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Harper CP, Day A, Tsingos M, Ding E, Zeng E, Stumpf SD, Qi Y, Robinson A, Greif J, Blodgett JAV. Critical analysis of polycyclic tetramate macrolactam biosynthetic gene cluster phylogeny and functional diversity. Appl Environ Microbiol 2024; 90:e0060024. [PMID: 38771054 PMCID: PMC11218653 DOI: 10.1128/aem.00600-24] [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: 04/06/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
Polycyclic tetramate macrolactams (PTMs) are bioactive natural products commonly associated with certain actinobacterial and proteobacterial lineages. These molecules have been the subject of numerous structure-activity investigations since the 1970s. New members continue to be pursued in wild and engineered bacterial strains, and advances in PTM biosynthesis suggest their outwardly simplistic biosynthetic gene clusters (BGCs) belie unexpected product complexity. To address the origins of this complexity and understand its influence on PTM discovery, we engaged in a combination of bioinformatics to systematically classify PTM BGCs and PTM-targeted metabolomics to compare the products of select BGC types. By comparing groups of producers and BGC mutants, we exposed knowledge gaps that complicate bioinformatics-driven product predictions. In sum, we provide new insights into the evolution of PTM BGCs while systematically accounting for the PTMs discovered thus far. The combined computational and metabologenomic findings presented here should prove useful for guiding future discovery.IMPORTANCEPolycyclic tetramate macrolactam (PTM) pathways are frequently found within the genomes of biotechnologically important bacteria, including Streptomyces and Lysobacter spp. Their molecular products are typically bioactive, having substantial agricultural and therapeutic interest. Leveraging bacterial genomics for the discovery of new related molecules is thus desirable, but drawing accurate structural predictions from bioinformatics alone remains challenging. This difficulty stems from a combination of previously underappreciated biosynthetic complexity and remaining knowledge gaps, compounded by a stream of yet-uncharacterized PTM biosynthetic loci gleaned from recently sequenced bacterial genomes. We engaged in the following study to create a useful framework for cataloging historic PTM clusters, identifying new cluster variations, and tracing evolutionary paths for these molecules. Our data suggest new PTM chemistry remains discoverable in nature. However, our metabolomic and mutational analyses emphasize the practical limitations of genomics-based discovery by exposing hidden complexity.
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Affiliation(s)
| | - Anna Day
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Maya Tsingos
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Edward Ding
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Elizabeth Zeng
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Spencer D. Stumpf
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Yunci Qi
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Adam Robinson
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jennifer Greif
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
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Yue H, Miller AL, Khetrapal V, Jayaseker V, Wright S, Du L. Biosynthesis, regulation, and engineering of natural products from Lysobacter. Nat Prod Rep 2022; 39:842-874. [PMID: 35067688 DOI: 10.1039/d1np00063b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Covering: up to August 2021Lysobacter is a genus of Gram-negative bacteria that was classified in 1987. Several Lysobacter species are emerging as new biocontrol agents for crop protection in agriculture. Lysobacter are prolific producers of new bioactive natural products that are largely underexplored. So far, several classes of structurally interesting and biologically active natural products have been isolated from Lysobacter. This article reviews the progress in Lysobacter natural product research over the past ten years, including molecular mechanisms for biosynthesis, regulation and mode of action, genome mining of cryptic biosynthetic gene clusters, and metabolic engineering using synthetic biology tools.
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Affiliation(s)
- Huan Yue
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Amanda Lynn Miller
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Vimmy Khetrapal
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Vishakha Jayaseker
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Stephen Wright
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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Yan Y, Wang H, Song Y, Zhu D, Shen Y, Li Y. Combinatorial Biosynthesis of Oxidized Combamides Using Cytochrome P450 Enzymes from Different Polycyclic Tetramate Macrolactam Pathways. ACS Synth Biol 2021; 10:2434-2439. [PMID: 34543003 DOI: 10.1021/acssynbio.1c00178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polycyclic tetramate macrolactams (PoTeMs) are a family of natural products containing a tetramic acid moiety and a polycyclic system. Due to the valuable biological activities of different PoTeMs and the genetic simplicity of their biosynthetic genes, it is highly desirable to manipulate the biosynthesis of PoTeMs by swapping modification genes between different pathways. Herein, by combining the cytochrome P450 (CYP) enzymes from different PoTeM pathways with the combamides' biosynthetic genes, the new combamides G (3), I (5), and J (6) along with the known combamides B (1), D (2), and H (4) were identified from the recombinant strains. Combamides G (3), H (4), and J (6) displayed cytotoxic activity against human cancer cell lines. Furthermore, our results demonstrated for the first time the substrate specificity of the PoTeM-related CYPs in vivo, which will facilitate the engineered biosynthesis of other PoTeMs in the future.
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Affiliation(s)
- Yaqian Yan
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Haoxin Wang
- State Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yuliang Song
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Deyu Zhu
- School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yuemao Shen
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yaoyao Li
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
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Ding W, Tu J, Zhang H, Wei X, Ju J, Li Q. Genome Mining and Metabolic Profiling Uncover Polycyclic Tetramate Macrolactams from Streptomyces koyangensis SCSIO 5802. Mar Drugs 2021; 19:md19080440. [PMID: 34436279 PMCID: PMC8399814 DOI: 10.3390/md19080440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022] Open
Abstract
We have previously shown deep-sea-derived Streptomyces koyangensis SCSIO 5802 to produce two types of active secondary metabolites, abyssomicins and candicidins. Here, we report the complete genome sequence of S. koyangensis SCSIO 5802 employing bioinformatics to highlight its potential to produce at least 21 categories of natural products. In order to mine novel natural products, the production of two polycyclic tetramate macrolactams (PTMs), the known 10-epi-HSAF (1) and a new compound, koyanamide A (2), was stimulated via inactivation of the abyssomicin and candicidin biosynthetic machineries. Detailed bioinformatics analyses revealed a PKS/NRPS gene cluster, containing 6 open reading frames (ORFs) and spanning ~16 kb of contiguous genomic DNA, as the putative PTM biosynthetic gene cluster (BGC) (termed herein sko). We furthermore demonstrate, via gene disruption experiments, that the sko cluster encodes the biosynthesis of 10-epi-HSAF and koyanamide A. Finally, we propose a plausible biosynthetic pathway to 10-epi-HSAF and koyanamide A. In total, this study demonstrates an effective approach to cryptic BGC activation enabling the discovery of new bioactive metabolites; genome mining and metabolic profiling methods play key roles in this strategy.
