncM's application scope for introducing macrocycles in other bioactive molecules.
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Affiliation(s)
- Patricia Arias-Orozco
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands
| | - Yunhai Yi
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands
| | - Fleur Ruijne
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands
| | - Rubén Cebrián
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands,Department
of Clinical Microbiology, Instituto de Investigación Biosanitaria,
ibs. GRANADA, San Cecilio University Hospital, Av. De la Innovación s/n, 18016 Granada, Spain
| | - Oscar P. Kuipers
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands,
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23
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Suryaletha K, Savithri AV, Nayar SA, Asokan S, Rajeswary D, Thomas S. Demystifying Bacteriocins of Human Microbiota by Genome Guided Prospects: An Impetus to Rekindle the Antimicrobial Research. Curr Protein Pept Sci 2022; 23:811-822. [PMID: 36278460 DOI: 10.2174/1389203724666221019111515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/14/2022] [Accepted: 09/06/2022] [Indexed: 11/07/2022]
Abstract
The human microbiome is a reservoir of potential bacteriocins that can counteract multidrug resistant bacterial pathogens. Unlike antibiotics, bacteriocins selectively inhibit a spectrum of competent bacteria and are said to safeguard gut commensals, reducing the chance of dysbiosis. Bacteriocinogenic probiotics or bacteriocins of human origin will be more pertinent in human physiological conditions for therapeutic applications to act against invading pathogens. Recent advancement in the omics approach enables the mining of diverse and novel bacteriocins by identifying biosynthetic gene clusters from the human microbial genome, pangenome or shotgun metagenome, which is a breakthrough in the discovery line of novel bacteriocins. This review summarizes the most recent trends and therapeutic potential of bacteriocins of human microbial origin, the advancement in the in silico algorithms and databases in the discovery of novel bacteriocin, and how to bridge the gap between the discovery of bacteriocin genes from big datasets and their in vitro production. Besides, the later part of the review discussed the various impediments in their clinical applications and possible solution to bring them into the frontline therapeutics to control infections, thereby meeting the challenges of global antimicrobial resistance.
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Affiliation(s)
- Karthika Suryaletha
- Cholera & Biofilm Research Laboratory, Pathogen Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Akhila Velappan Savithri
- Cholera & Biofilm Research Laboratory, Pathogen Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Seema A Nayar
- Department of Microbiology, Government Medical College, Thiruvananthapuram, Kerala, India
| | - Sijo Asokan
- Cholera & Biofilm Research Laboratory, Pathogen Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Divya Rajeswary
- Cholera & Biofilm Research Laboratory, Pathogen Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Sabu Thomas
- Cholera & Biofilm Research Laboratory, Pathogen Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
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24
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Vinogradov AA, Zhang Y, Hamada K, Chang JS, Okada C, Nishimura H, Terasaka N, Goto Y, Ogata K, Sengoku T, Onaka H, Suga H. De Novo Discovery of Thiopeptide Pseudo-natural Products Acting as Potent and Selective TNIK Kinase Inhibitors. J Am Chem Soc 2022; 144:20332-20341. [DOI: 10.1021/jacs.2c07937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Alexander A. Vinogradov
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yue Zhang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keisuke Hamada
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Jun Shi Chang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Chikako Okada
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Hirotaka Nishimura
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Naohiro Terasaka
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Toru Sengoku
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Hiroyasu Onaka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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25
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Romero-Rodríguez A, Martínez de la Peña C, Troncoso-Cotal S, Guzmán C, Sánchez S. Emerging alternatives against Clostridioides difficile infection. Anaerobe 2022; 78:102638. [DOI: 10.1016/j.anaerobe.2022.102638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022]
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26
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Nguyen DT, Le TT, Rice AJ, Hudson GA, van der Donk WA, Mitchell DA. Accessing Diverse Pyridine-Based Macrocyclic Peptides by a Two-Site Recognition Pathway. J Am Chem Soc 2022; 144:11263-11269. [PMID: 35713415 PMCID: PMC9247985 DOI: 10.1021/jacs.2c02824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Macrocyclic peptides
are sought-after molecular scaffolds for drug
discovery, and new methods to access diverse libraries are of increasing
interest. Here, we report the enzymatic synthesis of pyridine-based
macrocyclic peptides (pyritides) from linear precursor peptides. Pyritides
are a recently described class of ribosomally synthesized and post-translationally
modified peptides (RiPPs) and are related to the long-known thiopeptide
natural products. RiPP precursors typically contain an N-terminal
leader region that is physically engaged by the biosynthetic proteins
that catalyze modification of the C-terminal core region of the precursor
peptide. We demonstrate that pyritide-forming enzymes recognize both
the leader region and a C-terminal tripeptide motif, with each contributing
to site-selective substrate modification. Substitutions in the core
region were well-tolerated and facilitated the generation of a wide
range of pyritide analogues, with variations in macrocycle sequence
and size. A combination of the pyritide biosynthetic pathway with
azole-forming enzymes was utilized to generate a thiazole-containing
pyritide (historically known as a thiopeptide) with no similarity
in sequence and macrocycle size to the naturally encoded pyritides.
The broad substrate scope of the pyritide biosynthetic enzymes serves
as a future platform for macrocyclic peptide lead discovery and optimization.
