1
|
Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, da Silva EB, O'Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. Small molecule in situ resin capture provides a compound first approach to natural product discovery. Nat Commun 2024; 15:5230. [PMID: 38898025 DOI: 10.1038/s41467-024-49367-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Culture-based microbial natural product discovery strategies fail to realize the extraordinary biosynthetic potential detected across earth's microbiomes. Here we introduce Small Molecule In situ Resin Capture (SMIRC), a culture-independent method to obtain natural products directly from the environments in which they are produced. We use SMIRC to capture numerous compounds including two new carbon skeletons that were characterized using NMR and contain structural features that are, to the best of our knowledge, unprecedented among natural products. Applications across diverse marine habitats reveal biome-specific metabolomic signatures and levels of chemical diversity in concordance with sequence-based predictions. Expanded deployments, in situ cultivation, and metagenomics facilitate compound discovery, enhance yields, and link compounds to candidate producing organisms, although microbial community complexity creates challenges for the later. This compound-first approach to natural product discovery provides access to poorly explored chemical space and has implications for drug discovery and the detection of chemically mediated biotic interactions.
Collapse
Affiliation(s)
- Alexander Bogdanov
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Mariam N Salib
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alexander B Chase
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Earth Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Heinz Hammerlindl
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Mitchell N Muskat
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Stephanie Luedtke
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Tadeusz F Molinski
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Paul R Jensen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
2
|
Yang L, Yi L, Gong B, Chen L, Li M, Zhu X, Duan Y, Huang Y. Chalkophomycin Biosynthesis Revealing Unique Enzyme Architecture for a Hybrid Nonribosomal Peptide Synthetase and Polyketide Synthase. Molecules 2024; 29:1982. [PMID: 38731473 PMCID: PMC11085572 DOI: 10.3390/molecules29091982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Chalkophomycin is a novel chalkophore with antibiotic activities isolated from Streptomyces sp. CB00271, while its potential in studying cellular copper homeostasis makes it an important probe and drug lead. The constellation of N-hydroxylpyrrole, 2H-oxazoline, diazeniumdiolate, and methoxypyrrolinone functional groups into one compact molecular architecture capable of coordinating cupric ions draws interest to unprecedented enzymology responsible for chalkophomycin biosynthesis. To elucidate the biosynthetic machinery for chalkophomycin production, the chm biosynthetic gene cluster from S. sp. CB00271 was identified, and its involvement in chalkophomycin biosynthesis was confirmed by gene replacement. The chm cluster was localized to a ~31 kb DNA region, consisting of 19 open reading frames that encode five nonribosomal peptide synthetases (ChmHIJLO), one modular polyketide synthase (ChmP), six tailoring enzymes (ChmFGMNQR), two regulatory proteins (ChmAB), and four resistance proteins (ChmA'CDE). A model for chalkophomycin biosynthesis is proposed based on functional assignments from sequence analysis and structure modelling, and is further supported by analogy to over 100 chm-type gene clusters in public databases. Our studies thus set the stage to fully investigate chalkophomycin biosynthesis and to engineer chalkophomycin analogues through a synthetic biology approach.
Collapse
Affiliation(s)
- Long Yang
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China;
- Hefei Comprehensive National Science Center, Institute of Health and Medicine, Hefei 230093, China;
| | - Liwei Yi
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
- Department of Pharmacy, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Bang Gong
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
- College of Pharmacy, Hunan Vocational College of Science and Technology, Changsha 410004, China
| | - Lili Chen
- Hefei Comprehensive National Science Center, Institute of Health and Medicine, Hefei 230093, China;
| | - Miao Li
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha 410011, China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha 410011, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha 410011, China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha 410011, China
| | - Yong Huang
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China;
- Hefei Comprehensive National Science Center, Institute of Health and Medicine, Hefei 230093, China;
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
| |
Collapse
|
3
|
Bianchini G, Sánchez‐Baracaldo P. TreeViewer: Flexible, modular software to visualise and manipulate phylogenetic trees. Ecol Evol 2024; 14:e10873. [PMID: 38314311 PMCID: PMC10834882 DOI: 10.1002/ece3.10873] [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: 11/08/2023] [Accepted: 12/04/2023] [Indexed: 02/06/2024] Open
Abstract
Phylogenetic trees illustrate evolutionary relationships between taxa or genes. Tree figures are crucial when presenting results and data, and by creating clear and effective plots, researchers can describe many kinds of evolutionary patterns. However, producing tree plots can be a time-consuming task, especially as multiple different programs are often needed to adjust and illustrate all data associated with a tree. We present TreeViewer, a new software to draw phylogenetic trees. TreeViewer is flexible, modular, and user-friendly. Plots are produced as the result of a user-defined pipeline, which can be finely customised and easily applied to different trees. Every feature of the program is documented and easily accessible, either in the online manual or within the program's interface. We show how TreeViewer can be used to produce publication-ready figures, saving time by not requiring additional graphical post-processing tools. TreeViewer is freely available for Windows, macOS, and Linux operating systems and distributed under an AGPLv3 licence from https://treeviewer.org. It has a graphical user interface (GUI), as well as a command-line interface, which is useful to work with very large trees and for automated pipelines. A detailed user manual with examples and tutorials is also available. TreeViewer is mainly aimed at users wishing to produce highly customised, publication-quality tree figures using a single GUI software tool. Compared to other GUI tools, TreeViewer offers a richer feature set and a finer degree of customisation. Compared to command-line-based tools and software libraries, TreeViewer's graphical interface is more accessible. The flexibility of TreeViewer's approach to phylogenetic tree plotting enables the program to produce a wide variety of publication-ready figures. Users are encouraged to create their own custom modules to expand the functionalities of the program. This sets the scene for an ever-expanding and ever-adapting software framework that can easily adjust to respond to new challenges.
