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Ren Y, Liu R, Zheng Y, Wang H, Meng Q, Zhu T, Yin J, Cao X, Yu Z. Biosynthetic mechanism of the yellow pigments in the marine bacterium Pseudoalteromonas sp. strain T1lg65. Appl Environ Microbiol 2024; 90:e0177923. [PMID: 38193673 PMCID: PMC10880671 DOI: 10.1128/aem.01779-23] [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: 10/06/2023] [Accepted: 11/28/2023] [Indexed: 01/10/2024] Open
Abstract
The Pseudoalteromonas genus marine bacteria have attracted increasing interest because of their abilities to produce bioactive metabolites. The pigmented Pseudoalteromonas group encodes more secondary metabolite biosynthetic gene clusters (BGCs) than the non-pigmented group. Here, we report a yellow pigmented bacterium Pseudoalteromonas sp. strain T1lg65, which was isolated from a mangrove forest sediment. We showed that the yellow pigments of T1lg65 belong to the group of lipopeptide alterochromides. Further genetic analyses of the alterochromide BGC revealed that the yellow pigments are biosynthesized by aryl-polyene synthases and nonribosomal peptide synthases. Within the gene cluster, altA encodes a tyrosine ammonia acid lyase, which catalyzes synthesis of the precursor 4-hydroxycinnamic acid (4-HCA) from tyrosine in the alterochromide biosynthetic pathway. In addition, altN, encoding a putative flavin-dependent halogenase, was proven to be responsible for the bromination of alterochromides based on gene deletion, molecular docking, and site mutagenesis analyses. In summary, the biosynthetic pathway, precursor synthesis, and bromination mechanism of the lipopeptide alterochromides were studied in-depth. Our results expand the knowledge on biosynthesis of Pseudoalteromonas pigments and could promote the development of active pigments in the future.IMPORTANCEThe marine bacteria Pseudoalteromonas spp. are important biological resources because they are producers of bioactive natural products, including antibiotics, pigments, enzymes, and antimicrobial peptides. One group of the microbial pigments, alterochromides, holds a great value for their novel lipopeptide structures and antimicrobial activities. Previous studies were limited to the structural characterization of alterochromides and genome mining for the alterochromide biosynthesis. This work focused on the biosynthetic mechanism for alterochromide production, especially revealing functions of two key genes within the gene cluster for the alterochromide biosynthesis. On the one hand, our study provides a target for metabolic engineering of the alterochromide biosynthesis; on the other hand, the 4-HCA synthase AltA and brominase AltN show potential in the biocatalyst industry.
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Affiliation(s)
- Yixuan Ren
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Ruoyu Liu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yifan Zheng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Hang Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Qiu Meng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Tingheng Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Jianhua Yin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Xueqiang Cao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhiliang Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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2
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Karimian S, Farahmandzad N, Mohammadipanah F. Manipulation and epigenetic control of silent biosynthetic pathways in actinobacteria. World J Microbiol Biotechnol 2024; 40:65. [PMID: 38191749 DOI: 10.1007/s11274-023-03861-4] [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: 06/22/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024]
Abstract
Most biosynthetic gene clusters (BGCs) of Actinobacteria are either silent or expressed less than the detectable level. The non-genetic approaches including biological interactions, chemical agents, and physical stresses that can be used to awaken silenced pathways are compared in this paper. These non-genetic induction strategies often need screening approaches, including one strain many compounds (OSMAC), reporter-guided mutant selection, and high throughput elicitor screening (HiTES) have been developed. Different types of genetic manipulations applied in the induction of cryptic BGCs of Actinobacteria can be categorized as genome-wide pleiotropic and targeted approaches like manipulation of global regulatory systems, modulation of regulatory genes, ribosome and engineering of RNA polymerase or phosphopantheteine transferases. Targeted approaches including genome editing by CRISPR, mutation in transcription factors and modification of BGCs promoters, inactivation of the highly expressed biosynthetic pathways, deleting the suppressors or awakening the activators, heterologous expression, or refactoring of gene clusters can be applied for activation of pathways which are predicted to synthesize new bioactive structures in genome mining studies of Acinobacteria. In this review, the challenges and advantages of employing these approaches in induction of Actinobacteria BGCs are discussed. Further, novel natural products needed as drug for pharmaceutical industry or as biofertilizers in agricultural industry can be discovered even from known species of Actinobactera by the innovative approaches of metabolite biosynthesis elicitation.
