1
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Zeng P, Wang H, Zhang P, Leung SSY. Unearthing naturally-occurring cyclic antibacterial peptides and their structural optimization strategies. Biotechnol Adv 2024; 73:108371. [PMID: 38704105 DOI: 10.1016/j.biotechadv.2024.108371] [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: 11/10/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Natural products with antibacterial activity are highly desired globally to combat against multidrug-resistant (MDR) bacteria. Antibacterial peptide (ABP), especially cyclic ABP (CABP), is one of the abundant classes. Most of them were isolated from microbes, demonstrating excellent bactericidal effects. With the improved proteolytic stability, CABPs are normally considered to have better druggability than linear peptides. However, most clinically-used CABP-based antibiotics, such as colistin, also face the challenges of drug resistance soon after they reached the market, urgently requiring the development of next-generation succedaneums. We present here a detail review on the novel naturally-occurring CABPs discovered in the past decade and some of them are under clinical trials, exhibiting anticipated application potential. According to their chemical structures, they were broadly classified into five groups, including (i) lactam/lactone-based CABPs, (ii) cyclic lipopeptides, (iii) glycopeptides, (iv) cyclic sulfur-rich peptides and (v) multiple-modified CABPs. Their chemical structures, antibacterial spectrums and proposed mechanisms are discussed. Moreover, engineered analogs of these novel CABPs are also summarized to preliminarily analyze their structure-activity relationship. This review aims to provide a global perspective on research and development of novel CABPs to highlight the effectiveness of derivatives design in identifying promising antibacterial agents. Further research efforts in this area are believed to play important roles in fighting against the multidrug-resistance crisis.
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Affiliation(s)
- Ping Zeng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Honglan Wang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Pengfei Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sharon Shui Yee Leung
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong.
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2
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Sugrue I, Ross RP, Hill C. Bacteriocin diversity, function, discovery and application as antimicrobials. Nat Rev Microbiol 2024:10.1038/s41579-024-01045-x. [PMID: 38730101 DOI: 10.1038/s41579-024-01045-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2024] [Indexed: 05/12/2024]
Abstract
Bacteriocins are potent antimicrobial peptides that are produced by bacteria. Since their discovery almost a century ago, diverse peptides have been discovered and described, and some are currently used as commercial food preservatives. Many bacteriocins exhibit extensively post-translationally modified structures encoded on complex gene clusters, whereas others have simple linear structures. The molecular structures, mechanisms of action and resistance have been determined for a number of bacteriocins, but most remain incompletely characterized. These gene-encoded peptides are amenable to bioengineering strategies and heterologous expression, enabling metagenomic mining and modification of novel antimicrobials. The ongoing global antimicrobial resistance crisis demands that novel therapeutics be developed to combat infectious pathogens. New compounds that are target-specific and compatible with the resident microbiota would be valuable alternatives to current antimicrobials. As bacteriocins can be broad or narrow spectrum in nature, they are promising tools for this purpose. However, few bacteriocins have gone beyond preclinical trials and none is currently used therapeutically in humans. In this Review, we explore the broad diversity in bacteriocin structure and function, describe identification and optimization methods and discuss the reasons behind the lack of translation beyond the laboratory of these potentially valuable antimicrobials.
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Affiliation(s)
- Ivan Sugrue
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
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3
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Carson DV, Juarez RJ, Do T, Yang Z, James Link A. Antimicrobial Lasso Peptide Cloacaenodin Utilizes a Unique TonB-Dependent Transporter to Access Susceptible Bacteria. ACS Chem Biol 2024; 19:981-991. [PMID: 38527226 PMCID: PMC11031277 DOI: 10.1021/acschembio.4c00009] [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] [Indexed: 03/27/2024]
Abstract
The development of new antimicrobial agents effective against Gram-negative bacteria remains a major challenge in drug discovery. The lasso peptide cloacaenodin has potent antimicrobial activity against multiple strains in the Enterobacter genus, one of the ESKAPE pathogens. Here, we show that cloacaenodin uses a previously uncharacterized TonB-dependent transporter, which we name CloU, to cross the outer membrane (OM) of susceptible bacteria. Inner membrane transport is mediated by the protein SbmA. CloU is distinct from the known OM transporters (FhuA and PupB) utilized by other antimicrobial lasso peptides and thus offers important insight into the spectrum of activity of cloacaenodin. Using knowledge of the transport pathway to predict other cloacaenodin-susceptible strains, we demonstrate the activity of cloacaenodin against clinical isolates of Enterobacter and of a Kluyvera strain. Further, we use molecular dynamics simulations and mutagenesis of CloU to explain the variation in cloacaenodin susceptibility observed across different strains of Enterobacter. This work expands the currently limited understanding of lasso peptide uptake and advances the potential of cloacaenodin as an antibiotic.
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Affiliation(s)
- Drew V. Carson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Reecan J. Juarez
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Truc Do
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Zhongyue Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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4
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Baquero F, Beis K, Craik DJ, Li Y, Link AJ, Rebuffat S, Salomón R, Severinov K, Zirah S, Hegemann JD. The pearl jubilee of microcin J25: thirty years of research on an exceptional lasso peptide. Nat Prod Rep 2024; 41:469-511. [PMID: 38164764 DOI: 10.1039/d3np00046j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Covering: 1992 up to 2023Since their discovery, lasso peptides went from peculiarities to be recognized as a major family of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products that were shown to be spread throughout the bacterial kingdom. Microcin J25 was first described in 1992, making it one of the earliest known lasso peptides. No other lasso peptide has since then been studied to such an extent as microcin J25, yet, previous review articles merely skimmed over all the research done on this exceptional lasso peptide. Therefore, to commemorate the 30th anniversary of its first report, we give a comprehensive overview of all literature related to microcin J25. This review article spans the early work towards the discovery of microcin J25, its biosynthetic gene cluster, and the elucidation of its three-dimensional, threaded lasso structure. Furthermore, the current knowledge about the biosynthesis of microcin J25 and lasso peptides in general is summarized and a detailed overview is given on the biological activities associated with microcin J25, including means of self-immunity, uptake into target bacteria, inhibition of the Gram-negative RNA polymerase, and the effects of microcin J25 on mitochondria. The in vitro and in vivo models used to study the potential utility of microcin J25 in a (veterinary) medicine context are discussed and the efforts that went into employing the microcin J25 scaffold in bioengineering contexts are summed up.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- Network Center for Research in Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire OX11 0FA, UK
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, 4072 Brisbane, Queensland, Australia
| | - Yanyan Li
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - A James Link
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Raúl Salomón
- Instituto de Química Biológica "Dr Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán, Argentina
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany.
- Department of Pharmacy, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
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5
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Pfeiffer IPM, Schröder MP, Mordhorst S. Opportunities and challenges of RiPP-based therapeutics. Nat Prod Rep 2024. [PMID: 38411278 DOI: 10.1039/d3np00057e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Covering: up to 2024Ribosomally synthesised and post-translationally modified peptides (RiPPs) comprise a substantial group of peptide natural products exhibiting noteworthy bioactivities ranging from antiinfective to anticancer and analgesic effects. Furthermore, RiPP biosynthetic pathways represent promising production routes for complex peptide drugs, and the RiPP technology is well-suited for peptide engineering to produce derivatives with specific functions. Thus, RiPP natural products possess features that render them potentially ideal candidates for drug discovery and development. Nonetheless, only a small number of RiPP-derived compounds have successfully reached the market thus far. This review initially outlines the therapeutic opportunities that RiPP-based compounds can offer, whilst subsequently discussing the limitations that require resolution in order to fully exploit the potential of RiPPs towards the development of innovative drugs.