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Affiliation(s)
- Dinh T Nguyen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tung T Le
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andrew J Rice
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Graham A Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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27
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Vinogradov AA, Chang JS, Onaka H, Goto Y, Suga H. Accurate Models of Substrate Preferences of Post-Translational Modification Enzymes from a Combination of mRNA Display and Deep Learning. ACS CENTRAL SCIENCE 2022; 8:814-824. [PMID: 35756369 PMCID: PMC9228559 DOI: 10.1021/acscentsci.2c00223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Indexed: 05/15/2023]
Abstract
Promiscuous post-translational modification (PTM) enzymes often display nonobvious substrate preferences by acting on diverse yet well-defined sets of peptides and/or proteins. Understanding of substrate fitness landscapes for PTM enzymes is important in many areas of contemporary science, including natural product biosynthesis, molecular biology, and biotechnology. Here, we report an integrated platform for accurate profiling of substrate preferences for PTM enzymes. The platform features (i) a combination of mRNA display with next-generation sequencing as an ultrahigh throughput technique for data acquisition and (ii) deep learning for data analysis. The high accuracy (>0.99 in each of two studies) of the resulting deep learning models enables comprehensive analysis of enzymatic substrate preferences. The models can quantify fitness across sequence space, map modification sites, and identify important amino acids in the substrate. To benchmark the platform, we performed profiling of a Ser dehydratase (LazBF) and a Cys/Ser cyclodehydratase (LazDEF), two enzymes from the lactazole biosynthesis pathway. In both studies, our results point to complex enzymatic preferences, which, particularly for LazBF, cannot be reduced to a set of simple rules. The ability of the constructed models to dissect such complexity suggests that the developed platform can facilitate a wider study of PTM enzymes.
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Affiliation(s)
- Alexander A. Vinogradov
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jun Shi Chang
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyasu Onaka
- Department
of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative
Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yuki Goto
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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28
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Habibi Y, Weerasinghe NW, Uggowitzer KA, Thibodeaux CJ. Partially Modified Peptide Intermediates in Lanthipeptide Biosynthesis Alter the Structure and Dynamics of a Lanthipeptide Synthetase. J Am Chem Soc 2022; 144:10230-10240. [PMID: 35647706 DOI: 10.1021/jacs.2c00727] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lanthipeptide synthetases construct macrocyclic peptide natural products by catalyzing an iterative cascade of post-translational modifications. Class II lanthipeptide synthetases (LanM enzymes) catalyze multiple rounds of peptide dehydration and thioether macrocycle formation in a manner that guides precursor peptide maturation to the biologically active final product with high fidelity. The mechanistic details underlying the contradictory phenomena of substrate flexibility coupled with high biosynthetic fidelity have proven challenging to illuminate. In this work, we employ mass spectrometry to investigate how the structure of a maturing precursor lanthipeptide (HalA2) influences the local and global structure of its cognate lanthipeptide synthetase (HalM2). Using enzymatically synthesized HalA2 peptides that contain sets of native thioether macrocycles, we employ ion mobility mass spectrometry (IM-MS) to show that HalA2 macrocyclization alters the conformational landscape of the HalM2 enzyme in a systematic manner. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) studies show that local HalM2 structural dynamics also change in response to HalA2 post-translational modification. Notably, deuterium uptake in a critical HalM2 α-helical region depends on the number of thioether macrocycles present in the HalA2 core peptide. Binding of the isolated leader and core peptide portions of the modular HalA2 precursor led to a synergistic structuring of this α-helical region, providing evidence for distinct leader and core peptide binding sites that independently alter the dynamics of this functionally critical α-helix. The data support a mechanistic model where the sequential post-translational modification of HalA2 alters the conformational dynamics of HalM2 in regions of the enzyme that are known to be functionally critical.
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Affiliation(s)
- Yeganeh Habibi
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Nuwani W Weerasinghe
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Kevin A Uggowitzer
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Christopher J Thibodeaux
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
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29
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Zheng Y, Du Y, Qiu Z, Liu Z, Qiao J, Li Y, Caiyin Q. Nisin Variants Generated by Protein Engineering and Their Properties. Bioengineering (Basel) 2022; 9:bioengineering9060251. [PMID: 35735494 PMCID: PMC9219921 DOI: 10.3390/bioengineering9060251] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/28/2022] [Accepted: 06/08/2022] [Indexed: 02/07/2023] Open
Abstract
Nisin, a typical lantibiotic, has robust antimicrobial activity combined with limited cytotoxicity, and the development of resistance to it is slow. These properties make nisin a promising antimicrobial agent to control pathogenic microorganisms in dairy foods. However, its low solubility, poor stability and short half-life at neutral pH limit its application within the dairy industry. Protein engineering technology has revealed the potential of modifying nisin to improve its properties, and many valuable variants have emerged. This review summarizes progress in the generation of nisin variants for the dairy industry and for other purposes. These nisin variants with additional modification have improved properties and can even expand the inhibition spectrum range of nisin. Nisin, as the most thoroughly studied lantibiotic, and its variants can also guide the modification of other lantibiotics.
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Affiliation(s)
- Yue Zheng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (Y.Z.); (Z.Q.); (Z.L.); (J.Q.); (Y.L.)
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin 300072, China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China;
| | - Zekai Qiu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (Y.Z.); (Z.Q.); (Z.L.); (J.Q.); (Y.L.)
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin 300072, China
| | - Ziming Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (Y.Z.); (Z.Q.); (Z.L.); (J.Q.); (Y.L.)
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin 300072, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (Y.Z.); (Z.Q.); (Z.L.); (J.Q.); (Y.L.)
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin 300072, China
| | - Yanni Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (Y.Z.); (Z.Q.); (Z.L.); (J.Q.); (Y.L.)
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin 300072, China
| | - Qinggele Caiyin
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (Y.Z.); (Z.Q.); (Z.L.); (J.Q.); (Y.L.)
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin 300072, China
- Correspondence:
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30
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Viel JH, Kuipers OP. Mutational Studies of the Mersacidin Leader Reveal the Function of Its Unique Two-Step Leader Processing Mechanism. ACS Synth Biol 2022; 11:1949-1957. [PMID: 35504017 PMCID: PMC9127955 DOI: 10.1021/acssynbio.2c00088] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
The class II lanthipeptide
mersacidin, a ribosomally synthesized
and post-translationally modified peptide (RiPP), displays unique
intramolecular structures, including a very small lanthionine ring.
