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El-Hawary SS, Hassan MHA, Hudhud AO, Abdelmohsen UR, Mohammed R. Elicitation for activation of the actinomycete genome's cryptic secondary metabolite gene clusters. RSC Adv 2023; 13:5778-5795. [PMID: 36816076 PMCID: PMC9932869 DOI: 10.1039/d2ra08222e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 01/28/2023] [Indexed: 02/18/2023] Open
Abstract
This review summarizes the recent advances in the elicitation approaches used to activate the actinomycete genome's cryptic secondary metabolite gene clusters and shows the diversity of natural products obtained by various elicitation methods up to June 2022, such as co-cultivation of actinomycetes with actinomycetes, other non-actinomycete bacteria, fungi, cell-derived components, and/or algae. Chemical elicitation and molecular elicitation as transcription factor decoys, engineering regulatory genes, the promoter replacement strategy, global regulatory genes, and reporter-guided mutant selection were also reported. For researchers interested in this field, this review serves as a valuable resource for the latest studies and references.
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Affiliation(s)
- Seham S. El-Hawary
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo UniversityCairoEgypt
| | - Marwa H. A. Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef UniversityBeni-Suef 62511Egypt
| | - Ahmed O. Hudhud
- Department of Pharmacognosy, Faculty of Pharmacy, Merit UniversitySohag 82511Egypt
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University Minia 61519 Egypt .,Department of Pharmacognosy, Faculty of Pharmacy, Deraya University New Minia 61111 Egypt
| | - Rabab Mohammed
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University Beni-Suef 62511 Egypt
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Li Y, Lee SR, Han EJ, Seyedsayamdost MR. Momomycin, an Antiproliferative Cryptic Metabolite from the Oxytetracycline Producer Streptomyces rimosus. Angew Chem Int Ed Engl 2022; 61:e202208573. [PMID: 35903822 PMCID: PMC9489664 DOI: 10.1002/anie.202208573] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Indexed: 08/27/2023]
Abstract
Natural products provide an important source of pharmaceuticals and chemical tools. Traditionally, assessment of unexplored microbial phyla has led to new natural products. However, with every new microbe, the number of orphan biosynthetic gene clusters (BGC) grows. As such, the more difficult proposition is finding new molecules from well-studied strains. Herein, we targeted Streptomyces rimosus, the widely-used oxytetracycline producer, for the discovery of new natural products. Using MALDI-MS-guided high-throughput elicitor screening (HiTES), we mapped the global secondary metabolome of S. rimosus and structurally characterized products of three cryptic BGCs, including momomycin, an unusual cyclic peptide natural product with backbone modifications and several non-canonical amino acids. We elucidated important aspects of its biosynthesis and evaluated its bioactivity. Our studies showcase HiTES as an effective approach for unearthing new chemical matter from "drained" strains.
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Affiliation(s)
- Yuchen Li
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
| | - Seoung Rak Lee
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
| | - Esther J. Han
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544 (USA)
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3
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Paulus C, Myronovskyi M, Zapp J, Rodríguez Estévez M, Lopatniuk M, Rosenkränzer B, Palusczak A, Luzhetskyy A. Miramides A–D: Identification of Detoxin-like Depsipeptides after Heterologous Expression of a Hybrid NRPS-PKS Gene Cluster from Streptomyces mirabilis Lu17588. Microorganisms 2022; 10:microorganisms10091752. [PMID: 36144353 PMCID: PMC9503745 DOI: 10.3390/microorganisms10091752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/30/2022] Open
Abstract
Natural products derived from plants, fungi or bacteria have been used for years in the medicine, agriculture and food industries as they exhibit a variety of beneficial properties, such as antibiotic, antifungal, anticancer, herbicidal and immunosuppressive activities. Compared to synthetic compounds, natural products possess a greater chemical diversity, which is a reason why they are profitable templates for developing pharmaceutical drug candidates and ongoing research on them is inevitable. Performing heterologous expression with unknown gene clusters is the preferred method to activate gene clusters that are not expressed in the wild-type strain under laboratory conditions; thus, this method offers a way to discover new interesting metabolites. Here, we report the gene cluster assembly of a hybrid NRPS-PKS gene cluster from Streptomyces mirabilis Lu17588, which was heterologously expressed in Streptomyces albus Del14. Four new compounds were produced by the obtained strain, which were named miramides A–D. Isolation and structure elucidation revealed similarity of the isolated compounds to the known depsipeptides rimosamides/detoxins.