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Affiliation(s)
- Isabel P-M Pfeiffer
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| | - Maria-Paula Schröder
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| | - Silja Mordhorst
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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6
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Cha Y, Kim W, Park Y, Kim M, Son Y, Park W. Antagonistic actions of Paucibacter aquatile B51 and its lasso peptide paucinodin toward cyanobacterial bloom-forming Microcystis aeruginosa PCC7806. JOURNAL OF PHYCOLOGY 2024; 60:152-169. [PMID: 38073162 DOI: 10.1111/jpy.13412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/04/2023] [Accepted: 11/08/2023] [Indexed: 02/17/2024]
Abstract
Superior antagonistic activity against axenic Microcystis aeruginosa PCC7806 was observed with Paucibacter sp. B51 isolated from cyanobacterial bloom samples among 43 tested freshwater bacterial species. Complete genome sequencing, analyzing average nucleotide identity and digital DNA-DNA hybridization, designated the B51 strain as Paucibacter aquatile. Electron and fluorescence microscopic image analyses revealed the presence of the B51 strain in the vicinity of M. aeruginosa cells, which might provoke direct inhibition of the photosynthetic activity of the PCC7806 cells, leading to perturbation of cellular metabolisms and consequent cell death. Our speculation was supported by the findings that growth failure of the PCC7806 cells led to low pH conditions with fewer chlorophylls and down-regulation of photosystem genes (e.g., psbD and psaB) during their 48-h co-culture condition. Interestingly, the concentrated ethyl acetate extracts obtained from B51-grown supernatant exhibited a growth-inhibitory effect on PCC7806. The physical separation of both strains by a filter system led to no inhibitory activity of the B51 cells, suggesting that contact-mediated anti-cyanobacterial compounds might also be responsible for hampering the growth of the PCC7806 cells. Bioinformatic tools identified 12 gene clusters that possibly produce secondary metabolites, including a class II lasso peptide in the B51 genome. Further chemical analysis demonstrated anti-cyanobacterial activity from fractionated samples having a rubrivinodin-like lasso peptide, named paucinodin. Taken together, both contact-mediated inhibition of photosynthesis and the lasso peptide secretion of the B51 strain are responsible for the anti-cyanobacterial activity of P. aquatile B51.
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Affiliation(s)
- Yeji Cha
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Yerim Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Yongjun Son
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
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7
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Fernandez HN, Kretsch AM, Kunakom S, Kadjo AE, Mitchell DA, Eustáquio AS. High-Yield Lasso Peptide Production in a Burkholderia Bacterial Host by Plasmid Copy Number Engineering. ACS Synth Biol 2024; 13:337-350. [PMID: 38194362 PMCID: PMC10947786 DOI: 10.1021/acssynbio.3c00597] [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] [Indexed: 01/10/2024]
Abstract
The knotted configuration of lasso peptides confers thermal stability and proteolytic resistance, addressing two shortcomings of peptide-based drugs. However, low isolation yields hinder the discovery and development of lasso peptides. While testing Burkholderia sp. FERM BP-3421 as a bacterial host to produce the lasso peptide capistruin, an overproducer clone was previously identified. In this study, we show that an increase in the plasmid copy number partially contributed to the overproducer phenotype. Further, we modulated the plasmid copy number to recapitulate titers to an average of 160% relative to the overproducer, which is 1000-fold higher than previously reported with E. coli, reaching up to 240 mg/L. To probe the applicability of the developed tools for lasso peptide discovery, we targeted a new lasso peptide biosynthetic gene cluster from endosymbiont Mycetohabitans sp. B13, leading to the isolation of mycetolassin-15 and mycetolassin-18 in combined titers of 11 mg/L. These results validate Burkholderia sp. FERM BP-3421 as a production platform for lasso peptide discovery.
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Affiliation(s)
- Hannah N. Fernandez
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Ashley M. Kretsch
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sylvia Kunakom
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Adjo E. Kadjo
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Douglas A. Mitchell
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alessandra S. Eustáquio
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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8
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Kim B, Han SR, Lee H, Oh TJ. Insights into group-specific pattern of secondary metabolite gene cluster in Burkholderia genus. Front Microbiol 2024; 14:1302236. [PMID: 38293557 PMCID: PMC10826400 DOI: 10.3389/fmicb.2023.1302236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
Burkholderia is a versatile strain that has expanded into several genera. It has been steadily reported that the genome features of Burkholderia exhibit activities ranging from plant growth promotion to pathogenicity across various isolation areas. The objective of this study was to investigate the secondary metabolite patterns of 366 Burkholderia species through comparative genomics. Samples were selected based on assembly quality assessment and similarity below 80% in average nucleotide identity. Duplicate samples were excluded. Samples were divided into two groups using FastANI analysis. Group A included B. pseudomallei complex. Group B included B. cepacia complex. The limitations of MLST were proposed. The detection of genes was performed, including environmental and virulence-related genes. In the pan-genome analysis, each complex possessed a similar pattern of cluster for orthologous groups. Group A (n = 185) had 14,066 cloud genes, 2,465 shell genes, 682 soft-core genes, and 2,553 strict-core genes. Group B (n = 181) had 39,867 cloud genes, 4,986 shell genes, 324 soft-core genes, 222 core genes, and 2,949 strict-core genes. AntiSMASH was employed to analyze the biosynthetic gene cluster (BGC). The results were then utilized for network analysis using BiG-SCAPE and CORASON. Principal component analysis was conducted and a table was constructed using the results obtained from antiSMASH. The results were divided into Group A and Group B. We expected the various species to show similar patterns of secondary metabolite gene clusters. For in-depth analysis, a network analysis of secondary metabolite gene clusters was conducted, exemplified by BiG-SCAPE analysis. Depending on the species and complex, Burkholderia possessed several kinds of siderophore. Among them, ornibactin was possessed in most Burkholderia and was clustered into 4,062 clans. There was a similar pattern of gene clusters depending on the species. NRPS_04014 belonged to siderophore BGCs including ornibactin and indigoidine. However, it was observed that each family included a similar species. This suggests that, besides siderophores being species-specific, the ornibactin gene cluster itself might also be species-specific. The results suggest that siderophores are associated with environmental adaptation, possessing a similar pattern of siderophore gene clusters among species, which could provide another perspective on species-specific environmental adaptation mechanisms.
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Affiliation(s)
- Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
| | - So-Ra Han
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
| | - Hyun Lee
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
- Division of Computer Science and Engineering, SunMoon University, Asan, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, Republic of Korea
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9
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Prieto Maradona M, Querol A, Sijtsma L, Suarez JE, Sundh I, Barizzone F, Correia S, Herman L. Update of the list of qualified presumption of safety (QPS) recommended microbiological agents intentionally added to food or feed as notified to EFSA 19: Suitability of taxonomic units notified to EFSA until September 2023. EFSA J 2024; 22:e8517. [PMID: 38213415 PMCID: PMC10782250 DOI: 10.2903/j.efsa.2024.8517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024] Open
Abstract
The qualified presumption of safety (QPS) process was developed to provide a safety assessment approach for microorganisms intended for use in food or feed chains. The QPS approach is based on an assessment of published data for each taxonomic unit (TU), with respect to its taxonomic identity, the body of relevant knowledge and safety concerns. Safety concerns identified for a TU are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this Statement, no new information was found that would change the status of previously recommended QPS TUs. Of 71 microorganisms notified to EFSA between April and September 2023 (30 as feed additives, 22 as food enzymes or additives, 7 as novel foods and 12 from plant protection products [PPP]), 61 were not evaluated because: 26 were filamentous fungi, 1 was Enterococcus faecium, 5 were Escherichia coli, 1 was a bacteriophage (all excluded from the QPS evaluation) and 28 were TUs that already have a QPS status. The other 10 notifications belonged to 9 TUs which were evaluated for a possible QPS status: Ensifer adhaerens and Heyndrickxia faecalis did not get the QPS recommendation due to the limited body of knowledge about their occurrence in the food and/or feed chains and Burkholderia ubonensis also due to its ability to generate biologically active compounds with antimicrobial activity; Klebsiella pneumoniae, Serratia marcescens and Pseudomonas putida due to safety concerns. K. pneumoniae is excluded from future QPS evaluations. Chlamydomonas reinhardtii is recommended for QPS status with the qualification 'for production purposes only'; Clostridium tyrobutyricum is recommended for QPS status with the qualification 'absence of genetic determinants for toxigenic activity'; Candida oleophila has been added as a synonym of Yarrowia lipolytica. The Panel clarifies the extension of the QPS status for genetically modified strains.
