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Nuanjohn T, Suphrom N, Nakaew N, Pathom-Aree W, Pensupa N, Siangsuepchart A, Dell B, Jumpathong J. Actinomycins from Soil-Inhabiting Streptomyces as Sources of Antibacterial Pigments for Silk Dyeing. Molecules 2023; 28:5949. [PMID: 37630201 PMCID: PMC10459128 DOI: 10.3390/molecules28165949] [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: 06/23/2023] [Revised: 07/26/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Actinobacteria produce a broad spectrum of bioactive substances that are used in the pharmaceutical, agricultural, and biotechnology industries. This study investigates the production of bioactive substances in Streptomyces, isolated from soil under five tropical plants, focusing on their potential as natural antibacterial dyes for silk fabrics. Out of 194 isolates, 44 produced pigments on broken rice as a solid substrate culture. Eight antibacterial pigmented isolates from under Magnolia baillonii (TBRC 15924, TBRC 15927, TBRC 15931), Magnolia rajaniana (TBRC 15925, TBRC 15926, TBRC 15928, TBRC 15930), and Cinnamomum parthenoxylon (TBRC 15929) were studied in more detail. TBRC 15927 was the only isolate where all the crude extracts inhibited the growth of the test organisms, Staphylococcus epidermidis TISTR 518 and S. aureus DMST 4745. The bioactive compounds present in TBRC 15927 were identified through LC-MS/MS analysis as belonging to the actinomycin group, actinomycin D (or X1), X2, and X0β. Also, the ethyl acetate crude extract exhibited non-toxicity at an IC50 value of 0.029 ± 0.008 µg/mL on the mouse fibroblast L-929 assay. From the 16S rRNA gene sequence analysis, TBRC 15927 had 100% identity with Streptomyces gramineus JR-43T. Raw silk dyed with the positive antimicrobial TBRC 15927 extract (8.35 mg/mL) had significant (>99.99%) antibacterial properties. Streptomyces gramineus TBRC 15927 is the first actinomycin-producing strain reported to grow on broken rice and shows promise for antibacterial silk dyeing.
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Affiliation(s)
- Tananya Nuanjohn
- Department of Agricultural Science, Faculty of Agriculture, Natural Resources and Environment, Naresuan University, Phitsanulok 65000, Thailand
| | - Nungruthai Suphrom
- Department of Chemistry, Faculty of Science, Center of Excellence for Innovation in Chemistry, Naresuan University, Phitsanulok 65000, Thailand
| | - Nareeluk Nakaew
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Wasu Pathom-Aree
- Research Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nattha Pensupa
- Department of Agro-Industry, Faculty of Agriculture, Natural Resources and Environment, Naresuan University, Phitsanulok 65000, Thailand
| | - Apiradee Siangsuepchart
- Department of Agro-Industrial Biotechnology, Maejo University Phrae Campus, Phrae 54140, Thailand
| | - Bernard Dell
- School of Agricultural Sciences, Murdoch University, Perth 6150, Australia
| | - Juangjun Jumpathong
- Department of Agricultural Science, Faculty of Agriculture, Natural Resources and Environment, Naresuan University, Phitsanulok 65000, Thailand
- Center of Excellence in Research for Agricultural Biotechnology, Faculty of Agriculture, Natural Resources and Environment, Naresuan University, Phitsanulok 65000, Thailand
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102
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de Lima Júnior AA, de Sousa EC, de Oliveira THB, de Santana RCF, da Silva SKR, Coelho LCBB. Genus Streptomyces: Recent advances for biotechnological purposes. Biotechnol Appl Biochem 2023; 70:1504-1517. [PMID: 36924211 DOI: 10.1002/bab.2455] [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: 10/27/2022] [Revised: 02/06/2023] [Accepted: 02/26/2023] [Indexed: 03/18/2023]
Abstract
Actinomycetes are a distinct group of filamentous bacteria. The Streptomyces genus within this group has been extensively studied over the years, with substantial contributions to society and science. This genus is known for its antimicrobial production, as well as antitumor, biopesticide, and immunomodulatory properties. Therefore, the extraordinary plasticity of the Streptomyces genus has inspired new research techniques. The newest way of exploring Streptomyces has comprised the discovery of new natural metabolites and the application of emerging tools such as CRISPR technology in drug discovery. In this narrative review, we explore relevant published literature concerning the ongoing novelties of the Streptomyces genus.
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Affiliation(s)
- Apolonio Alves de Lima Júnior
- Departamento de Bioquímica, Centro de Biociências, CB, Universidade Federal de Pernambuco (UFPE), Avenida Professor Moraes Rego, S/N, Cidade Universitária, Recife, Pernambuco, Brazil
| | | | - Thales Henrique Barbosa de Oliveira
- Departamento de Bioquímica, Centro de Biociências, CB, Universidade Federal de Pernambuco (UFPE), Avenida Professor Moraes Rego, S/N, Cidade Universitária, Recife, Pernambuco, Brazil
| | | | | | - Luana Cassandra Breitenbach Barroso Coelho
- Departamento de Bioquímica, Centro de Biociências, CB, Universidade Federal de Pernambuco (UFPE), Avenida Professor Moraes Rego, S/N, Cidade Universitária, Recife, Pernambuco, Brazil
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103
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Lopatniuk M, Riedel F, Wildfeuer J, Stierhof M, Dahlem C, Kiemer AK, Luzhetskyy A. Development of a Streptomyces-based system for facile thioholgamide library generation and analysis. Metab Eng 2023; 78:48-60. [PMID: 37142115 DOI: 10.1016/j.ymben.2023.04.015] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/06/2023]
Abstract
Derivatizing natural products (NPs) is essential in structure-activity relationship (SAR) studies, compound optimization, and drug development. Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent one of the major classes of natural products. Thioholgamide represents thioamitide - a recently emerged family of RiPPs with unique structures and great potential in anticancer drug development. Although the method for generating the RiPP library by codon substitutions in the precursor peptide gene is straightforward, the techniques to perform RiPP derivatization in Actinobacteria remain limited and time-consuming. Here, we report a facile system for producing a library of randomized thioholgamide derivatives utilizing an optimized Streptomyces host. This technique enabled us to access all possible amino acid substitutions of the thioholgamide molecule, one position at a time. Out of 152 potential derivatives, 85 were successfully detected, revealing the impact of amino acid substitutions on thioholgamide post-translational modifications (PTMs). Moreover, new PTMs were observed among thioholgamide derivatives: thiazoline heterocycles, which have not yet been reported for thioamitides, and S-methylmethionine, which is very rare in nature. The obtained library was subsequently used for thioholgamide SAR studies and stability assays.
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Affiliation(s)
- Maria Lopatniuk
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Florian Riedel
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Julia Wildfeuer
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany; Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Marc Stierhof
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Charlotte Dahlem
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.
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104
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Schuntermann DB, Fischer JT, Bile J, Gaier SA, Shelley BA, Awawdeh A, Jahn M, Hoffman KS, Westhof E, Söll D, Clarke CR, Vargas-Rodriguez O. Mistranslation of the genetic code by a new family of bacterial transfer RNAs. J Biol Chem 2023; 299:104852. [PMID: 37224963 PMCID: PMC10404621 DOI: 10.1016/j.jbc.2023.104852] [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: 04/05/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 05/26/2023] Open
Abstract
The correct coupling of amino acids with transfer RNAs (tRNAs) is vital for translating genetic information into functional proteins. Errors during this process lead to mistranslation, where a codon is translated using the wrong amino acid. While unregulated and prolonged mistranslation is often toxic, growing evidence suggests that organisms, from bacteria to humans, can induce and use mistranslation as a mechanism to overcome unfavorable environmental conditions. Most known cases of mistranslation are caused by translation factors with poor substrate specificity or when substrate discrimination is sensitive to molecular changes such as mutations or posttranslational modifications. Here we report two novel families of tRNAs, encoded by bacteria from the Streptomyces and Kitasatospora genera, that adopted dual identities by integrating the anticodons AUU (for Asn) or AGU (for Thr) into the structure of a distinct proline tRNA. These tRNAs are typically encoded next to a full-length or truncated version of a distinct isoform of bacterial-type prolyl-tRNA synthetase. Using two protein reporters, we showed that these tRNAs translate asparagine and threonine codons with proline. Moreover, when expressed in Escherichia coli, the tRNAs cause varying growth defects due to global Asn-to-Pro and Thr-to-Pro mutations. Yet, proteome-wide substitutions of Asn with Pro induced by tRNA expression increased cell tolerance to the antibiotic carbenicillin, indicating that Pro mistranslation can be beneficial under certain conditions. Collectively, our results significantly expand the catalog of organisms known to possess dedicated mistranslation machinery and support the concept that mistranslation is a mechanism for cellular resiliency against environmental stress.
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Affiliation(s)
- Dominik B Schuntermann
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Department of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Jonathan T Fischer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Jonmatthew Bile
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Sarah A Gaier
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Brett A Shelley
- Genetic Improvement for Fruits and Vegetables Lab, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, USA
| | - Aya Awawdeh
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Martina Jahn
- Department of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | | | - Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Department of Chemistry, Yale University, New Haven, Connecticut, USA.
| | - Christopher R Clarke
- Genetic Improvement for Fruits and Vegetables Lab, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, USA
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
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105
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Avramova MM, Stevenson CEM, Chandra G, Holmes NA, Bush MJ, Findlay KC, Buttner MJ. Global Effects of the Developmental Regulator BldB in Streptomyces venezuelae. J Bacteriol 2023; 205:e0013523. [PMID: 37249447 PMCID: PMC10294661 DOI: 10.1128/jb.00135-23] [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: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/31/2023] Open
Abstract
In Streptomyces, the Bld (Bald) regulators control formation of the reproductive aerial hyphae. The functions of some of these regulators have been well characterized, but BldB has remained enigmatic. In addition to the bldB gene itself, Streptomyces venezuelae has 10 paralogs of bldB that sit next to paralogs of whiJ and abaA. Transcriptome sequencing (RNA-seq) revealed that loss of BldB function causes the dramatic transcriptional upregulation of the abaA paralogs and a novel inhibitor of sporulation, iosA, and that cooverexpression of just two of these genes, iosA and abaA6, was sufficient to recapitulate the bldB mutant phenotype. Further RNA-seq analysis showed that the transcription factor WhiJ9 is required for the activation of iosA seen in the bldB mutant, and biochemical studies showed that WhiJ9 mediates the activation of iosA expression by binding to direct repeats in the iosA-whiJ9 intergenic region. BldB and BldB9 hetero-oligomerize, providing a potential link between BldB and the iosA-whiJ9-bldB9 locus. This work greatly expands our overall understanding of the global effects of the BldB developmental regulator. IMPORTANCE To reproduce and disperse, the filamentous bacterium Streptomyces develops specialized reproductive structures called aerial hyphae. The formation of these structures is controlled by the bld (bald) genes, many of which encode transcription factors whose functions have been characterized. An exception is BldB, a protein whose biochemical function is unknown. In this study, we gain insight into the global effects of BldB function by examining the genome-wide transcriptional effects of deleting bldB. We identify a small set of genes that are dramatically upregulated in the absence of BldB. We show that their overexpression causes the bldB phenotype and characterize a transcription factor that mediates the upregulation of one of these target genes. Our results provide new insight into how BldB influences Streptomyces development.
