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Tan LL, Heng E, Leong CY, Ng V, Yang LK, Seow DCS, Koduru L, Kanagasundaram Y, Ng SB, Peh G, Lim YH, Wong FT. Application of Cas12j for Streptomyces Editing. Biomolecules 2024; 14:486. [PMID: 38672502 PMCID: PMC11048056 DOI: 10.3390/biom14040486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/09/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024] Open
Abstract
In recent years, CRISPR-Cas toolboxes for Streptomyces editing have rapidly accelerated natural product discovery and engineering. However, Cas efficiencies are oftentimes strain-dependent, and the commonly used Streptococcus pyogenes Cas9 (SpCas9) is notorious for having high levels of off-target toxicity effects. Thus, a variety of Cas proteins is required for greater flexibility of genetic manipulation within a wider range of Streptomyces strains. This study explored the first use of Acidaminococcus sp. Cas12j, a hypercompact Cas12 subfamily, for genome editing in Streptomyces and its potential in activating silent biosynthetic gene clusters (BGCs) to enhance natural product synthesis. While the editing efficiencies of Cas12j were not as high as previously reported efficiencies of Cas12a and Cas9, Cas12j exhibited higher transformation efficiencies compared to SpCas9. Furthermore, Cas12j demonstrated significantly improved editing efficiencies compared to Cas12a in activating BGCs in Streptomyces sp. A34053, a strain wherein both SpCas9 and Cas12a faced limitations in accessing the genome. Overall, this study expanded the repertoire of Cas proteins for genome editing in actinomycetes and highlighted not only the potential of recently characterized Cas12j in Streptomyces but also the importance of having an extensive genetic toolbox for improving the editing success of these beneficial microbes.
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Affiliation(s)
- Lee Ling Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore; (L.L.T.); (E.H.)
| | - Elena Heng
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore; (L.L.T.); (E.H.)
| | - Chung Yan Leong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Veronica Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Lay Kien Yang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Deborah Chwee San Seow
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Lokanand Koduru
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore; (L.L.T.); (E.H.)
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Guangrong Peh
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, Neuros #07-01, Singapore 138665, Singapore; (G.P.); (Y.H.L.)
| | - Yee Hwee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, Neuros #07-01, Singapore 138665, Singapore; (G.P.); (Y.H.L.)
| | - Fong Tian Wong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore; (L.L.T.); (E.H.)
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, Neuros #07-01, Singapore 138665, Singapore; (G.P.); (Y.H.L.)
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Hermans C, De Mol ML, Mispelaere M, De Rop AS, Rombaut J, Nusayr T, Creamer R, De Maeseneire SL, Soetaert WK, Hulpiau P. MariClus: Your One-Stop Platform for Information on Marine Natural Products, Their Gene Clusters and Producing Organisms. Mar Drugs 2023; 21:449. [PMID: 37623730 PMCID: PMC10455768 DOI: 10.3390/md21080449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND The marine environment hosts the vast majority of living species and marine microbes that produce natural products with great potential in providing lead compounds for drug development. With over 70% of Earth's surface covered in water and the high interaction rate associated with liquid environments, this has resulted in many marine natural product discoveries. Our improved understanding of the biosynthesis of these molecules, encoded by gene clusters, along with increased genomic information will aid us in uncovering even more novel compounds. RESULTS We introduce MariClus (https://www.mariclus.com), an online user-friendly platform for mining and visualizing marine gene clusters. The first version contains information on clusters and the predicted molecules for over 500 marine-related prokaryotes. The user-friendly interface allows scientists to easily search by species, cluster type or molecule and visualize the information in table format or graphical representation. CONCLUSIONS This new online portal simplifies the exploration and comparison of gene clusters in marine species for scientists and assists in characterizing the bioactive molecules they produce. MariClus integrates data from public sources, like GenBank, MIBiG and PubChem, with genome mining results from antiSMASH. This allows users to access and analyze various aspects of marine natural product biosynthesis and diversity.
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Affiliation(s)
- Cedric Hermans
- Bioinformatics Knowledge Center (BiKC), Campus Brugge Station, Howest University of Applied Sciences, Rijselstraat 5, 8200 Bruges, Belgium; (C.H.)
| | - Maarten Lieven De Mol
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Marieke Mispelaere
- Bioinformatics Knowledge Center (BiKC), Campus Brugge Station, Howest University of Applied Sciences, Rijselstraat 5, 8200 Bruges, Belgium; (C.H.)
| | - Anne-Sofie De Rop
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Jeltien Rombaut
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Tesneem Nusayr
- Life Sciences, Texas A&M-Corpus Christi, Corpus Christi, TX 78412, USA
| | - Rebecca Creamer
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM 88003, USA
| | - Sofie L. De Maeseneire
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Wim K. Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Paco Hulpiau
- Bioinformatics Knowledge Center (BiKC), Campus Brugge Station, Howest University of Applied Sciences, Rijselstraat 5, 8200 Bruges, Belgium; (C.H.)
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Lykins WR, Fox CB. Practical Considerations for Next-Generation Adjuvant Development and Translation. Pharmaceutics 2023; 15:1850. [PMID: 37514037 PMCID: PMC10385070 DOI: 10.3390/pharmaceutics15071850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/21/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Over the last several years, there has been increased interest from academia and the pharmaceutical/biotech industry in the development of vaccine adjuvants for new and emerging vaccine modalities. Despite this, vaccine adjuvant development still has some of the longest timelines in the pharmaceutical space, from discovery to clinical approval. The reasons for this are manyfold and range from complexities in translation from animal to human models, concerns about safety or reactogenicity, to challenges in sourcing the necessary raw materials at scale. In this review, we will describe the current state of the art for many adjuvant technologies and how they should be approached or applied in the development of new vaccine products. We postulate that there are many factors to be considered and tools to be applied earlier on in the vaccine development pipeline to improve the likelihood of clinical success. These recommendations may require a modified approach to some of the common practices in new product development but would result in more accessible and practical adjuvant-containing products.