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10
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Carson DV, Zhang Y, So L, Cheung-Lee WL, Cartagena AJ, Darst SA, Link AJ. Discovery, Characterization, and Bioactivity of the Achromonodins: Lasso Peptides Encoded by Achromobacter. JOURNAL OF NATURAL PRODUCTS 2023; 86:2448-2456. [PMID: 37870195 PMCID: PMC10949989 DOI: 10.1021/acs.jnatprod.3c00536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Through genome mining efforts, two lasso peptide biosynthetic gene clusters (BGCs) within two different species of Achromobacter, a genus that contains pathogenic organisms that can infect patients with cystic fibrosis, were discovered. Using gene-refactored BGCs in E. coli, these lasso peptides, which were named achromonodin-1 and achromonodin-2, were heterologously expressed. Achromonodin-1 is naturally encoded by certain isolates from the sputum of patients with cystic fibrosis. The NMR structure of achromonodin-1 was determined, demonstrating that it is a threaded lasso peptide with a large loop and short tail structure, reminiscent of previously characterized lasso peptides that inhibit RNA polymerase (RNAP). Achromonodin-1 inhibits RNAP in vitro and has potent, focused activity toward Achromobacter pulmonis, another isolate from the sputum of a cystic fibrosis patient. These efforts expand the repertoire of antimicrobial lasso peptides and provide insights into how Achromobacter isolates from certain ecological niches interact with each other.
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Affiliation(s)
- Drew V. Carson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Yi Zhang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Larry So
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Wai Ling Cheung-Lee
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Alexis Jaramillo Cartagena
- Laboratory of Molecular Biophysics and Tri-Institutional Training Program in Chemical Biology, Rockefeller University, New York, NY 10065, United States
| | - Seth A. Darst
- Laboratory of Molecular Biophysics and Tri-Institutional Training Program in Chemical Biology, Rockefeller University, New York, NY 10065, 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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11
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Yang ZJ, Shao Q, Jiang Y, Jurich C, Ran X, Juarez RJ, Yan B, Stull SL, Gollu A, Ding N. Mutexa: A Computational Ecosystem for Intelligent Protein Engineering. J Chem Theory Comput 2023; 19:7459-7477. [PMID: 37828731 PMCID: PMC10653112 DOI: 10.1021/acs.jctc.3c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Indexed: 10/14/2023]
Abstract
Protein engineering holds immense promise in shaping the future of biomedicine and biotechnology. This Review focuses on our ongoing development of Mutexa, a computational ecosystem designed to enable "intelligent protein engineering". In this vision, researchers will seamlessly acquire sequences of protein variants with desired functions as biocatalysts, therapeutic peptides, and diagnostic proteins through a finely-tuned computational machine, akin to Amazon Alexa's role as a versatile virtual assistant. The technical foundation of Mutexa has been established through the development of a database that combines and relates enzyme structures and their respective functions (e.g., IntEnzyDB), workflow software packages that enable high-throughput protein modeling (e.g., EnzyHTP and LassoHTP), and scoring functions that map the sequence-structure-function relationship of proteins (e.g., EnzyKR and DeepLasso). We will showcase the applications of these tools in benchmarking the convergence conditions of enzyme functional descriptors across mutants, investigating protein electrostatics and cavity distributions in SAM-dependent methyltransferases, and understanding the role of nonelectrostatic dynamic effects in enzyme catalysis. Finally, we will conclude by addressing the future steps and fundamental challenges in our endeavor to develop new Mutexa applications that assist the identification of beneficial mutants in protein engineering.
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Affiliation(s)
- Zhongyue J. Yang
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data
Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Qianzhen Shao
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Yaoyukun Jiang
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Christopher Jurich
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Xinchun Ran
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Reecan J. Juarez
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Bailu Yan
- Department
of Biostatistics, Vanderbilt University, Nashville, Tennessee 37205, United States
| | - Sebastian L. Stull
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Anvita Gollu
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ning Ding
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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12
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Choi GH, Holzapfel WH, Todorov SD. Diversity of the bacteriocins, their classification and potential applications in combat of antibiotic resistant and clinically relevant pathogens. Crit Rev Microbiol 2023; 49:578-597. [PMID: 35731254 DOI: 10.1080/1040841x.2022.2090227] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/18/2022] [Accepted: 06/13/2022] [Indexed: 12/19/2022]
Abstract
There is almost a century since discovery of penicillin by Alexander Fleming, a century of enthusiasm, abuse, facing development of antibiotic-resistance and clear conclusion that the modern medicine needs a new type of antimicrobials. Bacteriocins produced by Gram-positive and Gram-negative bacteria, Archaea and Eukaryotes were widely explored as potential antimicrobials with several applications in food industry. In last two decades bacteriocins showed their potential as promising alternative therapeutic for the treatment of antibiotic-resistant pathogens. Bacteriocins can be characterised as highly selective antimicrobials and therapeutics with low cytotoxicity. Most probably in order to solve the problems associated with the increasing number of antibiotic-resistant bacteria, the application of natural or bioengineered bacteriocins in addition to synergistically acting preparations of bacteriocins and conventional antibiotics, can be the next step in combat versus drug-resistant pathogens. In this overview we focussed on diversity of specific lactic acid bacteria and their bacteriocins. Moreover, some additional examples of bacteriocins from non-lactic acid, Gram-positive and Gram-negative bacteria, Archaea and eukaryotic organisms are presented and discussed. Therapeutic properties of bacteriocins, their bioengineering and combined applications, together with conventional antibiotics, were evaluated with the scope of application in human and veterinary medicine for combating (multi-)drug-resistant pathogens.
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Affiliation(s)
- Gee-Hyeun Choi
- ProBacLab, Department of Advanced Convergence, Handong Global University, Pohang, Republic of Korea
| | - Wilhelm Heinrich Holzapfel
- Human Effective Microbes, Department of Advanced Convergence, Handong Global University, Pohang, Republic of Korea
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13
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Cao L, Do T, Zhu A, Duan J, Alam N, Link AJ. Genome Mining and Discovery of Imiditides, a Family of RiPPs with a Class-Defining Aspartimide Modification. J Am Chem Soc 2023; 145:18834-18845. [PMID: 37595015 PMCID: PMC10947588 DOI: 10.1021/jacs.3c03991] [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] [Indexed: 08/20/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large and diverse class of natural products of ribosomal origin. In the past decade, various sophisticated machine-learning-based software packages have been established to discover novel RiPPs that do not resemble the known families. Here, we show that tailoring enzymes that cluster with various RiPP families can serve as effective bioinformatic seeds, providing a complementary approach for novel RiPP discovery. Leveraging the fact that O-methyltransferases homologous to protein isoaspartyl methyltransferases (PIMTs) are associated with lasso peptide, graspetide, and lanthipeptide biosynthetic gene clusters (BGCs), we utilized a C-terminal motif unique to RiPP-associated O-methyltransferases as the search query to discover a novel family of RiPPs, the imiditides. Our genome-mining algorithm reveals a total of 670 imiditide BGCs, distributed across Gram-positive bacterial genomes. In addition, we demonstrate the heterologous production of the founding member of the imiditide family, mNmaAM, encoded in the genome of Nonomuraea maritima. In contrast to other RiPP-associated PIMTs that recognize constrained peptides as substrates, the PIMT homologue in the mNmaAM BGC, NmaM, methylates a specific Asp residue on the linear precursor peptide, NmaA. The methyl ester is then turned into an aspartimide spontaneously. Substrate specificity is achieved by extensive charge-charge interactions between the precursor NmaA and the modifying enzyme NmaM suggested by both experiments and an AlphaFold model prediction. Our study shows that PIMT-mediated aspartimide formation is an emerging backbone modification strategy in the biosynthesis of multiple RiPP families.