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Affiliation(s)
- Wenjuan Ding
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (J.T.); (H.Z.)
- College of Oceanology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiajia Tu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (J.T.); (H.Z.)
| | - Huaran Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (J.T.); (H.Z.)
- College of Oceanology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyi Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (J.T.); (H.Z.)
- College of Oceanology, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 510301, China
- Correspondence: (J.J.); (Q.L.); Tel.: +86-20-8902-3028 (J.J. & Q.L.)
| | - Qinglian Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (J.T.); (H.Z.)
- Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 510301, China
- Correspondence: (J.J.); (Q.L.); Tel.: +86-20-8902-3028 (J.J. & Q.L.)
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Yue H, Jiang J, Taylor AJ, Leite ADL, Dodds ED, Du L. Outer Membrane Vesicle-Mediated Codelivery of the Antifungal HSAF Metabolites and Lytic Polysaccharide Monooxygenase in the Predatory Lysobacter enzymogenes. ACS Chem Biol 2021; 16:1079-1089. [PMID: 34032403 DOI: 10.1021/acschembio.1c00260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Lysobacter are new biocontrol agents known for their prolific production of lytic enzymes and bioactive metabolites. L. enzymogenes is a predator of fungi and produces several structurally distinct antimicrobial compounds, such as the antifungal HSAF (heat stable antifungal factor) and analogs. The mechanism by which L. enzymogenes interacts with fungal prey is not well understood. Here, we found that the production of HSAF and analogs in L. enzymogenes OH11 was significantly induced in media supplemented with ground fungal mycelia or chitin. In the OH11 genome, we identified a gene (LeLPMO10A) that was annotated to encode a chitin-binding protein. The stimulation of HSAF and analogs by chitin was diminished when LeLPMO10A was deleted. We expressed the gene in E. coli and demonstrated that purified LeLPMO10A oxidatively cleaved chitin into oligomeric products, including 1,5 δ-lactones and aldonic acids. The results revealed that LeLPMO10A encodes a lytic polysaccharide monooxygenase, which has not been reported in Lysobacter. The metabolite analysis, antifungal assay, and proteomic analysis showed that the antifungal compounds and the chitin-cleaving LeLPMO10A are colocalized in outer membrane vesicles. The enzymatic products that resulted from in vitro LeLPMO10A-cleaved chitin also significantly induced HSAF and analogs in OH11. Scanning electron microscopic analysis indicated that spherical vesicles were formed outside of OH11 cells, and fewer OH11 cells were observed to attach to fungal hyphae when LeLPMO10A was deleted. Together, the study revealed a previously uncharacterized synergistic strategy utilized by the predatory Lysobacter during interaction with fungal prey.
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Affiliation(s)
- Huan Yue
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Jiasong Jiang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Anna J. Taylor
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Aline De Lima Leite
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Eric D. Dodds
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States
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Jin H, Zhang W, Zhang G, Zhang L, Liu W, Zhang C. Engineered Biosynthesis of 5/5/6 Type Polycyclic Tetramate Macrolactams in an Ikarugamycin (5/6/5 Type)-Producing Chassis. Org Lett 2020; 22:1731-1735. [PMID: 32052979 DOI: 10.1021/acs.orglett.9b04672] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Hongbo Jin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Guangtao Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Wei Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-sen University, 135 West Xingang Road, Guangzhou 510006, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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Genome Mining of Marine-Derived Streptomyces sp. SCSIO 40010 Leads to Cytotoxic New Polycyclic Tetramate Macrolactams. Mar Drugs 2019; 17:md17120663. [PMID: 31775228 PMCID: PMC6950151 DOI: 10.3390/md17120663] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/10/2019] [Accepted: 11/16/2019] [Indexed: 01/09/2023] Open
Abstract
Polycyclic tetramate macrolactams (PTMs) biosynthetic gene cluster are widely distributed in different bacterial types, especially in Streptomyces species. The mining of the genomic data of marine-derived Streptomyces sp. SCSIO 40010 reveals the presence of a putative PTM-encoding biosynthetic gene cluster (ptm′ BGC) that features a genetic organization for potentially producing 5/5/6 type of carbocyclic ring-containing PTMs. A fermentation of Streptomyces sp. SCSIO 40010 led to the isolation and characterization of six new PTMs 1–6. Comprehensive spectroscopic analysis assigned their planar structures and relative configurations, and their absolute configurations were deduced by comparing the experimental electronic circular dichroism (ECD) spectra with the reported spectra of the known PTMs. Intriguingly, compounds 1–6 were determined to have a trans-orientation of H-10/H-11 at the first 5-membered ring, being distinct from the cis-orientation in their known PTM congeners. PTMs 1–5 displayed cytotoxicity against several cancer cell lines, with IC50 values that ranged from 2.47 to 17.68 µM.
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