When applied in the growing field of RiPP engineering, these can add
unique features to new-to-nature compounds with novel properties.
Recently, a heterologous expression system for mersacidin in Escherichia coli was developed to add its modification
enzymes to the RiPP engineering toolbox and further explore mersacidin
biosynthesis and leader-processing. The dedicated mersacidin transporter
and leader protease MrsT was shown to cleave the leader peptide only
partially upon export, transporting GDMEAA-mersacidin out of the cell.
The extracellular Bacillus amyloliquefaciens protease AprE was shown to release active mersacidin in a second
leader-processing step after transport. The conserved LanT cleavage
site in the mersacidin leader is present in many other class II lanthipeptides.
In contrast to mersacidin, the leader of these peptides is fully processed
in one step. This difference with mersacidin leader-processing raises
fundamentally interesting questions about the specifics of mersacidin
modification and processing, which is also crucial for its application
in RiPP engineering. Here, mutational studies of the mersacidin leader–core
interface were performed to answer these questions. Results showed
the GDMEAA sequence is crucial for both mersacidin modification and
leader processing, revealing a unique leader layout in which a LanM
recognition site is positioned downstream of the conserved leader-protease
LanT cleavage site. Moreover, by identifying residues and regions
that are crucial for mersacidin-type modifications, the wider application
of mersacidin modifications in RiPP engineering has been enabled.
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Affiliation(s)
- Jakob H. Viel
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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31
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Abbood N, Duy Vo T, Watzel J, Bozhueyuek KAJ, Bode HB. Type S Non‐Ribosomal Peptide Synthetases for the Rapid Generation of Tailormade Peptide Libraries**. Chemistry 2022; 28:e202103963. [PMID: 35176184 PMCID: PMC9315016 DOI: 10.1002/chem.202103963] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Indexed: 11/23/2022]
Abstract
Bacterial natural products in general, and non‐ribosomally synthesized peptides in particular, are structurally diverse and provide us with a broad range of pharmaceutically relevant bioactivities. Yet, traditional natural product research suffers from rediscovering the same scaffolds and has been stigmatized as inefficient, time‐, labour‐ and cost‐intensive. Combinatorial chemistry, on the other hand, can produce new molecules in greater numbers, cheaper and in less time than traditional natural product discovery, but also fails to meet current medical needs due to the limited biologically relevant chemical space that can be addressed. Consequently, methods for the high throughput generation of new natural products would offer a new approach to identifying novel bioactive chemical entities for the hit to lead phase of drug discovery programs. As a follow‐up to our previously published proof‐of‐principle study on generating bipartite type S non‐ribosomal peptide synthetases (NRPSs), we now envisaged the de novo generation of non‐ribosomal peptides (NRPs) on an unreached scale. Using synthetic zippers, we split NRPSs in up to three subunits and rapidly generated different bi‐ and tripartite NRPS libraries to produce 49 peptides, peptide derivatives, and de novo peptides at good titres up to 145 mg L−1. A further advantage of type S NRPSs not only is the possibility to easily expand the created libraries by re‐using previously created type S NRPS, but that functions of individual domains as well as domain‐domain interactions can be studied and assigned rapidly.
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Affiliation(s)
- Nadya Abbood
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Tien Duy Vo
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Jonas Watzel
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Kenan A. J. Bozhueyuek
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Helge B. Bode
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
- Senckenberg Gesellschaft für Naturforschung 60325 Frankfurt am Main Germany
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32
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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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33
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Hamry SR, Thibodeaux CJ. Biochemical and biophysical investigation of the HalM2 lanthipeptide synthetase using mass spectrometry. CAN J CHEM 2022. [DOI: 10.1139/cjc-2021-0124] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The rapid emergence of antimicrobial resistance in clinical settings has called for renewed efforts to discover and develop new antimicrobial compounds. Lanthipeptides present a promising, genetically encoded molecular scaffold for the engineering of structurally complex, biologically active peptides. These peptide natural products are constructed by enzymes (lanthipeptide synthetases) with relaxed substrate specificity that iteratively modify the precursor lanthipeptide to generate structures with defined sets of thioether macrocycles. The mechanistic features that guide the maturation of lanthipeptides into their proper, fully modified forms are obscured by the complexity of the multistep maturation and the large size and dynamic structures of the synthetases and precursor peptides. Over the past several years, our lab has been developing a suite of mass spectrometry-based techniques that are ideally suited to untangling the complex reaction sequences and molecular interactions that define lanthipeptide biosynthesis. This review focuses on our development and application of these mass spectrometry-based techniques to investigate the biochemical, kinetic, and biophysical properties of the haloduracin β class II lanthipeptide synthetase, HalM2.
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Affiliation(s)
- Sally R. Hamry
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - Christopher J. Thibodeaux
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
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34
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Cochrane W, Fitzgerald PR, Paegel BM. Antibacterial Discovery via Phenotypic DNA-Encoded Library Screening. ACS Chem Biol 2021; 16:2752-2756. [PMID: 34806373 PMCID: PMC8688339 DOI: 10.1021/acschembio.1c00714] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The global rise of multidrug resistant infections poses an imminent, existential threat. Numerous pipelines have failed to convert biochemically active molecules into bona fide antibacterials, owing to a lack of chemical material with antibacterial-like physical properties in high-throughput screening compound libraries. Here, we demonstrate scalable design and synthesis of an antibacterial-like solid-phase DNA-encoded library (DEL, 7488 members) and facile hit deconvolution from whole-cell Escherichia coli and Bacillus subtilis cytotoxicity screens. The screen output identified two low-micromolar inhibitors of B. subtilis growth and recapitulated known structure-activity relationships of the fluoroquinolone antibacterial class. This phenotypic DEL screening strategy is also potentially applicable to adherent cells and will broadly enable the discovery and optimization of cell-active molecules.