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Affiliation(s)
- Constanze Paulus
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Josef Zapp
- Department of Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany
| | - Marta Rodríguez Estévez
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Maria Lopatniuk
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Birgit Rosenkränzer
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Anja Palusczak
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany
- AMEG Department, Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbruecken, Germany
- Correspondence: ; Tel.: +49-681-302-70200
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Li Y, Lee SR, Han EJ, Seyedsayamdost MR. Momomycin, an Antiproliferative Cryptic Metabolite from the Oxytetracycline Producer Streptomyces rimosus. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yuchen Li
- Princeton University Chemistry UNITED STATES
| | | | | | - Mohammad R. Seyedsayamdost
- Princeton University Chemistry Washington UniversityFrick Chemistry Lab, Room 333 08544 Princeton UNITED STATES
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Lee SR, Seyedsayamdost MR. Induction of Diverse Cryptic Fungal Metabolites by Steroids and Channel Blockers. Angew Chem Int Ed Engl 2022; 61:e202204519. [PMID: 35509119 PMCID: PMC9276648 DOI: 10.1002/anie.202204519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 07/20/2023]
Abstract
Fungi offer a deep source of natural products but remain underutilized. Most biosynthetic gene clusters (BGCs) that can be detected are silent or "cryptic" in standard lab cultures and their products are thus not interrogated in routine screens. As genetic alterations are difficult and some strains can only be grown on agar, we have herein applied an agar-based high-throughput chemical genetic screen to identify inducers of fungal BGCs. Using R. solani and S. sclerotiorum as test cases, we report 13 cryptic metabolites in four compound groups, including sclerocyclane, a natural product with a novel scaffold. Steroids were the best elicitors and follow-up studies showed that plant-steroids trigger sclerocyclane synthesis, which shows antibiotic activity against B. plantarii, an ecological competitor of S. sclerotiorum. Our results open new paths to exploring the chemical ecology of fungal-plant interactions and provide a genetics-free approach for uncovering cryptic fungal metabolites.
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Affiliation(s)
- Seoung Rak Lee
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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Lee SR, Seyedsayamdost MR. Induction of Diverse Cryptic Fungal Metabolites by Steroids and Channel Blockers. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Seoung Rak Lee
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry Princeton University Princeton NJ 08544 USA
- Department of Molecular Biology Princeton University Princeton NJ 08544 USA
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A Glossary for Chemical Approaches towards Unlocking the Trove of Metabolic Treasures in Actinomycetes. Molecules 2021; 27:molecules27010142. [PMID: 35011373 PMCID: PMC8746466 DOI: 10.3390/molecules27010142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 12/02/2022] Open
Abstract
Actinobacterial natural products showed a critical basis for the discovery of new antibiotics as well as other lead secondary metabolites. Varied environmental and physiological signals touch the antibiotic machinery that faced a serious decline in the last decades. The reason was exposed by genomic sequencing data, which revealed that Actinomycetes harbor a large portion of silent biosynthetic gene clusters in their genomes that encrypt for secondary metabolites. These gene clusters are linked with a great reservoir of yet unknown molecules, and arranging them is considered a major challenge for biotechnology approaches. In the present paper, we discuss the recent strategies that have been taken to augment the yield of secondary metabolites via awakening these cryptic genes in Actinomycetes with emphasis on chemical signaling molecules used to induce the antibiotics biosynthesis. The rationale, types, applications and mechanisms are discussed in detail, to reveal the productive path for the unearthing of new metabolites, covering the literature until the end of 2020.
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Zhang C, Seyedsayamdost MR. Discovery of a Cryptic Depsipeptide from
Streptomyces ghanaensis
via MALDI‐MS‐Guided High‐Throughput Elicitor Screening. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009611] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Chen Zhang
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry Princeton University Princeton NJ 08544 USA
- Department of Molecular Biology Princeton University Princeton NJ 08544 USA
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Zhang C, Seyedsayamdost MR. Discovery of a Cryptic Depsipeptide from Streptomyces ghanaensis via MALDI-MS-Guided High-Throughput Elicitor Screening. Angew Chem Int Ed Engl 2020; 59:23005-23009. [PMID: 32790054 DOI: 10.1002/anie.202009611] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Indexed: 11/06/2022]
Abstract
Microbial genomes harbor an abundance of biosynthetic gene clusters, but most are expressed at low levels and need to be activated for characterization of their cognate natural products. In this work, we report the combination of high-throughput elicitor screening (HiTES) with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for the rapid identification of cryptic peptide natural products. Application to Streptomyces ghanaensis identified amygdalin as an elicitor of a novel non-ribosomal peptide, which we term cinnapeptin. Complete structural elucidation revealed cinnapeptin as a cyclic depsipeptide with an unusual 2-methyl-cinnamoyl group. Insights into its biosynthesis were provided by whole genome sequencing and gene deletion studies, while bioactivity assays showed antimicrobial activity against Gram-positive bacteria and fission yeast. MALDI-HiTES is a broadly applicable tool for the discovery of cryptic peptides encoded in microbial genomes.