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Affiliation(s)
- Li Cao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - Truc Do
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - Angela Zhu
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - Jianshu Duan
- Department of Geosciences, Princeton University, Princeton, NJ 08544, United States
| | - Nathan Alam
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
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14
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Cao L, Do T, Zhu AD, Alam N, Link AJ. Genome Mining and Discovery of Imiditides, a Novel Family of RiPPs with a Class-defining Aspartimide Modification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536058. [PMID: 37066262 PMCID: PMC10104114 DOI: 10.1101/2023.04.07.536058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a fascinating class of natural products of ribosomal origins. In the past decade, various sophisticated machine learning-based software packages have been established to discover novel RiPPs that do not resemble the known families. Instead, we argue that tailoring enzymes that cluster with various RiPP families can serve as effective bioinformatic seeds for novel RiPP discovery. Leveraging that O -methyltransferases homologous to protein isoaspartyl methyltransferases (PIMTs) are associated with lasso peptide, graspetide, and lanthipeptide biosynthetic gene clusters (BGCs), we utilized the C-terminal motif unique to RiPP-associated O -methyltransferases as the search query to discover a novel family of RiPPs, imiditides. Our genome-mining algorithm reveals a total of 670 imiditide BGCs, widely distributed in Gram-positive bacterial genomes. In addition, we demonstrate the heterologous production of the founding member of the imiditide family, mNmaA M , encoded in the genome of Nonomuraea maritima . In contrast to other RiPP associated PIMTs that recognize constrained peptides as substrates, the PIMT homolog in mNmaA M BGC, NmaM, methylates a specific Asp residue on the linear precursor peptide, NmaA. The methyl ester is then turned into an aspartimide spontaneously. The aspartimide moiety formed is unusually stable, leading to the accumulation of the aspartimidylated product in vivo . The substrate specificity is achieved by extensive charge-charge interactions between the precursor NmaA and the modifying enzyme NmaM suggested by both experimental validations as well as an AlphaFold model prediction. Our study suggests that PIMT-mediated aspartimide formation is an underappreciated backbone modification strategy in RiPP biosynthesis, compared to the well-studied backbone rigidification chemistries, such as thiazol(in)e and oxazol(in)e formations. Additionally, our findings suggest that aspartimide formation in Gram-positive bacterial proteomes are not limited to spontaneous protein aging and degradation. TOC Figure
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15
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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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16
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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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17
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Compilation of the Antimicrobial Compounds Produced by Burkholderia Sensu Stricto. Molecules 2023; 28:molecules28041646. [PMID: 36838633 PMCID: PMC9958762 DOI: 10.3390/molecules28041646] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/11/2023] Open
Abstract
Due to the increase in multidrug-resistant microorganisms, the investigation of novel or more efficient antimicrobial compounds is essential. The World Health Organization issued a list of priority multidrug-resistant bacteria whose eradication will require new antibiotics. Among them, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae are in the "critical" (most urgent) category. As a result, major investigations are ongoing worldwide to discover new antimicrobial compounds. Burkholderia, specifically Burkholderia sensu stricto, is recognized as an antimicrobial-producing group of species. Highly dissimilar compounds are among the molecules produced by this genus, such as those that are unique to a particular strain (like compound CF66I produced by Burkholderia cepacia CF-66) or antimicrobials found in a number of species, e.g., phenazines or ornibactins. The compounds produced by Burkholderia include N-containing heterocycles, volatile organic compounds, polyenes, polyynes, siderophores, macrolides, bacteriocins, quinolones, and other not classified antimicrobials. Some of them might be candidates not only for antimicrobials for both bacteria and fungi, but also as anticancer or antitumor agents. Therefore, in this review, the wide range of antimicrobial compounds produced by Burkholderia is explored, focusing especially on those compounds that were tested in vitro for antimicrobial activity. In addition, information was gathered regarding novel compounds discovered by genome-guided approaches.
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18
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Juarez RJ, Jiang Y, Tremblay M, Shao Q, Link AJ, Yang ZJ. LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling. J Chem Inf Model 2023; 63:522-530. [PMID: 36594886 PMCID: PMC10117200 DOI: 10.1021/acs.jcim.2c00945] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Lasso peptides are a subclass of ribosomally synthesized and post-translationally modified peptides with a slipknot conformation. With superior thermal stability, protease resistance, and antimicrobial activity, lasso peptides are promising candidates for bioengineering and pharmaceutical applications. To enable high-throughput computational prediction and design of lasso peptides, we developed a software, LassoHTP, for automatic lasso peptide structure construction and modeling. LassoHTP consists of three modules, including the scaffold constructor, mutant generator, and molecular dynamics (MD) simulator. With a user-provided sequence and conformational annotation, LassoHTP can either generate the structure and conformational ensemble as is or conduct random mutagenesis. We used LassoHTP to construct eight known lasso peptide structures de novo and to simulate their conformational ensembles for 100 ns MD simulations. For benchmarking, we calculated the root mean square deviation (RMSD) of these ensembles with reference to their experimental crystal or NMR PDB structures; we also compared these RMSD values against those of the MD ensembles that are initiated from the PDB structures. Dihedral principal component analysis was also conducted. The results show that the LassoHTP-initiated ensembles are similar to those of the PDB-initiated ensembles. LassoHTP offers a computational platform to develop strategies for lasso peptide prediction and design.
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Affiliation(s)
- Reecan J. Juarez
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Matthew Tremblay
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Chemistry and Molecular Biology, Princeton University, 207 Hoyt Laboratory, Princeton, New Jersey 08544, United States
| | - Zhongyue J. Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
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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: 3] [Impact Index Per Article: 3.0] [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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Carson DV, Patiño M, Elashal HE, Cartagena AJ, Zhang Y, Whitley ME, So L, Kayser-Browne AK, Earl AM, Bhattacharyya RP, Link AJ. Cloacaenodin, an Antimicrobial Lasso Peptide with Activity against Enterobacter. ACS Infect Dis 2023; 9:111-121. [PMID: 36519726 PMCID: PMC10038104 DOI: 10.1021/acsinfecdis.2c00446] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Using genome mining and heterologous expression, we report the discovery and production of a new antimicrobial lasso peptide from species related to the Enterobacter cloacae complex. Using NMR and mass spectrometric analysis, we show that this lasso peptide, named cloacaenodin, employs a threaded lasso fold which imparts proteolytic resistance that its unthreaded counterpart lacks. Cloacaenodin has selective, low micromolar, antimicrobial activity against species related to the E. cloacae complex, including species implicated in nosocomial infections and against clinical isolates of carbapenem-resistant Enterobacterales. We further used site-directed mutagenesis to probe the importance of specific residues to the peptide's biosynthesis, stability, and bioactivity.
