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Reyna-Campos AO, Ruiz-Villafan B, Macías-Rubalcava ML, Langley E, Rodríguez-Sanoja R, Sánchez S. Heterologous expression of lasso peptides with apparent participation in the morphological development in Streptomyces. AMB Express 2024; 14:97. [PMID: 39225916 PMCID: PMC11371967 DOI: 10.1186/s13568-024-01761-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Lasso peptides, ribosomally synthesized and post-translationally modified peptides, are primarily produced by bacteria and some archaea. Streptomyces lasso peptides have been known for their antimicrobial, anticancer, and antiviral properties. However, understanding their role in the morphology and production of secondary metabolites remains limited. We identified a previously unknown lasso peptide gene cluster in the genome of Streptomyces sp. L06. This gene cluster (LASS) produces two distinct lasso peptides, morphosin-1 and - 2. Notably, morphosin-2 is a member of a new subfamily of lasso peptides, with BGCs exhibiting a similar structure. When LASS was expressed in different Streptomyces hosts, it led to exciting phenotypic changes, including the absence of spores and damage in aerial mycelium development. In one of the hosts, LASS even triggered antibiotic formation. These findings open up a world of possibilities, suggesting the potential role of morphosins in shaping Streptomyces' morphological and biochemical development.
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Affiliation(s)
- Alma Ofelia Reyna-Campos
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), 04510, CdMx, Mexico
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, UNAM. , CdMx, 04510, Mexico
| | - Beatriz Ruiz-Villafan
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), 04510, CdMx, Mexico
| | | | - Elizabeth Langley
- Departmento de Investigación Básica, Instituto Nacional de Cancerología, CdMx, 14080, Mexico
| | - Romina Rodríguez-Sanoja
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), 04510, CdMx, Mexico
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), 04510, CdMx, Mexico.
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2
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Barrett SE, Mitchell DA. Advances in lasso peptide discovery, biosynthesis, and function. Trends Genet 2024:S0168-9525(24)00179-3. [PMID: 39218755 DOI: 10.1016/j.tig.2024.08.002] [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: 06/03/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
Lasso peptides are a large and sequence-diverse class of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products characterized by their slip knot-like shape. These unique, highly stable peptides are produced by bacteria for various purposes. Their stability and sequence diversity make them a potentially useful scaffold for biomedically relevant folded peptides. However, many questions remain about lasso peptide biosynthesis, ecological function, and diversification potential for biomedical and agricultural applications. This review discusses new insights and open questions about lasso peptide biosynthesis and biological function. The role that genome mining has played in the development of new methodologies for discovering and diversifying lasso peptides is also discussed.
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Affiliation(s)
- Susanna E Barrett
- Department of Chemistry at the University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology at University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Douglas A Mitchell
- Department of Chemistry at the University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology at University of Illinois Urbana-Champaign, Urbana, IL, USA.
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3
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Hoffmann A, Steffens U, Maček B, Franz-Wachtel M, Nieselt K, Harbig TA, Scherlach K, Hertweck C, Sahl HG, Bierbaum G. The unusual mode of action of the polyketide glycoside antibiotic cervimycin C. mSphere 2024; 9:e0076423. [PMID: 38722162 PMCID: PMC11237698 DOI: 10.1128/msphere.00764-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
Cervimycins A-D are bis-glycosylated polyketide antibiotics produced by Streptomyces tendae HKI 0179 with bactericidal activity against Gram-positive bacteria. In this study, cervimycin C (CmC) treatment caused a spaghetti-like phenotype in Bacillus subtilis 168, with elongated curved cells, which stayed joined after cell division, and exhibited a chromosome segregation defect, resulting in ghost cells without DNA. Electron microscopy of CmC-treated Staphylococcus aureus (3 × MIC) revealed swollen cells, misshapen septa, cell wall thickening, and a rough cell wall surface. Incorporation tests in B. subtilis indicated an effect on DNA biosynthesis at high cervimycin concentrations. Indeed, artificial downregulation of the DNA gyrase subunit B gene (gyrB) increased the activity of cervimycin in agar diffusion tests, and, in high concentrations (starting at 62.5 × MIC), the antibiotic inhibited S. aureus DNA gyrase supercoiling activity in vitro. To obtain a more global view on the mode of action of CmC, transcriptomics and proteomics of cervimycin treated versus untreated S. aureus cells were performed. Interestingly, 3 × MIC of cervimycin did not induce characteristic responses, which would indicate disturbance of the DNA gyrase activity in vivo. Instead, cervimycin induced the expression of the CtsR/HrcA heat shock operon and the expression of autolysins, exhibiting similarity to the ribosome-targeting antibiotic gentamicin. In summary, we identified the DNA gyrase as a target, but at low concentrations, electron microscopy and omics data revealed a more complex mode of action of cervimycin, which comprised induction of the heat shock response, indicating protein stress in the cell.IMPORTANCEAntibiotic resistance of Gram-positive bacteria is an emerging problem in modern medicine, and new antibiotics with novel modes of action are urgently needed. Secondary metabolites from Streptomyces species are an important source of antibiotics, like the cervimycin complex produced by Streptomyces tendae HKI 0179. The phenotypic response of Bacillus subtilis and Staphylococcus aureus toward cervimycin C indicated a chromosome segregation and septum formation defect. This effect was at first attributed to an interaction between cervimycin C and the DNA gyrase. However, omics data of cervimycin treated versus untreated S. aureus cells indicated a different mode of action, because the stress response did not include the SOS response but resembled the response toward antibiotics that induce mistranslation or premature chain termination and cause protein stress. In summary, these results point toward a possibly novel mechanism that generates protein stress in the cells and subsequently leads to defects in cell and chromosome segregation.
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Affiliation(s)
- Alina Hoffmann
- University Hospital Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Bonn, Germany
| | - Ursula Steffens
- University Hospital Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Bonn, Germany
| | - Boris Maček
- University of Tübingen, Proteome Center Tübingen, Tübingen, Germany
| | | | - Kay Nieselt
- University of Tübingen, Interfaculty Institute for Bioinformatics and Medical Informatics, Tübingen, Germany
| | - Theresa Anisja Harbig
- University of Tübingen, Interfaculty Institute for Bioinformatics and Medical Informatics, Tübingen, Germany
| | - Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
- Friedrich Schiller University Jena, Institute of Microbiology, Faculty of Biological Sciences, Jena, Germany
| | - Hans-Georg Sahl
- University of Bonn, Institute for Pharmaceutical Microbiology, Bonn, Germany
| | - Gabriele Bierbaum
- University Hospital Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Bonn, Germany
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4
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Kim W, Park Y, Jung J, Jeon CO, Toyofuku M, Lee J, Park W. Biological and Chemical Approaches for Controlling Harmful Microcystis Blooms. J Microbiol 2024; 62:249-260. [PMID: 38587591 DOI: 10.1007/s12275-024-00115-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 04/09/2024]
Abstract
The proliferation of harmful cyanobacterial blooms dominated by Microcystis aeruginosa has become an increasingly serious problem in freshwater ecosystems due to climate change and eutrophication. Microcystis-blooms in freshwater generate compounds with unpleasant odors, reduce the levels of dissolved O2, and excrete microcystins into aquatic ecosystems, potentially harming various organisms, including humans. Various chemical and biological approaches have thus been developed to mitigate the impact of the blooms, though issues such as secondary pollution and high economic costs have not been adequately addressed. Red clays and H2O2 are conventional treatment methods that have been employed worldwide for the mitigation of the blooms, while novel approaches, such as the use of plant or microbial metabolites and antagonistic bacteria, have also recently been proposed. Many of these methods rely on the generation of reactive oxygen species, the inhibition of photosynthesis, and/or the disruption of cellular membranes as their mechanisms of action, which may also negatively impact other freshwater microbiota. Nevertheless, the underlying molecular mechanisms of anticyanobacterial chemicals and antagonistic bacteria remain unclear. This review thus discusses both conventional and innovative approaches for the management of M. aeruginosa in freshwater bodies.
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Affiliation(s)
- Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Yerim Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Jaejoon Jung
- Department of Life Science, Chung-Ang University, Seoul, 02841, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 02841, Republic of Korea
| | - Masanori Toyofuku
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-0006, Japan
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, 43210, USA
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, 43210, USA
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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5
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Arbulu S, Kjos M. Revisiting the Multifaceted Roles of Bacteriocins : The Multifaceted Roles of Bacteriocins. MICROBIAL ECOLOGY 2024; 87:41. [PMID: 38351266 PMCID: PMC10864542 DOI: 10.1007/s00248-024-02357-4] [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: 12/08/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
Bacteriocins are gene-encoded antimicrobial peptides produced by bacteria. These peptides are heterogeneous in terms of structure, antimicrobial activities, biosynthetic clusters, and regulatory mechanisms. Bacteriocins are widespread in nature and may contribute to microbial diversity due to their capacity to target specific bacteria. Primarily studied as food preservatives and therapeutic agents, their function in natural settings is however less known. This review emphasizes the ecological significance of bacteriocins as multifunctional peptides by exploring bacteriocin distribution, mobility, and their impact on bacterial population dynamics and biofilms.
