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Surwase AJ, Thakur NL. Production of marine-derived bioactive peptide molecules for industrial applications: A reverse engineering approach. Biotechnol Adv 2024; 77:108449. [PMID: 39260778 DOI: 10.1016/j.biotechadv.2024.108449] [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: 07/13/2023] [Revised: 06/28/2024] [Accepted: 09/07/2024] [Indexed: 09/13/2024]
Abstract
This review examines a wide range of marine microbial-derived bioactive peptide molecules, emphasizing the significance of reverse engineering in their production. The discussion encompasses the advancements in Marine Natural Products (MNPs) bio-manufacturing through the integration of omics-driven microbial engineering and bioinformatics. The distinctive features of non-ribosomally synthesised peptides (NRPs), and ribosomally synthesised precursor peptides (RiPP) biosynthesis is elucidated and presented. Additionally, the article delves into the origins of common peptide modifications. It highlights various genome mining approaches for the targeted identification of Biosynthetic Gene Clusters (BGCs) and novel RiPP and NRPs-derived peptides. The review aims to demonstrate the advancements, prospects, and obstacles in engineering both RiPP and NRP biosynthetic pathways.
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Affiliation(s)
- Akash J Surwase
- CSIR-National Institute of Oceanography, Dona Paula 403004, Goa, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Narsinh L Thakur
- CSIR-National Institute of Oceanography, Dona Paula 403004, Goa, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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2
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Al Mamun A, Alam K, Koly FA, Showline Chaity F, Ferdous J, Islam S. Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in Streptomyces bacteria. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024:1-14. [PMID: 39140768 DOI: 10.1080/10286020.2024.2390510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024]
Abstract
Ribosomally synthesized post-translationally modified peptides (RiPPs) are a novel category of bioactive natural products (NPs). Streptomyces bacteria are a potential source of many bioactive NPs. Limited opportunities are available to characterize all the bioactive NP gene clusters. In this study, 410 sequences of Streptomyces were analyzed for RiPPs through genome mining using the National Center for Biotechnology Information (NCBI), by combining BAGEL and anti-SMASH. A total of 4098 RiPPs were found; including both classified (lanthipeptide, RiPP-like, bacteriocin, LAPs, lassopeptide, thiopeptides) and nonclassified RiPPs. Soil was identified as a rich habitat for RiPPs. These data may offer alternative future remedies for various health issues.
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Affiliation(s)
- Abdullah Al Mamun
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Khorshed Alam
- Bangladesh Standards and Testing Institution (BSTI), Dhaka, Bangladesh
| | - Farjana Akter Koly
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram Laboratories, Chattogram, Bangladesh
| | - Farjana Showline Chaity
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram Laboratories, Chattogram, Bangladesh
| | - Jannatul Ferdous
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram Laboratories, Chattogram, Bangladesh
| | - Saiful Islam
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram Laboratories, Chattogram, Bangladesh
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3
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Put H, Gerstmans H, Vande Capelle H, Fauvart M, Michiels J, Masschelein J. Bacillus subtilis as a host for natural product discovery and engineering of biosynthetic gene clusters. Nat Prod Rep 2024; 41:1113-1151. [PMID: 38465694 DOI: 10.1039/d3np00065f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that are either difficult or impossible to cultivate under laboratory conditions, or that produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms that are more easily cultured and engineered, larger quantities can be obtained and new analogues with potentially improved biological activity or other desirable properties can be generated. Moreover, expression of cryptic BGCs in a suitable host can facilitate the identification and characterization of novel natural products. Heterologous expression therefore represents a valuable tool for natural product discovery and engineering as it allows the study and manipulation of their biosynthetic pathways in a controlled setting, enabling innovative applications. Bacillus is a genus of Gram-positive bacteria that is widely used in industrial biotechnology as a host for the production of proteins from diverse origins, including enzymes and vaccines. However, despite numerous successful examples, Bacillus species remain underexploited as heterologous hosts for the expression of natural product BGCs. Here, we review important advantages that Bacillus species offer as expression hosts, such as high secretion capacity, natural competence for DNA uptake, and the increasing availability of a wide range of genetic tools for gene expression and strain engineering. We evaluate different strain optimization strategies and other critical factors that have improved the success and efficiency of heterologous natural product biosynthesis in B. subtilis. Finally, future perspectives for using B. subtilis as a heterologous host are discussed, identifying research gaps and promising areas that require further exploration.