Collapse
|
4
|
Syiemiong D, Rabha J. Unveiling nature's treasures: actinobacteria from Meghalaya's mining sites as sources of bioactive compounds. Arch Microbiol 2024; 206:64. [PMID: 38224372 DOI: 10.1007/s00203-023-03791-7] [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: 08/17/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 01/16/2024]
Abstract
Coal and sillimanite mining sites present unique ecological niches favoring the growth of actinobacteria, a group of Gram-positive bacteria known for producing a wide array of bioactive compounds. Isolating these bacteria from such environments could unveil novel compounds with potential biotechnological applications. This study involved the isolation of actinobacteria from two mining sites in Meghalaya, India. The dominant genera from both sites were Streptomyces, Amycolatopsis, Nocardia, and Streptosporangium. Metabolic pathway prediction from 16S rRNA gene revealed several pathways beneficial for plant growth. Exploration of biosynthetic genes indicated a prevalence of the type-II polyketide synthase gene. Sequencing the ketosynthase-alpha domain of the gene led to predictions of various bioactive secondary metabolites. Around 44% of the isolates demonstrated antimicrobial properties, with some also displaying plant growth-promoting traits. Amycolatopsis SD-15 exhibited promising results in planta when tested on tomato plants. These findings highlight the potential of actinobacteria from Meghalaya's mining sites across medical, agricultural, and industrial domains.
Collapse
Affiliation(s)
- Debulman Syiemiong
- Department of Botany, St. Edmund's College, Shillong, 793003, India.
- Microbial Ecology Laboratory, Department of Botany, Gauhati University, Guwahati, 781014, India.
| | - Jintu Rabha
- Microbial Ecology Laboratory, Department of Botany, Gauhati University, Guwahati, 781014, India
| |
Collapse
|
5
|
Li X, Gadar-Lopez AE, Chen L, Jayachandran S, Cruz-Morales P, Keasling JD. Mining natural products for advanced biofuels and sustainable bioproducts. Curr Opin Biotechnol 2023; 84:103003. [PMID: 37769513 DOI: 10.1016/j.copbio.2023.103003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/03/2023] [Accepted: 09/03/2023] [Indexed: 10/03/2023]
Abstract
Recently, there has been growing interest in the sustainable production of biofuels and bioproducts derived from renewable sources. Natural products, the largest and more structurally diverse group of metabolites, hold significant promise as sources for such bio-based products. However, there are two primary challenges in harnessing natural products' potential: precise mining of biosynthetic gene clusters (BGCs) that can be used as scaffolds or bioparts and their functional expression for biofuel and bioproduct manufacture. In this review, we explore recent advances in the development of bioinformatic tools for BGC mining and the manipulation of various hosts for natural product-based biofuels and bioproducts manufacture. Moreover, we discuss potential strategies for expanding the chemical diversity of biofuels and bioproducts and enhancing their overall yield.
Collapse
Affiliation(s)
- Xiaowei Li
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Adrian E Gadar-Lopez
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Ling Chen
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Sidharth Jayachandran
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark.