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Affiliation(s)
- Sanaz Karimian
- Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran
| | - Navid Farahmandzad
- Department of Biosystems Engineering, Auburn university, Auburn, AL 36849, USA
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran
| | - Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran.
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3
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Gasparek M, Steel H, Papachristodoulou A. Deciphering mechanisms of production of natural compounds using inducer-producer microbial consortia. Biotechnol Adv 2023; 64:108117. [PMID: 36813010 DOI: 10.1016/j.biotechadv.2023.108117] [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: 07/21/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023]
Abstract
Living organisms produce a wide range of metabolites. Because of their potential antibacterial, antifungal, antiviral, or cytostatic properties, such natural molecules are of high interest to the pharmaceutical industry. In nature, these metabolites are often synthesized via secondary metabolic biosynthetic gene clusters that are silent under the typical culturing conditions. Among different techniques used to activate these silent gene clusters, co-culturing of "producer" species with specific "inducer" microbes is a particularly appealing approach due to its simplicity. Although several "inducer-producer" microbial consortia have been reported in the literature and hundreds of different secondary metabolites with attractive biopharmaceutical properties have been described as a result of co-cultivating inducer-producer consortia, less attention has been devoted to the understanding of the mechanisms and possible means of induction for production of secondary metabolites in co-cultures. This lack of understanding of fundamental biological functions and inter-species interactions significantly limits the diversity and yield of valuable compounds using biological engineering tools. In this review, we summarize and categorize the known physiological mechanisms of production of secondary metabolites in inducer-producer consortia, and then discuss approaches that could be exploited to optimize the discovery and production of secondary metabolites.
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Affiliation(s)
- Miroslav Gasparek
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom.
| | - Harrison Steel
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
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Di Salvo E, Lo Vecchio G, De Pasquale R, De Maria L, Tardugno R, Vadalà R, Cicero N. Natural Pigments Production and Their Application in Food, Health and Other Industries. Nutrients 2023; 15:nu15081923. [PMID: 37111142 PMCID: PMC10144550 DOI: 10.3390/nu15081923] [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: 03/14/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
In addition to fulfilling their function of giving color, many natural pigments are known as interesting bioactive compounds with potential health benefits. These compounds have various applications. In recent times, in the food industry, there has been a spread of natural pigment application in many fields, such as pharmacology and toxicology, in the textile and printing industry and in the dairy and fish industry, with almost all major natural pigment classes being used in at least one sector of the food industry. In this scenario, the cost-effective benefits for the industry will be welcome, but they will be obscured by the benefits for people. Obtaining easily usable, non-toxic, eco-sustainable, cheap and biodegradable pigments represents the future in which researchers should invest.
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Affiliation(s)
- Eleonora Di Salvo
- Departement of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98168 Messina, Italy
| | - Giovanna Lo Vecchio
- Departement of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98168 Messina, Italy
| | - Rita De Pasquale
- Departement of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98168 Messina, Italy
| | - Laura De Maria
- Department of Veterinary Sciences, University of Messina, 98168 Messina, Italy
| | - Roberta Tardugno
- Department of Pharmacy-Drug Sciences, University of Bari, 70121 Bari, Italy
| | - Rossella Vadalà
- Departement of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98168 Messina, Italy
| | - Nicola Cicero
- Departement of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98168 Messina, Italy
- Science4life srl, University of Messina, 98168 Messina, Italy
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5
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Yu J, Hermann M, Smith R, Tomm H, Metwally H, Kolwich J, Liu C, Le Blanc JCY, Covey TR, Ross AC, Oleschuk R. Hyperspectral Visualization-Based Mass Spectrometry Imaging by LMJ-SSP: A Novel Strategy for Rapid Natural Product Profiling in Bacteria. Anal Chem 2023; 95:2020-2028. [PMID: 36634199 DOI: 10.1021/acs.analchem.2c04550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Mass spectrometry imaging (MSI) has been widely used to discover natural products (NPs) from underexplored microbiological sources. However, the technique is limited by incompatibility with complicated/uneven surface topography and labor-intensive sample preparation, as well as lengthy compound profiling procedures. Here, liquid micro-junction surface sampling probe (LMJ-SSP)-based MSI is used for rapid profiling of natural products from Gram-negative marine bacteria Pseudoalteromonas on nutrient agar media without any sample preparation. A conductance-based autosampling platform with 1 mm spatial resolution and an innovative multivariant analysis-driven method was used to create one hyperspectral image for the sampling area. NP discovery requires general spatial correlation between m/z and colony location but not highly precise spatial resolution. The hyperspectral image was used to annotate different m/z by straightforward color differences without the need to directly interrogate the spectra. To demonstrate the utility of our approach, the rapid analysis of Pseudoalteromonas rubra DSM6842, Pseudoalteromonas tunicata DSM14096, Pseudoalteromonas piscicida JCM20779, and Pseudoalteromonas elyakovii ATCC700519 cultures was directly performed on Agar. Various natural products, including prodiginine and tambjamine analogues, were quickly identified from the hyperspectral image, and the dynamic extracellular environment was shown with compound heatmaps. Hyperspectral visualization-based MSI is an efficient and sensitive strategy for direct and rapid natural product profiling from different Pseudoalteromonas strains.