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Affiliation(s)
- Wesley
G. Cochrane
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Patrick R. Fitzgerald
- Skaggs
Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| | - Brian M. Paegel
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Departments
of Chemistry & Biomedical Engineering, University of California, Irvine, California 92697, United States
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35
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Bauman KD, Butler KS, Moore BS, Chekan JR. Genome mining methods to discover bioactive natural products. Nat Prod Rep 2021; 38:2100-2129. [PMID: 34734626 PMCID: PMC8597713 DOI: 10.1039/d1np00032b] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Indexed: 12/22/2022]
Abstract
Covering: 2016 to 2021With genetic information available for hundreds of thousands of organisms in publicly accessible databases, scientists have an unprecedented opportunity to meticulously survey the diversity and inner workings of life. The natural product research community has harnessed this breadth of sequence information to mine microbes, plants, and animals for biosynthetic enzymes capable of producing bioactive compounds. Several orthogonal genome mining strategies have been developed in recent years to target specific chemical features or biological properties of bioactive molecules using biosynthetic, resistance, or transporter proteins. These "biosynthetic hooks" allow researchers to query for biosynthetic gene clusters with a high probability of encoding previously undiscovered, bioactive compounds. This review highlights recent case studies that feature orthogonal approaches that exploit genomic information to specifically discover bioactive natural products and their gene clusters.
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Affiliation(s)
- Katherine D Bauman
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Keelie S Butler
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, 27402, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, 27402, USA.
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36
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Molloy A, Harrison J, McGrath JS, Owen Z, Smith C, Liu X, Li X, Cox JAG. Microfluidics as a Novel Technique for Tuberculosis: From Diagnostics to Drug Discovery. Microorganisms 2021; 9:microorganisms9112330. [PMID: 34835455 PMCID: PMC8618277 DOI: 10.3390/microorganisms9112330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 12/29/2022] Open
Abstract
Tuberculosis (TB) remains a global healthcare crisis, with an estimated 5.8 million new cases and 1.5 million deaths in 2020. TB is caused by infection with the major human pathogen Mycobacterium tuberculosis, which is difficult to rapidly diagnose and treat. There is an urgent need for new methods of diagnosis, sufficient in vitro models that capably mimic all physiological conditions of the infection, and high-throughput drug screening platforms. Microfluidic-based techniques provide single-cell analysis which reduces experimental time and the cost of reagents, and have been extremely useful for gaining insight into monitoring microorganisms. This review outlines the field of microfluidics and discusses the use of this novel technique so far in M. tuberculosis diagnostics, research methods, and drug discovery platforms. The practices of microfluidics have promising future applications for diagnosing and treating TB.
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Affiliation(s)
- Antonia Molloy
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK; (A.M.); (J.H.)
| | - James Harrison
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK; (A.M.); (J.H.)
| | - John S. McGrath
- Sphere Fluidics Limited, The McClintock Building, Suite 7, Granta Park, Great Abington, Cambridge CB21 6GP, UK; (J.S.M.); (Z.O.); (C.S.); (X.L.); (X.L.)
| | - Zachary Owen
- Sphere Fluidics Limited, The McClintock Building, Suite 7, Granta Park, Great Abington, Cambridge CB21 6GP, UK; (J.S.M.); (Z.O.); (C.S.); (X.L.); (X.L.)
| | - Clive Smith
- Sphere Fluidics Limited, The McClintock Building, Suite 7, Granta Park, Great Abington, Cambridge CB21 6GP, UK; (J.S.M.); (Z.O.); (C.S.); (X.L.); (X.L.)
| | - Xin Liu
- Sphere Fluidics Limited, The McClintock Building, Suite 7, Granta Park, Great Abington, Cambridge CB21 6GP, UK; (J.S.M.); (Z.O.); (C.S.); (X.L.); (X.L.)
| | - Xin Li
- Sphere Fluidics Limited, The McClintock Building, Suite 7, Granta Park, Great Abington, Cambridge CB21 6GP, UK; (J.S.M.); (Z.O.); (C.S.); (X.L.); (X.L.)
| | - Jonathan A. G. Cox
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK; (A.M.); (J.H.)
- Correspondence: ; Tel.: +44-121-204-5011
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Le T, Jeanne Dit Fouque K, Santos-Fernandez M, Navo CD, Jiménez-Osés G, Sarksian R, Fernandez-Lima FA, van der Donk WA. Substrate Sequence Controls Regioselectivity of Lanthionine Formation by ProcM. J Am Chem Soc 2021; 143:18733-18743. [PMID: 34724611 DOI: 10.1021/jacs.1c09370] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Lanthipeptides belong to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs). The (methyl)lanthionine cross-links characteristic to lanthipeptides are essential for their stability and bioactivities. In most bacteria, lanthipeptides are maturated from single precursor peptides encoded in the corresponding biosynthetic gene clusters. However, cyanobacteria engage in combinatorial biosynthesis and encode as many as 80 substrate peptides with highly diverse sequences that are modified by a single lanthionine synthetase into lanthipeptides of different lengths and ring patterns. It is puzzling how a single enzyme could exert control over the cyclization processes of such a wide range of substrates. Here, we used a library of ProcA3.3 precursor peptide variants and show that it is not the enzyme ProcM but rather its substrate sequences that determine the regioselectivity of lanthionine formation. We also demonstrate the utility of trapped ion mobility spectrometry-tandem mass spectrometry (TIMS-MS/MS) as a fast and convenient method to efficiently separate lanthipeptide constitutional isomers, particularly in cases where the isomers cannot be resolved by conventional liquid chromatography. Our data allowed identification of factors that are important for the cyclization outcome, but also showed that there are no easily identifiable predictive rules for all sequences. Our findings provide a platform for future deep learning approaches to allow such prediction of ring patterns of products of combinatorial biosynthesis.