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Vermeulen R, Van Staden ADP, van Zyl LJ, Dicks LMT, Trindade M. Unusual Class I Lanthipeptides from the Marine Bacteria Thalassomonas viridans. ACS Synth Biol 2022; 11:3608-3616. [PMID: 36323319 PMCID: PMC9680876 DOI: 10.1021/acssynbio.2c00480] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Indexed: 11/06/2022]
Abstract
A novel class I lanthipeptide produced by the marine bacterium Thalassomonas viridans XOM25T was identified using genome mining. The putative lanthipeptides were heterologously coexpressed in Escherichia coli as GFP-prepeptide fusions along with the operon-encoded class I lanthipeptide modification machinery VdsCB. The core peptides, VdsA1 and VdsA2, were liberated from GFP using the NisP protease, purified, and analyzed by collision-induced tandem mass spectrometry. The operon-encoded cyclase and dehydratase, VdsCB, exhibited lanthipeptide synthetase activity via post-translational modification of the VdsA1 and VdsA2 core peptides. Modifications were directed by the conserved double glycine leader containing prepeptides of VdsA1 and VdsA2.
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Affiliation(s)
- Ross Vermeulen
- Department
of Microbiology, Stellenbosch University, Matieland 7602, South Africa
- Department
of Biotechnology, Institute for Microbial Biotechnology and Metagenomics
(IMBM), University of the Western Cape, Bellville 7535 South Africa
| | - Anton Du Preez Van Staden
- Department
of Microbiology, Stellenbosch University, Matieland 7602, South Africa
- Division
of Clinical Pharmacology, Department of Medicine, Faculty of Medicine
and Health Sciences, Stellenbosch University, Parow 7505, South Africa
| | - Leonardo Joaquim van Zyl
- Department
of Biotechnology, Institute for Microbial Biotechnology and Metagenomics
(IMBM), University of the Western Cape, Bellville 7535 South Africa
| | - Leon M. T. Dicks
- Department
of Microbiology, Stellenbosch University, Matieland 7602, South Africa
| | - Marla Trindade
- Department
of Biotechnology, Institute for Microbial Biotechnology and Metagenomics
(IMBM), University of the Western Cape, Bellville 7535 South Africa
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5
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Privalsky TM, Soohoo AM, Wang J, Walsh CT, Wright GD, Gordon EM, Gray NS, Khosla C. Prospects for Antibacterial Discovery and Development. J Am Chem Soc 2021; 143:21127-21142. [PMID: 34860516 PMCID: PMC8855840 DOI: 10.1021/jacs.1c10200] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The rising prevalence of multidrug-resistant bacteria is an urgent health crisis that can only be countered through renewed investment in the discovery and development of antibiotics. There is no panacea for the antibacterial resistance crisis; instead, a multifaceted approach is called for. In this Perspective we make the case that, in the face of evolving clinical needs and enabling technologies, numerous validated antibacterial targets and associated lead molecules deserve a second look. At the same time, many worthy targets lack good leads despite harboring druggable active sites. Creative and inspired techniques buoy discovery efforts; while soil screening efforts frequently lead to antibiotic rediscovery, researchers have found success searching for new antibiotic leads by studying underexplored ecological niches or by leveraging the abundance of available data from genome mining efforts. The judicious use of "polypharmacology" (i.e., the ability of a drug to alter the activities of multiple targets) can also provide new opportunities, as can the continued search for inhibitors of resistance enzymes with the capacity to breathe new life into old antibiotics. We conclude by highlighting available pharmacoeconomic models for antibacterial discovery and development while making the case for new ones.
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Affiliation(s)
- Thomas M. Privalsky
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
| | - Alexander M. Soohoo
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, United States
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 United States
| | - Christopher T. Walsh
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States,Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States
| | - Gerard D. Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Eric M. Gordon
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States,Department of Medicine, Stanford University, Stanford, CA 94305, United States
| | - Nathanael S. Gray
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States,Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, United States
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, United States,Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States,Corresponding Author: Correspondence to
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6
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Koch MJ, Hesketh-Best PJ, Smerdon G, Warburton PJ, Howell K, Upton M. Impact of growth media and pressure on the diversity and antimicrobial activity of isolates from two species of hexactinellid sponge. Microbiology (Reading) 2021; 167. [PMID: 34898418 PMCID: PMC8744994 DOI: 10.1099/mic.0.001123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Access to deep-sea sponges brings with it the potential to discover novel antimicrobial candidates, as well as novel cold- and pressure-adapted bacteria with further potential clinical or industrial applications. In this study, we implemented a combination of different growth media, increased pressure and high-throughput techniques to optimize recovery of isolates from two deep-sea hexactinellid sponges, Pheronema carpenteri and Hertwigia sp., in the first culture-based microbial analysis of these two sponges. Using 16S rRNA gene sequencing for isolate identification, we found a similar number of cultivable taxa from each sponge species, as well as improved recovery of morphotypes from P. carpenteri at 22-25 °C compared to other temperatures, which allows a greater potential for screening for novel antimicrobial compounds. Bacteria recovered under conditions of increased pressure were from the phyla Proteobacteria, Actinobacteria and Firmicutes, except at 4 %O2/5 bar, when the phylum Firmicutes was not observed. Cultured isolates from both sponge species displayed antimicrobial activity against Micrococcus luteus, Staphylococcus aureus and Escherichia coli.