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark; Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA 94720, USA; Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
| |
Collapse
|
6
|
Schwitalla JW, Le NTH, Um S, Schalk F, Brönstrup M, Baunach M, Beemelmanns C. Heterologous expression of the cryptic mdk gene cluster and structural revision of maduralactomycin A. RSC Adv 2023; 13:34136-34144. [PMID: 38019997 PMCID: PMC10663993 DOI: 10.1039/d3ra05931f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
After conducting an in silico analysis of the cryptic mdk cluster region and performing transcriptomic studies, an integrative Streptomyces BAC Vector containing the mdk gene sequence was constructed. The heterologous expression of the mdk cluster in Streptomyces albus J1074 resulted in the production of the angucyclic product, seongomycin, which allowed for the assesment of its antibacterial, antiproliferative, and antiviral activities. Heterologous production was further confirmed by targeted knock-out experiments involving key regulators of the biosynthetic pathways. We were further able to revise the core structure of maduralactomycin A, using a computational approach.
Collapse
Affiliation(s)
- Jan W Schwitalla
- Chemical Biology of Microbe-Host Interactions, Hans-Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) Campus E8 66123 Saarbrücken Germany
| | - Ngoc-Thao-Hien Le
- Department of Pharmaceutical Sciences, Natural Products and Food Research and Analysis (NatuRA), University of Antwerp Universiteitsplein 1 B-2610 Antwerp Belgium
| | - Soohyun Um
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University Incheon 21983 South Korea
| | - Felix Schalk
- Chemical Biology of Microbe-Host Interactions, Hans-Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research Inhoffenstrasse 7 D-38124 Braunschweig Germany
| | - Martin Baunach
- Institute of Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| | - Christine Beemelmanns
- Chemical Biology of Microbe-Host Interactions, Hans-Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) Campus E8 66123 Saarbrücken Germany
- Saarland University 66123 Saarbrücken Germany
| |
Collapse
|
7
|
Huang H, Yue L, Deng F, Wang X, Wang N, Chen H, Li H. NMR-Metabolomic Profiling and Genome Mining Drive the Discovery of Cyclic Decapeptides from a Marine Streptomyces. JOURNAL OF NATURAL PRODUCTS 2023; 86:2122-2130. [PMID: 37672645 DOI: 10.1021/acs.jnatprod.3c00310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
The integration of NMR-metabolomic and genomic analyses can provide enhanced identification of structural properties as well as key biosynthetic information, thus achieving the targeted discovery of new natural products. For this purpose, NMR-based metabolomic profiling of the marine-derived Streptomyces sp. S063 (CGMCC 14582) was performed, by which N-methylated peptides possessing unusual negative 1H NMR chemical shift values were tracked. Meanwhile, genome mining of this strain revealed the presence of an unknown NRPS gene cluster (len) with piperazic-acid-encoding genes (lenE and lenF). Under the guidance of the combined information, two cyclic decapeptides, lenziamides D1 (1) and B1 (2), were isolated from Streptomyces sp. S063, which contains piperazic acids with negative 1H NMR values. The structures of 1 and 2 were determined by extensive spectroscopic analysis combined with Marfey's method and ECD calculations. Furthermore, we provided a detailed model of lenziamide (1 and 2) biosynthesis in Streptomyces sp. S063. In the cytotoxicity evaluation, 1 and 2 showed moderate growth inhibition against the human cancer cells HEL, H1975, H1299, and drug-resistant A549-taxol with IC50 values of 8-24 μM.
Collapse
Affiliation(s)
- Huiming Huang
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China
| | - Liangguang Yue
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266100, China
| | - Fayu Deng
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266100, China
| | - Xiaoyu Wang
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China
| | - Ning Wang
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China
| | - Hu Chen
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266100, China
| | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| |
Collapse
|
8
|
Muangkaew P, De Roo V, Zhou L, Girard L, Cesa-Luna C, Höfte M, De Mot R, Madder A, Geudens N, Martins JC. Stereomeric Lipopeptides from a Single Non-Ribosomal Peptide Synthetase as an Additional Source of Structural and Functional Diversification in Pseudomonas Lipopeptide Biosynthesis. Int J Mol Sci 2023; 24:14302. [PMID: 37762605 PMCID: PMC10531924 DOI: 10.3390/ijms241814302] [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: 08/09/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
In Pseudomonas lipopeptides, the D-configuration of amino acids is generated by dedicated, dual-function epimerization/condensation (E/C) domains. The increasing attention to stereochemistry in lipopeptide structure elucidation efforts has revealed multiple examples where epimerization does not occur, even though an E/C-type domain is present. While the origin of the idle epimerization in those E/C-domains remains elusive, epimerization activity has so far shown a binary profile: it is either 'on' (active) or 'off' (inactive). Here, we report the unprecedented observation of an E/C-domain that acts 'on and off', giving rise to the production of two diastereoisomeric lipopeptides by a single non-ribosomal peptide synthetase system. Using dereplication based on solid-phase peptide synthesis and NMR fingerprinting, we first show that the two cyclic lipopeptides produced by Pseudomonas entomophila COR5 correspond to entolysin A and B originally described for P. entomophila L48. Next, we prove that both are diastereoisomeric homologues differing only in the configuration of a single amino acid. This configurational variability is maintained in multiple Pseudomonas strains and typically occurs in a 3:2 ratio. Bioinformatic analysis reveals a possible correlation with the composition of the flanking sequence of the N-terminal secondary histidine motif characteristic for dual-function E/C-type domains. In permeabilization assays, using propidium iodide entolysin B has a higher antifungal activity compared to entolysin A against Botrytis cinerea and Pyricularia oryzae spores. The fact that configurational homologues are produced by the same NRPS system in a Pseudomonas strain adds a new level of structural and functional diversification to those already known from substrate flexibility during the recruitment of the amino acids and fatty acids and underscores the importance of complete stereochemical elucidation of non-ribosomal lipopeptide structures.