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Affiliation(s)
- Tung Le
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Miguel Santos-Fernandez
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Claudio D Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Raymond Sarksian
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Francisco Alberto Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
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38
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Gomes Von Borowski R, Chat S, Schneider R, Nonin-Lecomte S, Bouaziz S, Giudice E, Rigon Zimmer A, Baggio Gnoatto SC, Macedo AJ, Gillet R. Capsicumicine, a New Bioinspired Peptide from Red Peppers Prevents Staphylococcal Biofilm In Vitro and In Vivo via a Matrix Anti-Assembly Mechanism of Action. Microbiol Spectr 2021; 9:e0047121. [PMID: 34704807 PMCID: PMC8549733 DOI: 10.1128/spectrum.00471-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/09/2021] [Indexed: 11/20/2022] Open
Abstract
Staphylococci are pathogenic biofilm-forming bacteria and a source of multidrug resistance and/or tolerance causing a broad spectrum of infections. These bacteria are enclosed in a matrix that allows them to colonize medical devices, such as catheters and tissues, and that protects against antibiotics and immune systems. Advances in antibiofilm strategies for targeting this matrix are therefore extremely relevant. Here, we describe the development of the Capsicum pepper bioinspired peptide "capsicumicine." By using microbiological, microscopic, and nuclear magnetic resonance (NMR) approaches, we demonstrate that capsicumicine strongly prevents methicillin-resistant Staphylococcus epidermidis biofilm via an extracellular "matrix anti-assembly" mechanism of action. The results were confirmed in vivo in a translational preclinical model that mimics medical device-related infection. Since capsicumicine is not cytotoxic, it is a promising candidate for complementary treatment of infectious diseases. IMPORTANCE Pathogenic biofilms are a global health care concern, as they can cause extensive antibiotic resistance, morbidity, mortality, and thereby substantial economic loss. So far, no effective treatments targeting the bacteria in biofilms have been developed. Plants are constantly attacked by a wide range of pathogens and have protective factors, such as peptides, to defend themselves. These peptides are common components in Capsicum baccatum (red pepper). Here, we provide insights into an antibiofilm strategy based on the development of capsicumicine, a natural peptide that strongly controls biofilm formation by Staphylococcus epidermidis, the most prevalent pathogen in device-related infections.
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Affiliation(s)
- Rafael Gomes Von Borowski
- Université de Rennes, CNRS, Institut de Génétique et de Développement de Rennes (IGDR), UMR6290, Rennes, France
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Sophie Chat
- Université de Rennes, CNRS, Institut de Génétique et de Développement de Rennes (IGDR), UMR6290, Rennes, France
| | - Rafael Schneider
- Université de Rennes, CNRS, Institut de Génétique et de Développement de Rennes (IGDR), UMR6290, Rennes, France
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Sylvie Nonin-Lecomte
- Université de Paris, CNRS, CiTCoM (Cibles Thérapeutiques et Conception de Médicaments) UMR 8038, Faculté de Pharmacie, Paris, France
| | - Serge Bouaziz
- Université de Paris, CNRS, CiTCoM (Cibles Thérapeutiques et Conception de Médicaments) UMR 8038, Faculté de Pharmacie, Paris, France
| | - Emmanuel Giudice
- Université de Rennes, CNRS, Institut de Génétique et de Développement de Rennes (IGDR), UMR6290, Rennes, France
| | - Aline Rigon Zimmer
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Simone Cristina Baggio Gnoatto
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Alexandre José Macedo
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Reynald Gillet
- Université de Rennes, CNRS, Institut de Génétique et de Développement de Rennes (IGDR), UMR6290, Rennes, France
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Arias-Orozco P, Inklaar M, Lanooij J, Cebrián R, Kuipers OP. Functional Expression and Characterization of the Highly Promiscuous Lanthipeptide Synthetase SyncM, Enabling the Production of Lanthipeptides with a Broad Range of Ring Topologies. ACS Synth Biol 2021; 10:2579-2591. [PMID: 34554737 PMCID: PMC8524650 DOI: 10.1021/acssynbio.1c00224] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Lanthipeptides are
ribosomally synthesized and post-translationally
modified peptides characterized by the presence of lanthionine rings
that provide stability and functionality. Genome mining techniques
have shown their huge diversity and potential for the discovery of
novel active molecules. However, in many cases, they are not easily
produced under laboratory conditions. The heterologous expression
of these molecules using well-characterized lanthipeptide biosynthetic
enzymes is rising as an alternative system for the design and production
of new lanthipeptides with biotechnological or clinical properties.
Nevertheless, the substrate-enzyme specificity limits the complete
modification of the desired peptides and hence, their full stability
and/or biological activity. New low substrate-selective biosynthetic
enzymes are therefore necessary for the heterologous production of
new-to-nature peptides. Here, we have identified, cloned, and heterologously
expressed in Lactococcus lactis the
most promiscuous lanthipeptide synthetase described to date, i.e.,
SyncM from the marine cyanobacteria Synechococcus MITS9509. We have characterized the functionality of SyncM by the
successful expression of 15 out of 18 different SyncA substrates,
subsequently determining the dehydration and cyclization processes
in six representatives of them. This characterization highlights the
very relaxed substrate specificity of SyncM toward its precursors
and the ability to catalyze the formation of exceptionally large rings
in a variety of topologies. Our results suggest that SyncM could be
an attractive enzyme to design and produce a wide variety of new-to-nature
lanthipeptides with a broad range of ring topologies.