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Affiliation(s)
- Matthew J Koch
- School of Biomedical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Poppy J Hesketh-Best
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Gary Smerdon
- Diving Diseases Research Centre Healthcare, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK
| | - Philip J Warburton
- School of Biomedical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Kerry Howell
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Mathew Upton
- School of Biomedical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
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Hug JJ, Frank NA, Walt C, Šenica P, Panter F, Müller R. Genome-Guided Discovery of the First Myxobacterial Biarylitide Myxarylin Reveals Distinct C-N Biaryl Crosslinking in RiPP Biosynthesis. Molecules 2021; 26:7483. [PMID: 34946566 DOI: 10.3390/molecules26247483] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 11/17/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a structurally diverse group of natural products. They feature a wide range of intriguing post-translational modifications, as exemplified by the biarylitides. These are a family of cyclic tripeptides found in Planomonospora, carrying a biaryl linkage between two aromatic amino acids. Recent genomic analyses revealed that the minimal biosynthetic prerequisite of biarylitide biosynthesis consists of only one ribosomally synthesized pentapeptide precursor as the substrate and a modifying cytochrome-P450-dependent enzyme. In silico analyses revealed that minimal biarylitide RiPP clusters are widespread among natural product producers across phylogenetic borders, including myxobacteria. We report here the genome-guided discovery of the first myxobacterial biarylitide MeYLH, termed Myxarylin, from Pyxidicoccus fallax An d48. Myxarylin was found to be an N-methylated tripeptide that surprisingly exhibits a C–N biaryl crosslink. In contrast to Myxarylin, previously isolated biarylitides are N-acetylated tripeptides that feature a C–C biaryl crosslink. Furthermore, the formation of Myxarylin was confirmed by the heterologous expression of the identified biosynthetic genes in Myxococcus xanthus DK1622. These findings expand the structural and biosynthetic scope of biarylitide-type RiPPs and emphasize the distinct biochemistry found in the myxobacterial realm.
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Frank NA, Széles M, Akone SH, Rasheed S, Hüttel S, Frewert S, Hamed MM, Herrmann J, Schuler SMM, Hirsch AKH, Müller R. Expanding the Myxochelin Natural Product Family by Nicotinic Acid Containing Congeners. Molecules 2021; 26:4929. [PMID: 34443518 PMCID: PMC8400222 DOI: 10.3390/molecules26164929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022] Open
Abstract
Myxobacteria represent a viable source of chemically diverse and biologically active secondary metabolites. The myxochelins are a well-studied family of catecholate-type siderophores produced by various myxobacterial strains. Here, we report the discovery, isolation, and structure elucidation of three new myxochelins N1-N3 from the terrestrial myxobacterium Corallococcus sp. MCy9049, featuring an unusual nicotinic acid moiety. Precursor-directed biosynthesis (PDB) experiments and total synthesis were performed in order to confirm structures, improve access to pure compounds for bioactivity testing, and to devise a biosynthesis proposal. The combined evaluation of metabolome and genome data covering myxobacteria supports the notion that the new myxochelin congeners reported here are in fact frequent side products of the known myxochelin A biosynthetic pathway in myxobacteria.
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Affiliation(s)
- Nicolas A. Frank
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Márió Széles
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Sergi H. Akone
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Department of Chemistry, Faculty of Science, University of Douala, Douala P.O. Box 24157, Cameroon
| | - Sari Rasheed
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Stephan Hüttel
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Simon Frewert
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Mostafa M. Hamed
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Jennifer Herrmann
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | | | - Anna K. H. Hirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
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Subko K, Wang X, Nielsen FH, Isbrandt T, Gotfredsen CH, Ramos MC, Mackenzie T, Vicente F, Genilloud O, Frisvad JC, Larsen TO. Mass Spectrometry Guided Discovery and Design of Novel Asperphenamate Analogs From Penicillium astrolabium Reveals an Extraordinary NRPS Flexibility. Front Microbiol 2021; 11:618730. [PMID: 33519780 PMCID: PMC7843940 DOI: 10.3389/fmicb.2020.618730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
Asperphenamate is a small peptide natural product that has gained much interest due to its antitumor activity. In the recent years numerous bioactive synthetic asperphenamate analogs have been reported, whereas only a handful of natural analogs either of microbial or plant origin has been discovered. Herein we describe a UHPLC-HRMS/MS and amino acid supplement approach for discovery and design of novel asperphenamate analogs. Chemical analysis of Penicillium astrolabium, a prolific producer of asperphenamate, revealed three previously described and two novel asperphenamate analogs produced in significant amounts, suggesting a potential for biosynthesis of further asperphenamate analogs by varying the amino acid availability. Subsequent growth on proteogenic and non-proteogenic amino acid enriched media, revealed a series of novel asperphenamate analogs, including single or double amino acid exchange, as well as benzoic acid exchange for nicotinic acid, with the latter observed from a natural source for the first time. In total, 22 new asperphenamate analogs were characterized by HRMS/MS, with one additionally confirmed by isolation and NMR structure elucidation. This study indicates an extraordinary nonribosomal peptide synthetase (NRPS) flexibility based on substrate availability, and therefore the potential for manipulating and designing novel peptide natural products in filamentous fungi.