Collapse
Affiliation(s)
- Penthip Muangkaew
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, B-9000 Ghent, Belgium; (P.M.); (V.D.R.); (A.M.)
| | - Vic De Roo
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, B-9000 Ghent, Belgium; (P.M.); (V.D.R.); (A.M.)
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, B-9000 Ghent, Belgium
| | - Lu Zhou
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium; (L.Z.); (M.H.)
| | - Léa Girard
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, B-3001 Heverlee, Belgium; (L.G.); (C.C.-L.); (R.D.M.)
| | - Catherine Cesa-Luna
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, B-3001 Heverlee, Belgium; (L.G.); (C.C.-L.); (R.D.M.)
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium; (L.Z.); (M.H.)
| | - René De Mot
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, B-3001 Heverlee, Belgium; (L.G.); (C.C.-L.); (R.D.M.)
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, B-9000 Ghent, Belgium; (P.M.); (V.D.R.); (A.M.)
| | - Niels Geudens
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, B-9000 Ghent, Belgium
| | - José C. Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, B-9000 Ghent, Belgium
| |
Collapse
|
9
|
Borgio JF, Alhujaily R, Alquwaie R, Alabdullah MJ, AlHasani E, Alothman W, Alaqeel RK, Alfaraj AS, Kaabi A, Alhur NF, Akhtar S, AlJindan R, Almofty S, Almandil NB, AbdulAzeez S. Mining the nanotube-forming Bacillus amyloliquefaciens MR14M3 genome for determining anti- Candida auris and anti- Candida albicans potential by pathogenicity and comparative genomics analysis. Comput Struct Biotechnol J 2023; 21:4261-4276. [PMID: 37701018 PMCID: PMC10493893 DOI: 10.1016/j.csbj.2023.08.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023] Open
Abstract
There is a global health concern associated with the emergence of the multidrug-resistant (MDR) fungus Candida auris, which has significant mortality rates. Finding innovative and distinctive anti-Candida compounds is essential for treating infections caused by MDR C. auris. A bacterial strain with anti-Candida activity was isolated and identified using 16 S rRNA gene sequencing. The whole genome was sequenced to identify biosynthesis-related gene clusters. The pathogenicity and cytotoxicity of the isolate were analyzed in Candida and HFF-1 cell lines, respectively. This study set out to show that whole-genome sequencing, cytotoxicity testing, and pathogenicity analysis combined with genome mining and comparative genomics can successfully identify biosynthesis-related gene clusters in native bacterial isolates that encode antifungal natural compounds active against Candida albicans and C. auris. The native isolate MR14M3 has the ability to inhibit C. auris (zone of inhibition 25 mm) and C. albicans (zone of inhibition 25 mm). The 16 S rRNA gene sequence of MR14M3 aligned with Bacillus amyloliquefaciens with similarity (100%). Bacillus amyloliquefaciens MR14M3 establishes bridges of intercellular nanotubes (L 258.56 ± 35.83 nm; W 25.32 ± 6.09 nm) connecting neighboring cells. Candida cell size was reduced significantly, and crushed phenotypes were observed upon treatment with the defused metabolites of B. amyloliquefaciens MR14M3. Furthermore, the pathogenicity of B. amyloliquefaciens MR14M3 on Candida cells was observed through cell membrane disruption and lysed yeast cells. The whole-genome alignment of the MR14M3 genome (3981,643 bp) using 100 genes confirmed its affiliation with Bacillus amyloliquefaciens. Genome mining analysis revealed that MR14M3-coded secondary metabolites are involved in the biosynthesis of polyketides (PKs) and nonribosomal peptide synthases (NRPSs), including 11 biosynthesis-related gene clusters with one hundred percent similarity. Highly conserved biosynthesis-related gene clusters with anti-C. albicans and anti-C. auris potentials and cytotoxic-free activity of B. amyloliquefaciens MR14M3 proposes the utilization of Bacillus amyloliquefaciens MR14M3 as a biofactory for an anti-Candida auris and anti-C. albicans compound synthesizer.