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Affiliation(s)
- Sara Arbulu
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
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6
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Rathinam AJ, Santhaseelan H, Dahms HU, Dinakaran VT, Murugaiah SG. Bioprospecting of unexplored halophilic actinobacteria against human infectious pathogens. 3 Biotech 2023; 13:398. [PMID: 37974926 PMCID: PMC10645811 DOI: 10.1007/s13205-023-03812-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023] Open
Abstract
Human pathogenic diseases received much attention recently due to their uncontrolled spread of antimicrobial resistance (AMR) which causes several threads every year. Effective alternate antimicrobials are urgently required to combat those disease causing infectious microbes. Halophilic actinobacteria revealed huge potentials and unexplored cultivable/non-cultivable actinobacterial species producing enormous antimicrobials have been proved in several genomics approaches. Potential gene clusters, PKS and NRPKS from Nocardia, Salinospora, Rhodococcus, and Streptomyces have wide range coding genes of secondary metabolites. Biosynthetic pathways identification via various approaches like genome mining, In silico, OSMAC (one strain many compound) analysis provides better identification of knowing the active metabolites using several databases like AMP, APD and CRAMPR, etc. Genome constellations of actinobacteria particularly the prediction of BGCs (Biosynthetic Gene Clusters) to mine the bioactive molecules such as pigments, biosurfactants and few enzymes have been reported for antimicrobial activity. Saltpan, saltlake, lagoon and haloalkali environment exploring potential actinobacterial strains Micromonospora, Kocuria, Pseudonocardia, and Nocardiopsis revealed several acids and ester derivatives with antimicrobial potential. Marine sediments and marine macro organisms have been found as significant population holders of potential actinobacterial strains. Deadly infectious diseases (IDs) including tuberculosis, ventilator-associated pneumonia and Candidiasis, have been targeted by halo-actinobacterial metabolites with promising results. Methicillin resistant Staphylococus aureus and virus like Encephalitic alphaviruses were potentially targeted by halophilic actinobacterial metabolites by the compound Homoseongomycin from sponge associated antinobacterium. In this review, we discuss the potential antimicrobial properties of various biomolecules extracted from the unexplored halophilic actinobacterial strains specifically against human infectious pathogens along with prospective genomic constellations.
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Affiliation(s)
- Arthur James Rathinam
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Henciya Santhaseelan
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708 Taiwan
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7
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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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8
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Zhen C, Chen XK, Ge XF, Liu WZ. Streptomonospora mangrovi sp. nov., isolated from mangrove soil showing similar metabolic capabilities, but distinct secondary metabolites profiles. Arch Microbiol 2023; 205:148. [PMID: 36991151 DOI: 10.1007/s00203-023-03501-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/31/2023]
Abstract
A novel actinomycete, designated strain S1-112 T, was isolated from a mangrove soil sample from Hainan, China, and characterized using a polyphasic approach. Strain S1-112 T showed the highest similarity of the 16S rRNA gene to Streptomonospora nanhaiensis 12A09T (99.24%). Their close relationship was further supported by phylogenetic analyses, which placed these two strains within a stable clade. The highest values of digital DNA-DNA hybridization (dDDH, 41.4%) and average nucleotide identity (ANI, 90.55%) were detected between strain S1-112 T and Streptomonospora halotolerans NEAU-Jh2-17 T. Genotypic and phenotypic characteristics demonstrated that strain S1-112 T could be distinguished from its closely related relatives. We also profiled the pan-genome and metabolic features of genomic assemblies of strains belonging to the genus Streptomonospora, indicating similar functional capacities and metabolic activities. However, all of these strains showed promising potential for producing diverse types of secondary metabolites. In conclusion, strain S1-112 T represents a novel species of the genus Streptomonospora, for which the name Streptomonospora mangrovi sp. nov. was proposed. The type strain is S1-112 T (= JCM 34292 T).
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Affiliation(s)
- Cheng Zhen
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Xin-Kai Chen
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Xian-Feng Ge
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Wen-Zheng Liu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China.
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9
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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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10
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Carson DV, Patiño M, Elashal HE, Cartagena AJ, Zhang Y, Whitley ME, So L, Kayser-Browne AK, Earl AM, Bhattacharyya RP, Link AJ. Cloacaenodin, an Antimicrobial Lasso Peptide with Activity against Enterobacter. ACS Infect Dis 2023; 9:111-121. [PMID: 36519726 PMCID: PMC10038104 DOI: 10.1021/acsinfecdis.2c00446] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Using genome mining and heterologous expression, we report the discovery and production of a new antimicrobial lasso peptide from species related to the Enterobacter cloacae complex. Using NMR and mass spectrometric analysis, we show that this lasso peptide, named cloacaenodin, employs a threaded lasso fold which imparts proteolytic resistance that its unthreaded counterpart lacks. Cloacaenodin has selective, low micromolar, antimicrobial activity against species related to the E. cloacae complex, including species implicated in nosocomial infections and against clinical isolates of carbapenem-resistant Enterobacterales. We further used site-directed mutagenesis to probe the importance of specific residues to the peptide's biosynthesis, stability, and bioactivity.
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Affiliation(s)
- Drew V. Carson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Monica Patiño
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Hader E. Elashal
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Alexis Jaramillo Cartagena
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Yi Zhang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Megan E. Whitley
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Larry So
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Angelo K. Kayser-Browne
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Roby P. Bhattacharyya
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Infectious Diseases Division, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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11
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Cervimycin-Resistant Staphylococcus aureus Strains Display Vancomycin-Intermediate Resistant Phenotypes. Microbiol Spectr 2022; 10:e0256722. [PMID: 36173303 PMCID: PMC9603734 DOI: 10.1128/spectrum.02567-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Resistance to antibiotics is an increasing problem and necessitates novel antibacterial therapies. The polyketide antibiotics cervimycin A to D are natural products of Streptomyces tendae HKI 0179 with promising activity against multidrug-resistant staphylococci and vancomycin-resistant enterococci. To initiate mode of action studies, we selected cervimycin C- and D-resistant (CmR) Staphylococcus aureus strains. Genome sequencing of CmR mutants revealed amino acid exchanges in the essential histidine kinase WalK, the Clp protease proteolytic subunit ClpP or the Clp ATPase ClpC, and the heat shock protein DnaK. Interestingly, all characterized CmR mutants harbored a combination of mutations in walK and clpP or clpC. In vitro and in vivo analyses showed that the mutations in the Clp proteins abolished ClpP or ClpC activity, and the deletion of clpP rendered S. aureus but not all Bacillus subtilis strains cervimycin-resistant. The essential gene walK was the second mutational hotspot in the CmR S. aureus strains, which decreased WalK activity in vitro and generated a vancomycin-intermediate resistant phenotype, with a thickened cell wall, a lower growth rate, and reduced cell lysis. Transcriptomic and proteomic analyses revealed massive alterations in the CmR strains compared to the parent strain S. aureus SG511, with major shifts in the heat shock regulon, the metal ion homeostasis, and the carbohydrate metabolism. Taken together, mutations in the heat shock genes clpP, clpC, and dnaK, and the walK kinase gene in CmR mutants induced a vancomycin-intermediate resistant phenotype in S. aureus, suggesting cell wall metabolism or the Clp protease system as primary target of cervimycin. IMPORTANCE Staphylococcus aureus is a frequent cause of infections in both the community and hospital setting. Resistance development of S. aureus to various antibiotics is a severe problem for the treatment of this pathogen worldwide. New powerful antimicrobial agents against Gram-positives are needed, since antibiotics like vancomycin fail to cure vancomycin-intermediate resistant S. aureus (VISA) and vancomycin-resistant enterococci (VRE) infections. One candidate substance with promising activity against these organisms is cervimycin, which is an antibiotic complex with a yet unknown mode of action. In our study, we provide first insights into the mode of action of cervimycins. By characterizing cervimycin-resistant S. aureus strains, we revealed the Clp system and the essential kinase WalK as mutational hotspots for cervimycin resistance in S. aureus. It further emerged that cervimycin-resistant S. aureus strains show a VISA phenotype, indicating a role of cervimycin in perturbing the bacterial cell envelope.