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Affiliation(s)
- Jian Yu
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Matthias Hermann
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Rachael Smith
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Hailey Tomm
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Haidy Metwally
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Jennifer Kolwich
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Chang Liu
- SCIEX, Concord, Ontario L4K 4 V8, Canada
| | | | | | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Richard Oleschuk
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
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6
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Muñoz-Miranda LA, Iñiguez-Moreno M. An extensive review of marine pigments: sources, biotechnological applications, and sustainability. AQUATIC SCIENCES 2023; 85:68. [PMID: 37096011 PMCID: PMC10112328 DOI: 10.1007/s00027-023-00966-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
The global demand for food and healthcare products based on natural compounds means that the industrial and scientific sectors are on a continuous search for natural colored compounds that can contribute to the replacement of synthetic colors. Natural pigments are a heterogeneous group of chemical molecules, widely distributed in nature. Recently, the interest in marine organisms has increased as they represent the most varied environment in the world and provide a wide range of colored compounds with bioactive properties and biotechnological applications in areas such as the food, pharmaceutical, cosmetic, and textile industries. The use of marine-derived pigments has increased during the last two decades because they are environmentally safe and healthy compounds. This article provides a comprehensive review of the current knowledge of sources, applications, and sustainability of the most important marine pigments. In addition, alternatives to protect these compounds from environmental conditions and their applications in the industrial sector are reviewed.
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Affiliation(s)
- Luis Alfonso Muñoz-Miranda
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, 44340 Jalisco Mexico
| | - Maricarmen Iñiguez-Moreno
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnológico de Monterrey, Monterrey, 64849 Mexico
- School of Engineering and Sciences, Tecnológico de Monterrey, Monterrey, 64849 Mexico
- Universidad Politécnica del Estado de Nayarit, Tepic, 63506 Nayarit Mexico
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7
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Lee TA, Steel H. Cybergenetic control of microbial community composition. Front Bioeng Biotechnol 2022; 10:957140. [PMID: 36277404 PMCID: PMC9582452 DOI: 10.3389/fbioe.2022.957140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
The use of bacterial communities in bioproduction instead of monocultures has potential advantages including increased productivity through division of labour, ability to utilise cheaper substrates, and robustness against perturbations. A key challenge in the application of engineered bacterial communities is the ability to reliably control the composition of the community in terms of its constituent species. This is crucial to prevent faster growing species from outcompeting others with a lower relative fitness, and to ensure that all species are present at an optimal ratio during different steps in a biotechnological process. In contrast to purely biological approaches such as synthetic quorum sensing circuits or paired auxotrophies, cybergenetic control techniques - those in which computers interface with living cells-are emerging as an alternative approach with many advantages. The community composition is measured through methods such as fluorescence intensity or flow cytometry, with measured data fed real-time into a computer. A control action is computed using a variety of possible control algorithms and then applied to the system, with actuation taking the form of chemical (e.g., inducers, nutrients) or physical (e.g., optogenetic, mechanical) inputs. Subsequent changes in composition are then measured and the cycle repeated, maintaining or driving the system to a desired state. This review discusses recent and future developments in methods for implementing cybergenetic control systems, contrasts their capabilities with those of traditional biological methods of population control, and discusses future directions and outstanding challenges for the field.