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Affiliation(s)
- Karolina Subko
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Xinhui Wang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Frederik H Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thomas Isbrandt
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | | | | | | | | | - Jens C Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thomas O Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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10
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Kautsar SA, van der Hooft JJJ, de Ridder D, Medema MH. BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters. Gigascience 2021; 10:giaa154. [PMID: 33438731 PMCID: PMC7804863 DOI: 10.1093/gigascience/giaa154] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/29/2020] [Accepted: 11/29/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Genome mining for biosynthetic gene clusters (BGCs) has become an integral part of natural product discovery. The >200,000 microbial genomes now publicly available hold information on abundant novel chemistry. One way to navigate this vast genomic diversity is through comparative analysis of homologous BGCs, which allows identification of cross-species patterns that can be matched to the presence of metabolites or biological activities. However, current tools are hindered by a bottleneck caused by the expensive network-based approach used to group these BGCs into gene cluster families (GCFs). RESULTS Here, we introduce BiG-SLiCE, a tool designed to cluster massive numbers of BGCs. By representing them in Euclidean space, BiG-SLiCE can group BGCs into GCFs in a non-pairwise, near-linear fashion. We used BiG-SLiCE to analyze 1,225,071 BGCs collected from 209,206 publicly available microbial genomes and metagenome-assembled genomes within 10 days on a typical 36-core CPU server. We demonstrate the utility of such analyses by reconstructing a global map of secondary metabolic diversity across taxonomy to identify uncharted biosynthetic potential. BiG-SLiCE also provides a "query mode" that can efficiently place newly sequenced BGCs into previously computed GCFs, plus a powerful output visualization engine that facilitates user-friendly data exploration. CONCLUSIONS BiG-SLiCE opens up new possibilities to accelerate natural product discovery and offers a first step towards constructing a global and searchable interconnected network of BGCs. As more genomes are sequenced from understudied taxa, more information can be mined to highlight their potentially novel chemistry. BiG-SLiCE is available via https://github.com/medema-group/bigslice.
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Affiliation(s)
- Satria A Kautsar
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, sThe Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
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11
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Buijs Y, Isbrandt T, Zhang SD, Larsen TO, Gram L. The Antibiotic Andrimid Produced by Vibrio coralliilyticus Increases Expression of Biosynthetic Gene Clusters and Antibiotic Production in Photobacterium galatheae. Front Microbiol 2020; 11:622055. [PMID: 33424823 PMCID: PMC7793655 DOI: 10.3389/fmicb.2020.622055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/30/2020] [Indexed: 01/12/2023] Open
Abstract
The development and spread of multidrug resistant pathogens have reinforced the urgency to find novel natural products with antibiotic activity. In bacteria, orphan biosynthetic gene clusters (BGCs) far outnumber the BGCs for which chemistry is known, possibly because they are transcriptionally silent under laboratory conditions. A strategy to trigger the production of this biosynthetic potential is to challenge the microorganism with low concentrations of antibiotics, and by using a Burkholderia genetic reporter strain (Seyedsayamdost, Proc Natl Acad Sci 111:7266-7271), we found BGC unsilencing activity for the antimicrobial andrimid, produced by the marine bacterium Vibrio coralliilyticus. Next, we challenged another marine Vibrionaceae, Photobacterium galatheae, carrier of seven orphan BGCs with sub-inhibitory concentrations of andrimid. A combined approach of transcriptional and chemical measurements of andrimid-treated P. galatheae cultures revealed a 10-fold upregulation of an orphan BGC and, amongst others, a 1.6-2.2-fold upregulation of the gene encoding the core enzyme for biosynthesis of holomycin. Also, addition of andrimid caused an increase, based on UV-Vis peak area, of 4-fold in production of the antibiotic holomycin. Transcriptional measurements of stress response related genes in P. galatheae showed a co-occurrence of increased transcript levels of rpoS (general stress response) and andrimid induced holomycin overproduction, while in trimethoprim treated cultures attenuation of holomycin production coincided with a transcriptional increase of recA (SOS stress response). This study shows that using antimicrobial compounds as activators of secondary metabolism can be a useful strategy in eliciting biosynthetic gene clusters and facilitate natural product discovery. Potentially, such interactions could also have ecological relevant implications.
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Affiliation(s)
| | | | | | | | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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12
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Wang S, Fang Q, Lu Z, Gao Y, Trembleau L, Ebel R, Andersen JH, Philips C, Law S, Deng H. Discovery and Biosynthetic Investigation of a New Antibacterial Dehydrated Non-Ribosomal Tripeptide. Angew Chem Int Ed Engl 2020; 60:3229-3237. [PMID: 33107670 DOI: 10.1002/anie.202012902] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Indexed: 11/07/2022]
Abstract
Dehydroalanine (Dha) and dehydrobutyrine (Dhb) display considerable flexibility in a variety of chemical and biological reactions. Natural products containing Dha and/or Dhb residues are often found to display diverse biological activities. While the (Z) geometry is predominant in nature, only a handful of metabolites containing (E)-Dhb have been found thus far. Here we report discovery of a new antimicrobial peptide, albopeptide, through NMR analysis and chemical synthesis, which contains two contiguous unsaturated residues, Dha-(E)-Dhb. It displays narrow-spectrum activity against vancomycin-resistant Enterococcus faecium. In-vitro biochemical assays show that albopeptide originates from a noncanonical NRPS pathway featuring dehydration processes and catalysed by unusual condensation domains. Finally, we provide evidence of the occurrence of a previously untapped group of short unsaturated peptides in the bacterial kingdom, suggesting an important biological function in bacteria.