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Affiliation(s)
- Patricia Arias-Orozco
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Maartje Inklaar
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Judith Lanooij
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Rubén Cebrián
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
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40
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Vinogradov AA, Nagano M, Goto Y, Suga H. Site-Specific Nonenzymatic Peptide S/O-Glutamylation Reveals the Extent of Substrate Promiscuity in Glutamate Elimination Domains. J Am Chem Soc 2021; 143:13358-13369. [PMID: 34392675 DOI: 10.1021/jacs.1c06470] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Formation of dehydroalanine and dehydrobutyrine residues via tRNA-dependent dehydration of serine and threonine is a key post-translational modification in the biosynthesis of lanthipeptide and thiopeptide RiPPs. The dehydration process involves two reactions, wherein the O-glutamyl Ser/Thr intermediate, accessed by a dedicated enzyme utilizing Glu-tRNAGlu as the acyl donor, is recognized by the second enzyme, referred to as the glutamate elimination domain (ED), which catalyzes the eponymous reaction yielding a dehydroamino acid. Many details of ED catalysis remain unexplored because the scope of available substrates for testing is limited to those that the upstream enzymes can furnish. Here, we report two complementary strategies for direct, nonenzymatic access to diverse ED substrates. We establish that a thiol-thioester exchange reaction between a Cys-containing peptide and an α thioester of glutamic acid leads an S-glutamylated intermediate which can act as a substrate for EDs. Furthermore, we show that the native O-glutamylated substrates can be accessible from S-glutamylated peptides upon a site-specific S-to-O acyl transfer reaction. Combined with flexible in vitro translation utilized for rapid peptide production, these chemistries enabled us to dissect the substrate recognition requirements of three known EDs. Our results establish that EDs are uniquely promiscuous enzymes capable of acting on substrates with arbitrary amino acid sequences and performing retro-Michael reaction beyond the canonical glutamate elimination. To facilitate substrate recruitment, EDs apparently engage in nonspecific hydrophobic interactions with their substrates. Altogether, our results establish the substrate scope of EDs and provide clues to their catalysis.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masanobu Nagano
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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41
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Zhao X, Xu Y, Viel JH, Kuipers OP. Semisynthetic Macrocyclic Lipo-lanthipeptides Display Antimicrobial Activity Against Bacterial Pathogens. ACS Synth Biol 2021; 10:1980-1991. [PMID: 34347446 PMCID: PMC8383303 DOI: 10.1021/acssynbio.1c00161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A large number of antimicrobial peptides depend on intramolecular disulfide bonds for their biological activity. However, the relative instability of disulfide bonds has limited the potential of some of these peptides to be developed into therapeutics. Conversely, peptides containing intramolecular (methyl)lanthionine-based bonds, lanthipeptides, are highly stable under a broader range of biological and physical conditions. Here, the class-II lanthipeptide synthetase CinM, from the cinnamycin gene cluster, was employed to create methyllanthionine stabilized analogues of disulfide-bond-containing antimicrobial peptides. The resulting analogues were subsequently modified in vitro by adding lipid tails of variable lengths through chemical addition. Finally, the created compounds were characterized by MIC tests against several relevant pathogens, killing assays, membrane permeability assays, and hemolysis assays. It was found that CinM could successfully install methyllanthionine bonds at the intended positions of the analogues and that the lipidated macrocyclic core peptides have bactericidal activity against tested Gram-positive and Gram-negative pathogenic bacteria. Additionally, fluorescence microscopy assays revealed that the lipidated compounds disrupt the bacterial membrane and lyse bacterial cells, hinting toward a potential mode of action. Notably, the semisynthesized macrocyclic lipo-lanthipeptides show low hemolytic activity. These results show that the methods developed here extend the toolbox for novel antimicrobial development and might enable the further development of novel compounds with killing activity against relevant pathogenic bacteria.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Yanli Xu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Jakob H. Viel
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
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Stucki A, Jusková P, Nuti N, Schmitt S, Dittrich PS. Synchronized Reagent Delivery in Double Emulsions for Triggering Chemical Reactions and Gene Expression. SMALL METHODS 2021; 5:e2100331. [PMID: 34927870 DOI: 10.1002/smtd.202100331] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/21/2021] [Indexed: 06/14/2023]
Abstract
Microfluidic methods for the formation of single and double emulsion (DE) droplets allow for the encapsulation and isolation of reactants inside nanoliter compartments. Such methods have greatly enhanced the toolbox for high-throughput screening for cell or enzyme engineering and drug discovery. However, remaining challenges in the supply of reagents into these enclosed compartments limit the applicability of droplet microfluidics. Here, a strategy is introduced for on-demand delivery of reactants in DEs. Lipid vesicles are used as reactant carriers, which are co-encapsulated in double emulsions and release their cargo upon addition of an external trigger, here the anionic surfactant sodium dodecyl sulfate (SDS). The reagent present inside the lipid vesicles stays isolated from the remaining content of the DE vessel until SDS enters the DE lumen and solubilizes the vesicles' lipid bilayer. The versatility of the method is demonstrated with two critical applications chosen as representative assays for high-throughput screening: the induction of gene expression in bacteria and the initiation of an enzymatic reaction. This method not only allows for the release of the lipid vesicle content inside DEs to be synchronized for all DEs but also for the release to be triggered at any desired time.
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Affiliation(s)
- Ariane Stucki
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, Basel, CH-4058, Switzerland
- NCCR Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
| | - Petra Jusková
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Nicola Nuti
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Steven Schmitt
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zürich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, Basel, CH-4058, Switzerland
- NCCR Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
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Li C, Alam K, Zhao Y, Hao J, Yang Q, Zhang Y, Li R, Li A. Mining and Biosynthesis of Bioactive Lanthipeptides From Microorganisms. Front Bioeng Biotechnol 2021; 9:692466. [PMID: 34395400 PMCID: PMC8358304 DOI: 10.3389/fbioe.2021.692466] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/29/2021] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial resistance is one of the most serious public health issues in the worldwide and only a few new antimicrobial drugs have been discovered in recent decades. To overcome the ever-increasing emergence of multidrug-resistant (MDR) pathogens, discovery of new natural products (NPs) against MDR pathogens with new technologies is in great demands. Lanthipeptides which are ribosomally synthesized and post-translationally modified peptides (RiPPs) display high diversity in their chemical structures and mechanisms of action. Genome mining and biosynthetic engineering have also yielded new lanthipeptides, which are a valuable source of drug candidates. In this review we cover the recent advances in the field of microbial derived lanthipeptide discovery and development.