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12
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Nanudorn P, Thiengmag S, Biermann F, Erkoc P, Dirnberger SD, Phan TN, Fürst R, Ueoka R, Helfrich EJN. Atropopeptides are a Novel Family of Ribosomally Synthesized and Posttranslationally Modified Peptides with a Complex Molecular Shape. Angew Chem Int Ed Engl 2022; 61:e202208361. [PMID: 35939298 PMCID: PMC9826248 DOI: 10.1002/anie.202208361] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 01/11/2023]
Abstract
Biomacromolecules are known to feature complex three-dimensional shapes that are essential for their function. Among natural products, ambiguous molecular shapes are a rare phenomenon. The hexapeptide tryptorubin A can adopt one of two unusual atropisomeric configurations. Initially hypothesized to be a non-ribosomal peptide, we show that tryptorubin A is the first characterized member of a new family of ribosomally synthesized and posttranslationally modified peptides (RiPPs) that we named atropopeptides. The sole modifying enzyme encoded in the gene cluster, a cytochrome P450 monooxygenase, is responsible for the atropospecific formation of one carbon-carbon and two carbon-nitrogen bonds. The characterization of two additional atropopeptide biosynthetic pathways revealed a two-step maturation process. Atropopeptides promote pro-angiogenic cell functions as indicated by an increase in endothelial cell proliferation and undirected migration. Our study expands the biochemical space of RiPP-modifying enzymes and paves the way towards the chemoenzymatic utilization of atropopeptide-modifying P450s.
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Affiliation(s)
- Pakjira Nanudorn
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Sirinthra Thiengmag
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Friederike Biermann
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Pelin Erkoc
- LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany,Institute of Pharmaceutical BiologyGoethe University FrankfurtMax-von-Laue Strasse 960438FrankfurtGermany
| | - Sabrina D. Dirnberger
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Thao N. Phan
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Robert Fürst
- LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany,Institute of Pharmaceutical BiologyGoethe University FrankfurtMax-von-Laue Strasse 960438FrankfurtGermany
| | - Reiko Ueoka
- School of Marine BiosciencesKitasato University1-15-1 Kitasato, Minami-kuSagamiharaKanagawa, 252-0373Japan
| | - Eric J. N. Helfrich
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
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13
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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: 62] [Impact Index Per Article: 31.0] [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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14
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Nanudorn P, Thiengmag S, Biermann F, Erkoc P, Dirnberger SD, Phan TN, Fürst R, Ueoka R, Helfrich EJN. Atropopeptides are a Novel Family of Ribosomally Synthesized and Posttranslationally Modified Peptides with a Complex Molecular Shape. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Pakjira Nanudorn
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute for Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Sirinthra Thiengmag
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute for Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Friederike Biermann
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute for Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Pelin Erkoc
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute of Pharmaceutical Biology Biozentrum Building 230Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Sabrina Doris Dirnberger
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute for Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Thao Ngoc Phan
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute for Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Robert Fürst
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute of Pharmaceutical Biology Biozentrum Building 230Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Reiko Ueoka
- Kitasato University: Kitasato Daigaku School of Marine Biosciences 1-15-1 KitasatoMinami-kuSagamihara 252-0373 Kanagawa JAPAN
| | - Eric Jan Nikolaus Helfrich
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
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15
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Andersen FD, Pedersen KD, Wilkens Juhl D, Mygind T, Chopin P, B Svenningsen E, Poulsen TB, Braad Lund M, Schramm A, Gotfredsen CH, Tørring T. Triculamin: An Unusual Lasso Peptide with Potent Antimycobacterial Activity. JOURNAL OF NATURAL PRODUCTS 2022; 85:1514-1521. [PMID: 35748039 DOI: 10.1021/acs.jnatprod.2c00065] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Lasso peptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) produced by microorganisms. Here we show that the two natural products triculamin and alboverticillin, originally isolated in 1967 and 1958, respectively, with potent and specific activity against mycobacteria are in fact the same lasso peptide. We solved the structure using 2D NMR spectroscopy and expanded on the previously reported bioactivity. Through genome sequencing, we identify the responsible biosynthetic gene clusters, which curiously revealed that, unlike any known lasso peptides, their precursor peptides appear to have a follower instead of a leader peptide.
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Affiliation(s)
- Frederikke D Andersen
- Department of Biological and Chemical Engineering, Aarhus University, 8000 Aarhus C, Denmark
| | - Katja D Pedersen
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Dennis Wilkens Juhl
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
- Interdisciplinary Nanoscience Centre, Aarhus University, 8000 Aarhus C, Denmark
| | - Tobias Mygind
- Department of Biological and Chemical Engineering, Aarhus University, 8000 Aarhus C, Denmark
| | - Paul Chopin
- Department of Biological and Chemical Engineering, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Thomas B Poulsen
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Marie Braad Lund
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Andreas Schramm
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Thomas Tørring
- Department of Biological and Chemical Engineering, Aarhus University, 8000 Aarhus C, Denmark
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16
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Dutta B, Bandopadhyay R. Biotechnological potentials of halophilic microorganisms and their impact on mankind. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2022; 11:75. [PMID: 35669848 PMCID: PMC9152817 DOI: 10.1186/s43088-022-00252-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 05/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background Halophiles are extremophilic organisms represented by archaea, bacteria and eukaryotes that thrive in hypersaline environment. They apply different osmoadaptation strategies to survive in hostile conditions. Habitat diversity of halophilic microorganisms in hypersaline system provides information pertaining the evolution of life on Earth. Main body The microbiome-gut-brain axis interaction contributes greatly to the neurodegenerative diseases. Gut resident halophilic bacteria are used as alternative medication for chronic brain diseases. Halophiles can be used in pharmaceuticals, drug delivery, agriculture, saline waste water treatment, biodegradable plastic production, metal recovery, biofuel energy generation, concrete crack repair and other sectors. Furthermore, versatile biomolecules, mainly enzymes characterized by broad range of pH and thermostability, are suitable candidate for industrial purposes. Reflectance pattern of halophilic archaeal pigment rhodopsin is considered as potential biosignature for Earth-like planets. Short conclusions This review represents important osmoadaptation strategies acquired by halophilic archaea and bacteria and their potential biotechnological applications to resolve present day challenges. Graphical Abstract
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Affiliation(s)
- Bhramar Dutta
- Department of Botany, The University of Burdwan, Purba Bardhaman, West Bengal 713104 India
| | - Rajib Bandopadhyay
- Department of Botany, The University of Burdwan, Purba Bardhaman, West Bengal 713104 India
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17
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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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18
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Xiu H, Wang M, Fage CD, He Y, Niu X, Han M, Li F, An X, Fan H, Song L, Zheng G, Zhu S, Tong Y. Discovery and Characterization of Rubrinodin Provide Clues into the Evolution of Lasso Peptides. Biochemistry 2022; 61:595-607. [PMID: 35298141 DOI: 10.1021/acs.biochem.2c00029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lasso peptides are unique natural products that comprise a class of ribosomally synthesized and post-translationally modified peptides. Their defining three-dimensional structure is a lariat knot, in which the C-terminal tail is threaded through a macrolactam ring formed between the N-terminal amino group and an Asp or Glu side chain (i.e., an isopeptide bond). Recent genome mining strategies have revealed various types of lasso peptide biosynthetic gene clusters and have thus redefined the known chemical space of lasso peptides. To date, over 20 different types of these gene clusters have been discovered, including several different clades from Proteobacteria. Despite the diverse architectures of these gene clusters, which may or may not encode various tailoring enzymes, most currently known lasso peptides are synthesized by two discrete clades defined by the presence of an ATP-binding cassette transporter or its absence and (sometimes) concurrent appearance of an isopeptidase, raising questions about their evolutionary history. Herein, we discovered and characterized the lasso peptide rubrinodin, which is assembled by a gene cluster encoding both an ATP-binding cassette transporter and an isopeptidase. Our bioinformatics analyses of this and other representative cluster types provided new clues into the evolutionary history of lasso peptides. Furthermore, our structural and biochemical investigations of rubrinodin permitted the conversion of this thermolabile lasso peptide into a more thermostable scaffold.
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Affiliation(s)
- Huanhuan Xiu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Mengjiao Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | | | - Yile He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meng Han
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Fei Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Guojun Zheng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Shaozhou Zhu
- National Institutes for Food and Drug Control, Beijing 102629, People's Republic of China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
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19
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Recent Antimicrobial Responses of Halophilic Microbes in Clinical Pathogens. Microorganisms 2022; 10:microorganisms10020417. [PMID: 35208871 PMCID: PMC8874722 DOI: 10.3390/microorganisms10020417] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 01/27/2023] Open
Abstract
Microbial pathogens that cause severe infections and are resistant to drugs are simultaneously becoming more active. This urgently calls for novel effective antibiotics. Organisms from extreme environments are known to synthesize novel bioprospecting molecules for biomedical applications due to their peculiar characteristics of growth and physiological conditions. Antimicrobial developments from hypersaline environments, such as lagoons, estuaries, and salterns, accommodate several halophilic microbes. Salinity is a distinctive environmental factor that continuously promotes the metabolic adaptation and flexibility of halophilic microbes for their survival at minimum nutritional requirements. A genetic adaptation to extreme solar radiation, ionic strength, and desiccation makes them promising candidates for drug discovery. More microbiota identified via sequencing and ‘omics’ approaches signify the hypersaline environments where compounds are produced. Microbial genera such as Bacillus, Actinobacteria, Halorubrum and Aspergillus are producing a substantial number of antimicrobial compounds. Several strategies were applied for producing novel antimicrobials from halophiles including a consortia approach. Promising results indicate that halophilic microbes can be utilised as prolific sources of bioactive metabolites with pharmaceutical potentialto expand natural product research towards diverse phylogenetic microbial groups which inhabit salterns. The present study reviews interesting antimicrobial compounds retrieved from microbial sources of various saltern environments, with a discussion of their potency in providing novel drugs against clinically drug-resistant microbes.