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Affiliation(s)
- Marieta M. Avramova
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Clare E. M. Stevenson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Neil A. Holmes
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Matthew J. Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Kim C. Findlay
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Mark J. Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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106
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Kronheim S, Solomon E, Ho L, Glossop M, Davidson AR, Maxwell KL. Complete genomes and comparative analyses of Streptomyces phages that influence secondary metabolism and sporulation. Sci Rep 2023; 13:9820. [PMID: 37330527 PMCID: PMC10276819 DOI: 10.1038/s41598-023-36938-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 04/20/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
Bacteria in the genus Streptomyces are found ubiquitously in nature and are known for the number and diversity of specialized metabolites they produce, as well as their complex developmental lifecycle. Studies of the viruses that prey on Streptomyces, known as phages, have aided the development of tools for genetic manipulation of these bacteria, as well as contributing to a deeper understanding of Streptomyces and their behaviours in the environment. Here, we present the genomic and biological characterization of twelve Streptomyces phages. Genome analyses reveal that these phages are closely related genetically, while experimental approaches show that they have broad overlapping host ranges, infect early in the Streptomyces lifecycle, and induce secondary metabolite production and sporulation in some Streptomyces species. This work expands the group of characterized Streptomyces phages and improves our understanding of Streptomyces phage-host dynamics.
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Affiliation(s)
- Sarah Kronheim
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Ethan Solomon
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Louis Ho
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Michelle Glossop
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Alan R Davidson
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada.
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107
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Gao WL, Fang JL, Zhu CY, Xu WF, Lyu ZY, Chan XA, Zhao QW, Li YQ. Identification and Characterization of a New Regulator, TagR, for Environmental Stress Resistance Based on the DNA Methylome of Streptomyces roseosporus. Microbiol Spectr 2023; 11:e0038023. [PMID: 37154757 PMCID: PMC10269677 DOI: 10.1128/spectrum.00380-23] [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: 01/24/2023] [Accepted: 04/10/2023] [Indexed: 05/10/2023] Open
Abstract
DNA methylation is a defense that microorganisms use against extreme environmental stress, and improving resistance against environmental stress is essential for industrial actinomycetes. However, research on strain optimization utilizing DNA methylation for breakthroughs is rare. Based on DNA methylome analysis and KEGG pathway assignment in Streptomyces roseosporus, we discovered an environmental stress resistance regulator, TagR. A series of in vivo and in vitro experiments identified TagR as a negative regulator, and it is the first reported regulator of the wall teichoic acid (WTA) ABC transport system. Further study showed that TagR had a positive self-regulatory loop and m4C methylation in the promoter improved its expression. The ΔtagR mutant exhibited better hyperosmotic resistance and higher decanoic acid tolerance than the wild type, which led to a 100% increase in the yield of daptomycin. Moreover, enhancing the expression of the WTA transporter resulted in better osmotic stress resistance in Streptomyces lividans TK24, indicating the potential for wide application of the TagR-WTA transporter regulatory pathway. This research confirmed the feasibility and effectiveness of mining regulators of environmental stress resistance based on the DNA methylome, characterized the mechanism of TagR, and improved the resistance and daptomycin yield of strains. Furthermore, this research provides a new perspective on the optimization of industrial actinomycetes. IMPORTANCE This study established a novel strategy for screening regulators of environmental stress resistance based on the DNA methylome and discovered a new regulator, TagR. The TagR-WTA transporter regulatory pathway improved the resistance and antibiotic yield of strains and has the potential for wide application. Our research provides a new perspective on the optimization and reconstruction of industrial actinomycetes.
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Affiliation(s)
- Wen-Li Gao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Jiao-Le Fang
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Chen-Yang Zhu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Wei-Feng Xu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Zhong-Yuan Lyu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Xin-Ai Chan
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Qing-Wei Zhao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
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108
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Thakur M, Kumar P, Rajput D, Yadav V, Dhaka N, Shukla R, Kumar Dubey K. Genome-guided approaches and evaluation of the strategies to influence bioprocessing assisted morphological engineering of Streptomyces cell factories. Bioresour Technol 2023; 376:128836. [PMID: 36898554 DOI: 10.1016/j.biortech.2023.128836] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
Streptomyces genera serve as adaptable cell factories for secondary metabolites with various and distinctive chemical structures that are relevant to the pharmaceutical industry. Streptomyces' complex life cycle necessitated a variety of tactics to enhance metabolite production. Identification of metabolic pathways, secondary metabolite clusters, and their controls have all been accomplished using genomic methods. Besides this, bioprocess parameters were also optimized for the regulation of morphology. Kinase families were identified as key checkpoints in the metabolic manipulation (DivIVA, Scy, FilP, matAB, and AfsK) and morphology engineering of Streptomyces. This review illustrates the role of different physiological variables during fermentation in the bioeconomy coupled with genome-based molecular characterization of biomolecules responsible for secondary metabolite production at different developmental stages of the Streptomyces life cycle.
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Affiliation(s)
- Mony Thakur
- Department of Microbiology, Central University of Haryana, Mahendergarh 123031, India
| | - Punit Kumar
- Department of Morphology and Physiology, Karaganda Medical University, Karaganda 100008 Kazakhstan
| | - Deepanshi Rajput
- Bioprocess Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vinod Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh 123031, India
| | - Namrata Dhaka
- Department of Biotechnology, Central University of Haryana, Mahendergarh 123031, India
| | - Rishikesh Shukla
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura- 281406, U.P., India
| | - Kashyap Kumar Dubey
- Bioprocess Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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109
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Kumar V, Fox BG, Takasuka TE. Consolidated bioprocessing of plant biomass to polyhydroxyalkanoate by co-culture of Streptomyces sp. SirexAA-E and Priestia megaterium. Bioresour Technol 2023; 376:128934. [PMID: 36940873 DOI: 10.1016/j.biortech.2023.128934] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
Polyhydroxyalkanoate (PHA) production from plant biomass is an ideal way to realize sustainable PHA-based bioplastic. The present study demonstrated consolidated bioconversion of plant biomass to PHA by co-culturing two specialized bacteria, cellulolytic Streptomyces sp. SirexAA-E and PHA producing Priestia megaterium. In monoculture, S. sp. SirexAA-E does not produce PHA, while P. megaterium did not grow on plant polysaccharides. The co-culture showed poly(3-hydroxybutyrate) (PHB) production using purified polysaccharides, including cellulose, xylan, mannan and their combinations, and plant biomass (Miscanthus, corn stalk and corn leaves) as sole carbon sources, confirmed by GC-MS. The co-culture inoculated with 1:4 (v/v) ratio of S. sp. SirexAA-E to P. megaterium produced 40 mg PHB/g Miscanthus using 0.5% biomass loading. Realtime PCR showed ∼85% S. sp. SirexAA-E and ∼15% P. megaterium in the co-culture. Thus, this study provides a concept of proof for one-pot bioconversion of plant biomass into PHB without separate saccharification processes.
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Affiliation(s)
- Vijay Kumar
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Brian G Fox
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan; US-DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; Global Station for Food, Land and Water Resources, Hokkaido University, Sapporo, Japan
| | - Taichi E Takasuka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan; Global Station for Food, Land and Water Resources, Hokkaido University, Sapporo, Japan.
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110
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Yang P, Wang X, Ye J, Rao S, Zhou J, Du G, Liu S. Enhanced Thermostability and Catalytic Activity of Streptomyces mobaraenesis Transglutaminase by Rationally Engineering Its Flexible Regions. J Agric Food Chem 2023; 71:6366-6375. [PMID: 37039372 DOI: 10.1021/acs.jafc.3c00260] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Streptomyces mobaraenesis transglutaminase can catalyze the cross-linking of proteins, which has been widely used in food processing. In this study, we rationally modified flexible regions to further improve the thermostability of FRAPD-TGm2 (S2P-S23V-Y24N-E28T-S199A-A265P-A287P-K294L), a stable mutant of the transglutaminase constructed in our previous study. First, five flexible regions of FRAPD-TGm2 were identified by molecular dynamics simulations at 330 and 360 K. Second, a script based on Rosetta Cartesian_ddg was developed for virtual saturation mutagenesis within the flexible regions far from the substrate binding pocket, generating the top 18 mutants with remarkable decreases in folding free energy. Third, from the top 18 mutants, we identified two mutants (S116A and S179L) with increased thermostability and activity. Finally, the above favorable mutations were combined to obtain FRAPD-TGm2-S116A-S179L (FRAPD-TGm2A), exhibiting a half-life of 132.38 min at 60 °C (t1/2(60 °C)) and a specific activity of 79.15 U/mg, 84 and 21% higher than those of FRAPD-TGm2, respectively. Therefore, the current result may benefit the application of S. mobaraenesis transglutaminase at high temperatures.