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Affiliation(s)
- Caiyun Li
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Khorshed Alam
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yiming Zhao
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jinfang Hao
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qing Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ruijuan Li
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Aiying Li
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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44
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Dorau R, Liu J, Solem C, Jensen PR. Metabolic Engineering of Lactic Acid Bacteria. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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45
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Sedlmayer F, Woischnig AK, Unterreiner V, Fuchs F, Baeschlin D, Khanna N, Fussenegger M. 5-Fluorouracil blocks quorum-sensing of biofilm-embedded methicillin-resistant Staphylococcus aureus in mice. Nucleic Acids Res 2021; 49:e73. [PMID: 33856484 PMCID: PMC8287944 DOI: 10.1093/nar/gkab251] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 03/02/2021] [Accepted: 03/29/2021] [Indexed: 02/05/2023] Open
Abstract
Antibiotic-resistant pathogens often escape antimicrobial treatment by forming protective biofilms in response to quorum-sensing communication via diffusible autoinducers. Biofilm formation by the nosocomial pathogen methicillin-resistant Staphylococcus aureus (MRSA) is triggered by the quorum-sensor autoinducer-2 (AI-2), whose biosynthesis is mediated by methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) and S-ribosylhomocysteine lyase (LuxS). Here, we present a high-throughput screening platform for small-molecular inhibitors of either enzyme. This platform employs a cell-based assay to report non-toxic, bioavailable and cell-penetrating inhibitors of AI-2 production, utilizing engineered human cells programmed to constitutively secrete AI-2 by tapping into the endogenous methylation cycle via ectopic expression of codon-optimized MTAN and LuxS. Screening of a library of over 5000 commercial compounds yielded 66 hits, including the FDA-licensed cytostatic anti-cancer drug 5-fluorouracil (5-FU). Secondary screening and validation studies showed that 5-FU is a potent quorum-quencher, inhibiting AI-2 production and release by MRSA, Staphylococcus epidermidis, Escherichia coli and Vibrio harveyi. 5-FU efficiently reduced adherence and blocked biofilm formation of MRSA in vitro at an order-of-magnitude-lower concentration than that clinically relevant for anti-cancer therapy. Furthermore, 5-FU reestablished antibiotic susceptibility and enabled daptomycin-mediated prevention and clearance of MRSA infection in a mouse model of human implant-associated infection.
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Affiliation(s)
- Ferdinand Sedlmayer
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Anne-Kathrin Woischnig
- Laboratory of Infection Biology, Department of Biomedicine, University and University Hospital Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland
| | - Vincent Unterreiner
- Novartis Institutes for BioMedical Research (NIBR), Chemical Biology and Therapeutics (CBT), CH-4033, Basel, Switzerland
| | - Florian Fuchs
- Novartis Institutes for BioMedical Research (NIBR), Chemical Biology and Therapeutics (CBT), CH-4033, Basel, Switzerland
| | - Daniel Baeschlin
- Novartis Institutes for BioMedical Research (NIBR), Chemical Biology and Therapeutics (CBT), CH-4033, Basel, Switzerland
| | - Nina Khanna
- Laboratory of Infection Biology, Department of Biomedicine, University and University Hospital Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Basel, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
- Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
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46
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Zhao X, Kuipers OP. Nisin- and Ripcin-Derived Hybrid Lanthipeptides Display Selective Antimicrobial Activity against Staphylococcus aureus. ACS Synth Biol 2021; 10:1703-1714. [PMID: 34156232 PMCID: PMC8291769 DOI: 10.1021/acssynbio.1c00080] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Lanthipeptides are
(methyl)lanthionine ring-containing ribosomally
synthesized and post-translationally modified peptides (RiPPs). Many
lanthipeptides show strong antimicrobial activity against bacterial
pathogens, including antibiotic-resistant bacterial pathogens. The
group of disulfide-bond-containing antimicrobial peptides (AMPs) is
well-known in nature and forms a rich source of templates for the
production of novel peptides with corresponding (methyl)lanthionine
analogues instead of disulfides. Here, we show that novel macrocyclic
lanthipeptides (termed thanacin and ripcin) can be synthesized using
the known antimicrobials thanatin and rip-thanatin as templates. Notably,
the synthesized nisin(1–20)–ripcin hybrid lanthipeptides
(ripcin B–G) showed selective antimicrobial activity against S. aureus, including an antibiotic-resistant MRSA
strain. Interestingly, ripcin B–G, which are hybrid peptides
of nisin(1–20) and ripcin that are each inactive against Gram-negative
pathogens, showed substantial antimicrobial activity against the tested
Gram-negative pathogens. Moreover, ripcin B–G was highly resistant
against the nisin resistance protein (NSR; a peptidase that removes
the C-terminal 6 amino acids of nisin and strongly reduces its antimicrobial
activity), opposed to nisin itself. This study provides an example
of converting disulfide-bond-based AMPs into (methyl)lanthionine-based
macrocyclic hybrid lanthipeptides and can yield antimicrobial peptides
with selective antimicrobial activity against S. aureus.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
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Zhao X, Kuipers OP. Synthesis of silver-nisin nanoparticles with low cytotoxicity as antimicrobials against biofilm-forming pathogens. Colloids Surf B Biointerfaces 2021; 206:111965. [PMID: 34237525 DOI: 10.1016/j.colsurfb.2021.111965] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/02/2021] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
Wound infection is a serious threat to patients, in particular those with septic wound infections, which result in high mortality rates. Moreover, the treatment of wound infections with antimicrobial-resistant and/or biofilm-forming pathogens can be challenging. Nisin, a potent antimicrobial against Gram-positive bacterial pathogens, has been used in the food industry as a preservative for decades. Silver has been approved by the FDA as a topical antimicrobial. Here, we show that silver-nisin nanoparticles (Ag-nisin NP), with an average diameter of 60 nm, can be quickly synthesized with the assistance of a simple microwave. Ag-nisin NP act as bactericidal antibiotics against the tested pathogens. In contrast, resistance was observed in S. aureus and A. baumannii that were treated with silver nitrate alone. In addition, Ag-nisin NP showed potent antibiofilm activity against S. aureus, P. aeruginosa, A. baumannii, K. pneumoniae, and E. coli, which are pathogens occurring in wound infections. Notably, the synthesized Ag-nisin NP showed lower cytotoxicity than silver nitrate to human cells. This formulation provides an alternative and safe measurement for biofilm-infected wound control.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, the Netherlands.