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Affiliation(s)
- Drew V. Carson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Monica Patiño
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Hader E. Elashal
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Alexis Jaramillo Cartagena
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Yi Zhang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Megan E. Whitley
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Larry So
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Angelo K. Kayser-Browne
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Roby P. Bhattacharyya
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Infectious Diseases Division, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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21
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Xu Z, Eichler B, Klausner EA, Duffy-Matzner J, Zheng W. Lead/Drug Discovery from Natural Resources. Molecules 2022; 27:molecules27238280. [PMID: 36500375 PMCID: PMC9736696 DOI: 10.3390/molecules27238280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
Natural products and their derivatives have been shown to be effective drug candidates against various diseases for many years. Over a long period of time, nature has produced an abundant and prosperous source pool for novel therapeutic agents with distinctive structures. Major natural-product-based drugs approved for clinical use include anti-infectives and anticancer agents. This paper will review some natural-product-related potent anticancer, anti-HIV, antibacterial and antimalarial drugs or lead compounds mainly discovered from 2016 to 2022. Structurally typical marine bioactive products are also included. Molecular modeling, machine learning, bioinformatics and other computer-assisted techniques that are very important in narrowing down bioactive core structural scaffolds and helping to design new structures to fight against key disease-associated molecular targets based on available natural products are considered and briefly reviewed.
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Affiliation(s)
- Zhihong Xu
- Department of Chemistry and Biochemistry, Augustana University, 2001 S Summit Ave., Sioux Falls, SD 57197, USA
- Institute of Interventional & Vascular Surgery, Tongji University, Shanghai 200072, China
- Department of Pharmaceutical Sciences, South College School of Pharmacy, 400 Goody’s Lane, Knoxville, TN 37922, USA
- Correspondence: ; Tel.: +1-(605)-274-5008
| | - Barrett Eichler
- Department of Chemistry and Biochemistry, Augustana University, 2001 S Summit Ave., Sioux Falls, SD 57197, USA
| | - Eytan A. Klausner
- Department of Pharmaceutical Sciences, South College School of Pharmacy, 400 Goody’s Lane, Knoxville, TN 37922, USA
| | - Jetty Duffy-Matzner
- Department of Chemistry and Biochemistry, Augustana University, 2001 S Summit Ave., Sioux Falls, SD 57197, USA
| | - Weifan Zheng
- Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, 1801 Fayetteville St., Durham, NC 27707, USA
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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22
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Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK. Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides. Chem Rev 2022; 122:14722-14814. [PMID: 36049139 PMCID: PMC9897510 DOI: 10.1021/acs.chemrev.2c00210] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.
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Affiliation(s)
- Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Emily K. Desormeaux
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Adam DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
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Do T, Thokkadam A, Leach R, Link AJ. Phenotype-Guided Comparative Genomics Identifies the Complete Transport Pathway of the Antimicrobial Lasso Peptide Ubonodin in Burkholderia. ACS Chem Biol 2022; 17:2332-2343. [PMID: 35802499 PMCID: PMC9454059 DOI: 10.1021/acschembio.2c00420] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New antibiotics are needed as bacterial infections continue to be a leading cause of death, but efforts to develop compounds with promising antibacterial activity are hindered by a poor understanding of─and limited strategies for elucidating─their modes of action. We recently discovered a novel lasso peptide, ubonodin, that is active against opportunistic human lung pathogens from the Burkholderia cepacia complex (Bcc). Ubonodin inhibits RNA polymerase, but only select strains were susceptible, indicating that having a conserved cellular target does not guarantee activity. Given the cytoplasmic target, we hypothesized that cellular uptake of ubonodin determines susceptibility. Although Bcc strains harbor numerous nutrient uptake systems, these organisms lack close homologues of the single known lasso peptide membrane receptor, FhuA. Thus, a straightforward homology-driven approach failed to uncover the identity of the ubonodin transporter(s). Here, we used phenotype-guided comparative genomics to identify genes uniquely associated with ubonodin-susceptible Bcc strains, leading to the identification of PupB as the ubonodin outer membrane (OM) receptor in Burkholderia. The loss of PupB renders B. cepacia resistant to ubonodin, whereas expressing PupB sensitizes a resistant strain. We also examine how a conserved iron-regulated transcriptional pathway controls PupB to further tune ubonodin susceptibility. PupB is only the second lasso peptide OM receptor to be uncovered and the first outside of enterobacteria. Finally, we elucidate the full transport pathway for ubonodin by identifying its inner membrane receptor YddA in Burkholderia. Our work provides a complete picture of the mode of action of ubonodin and establishes a general framework for deciphering the transport pathways of other natural products with cytoplasmic targets.
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Affiliation(s)
- Truc Do
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - Alina Thokkadam
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - Robert Leach
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
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24
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Johnston CW, Badran AH. Natural and engineered precision antibiotics in the context of resistance. Curr Opin Chem Biol 2022; 69:102160. [PMID: 35660248 DOI: 10.1016/j.cbpa.2022.102160] [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: 12/02/2021] [Revised: 04/18/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022]
Abstract
Antibiotics are essential weapons in our fight against infectious disease, yet the consequences of broad-spectrum antibiotic use on microbiome stability and pathogen resistance are prompting investigations into more selective alternatives. Echoing the advent of precision medicine in oncology, precision antibiotics with focused activities are emerging as a means of addressing infections without damaging microbiomes or incentivizing resistance. Historically, antibiotic design principles have been gleaned from Nature, and reinvestigation of overlooked antibacterials is now providing scaffolds and targets for the design of pathogen-specific drugs. In this perspective, we summarize the biosynthetic and antibacterial mechanisms used to access these activities, and discuss how such strategies may be co-opted through engineering approaches to afford precision antibiotics.
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Affiliation(s)
- Chad W Johnston
- Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Ahmed H Badran
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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25
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Hegemann JD. Combined thermal and carboxypeptidase Y stability assays for probing the threaded fold of lasso peptides. Methods Enzymol 2022; 663:177-204. [PMID: 35168788 DOI: 10.1016/bs.mie.2021.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Lasso peptides are natural products belonging to the superfamily of ribosomally synthesized and post-translationally modified peptides (RiPPs). The defining characteristic of lasso peptides is their threaded structure, which is reminiscent of a lariat knot. When working with lasso peptides, it is therefore of major importance to understand and evidence their threaded folds. While the full elucidation of their three-dimensional structures via NMR spectroscopy or crystallization remains the gold standard, these methods are time-consuming, require large quantities of highly pure lasso peptides, and therefore might not always be applicable. Instead, the unique properties of lasso peptides in context of their behavior at elevated temperatures and toward carboxypeptidase Y treatment can be leveraged as a tool to investigate and evidence the threaded lasso fold using only minute amounts of compound that does not need to be purified first. This chapter will provide insights into the thermal stability properties of lasso peptides and their behavior when treated with carboxypeptidase Y in comparison to a branched-cyclic peptide with the same amino acid sequence. Furthermore, it will be described in detail how to set up a combined thermal and carboxypeptidase Y stability assay and how to analyze its outcomes.
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Affiliation(s)
- Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany.