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Affiliation(s)
- Hanne Put
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
- Biosensors Group, KU Leuven, 3001 Leuven, Belgium
| | - Hanne Vande Capelle
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- imec, 3001 Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Joleen Masschelein
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
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4
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Diab MK, Mead HM, Ahmad Khedr MM, Abu-Elsaoud AM, El-Shatoury SA. Actinomycetes are a natural resource for sustainable pest control and safeguarding agriculture. Arch Microbiol 2024; 206:268. [PMID: 38762847 DOI: 10.1007/s00203-024-03975-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/22/2024] [Indexed: 05/20/2024]
Abstract
Actinomycetes, a diverse group of bacteria with filamentous growth characteristics, have long captivated researchers and biochemists for their prolific production of secondary metabolites. Among the myriad roles played by actinomycete secondary metabolites, their historical significance in the field of biocontrol stands out prominently. The fascinating journey begins with the discovery of antibiotics, where renowned compounds like streptomycin, tetracycline, and erythromycin revolutionized medicine and agriculture. The history of biocontrol traces its roots back to the early twentieth century, when scientists recognized the potential of naturally occurring agents to combat pests and diseases. The emergence of synthetic pesticides in the mid-twentieth century temporarily overshadowed interest in biocontrol. However, with growing environmental concerns and the realization of the negative ecological impacts of chemical pesticides, the pendulum swung back towards exploring sustainable alternatives. Beyond their historical role as antibiotics, actinomycete-produced secondary metabolites encompass a rich repertoire with biopesticide potential. The classification of these compounds based on chemical structure and mode of action is highlighted, demonstrating their versatility against both plant pathogens and insect pests. Additionally, this review provides in-depth insights into how endophytic actinomycete strains play a pivotal role in biocontrol strategies. Case studies elucidate their effectiveness in inhibiting Spodoptera spp. and nematodes through the production of bioactive compounds. By unraveling the multifunctional roles of endophytic actinomycetes, this review contributes compelling narrative knowledge to the field of sustainable agriculture, emphasizing the potential of these microbial allies in crafting effective, environmentally friendly biocontrol strategies for combating agricultural pests.
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Affiliation(s)
- Mohamed Khaled Diab
- Agricultural Research Center, Pest Physiology Department, Plant Protection Research Institute, Giza, 12311, Egypt.
| | - Hala Mohamed Mead
- Agricultural Research Center, Pest Physiology Department, Plant Protection Research Institute, Giza, 12311, Egypt
| | - Mohamad M Ahmad Khedr
- Agricultural Research Center, Cotton Leafworm Department, Plant Protection Research Institute, Giza, 12311, Egypt
| | | | - Sahar Ahmed El-Shatoury
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
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Ramírez-Rendón D, Guzmán-Chávez F, García-Ausencio C, Rodríguez-Sanoja R, Sánchez S. The untapped potential of actinobacterial lanthipeptides as therapeutic agents. Mol Biol Rep 2023; 50:10605-10616. [PMID: 37934370 PMCID: PMC10676316 DOI: 10.1007/s11033-023-08880-w] [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: 08/26/2023] [Accepted: 10/03/2023] [Indexed: 11/08/2023]
Abstract
The increase in bacterial resistance generated by the indiscriminate use of antibiotics in medical practice set new challenges for discovering bioactive natural products as alternatives for therapeutics. Lanthipeptides are an attractive natural product group that has been only partially explored and shows engaging biological activities. These molecules are small peptides with potential application as therapeutic agents. Some members show antibiotic activity against problematic drug-resistant pathogens and against a wide variety of viruses. Nevertheless, their biological activities are not restricted to antimicrobials, as their contribution to the treatment of cystic fibrosis, cancer, pain symptoms, control of inflammation, and blood pressure has been demonstrated. The study of biosynthetic gene clusters through genome mining has contributed to accelerating the discovery, enlargement, and diversification of this group of natural products. In this review, we provide insight into the recent advances in the development and research of actinobacterial lanthipeptides that hold great potential as therapeutics.
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Affiliation(s)
- Dulce Ramírez-Rendón
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico City, México
| | - Fernando Guzmán-Chávez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico City, México
| | - Carlos García-Ausencio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico City, México
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico City, México
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico City, México.
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6
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Lopatniuk M, Riedel F, Wildfeuer J, Stierhof M, Dahlem C, Kiemer AK, Luzhetskyy A. Development of a Streptomyces-based system for facile thioholgamide library generation and analysis. Metab Eng 2023; 78:48-60. [PMID: 37142115 DOI: 10.1016/j.ymben.2023.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/06/2023]
Abstract
Derivatizing natural products (NPs) is essential in structure-activity relationship (SAR) studies, compound optimization, and drug development. Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent one of the major classes of natural products. Thioholgamide represents thioamitide - a recently emerged family of RiPPs with unique structures and great potential in anticancer drug development. Although the method for generating the RiPP library by codon substitutions in the precursor peptide gene is straightforward, the techniques to perform RiPP derivatization in Actinobacteria remain limited and time-consuming. Here, we report a facile system for producing a library of randomized thioholgamide derivatives utilizing an optimized Streptomyces host. This technique enabled us to access all possible amino acid substitutions of the thioholgamide molecule, one position at a time. Out of 152 potential derivatives, 85 were successfully detected, revealing the impact of amino acid substitutions on thioholgamide post-translational modifications (PTMs). Moreover, new PTMs were observed among thioholgamide derivatives: thiazoline heterocycles, which have not yet been reported for thioamitides, and S-methylmethionine, which is very rare in nature. The obtained library was subsequently used for thioholgamide SAR studies and stability assays.