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Affiliation(s)
- Shan Wang
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, Scotland, UK
| | - Qing Fang
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, Scotland, UK
| | - Zhou Lu
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, Scotland, UK.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Yingli Gao
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, Scotland, UK.,College of Marine Life and Fisheries, Jiangsu Ocean University, Lianyungang, Jiangsu Province, China
| | - Laurent Trembleau
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, Scotland, UK
| | - Rainer Ebel
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, Scotland, UK
| | | | - Carol Philips
- NCIMB Ltd., Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen, AB21 9YA, Scotland, UK
| | - Samantha Law
- NCIMB Ltd., Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen, AB21 9YA, Scotland, UK
| | - Hai Deng
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, Scotland, UK
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13
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Alkayyali T, Pope E, Wheatley SK, Cartmell C, Haltli B, Kerr RG, Ahmadi A. Development of a microbe domestication pod (MD Pod) for in situ cultivation of micro-encapsulated marine bacteria. Biotechnol Bioeng 2020; 118:1166-1176. [PMID: 33241862 DOI: 10.1002/bit.27633] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/01/2020] [Accepted: 11/20/2020] [Indexed: 11/10/2022]
Abstract
Microbial marine natural products hold significant potential for the discovery of new bioactive therapeutics such as antibiotics. Unfortunately, this discovery is hindered by the inability to culture the majority of microbes using traditional laboratory approaches. While many new methods have been developed to increase cultivability, a high-throughput in situ incubation chamber capable of simultaneously isolating individual microbes while allowing cellular communication has not previously been reported. Development of such a device would expedite the discovery of new microbial taxa and, thus, facilitate access to their associated natural products. In this study, this concept is achieved by the development of a new device termed by the authors as the microbe domestication (MD) Pod. The MD Pod enables single-cell cultivation by isolating marine bacterial cells in agarose microbeads produced using microfluidics, while allowing potential transmission of chemical signals between cells during in situ incubation in a chamber, or "Pod," that is deployed in the environment. The design of the MD Pod was optimized to ensure the use of biocompatible materials, allow for simple assembly in a field setting, and maintain sterility throughout incubation. The encapsulation process was designed to ensure that the viability of marine sediment bacteria was not adversely impacted by the encapsulation process. The process was validated using representative bacteria isolated from temperate marine sediment samples: Marinomonas polaris, Psychrobacter aquimaris, and Bacillus licheniformis. The overall process appeared to promote metabolic activity of most representative species. Thus, microfluidic encapsulation of marine bacteria and subsequent in situ incubation in the MD Pod is expected to accelerate marine natural products discovery by increasing the cultivability of marine bacteria.
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Affiliation(s)
- Tartela Alkayyali
- Faculty of Sustainable Design Engineering, University of Prince Edward Island, Prince Edward Island, Canada
| | - Emily Pope
- Departments of Biomedical Sciences, University of Prince Edward Island, Prince Edward Island, Canada
| | - Sydney K Wheatley
- Faculty of Sustainable Design Engineering, University of Prince Edward Island, Prince Edward Island, Canada
| | - Christopher Cartmell
- Departments of Chemistry, University of Prince Edward Island, Prince Edward Island, Canada
| | - Bradley Haltli
- Departments of Biomedical Sciences, University of Prince Edward Island, Prince Edward Island, Canada.,Nautilus Biosciences Croda, Prince Edward Island, Canada
| | - Russell G Kerr
- Departments of Biomedical Sciences, University of Prince Edward Island, Prince Edward Island, Canada.,Departments of Chemistry, University of Prince Edward Island, Prince Edward Island, Canada.,Nautilus Biosciences Croda, Prince Edward Island, Canada
| | - Ali Ahmadi
- Faculty of Sustainable Design Engineering, University of Prince Edward Island, Prince Edward Island, Canada
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14
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Quigley J, Peoples A, Sarybaeva A, Hughes D, Ghiglieri M, Achorn C, Desrosiers A, Felix C, Liang L, Malveira S, Millett W, Nitti A, Tran B, Zullo A, Anklin C, Spoering A, Ling LL, Lewis K. Novel Antimicrobials from Uncultured Bacteria Acting against Mycobacterium tuberculosis. mBio 2020; 11:e01516-20. [PMID: 32753498 PMCID: PMC7407088 DOI: 10.1128/mbio.01516-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/06/2020] [Indexed: 12/13/2022] Open
Abstract
Mycobacterium tuberculosis, which causes tuberculosis (TB), is estimated to infect one-third of the world's population. The overall burden and the emergence of drug-resistant strains of Mycobacterium tuberculosis underscore the need for new therapeutic options against this important human pathogen. Our recent work demonstrated the success of natural product discovery in identifying novel compounds with efficacy against Mycobacterium tuberculosis Here, we improve on these methods by combining improved isolation and Mycobacterium tuberculosis selective screening to identify three new anti-TB compounds: streptomycobactin, kitamycobactin, and amycobactin. We were unable to obtain mutants resistant to streptomycobactin, and its target remains to be elucidated. We identify the target of kitamycobactin to be the mycobacterial ClpP1P2C1 protease and confirm that kitamycobactin is an analog of the previously identified compound lassomycin. Further, we identify the target of amycobactin to be the essential protein secretion pore SecY. We show further that amycobactin inhibits protein secretion via the SecY translocon. Importantly, this inhibition is bactericidal to nonreplicating Mycobacterium tuberculosis This is the first compound, to our knowledge, that targets the Sec protein secretion machinery in Mycobacterium tuberculosis This work underscores the ability of natural product discovery to deliver not only new compounds with activity against Mycobacterium tuberculosis but also compounds with novel targets.IMPORTANCE Decreasing discovery rates and increasing resistance have underscored the need for novel therapeutic options to treat Mycobacterium tuberculosis infection. Here, we screen extracts from previously uncultured soil microbes for specific activity against Mycobacterium tuberculosis, identifying three novel compounds. We further define the mechanism of action of one compound, amycobactin, and demonstrate that it inhibits protein secretion through the Sec translocation machinery.
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Affiliation(s)
- Jeffrey Quigley
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Aaron Peoples
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Asel Sarybaeva
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Dallas Hughes
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Meghan Ghiglieri
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | | | | | - Cintia Felix
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Libang Liang
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Stephanie Malveira
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - William Millett
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Anthony Nitti
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Baldwin Tran
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Ashley Zullo
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Clemens Anklin
- Bruker Biospin Corporation, Billerica, Massachusetts, USA
| | - Amy Spoering
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Losee Lucy Ling
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
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15
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Abstract
Type I polyketide synthases (T1PKSs) are one of the most extensively studied PKSs, which can act either iteratively or via an assembly-line mechanism. Domains in the T1PKSs can readily be predicted by computational tools based on their highly conserved sequences. However, to distinguish between iterative and noniterative at the module level remains an overwhelming challenge, which may account for the seemingly biased distribution of T1PKSs in fungi and bacteria: small iterative monomodular T1PKSs that are responsible for the enormously diverse fungal natural products exist almost exclusively in fungi. Here we report the discovery of iterative T1PKSs that are unexpectedly both abundant and widespread in Streptomyces Seven of 11 systematically selected T1PKS monomodules from monomodular T1PKS biosynthetic gene clusters (BGCs) were experimentally confirmed to be iteratively acting, synthesizing diverse branched/nonbranched linear intermediates, and two of them produced bioactive allenic polyketides and citreodiols as end products, respectively. This study indicates the huge potential of iterative T1PKS BGCs from streptomycetes in the discovery of novel polyketides.