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26
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Biosynthesis of Ditropolonyl Sulfide, an Antibacterial Compound Produced by Burkholderia cepacia Complex Strain R-12632. Appl Environ Microbiol 2021; 87:e0116921. [PMID: 34524894 DOI: 10.1128/aem.01169-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Burkholderia cepacia complex strain R-12632 produces ditropolonyl sulfide, an unusual sulfur-containing tropone, via a yet-unknown biosynthetic pathway. Ditropolonyl sulfide purified from a culture of strain R-12632 inhibits the growth of various Gram-positive and Gram-negative resistant bacteria, with MIC values as low as 16 μg/ml. In the present study, we used a transposon mutagenesis approach combined with metabolite analyses to identify the genetic basis for antibacterial activity of strain R-12632 against Gram-negative bacterial pathogens. Fifteen of the 8304 transposon mutants investigated completely lost antibacterial activity against Klebsiella pneumoniae LMG 2095. In these loss-of-activity mutants, nine genes were interrupted. Four of those genes were involved in assimilatory sulfate reduction, two were involved in phenylacetic acid (PAA) catabolism, and one was involved in glutathione metabolism. Via semipreparative fractionation and metabolite identification, it was confirmed that inactivation of the PAA degradation pathway or glutathione metabolism led to loss of ditropolonyl sulfide production. Based on earlier studies on the biosynthesis of tropolone compounds, the requirement for a functional PAA catabolic pathway for antibacterial activity in strain R-12632 indicated that this pathway likely provides the tropolone backbone for ditropolonyl sulfide. Loss of activity observed in mutants defective in assimilatory sulfate reduction and glutathione biosynthesis suggested that cysteine and glutathione are potential sources of the sulfur atom linking the two tropolone moieties. The demonstrated antibacterial activity of the unusual antibacterial compound ditropolonyl sulfide warrants further studies into its biosynthesis and biological role. IMPORTANCE Burkholderia bacteria are historically known for their biocontrol properties and have been proposed as a promising and underexplored source of bioactive specialized metabolites. Burkholderia cepacia complex strain R-12632 inhibits various Gram-positive and Gram-negative resistant pathogens and produces numerous specialized metabolites, among which is ditropolonyl sulfide. This unusual antimicrobial has been poorly studied and its biosynthetic pathway remains unknown. In the present study, we performed transposon mutagenesis of strain R-12632 and performed genome and metabolite analyses of loss-of-activity mutants to study the genetic basis for antibacterial activity. Our results indicate that phenylacetic acid catabolism, assimilatory sulfate reduction, and glutathione metabolism are necessary for ditropolonyl sulfide production. These findings contribute to understanding of the biosynthesis and biological role of this unusual antimicrobial.
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27
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Wang M, Fage CD, He Y, Mi J, Yang Y, Li F, An X, Fan H, Song L, Zhu S, Tong Y. Recent Advances and Perspectives on Expanding the Chemical Diversity of Lasso Peptides. Front Bioeng Biotechnol 2021; 9:741364. [PMID: 34631682 PMCID: PMC8498205 DOI: 10.3389/fbioe.2021.741364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/13/2021] [Indexed: 12/16/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing family of natural products that exhibit a range of structures and bioactivities. Initially assembled from the twenty proteinogenic amino acids in a ribosome-dependent manner, RiPPs assume their peculiar bioactive structures through various post-translational modifications. The essential modifications representative of each subfamily of RiPP are performed on a precursor peptide by the so-called processing enzymes; however, various tailoring enzymes can also embellish the precursor peptide or processed peptide with additional functional groups. Lasso peptides are an interesting subfamily of RiPPs characterized by their unique lariat knot-like structure, wherein the C-terminal tail is inserted through a macrolactam ring fused by an isopeptide bond between the N-terminal amino group and an acidic side chain. Until recently, relatively few lasso peptides were found to be tailored with extra functional groups. Nevertheless, the development of new routes to diversify lasso peptides and thus introduce novel or enhanced biological, medicinally relevant, or catalytic properties is appealing. In this review, we highlight several strategies through which lasso peptides have been successfully modified and provide a brief overview of the latest findings on the tailoring of these peptides. We also propose future directions for lasso peptide tailoring as well as potential applications for these peptides in hybrid catalyst design.
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Affiliation(s)
- Mengjiao Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Christopher D Fage
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
| | - Yile He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jinhui Mi
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yang Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Fei Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.,Clinical Laboratory Center, Taian City Central Hospital, Taian, China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shaozhou Zhu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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28
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Mullins AJ, Mahenthiralingam E. The Hidden Genomic Diversity, Specialized Metabolite Capacity, and Revised Taxonomy of Burkholderia Sensu Lato. Front Microbiol 2021; 12:726847. [PMID: 34650530 PMCID: PMC8506256 DOI: 10.3389/fmicb.2021.726847] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Burkholderia sensu lato is a collection of closely related genera within the family Burkholderiaceae that includes species of environmental, industrial, biotechnological, and clinical importance. Multiple species within the complex are the source of diverse specialized metabolites, many of which have been identified through genome mining of their biosynthetic gene clusters (BGCs). However, the full, true genomic diversity of these species and genera, and their biosynthetic capacity have not been investigated. This study sought to cluster and classify over 4000 Burkholderia sensu lato genome assemblies into distinct genomic taxa representing named and uncharacterized species. We delineated 235 species groups by average nucleotide identity analyses that formed seven distinct phylogenomic clades, representing the genera of Burkholderia sensu lato: Burkholderia, Paraburkholderia, Trinickia, Caballeronia, Mycetohabitans, Robbsia, and Pararobbisa. A total of 137 genomic taxa aligned with named species possessing a sequenced type strain, while 93 uncharacterized species groups were demarcated. The 95% ANI threshold proved capable of delineating most genomic species and was only increased to resolve several closely related species. These analyses enabled the assessment of species classifications of over 4000 genomes, and the correction of over 400 genome taxonomic assignments in public databases into existing and uncharacterized genomic species groups. These species groups were genome mined for BGCs, their specialized metabolite capacity calculated per species and genus, and the number of distinct BGCs per species estimated through kmer-based de-replication. Mycetohabitans species dedicated a larger proportion of their relatively small genomes to specialized metabolite biosynthesis, while Burkholderia species harbored more BGCs on average per genome and possessed the most distinct BGCs per species compared to the remaining genera. Exploring the hidden genomic diversity of this important multi-genus complex contributes to our understanding of their taxonomy and evolutionary relationships, and supports future efforts toward natural product discovery.
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29
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de Siqueira KA, Liotti RG, de Sousa JR, Vendruscullo SJ, de Souza GB, de Vasconcelos LG, Januário AH, de Oliveira Mendes TA, Soares MA. Streptomyces griseocarneus R132 expresses antimicrobial genes and produces metabolites that modulate Galleria mellonella immune system. 3 Biotech 2021; 11:396. [PMID: 34422537 DOI: 10.1007/s13205-021-02942-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/25/2021] [Indexed: 10/20/2022] Open
Abstract
Actinobacteria is a phylum composed of aerobic, Gram-positive, and filamentous bacteria with a broad spectrum of biological activity, including antioxidant, antitumor, and antibiotic. The crude extract of Streptomyces griseocarneus R132 was fractionated on a C18 silica column and the isolated compound was identified by 1H and 13C nuclear magnetic resonance as 3-(phenylprop-2-enoic acid), also known as trans-cinnamic acid. Antimicrobial activity against human pathogens was assayed in vitro (disk-diffusion qualitative test) and in vivo using Galleria mellonella larvae (RT-qPCR). The methanol fractions 132-F30%, 132-F50%, 132-F70%, and 132-F100% inhibited the Escherichia coli (ATCC 25922) and Staphylococcus aureus (MRSA) growth in vitro the most effectively. Compared with the untreated control (60-80% of larvae death), the fractions and isolated trans-cinnamic acid increased the survival rate and modulated the immune system of G. mellonella larvae infected with pathogenic microorganisms. The anti-infection effect of the S. griseocarneus R132 fermentation product led us to sequence its genome, which was assembled and annotated using the Rast and antiSMASH platforms. The assembled genome consisted of 227 scaffolds represented on a linear chromosome of 8.85 Mb and 71.3% of GC. We detected conserved domains typical of enzymes that produce molecules with biological activity, such as polyketides and non-ribosomal and ribosomal peptides, indicating a great potential for obtaining new antibiotics and molecules with biotechnological application. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02942-1.