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Affiliation(s)
- Maria Lopatniuk
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Florian Riedel
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Julia Wildfeuer
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany; Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Marc Stierhof
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Charlotte Dahlem
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.
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7
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Yang Y, Kessler MGC, Marchán-Rivadeneira MR, Han Y. Combating Antimicrobial Resistance in the Post-Genomic Era: Rapid Antibiotic Discovery. Molecules 2023; 28:molecules28104183. [PMID: 37241928 DOI: 10.3390/molecules28104183] [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: 04/24/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Constantly evolving drug-resistant "superbugs" have caused an urgent demand for novel antimicrobial agents. Natural products and their analogs have been a prolific source of antimicrobial agents, even though a high rediscovery rate and less targeted research has made the field challenging in the pre-genomic era. With recent advancements in technology, natural product research is gaining new life. Genome mining has allowed for more targeted excavation of biosynthetic potential from natural sources that was previously overlooked. Researchers use bioinformatic algorithms to rapidly identify and predict antimicrobial candidates by studying the genome before even entering the lab. In addition, synthetic biology and advanced analytical instruments enable the accelerated identification of novel antibiotics with distinct structures. Here, we reviewed the literature for noteworthy examples of novel antimicrobial agents discovered through various methodologies, highlighting the candidates with potent effectiveness against antimicrobial-resistant pathogens.
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Affiliation(s)
- Yuehan Yang
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
| | - Mara Grace C Kessler
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Honors Tutorial College, Ohio University, Athens, OH 45701, USA
| | - Maria Raquel Marchán-Rivadeneira
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
- Center for Research on Health in Latinamerica (CISeAL)-Biological Science Department, Pontificia Universidad Católica del Ecuador (PUCE), Quito 170143, Ecuador
| | - Yong Han
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
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Pashou E, Reich SJ, Reiter A, Weixler D, Eikmanns BJ, Oldiges M, Riedel CU, Goldbeck O. Identification and Characterization of Corynaridin, a Novel Linaridin from Corynebacterium lactis. Microbiol Spectr 2023; 11:e0175622. [PMID: 36541778 PMCID: PMC9927463 DOI: 10.1128/spectrum.01756-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Genome analysis of Corynebacterium lactis revealed a bacteriocin gene cluster encoding a putative bacteriocin of the linaridin family of ribosomally synthesized and posttranslationally modified peptides (RiPPs). The locus harbors typical linaridin modification enzymes but lacks genes for a decarboxylase and methyltransferase, which is unusual for type B linaridins. Supernatants of Corynebacterium lactis RW3-42 showed antimicrobial activity against Corynebacterium glutamicum. Deletion of the precursor gene crdA clearly linked the antimicrobial activity of the producer strain to the identified gene cluster. Following purification, we observed potent activity of the peptide against Actinobacteria, mainly other members of the genus Corynebacterium, including the pathogenic species Corynebacterium striatum and Corynebacterium amycolatum. Also, low activity against some Firmicutes was observed, but there was no activity against Gram-negative species. The peptide is resilient towards heat but sensitive to proteolytic degradation by trypsin and proteinase K. Analysis by mass spectrometry indicates that corynaridin is processed by cleaving off the leader sequence at a conserved motif and posttranslationally modified by dehydration of all threonine and serin residues, resulting in a monoisotopic mass of 3,961.19 Da. Notably, time-kill kinetics and experiments using live biosensors to monitor membrane integrity suggest bactericidal activity that does not involve formation of pores in the cytoplasmic membrane. As Corynebacterium species are ubiquitous in nature and include important commensals and pathogens of mammalian organisms, secretion of bacteriocins by species of this genus could be a hitherto neglected trait with high relevance for intra- and interspecies competition and infection. IMPORTANCE Bacteriocins are antimicrobial peptides produced by bacteria to fend off competitors in ecological niches and are considered to be important factors influencing the composition of microbial communities. However, bacteriocin production by bacteria of the genus Corynebacterium has been a hitherto neglected trait, although its species are ubiquitous in nature and make up large parts of the microbiome of humans and animals. In this study, we describe and characterize a novel linaridin family bacteriocin from Corynebacterium lactis and show its narrow-spectrum activity, mainly against other actinobacteria. Moreover, we were able to extend the limited knowledge on linaridin bioactivity in general and for the first time describe the bactericidal activity of such a bacteriocin. Interestingly, the peptide, which was named corynaridin, appears bactericidal, but without formation of pores in the bacterial membrane.