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48
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van Staden ADP, van Zyl WF, Trindade M, Dicks LMT, Smith C. Therapeutic Application of Lantibiotics and Other Lanthipeptides: Old and New Findings. Appl Environ Microbiol 2021; 87:e0018621. [PMID: 33962984 PMCID: PMC8231447 DOI: 10.1128/aem.00186-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Lanthipeptides are ribosomally synthesized and posttranslationally modified peptides, with modifications that are incorporated during biosynthesis by dedicated enzymes. Various modifications of the peptides are possible, resulting in a highly diverse group of bioactive peptides that offer a potential reservoir for use in the fight against a plethora of diseases. Their activities range from the antimicrobial properties of lantibiotics, especially against antibiotic-resistant strains, to antiviral activity, immunomodulatory properties, antiallodynic effects, and the potential to alleviate cystic fibrosis symptoms. Lanthipeptide biosynthetic genes are widespread within bacterial genomes, providing a substantial repository for novel bioactive peptides. Using genome mining tools, novel bioactive lanthipeptides can be identified, and coupled with rapid screening and heterologous expression technologies, the lanthipeptide drug discovery pipeline can be significantly sped up. Lanthipeptides represent a group of bioactive peptides that hold great potential as biotherapeutics, especially at a time when novel and more effective therapies are required. With this review, we provide insight into the latest developments made toward the therapeutic applications and production of lanthipeptides, specifically looking at heterologous expression systems.
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Affiliation(s)
- Anton Du Preez van Staden
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
- Division of Clinical Pharmacology, Department Medicine, Stellenbosch University, Stellenbosch, South Africa
| | - Winschau F. van Zyl
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
| | - Leon M. T. Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Carine Smith
- Division of Clinical Pharmacology, Department Medicine, Stellenbosch University, Stellenbosch, South Africa
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49
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Liu D, Rubin GM, Dhakal D, Chen M, Ding Y. Biocatalytic synthesis of peptidic natural products and related analogues. iScience 2021; 24:102512. [PMID: 34041453 PMCID: PMC8141463 DOI: 10.1016/j.isci.2021.102512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Peptidic natural products (PNPs) represent a rich source of lead compounds for the discovery and development of therapeutic agents for the treatment of a variety of diseases. However, the chemical synthesis of PNPs with diverse modifications for drug research is often faced with significant challenges, including the unavailability of constituent nonproteinogenic amino acids, inefficient cyclization protocols, and poor compatibility with other functional groups. Advances in the understanding of PNP biosynthesis and biocatalysis provide a promising, sustainable alternative for the synthesis of these compounds and their analogues. Here we discuss current progress in using native and engineered biosynthetic enzymes for the production of both ribosomally and nonribosomally synthesized peptides. In addition, we highlight new in vitro and in vivo approaches for the generation and screening of PNP libraries.
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Affiliation(s)
- Dake Liu
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Garret M. Rubin
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
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50
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Weerasinghe NW, Habibi Y, Uggowitzer KA, Thibodeaux CJ. Exploring the Conformational Landscape of a Lanthipeptide Synthetase Using Native Mass Spectrometry. Biochemistry 2021; 60:1506-1519. [PMID: 33887902 DOI: 10.1021/acs.biochem.1c00085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lanthipeptides are ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. These genetically encoded peptides are biosynthesized by multifunctional enzymes (lanthipeptide synthetases) that possess relaxed substrate specificity and catalyze iterative rounds of post-translational modification. Recent evidence has suggested that some lanthipeptide synthetases are structurally dynamic enzymes that are allosterically activated by precursor peptide binding and that conformational sampling of the enzyme-peptide complex may play an important role in defining the efficiency and sequence of biosynthetic events. These "biophysical" processes, while critical for defining the activity and function of the synthetase, remain very challenging to study with existing methodologies. Herein, we show that native mass spectrometry coupled to ion mobility (native IM-MS) provides a powerful and sensitive means for investigating the conformational landscapes and intermolecular interactions of lanthipeptide synthetases. Namely, we demonstrate that the class II lanthipeptide synthetase (HalM2) and its noncovalent complex with the cognate HalA2 precursor peptide can be delivered into the gas phase in a manner that preserves native structures and intermolecular enzyme-peptide contacts. Moreover, gas phase ion mobility studies of the natively folded ions demonstrate that peptide binding and mutations to dynamic structural elements of HalM2 alter the conformational landscape of the enzyme. Cumulatively, these data support previous claims that lanthipeptide synthetases are structurally dynamic enzymes that undergo functionally relevant conformational changes in response to precursor peptide binding. This work establishes native IM-MS as a versatile approach for characterizing intermolecular interactions and for unraveling the relationships between protein structure and biochemical function in RiPP biosynthetic systems.
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Affiliation(s)
- Nuwani W Weerasinghe
- Department of Chemistry and Centre de Recherche en Biologie Structurale, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Yeganeh Habibi
- Department of Chemistry and Centre de Recherche en Biologie Structurale, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Kevin A Uggowitzer
- Department of Chemistry and Centre de Recherche en Biologie Structurale, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Christopher J Thibodeaux
- Department of Chemistry and Centre de Recherche en Biologie Structurale, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
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