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Affiliation(s)
- Penghui Yang
- Engineering Research Center of Ministry of Education on Food Synthetic Biorheology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xinglong Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biorheology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jiacai Ye
- Engineering Research Center of Ministry of Education on Food Synthetic Biorheology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shengqi Rao
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biorheology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Guocheng Du
- Engineering Research Center of Ministry of Education on Food Synthetic Biorheology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Song Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biorheology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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Xu W, Sun C, Gao W, Scharf DH, Zhu C, Bu Q, Zhao Q, Li Y. Degradation mechanism of AtrA mediated by ClpXP and its application in daptomycin production in Streptomyces roseosporus. Protein Sci 2023; 32:e4617. [PMID: 36882943 PMCID: PMC10031807 DOI: 10.1002/pro.4617] [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: 11/01/2022] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
The efficiency of drug biosynthesis depends on different transcriptional regulatory pathways in Streptomyces, and the protein degradation system adds another layer of complexity to the regulatory processes. AtrA, a transcriptional regulator in the A-factor regulatory cascade, stimulates the production of daptomycin by binding to the dptE promoter in Streptomyces roseosporus. Using pull-down assays, bacterial two-hybrid system and knockout verification, we demonstrated that AtrA is a substrate for ClpP protease. Furthermore, we showed that ClpX is necessary for AtrA recognition and subsequent degradation. Bioinformatics analysis, truncating mutation, and overexpression proved that the AAA motifs of AtrA were essential for initial recognition in the degradation process. Finally, overexpression of mutated atrA (AAA-QQQ) in S. roseosporus increased the yield of daptomycin by 225% in shake flask and by 164% in the 15 L bioreactor. Thus, improving the stability of key regulators is an effective method to promote the ability of antibiotic synthesis.
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Affiliation(s)
- Wei‐Feng Xu
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
- Institute of Pharmaceutical BiotechnologyZhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Chen‐Fan Sun
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
- Institute of Pharmaceutical BiotechnologyZhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Wen‐Li Gao
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
- Institute of Pharmaceutical BiotechnologyZhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Daniel H. Scharf
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
- Institute of Pharmaceutical BiotechnologyZhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Chen‐Yang Zhu
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
- Institute of Pharmaceutical BiotechnologyZhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Qing‐Ting Bu
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
- Institute of Pharmaceutical BiotechnologyZhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Qing‐Wei Zhao
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
| | - Yong‐Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
- Institute of Pharmaceutical BiotechnologyZhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
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112
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Tang SK, Zhi XY, Zhang Y, Makarova KS, Liu BB, Zheng GS, Zhang ZP, Zheng HJ, Wolf YI, Zhao YR, Jiang SH, Chen XM, Li EY, Zhang T, Chen PR, Feng YZ, Xiang MX, Lin ZQ, Shi JH, Chang C, Zhang X, Li R, Lou K, Wang Y, Chang L, Yin M, Yang LL, Gao HY, Zhang ZK, Tao TS, Guan TW, He FC, Lu YH, Cui HL, Koonin EV, Zhao GP, Xu P. Cellular differentiation into hyphae and spores in halophilic archaea. Nat Commun 2023; 14:1827. [PMID: 37005419 PMCID: PMC10067837 DOI: 10.1038/s41467-023-37389-w] [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: 06/15/2022] [Accepted: 03/14/2023] [Indexed: 04/04/2023] Open
Abstract
Several groups of bacteria have complex life cycles involving cellular differentiation and multicellular structures. For example, actinobacteria of the genus Streptomyces form multicellular vegetative hyphae, aerial hyphae, and spores. However, similar life cycles have not yet been described for archaea. Here, we show that several haloarchaea of the family Halobacteriaceae display a life cycle resembling that of Streptomyces bacteria. Strain YIM 93972 (isolated from a salt marsh) undergoes cellular differentiation into mycelia and spores. Other closely related strains are also able to form mycelia, and comparative genomic analyses point to gene signatures (apparent gain or loss of certain genes) that are shared by members of this clade within the Halobacteriaceae. Genomic, transcriptomic and proteomic analyses of non-differentiating mutants suggest that a Cdc48-family ATPase might be involved in cellular differentiation in strain YIM 93972. Additionally, a gene encoding a putative oligopeptide transporter from YIM 93972 can restore the ability to form hyphae in a Streptomyces coelicolor mutant that carries a deletion in a homologous gene cluster (bldKA-bldKE), suggesting functional equivalence. We propose strain YIM 93972 as representative of a new species in a new genus within the family Halobacteriaceae, for which the name Actinoarchaeum halophilum gen. nov., sp. nov. is herewith proposed. Our demonstration of a complex life cycle in a group of haloarchaea adds a new dimension to our understanding of the biological diversity and environmental adaptation of archaea.
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Affiliation(s)
- Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Bing-Bing Liu
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, China
| | - Guo-Song Zheng
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhen-Peng Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Hua-Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 201203, China
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Yu-Rong Zhao
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Song-Hao Jiang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China
| | - Xi-Ming Chen
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - En-Yuan Li
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Tao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Pei-Ru Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China
| | - Yu-Zhou Feng
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Ming-Xian Xiang
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Zhi-Qian Lin
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Jia-Hui Shi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Xue Zhang
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, China
| | - Rui Li
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Kai Lou
- Xinjiang Institute of Microbiology, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Yun Wang
- Xinjiang Institute of Microbiology, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Min Yin
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Ling-Ling Yang
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Hui-Ying Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Zhong-Kai Zhang
- Biotechnology and Genetic Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Tian-Shen Tao
- Department of Microbiology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China
| | - Tong-Wei Guan
- College of Food and Biological Engineering, Xihua University, Chengdu, 610039, China
| | - Fu-Chu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Yin-Hua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA.
| | - Guo-Ping Zhao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200032, China.
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China.
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China.
- Department of Microbiology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China.
- Guizhou University, School of Medicine, Guiyang, 550025, China.
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China.
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113
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Wojnowska M, Feng X, Chen Y, Deng H, O'Hagan D. Identification of Genes Essential for Fluorination and Sulfamylation within the Nucleocidin Gene Clusters of Streptomyces calvus and Streptomyces virens. Chembiochem 2023; 24:e202200684. [PMID: 36548247 PMCID: PMC10946740 DOI: 10.1002/cbic.202200684] [Citation(s) in RCA: 2] [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: 11/21/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 12/24/2022]
Abstract
The gene cluster in Streptomyces calvus associated with the biosynthesis of the fluoro- and sulfamyl-metabolite nucleocidin was interrogated by systematic gene knockouts. Out of the 26 gene deletions, most did not affect fluorometabolite production, nine abolished sulfamylation but not fluorination, and three precluded fluorination, but had no effect on sulfamylation. In addition to nucI, nucG, nucJ, nucK, nucL, nucN, nucO, nucQ and nucP, we identified two genes (nucW, nucA), belonging to a phosphoadenosine phosphosulfate (PAPS) gene cluster, as required for sulfamyl assembly. Three genes (orf(-3), orf2 and orf3) were found to be essential for fluorination, although the activities of their protein products are unknown. These genes as well as nucK, nucN, nucO and nucPNP, whose knockouts produced results differing from those described in a recent report, were also deleted in Streptomyces virens - with confirmatory outcomes. This genetic profile should inform biochemistry aimed at uncovering the enzymology behind nucleocidin biosynthesis.
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Affiliation(s)
- Marta Wojnowska
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| | - Xuan Feng
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| | - Yawen Chen
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| | - Hai Deng
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| | - David O'Hagan
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
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Abstract
Streptomyces bacteria are a major microbial source of natural products, which are encoded within so-called biosynthetic gene clusters (BGCs). This highlight discusses the emergence of native Streptomyces cell-free systems as a new tool to accelerate the study of the fundamental chemistry and biology of natural product biosynthesis from these bacteria. Cell-free systems provide a prototyping platform to study plug-and-play reactions in microscale reactions. So far, Streptomyces cell-free systems have been used to rapidly characterise gene expression regulation, access secondary metabolite biosynthetic enzymes, and catalyse cell-free transcription, translation, and biosynthesis of example natural products. With further progress, we anticipate the development of more complex systems to complement existing experimental tools for the discovery and engineering of natural product biosynthesis from Streptomyces and related high G + C (%) bacteria.
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Affiliation(s)
- Simon J Moore
- School of Biosciences, University of Kent, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, UK.
| | - Hung-En Lai
- School of Biological Sciences, Victoria University of Wellington, New Zealand
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, China
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115
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Cao M, Yang D, Adhikari A, Ye F, Zheng C, Yan W, Meng S, Su P, Shen B. Neogrisemycin, a Trisulfide-Bridged Angucycline, Produced upon Expressing the Thioangucycline Biosynthetic Gene Cluster in Streptomyces albus J1074. Org Lett 2023; 25:961-965. [PMID: 36735280 PMCID: PMC10115141 DOI: 10.1021/acs.orglett.2c04303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Neogrisemycin (1) was isolated from recombinant Streptomyces albus J1074 strain SB4061 expressing an engineered thioangucycline (TAC) biosynthetic gene cluster (BGC). The structure and absolute configuration of 1 were established by a combination of mass spectrometry, nuclear magnetic resonance, and single-crystal X-ray diffraction analyses. Like the TACs, 1 was also proposed to derive non-enzymatically from the common epoxide (8), the nascent product encoded by the tac BGC, mediated by endogenous hydrogen trisulfide.
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Affiliation(s)
| | | | - Ajeeth Adhikari
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, Florida 33458, United States
| | | | | | | | | | | | - Ben Shen
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, Florida 33458, United States
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116
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Li Y, Xu Z, Chen P, Zuo C, Chen L, Yan W, Jiao R, Ye Y. Genome Mining and Heterologous Expression Guided the Discovery of Antimicrobial Naphthocyclinones from Streptomyces eurocidicus CGMCC 4.1086. J Agric Food Chem 2023; 71:2914-2923. [PMID: 36731876 DOI: 10.1021/acs.jafc.2c06928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A type II polyketide synthase biosynthetic gene cluster (nap) was identified in Streptomyces eurocidicus CGMCC 4.1086 via genome mining. The heterologous expression of the cryptic nap gene cluster in Streptomyces albus J1074 generated dimerized aromatic polyketide naphthocyclinones (1-3), whose structures were determined via extensive analysis using nuclear magnetic resonance and high-resolution electrospray ionization mass spectroscopy. The biological pathway of naphthocyclinone synthesis was revealed via in vivo gene deletion, in vitro biochemical reactions, and comparative genomics. Remarkably, 3 played a crucial role in inhibiting Phytophthora capsici and Phytophthora sojae, with EC50 values of 6.1 and 20.2 μg/mL, respectively. Furthermore, 3 exhibited a potent protective effect against P. capsici and P. sojae in greenhouse tests.