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Affiliation(s)
- Efthimia Pashou
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Sebastian J. Reich
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Alexander Reiter
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Dominik Weixler
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | | | - Marco Oldiges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Christian U. Riedel
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Oliver Goldbeck
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
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González-Salazar LA, Quezada M, Rodríguez-Orduña L, Ramos-Aboites H, Capon RJ, Souza-Saldívar V, Barona-Gomez F, Licona-Cassani C. Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments. Microb Genom 2023; 9:mgen000921. [PMID: 36748531 PMCID: PMC9973853 DOI: 10.1099/mgen.0.000921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Calculations predict that testing of 5 000-10 000 molecules and >1 billion US dollars (£0.8 billion, £1=$1.2) are required for one single drug to come to the market. A solution to this problem is to establish more efficient protocols that reduce the high rate of re-isolation and continuous rediscovery of natural products during early stages of the drug development process. The study of 'rare actinobacteria' has emerged as a possible approach for increasing the discovery rate of drug leads from natural sources. Here, we define a simple genomic metric, defined as biosynthetic novelty index (BiNI), that can be used to rapidly rank strains according to the novelty of the subset of encoding biosynthetic clusters. By comparing a subset of high-quality genomes from strains of different taxonomic and ecological backgrounds, we used the BiNI score to support the notion that rare actinobacteria encode more biosynthetic gene cluster (BGC) novelty. In addition, we present the isolation and genomic characterization, focused on specialized metabolites and phenotypic screening, of two isolates belonging to genera Lentzea and Actinokineospora from a highly oligotrophic environment. Our results show that both strains harbour a unique subset of BGCs compared to other members of the genera Lentzea and Actinokineospora. These BGCs are responsible for potent antimicrobial and cytotoxic bioactivity. The experimental data and analysis presented in this study contribute to the knowledge of genome mining analysis in rare actinobacteria and, most importantly, can serve to direct sampling efforts to accelerate early stages of the drug discovery pipeline.
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Affiliation(s)
- Luz A González-Salazar
- Industrial Genomics Laboratory, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, Mexico
| | - Michelle Quezada
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lorena Rodríguez-Orduña
- Industrial Genomics Laboratory, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, Mexico
| | - Hilda Ramos-Aboites
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanza (LANGEBIO), Cinvestav-IPN, Irapuato, Mexico
| | - Robert J Capon
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Valeria Souza-Saldívar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Francisco Barona-Gomez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanza (LANGEBIO), Cinvestav-IPN, Irapuato, Mexico.,Present address: Microbial Diversity and Specialized Metabolism Laboratory, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Cuauhtémoc Licona-Cassani
- Industrial Genomics Laboratory, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, Mexico.,Division of Integrative Biology, Institute for Obesity Research, Tecnológico de Monterrey, Nuevo León, Mexico
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10
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Sánchez-Suárez J, Díaz L, Coy-Barrera E, Villamil L. Specialized Metabolism of Gordonia Genus: An Integrated Survey on Chemodiversity Combined with a Comparative Genomics-Based Analysis. BIOTECH 2022; 11:53. [PMID: 36412754 PMCID: PMC9680422 DOI: 10.3390/biotech11040053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
Members of the phylum Actinomycetota (formerly Actinobacteria) have historically been the most prolific providers of small bioactive molecules. Although the genus Streptomyces is the best-known member for this issue, other genera, such as Gordonia, have shown interesting potential in their specialized metabolism. Thus, we combined herein the result of a comprehensive literature survey on metabolites derived from Gordonia strains with a comparative genomic analysis to examine the potential of the specialized metabolism of the genus Gordonia. Thirty Gordonia-derived compounds of different classes were gathered (i.e., alkaloids, amides, phenylpropanoids, and terpenoids), exhibiting antimicrobial and cytotoxic activities, and several were also isolated from Streptomyces (e.g., actinomycin, nocardamin, diolmycin A1). With the genome data, we estimated an open pan-genome of 57,901 genes, most of them being part of the cloud genome. Regarding the BGCs content, 531 clusters were found, including Terpenes, RiPP-like, and NRPS clusters as the most frequent clusters. Our findings demonstrated that Gordonia is a poorly studied genus in terms of its specialized metabolism production and potential applications. Nevertheless, given their BGCs content, Gordonia spp. are a valuable biological resource that could expand the chemical spectrum of the phylum Actinomycetota, involving novel BGCs for inspiring innovative outlines for synthetic biology and further use in biotechnological initiatives. Therefore, further studies and more efforts should be made to explore different environments and evaluate other bioactivities.