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30
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Cao L, Beiser M, Koos JD, Orlova M, Elashal HE, Schröder HV, Link AJ. Cellulonodin-2 and Lihuanodin: Lasso Peptides with an Aspartimide Post-Translational Modification. J Am Chem Soc 2021; 143:11690-11702. [PMID: 34283601 PMCID: PMC9206484 DOI: 10.1021/jacs.1c05017] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Lasso peptides are a family of ribosomally synthesized and post-translationally modified peptides (RiPPs) defined by their threaded structure. Besides the class-defining isopeptide bond, other post-translational modifications (PTMs) that further tailor lasso peptides have been previously reported. Using genome mining tools, we identified a subset of lasso peptide biosynthetic gene clusters (BGCs) that are colocalized with genes encoding protein l-isoaspartyl methyltransferase (PIMT) homologues. PIMTs have an important role in protein repair, restoring isoaspartate residues formed from asparagine deamidation to aspartate. Here we report a new function for PIMT enzymes in the post-translational modification of lasso peptides. The PIMTs associated with lasso peptide BGCs first methylate an l-aspartate side chain found within the ring of the lasso peptide. The methyl ester is then converted into a stable aspartimide moiety, endowing the lasso peptide ring with rigidity relative to its unmodified counterpart. We describe the heterologous expression and structural characterization of two examples of aspartimide-modified lasso peptides from thermophilic Gram-positive bacteria. The lasso peptide cellulonodin-2 is encoded in the genome of actinobacterium Thermobifida cellulosilytica, while lihuanodin is encoded in the genome of firmicute Lihuaxuella thermophila. Additional genome mining revealed PIMT-containing lasso peptide BGCs in 48 organisms. In addition to heterologous expression, we have reconstituted PIMT-mediated aspartimide formation in vitro, showing that lasso peptide-associated PIMTs transfer methyl groups very rapidly as compared to canonical PIMTs. Furthermore, in stark contrast to other characterized lasso peptide PTMs, the methyltransferase functions only on lassoed substrates.
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Affiliation(s)
- Li Cao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - Moshe Beiser
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Joseph D. Koos
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
| | - Margarita Orlova
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - Hader E. Elashal
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - Hendrik V. Schröder
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
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31
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Bach E, Passaglia LMP, Jiao J, Gross H. Burkholderia in the genomic era: from taxonomy to the discovery of new antimicrobial secondary metabolites. Crit Rev Microbiol 2021; 48:121-160. [PMID: 34346791 DOI: 10.1080/1040841x.2021.1946009] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Species of Burkholderia are highly versatile being found not only abundantly in soil, but also as plants and animals' commensals or pathogens. Their complex multireplicon genomes harbour an impressive number of polyketide synthase (PKS) and nonribosomal peptide-synthetase (NRPS) genes coding for the production of antimicrobial secondary metabolites (SMs), which have been successfully deciphered by genome-guided tools. Moreover, genome metrics supported the split of this genus into Burkholderia sensu stricto (s.s.) and five new other genera. Here, we show that the successful antimicrobial SMs producers belong to Burkholderia s.s. Additionally, we reviewed the occurrence, bioactivities, modes of action, structural, and biosynthetic information of thirty-eight Burkholderia antimicrobial SMs shedding light on their diversity, complexity, and uniqueness as well as the importance of genome-guided strategies to facilitate their discovery. Several Burkholderia NRPS and PKS display unusual features, which are reflected in their structural diversity, important bioactivities, and varied modes of action. Up to now, it is possible to observe a general tendency of Burkholderia SMs being more active against fungi. Although the modes of action and biosynthetic gene clusters of many SMs remain unknown, we highlight the potential of Burkholderia SMs as alternatives to fight against new diseases and antibiotic resistance.
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Affiliation(s)
- Evelise Bach
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Junjing Jiao
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Harald Gross
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
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32
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Cao L, Do T, Link AJ. Mechanisms of action of ribosomally synthesized and posttranslationally modified peptides (RiPPs). J Ind Microbiol Biotechnol 2021; 48:6121428. [PMID: 33928382 PMCID: PMC8183687 DOI: 10.1093/jimb/kuab005] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/22/2021] [Indexed: 12/19/2022]
Abstract
Natural products remain a critical source of medicines and drug leads. One of the most rapidly growing superclasses of natural products is RiPPs: ribosomally synthesized and posttranslationally modified peptides. RiPPs have rich and diverse bioactivities. This review highlights examples of the molecular mechanisms of action that underly those bioactivities. Particular emphasis is placed on RiPP/target interactions for which there is structural information. This detailed mechanism of action work is critical toward the development of RiPPs as therapeutics and can also be used to prioritize hits in RiPP genome mining studies.
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Affiliation(s)
- Li Cao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Truc Do
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - A James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.,Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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33
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Stariha LM, McCafferty DG. Discovery of the Class I Antimicrobial Lasso Peptide Arcumycin. Chembiochem 2021; 22:2632-2640. [PMID: 34133845 DOI: 10.1002/cbic.202100132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/27/2021] [Indexed: 12/13/2022]
Abstract
Lasso peptides are a structurally diverse superfamily of conformationally constrained peptide natural products, of which a subset exhibits broad antimicrobial activity. Although advances in bioinformatics have increased our knowledge of strains harboring the biosynthetic machinery for lasso peptide production, relating peptide sequence to bioactivity remains a continuous challenge. To this end, genome mining investigation of Actinobacteria-produced antimicrobial lasso peptides was performed to correlate predicted structure with antibiotic activity. Bioinformatic evaluation revealed eight putative novel class I lasso peptide sequences. Fermentation of one of these hits, Streptomyces NRRL F-5639, resulted in the production of a novel class I lasso peptide, arcumycin. Arcumycin exhibited antibiotic activity against Gram-positive bacteria including Bacillus subtilis (4 μg/mL), Staphylococcus aureus (8 μg/mL), and Micrococcus luteus (8 μg/mL). Arcumycin treatment of B. subtilis liaI-β-gal promoter fusion reporter strain resulted in upregulation of the liaRS system by the promoter liaI, indicating arcumycin interferes with lipid II biosynthesis. Cumulatively, the results illustrate the relationship between phylogenetically related lasso peptides and their bioactivity as validated through the isolation, structural determination, and evaluation of bioactivity of the novel class I antimicrobial lasso peptide arcumycin.
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Affiliation(s)
- Lydia M Stariha
- Department of Chemistry, Duke University, Durham, NC, 27708-0346, USA
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34
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BING, a novel antimicrobial peptide isolated from Japanese medaka plasma, targets bacterial envelope stress response by suppressing cpxR expression. Sci Rep 2021; 11:12219. [PMID: 34108601 PMCID: PMC8190156 DOI: 10.1038/s41598-021-91765-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/25/2021] [Indexed: 12/16/2022] Open
Abstract
Antimicrobial peptides (AMPs) have emerged as a promising alternative to small molecule antibiotics. Although AMPs have previously been isolated in many organisms, efforts on the systematic identification of AMPs in fish have been lagging. Here, we collected peptides from the plasma of medaka (Oryzias latipes) fish. By using mass spectrometry, 6399 unique sequences were identified from the isolated peptides, among which 430 peptides were bioinformatically predicted to be potential AMPs. One of them, a thermostable 13-residue peptide named BING, shows a broad-spectrum toxicity against pathogenic bacteria including drug-resistant strains, at concentrations that presented relatively low toxicity to mammalian cell lines and medaka. Proteomic analysis indicated that BING treatment induced a deregulation of periplasmic peptidyl-prolyl isomerases in gram-negative bacteria. We observed that BING reduced the RNA level of cpxR, an upstream regulator of envelope stress responses. cpxR is known to play a crucial role in the development of antimicrobial resistance, including the regulation of genes involved in drug efflux. BING downregulated the expression of efflux pump components mexB, mexY and oprM in P. aeruginosa and significantly synergised the toxicity of antibiotics towards these bacteria. In addition, exposure to sublethal doses of BING delayed the development of antibiotic resistance. To our knowledge, BING is the first AMP shown to suppress cpxR expression in Gram-negative bacteria. This discovery highlights the cpxR pathway as a potential antimicrobial target.