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Affiliation(s)
- Yu Li
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| | - Zifei Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ping Chen
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| | - Chen Zuo
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| | - Liyifan Chen
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| | - Wei Yan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| | - Ruihua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yonghao Ye
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
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Mehdiratta K, Nain S, Sharma M, Singh S, Srivastava S, Dhamale BD, Mohanty D, Kamat SS, Natarajan VT, Sharma R, Gokhale RS. Respiratory Quinone Switches from Menaquinone to Polyketide Quinone during the Development Cycle in Streptomyces sp. Strain MNU77. Microbiol Spectr 2023; 11:e0259722. [PMID: 36507669 PMCID: PMC9927152 DOI: 10.1128/spectrum.02597-22] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Type III polyketide synthases (PKSs) found across Streptomyces species are primarily known for synthesis of a vast repertoire of clinically and industrially relevant secondary metabolites. However, our understanding of the functional relevance of these bioactive metabolites in Streptomyces physiology is still limited. Recently, a role of type III PKS harboring gene cluster in producing alternate electron carrier, polyketide quinone (PkQ) was established in a related member of the Actinobacteria, Mycobacteria, highlighting the critical role these secondary metabolites play in primary cellular metabolism of the producer organism. Here, we report the developmental stage-specific transcriptional regulation of homologous type III PKS containing gene cluster in freshwater Streptomyces sp. strain MNU77. Gene expression analysis revealed the type III PKS gene cluster to be stringently regulated, with significant upregulation observed during the dormant sporulation stage of Streptomyces sp. MNU77. In contrast, the expression levels of only known electron carrier, menaquinone biosynthetic genes were interestingly found to be downregulated. Our liquid chromatography-high-resolution mass spectrometry (LC-HRMS) analysis of a metabolite extract from the Streptomyces sp. MNU77 spores also showed 10 times more metabolic abundance of PkQs than menaquinones. Furthermore, through heterologous complementation studies, we demonstrate that Streptomyces sp. MNU77 type III PKS rescues a respiratory defect of the Mycobacterium smegmatis type III PKS deletion mutant. Together, our studies reveal that freshwater Streptomyces sp. MNU77 robustly produces novel PkQs during the sporulation stage, suggesting utilization of PkQs as alternate electron carriers across Actinobacteria during dormant hypoxic conditions. IMPORTANCE The complex developmental life cycle of Streptomyces sp. mandates efficient cellular respiratory reconfiguration for a smooth transition from aerated nutrient-rich vegetative hyphal growth to the hypoxic-dormant sporulation stage. Polyketide quinones (PkQs) have recently been identified as a class of alternate electron carriers from a related member of the Actinobacteria, Mycobacteria, that facilitates maintenance of membrane potential in oxygen-deficient niches. Our studies with the newly identified freshwater Streptomyces sp. strain MNU77 show conditional transcriptional upregulation and metabolic abundance of PkQs in the spore state of the Streptomyces life cycle. In parallel, the levels of menaquinones, the only known Streptomyces electron carrier, were downregulated, suggesting deployment of PkQs as universal electron carriers in low-oxygen, unfavorable conditions across the Actinobacteria family.
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Affiliation(s)
- Kritee Mehdiratta
- National Institute of Immunology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sonam Nain
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Meenakshi Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shubham Singh
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | | | | | | | - Siddhesh S. Kamat
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Vivek T. Natarajan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Rakesh Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Rajesh S. Gokhale
- National Institute of Immunology, New Delhi, India
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
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Feng XL, Zhang RQ, Wang DC, Dong WG, Wang ZX, Zhai YJ, Han WB, Yin X, Tian J, Wei J, Gao JM, Qi J. Genomic and Metabolite Profiling Reveal a Novel Streptomyces Strain, QHH-9511, from the Qinghai-Tibet Plateau. Microbiol Spectr 2023; 11:e0276422. [PMID: 36622153 PMCID: PMC9927492 DOI: 10.1128/spectrum.02764-22] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/15/2022] [Indexed: 01/10/2023] Open
Abstract
The prevalence of superbugs, represented by methicillin-resistant Staphylococcus aureus (MRSA), has become a serious clinical and public safety concern with rising incidence in hospitals. Polyketides with diverse chemical structures harbor many antimicrobial activities, including those of rifampin and rapamycin against MRSA. Streptomyces sp. QHH-9511 was isolated from a niche habitat in the Qinghai-Tibet Plateau and used to produce antibacterial metabolites. Herein, an integrated approach combining genome mining and metabolic analysis were employed to decipher the chemical origin of the antibacterial components with pigmented properties in strain QHH-9511, a novel Streptomyces species from a lichen symbiont on the Qinghai-Tibet Plateau. Genomic phylogeny assembled at the chromosome level revealed its unique evolutionary state. Further genome mining uncovered 36 candidate gene clusters, most of which were uncharacterized. Meanwhile, based on liquid chromatography coupled to diode array detection mass spectrometry, a series of granaticins, BSMs, chromones, phaeochromycins, and related molecules were discovered by using the Global Natural Product Social molecular networking platform. Subsequently, several pigment compounds were isolated and identified by high-resolution mass spectrometry and/or nuclear magnetic resonance, among which the structure-activity relationships of seven aromatic polyketides showed that the fused lactone ring of the C-2 carboxyl group could increase antibacterial activity. Genetic experiments indicated that all seven aromatic polyketides are a series of metabolic shunts produced by a single type II polyketide synthase (PKS) cluster. Comparative genomic analysis of granaticin producers showed that the granaticin gene cluster is widely distributed. This study provides an efficient method to combine genome mining and metabolic profiling techniques to uncover bioactive metabolites derived from specific habitats, while deepening our understanding of aromatic polyketide biosynthesis. IMPORTANCE Undescribed microorganisms from special habitats are being screened for anti-superbug drug molecules. In a project to screen actinomycetes for anti-MRSA activity, we isolated a Streptomyces strain from Qinghai Lake lichens. The phylogeny based on the genome assembled at the chromosome level revealed this strain's unique evolutionary state. The chemical origins of the antibacterial components with pigment properties in strain QHH-9511 were determined using an integrated approach combining genome mining and metabolic analysis. Further genome mining uncovered 36 secondary metabolite gene clusters, the majority of which were previously unknown. A series of aromatic compounds were discovered using molecular network analysis, separation, and extraction. Genetic experiments revealed that all seven aromatic polyketides are a series of metabolic shunts produced by a single cluster of type II PKSs. This study describes a method for identifying novel Streptomyces from specific habitats by combining genome mining with metabolic profiling techniques.
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Affiliation(s)
- Xi-Long Feng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Rui-Qi Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Da-Cheng Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Wei-Ge Dong
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhen-Xin Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yi-Jie Zhai
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Wen-Bo Han
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Xia Yin
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Junmian Tian
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Jing Wei
- College of Biology Pharmacy & Food Engineering, Shangluo University, Shangluo, Shaanxi, China
- Qinba Mountains of Bio-Resource Collaborative Innovation Center of Southern Shaanxi Province, Hanzhong, Shaanxi, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi, China
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Song Y, Zhang X, Zhang Z, Shentu X, Yu X. Physiology and Transcriptional Analysis of ppGpp-Related Regulatory Effects in Streptomyces diastatochromogenes 1628. Microbiol Spectr 2023; 11:e0120022. [PMID: 36475882 PMCID: PMC9927088 DOI: 10.1128/spectrum.01200-22] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
ppGpp is a ubiquitous small nucleotide messenger that mediates cellular self-protective responses under environmental stress. However, the mechanisms of ppGpp that control transcription and other metabolic processes depend on the species, and ppGpp regulates the same process via different mechanisms. The level of ppGpp is regulated by RelA/SpoT homolog (RSH) enzymes that synthesize and hydrolyze the alarmone. Here, we constructed a ppGpp0 strain and monitored the effects of ppGpp on the transcriptional level, physiology, and secondary metabiotic production in the antibiotic producer Streptomyces diastatochromogenes 1628. The results showed the cell division and growth of ppGpp0 increased by measurement of gene transcription and DCWs. The utilization of nitrogen was affected depending on the nitrogen type with a significantly higher DCW of the ppGpp0 mutant in the medium supplied with the yeast extract and a lower growth rate in the inorganic nitrogen ammonium salt. The ppGpp-mediated stringent response could not affect the usage of carbon resources. More importantly, ppGpp0 inhibited the expression of antibiotic clusters and the production of toyocamycin and tetramycin P. The antibiotic resistance was also significantly downregulated in the ppGpp0 mutant. In conclusion, this study showed detailed changes in ppGpp-mediated stringent responses on S. diastatochromogenes 1628 cell growth, nutrient utilization, morphological characteristics, antibiotic production, and resistance, which will provide insights into the role of ppGpp in Streptomyces. IMPORTANCE The ppGpp-mediated stringent response is widely distributed in Escherichia coli, Bacillus subtilis, Streptomyces, Staphylococcus aureus, etc. Stringent responses give strains the ability to resist environmental stresses, and survival from nutrition starvation, virulence, long-term persistence, biofilm formation, and gut colonization. ppGpp has many targets in cells and can reprogram DNA replication, transcription, ribosome biogenesis and function, and lipid metabolism. However, the mechanism of ppGpp to control transcription and other metabolic processes depends on the bacterial species and regulates the same process via a different mechanism. In Streptomyces, how ppGpp regulates the transcription remains to be elucidated. However, because ppGpp regulates many genes involved in primary and secondary metabolism, we compared the transcription and cell division, cell growth, morphological differentiation, antibiotic resistance, and secondary synthesis in the wild-type S. diastatochromogenes and ppGpp0 strains.