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Affiliation(s)
- Jeysson Sánchez-Suárez
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia
| | - Luis Díaz
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Universidad Militar Nueva Granada, Cajicá 250247, Colombia
| | - Luisa Villamil
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia
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Ossai J, Khatabi B, Nybo SE, Kharel MK. Renewed interests in the discovery of bioactive actinomycete metabolites driven by emerging technologies. J Appl Microbiol 2022; 132:59-77. [PMID: 34265147 PMCID: PMC8714619 DOI: 10.1111/jam.15225] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/25/2021] [Accepted: 07/12/2021] [Indexed: 01/03/2023]
Abstract
Actinomycetes are prolific sources of bioactive molecules. Traditional workflows including bacterial isolation, fermentation, metabolite identification and structure elucidation have resulted in high rates of natural product rediscovery in recent years. Recent advancements in multi-omics techniques have uncovered cryptic gene clusters within the genomes of actinomycetes, potentially introducing vast resources for the investigation of bioactive molecules. While developments in culture techniques have allowed for the fermentation of difficult-to-culture actinomycetes, high-throughput metabolite screening has offered plenary tools to accelerate hits discovery. A variety of new bioactive molecules have been isolated from actinomycetes of unique environmental origins, such as endophytic and symbiotic actinomycetes. Synthetic biology and genome mining have also emerged as new frontiers for the discovery of bioactive molecules. This review covers the highlights of recent developments in actinomycete-derived natural product drug discovery.
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Affiliation(s)
- Jenifer Ossai
- University of Maryland Eastern Shore, School of Agriculture and Natural Sciences, One Backbone Road, Princess Anne, MD 21853, USA
| | - Behnam Khatabi
- University of Maryland Eastern Shore, School of Agriculture and Natural Sciences, One Backbone Road, Princess Anne, MD 21853, USA
| | - S. Eric Nybo
- Ferris State University, College of Pharmacy, Big Rapids, Michigan, USA
| | - Madan K. Kharel
- University of Maryland Eastern Shore, School of Pharmacy and Health Professions, Department of Pharmaceutical Sciences, One Backbone Road, Princess Anne, MD 21853, USA,Corresponding author:
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Major D, Flanzbaum L, Lussier L, Davies C, Caldo KMP, Acedo JZ. Transporter Protein-Guided Genome Mining for Head-to-Tail Cyclized Bacteriocins. Molecules 2021; 26:7218. [PMID: 34885800 PMCID: PMC8659200 DOI: 10.3390/molecules26237218] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 12/02/2022] Open
Abstract
Head-to-tail cyclized bacteriocins are ribosomally synthesized antimicrobial peptides that are defined by peptide backbone cyclization involving the N- and C- terminal amino acids. Their cyclic nature and overall three-dimensional fold confer superior stability against extreme pH and temperature conditions, and protease degradation. Most of the characterized head-to-tail cyclized bacteriocins were discovered through a traditional approach that involved the screening of bacterial isolates for antimicrobial activity and subsequent isolation and characterization of the active molecule. In this study, we performed genome mining using transporter protein sequences associated with experimentally validated head-to-tail cyclized bacteriocins as driver sequences to search for novel bacteriocins. Biosynthetic gene cluster analysis was then performed to select the high probability functional gene clusters. A total of 387 producer strains that encode putative head-to-tail cyclized bacteriocins were identified. Sequence and phylogenetic analyses revealed that this class of bacteriocins is more diverse than previously thought. Furthermore, our genome mining strategy captured hits that were not identified in precursor-based bioprospecting, showcasing the utility of this approach to expanding the repertoire of head-to-tail cyclized bacteriocins. This work sets the stage for future isolation of novel head-to-tail cyclized bacteriocins to serve as possible alternatives to traditional antibiotics and potentially help address the increasing threat posed by resistant pathogens.
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Affiliation(s)
- Daniel Major
- Department of Biology, Mount Royal University, Calgary, AB T3E 6K6, Canada; (D.M.); (L.F.); (C.D.)
| | - Lara Flanzbaum
- Department of Biology, Mount Royal University, Calgary, AB T3E 6K6, Canada; (D.M.); (L.F.); (C.D.)
| | - Leah Lussier
- Department of Chemistry and Physics, Mount Royal University, Calgary, AB T3E 6K6, Canada;
| | - Carly Davies
- Department of Biology, Mount Royal University, Calgary, AB T3E 6K6, Canada; (D.M.); (L.F.); (C.D.)