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35
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Telhig S, Ben Said L, Zirah S, Fliss I, Rebuffat S. Bacteriocins to Thwart Bacterial Resistance in Gram Negative Bacteria. Front Microbiol 2020; 11:586433. [PMID: 33240239 PMCID: PMC7680869 DOI: 10.3389/fmicb.2020.586433] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/16/2020] [Indexed: 12/16/2022] Open
Abstract
An overuse of antibiotics both in human and animal health and as growth promoters in farming practices has increased the prevalence of antibiotic resistance in bacteria. Antibiotic resistant and multi-resistant bacteria are now considered a major and increasing threat by national health agencies, making the need for novel strategies to fight bugs and super bugs a first priority. In particular, Gram-negative bacteria are responsible for a high proportion of nosocomial infections attributable for a large part to Enterobacteriaceae, such as pathogenic Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. To cope with their highly competitive environments, bacteria have evolved various adaptive strategies, among which the production of narrow spectrum antimicrobial peptides called bacteriocins and specifically microcins in Gram-negative bacteria. They are produced as precursor peptides that further undergo proteolytic cleavage and in many cases more or less complex posttranslational modifications, which contribute to improve their stability and efficiency. Many have a high stability in the gastrointestinal tract where they can target a single pathogen whilst only slightly perturbing the gut microbiota. Several microcins and antibiotics can bind to similar bacterial receptors and use similar pathways to cross the double-membrane of Gram-negative bacteria and reach their intracellular targets, which they also can share. Consequently, bacteria may use common mechanisms of resistance against microcins and antibiotics. This review describes both unmodified and modified microcins [lasso peptides, siderophore peptides, nucleotide peptides, linear azole(in)e-containing peptides], highlighting their potential as weapons to thwart bacterial resistance in Gram-negative pathogens and discusses the possibility of cross-resistance and co-resistance occurrence between antibiotics and microcins in Gram-negative bacteria.
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Affiliation(s)
- Soufiane Telhig
- Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
- Laboratory Molecules of Communication and Adaptation of Microorganisms, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Laila Ben Said
- Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
| | - Séverine Zirah
- Laboratory Molecules of Communication and Adaptation of Microorganisms, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Ismail Fliss
- Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
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36
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How to harness biosynthetic gene clusters of lasso peptides. ACTA ACUST UNITED AC 2020; 47:703-714. [DOI: 10.1007/s10295-020-02292-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023]
Abstract
Abstract
Lasso peptides produced by bacteria have a very unique cyclic structure (“lasso” structure) and are resistant to protease. To date, a number of lasso peptides have been isolated from proteobacteria and actinobacteria. Many lasso peptides exhibit various biological activities, such as antibacterial activity, and are expected to have various applications. Based on study of genome mining, large numbers of biosynthetic gene cluster of lasso peptides are revealed to distribute over genomes of proteobacteria and actinobacteria. However, the biosynthetic gene clusters are cryptic in most cases. Therefore, the combination of genome mining and heterologous production is efficient method for the production of lasso peptides. To utilize lasso peptide as fine chemical, there have been several attempts to add new function to lasso peptide by genetic engineering. Currently, a more efficient lasso peptide production system is being developed to harness cryptic biosynthetic gene clusters of lasso peptide. In this review, the overview of lasso peptide study is discussed.
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Cheng C, Hua ZC. Lasso Peptides: Heterologous Production and Potential Medical Application. Front Bioeng Biotechnol 2020; 8:571165. [PMID: 33117783 PMCID: PMC7549694 DOI: 10.3389/fbioe.2020.571165] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/04/2020] [Indexed: 12/15/2022] Open
Abstract
Lasso peptides are natural products found in bacteria. They belong to a specific family of ribosomally-synthesized and posttranslationally-modified peptides with an unusual lasso structure. Lasso peptides possess remarkable thermal and proteolytic stability and various biological activities, such as antimicrobial activity, enzyme inhibition, receptor blocking, anticancer properties and HIV antagonism. They have promising potential therapeutic effects on gastrointestinal diseases, tuberculosis, Alzheimer’s disease, cardiovascular disease, fungal infections and cancer. Lasso peptides with high stability have been shown to be good carriers for other bioactive peptides. These make them attractive candidates for pharmaceutical research. This review aimed to describe the strategies used for the heterologous production of lasso peptides. Also, it indicated their therapeutical potential and their capacity to use as an efficient scaffold for epitope grafting.
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Affiliation(s)
- Cheng Cheng
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zi-Chun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.,School of Biopharmacy, China Pharmaceutical University, Nanjing, China.,Changzhou High-Tech Research Institute of Nanjing University, Changzhou, China.,Jiangsu Target Pharma Laboratories Inc., Changzhou, China
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Fuwa H, Hemmi H, Kaweewan I, Kozaki I, Honda H, Kodani S. Heterologous production of new lasso peptide koreensin based on genome mining. J Antibiot (Tokyo) 2020; 74:42-50. [PMID: 32855516 DOI: 10.1038/s41429-020-00363-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 11/09/2022]
Abstract
Lasso peptides are a class of ribosomally biosynthesized and posttranslationally modified peptides with a knot structure as a common motif. Based on a genome search, a new biosynthetic gene cluster of lasso peptide was found in the genome of the proteobacterium Sphingomonas koreensis. Interestingly, the amino acid sequence of the precursor peptide gene includes two cell adhesion motif sequences (KGD and DGR). Heterologous production of the new lasso peptide was performed using the cryptic biosynthetic gene cluster of S. koreensis. As a result, a new lasso peptide named koreensin was produced by the gene expression system in the host strain Sphingomonas subterranea. The structure of koreensin was determined by NMR and ESI-MS analysis. The three-dimensional structure of koreensin was obtained based on an NOE experiment and the coupling constants. A variant peptide (koreensin-RGD), which had RGD instead of KGD, was produced by heterologous production with site-directed mutagenesis experiment. Koreensin and koreensin-RGD did not show cell adhesion inhibitory activity, although the molecules possessed cell adhesion motifs. The possible presence of a salt bridge between the motifs in koreensin was indicated, and it may prevent the cell adhesion motif from functioning.
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Affiliation(s)
- Hiroki Fuwa
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hikaru Hemmi
- Food Research Institute, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Issara Kaweewan
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Ikko Kozaki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Hiroyuki Honda
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan. .,Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan. .,Academic Institute, Shizuoka University, Shizuoka, Japan.
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Abstract
Burkholderia bacteria are an emerging source of natural products with applications in agriculture and medicine. The heterologous expression of biosynthetic gene clusters can streamline natural product discovery; however, production yields with the commonly used Escherichia coli host are usually low. Following the current paradigm that one host does not fit all, we aim to develop a Burkholderia host to ultimately tap into the biosynthetic potential of Burkholderia genomes, which can contain up to 27 biosynthetic gene clusters per genome. Because a close phylogenetic relationship is expected to improve the odds of success due to compatible gene expression and precursor supply, we tested Burkholderia sp. FERM BP-3421, a nonpathogenic isolate previously used to produce natural products at industrial scales. We show here that FERM BP-3421 can produce the model lasso peptide capistruin in yields that are at least 65 times and up to 580 times higher than the previously used E. coli host.
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Affiliation(s)
- Sylvia Kunakom
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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