Collapse
Affiliation(s)
- J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
- Department of Epidemic Diseases Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Rahaf Alhujaily
- Summer Research Program, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Rahaf Alquwaie
- Master Program of Biotechnology, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Maryam Jawad Alabdullah
- Summer Research Program, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Eman AlHasani
- Master Program of Biotechnology, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Wojod Alothman
- Summer Research Program, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Rawan Khalid Alaqeel
- Summer Research Program, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Aqeelah Salman Alfaraj
- Summer Research Program, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Ayidah Kaabi
- Summer Research Program, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Norah F. Alhur
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Sultan Akhtar
- Department of Biophysics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Reem AlJindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 40017, Saudi Arabia)
| | - Sarah Almofty
- Department of Stem Cell Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Noor B. Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| |
Collapse
|
10
|
Paguirigan JAG, Kim JA, Hur JS, Kim W. Identification of a biosynthetic gene cluster for a red pigment cristazarin produced by a lichen-forming fungus Cladonia metacorallifera. PLoS One 2023; 18:e0287559. [PMID: 37352186 PMCID: PMC10289310 DOI: 10.1371/journal.pone.0287559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/07/2023] [Indexed: 06/25/2023] Open
Abstract
Lichens are known to produce many novel bioactive metabolites. To date, approximately 1,000 secondary metabolites have been discovered, which are predominantly produced by the lichen mycobionts. However, despite the extensive studies on production of lichen secondary metabolites, little is known about the responsible biosynthetic gene clusters (BGCs). Here, we identified a putative BGC that is implicated in production of a red pigment, cristazarin (a naphthazarin derivative), in Cladonia metacorallifera. Previously, cristazarin was shown to be specifically induced in growth media containing fructose as a sole carbon source. Thus, we performed transcriptome analysis of C. metacorallifera growing on different carbon sources including fructose to identify the BGC for cristazarin. Among 39 polyketide synthase (PKS) genes found in the genome of C. metacorallifera, a non-reducing PKS (coined crz7) was highly expressed in growth media containing either fructose or glucose. The borders of a cristazarin gene cluster were delimited by co-expression patterns of neighboring genes of the crz7. BGCs highly conserved to the cristazarin BGC were also found in C. borealis and C. macilenta, indicating that these related species also have metabolic potentials to produce cristazarin. Phylogenetic analysis revealed that the Crz7 is sister to fungal PKSs that biosynthesize an acetylated tetrahydoxynaphthalene as a precursor of melanin pigment. Based on the phylogenetic placement of the Crz7 and putative functions of its neighboring genes, we proposed a plausible biosynthetic route for cristazarin. In this study, we identified a lichen-specific BGC that is likely involved in the biosynthesis of a naphthazarin derivative, cristazarin, and confirmed that transcriptome profiling under inducing and non-inducing conditions is an effective strategy for linking metabolites of interest to biosynthetic genes.
Collapse
Affiliation(s)
- Jaycee Augusto Gumiran Paguirigan
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Jung A. Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
| |
Collapse
|
11
|
Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, Barbosa da Silva E, O’Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. Small Molecule in situ Resin Capture - A Compound First Approach to Natural Product Discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.02.530684. [PMID: 37398257 PMCID: PMC10312467 DOI: 10.1101/2023.03.02.530684] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Microbial natural products remain an important resource for drug discovery. Yet, commonly employed discovery techniques are plagued by the rediscovery of known compounds, the relatively few microbes that can be cultured, and laboratory growth conditions that do not elicit biosynthetic gene expression among myriad other challenges. Here we introduce a culture independent approach to natural product discovery that we call the Small Molecule In situ Resin Capture (SMIRC) technique. SMIRC exploits in situ environmental conditions to elicit compound production and represents a new approach to access poorly explored chemical space by capturing natural products directly from the environments in which they are produced. In contrast to traditional methods, this compound-first approach can capture structurally complex small molecules across all domains of life in a single deployment while relying on Nature to provide the complex and poorly understood environmental cues needed to elicit biosynthetic gene expression. We illustrate the effectiveness of SMIRC in marine habitats with the discovery of numerous new compounds and demonstrate that sufficient compound yields can be obtained for NMR-based structure assignment. Two new compound classes are reported including one novel carbon skeleton that possesses a functional group not previously observed among natural products and a second that possesses potent biological activity. We introduce expanded deployments, in situ cultivation, and metagenomics as methods to facilitate compound discovery, enhance yields, and link compounds to producing organisms. This compound first approach can provide unprecedented access to new natural product chemotypes with broad implications for drug discovery.