| | - Kristian Mark P. Caldo
- Department of Agriculture, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Jeella Z. Acedo
- Department of Chemistry and Physics, Mount Royal University, Calgary, AB T3E 6K6, Canada;
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Caicedo-Montoya C, Manzo-Ruiz M, Ríos-Estepa R. Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds. Front Microbiol 2021; 12:677558. [PMID: 34659136 PMCID: PMC8510958 DOI: 10.3389/fmicb.2021.677558] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/30/2021] [Indexed: 01/07/2023] Open
Abstract
Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in turn permits reliable comparative genomics studies and an improved prediction of biosynthetic gene clusters (BGCs) through genome mining approaches. In this work, we used 121 genome sequences of the genus Streptomyces in a comparative genomics study with the aim of estimating the genomic diversity by protein domains content, sequence similarity of proteins and conservation of Intergenic Regions (IGRs). We also searched for BGCs but prioritizing those with potential antibiotic activity. Our analysis revealed that the pan-genome of the genus Streptomyces is clearly open, with a high quantity of unique gene families across the different species and that the IGRs are rarely conserved. We also described the phylogenetic relationships of the analyzed genomes using multiple markers, obtaining a trustworthy tree whose relationships were further validated by Average Nucleotide Identity (ANI) calculations. Finally, 33 biosynthetic gene clusters were detected to have potential antibiotic activity and a predicted mode of action, which might serve up as a guide to formulation of related experimental studies.
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Affiliation(s)
- Carlos Caicedo-Montoya
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Monserrat Manzo-Ruiz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rigoberto Ríos-Estepa
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
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14
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Chen Y, Wang J, Li G, Yang Y, Ding W. Current Advancements in Sactipeptide Natural Products. Front Chem 2021; 9:595991. [PMID: 34095082 PMCID: PMC8172795 DOI: 10.3389/fchem.2021.595991] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 04/09/2021] [Indexed: 11/18/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing class of natural products that benefited from genome sequencing technology in the past two decades. RiPPs are widely distributed in nature and show diverse chemical structures and rich biological activities. Despite the various structural characteristic of RiPPs, they follow a common biosynthetic logic: a precursor peptide containing an N-terminal leader peptide and a C-terminal core peptide; in some cases,a follower peptide is after the core peptide. The precursor peptide undergoes a series of modification, transport, and cleavage steps to form a mature natural product with specific activities. Sactipeptides (Sulfur-to-alpha carbon thioether cross-linked peptides) belong to RiPPs that show various biological activities such as antibacterial, spermicidal and hemolytic properties. Their common hallmark is an intramolecular thioether bond that crosslinks the sulfur atom of a cysteine residue to the α-carbon of an acceptor amino acid, which is catalyzed by a rSAM enzyme. This review summarizes recent achievements concerning the discovery, distribution, structural elucidation, biosynthesis and application prospects of sactipeptides.
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Affiliation(s)
- Yunliang Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, China
| | - Jinxiu Wang
- Northwest Institute of Eco-Environmental and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Guoquan Li
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, China
| | - Yunpeng Yang
- Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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15
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Genomic insight into a novel actinobacterium, Actinomadura rubrisoli sp. nov., reveals high potential for bioactive metabolites. Antonie van Leeuwenhoek 2021; 114:195-208. [DOI: 10.1007/s10482-020-01511-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/10/2020] [Indexed: 10/22/2022]
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16
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Pipiya SO, Terekhov SS, Mokrushina YA, Knorre VD, Smirnov IV, Gabibov AG. Engineering Artificial Biodiversity of Lantibiotics to Expand Chemical Space of DNA-Encoded Antibiotics. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:1319-1334. [PMID: 33280576 DOI: 10.1134/s0006297920110048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The discovery of antibiotics was one of the fundamental stages in the development of humanity, leading to a dramatic increase in the life expectancy of millions of people all over the world. The uncontrolled use of antibiotics resulted in the selection of resistant strains of bacteria, limiting the effectiveness of antimicrobial therapy nowadays. Antimicrobial peptides (AMPs) were considered promising candidates for next-generation antibiotics for a long time. However, the practical application of AMPs is restricted by their low therapeutic indices, impaired pharmacokinetics, and pharmacodynamics, which is predetermined by their peptide structure. Nevertheless, the DNA-encoded nature of AMPs enables creating broad repertoires of artificial biodiversity of antibiotics, making them versatile templates for the directed evolution of antibiotic activity. Lantibiotics are a unique class of AMPs with an expanded chemical space. A variety of post-translational modifications, mechanisms of action on bacterial membranes, and DNA-encoded nature make them a convenient molecular template for creating highly representative libraries of antimicrobial compounds. Isolation of new drug candidates from this synthetic biodiversity is extremely attractive but requires high-throughput screening of antibiotic activity. The combination of synthetic biology and ultrahigh-throughput microfluidics allows implementing the concept of directed evolution of lantibiotics for accelerated creation of new promising drug candidates.