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20
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Rajwani R, Ohlemacher SI, Zhao G, Liu HB, Bewley CA. Genome-Guided Discovery of Natural Products through Multiplexed Low-Coverage Whole-Genome Sequencing of Soil Actinomycetes on Oxford Nanopore Flongle. mSystems 2021; 6:e0102021. [PMID: 34812649 PMCID: PMC8609971 DOI: 10.1128/msystems.01020-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/31/2021] [Indexed: 12/02/2022] Open
Abstract
Genome mining is an important tool for discovery of new natural products; however, the number of publicly available genomes for natural product-rich microbes such as actinomycetes, relative to human pathogens with smaller genomes, is small. To obtain contiguous DNA assemblies and identify large (ca. 10 to greater than 100 kb) biosynthetic gene clusters (BGCs) with high GC (>70%) and high-repeat content, it is necessary to use long-read sequencing methods when sequencing actinomycete genomes. One of the hurdles to long-read sequencing is the higher cost. In the current study, we assessed Flongle, a recently launched platform by Oxford Nanopore Technologies, as a low-cost DNA sequencing option to obtain contiguous DNA assemblies and analyze BGCs. To make the workflow more cost-effective, we multiplexed up to four samples in a single Flongle sequencing experiment while expecting low-sequencing coverage per sample. We hypothesized that contiguous DNA assemblies might enable analysis of BGCs even at low sequencing depth. To assess the value of these assemblies, we collected high-resolution mass spectrometry data and conducted a multi-omics analysis to connect BGCs to secondary metabolites. In total, we assembled genomes for 20 distinct strains across seven sequencing experiments. In each experiment, 50% of the bases were in reads longer than 10 kb, which facilitated the assembly of reads into contigs with an average N50 value of 3.5 Mb. The programs antiSMASH and PRISM predicted 629 and 295 BGCs, respectively. We connected BGCs to metabolites for N,N-dimethyl cyclic-di-tryptophan, two novel lasso peptides, and three known actinomycete-associated siderophores, namely, mirubactin, heterobactin, and salinichelin. IMPORTANCE Short-read sequencing of GC-rich genomes such as those from actinomycetes results in a fragmented genome assembly and truncated biosynthetic gene clusters (often 10 to >100 kb long), which hinders our ability to understand the biosynthetic potential of a given strain and predict the molecules that can be produced. The current study demonstrates that contiguous DNA assemblies, suitable for analysis of BGCs, can be obtained through low-coverage, multiplexed sequencing on Flongle, which provides a new low-cost workflow ($30 to 40 per strain) for sequencing actinomycete strain libraries.
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Affiliation(s)
- Rahim Rajwani
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shannon I. Ohlemacher
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Gengxiang Zhao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Hong-Bing Liu
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Carole A. Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
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21
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Lach J, Jęcz P, Strapagiel D, Matera-Witkiewicz A, Stączek P. The Methods of Digging for "Gold" within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools. Genes (Basel) 2021; 12:1756. [PMID: 34828362 PMCID: PMC8619533 DOI: 10.3390/genes12111756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/18/2021] [Accepted: 10/30/2021] [Indexed: 02/06/2023] Open
Abstract
Halophiles, the salt-loving organisms, have been investigated for at least a hundred years. They are found in all three domains of life, namely Archaea, Bacteria, and Eukarya, and occur in saline and hypersaline environments worldwide. They are already a valuable source of various biomolecules for biotechnological, pharmaceutical, cosmetological and industrial applications. In the present era of multidrug-resistant bacteria, cancer expansion, and extreme environmental pollution, the demand for new, effective compounds is higher and more urgent than ever before. Thus, the unique metabolism of halophilic microorganisms, their low nutritional requirements and their ability to adapt to harsh conditions (high salinity, high pressure and UV radiation, low oxygen concentration, hydrophobic conditions, extreme temperatures and pH, toxic compounds and heavy metals) make them promising candidates as a fruitful source of bioactive compounds. The main aim of this review is to highlight the nucleic acid sequencing experimental strategies used in halophile studies in concert with the presentation of recent examples of bioproducts and functions discovered in silico in the halophile's genomes. We point out methodological gaps and solutions based on in silico methods that are helpful in the identification of valuable bioproducts synthesized by halophiles. We also show the potential of an increasing number of publicly available genomic and metagenomic data for halophilic organisms that can be analysed to identify such new bioproducts and their producers.
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Affiliation(s)
- Jakub Lach
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, 93-338 Lodz, Poland; (P.J.); (P.S.)
- Biobank Lab, Department of Molecular Biophysics, Faculty of Environmental Protection, University of Lodz, 93-338 Lodz, Poland;
| | - Paulina Jęcz
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, 93-338 Lodz, Poland; (P.J.); (P.S.)
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Environmental Protection, University of Lodz, 93-338 Lodz, Poland;
| | - Agnieszka Matera-Witkiewicz
- Screening Laboratory of Biological Activity Tests and Collection of Biological Material, Faculty of Pharmacy, Wroclaw Medical University, 50-368 Wroclaw, Poland;
| | - Paweł Stączek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, 93-338 Lodz, Poland; (P.J.); (P.S.)
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22
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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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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: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [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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24
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Li Y, Han Y, Zeng Z, Li W, Feng S, Cao W. Discovery and Bioactivity of the Novel Lasso Peptide Microcin Y. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8758-8767. [PMID: 34314160 DOI: 10.1021/acs.jafc.1c02659] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Lasso peptides, a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) secreted by bacteria, have antimicrobial activity. Here, a novel lasso peptide, microcin Y (MccY), was discovered and characterized. The gene cluster for MccY synthesis was cloned for expression in Escherichia coli. This peptide was purified by HPLC and characterized by Q-TOF. MIC assays showed that some Bacillus, Staphylococcus, Pseudomonas, Shigella, and Salmonella strains were sensitive to MccY. Interestingly, Salmonellatyphimurium and Salmonella infantis were efficiently inhibited by MccY, while they were not affected by MccJ25, a lasso peptide that has antibacterial effects on many Salmonella strains. Furthermore, MccY-resistant strains of S. typhimurium were screened, and mutations were found in FhuA and SbmA, indicating the importance of these transporters for MccY absorption. This novel peptide can greatly broaden the antimicrobial spectrum of MccJ25 in Salmonella and is expected to be used in food preservation and animal feed additive areas.
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Affiliation(s)
- Yu Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Yu Han
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Zhiwei Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Wenjing Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Saixiang Feng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, People's Republic of China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Weisheng Cao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, People's Republic of China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou 510642, People's Republic of China
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25
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Case-Control Microbiome Study of Chronic Otitis Media with Effusion in Children Points at Streptococcus salivarius as a Pathobiont-Inhibiting Species. mSystems 2021; 6:6/2/e00056-21. [PMID: 33879499 PMCID: PMC8546964 DOI: 10.1128/msystems.00056-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Chronic otitis media with effusion (OME) has been associated with a shift in microbiome composition and microbial interaction in the upper respiratory tract (URT). While most studies have focused on potential pathogens, this study aimed to find bacteria that could be protective against OME through a case-control microbiome study and characterization of isolates from healthy subjects. The URT and ear microbiome profiles of 70 chronic OME patients and 53 controls were compared by 16S rRNA amplicon sequencing. Haemophilus influenzae was the most frequent classic middle ear pathobiont. However, other taxa, especially Alloiococcus otitis, were also frequently detected in the ear canal of OME patients. Streptococci of the salivarius group and Acinetobacter lwoffii were more abundant in the nasopharynx of healthy controls than in OME patients. In addition to the microbiome analysis, 142 taxa were isolated from healthy individuals, and 79 isolates of 13 different Streptococcus species were tested for their pathobiont-inhibiting potential. Of these, Streptococcus salivarius isolates showed a superior capacity to inhibit the growth of H. influenzae, Moraxella catarrhalis, Streptococcus pneumoniae, Streptococcus pyogenes, Staphylococcus aureus, A. otitis, and Corynebacterium otitidis. S. salivarius strains thus show potential as a probiotic for prevention or treatment of OME based on their overrepresentation in the healthy nasopharynx and their ability to inhibit the growth of respiratory pathobionts. (This study has been registered at ClinicalTrials.gov under registration no. NCT03109496.) IMPORTANCE The majority of probiotics marketed today target gastrointestinal health. This study searched for bacteria native to the human upper respiratory tract, with a beneficial potential for respiratory and middle ear health. Comparison of the microbiomes of children with chronic otitis media with effusion (OME) and of healthy controls identified Streptococcus salivarius as a health-associated and prevalent inhabitant of the human nasopharynx. However, beneficial potential should be assessed at strain level. Here, we also isolated specific S. salivarius strains from the healthy individuals in our study. These isolates showed a beneficial safety profile and efficacy potential to inhibit OME pathogens in vitro. These properties will now have to be evaluated and confirmed in human clinical studies.