Collapse
Affiliation(s)
- Alexander Bogdanov
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mariam N. Salib
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexander B. Chase
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Earth Sciences, Southern Methodist University, Dallas, TX 75275, USA
| | - Heinz Hammerlindl
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mitchell N. Muskat
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephanie Luedtke
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Lani F. Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven J. Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tadeusz F. Molinski
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Paul R. Jensen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
12
|
He R, Zhang J, Shao Y, Gu S, Song C, Qian L, Yin WB, Li Z. Knowledge-guided data mining on the standardized architecture of NRPS: Subtypes, novel motifs, and sequence entanglements. PLoS Comput Biol 2023; 19:e1011100. [PMID: 37186644 DOI: 10.1371/journal.pcbi.1011100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 05/25/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Non-ribosomal peptide synthetase (NRPS) is a diverse family of biosynthetic enzymes for the assembly of bioactive peptides. Despite advances in microbial sequencing, the lack of a consistent standard for annotating NRPS domains and modules has made data-driven discoveries challenging. To address this, we introduced a standardized architecture for NRPS, by using known conserved motifs to partition typical domains. This motif-and-intermotif standardization allowed for systematic evaluations of sequence properties from a large number of NRPS pathways, resulting in the most comprehensive cross-kingdom C domain subtype classifications to date, as well as the discovery and experimental validation of novel conserved motifs with functional significance. Furthermore, our coevolution analysis revealed important barriers associated with re-engineering NRPSs and uncovered the entanglement between phylogeny and substrate specificity in NRPS sequences. Our findings provide a comprehensive and statistically insightful analysis of NRPS sequences, opening avenues for future data-driven discoveries.
Collapse
Affiliation(s)
- Ruolin He
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jinyu Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, PR China
| | - Yuanzhe Shao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Shaohua Gu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Long Qian
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, PR China
| | - Zhiyuan Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| |
Collapse
|
13
|
Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F, Alanjary M, Fetter A, Terlouw BR, Metcalf WW, Helfrich EJN, van Wezel GP, Medema MH, Weber T. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023:7151336. [PMID: 37140036 DOI: 10.1093/nar/gkad344] [Citation(s) in RCA: 266] [Impact Index Per Article: 266.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/31/2023] [Accepted: 04/26/2023] [Indexed: 05/05/2023] Open
Abstract
Microorganisms produce small bioactive compounds as part of their secondary or specialised metabolism. Often, such metabolites have antimicrobial, anticancer, antifungal, antiviral or other bio-activities and thus play an important role for applications in medicine and agriculture. In the past decade, genome mining has become a widely-used method to explore, access, and analyse the available biodiversity of these compounds. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' (https://antismash.secondarymetabolites.org/) has supported researchers in their microbial genome mining tasks, both as a free to use web server and as a standalone tool under an OSI-approved open source licence. It is currently the most widely used tool for detecting and characterising biosynthetic gene clusters (BGCs) in archaea, bacteria, and fungi. Here, we present the updated version 7 of antiSMASH. antiSMASH 7 increases the number of supported cluster types from 71 to 81, as well as containing improvements in the areas of chemical structure prediction, enzymatic assembly-line visualisation and gene cluster regulation.