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Affiliation(s)
- S O Pipiya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - S S Terekhov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Yu A Mokrushina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - V D Knorre
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - I V Smirnov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - A G Gabibov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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17
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Walker MC, Eslami SM, Hetrick KJ, Ackenhusen SE, Mitchell DA, van der Donk WA. Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family. BMC Genomics 2020; 21:387. [PMID: 32493223 PMCID: PMC7268733 DOI: 10.1186/s12864-020-06785-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 05/18/2020] [Indexed: 02/08/2023] Open
Abstract
Background Lanthipeptides belong to the ribosomally synthesized and post-translationally modified peptide group of natural products and have a variety of biological activities ranging from antibiotics to antinociceptives. These peptides are cyclized through thioether crosslinks and can bear other secondary post-translational modifications. While lanthipeptide biosynthetic gene clusters can be identified by the presence of genes encoding characteristic enzymes involved in the post-translational modification process, locating the precursor peptides encoded within these clusters is challenging due to their short length and high sequence variability, which limits the high-throughput exploration of lanthipeptide biosynthesis. To address this challenge, we enhanced the predictive capabilities of Rapid ORF Description & Evaluation Online (RODEO) to identify members of all four known classes of lanthipeptides. Results Using RODEO, we mined over 100,000 bacterial and archaeal genomes in the RefSeq database. We identified nearly 8500 lanthipeptide precursor peptides. These precursor peptides were identified in a broad range of bacterial phyla as well as the Euryarchaeota phylum of archaea. Bacteroidetes were found to encode a large number of these biosynthetic gene clusters, despite making up a relatively small portion of the genomes in this dataset. A number of these precursor peptides are similar to those of previously characterized lanthipeptides, but even more were not, including potential antibiotics. One such new antimicrobial lanthipeptide was purified and characterized. Additionally, examination of the biosynthetic gene clusters revealed that enzymes installing secondary post-translational modifications are more widespread than initially thought. Conclusion Lanthipeptide biosynthetic gene clusters are more widely distributed and the precursor peptides encoded within these clusters are more diverse than previously appreciated, demonstrating that the lanthipeptide sequence-function space remains largely underexplored.
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Affiliation(s)
- Mark C Walker
- Department of Chemistry and Chemical Biology, University of New Mexico, 346 Clark Hall, 300 Terrace St. NE, Albuquerque, NM, 87131, USA. .,Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA.
| | - Sara M Eslami
- Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA
| | - Kenton J Hetrick
- Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA
| | - Sarah E Ackenhusen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL, 61801, USA
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18
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Ay H, Nouioui I, Klenk HP, Cetin D, Igual JM, Sahin N, Isik K. Genome-based classification of Micromonospora craterilacus sp. nov., a novel actinobacterium isolated from Nemrut Lake. Antonie Van Leeuwenhoek 2020; 113:791-801. [PMID: 32060815 DOI: 10.1007/s10482-020-01390-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 01/28/2020] [Indexed: 11/28/2022]
Abstract
A novel actinobacterial strain, designated NA12T, was isolated from coastal sediment sample of Nemrut Lake, a crater lake in eastern Anatolia, Turkey. The taxonomic position of the strain was established using a polyphasic approach. Cultural and chemotaxonomic characteristics of the strain were consistent with its classification within the family Micromonosporaceae. The 16S rRNA gene sequence analysis of strain NA12T showed that the strain closely related to M. radicis AZ1-13T, M. zingiberis PLAI 1-1T, M. craniella LHW63014T and M. endophytica 202201T with pairwise sequence identity values ranging from 99.4 to 99.3%. Digital DNA-DNA hybridization values between strain NA12T and the closely related type strains were ranged from 41.0 to 18.3% while the average nucleotide identity values were between 87.3 and 86.5%, which are well below the designed cut-off points of 70 and 95%, respectively. The G + C content of genomic DNA was 71.5%. Whole-cell hydrolysates of strain NA12T contained 3-hydroxydiaminopimelic acid and meso-diaminopimelic acid. Cell-wall sugars were composed of arabinose, fucose, glucose, mannose, rhamnose and xylose. The polar lipid profile contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, glycophospholipid, amino-phospholipid and two unidentified phospholipids. The predominant menaquinones were MK-9(H6) and MK-9(H4). Major fatty acids were iso-C16:0 and C17:1ω8c. Based upon the consensus of phenotypic and phylogenetic analyses as well as whole genome comparisons, strain NA12T (DSM 100982T = KCTC 39647T) is proposed to represent the type strain of a novel species, Micromonospora craterilacus sp. nov.
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Affiliation(s)
- Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, Samsun, Turkey.