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8
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Alviz-Gazitua P, González A, Lee MR, Aranda CP. Molecular Relationships in Biofilm Formation and the Biosynthesis of Exoproducts in Pseudoalteromonas spp. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:431-447. [PMID: 35486299 DOI: 10.1007/s10126-022-10097-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Most members of the Pseudoalteromonas genus have been isolated from living surfaces as members of epiphytic and epizooic microbiomes on marine macroorganisms. Commonly Pseudoalteromonas isolates are reported as a source of bioactive exoproducts, i.e., secondary metabolites, such as exopolymeric substances and extracellular enzymes. The experimental conditions for the production of these agents are commonly associated with sessile metabolic states such as biofilms or liquid cultures in the stationary growth phase. Despite this, the molecular mechanisms that connect biofilm formation and the biosynthesis of exoproducts in Pseudoalteromonas isolates have rarely been mentioned in the literature. This review compiles empirical evidence about exoproduct biosynthesis conditions and molecular mechanisms that regulate sessile metabolic states in Pseudoalteromonas species, to provide a comprehensive perspective on the regulatory convergences that generate the recurrent coexistence of both phenomena in this bacterial genus. This synthesis aims to provide perspectives on the extent of this phenomenon for the optimization of bioprospection studies and biotechnology processes based on these bacteria.
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Affiliation(s)
- P Alviz-Gazitua
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avda. Fuchslocher 1305, P. Box 5290000, Osorno, Chile
| | - A González
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avda. Fuchslocher 1305, P. Box 5290000, Osorno, Chile
| | - M R Lee
- Centro i~mar, Universidad de Los Lagos, Camino a Chinquihue km 6, P. Box 5480000, Puerto Montt, Chile
| | - C P Aranda
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avda. Fuchslocher 1305, P. Box 5290000, Osorno, Chile.
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9
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Deshmukh SK, Dufossé L, Chhipa H, Saxena S, Mahajan GB, Gupta MK. Fungal Endophytes: A Potential Source of Antibacterial Compounds. J Fungi (Basel) 2022; 8:164. [PMID: 35205918 PMCID: PMC8877021 DOI: 10.3390/jof8020164] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 02/04/2023] Open
Abstract
Antibiotic resistance is becoming a burning issue due to the frequent use of antibiotics for curing common bacterial infections, indicating that we are running out of effective antibiotics. This has been more obvious during recent corona pandemics. Similarly, enhancement of antimicrobial resistance (AMR) is strengthening the pathogenicity and virulence of infectious microbes. Endophytes have shown expression of various new many bioactive compounds with significant biological activities. Specifically, in endophytic fungi, bioactive metabolites with unique skeletons have been identified which could be helpful in the prevention of increasing antimicrobial resistance. The major classes of metabolites reported include anthraquinone, sesquiterpenoid, chromone, xanthone, phenols, quinones, quinolone, piperazine, coumarins and cyclic peptides. In the present review, we reported 451 bioactive metabolites isolated from various groups of endophytic fungi from January 2015 to April 2021 along with their antibacterial profiling, chemical structures and mode of action. In addition, we also discussed various methods including epigenetic modifications, co-culture, and OSMAC to induce silent gene clusters for the production of noble bioactive compounds in endophytic fungi.
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Affiliation(s)
- Sunil K Deshmukh
- TERI-Deakin Nano Biotechnology Centre, The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi 110003, Delhi, India
- Agpharm Bioinnovations LLP, Incubatee: Science and Technology Entrepreneurs Park (STEP), Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
| | - Laurent Dufossé
- Chimie et Biotechnologie des Produits Naturels (CHEMBIOPRO Lab) & ESIROI Agroalimentaire, Université de la Réunion, 15 Avenue René Cassin, 97744 Saint-Denis, France
| | - Hemraj Chhipa
- College of Horticulture and Forestry, Agriculture University Kota, Jhalawar 322360, Rajasthan, India
| | - Sanjai Saxena
- Agpharm Bioinnovations LLP, Incubatee: Science and Technology Entrepreneurs Park (STEP), Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
| | - Girish B Mahajan
- HiMedia Laboratories Pvt. Ltd., Mumbai 400086, Maharashtra, India
| | - Manish Kumar Gupta
- SGT College of Pharmacy, SGT University, Gurugram 122505, Haryana, India
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10
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Johnson RA, Chan AN, Ward RD, McGlade CA, Hatfield BM, Peters JM, Li B. Inhibition of Isoleucyl-tRNA Synthetase by the Hybrid Antibiotic Thiomarinol. J Am Chem Soc 2021; 143:12003-12013. [PMID: 34342433 DOI: 10.1021/jacs.1c02622] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hybrid antibiotics are an emerging antimicrobial strategy to overcome antibiotic resistance. The natural product thiomarinol A is a hybrid of two antibiotics: holothin, a dithiolopyrrolone (DTP), and marinolic acid, a close analogue of the drug mupirocin that is used to treat methicillin-resistant Staphylococcus aureus (MRSA). DTPs disrupt metal homeostasis by chelating metal ions in cells, whereas mupirocin targets the essential enzyme isoleucyl-tRNA synthetase (IleRS). Thiomarinol A is over 100-fold more potent than mupirocin against mupirocin-sensitive MRSA; however, its mode of action has been unknown. We show that thiomarinol A targets IleRS. A knockdown of the IleRS-encoding gene, ileS, exhibited sensitivity to a synthetic analogue of thiomarinol A in a chemical genomics screen. Thiomarinol A inhibits MRSA IleRS with a picomolar Ki and binds to IleRS with low femtomolar affinity, 1600 times more tightly than mupirocin. We find that thiomarinol A remains effective against high-level mupirocin-resistant MRSA and provide evidence to support a dual mode of action for thiomarinol A that may include both IleRS inhibition and metal chelation. We demonstrate that MRSA develops resistance to thiomarinol A to a substantially lesser degree than mupirocin and the potent activity of thiomarinol A requires hybridity between DTP and mupirocin. Our findings identify a mode of action of a natural hybrid antibiotic and demonstrate the potential of hybrid antibiotics to combat antibiotic resistance.