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16
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Gregory K, Salvador LA, Akbar S, Adaikpoh BI, Stevens DC. Survey of Biosynthetic Gene Clusters from Sequenced Myxobacteria Reveals Unexplored Biosynthetic Potential. Microorganisms 2019; 7:E181. [PMID: 31238501 PMCID: PMC6616573 DOI: 10.3390/microorganisms7060181] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 01/31/2023] Open
Abstract
Coinciding with the increase in sequenced bacteria, mining of bacterial genomes for biosynthetic gene clusters (BGCs) has become a critical component of natural product discovery. The order Myxococcales, a reputable source of biologically active secondary metabolites, spans three suborders which all include natural product producing representatives. Utilizing the BiG-SCAPE-CORASON platform to generate a sequence similarity network that contains 994 BGCs from 36 sequenced myxobacteria deposited in the antiSMASH database, a total of 843 BGCs with lower than 75% similarity scores to characterized clusters within the MIBiG database are presented. This survey provides the biosynthetic diversity of these BGCs and an assessment of the predicted chemical space yet to be discovered. Considering the mere snapshot of myxobacteria included in this analysis, these untapped BGCs exemplify the potential for natural product discovery from myxobacteria.
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Affiliation(s)
- Katherine Gregory
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Laura A Salvador
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Shukria Akbar
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Barbara I Adaikpoh
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - D Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
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17
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Liang L, Sproule A, Haltli B, Marchbank DH, Berrué F, Overy DP, McQuillan K, Lanteigne M, Duncan N, Correa H, Kerr RG. Discovery of a New Natural Product and a Deactivation of a Quorum Sensing System by Culturing a "Producer" Bacterium With a Heat-Killed "Inducer" Culture. Front Microbiol 2019; 9:3351. [PMID: 30705672 PMCID: PMC6344404 DOI: 10.3389/fmicb.2018.03351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/31/2018] [Indexed: 11/28/2022] Open
Abstract
Herein we describe a modified bacterial culture methodology as a tool to discover new natural products via supplementing actinomycete fermentation media with autoclaved cultures of “inducer” microbes. Using seven actinomycetes and four inducer microbes, we detected 28 metabolites that were induced in UHPLC-HRESIMS-based analysis of bacterial fermentations. Metabolomic analysis indicated that each inducer elicited a unique response from the actinomycetes and that some chemical responses were specific to each inducer-producer combination. Among these 28 metabolites, hydrazidomycin D, a new hydrazide-containing natural product was isolated from the pair Streptomyces sp. RKBH-B178 and Mycobacterium smegmatis. This result validated the effectiveness of the strategy in discovering new natural products. From the same set of induced metabolites, an in-depth investigation of a fermentation of Streptomyces sp. RKBH-B178 and autoclaved Pseudomonas aeruginosa led to the discovery of a glucuronidated analog of the pseudomonas quinolone signal (PQS). We demonstrated that RKBH-B178 is able to biotransform the P. aeruginosa quorum sensing molecules, 2-heptyl-4-quinolone (HHQ), and PQS to form PQS-GlcA. Further, PQS-GlcA was shown to have poor binding affinity to PqsR, the innate receptor of HHQ and PQS.
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Affiliation(s)
- Libang Liang
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Amanda Sproule
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Brad Haltli
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada.,Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada.,Nautilus Biosciences Croda, Charlottetown, PE, Canada
| | - Douglas H Marchbank
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada.,Nautilus Biosciences Croda, Charlottetown, PE, Canada
| | - Fabrice Berrué
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada
| | - David P Overy
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada.,Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | | | - Martin Lanteigne
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Noelle Duncan
- Nautilus Biosciences Croda, Charlottetown, PE, Canada
| | | | - Russell G Kerr
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada.,Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada.,Nautilus Biosciences Croda, Charlottetown, PE, Canada
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18
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Du C, van Wezel GP. Mining for Microbial Gems: Integrating Proteomics in the Postgenomic Natural Product Discovery Pipeline. Proteomics 2018; 18:e1700332. [PMID: 29708658 PMCID: PMC6175363 DOI: 10.1002/pmic.201700332] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/09/2018] [Indexed: 12/23/2022]
Abstract
Natural products (NPs) are a major source of compounds for medical, agricultural, and biotechnological industries. Many of these compounds are of microbial origin, and, in particular, from Actinobacteria or filamentous fungi. To successfully identify novel compounds that correlate to a bioactivity of interest, or discover new enzymes with desired functions, systematic multiomics approaches have been developed over the years. Bioinformatics tools harness the rapidly expanding wealth of genome sequence information, revealing previously unsuspected biosynthetic diversity. Varying growth conditions or application of elicitors are applied to activate cryptic biosynthetic gene clusters, and metabolomics provide detailed insights into the NPs they specify. Combining these technologies with proteomics-based approaches to profile the biosynthetic enzymes provides scientists with insights into the full biosynthetic potential of microorganisms. The proteomics approaches include enrichment strategies such as employing activity-based probes designed by chemical biology, as well as unbiased (quantitative) proteomics methods. In this review, the opportunities and challenges in microbial NP research are discussed, and, in particular, the application of proteomics to link biosynthetic enzymes to the molecules they produce, and vice versa.