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Affiliation(s)
- Yang Song
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China Jiliang University, Hangzhou, China
| | - Xiangli Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China Jiliang University, Hangzhou, China
| | - Zixuan Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China Jiliang University, Hangzhou, China
| | - Xuping Shentu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China Jiliang University, Hangzhou, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China Jiliang University, Hangzhou, China
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Zheng S, Zhao H, Yuan Z, Si X, Li Z, Song J, Zhu Y, Wu H. The Analysis of the Glycosyltransferase Gene Function From a Novel Granaticin Producer, Streptomyces Vilmorinianum. YP1. Curr Microbiol 2023; 80:103. [PMID: 36781498 DOI: 10.1007/s00284-023-03192-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 12/15/2022] [Indexed: 02/15/2023]
Abstract
Glycosylation is common among the synthesis of natural product and imparts the bioactivity for natural product. As for granaticin, a natural product with great bioactivity, glycosylation is an unusual sugar attachment and remains enigmatic. Orf14 in the gra cluster is the predicted glycosyltransferase but without being identified. Recently, we isolated and identified a novel granaticin producer Streptomyces vilmorinianum YP1. Orf14 gene in gra cluster of YP1 is knocked out and complemented. The instrumental analysis of the blue product synthesized by orf14-deficient mutant exhibits the none-granaticin detection and deglycosylated intermediates accumulation. The bioactivity and stability test suggests the weaker or none antibacterial activity and cytotoxicity of this blue product with greater ultraviolet stability and thermostability than granaticin and derivatives produced by YP1. All the result indicates that orf14 encodes glycosyltransferase and glycosylation played an important role in the bioactivity of granaticin. Meanwhile, the blue pigment, deglycosylated intermediates, has favorable processing characteristics. Our finding supplies the function of orf14 and glycosylation, but also indicates a promising candidate of edible blue pigment applicated in food industry.
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Affiliation(s)
- Shenglan Zheng
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Hongling Zhao
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Zuoyun Yuan
- Department of Science Technology and Innovation, Future Science and Technology Park South, COFCO Nutrition and Health Research Institute, BeiQiJia, ChangPing, BeiJing, 102209, China
| | - Xuechen Si
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Zongxian Li
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Jingyi Song
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, No.33, Fucheng Road, Beijing, 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, 100048, China
| | - Yunping Zhu
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, 100048, China.
- College of Food and Health, Beijing Technology and Business University, No. 33, Fucheng Road, Haidian District, Beijing, 100048, China.
| | - Hua Wu
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, No.33, Fucheng Road, Beijing, 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, 100048, China
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Liu J, Wang Y, He H, Dong S, Tang L, Yang E, Wang W, Zhang B. The leucine-responsive regulatory protein SCAB_Lrp modulates thaxtomin biosynthesis, pathogenicity, and morphological development in Streptomyces scabies. Mol Plant Pathol 2023; 24:167-178. [PMID: 36478143 PMCID: PMC9831280 DOI: 10.1111/mpp.13285] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/16/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Streptomyces scabies is the best-characterized plant-pathogenic streptomycete, which is a special species among the large genus Streptomyces. The pathogenicity of S. scabies relies on the production of the secondary metabolite thaxtomin A. Little is known about the molecular mechanisms underlying the regulation of thaxtomin biosynthesis in S. scabies beyond the pathway-specific activator TxtR and the cellulose utilization repressor CebR. The leucine-responsive regulatory protein (Lrp) family modulates secondary metabolism in nonpathogenic streptomycetes. However, the regulatory relationship between the Lrp and pathogenic streptomycetes remains unknown. In this study, we demonstrated that SCAB_Lrp (SCAB_77931) from S. scabies significantly affects thaxtomin biosynthesis, pathogenicity, and morphological development. SCAB_Lrp deletion resulted in a dramatic decline in thaxtomin A production and a low-virulence phenotype of S. scabies. An in-depth dissection of the regulatory mechanism of SCAB_Lrp revealed that it positively regulates the transcription of the thaxtomin biosynthetic gene cluster by directly binding to the promoter of the cluster-situated regulator gene txtR. SCAB_Lrp also controls the morphological development of S. scabies by directly activating the transcription of amfC, whiB, and ssgB. SCAB_Lrp directly controls the transcription of its own gene by binding a specific sequence (5'-GGACAGTCGCCGTGCTACG-3'). Moreover, phenylalanine and methionine have been characterized as SCAB_Lrp effectors by strengthening the binding affinity and complex status between SCAB_Lrp and DNA. Our findings characterize a multifunctional regulatory protein, SCAB_Lrp, that controls secondary metabolism, pathogenicity, and sporulation in S. scabies and provide new insights into the complex regulatory network that modulates thaxtomin phytotoxins in pathogenic Streptomyces.
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Affiliation(s)
- Jing Liu
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Yunxia Wang
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Haoyang He
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Shengnan Dong
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Lijuan Tang
- Institute of Physical Science and Information Technology, School of Life SciencesAnhui UniversityHefeiChina
| | - Endong Yang
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Weiyun Wang
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Buchang Zhang
- Institute of Physical Science and Information Technology, School of Life SciencesAnhui UniversityHefeiChina
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Martinet L, Naômé A, Rezende LCD, Tellatin D, Pignon B, Docquier JD, Sannio F, Baiwir D, Mazzucchelli G, Frédérich M, Rigali S. Lunaemycins, New Cyclic Hexapeptide Antibiotics from the Cave Moonmilk-Dweller Streptomyces lunaelactis MM109 T. Int J Mol Sci 2023; 24:ijms24021114. [PMID: 36674628 PMCID: PMC9866976 DOI: 10.3390/ijms24021114] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Streptomyces lunaelactis strains have been isolated from moonmilk deposits, which are calcium carbonate speleothems used for centuries in traditional medicine for their antimicrobial properties. Genome mining revealed that these strains are a remarkable example of a Streptomyces species with huge heterogeneity regarding their content in biosynthetic gene clusters (BGCs) for specialized metabolite production. BGC 28a is one of the cryptic BGCs that is only carried by a subgroup of S. lunaelactis strains for which in silico analysis predicted the production of nonribosomal peptide antibiotics containing the non-proteogenic amino acid piperazic acid (Piz). Comparative metabolomics of culture extracts of S. lunaelactis strains either holding or not holding BGC 28a combined with MS/MS-guided peptidogenomics and 1H/13C NMR allowed us to identify the cyclic hexapeptide with the amino acid sequence (D-Phe)-(L-HO-Ile)-(D-Piz)-(L-Piz)-(D-Piz)-(L-Piz), called lunaemycin A, as the main compound synthesized by BGC 28a. Molecular networking further identified 18 additional lunaemycins, with 14 of them having their structure elucidated by HRMS/MS. Antimicrobial assays demonstrated a significant bactericidal activity of lunaemycins against Gram-positive bacteria, including multi-drug resistant clinical isolates. Our work demonstrates how an accurate in silico analysis of a cryptic BGC can highly facilitate the identification, the structural elucidation, and the bioactivity of its associated specialized metabolites.
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Affiliation(s)
- Loïc Martinet
- InBioS—Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000 Liege, Belgium
- Hedera-22, Boulevard du Rectorat 27b, B-4000 Liege, Belgium
| | - Aymeric Naômé
- InBioS—Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000 Liege, Belgium
- Hedera-22, Boulevard du Rectorat 27b, B-4000 Liege, Belgium
| | | | - Déborah Tellatin
- InBioS—Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000 Liege, Belgium
| | - Bernard Pignon
- InBioS—Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000 Liege, Belgium
| | - Jean-Denis Docquier
- InBioS—Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000 Liege, Belgium
- Dipartimento di Biotecnologie Mediche, University of Siena, Viale Bracci 16, 53100 Siena, Italy
| | - Filomena Sannio
- Dipartimento di Biotecnologie Mediche, University of Siena, Viale Bracci 16, 53100 Siena, Italy
| | - Dominique Baiwir
- GIGA Proteomics Facility, University of Liege, B-4000 Liege, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, B-4000 Liege, Belgium
| | - Michel Frédérich
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines (CIRM), University of Liege, B-4000 Liege, Belgium
| | - Sébastien Rigali
- InBioS—Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000 Liege, Belgium
- Hedera-22, Boulevard du Rectorat 27b, B-4000 Liege, Belgium
- Correspondence:
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Rebets Y, Kormanec J, Lutzhetskyy A, Bernaerts K, Anné J. Cloning and Expression of Metagenomic DNA in Streptomyces lividans and Its Subsequent Fermentation for Optimized Production. Methods Mol Biol 2023; 2555:213-260. [PMID: 36306090 DOI: 10.1007/978-1-0716-2795-2_16] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The choice of an expression system for the metagenomic DNA of interest is of vital importance for the detection of any particular gene or gene cluster. Most of the screens to date have used the Gram-negative bacterium Escherichia coli as a host for metagenomic gene libraries. However, the use of E. coli introduces a potential host bias since only 40% of the enzymatic activities may be readily recovered by random cloning in E. coli. To recover some of the remaining 60%, alternative cloning hosts such as Streptomyces spp. have been used. Streptomycetes are high-GC Gram-positive bacteria belonging to the Actinomycetales and they have been studied extensively for more than 25 years as an alternative expression system. They are extremely well suited for the expression of DNA from other actinomycetes and genomes of high GC content. Furthermore, due to its high innate, extracellular secretion capacity, Streptomyces can be a better system than E. coli for the production of many extracellular proteins. In this article, an overview is given about the materials and methods for growth and successful expression and secretion of heterologous proteins from diverse origin using Streptomyces lividans as a host. More in detail, an overview is given about the protocols of transformation, type of plasmids used and of vectors useful for integration of DNA into the host chromosome, and accompanying cloning strategies. In addition, various control elements for gene expression including synthetic promoters are discussed, and methods to compare their strength are described. Stable and efficient marker-less integration of the gene of interest under the control of the promoter of choice into S. lividans chromosome via homologous recombination using pAMR23A-based system will be explained. Finally, a basic protocol for bench-top bioreactor experiments which can form the start in the production process optimization and up-scaling will be provided.
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Affiliation(s)
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Andriy Lutzhetskyy
- Department of Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), University of Saarland, Saarbrücken, Germany
| | - Kristel Bernaerts
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety Division, KU Leuven, Leuven, Belgium
| | - Jozef Anné
- Department of Microbiology, Immunology and Transplantation, lab. Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium.