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Leonard TE, Siratan E, Hartiadi LY, Crystalia AA. Insights into antimicrobial peptides in fighting anthrax: A review. Drug Dev Res 2021; 82:754-766. [PMID: 33580543 DOI: 10.1002/ddr.21803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/31/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022]
Abstract
Anthrax is an infectious disease occurring worldwide and is a threat to global society due to its possible misuse as a biological weapon. Bacillus anthracis is the etiologic agent of this disease which can be transmitted via inhalation, ingestion, and skin contact. Globally, it is estimated around 2000 anthrax cases occur per year. Upon infection, the organism can cause cytolysis of macrophage and produce exotoxin capable of inducing edema and lymphatic blockage. Another challenge posed by the organism is the ability to form spores in harsh conditions. Various antibiotics have been used to fight the disease. However, like many other microbes, B. anthracis may develop resistance, thus the discovery of new therapeutics is urgently required. Antimicrobial peptides (AMPs) have been discovered since 1980s and attracted researchers in the antimicrobial field. In this review, the work and studies on the attempts to discover potent AMPs to treat anthrax together with the brief overview of the synthesis and modification pathways of several AMPs have been presented.
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Affiliation(s)
- Theodore Ebenezer Leonard
- Department of Pharmacy, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | - Elsabda Siratan
- Department of Pharmacy, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | - Leonny Yulita Hartiadi
- Department of Pharmacy, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | - Audrey Amira Crystalia
- Department of Pharmacy, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
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27
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 399] [Impact Index Per Article: 133.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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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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29
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Yang Y, Babich O, Sukhikh S, Zimina M, Milentyeva I. Antibiotic activity and resistance of lactic acid bacteria and other antagonistic bacteriocin-producing microorganisms. FOODS AND RAW MATERIALS 2020. [DOI: 10.21603/2308-4057-2020-2-377-384] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Introduction. Increased resistance of microorganisms to traditional antibiotics has created a practical need for isolating and synthesizing new antibiotics. We aimed to study the antibiotic activity and resistance of bacteriocins produced by lactic acid bacteria and other microorganisms.
Study objects and methods. We studied the isolates of the following microorganism strains: Bacillus subtilis, Penicillium glabrum, Penicillium lagena, Pseudomonas koreenis, Penicillium ochrochloron, Leuconostoc lactis, Lactobacillus plantarum, Leuconostoc mesenteroides, Pediococcus acidilactici, Leuconostoc mesenteroides, Pediococcus pentosaceus, Lactobacillus casei, Lactobacillus fermentum, Bacteroides hypermegas, Bacteroides ruminicola, Pediococcus damnosus, Bacteroides paurosaccharolyticus, Halobacillus profundi, Geobacillus stearothermophilus, and Bacillus caldotenax. Pathogenic test strains included Escherichia coli, Salmonella enterica, Staphylococcus aureus, Pseudomonas aeruginosa, Bacillus mycoides, Alcaligenes faecalis, and Proteus vulgaris. The titer of microorganisms was determined by optical density measurements at 595 nm.
Results and discussion. We found that eleven microorganisms out of twenty showed high antimicrobial activity against all test strains of pathogenic and opportunistic microorganisms. All the Bacteroides strains exhibited little antimicrobial activity against Gramnegative test strains, while Halobacillus profundi had an inhibitory effect on Gram-positive species only. The Penicillium strains also displayed a slight antimicrobial effect on pathogenic test strains.
Conclusion. The antibiotic resistance of the studied lactic acid bacteria and other bacteriocin-producing microorganisms allows for their use in the production of pharmaceutical antibiotic drugs.
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30
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Cheng C, Hua ZC. Lasso Peptides: Heterologous Production and Potential Medical Application. Front Bioeng Biotechnol 2020; 8:571165. [PMID: 33117783 PMCID: PMC7549694 DOI: 10.3389/fbioe.2020.571165] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/04/2020] [Indexed: 12/15/2022] Open
Abstract
Lasso peptides are natural products found in bacteria. They belong to a specific family of ribosomally-synthesized and posttranslationally-modified peptides with an unusual lasso structure. Lasso peptides possess remarkable thermal and proteolytic stability and various biological activities, such as antimicrobial activity, enzyme inhibition, receptor blocking, anticancer properties and HIV antagonism. They have promising potential therapeutic effects on gastrointestinal diseases, tuberculosis, Alzheimer’s disease, cardiovascular disease, fungal infections and cancer. Lasso peptides with high stability have been shown to be good carriers for other bioactive peptides. These make them attractive candidates for pharmaceutical research. This review aimed to describe the strategies used for the heterologous production of lasso peptides. Also, it indicated their therapeutical potential and their capacity to use as an efficient scaffold for epitope grafting.
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Affiliation(s)
- Cheng Cheng
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zi-Chun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.,School of Biopharmacy, China Pharmaceutical University, Nanjing, China.,Changzhou High-Tech Research Institute of Nanjing University, Changzhou, China.,Jiangsu Target Pharma Laboratories Inc., Changzhou, China
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31
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Cutting the Gordian knot: early and complete amino acid sequence confirmation of class II lasso peptides by HCD fragmentation. J Antibiot (Tokyo) 2020; 73:772-779. [DOI: 10.1038/s41429-020-00369-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023]
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32
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Wilson ZE, Brimble MA. Molecules derived from the extremes of life: a decade later. Nat Prod Rep 2020; 38:24-82. [PMID: 32672280 DOI: 10.1039/d0np00021c] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: Early 2008 until the end of 2019Microorganisms which survive (extreme-tolerant) or even prefer (extremophilic) living at the limits of pH, temperature, salinity and pressure found on earth have proven to be a rich source of novel structures. In this update we summarise the wide variety of new molecules which have been isolated from extremophilic and extreme-tolerant microorganisms since our original 2009 review, highlighting the range of bioactivities these molecules have been reported to possess.
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Affiliation(s)
- Zoe E Wilson
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand.
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33
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Waliczek M, Wierzbicka M, Arkuszewski M, Kijewska M, Jaremko Ł, Rajagopal P, Szczepski K, Sroczyńska A, Jaremko M, Stefanowicz P. Attempting to synthesize lasso peptides using high pressure. PLoS One 2020; 15:e0234901. [PMID: 32579565 PMCID: PMC7314030 DOI: 10.1371/journal.pone.0234901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/20/2020] [Indexed: 12/30/2022] Open
Abstract
Lasso peptides are unique in that the tail of the lasso peptide threads through its macrolactam ring. The unusual structure and biological activity of lasso peptides have generated increased interest from the scientific community in recent years. Because of this, many new types of lasso peptides have been discovered. These peptides can be synthesized by microorganisms efficiently, and yet, their chemical assembly is challenging. Herein, we investigated the possibility of high pressure inducing the cyclization of linear precursors of lasso peptides. Unlike other molecules like rotaxanes which mechanically interlock at high pressure, the threaded lasso peptides did not form, even at pressures the high pressure up to 14 000 kbar.
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Affiliation(s)
| | | | | | - Monika Kijewska
- Faculty of Chemistry, University of Wrocław, Wroclaw, Poland
| | - Łukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Priyadharshni Rajagopal
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kacper Szczepski
- Faculty of Chemistry, University of Wrocław, Wroclaw, Poland
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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34
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Matroodi S, Siitonen V, Baral B, Yamada K, Akhgari A, Metsä-Ketelä M. Genotyping-Guided Discovery of Persiamycin A From Sponge-Associated Halophilic Streptomonospora sp. PA3. Front Microbiol 2020; 11:1237. [PMID: 32582127 PMCID: PMC7296137 DOI: 10.3389/fmicb.2020.01237] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/14/2020] [Indexed: 12/16/2022] Open
Abstract
Microbial natural products have been a cornerstone of the pharmaceutical industry, but the supply of novel bioactive secondary metabolites has diminished due to extensive exploration of the most easily accessible sources, namely terrestrial Streptomyces species. The Persian Gulf is a unique habitat for marine sponges, which contain diverse communities of microorganisms including marine Actinobacteria. These exotic ecosystems may cradle rare actinomycetes with high potential to produce novel secondary metabolites. In this study, we harvested 12 different species of sponges from two locations in the Persian Gulf and isolated 45 symbiotic actinomycetes to assess their biodiversity and sponge-microbe relationships. The isolates were classified into Nocardiopsis (24 isolates), Streptomyces (17 isolates) and rare genera (4 isolates) by 16S rRNA sequencing. Antibiotic activity tests revealed that culture extracts from half of the isolates displayed growth inhibitory effects against seven pathogenic bacteria. Next, we identified five strains with the genetic potential to produce aromatic polyketides by genotyping ketosynthase genes responsible for synthesis of carbon scaffolds. The combined data led us to focus on Streptomonospora sp. PA3, since the genus has rarely been examined for its capacity to produce secondary metabolites. Analysis of culture extracts led to the discovery of a new bioactive aromatic polyketide denoted persiamycin A and 1-hydroxy-4-methoxy-2-naphthoic acid. The genome harbored seven gene clusters involved in secondary metabolism, including a tetracenomycin-type polyketide synthase pathway likely involved in persiamycin formation. The work demonstrates the use of multivariate data and underexplored ecological niches to guide the drug discovery process for antibiotics and anticancer agents.