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Affiliation(s)
- Chao Du
- Microbial Biotechnology & Health Programme Institute of BiologyLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
| | - Gilles P. van Wezel
- Microbial Biotechnology & Health Programme Institute of BiologyLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
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19
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Marfil-Santana MD, O'Connor-Sánchez A, Ramírez-Prado JH, De Los Santos-Briones C, López-Aguiar LK, Rojas-Herrera R, Lago-Lestón A, Prieto-Davó A. A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products. J Microbiol 2016; 54:774-781. [PMID: 27796931 DOI: 10.1007/s12275-016-6092-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 07/27/2016] [Accepted: 08/26/2016] [Indexed: 11/30/2022]
Abstract
The need for new antibiotics has sparked a search for the microbes that might potentially produce them. Current sequencing technologies allow us to explore the biotechnological potential of microbial communities in diverse environments without the need for cultivation, benefitting natural product discovery in diverse ways. A relatively recent method to search for the possible production of novel compounds includes studying the diverse genes belonging to polyketide synthase pathways (PKS), as these complex enzymes are an important source of novel therapeutics. In order to explore the biotechnological potential of the microbial community from the largest underground aquifer in the world located in the Yucatan, we used a polyphasic approach in which a simple, non-computationally intensive method was coupled with direct amplification of environmental DNA to assess the diversity and novelty of PKS type I ketosynthase (KS) domains. Our results suggest that the bioinformatic method proposed can indeed be used to assess the novelty of KS enzymes; nevertheless, this in silico study did not identify some of the KS diversity due to primer bias and stringency criteria outlined by the metagenomics pipeline. Therefore, additionally implementing a method involving the direct cloning of KS domains enhanced our results. Compared to other freshwater environments, the aquifer was characterized by considerably less diversity in relation to known ketosynthase domains; however, the metagenome included a family of KS type I domains phylogenetically related, but not identical, to those found in the curamycin pathway, as well as an outstanding number of thiolases. Over all, this first look into the microbial community found in this large Yucatan aquifer and other fresh water free living microbial communities highlights the potential of these previously overlooked environments as a source of novel natural products.
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Affiliation(s)
- Miguel David Marfil-Santana
- Center for Scientific Investigation of Yucatan (CICY), Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, C.P. 97200, Mexico
| | - Aileen O'Connor-Sánchez
- Center for Scientific Investigation of Yucatan (CICY), Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, C.P. 97200, Mexico
| | - Jorge Humberto Ramírez-Prado
- Center for Scientific Investigation of Yucatan (CICY), Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, C.P. 97200, Mexico
| | - Cesar De Los Santos-Briones
- Center for Scientific Investigation of Yucatan (CICY), Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, C.P. 97200, Mexico
| | - Lluvia Korynthia López-Aguiar
- School of Chemistry, National Autonomous University of Mexico (UNAM), Campus Sisal, Puerto de Abrigo s/n Municipio de Hunucmá, Sisal, Yucatan, C.P. 97356, Mexico
| | - Rafael Rojas-Herrera
- School of Chemical Engeneering, Autonomous University of Yucatan (UADY), Periférico Norte Kilometro 33.5, Chuburná de Hidalgo Inn, Mérida, Yucatán, C.P. 97203, Mexico
| | - Asunción Lago-Lestón
- Post Graduate Studies and Research Center of Ensenada (CICESE), Ensenada, Baja California, C.P. 22860, Mexico
| | - Alejandra Prieto-Davó
- School of Chemistry, National Autonomous University of Mexico (UNAM), Campus Sisal, Puerto de Abrigo s/n Municipio de Hunucmá, Sisal, Yucatan, C.P. 97356, Mexico.
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Prieto-Davó A, Dias T, Gomes SE, Rodrigues S, Parera-Valadez Y, Borralho PM, Pereira F, Rodrigues CMP, Santos-Sanches I, Gaudêncio SP. The Madeira Archipelago As a Significant Source of Marine-Derived Actinomycete Diversity with Anticancer and Antimicrobial Potential. Front Microbiol 2016; 7:1594. [PMID: 27774089 PMCID: PMC5053986 DOI: 10.3389/fmicb.2016.01594] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/23/2016] [Indexed: 12/21/2022] Open
Abstract
Marine-derived actinomycetes have demonstrated an ability to produce novel compounds with medically relevant biological activity. Studying the diversity and biogeographical patterns of marine actinomycetes offers an opportunity to identify genera that are under environmental pressures, which may drive adaptations that yield specific biosynthetic capabilities. The present study describes research efforts to explore regions of the Atlantic Ocean, specifically around the Madeira Archipelago, where knowledge of the indigenous actinomycete diversity is scarce. A total of 400 actinomycetes were isolated, sequenced, and screened for antimicrobial and anticancer activities. The three most abundant genera identified were Streptomyces, Actinomadura, and Micromonospora. Phylogenetic analyses of the marine OTUs isolated indicated that the Madeira Archipelago is a new source of actinomycetes adapted to life in the ocean. Phylogenetic differences between offshore (>100 m from shore) and nearshore (< 100 m from shore) populations illustrates the importance of sampling offshore in order to isolate new and diverse bacterial strains. Novel phylotypes from chemically rich marine actinomycete groups like MAR4 and the genus Salinispora were isolated. Anticancer and antimicrobial assays identified Streptomyces, Micromonospora, and Salinispora as the most biologically active genera. This study illustrates the importance of bioprospecting efforts at unexplored regions of the ocean to recover bacterial strains with the potential to produce novel and interesting chemistry.