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Yang M, Zhang W, Lv Z, Shi L, Zhang K, Ge B. Induced Defense Response in Soybean to Sclerotinia sclerotiorum Using Wuyiencin from Streptomyces albulus CK-15. Plant Dis 2023; 107:107-115. [PMID: 35771107 DOI: 10.1094/pdis-03-22-0582-re] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Sclerotinia sclerotiorum (Lib) de Bary, a destructive fungal pathogen with an extensive host range, causes major economic losses to crop production activities globally. Streptomyces spp. produce secondary metabolites with diverse structures and biological activities with potential applications in the control of crop disease. This study explored the potential application of wuyiencin, a secondary metabolite of Streptomyces albulus CK-15, to induce defense responses in soybean against S. sclerotiorum. Lesion size was reduced by nearly 60% in wuyiencin-treated soybean plants compared with plants infected with S. sclerotiorum only in greenhouse experiments. Wuyiencin induced callose deposition at 6 h postinoculation and increased reactive-oxygen-scavenging enzyme activities, including superoxide dismutase, catalase, and peroxidase. Moreover, wuyiencin inoculated before S. sclerotiorum infection significantly increased polyphenol oxidase, phenylalanine ammonia lyase, chitinase, and β-1,3-glucanase activity, suggesting their involvement in soybean defense responses to S. sclerotiorum. Further, qRT-PCR results showed expression levels of the hormone signaling markers CO11, MYC2, PR4, PR1, NPR1, and ERF1 were upregulated in infected leaves treated with wuyiencin.
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Affiliation(s)
- Miaoling Yang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Wei Zhang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Zhaoyang Lv
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Liming Shi
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Kecheng Zhang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Beibei Ge
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
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Li Y, Xu Z, Chen L, Zhu M, Wang D, Jing M, Chen Y, Sun Z, Wang Y, He B, Yan W, Jiao R, Ye Y. New metabolites from Streptomyces pseudovenezuelae NA07424 and their potential activity of inducing resistance in plants against Phytophthora capsici. Pest Manag Sci 2023; 79:349-356. [PMID: 36153708 DOI: 10.1002/ps.7204] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 09/19/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The lack of novel fungicide and appearance of resistance are the most emergent problems in the control of Phytophthora diseases. Plant immunity elicitors that induce systemic resistance in plants are regarded as the new strategy for plant disease control. Streptomyces can produce a variety of bioactive natural products, which are important resources for lead compounds of plant immunity elicitors. RESULTS A novel peptidendrocin C (1) together with the known analog peptidendrocin B (2) were isolated from Streptomyces pseudovenezuelae NA07424. Their structures were confirmed by spectroscopic data and Marfey's reaction. In bioactive assays, compound 1 played an important role in inducing systemic resistance of Nicotiana benthamiana against Phytophthora capsici growth, with a 90.5% inhibition ratio at 400 μg/mL, while compound 2 showed moderate activity, inhibiting P. capsici growth by a 50.8% decrease at 400 μg/mL. Simultaneously, two compounds promoted enhanced expression of the PR1 gene and callose accumulation in N. benthamiana and Arabidopsis thaliana. In this paper, we also provide the first insights into their biosynthesis by confirming their biosynthesis gene cluster and related functional genes. CONCLUSION Our findings show that 1 and 2 have the potential to be used as lead compounds for development of new plant immunity elicitors to control Phytophthora diseases. The study of the biosynthesis pathway lays the groundwork for further application of the bioactive natural products. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Yu Li
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, P. R. China
| | - Zifei Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing, China
| | - Liyifan Chen
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, P. R. China
| | - Mengyue Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing, China
| | - Dacheng Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
| | - Maofeng Jing
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yiliang Chen
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, P. R. China
| | - Ziqian Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yiming Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
| | - Bo He
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, P. R. China
| | - Wei Yan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, P. R. China
| | - Ruihua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yonghao Ye
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, P. R. China
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Kresna IDM, Wuisan ZG, Schäberle TF. Production of Antimicrobial Compounds by Homologous and Heterologous Expression. Methods Mol Biol 2023; 2601:55-73. [PMID: 36445579 DOI: 10.1007/978-1-0716-2855-3_4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Natural product discovery campaigns aim to identify compounds with the desired bioactivity, for example, metabolites with antibiotic activity. The major driver of many projects is still the finding of bioactive extracts, which will be followed up to isolate the activity-causing agent as pure compound. However, nowadays also additional strategies can be used to increase the probability of success. Metabolomic approaches indicate chemical novelty, and genomics allow identification of putative biosynthetic gene clusters (BGCs) of interest, even though the corresponding metabolite is unknown. Whatever the entry to the campaign is, at one point the scientists need to have the desired compound in hand to analyze it in detail. Hence, expression must be achieved to yield the compound of interest, either to link it to the corresponding putative BGC or to overcome the bottleneck of sparse compound supply. Therefore, homologous and heterologous expression approaches are feasible ways forward to increase production yield, shorten fermentation time, or to get BGCs expressed at all for which no suitable fermentation condition was identified.In this chapter, expression approaches in bacteria are described to biosynthesize compounds of interest. Homologous expression, by genetic manipulation of the original Streptomyces producer strain, and heterologous expression in the microbial workhorse Escherichia coli are exemplified.
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Affiliation(s)
- I Dewa M Kresna
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Zerlina G Wuisan
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, Giessen, Germany
- German Center of Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, Giessen, Germany.
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany.
- German Center of Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany.
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127
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Antonov IV, O’Loughlin S, Gorohovski AN, O’Connor PB, Baranov PV, Atkins JF. Streptomyces rare codon UUA: from features associated with 2 adpA related locations to candidate phage regulatory translational bypassing. RNA Biol 2023; 20:926-942. [PMID: 37968863 PMCID: PMC10732093 DOI: 10.1080/15476286.2023.2270812] [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: 11/17/2022] [Accepted: 10/02/2023] [Indexed: 11/17/2023] Open
Abstract
In Streptomyces species, the cell cycle involves a switch from an early and vegetative state to a later phase where secondary products including antibiotics are synthesized, aerial hyphae form and sporulation occurs. AdpA, which has two domains, activates the expression of numerous genes involved in the switch from the vegetative growth phase. The adpA mRNA of many Streptomyces species has a UUA codon in a linker region between 5' sequence encoding one domain and 3' sequence encoding its other and C-terminal domain. UUA codons are exceptionally rare in Streptomyces, and its functional cognate tRNA is not present in a fully modified and acylated form, in the early and vegetative phase of the cell cycle though it is aminoacylated later. Here, we report candidate recoding signals that may influence decoding of the linker region UUA. Additionally, a short ORF 5' of the main ORF has been identified with a GUG at, or near, its 5' end and an in-frame UUA near its 3' end. The latter is commonly 5 nucleotides 5' of the main ORF start. Ribosome profiling data show translation of that 5' region. Ten years ago, UUA-mediated translational bypassing was proposed as a sensor by a Streptomyces phage of its host's cell cycle stage and an effector of its lytic/lysogeny switch. We provide the first experimental evidence supportive of this proposal.
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Affiliation(s)
- Ivan V. Antonov
- Russian Academy of Science, Institute of Bioengineering, Research Center of Biotechnology, Moscow, Russia
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Sinéad O’Loughlin
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Alessandro N. Gorohovski
- Russian Academy of Science, Institute of Bioengineering, Research Center of Biotechnology, Moscow, Russia
- Structural Biology and BioComputing Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Pavel V. Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - John F. Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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Alam K, Islam MM, Islam S, Hao J, Abbasi MN, Hayat M, Shoaib M, Zhang Y, Li A. Comparative genomics with evolutionary lineage in Streptomyces bacteria reveals high biosynthetic potentials. World J Microbiol Biotechnol 2022; 39:64. [PMID: 36581678 DOI: 10.1007/s11274-022-03433-y] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/06/2022] [Indexed: 12/31/2022]
Abstract
Genome mining in silico approaches allow scientists to proficiently evaluate the genomic potency of secondary bioactive chemical producers and find new bioactive compounds in different bacteria. Streptomyces is one of the most ubiquitous bacterial genera in the environments, and well-known as prolific producers of diverse and valuable natural products (NPs) with significant biological activities. Mining and prioritizing of NP biosynthetic gene clusters (BGCs) would be the most important stage in the identification of novel compounds. Comparative genomics and genetic similarity network analysis of 62 Streptomyces public reference genomes demonstrated that individuals of these species exhibit a huge number of distinct NP BGCs, the most of which are cryptic and unconnected to any reported NPs with high phylogenetic variation among individuals. It was assumed that substantial heterogeneity across the varieties of species of Streptomyces drives outstanding biosynthetic and metabolic potential, making them plausible candidates for the identification of novel molecules.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Md Mahmudul Islam
- Department of Microbiology, Rajshahi Institute of Biosciences (RIB), Affiliated University of Rajshahi, Rajshahi, 6212, Bangladesh
| | - Saiful Islam
- Chattogram Laboratories, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram, 4220, Bangladesh
| | - Jinfang Hao
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Muhammad Nazeer Abbasi
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Muhammad Hayat
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Muhammad Shoaib
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237, People's Republic of China.
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129
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Goel N, Singh R, Sood S, Khare SK. Investigation of Streptomyces sp. Strain EMB24 Secondary Metabolite Profile Has Unraveled Its Extraordinary Antibacterial Potency Against Drug-Resistant Bacteria. Mar Biotechnol (NY) 2022; 24:1168-1175. [PMID: 36220897 PMCID: PMC9553293 DOI: 10.1007/s10126-022-10168-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
With the overuse and misuse of antibiotics amid COVID-19 pandemic, the antimicrobial resistance, which is already a global challenge, has accelerated its pace significantly. Finding novel and potential antibiotics seems one of the probable solutions. In this work, a novel Streptomyces sp. strain EMB24 was isolated and found to be an excellent source of antimicrobials as confirmed by agar-plug assay. It showed antibacterial activity against infection-causing bacteria, namely Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. In addition, Streptomyces sp. strain EMB24 inhibited the growth methicillin-resistant Staphylococcus aureus (MRSA), tetracycline-resistant Neisseria gonorrhoeae, and ampicillin-resistant Neisseria gonorrhoeae. Furthermore, to get deep insights about the genome and biosynthetic gene clusters producing antibiotics, whole genome sequencing was done. The strain EMB24 is closely related to the Streptomyces longispororuber as revealed by phylogenetic analysis which is a potential source of antibiotics and pigments as undecylprodigiosin and metacycloprodigiosin belonging to the class prodigiosin. Naphthyridinomycin, alkylresorcinols, desferrioxamine B and E, venezuelin, aborycin, MS-271, and siamycin are potent therapeutics that shared 100% similarity with the reference strain as revealed by the online antiSMASH tool.