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Affiliation(s)
- Rachel A Johnson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Andrew N Chan
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ryan D Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Caylie A McGlade
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Breanne M Hatfield
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jason M Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin 53726, United States
| | - Bo Li
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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11
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Mai PY, Le Goff G, Poupon E, Lopes P, Moppert X, Costa B, Beniddir MA, Ouazzani J. Solid-Phase Extraction Embedded Dialysis (SPEED), an Innovative Procedure for the Investigation of Microbial Specialized Metabolites. Mar Drugs 2021; 19:md19070371. [PMID: 34206861 PMCID: PMC8304039 DOI: 10.3390/md19070371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
Solid-phase extraction embedded dialysis (SPEED technology) is an innovative procedure developed to physically separate in-situ, during the cultivation, the mycelium of filament forming microorganisms, such as actinomycetes and fungi, and the XAD-16 resin used to trap the secreted specialized metabolites. SPEED consists of an external nylon cloth and an internal dialysis tube containing the XAD resin. The dialysis barrier selects the molecular weight of the trapped compounds, and prevents the aggregation of biomass or macromolecules on the XAD beads. The external nylon promotes the formation of a microbial biofilm, making SPEED a biofilm supported cultivation process. SPEED technology was applied to the marine Streptomyces albidoflavus 19-S21, isolated from a core of a submerged Kopara sampled at 20 m from the border of a saltwater pond. The chemical space of this strain was investigated effectively using a dereplication strategy based on molecular networking and in-depth chemical analysis. The results highlight the impact of culture support on the molecular profile of Streptomyces albidoflavus 19-S21 secondary metabolites.
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Affiliation(s)
- Phuong-Y. Mai
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France; (P.-Y.M.); (G.L.G.); (P.L.)
- Équipe “Chimie des Substances Naturelles” BioCIS, CNRS, Université Paris-Saclay, 5 Rue J.-B. Clément, 92290 Châtenay-Malabry, France; (E.P.); (M.A.B.)
| | - Géraldine Le Goff
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France; (P.-Y.M.); (G.L.G.); (P.L.)
| | - Erwan Poupon
- Équipe “Chimie des Substances Naturelles” BioCIS, CNRS, Université Paris-Saclay, 5 Rue J.-B. Clément, 92290 Châtenay-Malabry, France; (E.P.); (M.A.B.)
| | - Philippe Lopes
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France; (P.-Y.M.); (G.L.G.); (P.L.)
| | - Xavier Moppert
- PACIFIC BIOTECH SAS, BP 140 289, 98 701 Arue, Tahiti, French Polynesia; (X.M.); (B.C.)
| | - Bernard Costa
- PACIFIC BIOTECH SAS, BP 140 289, 98 701 Arue, Tahiti, French Polynesia; (X.M.); (B.C.)
| | - Mehdi A. Beniddir
- Équipe “Chimie des Substances Naturelles” BioCIS, CNRS, Université Paris-Saclay, 5 Rue J.-B. Clément, 92290 Châtenay-Malabry, France; (E.P.); (M.A.B.)
| | - Jamal Ouazzani
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France; (P.-Y.M.); (G.L.G.); (P.L.)