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Demet Cetin
- Division of Science Education, Department of Mathematics and Science Education, Gazi Faculty of Education, Gazi University, 06500, Ankara, Turkey
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiologia de Salamanca, Consejo Superior de Investigaciones Cientificas (IRNASA-CSIC), Salamanca, Spain
| | - Nevzat Sahin
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, Samsun, Turkey
| | - Kamil Isik
- Department of Biology, Faculty of Science and Arts, Ondokuz Mayis University, Samsun, Turkey
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Identification and Heterologous Expression of the Biosynthetic Gene Cluster Encoding the Lasso Peptide Humidimycin, a Caspofungin Activity Potentiator. Antibiotics (Basel) 2020; 9:antibiotics9020067. [PMID: 32046042 PMCID: PMC7168211 DOI: 10.3390/antibiotics9020067] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 12/19/2022] Open
Abstract
Humidimycin (MDN-0010) is a ribosomally synthesized and post-translationally modified peptide (RiPP) belonging to class I lasso peptides, and is structurally related to siamycins, which have been shown to have strong antimicrobial activities against Gram-positive bacteria and to possess anti-HIV activity. Humidimycin was isolated from the strain Streptomyces humidus CA-100629, and was shown to synergize the activity of the fungal cell wall inhibitor caspofungin. In this work, the biosynthetic gene cluster of humidimycin was identified by genome mining of S. humidus CA-100629, cloned by Gibson assembly, and heterologously expressed.
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20
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Huo L, Zhao X, Acedo JZ, Estrada P, Nair SK, van der Donk WA. Characterization of a Dehydratase and Methyltransferase in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides in Lachnospiraceae. Chembiochem 2020; 21:190-199. [PMID: 31532570 PMCID: PMC6980331 DOI: 10.1002/cbic.201900483] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Indexed: 12/15/2022]
Abstract
As a result of the exponential increase in genomic data, discovery of novel ribosomally synthesized and post-translationally modified peptide natural products (RiPPs) has progressed rapidly in the past decade. The lanthipeptides are a major subset of RiPPs. Through genome mining we identified a novel lanthipeptide biosynthetic gene cluster (lah) from Lachnospiraceae bacterium C6A11, an anaerobic bacterium that is a member of the human microbiota and which is implicated in the development of host disease states such as type 2 diabetes and resistance to Clostridium difficile colonization. The lah cluster encodes at least seven putative precursor peptides and multiple post-translational modification (PTM) enzymes. Two unusual class II lanthipeptide synthetases LahM1/M2 and a substrate-tolerant S-adenosyl-l-methionine (SAM)-dependent methyltransferase LahSB are biochemically characterized in this study. We also present the crystal structure of LahSB in complex with product S-adenosylhomocysteine. This study sets the stage for further exploration of the final products of the lah pathway as well as their potential physiological functions in human/animal gut microbiota.
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Affiliation(s)
- Liujie Huo
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
- State Key Laboratory for Microbial Technology (SKLMT), Institute of Microbial Technology, Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao, 266237, P. R. China
| | - Xiling Zhao
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Jeella Z Acedo
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Paola Estrada
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
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21
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Acedo JZ, Bothwell IR, An L, Trouth A, Frazier C, van der Donk WA. O-Methyltransferase-Mediated Incorporation of a β-Amino Acid in Lanthipeptides. J Am Chem Soc 2019; 141:16790-16801. [PMID: 31568727 DOI: 10.1021/jacs.9b07396] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Lanthipeptides represent a large class of cyclic natural products defined by the presence of lanthionine (Lan) and methyllanthionine (MeLan) cross-links. With the advances in DNA sequencing technologies and genome mining tools, new biosynthetic enzymes capable of installing unusual structural features are continuously being discovered. In this study, we investigated an O-methyltransferase that is a member of the most prominent auxiliary enzyme family associated with class I lanthipeptide biosynthetic gene clusters. Despite the prevalence of these enzymes, their function has not been established. Herein, we demonstrate that the O-methyltransferase OlvSA encoded in the olv gene cluster from Streptomyces olivaceus NRRL B-3009 catalyzes the rearrangement of a highly conserved aspartate residue to a β-amino acid, isoaspartate, in the lanthipeptide OlvA(BCSA). We elucidated the NMR solution structure of the GluC-digested peptide, OlvA(BCSA)GluC, which revealed a unique ring topology comprising four interlocking rings and positions the isoaspartate residue in a solvent exposed loop that is stabilized by a MeLan ring. Gas chromatography-mass spectrometry analysis further indicated that OlvA(BCSA) contains two dl-MeLan rings and two Lan rings with an unusual ll-stereochemistry. Lastly, in vitro reconstitution of OlvSA activity showed that it is a leader peptide-independent and S-adenosyl methionine-dependent O-methyltransferase that mediates the conversion of a highly conserved aspartate residue in a cyclic substrate into a succinimide, which is hydrolyzed to generate an Asp or isoAsp containing peptide. This overall transformation converts an α-amino acid into a β-amino acid in a ribosomally synthesized peptide, via an electrophilic intermediate that may be the intended product.
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Affiliation(s)
- Jeella Z Acedo
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Ian R Bothwell
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Linna An
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Abby Trouth
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Clara Frazier
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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