Collapse
Affiliation(s)
- Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs.Lyngby, Denmark
| | - Simon Shaw
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs.Lyngby, Denmark
| | - Hannah E Augustijn
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Zachary L Reitz
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Friederike Biermann
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Institute of Molecular Bio Science, Goethe-University Frankfurt, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics. Frankfurt am Main, Germany
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Artem Fetter
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Institute of Technical Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Barbara R Terlouw
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - William W Metcalf
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Eric J N Helfrich
- Institute of Molecular Bio Science, Goethe-University Frankfurt, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics. Frankfurt am Main, Germany
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs.Lyngby, Denmark
| |
Collapse
|
14
|
Vind K, Brunati C, Simone M, Sosio M, Donadio S, Iorio M. Megalochelin, a Tridecapeptide Siderophore from a Talented Streptomycete. ACS Chem Biol 2023; 18:861-874. [PMID: 36920304 PMCID: PMC10127220 DOI: 10.1021/acschembio.2c00958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/06/2023] [Indexed: 03/16/2023]
Abstract
Streptomycetes are bacteria known for their extraordinary biosynthetic capabilities. Herein, we describe the genome and metabolome of a particularly talented strain, Streptomyces ID71268. Its 8.4-Mbp genome harbors 32 bioinformatically predicted biosynthetic gene clusters (BGCs), out of which 10 are expressed under a single experimental condition. In addition to five families of known metabolites with previously assigned BGCs (nigericin, azalomycin F, ectoine, SF2766, and piericidin), we were able to predict BGCs for three additional metabolites: streptochlorin, serpetene, and marinomycin. The strain also produced two families of presumably novel metabolites, one of which was associated with growth inhibitory activity against the human opportunistic pathogen Acinetobacter baumannii in an iron-dependent manner. Bioassay-guided fractionation, followed by extensive liquid chromatography-mass spectrometry (LC-MS) and NMR analyses, established that the molecule responsible for the observed antibacterial activity is an unusual tridecapeptide siderophore with a ring-and-tail structure: the heptapeptide ring is formed through a C-C bond between a 2,3-dihydroxybenzoate (DHB) cap on Gly1 and the imidazole moiety of His7, while the hexapeptide tail is sufficient for binding iron. This molecule, named megalochelin, is the largest known siderophore. The megalochelin BGC encodes a 13-module nonribosomal peptide synthetase for the synthesis of the tridecapeptide, and a copper-dependent oxidase, likely responsible for the DHB-imidazole cross-link, whereas the genes for synthesis of the DHB starter unit are apparently specified in trans by a different BGC. Our results suggest that prolific producers of specialized metabolites may conceal hidden treasures within a background of known compounds.
Collapse
Affiliation(s)
- Kristiina Vind
- NAICONS
Srl, 20139 Milan, Italy
- Host-Microbe
Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
15
|
El Samak M, Zakeer S, Hanora A, Solyman SM. Metagenomic and metatranscriptomic exploration of the Egyptian Red Sea sponge Theonella sp. associated microbial community. Mar Genomics 2023; 70:101032. [PMID: 37084583 DOI: 10.1016/j.margen.2023.101032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/02/2023] [Accepted: 04/12/2023] [Indexed: 04/23/2023]
Abstract
Marine sponges associated microorganisms are considered to be prolific source of bioactive natural products. Omics-based techniques such as metagenomics and metatranscriptomics have been used as effective tools to discover natural products. In this study, we used integrated metagenomic and metatranscriptomic analysis of three samples of the Egyptian Red Sea sponge Theonella sp. microbiome to obtain a complete picture of its biosynthetic activity to produce bioactive compounds. Our data revealed high biodiversity of the Egyptian sponge microbiota represented by 38 bacterial phyla with Candidate Phylum Poribacteria as the most abundant phyla with an average of 27.5% of the microbial community. The analysis also revealed high biosynthetic activity of the sponge microbiome through detecting different types of biosynthetic gene clusters (BGCs) with predicted antibacterial, cytotoxic and inhibitory bioactivity and the majority of these clusters were found to be actively transcribed. The complete BGCs of the cytotoxic theonellamide and misakinolide were detected and found to be actively transcribed. The majority of the detected BGCs were predicted to be novel as they did not show any similarity with any known cluster in the MIBiG database.
Collapse
Affiliation(s)
- Manar El Samak
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt
| | - Samira Zakeer
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt
| | - Amro Hanora
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt.
| | - Samar M Solyman
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt; Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University- Elkantara branch, Egypt
| |
Collapse
|
16
|
Chase AB, Bogdanov A, Demko AM, Jensen PR. Biogeographic patterns of biosynthetic potential and specialized metabolites in marine sediments. THE ISME JOURNAL 2023:10.1038/s41396-023-01410-3. [PMID: 37061583 DOI: 10.1038/s41396-023-01410-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/17/2023]
Abstract
While the field of microbial biogeography has largely focused on the contributions of abiotic factors to community patterns, the potential influence of biotic interactions in structuring microbial communities, such as those mediated by the production of specialized metabolites, remains largely unknown. Here, we examined the relationship between microbial community structure and specialized metabolism at local spatial scales in marine sediment samples collected from the Long-Term Ecological Research (LTER) site in Moorea, French Polynesia. By employing a multi-omic approach to characterize the taxonomic, functional, and specialized metabolite composition within sediment communities, we find that biogeographic patterns were driven by local scale processes (e.g., biotic interactions) and largely independent of dispersal limitation. Specifically, we observed high variation in biosynthetic potential (based on Bray-Curtis dissimilarity) between samples, even within 1 m2 plots, that reflected uncharacterized chemical space associated with site-specific metabolomes. Ultimately, connecting biosynthetic potential to community metabolomes facilitated the in situ detection of natural products and revealed new insights into the complex metabolic dynamics associated with sediment microbial communities. Our study demonstrates the potential to integrate biosynthetic genes and metabolite production into assessments of microbial community dynamics.