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Affiliation(s)
- Alejandra Prieto-Davó
- Laboratorio de Productos Naturales Marinos, Facultad de Química, Universidad Nacional Autónoma de México, Unidad Sisal Sisal, Mexico
| | - Tiago Dias
- LAQV-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de LisboaCaparica, Portugal; UCIBIO-REQUIMTE, Department of Life Sciences, Faculty of Science and Technology, Universidade NOVA de LisboaCaparica, Portugal
| | - Sofia E Gomes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa Lisbon, Portugal
| | - Sara Rodrigues
- LAQV-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de LisboaCaparica, Portugal; UCIBIO-REQUIMTE, Department of Life Sciences, Faculty of Science and Technology, Universidade NOVA de LisboaCaparica, Portugal
| | - Yessica Parera-Valadez
- Laboratorio de Productos Naturales Marinos, Facultad de Química, Universidad Nacional Autónoma de México, Unidad Sisal Sisal, Mexico
| | - Pedro M Borralho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de LisboaLisbon, Portugal; Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de LisboaLisbon, Portugal
| | - Florbela Pereira
- LAQV-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de Lisboa Caparica, Portugal
| | - Cecilia M P Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de LisboaLisbon, Portugal; Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de LisboaLisbon, Portugal
| | - Ilda Santos-Sanches
- UCIBIO-REQUIMTE, Department of Life Sciences, Faculty of Science and Technology, Universidade NOVA de Lisboa Caparica, Portugal
| | - Susana P Gaudêncio
- LAQV-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de LisboaCaparica, Portugal; UCIBIO-REQUIMTE, Department of Life Sciences, Faculty of Science and Technology, Universidade NOVA de LisboaCaparica, Portugal
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Skinnider MA, Johnston CW, Edgar RE, Dejong CA, Merwin NJ, Rees PN, Magarvey NA. Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining. Proc Natl Acad Sci U S A 2016; 113:E6343-51. [PMID: 27698135 DOI: 10.1073/pnas.1609014113] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Microbial natural products are an evolved resource of bioactive small molecules, which form the foundation of many modern therapeutic regimes. Ribosomally synthesized and posttranslationally modified peptides (RiPPs) represent a class of natural products which have attracted extensive interest for their diverse chemical structures and potent biological activities. Genome sequencing has revealed that the vast majority of genetically encoded natural products remain unknown. Many bioinformatic resources have therefore been developed to predict the chemical structures of natural products, particularly nonribosomal peptides and polyketides, from sequence data. However, the diversity and complexity of RiPPs have challenged systematic investigation of RiPP diversity, and consequently the vast majority of genetically encoded RiPPs remain chemical "dark matter." Here, we introduce an algorithm to catalog RiPP biosynthetic gene clusters and chart genetically encoded RiPP chemical space. A global analysis of 65,421 prokaryotic genomes revealed 30,261 RiPP clusters, encoding 2,231 unique products. We further leverage the structure predictions generated by our algorithm to facilitate the genome-guided discovery of a molecule from a rare family of RiPPs. Our results provide the systematic investigation of RiPP genetic and chemical space, revealing the widespread distribution of RiPP biosynthesis throughout the prokaryotic tree of life, and provide a platform for the targeted discovery of RiPPs based on genome sequencing.
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Abstract
In this perspective, we highlight recent examples and trends in metabolic engineering and synthetic biology that demonstrate the synthetic potential of enzyme and pathway engineering for natural product discovery. In doing so, we introduce natural paradigms of secondary metabolism whereby simple carbon substrates are combined into complex molecules through “scaffold diversification”, and subsequent “derivatization” of these scaffolds is used to synthesize distinct complex natural products. We provide examples in which modern pathway engineering efforts including combinatorial biosynthesis and biological retrosynthesis can be coupled to directed enzyme evolution and rational enzyme engineering to allow access to the “privileged” chemical space of natural products in industry-proven microbes. Finally, we forecast the potential to produce natural product-like discovery platforms in biological systems that are amenable to single-step discovery, validation, and synthesis for streamlined discovery and production of biologically active agents.
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Affiliation(s)
- Jason R King
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven Edgar
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kangjian Qiao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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Vestola J, Shishido TK, Jokela J, Fewer DP, Aitio O, Permi P, Wahlsten M, Wang H, Rouhiainen L, Sivonen K. Hassallidins, antifungal glycolipopeptides, are widespread among cyanobacteria and are the end-product of a nonribosomal pathway. Proc Natl Acad Sci U S A 2014; 111:E1909-17. [PMID: 24742428 DOI: 10.1073/pnas.1320913111] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyanobacteria produce a wide variety of cyclic peptides, including the widespread hepatotoxins microcystins and nodularins. Another class of peptides, cyclic glycosylated lipopeptides called hassallidins, show antifungal activity. Previously, two hassallidins (A and B) were reported from an epilithic cyanobacterium Hassallia sp. and found to be active against opportunistic human pathogenic fungi. Bioinformatic analysis of the Anabaena sp. 90 genome identified a 59-kb cryptic inactive nonribosomal peptide synthetase gene cluster proposed to be responsible for hassallidin biosynthesis. Here we describe the hassallidin biosynthetic pathway from Anabaena sp. SYKE748A, as well as the large chemical variation and common occurrence of hassallidins in filamentous cyanobacteria. Analysis demonstrated that 20 strains of the genus Anabaena carry hassallidin synthetase genes and produce a multitude of hassallidin variants that exhibit activity against Candida albicans. The compounds discovered here were distinct from previously reported hassallidins A and B. The IC50 of hassallidin D was 0.29-1.0 µM against Candida strains. A large variation in amino acids, sugars, their degree of acetylation, and fatty acid side chain length was detected. In addition, hassallidins were detected in other cyanobacteria including Aphanizomenon, Cylindrospermopsis raciborskii, Nostoc, and Tolypothrix. These compounds may protect some of the most important bloom-forming and globally distributed cyanobacteria against attacks by parasitic fungi.
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