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Affiliation(s)
- Nikky Goel
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Rajendra Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Seema Sood
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sunil Kumar Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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130
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Tsunoda T, Asamizu S, Mahmud T. Biochemical Characterization of GacI, a Bifunctional Glycosyltransferase-Phosphatase Enzyme Involved in Acarbose Biosynthesis in Streptomyces glaucescens GLA.O. Biochemistry 2022; 61:2628-2635. [PMID: 36288494 PMCID: PMC9669214 DOI: 10.1021/acs.biochem.2c00473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acarbose, a pseudotetrasaccharide produced by several strains of Actinoplanes and Streptomyces, is an α-glucosidase inhibitor clinically used to control type II diabetes. Bioinformatic analysis of the biosynthetic gene clusters of acarbose in Actinoplanes sp. SE50/110 (the acb cluster) and Streptomyces glaucescens GLA.O (the gac cluster) revealed their distinct genetic organizations and presumably biosynthetic pathways. However, to date, only the acarbose pathway in the SE50/110 strain has been extensively studied. Here, we report that GacI, one of the proteins that appear to be different between the two pathways, is a bifunctional glycosyltransferase family 5 (GT5)-phosphatase (PP) enzyme that functions at two different steps in acarbose biosynthesis in S. glaucescens GLA.O. In the acb pathway, the GT and the PP reactions are performed by two different enzymes. Truncated GacI proteins having only the GT or the PP domain showed comparable catalytic activity with the full-length GacI, indicating that domain separation does not significantly affect their respective catalytic activity. GacI, which is widely distributed in many Streptomyces, represents the first example of naturally occurring GT5-PP bifunctional enzymes biochemically characterized.
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Affiliation(s)
- Takeshi Tsunoda
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Shumpei Asamizu
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
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131
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Cuervo L, Méndez C, Salas JA, Olano C, Malmierca MG. Volatile Compounds in Actinomycete Communities: A New Tool for Biosynthetic Gene Cluster Activation, Cooperative Growth Promotion, and Drug Discovery. Cells 2022; 11:3510. [PMID: 36359906 PMCID: PMC9655753 DOI: 10.3390/cells11213510] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 07/30/2023] Open
Abstract
The increasing appearance of multiresistant pathogens, as well as emerging diseases, has highlighted the need for new strategies to discover natural compounds that can be used as therapeutic alternatives, especially in the genus Streptomyces, which is one of the largest producers of bioactive metabolites. In recent years, the study of volatile compounds (VOCs) has raised interest because of the variety of their biological properties in addition to their involvement in cell communication. In this work, we analyze the implications of VOCs as mediating molecules capable of inducing the activation of biosynthetic pathways of bioactive compounds in surrounding Actinomycetes. For this purpose, several strains of Streptomyces were co-cultured in chamber devices that allowed VOC exchange while avoiding physical contact. In several of those strains, secondary metabolism was activated by VOCs emitted by companion strains, resulting in increased antibiotic production and synthesis of new VOCs. This study shows a novel strategy to exploit the metabolic potential of Actinomycetes as well as emphasizes the importance of studying the interactions between different microorganisms sharing the same ecological niche.
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Affiliation(s)
- Lorena Cuervo
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Carmen Méndez
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - José A. Salas
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Carlos Olano
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Mónica G. Malmierca
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
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132
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Clarke CR, Kramer CG, Kotha RR, Luthria DL. The Phytotoxin Thaxtomin A Is the Primary Virulence Determinant for Scab Disease of Beet, Carrot, and Radish Caused by Streptomyces scabiei. Phytopathology 2022; 112:2288-2295. [PMID: 35694886 DOI: 10.1094/phyto-03-22-0072-r] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Several species of Streptomyces cause common scab, a major disease of potato, primarily through the phytotoxic effects of the phytotoxin thaxtomin A. Several phytopathogenic Streptomyces species have also been implicated as the causative agents of scab diseases of taproot crops including beet, carrot, radish, parsnip, and turnip. But the molecular mechanisms employed by Streptomyces to infect these crops is unknown. In this work, we tested the hypothesis that thaxtomin A biosynthesis is also necessary for Streptomyces-caused scab of beet, carrot, radish, and turnip. Thaxtomin A induced plant stunting and cell death of all four of these species. Streptomyces mutants in which the transcriptional regulator of thaxtomin A biosynthesis is disrupted were nonvirulent on all four crops, and complementation of the transcriptional regulator rescued thaxtomin A biosynthesis and plant pathogenicity to wild-type levels. These results demonstrate that thaxtomin A is the primary virulence determinant of scab disease of these other crops.
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Affiliation(s)
- Christopher R Clarke
- Genetic Improvement for Fruits and Vegetables Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD
| | - Charles G Kramer
- Genetic Improvement for Fruits and Vegetables Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD
| | - Raghavendhar R Kotha
- Food Composition and Methods Development Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD
| | - Devanand L Luthria
- Food Composition and Methods Development Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD
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133
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Abbasi S, Nasirzadeh F, Boojar MMA, Kafi SA, Karimi E, Khelghatibana F, Sadeghi A. Streptomyces strains can improve the quality properties and antifungal bioactivities of tomato fruits by impacting WRKY70 transcription factor gene and nitrate accumulation. Plant Physiol Biochem 2022; 188:31-37. [PMID: 35964362 DOI: 10.1016/j.plaphy.2022.07.033] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/09/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
The current study evaluated the effect of plant growth-promoting (PGP) strains of Streptomyces on yield, quality, and nitrate content of fruits, plant-microbe responses, and antifungal effect against blight disease caused by fungus pathogen Alternaria solani on tomato fruits in commercial greenhouse conditions. Greenhouse trials were done with four treatments including strains Y28, IC10, IT25, and commercial bio-fertilizer (Barvar NPK®) on tomato plants. In PGP treatments, the number of infected fruits significantly reduced (60%) compared to Barvar and control. Strain Y28 improved the quality of tomatoes more than other treatments. All three PGP treatments contained a higher level of total sugar concentration and antioxidant enzyme activities than Barvar and control. In contrast, PGP strains, especially Y28, significantly reduced nitrate accumulation (25%) compared to Barvar and control tomatoes. Streptomyces treatments induced more than a 20-fold increase in UDP and WRKY70 transcription factor gene expression relative to the control (P < 0.01). Based on the results, microbe-dependent plant defense induced by these strains is positively correlated to WRKY70 expression and nitrate reduction in commercial greenhouse conditions. These findings suggest that the commercial application of specific strains not only can illustrate an eco-friendly solution to induce resistance against fungal pathogens but also improve the quality properties of food plants with lower nitrate content.
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Affiliation(s)
- Sakineh Abbasi
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran; Department of Microbial Biotechnology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Farhad Nasirzadeh
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | | | - Sahar Alipour Kafi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Ebrahim Karimi
- Department of Microbial Biotechnology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Fatemeh Khelghatibana
- Plant Protection Lab, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Akram Sadeghi
- Department of Microbial Biotechnology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
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134
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Anupong W, Jutamas K, On-Uma R, Sabour A, Alshiekheid M, Karuppusamy I, Lan Chi NT, Pugazhendhi A. Sustainable bioremediation approach to treat the sago industry effluents and evaluate the possibility of yielded biomass as a single cell protein (SCP) using cyanide tolerant Streptomyces tritici D5. Chemosphere 2022; 304:135248. [PMID: 35679978 DOI: 10.1016/j.chemosphere.2022.135248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/23/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
This sustainable approach was performed to evaluate the bioremediation potential of cyanide resistant bacterial species on sago industry effluents and assess the possibility of using the yielded biomass as single cell protein (SCP). The predominant cyanide tolerant bacterium enumerated from muddy soil was identified as Streptomyces tritici D5 through 16S rRNA sequencing. The identified S. tritici D5 strains showed excellent resistant and degradation potential at 100 mM concentration of potassium cyanide. Furthermore, the physicochemical properties analysis of sago industry effluents results revealed that the most of the parameters were crossing the permissible limits of Pollution control board of India. The bioremediation process was performed at various temperatures at 25 °C, 35 °C, and 45 °C for a period of 30 days of continuous bioremediation process with the aid of an aerator. Surprisingly, the best organic pollutant reduction was found at 35 °C and 45 °C, with 25 °C following close behind. Remarkably, the dissolved oxygen (DO) level was gradually increased from 2.24 to 12.04 mg L-1 at 35 °C in 30 days of the remediation process. The pH and ammonia were also significantly increased during the bioremediation process in 30 days of treatment. Similarly, at 35 °C of bioremediation process the S. tritici D5 yielded maximum dried biomass (6.9 g L-1) with the total crude protein (SCP) as 4.8 g L-1 (69.56%) in 30 days of growth. These findings stated that S. tritici D5 can treat sago industry effluents and that the biomass produced may be considered SCP after some in-vitro and in-vivo analyses.
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Affiliation(s)
- Wongchai Anupong
- Department of Agricultural Economy and Development, Faculty of Agriculture, Chiang Mai University, 50200, Thailand; Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Khumchai Jutamas
- Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, 50200, Thailand; Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Ruangwong On-Uma
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, 50200, Thailand; Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Amal Sabour
- Department of Botany and Microbiology, College of Science, King Saud University, PO Box -2455, Riyadh, 11451, Saudi Arabia
| | - Maha Alshiekheid
- Department of Botany and Microbiology, College of Science, King Saud University, PO Box -2455, Riyadh, 11451, Saudi Arabia
| | - Indira Karuppusamy
- Research Center for Strategic Materials, Corrosion Resistant Steel Group, National Institute for Materials Science (NIMS), Tsukuba, Japan
| | - Nguyen Thuy Lan Chi
- School of Engineering and Technology, Van Lang University, Ho Chi Minh City, Vietnam.
| | - Arivalagan Pugazhendhi
- Emerging Materials for Energy and Environmental Applications Research Group, School of Engineering and Technology, Van Lang University, Ho Chi Minh City, Vietnam.