Collapse
Affiliation(s)
- Alexander B Chase
- Department of Earth Sciences, Southern Methodist University, Dallas, TX, USA.
| | - Alexander Bogdanov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Alyssa M Demko
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA, USA
| |
Collapse
|
17
|
Computational Approaches to Enzyme Inhibition by Marine Natural Products in the Search for New Drugs. Mar Drugs 2023; 21:md21020100. [PMID: 36827141 PMCID: PMC9961086 DOI: 10.3390/md21020100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/03/2023] Open
Abstract
The exploration of biologically relevant chemical space for the discovery of small bioactive molecules present in marine organisms has led not only to important advances in certain therapeutic areas, but also to a better understanding of many life processes. The still largely untapped reservoir of countless metabolites that play biological roles in marine invertebrates and microorganisms opens new avenues and poses new challenges for research. Computational technologies provide the means to (i) organize chemical and biological information in easily searchable and hyperlinked databases and knowledgebases; (ii) carry out cheminformatic analyses on natural products; (iii) mine microbial genomes for known and cryptic biosynthetic pathways; (iv) explore global networks that connect active compounds to their targets (often including enzymes); (v) solve structures of ligands, targets, and their respective complexes using X-ray crystallography and NMR techniques, thus enabling virtual screening and structure-based drug design; and (vi) build molecular models to simulate ligand binding and understand mechanisms of action in atomic detail. Marine natural products are viewed today not only as potential drugs, but also as an invaluable source of chemical inspiration for the development of novel chemotypes to be used in chemical biology and medicinal chemistry research.
Collapse
|
18
|
Singh HW, Creamer KE, Chase AB, Klau LJ, Podell S, Jensen PR. Metagenomic Data Reveal Type I Polyketide Synthase Distributions Across Biomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523365. [PMID: 36711755 PMCID: PMC9882069 DOI: 10.1101/2023.01.09.523365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Microbial polyketide synthase (PKS) genes encode the biosynthesis of many biomedically important natural products, yet only a small fraction of nature's polyketide biosynthetic potential has been realized. Much of this potential originates from type I PKSs (T1PKSs), which can be delineated into different classes and subclasses based on domain organization and structural features of the compounds encoded. Notably, phylogenetic relationships among PKS ketosynthase (KS) domains provide a method to classify the larger and more complex genes in which they occur. Increased access to large metagenomic datasets from diverse habitats provides opportunities to assess T1PKS biosynthetic diversity and distributions through the analysis of KS domain sequences. Here, we used the webtool NaPDoS2 to detect and classify over 35,000 type I KS domains from 137 metagenomic data sets reported from eight diverse biomes. We found biome-specific separation with soils enriched in modular cis -AT and hybrid cis -AT KSs relative to other biomes and marine sediments enriched in KSs associated with PUFA and enediyne biosynthesis. By extracting full-length KS domains, we linked the phylum Actinobacteria to soil-specific enediyne and cis -AT clades and identified enediyne and monomodular KSs in phyla from which the associated compound classes have not been reported. These sequences were phylogenetically distinct from those associated with experimentally characterized PKSs suggesting novel structures or enzyme functions remain to be discovered. Lastly, we employed our metagenome-extracted KS domains to evaluate commonly used type I KS PCR primers and identified modifications that could increase the KS sequence diversity recovered from amplicon libraries. Importance Polyketides are a crucial source of medicines, agrichemicals, and other commercial products. Advances in our understanding of polyketide biosynthesis coupled with the accumulation of metagenomic sequence data provide new opportunities to assess polyketide biosynthetic potential across biomes. Here, we used the webtool NaPDoS2 to assess type I PKS diversity and distributions by detecting and classifying KS domains across 137 metagenomes. We show that biomes are differentially enriched in KS domain classes, providing a roadmap for future biodiscovery strategies. Further, KS phylogenies reveal both biome-specific clades that do not include biochemically characterized PKSs, highlighting the biosynthetic potential of poorly explored environments. The large metagenome-derived KS dataset allowed us to identify regions of commonly used type I KS PCR primers that could be modified to capture a larger extent of KS diversity. These results facilitate both the search for novel polyketides and our understanding of the biogeographical distribution of PKSs across earth's major biomes.
Collapse
|
19
|
Humicolopsis cephalosporioides synthesizes DHN-melanin in its chlamydospores. Mycol Prog 2023. [DOI: 10.1007/s11557-022-01853-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|