- Correspondence: ; Tel.: +33-6-82-81-65-90
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12
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Condren AR, Costa MS, Sanchez NR, Konkapaka S, Gallik KL, Saxena A, Murphy BT, Sanchez LM. Addition of insoluble fiber to isolation media allows for increased metabolite diversity of lab-cultivable microbes derived from zebrafish gut samples. Gut Microbes 2020; 11:1064-1076. [PMID: 32202200 PMCID: PMC7524352 DOI: 10.1080/19490976.2020.1740073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
There is a gap in measured microbial diversity when comparing genomic sequencing techniques versus cultivation from environmental samples in a laboratory setting. Standardized methods in artificial environments may not recapitulate the environmental conditions that native microbes require for optimal growth. For example, the intestinal tract houses microbes at various pH values as well as minimal oxygen and light environments. These microbes are also exposed to an atypical source of carbon: dietary fiber compacted in fecal matter. To investigate how the addition of insoluble fiber to isolation media could affect the cultivation of microbes from zebrafish intestines, an isolate library was built and analyzed using the bioinformatics pipeline IDBac. While all isolation media encouraged the growth of species from several phyla, the extent of growth was greater with the addition of fiber allowing for easier isolation. Furthermore, fiber addition altered the metabolism of the cultivated gut-derived microbes and induced the production of unique metabolites that were not produced when microbes were otherwise grown on standard isolation media. Addition of this inexpensive carbon source to the media supported the cultivation of a diverse community whose secondary metabolite production may more closely replicate their metabolite production in vivo.
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Affiliation(s)
- Alanna R. Condren
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Maria S Costa
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA,Faculty of Pharmaceutical Sciences, University of Iceland, Reykjavik, Iceland
| | - Natalia Rivera Sanchez
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Sindhu Konkapaka
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Kristin L Gallik
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Ankur Saxena
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Brian T Murphy
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA,CONTACT Laura M Sanchez Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL60612, USA
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Advances in microbial culturing conditions to activate silent biosynthetic gene clusters for novel metabolite production. ACTA ACUST UNITED AC 2019; 46:1381-1400. [DOI: 10.1007/s10295-019-02198-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/24/2019] [Indexed: 02/08/2023]
Abstract
Abstract
Natural products (NPs) produced by bacteria and fungi are often used as therapeutic agents due to their complex structures and wide range of bioactivities. Enzymes that build NPs are encoded by co-localized biosynthetic gene clusters (BGCs), and genome sequencing has recently revealed that many BGCs are “silent” under standard laboratory conditions. There are numerous methods used to activate “silent” BGCs that rely either upon altering culture conditions or genetic modification. In this review, we discuss several recent microbial cultivation methods that have been used to expand the scope of NPs accessible in the laboratory. These approaches are divided into three categories: addition of a physical scaffold, addition of small molecule elicitors, and co-cultivation with another microbe.
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14
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Isolation and characterization of violacein from an Antarctic Iodobacter: a non-pathogenic psychrotolerant microorganism. Extremophiles 2019; 24:43-52. [DOI: 10.1007/s00792-019-01111-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/17/2019] [Indexed: 10/26/2022]
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15
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Timmermans ML, Picott KJ, Ucciferri L, Ross AC. Culturing marine bacteria from the genus Pseudoalteromonas on a cotton scaffold alters secondary metabolite production. Microbiologyopen 2018; 8:e00724. [PMID: 30270573 PMCID: PMC6528606 DOI: 10.1002/mbo3.724] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 07/23/2018] [Accepted: 08/03/2018] [Indexed: 01/13/2023] Open
Abstract
The discovery of secondary metabolites from marine microorganisms is beset by numerous challenges including difficulties cultivating and subsequently eliciting expression of biosynthetic genes from marine microbes in the laboratory. In this paper, we describe a method of culturing three species from the marine bacterial genus Pseudoalteromonas using cotton scaffold supplemented liquid media. This simple cultivation method was designed to mimic the natural behavior of some members of the genus wherein they form epibiotic/symbiotic associations with higher organisms such as sponges and corals or attach to solid structures as a biofilm. Our scaffolded cultivation is highly effective at stimulating an attachment/biofilm phenotype and causes large changes to metabolite profiles for the microbes investigated. Metabolite changes include alteration to the production levels of known molecules such as violacein, thiomarinol A, and the alterochromide and prodiginine families of molecules. Finally and critically, our technique stimulates the production of unknown compounds that will serve as leads for future natural product discovery. These results suggest our cultivation approach could potentially be used as a general strategy for the activation of silent gene clusters in marine microbes to facilitate access to their full natural product biosynthetic capacity.
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Affiliation(s)
| | | | - Lorena Ucciferri
- Department of Chemistry, Queen's University, Kingston, ON, Canada
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ON, Canada
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