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Affiliation(s)
- Soheila Matroodi
- Laboratory of Biotechnology, Department of Marine Biology, Faculty of Marine Science and Oceanography, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Vilja Siitonen
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Bikash Baral
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Keith Yamada
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Amir Akhgari
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Mikko Metsä-Ketelä
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
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35
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Corral P, Amoozegar MA, Ventosa A. Halophiles and Their Biomolecules: Recent Advances and Future Applications in Biomedicine. Mar Drugs 2019; 18:md18010033. [PMID: 31906001 PMCID: PMC7024382 DOI: 10.3390/md18010033] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/21/2019] [Accepted: 12/28/2019] [Indexed: 12/18/2022] Open
Abstract
The organisms thriving under extreme conditions better than any other organism living on Earth, fascinate by their hostile growing parameters, physiological features, and their production of valuable bioactive metabolites. This is the case of microorganisms (bacteria, archaea, and fungi) that grow optimally at high salinities and are able to produce biomolecules of pharmaceutical interest for therapeutic applications. As along as the microbiota is being approached by massive sequencing, novel insights are revealing the environmental conditions on which the compounds are produced in the microbial community without more stress than sharing the same substratum with their peers, the salt. In this review are reported the molecules described and produced by halophilic microorganisms with a spectrum of action in vitro: antimicrobial and anticancer. The action mechanisms of these molecules, the urgent need to introduce alternative lead compounds and the current aspects on the exploitation and its limitations are discussed.
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Affiliation(s)
- Paulina Corral
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy;
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Mohammad A. Amoozegar
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran 14155-6955, Iran;
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
- Correspondence: ; Tel.: +34-954556765
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36
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Hegemann JD. Factors Governing the Thermal Stability of Lasso Peptides. Chembiochem 2019; 21:7-18. [DOI: 10.1002/cbic.201900364] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Julian D. Hegemann
- Technische Universität BerlinInstitute of Chemistry Strasse des 17. Juni 124/TC2 10623 Berlin Germany
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37
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Tan S, Moore G, Nodwell J. Put a Bow on It: Knotted Antibiotics Take Center Stage. Antibiotics (Basel) 2019; 8:antibiotics8030117. [PMID: 31405236 PMCID: PMC6784204 DOI: 10.3390/antibiotics8030117] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/06/2019] [Accepted: 08/09/2019] [Indexed: 01/15/2023] Open
Abstract
Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large class of natural products produced across all domains of life. The lasso peptides, a subclass of RiPPs with a lasso-like structure, are structurally and functionally unique compared to other known peptide antibiotics in that the linear peptide is literally "tied in a knot" during its post-translational maturation. This underexplored class of peptides brings chemical diversity and unique modes of action to the antibiotic space. To date, eight different lasso peptides have been shown to target three known molecular machines: RNA polymerase, the lipid II precursor in peptidoglycan biosynthesis, and the ClpC1 subunit of the Clp protease involved in protein homeostasis. Here, we discuss the current knowledge on lasso peptide biosynthesis as well as their antibiotic activity, molecular targets, and mechanisms of action.
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Affiliation(s)
- Stephanie Tan
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Gaelen Moore
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Justin Nodwell
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
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38
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Sumida T, Dubiley S, Wilcox B, Severinov K, Tagami S. Structural Basis of Leader Peptide Recognition in Lasso Peptide Biosynthesis Pathway. ACS Chem Biol 2019; 14:1619-1627. [PMID: 31188556 DOI: 10.1021/acschembio.9b00348] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) with a unique 3D-interlocked structure, in which an N-terminal macrolactam ring is threaded by a linear C-terminal part. The unique structure of lasso peptides is introduced into ribosomally translated precursor peptides by lasso peptide synthetase encompassing proteins B and C or B1, B2, and C when the B enzyme is split into two distinct proteins. The B1 protein recognizes the leader sequence of the precursor peptide, and then the B2 protein cleaves it. The C protein catalyzes the formation of the macrolactam ring. However, the detailed mechanism of lasso peptide maturation has remained elusive, due to the lack of structural information about the responsible proteins. Here we report the crystal structure of the B1 protein from the thermophilic actinobacteria, Thermobifida fusca (TfuB1), complexed with the leader peptide (TfuA-Leader), which revealed the detailed mechanism of leader peptide recognition. The structure of TfuB1 consists of an N-terminal β-sheet and three C-terminal helices. The leader peptide is docked on one edge of the N-terminal β-sheet of TfuB1, as an additional β strand. Three conserved amino acid residues of the leader peptide (TfuA Tyr-17, Pro-14, and Leu-12) fit well on the hydrophobic cleft between the β-sheet and adjacent helices. Biochemical analysis demonstrated that these conserved residues are essential for affinity between TfuB1 and the TfuA-Leader. Furthermore, we found that TfuB1 and the leader peptide jointly form a hydrophobic patch on the β-sheet, which includes the highly conserved TfuA Phe-6 and TfuB1 Tyr33. Homology modeling and mutational analysis of the B1 protein from a firmicute, Bacillus pseudomycoides (PsmB1), revealed that the hydrophobic patch is conserved in a wide range of species and involved in the cleavage activity of the B2 protein, indicating it forms the interaction surface for the B2 protein or the core part of the precursor peptide.
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Affiliation(s)
- Tomomi Sumida
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Svetlana Dubiley
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
- Institute of Gene Biology, Russian Academy of Science, Moscow 119334, Russia
| | - Brendan Wilcox
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
| | - Konstantin Severinov
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
- Institute of Gene Biology, Russian Academy of Science, Moscow 119334, Russia
- Waksman Institute for Microbiology, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
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Tan S, Ludwig KC, Müller A, Schneider T, Nodwell JR. The Lasso Peptide Siamycin-I Targets Lipid II at the Gram-Positive Cell Surface. ACS Chem Biol 2019; 14:966-974. [PMID: 31026131 DOI: 10.1021/acschembio.9b00157] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribosomally synthesized post-translationally modified peptides (RiPPs) are a diverse class of biologically active molecules produced by many environmental bacteria. While thousands of these compounds have been identified, mostly through genome mining, a relatively small number has been investigated at the molecular level. One less understood class of RiPPs is the lasso peptides. These are 20-25 amino acid residue compounds bearing an N-terminal macrocyclic ring and a C-terminal tail that is threaded through the ring. We have carried out a detailed investigation on the mechanism of action of the siamycin-I lasso peptide. We demonstrate that siamycin-I interacts with lipid II, the central building block of the major cell wall component peptidoglycan, which is readily accessible on the outside of the cell. This interaction compromises cell wall biosynthesis in a manner that activates the liaI stress response. Additionally, resistance to siamycin-I can be brought about by mutations in the essential WalKR two-component system that causes thickening of the cell wall. Siamycin-I is the first lasso peptide that has been shown to inhibit cell wall biosynthesis.
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Affiliation(s)
- Stephanie Tan
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
| | - Kevin C. Ludwig
- Institute for Pharmaceutical Microbiology, University of Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Anna Müller
- Institute for Pharmaceutical Microbiology, University of Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany
| | - Justin R. Nodwell
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
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Zhu S, Su Y, Shams S, Feng Y, Tong Y, Zheng G. Lassomycin and lariatin lasso peptides as suitable antibiotics for combating mycobacterial infections: current state of biosynthesis and perspectives for production. Appl Microbiol Biotechnol 2019; 103:3931-3940. [PMID: 30915503 DOI: 10.1007/s00253-019-09771-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/12/2019] [Accepted: 03/12/2019] [Indexed: 11/30/2022]
Abstract
Lasso peptides are ribosomally synthesized and post-translationally modified natural products with a characteristic slipknot-like structure, which confers these peptides remarkable stability and diverse pharmacologically relevant bioactivities. Among all the reported lasso peptides, lassomycin and lariatins are unique lasso peptides that exhibit noticeable anti-tuberculosis (TB) activity. Due to the unique threaded structure and the unusual bactericidal mechanism toward Mycobacterium tuberculosis, these peptides have drawn considerable interest, not only in the field of total synthesis but also in several other fields including biosynthesis, bioengineering, and structure-activity studies. During the past few years, significant progress has been made in understanding the biosynthetic mechanism of these intriguing compounds, which has provided a solid foundation for future work. This review highlights recent achievements in the discovery, structure elucidation, biological activity, and the unique anti-TB mechanism of lasso peptides. Moreover, the discovery of their biosynthetic pathway has laid the foundation for combinatorial biosynthesis of their analogs, which provides new perspectives for the production of novel anti-TB lasso peptides.