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Affiliation(s)
- Chen Zhang
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
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Mao D, Yoshimura A, Wang R, Seyedsayamdost MR. Reporter-Guided Transposon Mutant Selection for Activation of Silent Gene Clusters in Burkholderia thailandensis. Chembiochem 2020; 21:1826-1831. [PMID: 31984619 DOI: 10.1002/cbic.201900748] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Indexed: 01/01/2023]
Abstract
Most natural product biosynthetic gene clusters that can be observed bioinformatically are silent. This insight has prompted the development of several methodologies for inducing their expression. One of the more recent methods, termed reporter-guided mutant selection (RGMS), entails creation of a library of mutants that is then screened for the desired phenotype via reporter gene expression. Herein, we apply a similar approach to Burkholderia thailandensis and, using transposon mutagenesis, mutagenize three strains, each carrying a fluorescent reporter in the malleilactone (mal), capistruin (cap), or an unidentified ribosomal peptide (tomm) gene cluster. We show that even a small library of <500 mutants can be used to induce expression of each cluster. We also explore the mechanism of activation and find that inhibition of pyrimidine biosynthesis is linked to the induction of the mal cluster. Both a transposon insertion into pyrF as well as small-molecule-mediated inhibition of PyrF trigger malleilactone biosynthesis. Our results pave the way toward the broad application of RGMS and related approaches to Burkholderia spp.
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Affiliation(s)
- Dainan Mao
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Aya Yoshimura
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Rurun Wang
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
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Cheng Y, Yuan P, Xu X, Guo S, Pang K, Guo H, Zhang Z, Wu X, Zheng L, Song R. S-Edge-rich Mo xS y arrays vertically grown on carbon aerogels as superior bifunctional HER/OER electrocatalysts. NANOSCALE 2019; 11:20284-20294. [PMID: 31633137 DOI: 10.1039/c9nr07277b] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molybdenum disulfide (MoS2) is a potential earth-abundant electrocatalyst for the hydrogen evolution reaction (HER), but the lack of in-depth understanding of its intrinsic activity still impedes the further optimization and design of MoS2-based electrocatalysts. Herein, we report a facile in situ hydrothermal synthetic method to prepare vertical MoxSy arrays grown on guar gum-derived carbon aerogels (GCA), termed MoxSy@GCA. The obtained well-assembled MoxSy@GCA architectures consist of uniform, few-layered and S-edge-rich MoxSy nanoflakes with a length of approximately 100 nm, which effectively prevent the inherent stacking among MoxSy layers and connect the charge transfer path between interlayers, thus endowing MoxSy@GCA with a huge number of active sites and high conductivity. Benefitting from all these advantages, the optimal Mo4S16@GCA exhibited extraordinary HER/OER performances, including a low onset potential for both the HER (24.28 mV) and OER (1.53 V), and a low overpotential at 10 mA cm-2 for the HER (54.13 mV) and OER (370 mV), which are both extremely close to that of the noble Pt/C. Furthermore, a series of operando Raman spectroscopy measurements on Mo4S16@GCA were conducted to identify the intrinsic HER/OER-active sites during the HER and OER process. The results show that the S-H bond is generated simultaneously as HER/OER excitation, indicating the rich S-edge may be the intrinsic active site, which will accelerate the HER/OER kinetic process. Density functional theory (DFT) calculations revealed that the observed superb HER/OER activity can be attributed to the synergistic effect of rich S-edge of MoxSy and confinement effect of GCA, which collaboratively promote the proton adsorption and electrocatalytic kinetics. Reasonably, this study will have profound guiding value for the rational tailoring of the microstructure and size of transition metal electrocatalysts via hierarchical porous carbon aerogels.
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Affiliation(s)
- Yu Cheng
- School of Chemical Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing, 100049, PR China.
| | - Pengfei Yuan
- International Joint Research Laboratory for Quantum Functional Materials of Henan Province, and School of Physics and Engineering, Zhengzhou University, Zhengzhou 450001, PR China
| | - Xiaohui Xu
- School of Chemical Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing, 100049, PR China.
| | - Sijie Guo
- Institute of Chemistry, Chinese Academy of Sciences (CAS), 2 Zhongguancun North Road, Haidian District, Beijing, 100190, PR China
| | - Kanglei Pang
- School of Chemical Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing, 100049, PR China. and Sino-Danish College (SDC), University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing, 100049, PR China
| | - Haoran Guo
- School of Chemical Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing, 100049, PR China.
| | - Zhiguo Zhang
- School of Chemical Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing, 100049, PR China.
| | - Xiao Wu
- Research Institute of Aerospace Special Materials and Processing Technology, Beijing 100074, P. R. China
| | - Lirong Zheng
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, PR China
| | - Rui Song
- School of Chemical Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing, 100049, PR China.
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