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Affiliation(s)
- Shaozhou Zhu
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
| | - Yu Su
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Saira Shams
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yue Feng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yigang Tong
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Guojun Zheng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
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Discovery and characterization of a novel C-terminal peptide carboxyl methyltransferase in a lassomycin-like lasso peptide biosynthetic pathway. Appl Microbiol Biotechnol 2019; 103:2649-2664. [DOI: 10.1007/s00253-019-09645-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/02/2019] [Accepted: 01/10/2019] [Indexed: 12/28/2022]
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Acedo JZ, Chiorean S, Vederas JC, van Belkum MJ. The expanding structural variety among bacteriocins from Gram-positive bacteria. FEMS Microbiol Rev 2019; 42:805-828. [PMID: 30085042 DOI: 10.1093/femsre/fuy033] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/30/2018] [Indexed: 12/21/2022] Open
Abstract
Bacteria use various strategies to compete in an ecological niche, including the production of bacteriocins. Bacteriocins are ribosomally synthesized antibacterial peptides, and it has been postulated that the majority of Gram-positive bacteria produce one or more of these natural products. Bacteriocins can be used in food preservation and are also considered as potential alternatives to antibiotics. The majority of bacteriocins from Gram-positive bacteria had been traditionally divided into two major classes, namely lantibiotics, which are post-translationally modified bacteriocins, and unmodified bacteriocins. The last decade has seen an expanding number of ribosomally synthesized and post-translationally modified peptides (RiPPs) in Gram-positive bacteria that have antibacterial activity. These include linear azol(in)e-containing peptides, thiopeptides, bottromycins, glycocins, lasso peptides and lipolanthines. In addition, the three-dimensional (3D) structures of a number of modified and unmodified bacteriocins have been elucidated in recent years. This review gives an overview on the structural variety of bacteriocins from Gram-positive bacteria. It will focus on the chemical and 3D structures of these peptides, and their interactions with receptors and membranes, structure-function relationships and possible modes of action.
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Affiliation(s)
- Jeella Z Acedo
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, T6G 2G2, Canada
| | - Sorina Chiorean
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, T6G 2G2, Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, T6G 2G2, Canada
| | - Marco J van Belkum
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, T6G 2G2, Canada
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Koos JD, Link AJ. Heterologous and in Vitro Reconstitution of Fuscanodin, a Lasso Peptide from Thermobifida fusca. J Am Chem Soc 2018; 141:928-935. [PMID: 30532970 DOI: 10.1021/jacs.8b10724] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Lasso peptides are a class of ribosomally derived natural products typified by their threaded rotaxane structure. The conversion of a linear precursor peptide into a lasso peptide structure requires two enzymatic activities: cleavage of the precursor via a cysteine protease and cyclization via isopeptide bond formation. In vitro studies of lasso peptide enzymology have been hampered by difficulties in obtaining pure, soluble enzymes. We reasoned that thermophilic bacteria would be a good source for well-behaved lasso peptide biosynthetic enzymes. The genome of the thermophilic actinobacterium Thermobifida fusca encodes for a lasso peptide with an unprecedented Trp residue at its N-terminus, a peptide we have named fuscanodin. Here we reconstitute fuscanodin biosynthesis in vitro with purified components, establishing a minimal fuscanodin synthetase. These experiments have allowed us to probe the kinetics of lasso peptide biosynthesis for the first time, and we report initial rates of fuscanodin biosynthesis. The fuscanodin biosynthetic enzymes are insensitive to substrate concentration and operate in a near single-turnover regime in vitro. While lasso peptides are often touted for their stability to both chaotropic and thermal challenges, fuscanodin is found to undergo a conformational change consistent with lasso peptide unthreading in organic solvents at room temperature.
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Kaweewan I, Hemmi H, Komaki H, Harada S, Kodani S. Isolation and structure determination of a new lasso peptide specialicin based on genome mining. Bioorg Med Chem 2018; 26:6050-6055. [PMID: 30448257 DOI: 10.1016/j.bmc.2018.11.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/05/2018] [Accepted: 11/06/2018] [Indexed: 10/27/2022]
Abstract
Based on genome mining, a new lasso peptide specialicin was isolated from the extract of Streptomyces specialis. The structure of specialicin was established by ESI-MS and NMR analyses to be a lasso peptide with the length of 21 amino acids, containing an isopeptide bond and two disulfide bonds in the molecule. The stereochemistries of the constituent amino acids except for Trp were determined to be L and the stereochemistry of Trp at C-terminus was determined to be D. Three dimensional structure of specialicin was determined based on NOE experimental data, which indicated that specialicin possessed the similar conformational structure with siamycin I. Specialicin showed the antibacterial activity against Micrococcus luteus and the moderate anti-HIV activity against HIV-1 NL4-3. The biosynthetic gene cluster of specialicin was proposed from the genome sequence data of S. specialis.
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Affiliation(s)
- Issara Kaweewan
- Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, 432-8561 Shizuoka, Japan
| | - Hikaru Hemmi
- Food Research Institute, NARO, 2-1-12 Kan-nondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shigeyoshi Harada
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Shinya Kodani
- Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, 432-8561 Shizuoka, Japan; Academic Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529 Japan.
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Kodani S, Hemmi H, Miyake Y, Kaweewan I, Nakagawa H. Heterologous production of a new lasso peptide brevunsin in Sphingomonas subterranea. ACTA ACUST UNITED AC 2018; 45:983-992. [DOI: 10.1007/s10295-018-2077-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/30/2018] [Indexed: 11/29/2022]
Abstract
Abstract
A shuttle vector pHSG396Sp was constructed to perform gene expression using Sphingomonas subterranea as a host. A new lasso peptide biosynthetic gene cluster, derived from Brevundimonas diminuta, was amplified by PCR and integrated to afford a expression vector pHSG396Sp-12697L. The new lasso peptide brevunsin was successfully produced by S. subterranea, harboring the expression vector, with a high production yield (10.2 mg from 1 L culture). The chemical structure of brevunsin was established by NMR and MS/MS experiments. Based on the information obtained from the NOE experiment, the three-dimensional structure of brevunsin was determined, which indicated that brevunsin possessed a typical lasso structure. This expression vector system provides a new heterologous production method for unexplored lasso peptides that are encoded by bacterial genomes.
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Affiliation(s)
- Shinya Kodani
- College of Agriculture Academic Institute, Shizuoka University 836 Ohya, Suruga-ku 422-8529 Shizuoka Japan
- 0000 0001 0656 4913 grid.263536.7 Graduate School of Integrated Science and Technology Shizuoka University 422-8529 Shizuoka Japan
- 0000 0001 0656 4913 grid.263536.7 Graduate School of Science and Technology Shizuoka University 422-8529 Shizuoka Japan
| | - Hikaru Hemmi
- 0000 0001 2222 0432 grid.416835.d Food Research Institute, National Agriculture and Food Research Organization (NARO) 305-8642 Ibaraki Japan
| | - Yuto Miyake
- 0000 0001 0656 4913 grid.263536.7 Graduate School of Integrated Science and Technology Shizuoka University 422-8529 Shizuoka Japan
| | - Issara Kaweewan
- 0000 0001 0656 4913 grid.263536.7 Graduate School of Science and Technology Shizuoka University 422-8529 Shizuoka Japan
| | - Hiroyuki Nakagawa
- 0000 0001 2222 0432 grid.416835.d Food Research Institute, National Agriculture and Food Research Organization (NARO) 305-8642 Ibaraki Japan
- 0000 0001 2222 0432 grid.416835.d Advanced Analysis Center National Agriculture and Food Research Organization (NARO) 305-8642 Ibaraki Japan
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Son S, Jang M, Lee B, Hong YS, Ko SK, Jang JH, Ahn JS. Ulleungdin, a Lasso Peptide with Cancer Cell Migration Inhibitory Activity Discovered by the Genome Mining Approach. JOURNAL OF NATURAL PRODUCTS 2018; 81:2205-2211. [PMID: 30251851 DOI: 10.1021/acs.jnatprod.8b00449] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The advances of genomic sequence analyses and genome mining tools have enabled the exploration of untapped microbial natural products. Through genome mining studies to discover cryptic natural products, we found biosynthetic genes encoding a new lasso peptide in the genome sequence of a soil bacterium, Streptomyces sp. KCB13F003 isolated from Ulleung Island (a small volcanic island), Korea. The production and purification of the encoded peptide, named ulleungdin, were achieved by optimizing the culture conditions followed by LC-MS-targeted isolation. Structure elucidation was performed by NMR spectroscopic and MS spectrometric analyses and chemical means (Marfey's and GITC derivatizations), proving ulleungdin to be a new 15-mer class II lasso peptide with a threaded structure. Biological evaluation with the cell invasion assay and time-lapse cell tracking analysis revealed that ulleungdin has significant inhibitory activities against cancer cell invasion and migration.
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Affiliation(s)
- Sangkeun Son
- Anticancer Agent Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116 , Korea
| | - Mina Jang
- Anticancer Agent Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116 , Korea
- Department of Biomolecular Science, KRIBB School of Bioscience , Korea University of Science and Technology (UST) , Daejeon 34141 , Korea
| | - Byeongsan Lee
- Anticancer Agent Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116 , Korea
| | - Young-Soo Hong
- Anticancer Agent Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116 , Korea
- Department of Biomolecular Science, KRIBB School of Bioscience , Korea University of Science and Technology (UST) , Daejeon 34141 , Korea
| | - Sung-Kyun Ko
- Anticancer Agent Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116 , Korea
- Department of Biomolecular Science, KRIBB School of Bioscience , Korea University of Science and Technology (UST) , Daejeon 34141 , Korea
| | - Jae-Hyuk Jang
- Anticancer Agent Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116 , Korea
- Department of Biomolecular Science, KRIBB School of Bioscience , Korea University of Science and Technology (UST) , Daejeon 34141 , Korea
| | - Jong Seog Ahn
- Anticancer Agent Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116 , Korea
- Department of Biomolecular Science, KRIBB School of Bioscience , Korea University of Science and Technology (UST) , Daejeon 34141 , Korea
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Hudson GA, Mitchell DA. RiPP antibiotics: biosynthesis and engineering potential. Curr Opin Microbiol 2018; 45:61-69. [PMID: 29533845 PMCID: PMC6131089 DOI: 10.1016/j.mib.2018.02.010] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 02/23/2018] [Indexed: 01/14/2023]
Abstract
The threat of antibiotic resistant bacterial infections continues to underscore the need for new treatment options. Historically, small molecule metabolites from microbes have provided a rich source of antibiotic compounds, and as a result, significant effort has been invested in engineering the responsible biosynthetic pathways to generate novel analogs with attractive pharmacological properties. Unfortunately, biosynthetic stringency has limited the capacity of non-ribosomal peptide synthetases and polyketide synthases from producing substantially different analogs in large numbers. Another class of natural products, the ribosomally synthesized and post-translationally modified peptides (RiPPs), have rapidly expanded in recent years with many natively displaying potent antibiotic activity. RiPP biosynthetic pathways are modular and intrinsically tolerant to alternative substrates. Several prominent RiPPs with antibiotic activity will be covered in this review with a focus on their biosynthetic plasticity. While only a few RiPP enzymes have been thoroughly investigated mechanistically, this knowledge has already been harnessed to generate new-to-nature compounds. Through the use of synthetic biology approaches, on-going efforts in RiPP engineering hold great promise in unlocking the potential of this natural product class.
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Affiliation(s)
- Graham A Hudson
- Department of Chemistry, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States; Department of Microbiology, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States.
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48
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Martin-Gómez H, Linne U, Albericio F, Tulla-Puche J, Hegemann JD. Investigation of the Biosynthesis of the Lasso Peptide Chaxapeptin Using an E. coli-Based Production System. JOURNAL OF NATURAL PRODUCTS 2018; 81:2050-2056. [PMID: 30178995 DOI: 10.1021/acs.jnatprod.8b00392] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Lasso peptides are natural products belonging to the family of ribosomally synthesized and posttranslationally modified peptides (RiPPs) and are defined by their unique topology. Even though lasso peptide biosynthetic gene clusters are found in many different kinds of bacteria, most of the hitherto studied lasso peptides were of proteobacterial or actinobacterial origin. Despite this, no E. coli-based production system has been reported for actinobacterial lasso peptides, while there are numerous examples of this for proteobacterial lasso peptides. Here, a heterologous production system of the lasso peptide chaxapeptin was established in E. coli. Chaxapeptin, originally isolated from Streptomyces leeuwenhoekii strain C58, is closely related to the lasso peptide sungsanpin (produced by a marine Streptomyces sp.) and shares its inhibitory activity against cell invasion by the human lung cancer cell line A549. Our production system not only allowed isolation of the mature lasso peptide outside of the native producer with a yield of 0.1 mg/L (compared to 0.7 mg/L from S. leeuwenhoekii) but also was used for a mutational study to identify residues in the precursor peptide that are important for biosynthesis. In addition to these experiments, the stability of chaxapeptin against thermal denaturation and proteases was assessed.
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Affiliation(s)
- Helena Martin-Gómez
- Institute for Research in Biomedicine , Baldiri Reixac 10 , 08028 Barcelona , Spain
- Department of Chemistry , Philipps-University Marburg , Hans-Meerwein-Strasse 4 , 35032 Marburg , Germany
| | - Uwe Linne
- Department of Chemistry , Philipps-University Marburg , Hans-Meerwein-Strasse 4 , 35032 Marburg , Germany
| | - Fernando Albericio
- Department of Inorganic and Organic Chemistry-Organic Chemistry Section , University of Barcelona , Martí i Franquès 1-11 , 08028 Barcelona , Spain
- CIBER-BBN, Networking Centre on Bioengineering , Biomaterials and Nanomedicine , Baldiri Reixac 10 , 08028 Barcelona , Spain
- School of Chemistry and Physics , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Judit Tulla-Puche
- Department of Inorganic and Organic Chemistry-Organic Chemistry Section , University of Barcelona , Martí i Franquès 1-11 , 08028 Barcelona , Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB) , 08028 Barcelona , Spain
| | - Julian D Hegemann
- Department of Chemistry , Philipps-University Marburg , Hans-Meerwein-Strasse 4 , 35032 Marburg , Germany
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 S. Mathews Avenue , Urbana , Illinois 61801 , United States
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49
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Hegemann JD, Schwalen CJ, Mitchell DA, van der Donk WA. Elucidation of the roles of conserved residues in the biosynthesis of the lasso peptide paeninodin. Chem Commun (Camb) 2018; 54:9007-9010. [PMID: 30046789 DOI: 10.1039/c8cc04411b] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Substrate binding assays, in vitro proteolytic processing assays, and heterologous lasso peptide production were used to investigate the roles of conserved precursor peptide residues during paeninodin maturation. Specifically, we delineate which residues are important for substrate recognition, proteolysis, and lasso peptide macrocyclization.
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Affiliation(s)
- Julian D Hegemann
- Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, USA. and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, USA.
| | - Christopher J Schwalen
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, USA. and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, USA. and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Wilfred A van der Donk
- Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, USA. and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, USA. and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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50
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Mevaere J, Goulard C, Schneider O, Sekurova ON, Ma H, Zirah S, Afonso C, Rebuffat S, Zotchev SB, Li Y. An orthogonal system for heterologous expression of actinobacterial lasso peptides in Streptomyces hosts. Sci Rep 2018; 8:8232. [PMID: 29844351 PMCID: PMC5974421 DOI: 10.1038/s41598-018-26620-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/15/2018] [Indexed: 12/05/2022] Open
Abstract
Lasso peptides are ribosomally synthesized and post-translationally modified peptides produced by bacteria. They are characterized by an unusual lariat-knot structure. Targeted genome scanning revealed a wide diversity of lasso peptides encoded in actinobacterial genomes, but cloning and heterologous expression of these clusters turned out to be problematic. To circumvent this, we developed an orthogonal expression system for heterologous production of actinobacterial lasso peptides in Streptomyces hosts based on a newly-identified regulatory circuit from Actinoalloteichus fjordicus. Six lasso peptide gene clusters, mainly originating from marine Actinobacteria, were chosen for proof-of-concept studies. By varying the Streptomyces expression hosts and a small set of culture conditions, three new lasso peptides were successfully produced and characterized by tandem MS. The newly developed expression system thus sets the stage to uncover and bioengineer the chemo-diversity of actinobacterial lasso peptides. Moreover, our data provide some considerations for future bioprospecting efforts for such peptides.
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Affiliation(s)
- Jimmy Mevaere
- Laboratory « Molecules of Communication and Adaptation of Microorganisms » (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Christophe Goulard
- Laboratory « Molecules of Communication and Adaptation of Microorganisms » (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Olha Schneider
- Department of Biotechnology, Norwegian University of Science and Technology NTNU, N-7491, Trondheim, Norway
| | - Olga N Sekurova
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Haiyan Ma
- Laboratory « Molecules of Communication and Adaptation of Microorganisms » (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, 75005, Paris, France.,Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Séverine Zirah
- Laboratory « Molecules of Communication and Adaptation of Microorganisms » (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Carlos Afonso
- Normandie Université, INSA Rouen, UNIROUEN, CNRS, COBRA, Rouen, France
| | - Sylvie Rebuffat
- Laboratory « Molecules of Communication and Adaptation of Microorganisms » (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Sergey B Zotchev
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria.
| | - Yanyan Li
- Laboratory « Molecules of Communication and Adaptation of Microorganisms » (MCAM, UMR 7245 CNRS-MNHN), Sorbonne Universités, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, 75005, Paris, France.
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