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135
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Feng S, Dong P, Jin L, Li Z. Complete Genome Sequence Data of a Newly Isolated Streptomyces violascens Strain A10, a Potential Biological Control Agent for Fungal and Oomycete Diseases. Plant Dis 2022; 106:2498-2501. [PMID: 35895328 DOI: 10.1094/pdis-11-21-2561-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Shun Feng
- School of Horticulture, Hainan University, Haikou 570228, China
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Pan Dong
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Liang Jin
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
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136
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Yun T, Jing T, Zhou D, Zhang M, Zhao Y, Li K, Zang X, Zhang L, Xie J, Wang W. Potential Biological Control of Endophytic Streptomyces sp. 5-4 Against Fusarium Wilt of Banana Caused by Fusarium oxysporum f. sp. cubense Tropical Race 4. Phytopathology 2022; 112:1877-1885. [PMID: 35471064 DOI: 10.1094/phyto-11-21-0464-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fusarium wilt of banana caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is one of the most disastrous fungal diseases. Biological control is a promising strategy for controlling Fusarium wilt of banana. To explore endophytic actinomycetes as biocontrol resources against Foc TR4, antagonistic strains were isolated from different tissues of medicinal plants. Here, a total of 144 actinomycetes were isolated and belonged to Nonomuraea, Kitasatospora, and Streptomyces. Forty-three isolates exhibited antifungal activities against Foc TR4. The strain labeled with 5-4 isolated from roots of Piper austrosinense had a broad-spectrum antifungal activity by the production of chitinase and β-1,3-glucanase and was identified as Streptomyces hygroscopicus subsp. hygroscopicus 5-4. Furthermore, disease index of banana wilt was significantly reduced by application of strain 5-4 in comparison with application of Foc TR4 alone. Exogenous application of strain 5-4 increased the expression levels of defense genes such as (PAL), peroxidase (POD), pathogenesis-related protein 1 (PR-1), hydrolytic enzymes (β-1,3-glucanase), lysin motif receptor kinase 1 (LYK-1), and mitogen-activated protein kinase 1 (MPK-1). The antifungal mechanism assay demonstrated that extracts of strain 5-4 inhibited spore gemination and hyphal growth of Foc TR4, and caused abnormally swollen, deformity, and rupture of Foc TR4 hypha. Thus, S. hygroscopicus subsp. hygroscopicus 5-4 could be used as a potential biological agent for controlling Fusarium wilt of banana.
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Affiliation(s)
- Tianyan Yun
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Tao Jing
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Dengbo Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
| | - Miaoyi Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
| | - Yankun Zhao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
| | - Kai Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
| | - Xiaoping Zang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Lu Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Jianghui Xie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
| | - Wei Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
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Zhou W, Alharbi HA, Hummingbird E, Keatinge-Clay AT, Mahmud T. Functional Studies and Revision of the NFAT-133/TM-123 Biosynthetic Pathway in Streptomyces pactum. ACS Chem Biol 2022; 17:2039-2045. [PMID: 35904416 PMCID: PMC9391300 DOI: 10.1021/acschembio.2c00454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biosynthetic gene cluster of NFAT-133, an inhibitor of the nuclear factor of activated T cells, was recently identified in Streptomyces pactum ATCC 27456. This cluster is conspicuous by its highly disordered noncollinear type I modular polyketide synthase (PKS) genes that encode PKSs with one module more than those expected for the heptaketide NFAT-133 biosynthesis. Thus, the major metabolite NFAT-133 was proposed to derive from an octaketide analogue, TM-123. Here, we report that further bioinformatic analysis and gene inactivation studies suggest that NFAT-133 is not derived from TM-123 but rather a product of programmed KS7 extension skipping of a nascent heptaketide from the PKS assembly line that produces TM-123. Furthermore, identification of NFAT-133/TM-123 analogues from mutants of the ATCC 27456 strain suggests that NftN (a putative dehydrogenase), NftE (a cytochrome P450), and NftG (a putative hydrolase/decarboxylase) function "in trans" during the polyketide chain assembly processes.
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Affiliation(s)
- Wei Zhou
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Hattan A. Alharbi
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Eshe Hummingbird
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | | | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
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McHugh RE, Munnoch JT, Braes RE, McKean IJW, Giard J, Taladriz-Sender A, Peschke F, Burley GA, Roe AJ, Hoskisson PA. Biosynthesis of Aurodox, a Type III Secretion System Inhibitor from Streptomyces goldiniensis. Appl Environ Microbiol 2022; 88:e0069222. [PMID: 35867559 PMCID: PMC9361827 DOI: 10.1128/aem.00692-22] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/26/2022] [Indexed: 11/20/2022] Open
Abstract
The global increase in antimicrobial-resistant infections means that there is a need to develop new antimicrobial molecules and strategies to combat the issue. Aurodox is a linear polyketide natural product that is produced by Streptomyces goldiniensis, yet little is known about aurodox biosynthesis or the nature of the biosynthetic gene cluster (BGC) that encodes its production. To gain a deeper understanding of aurodox biosynthesis by S. goldiniensis, the whole genome of the organism was sequenced, revealing the presence of an 87 kb hybrid polyketide synthase/non-ribosomal peptide synthetase (PKS/NRPS) BGC. The aurodox BGC shares significant homology with the kirromycin BGC from S. collinus Tϋ 365. However, the genetic organization of the BGC differs significantly. The candidate aurodox gene cluster was cloned and expressed in a heterologous host to demonstrate that it was responsible for aurodox biosynthesis and disruption of the primary PKS gene (aurAI) abolished aurodox production. These data supported a model whereby the initial core biosynthetic reactions involved in aurodox biosynthesis followed that of kirromycin. Cloning aurM* from S. goldiniensis and expressing this in the kirromycin producer S. collinus Tϋ 365 enabled methylation of the pyridone group, suggesting this is the last step in biosynthesis. This methylation step is also sufficient to confer the unique type III secretion system inhibitory properties to aurodox. IMPORTANCE Enterohemorrhagic Escherichia coli (EHEC) is a significant global pathogen for which traditional antibiotic treatment is not recommended. Aurodox inhibits the ability of EHEC to establish infection in the host gut through the specific targeting of the type III secretion system while circumventing the induction of toxin production associated with traditional antibiotics. These properties suggest aurodox could be a promising anti-virulence compound for EHEC, which merits further investigation. Here, we characterized the aurodox biosynthetic gene cluster from Streptomyces goldiniensis and established the key enzymatic steps of aurodox biosynthesis that give rise to the unique anti-virulence activity. These data provide the basis for future chemical and genetic approaches to produce aurodox derivatives with increased efficacy and the potential to engineer novel elfamycins.
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Affiliation(s)
- Rebecca E. McHugh
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - John T. Munnoch
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Robyn E. Braes
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Iain J. W. McKean
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Josephine Giard
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | | | - Frederik Peschke
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Glenn A. Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Andrew J. Roe
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
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139
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Liang Q, Liu G, Guo Z, Wang Y, Xu Z, Ren Y, Zhang Q, Cui M, Zhao X, Xu D. Application of potential probiotic strain Streptomyces sp. SH5 on anti-Aeromonas infection in zebrafish larvae. Fish Shellfish Immunol 2022; 127:375-385. [PMID: 35777708 DOI: 10.1016/j.fsi.2022.06.049] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/11/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Pre-treatment of Streptomyces sp. SH5 on zebrafish lead to a significant enhancement of larvae survival upon Aeromonas hydrophila challenging. SH5 was able to colonize in zebrafish approximately at 1 × 102.6 cells per fish for at least seven days. The presence of SH5 strongly repelled the A. hydrophila colonization in zebrafish, and maximally, a 67.53% reduction rate was achieved. A more diversified flora was discovered in the SH5-treated zebrafish larvae at both phylum and genus levels. The expression of immune response genes of SH5-treated zebrafish, including TLR3, lysozyme and NOS2α, were enhanced at initial stage, while, that of various inflammatory stimuli genes including 1L-1β, 1L-6 and MyD88 were decreased at all tested timepoints. SH5 was shown to inhibit virulence factors production and the expression of corresponding virulence genes in A. hydrophila, suggesting its quorum sensing inhibitory potential. These results indicated favorable application perspectives of SH5 in resisting pathogenic infection in aquaculture.
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Affiliation(s)
- Qiting Liang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, PR China; State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Key Laboratory of Drinking Water Source Safety Control, Shenzhen Academy of Environmental Sciences, Shenzhen, 518001, PR China
| | - Ganxing Liu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, PR China
| | - Zheng Guo
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, PR China
| | - Yuting Wang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, PR China
| | - Zhongheng Xu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, PR China
| | - Yuxian Ren
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, PR China
| | - Qizhong Zhang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, PR China.
| | - Miao Cui
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, PR China.
| | - Xinqing Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
| | - Delin Xu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, PR China.
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Luković J, Potočnik I, Šantrić L, Radivojević L, Todorović B, Milijašević-Marčić S, Szűcs A, Kredics L, Vágvölgyi C, Hatvani L. Response of the mushroom pathogen Cladobotryum mycophilum to prochloraz and metrafenone fungicides and Streptomyces flavovirens actinobacteria. J Environ Sci Health B 2022; 57:636-643. [PMID: 35833259 DOI: 10.1080/03601234.2022.2096360] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
After an outbreak of cobweb disease of cultivated button mushroom in Serbia in 2003, the isolated fungal pathogen was initially identified as Cladobotryum dendroides (teleomorph Hypomyces rosellus) based on morpho-physiological traits. Molecular analysis indicated re-classification of two strains (isolated in 2004 and 2007) as Cladobotryum mycophilum (teleomorph Hypomyces odoratus). However, subsequent analysis of further five strains (isolated over the period 2003-2010) within the frames of the present study, also confirmed their identification as the exclusive cobweb causal agent C. mycophilum. After artificial inoculation, the symptoms observed on harvested and growing mushrooms were consistent with the appearance of cobweb disease. Pathogen sensitivity to fungicides was estimated by probit analyses. Fungicide susceptibility tests showed that C. mycophilum strains were highly sensitive both to prochloraz (ED50<0.087 µg mL-1) and the newly introduced metrafenone (ED50<0.15 µg mL-1). Furthermore, the growth of all examined strains of C. mycophilum was significantly inhibited by the indigenous actinobacterial strain Streptomyces flavovirens A06. A dual culture assay showed after 72 h that the percentage of radial growth inhibition of the pathogen ranged from 22.38 to 55.73%. Our findings suggest that the antagonistic S. flavovirens A06 might be a potential candidate for controlling the cobweb disease of cultivated button mushroom.
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Affiliation(s)
- Jelena Luković
- Institute of Pesticides and Environmental Protection, Belgrade, Serbia
| | - Ivana Potočnik
- Institute of Pesticides and Environmental Protection, Belgrade, Serbia
| | - Ljiljana Šantrić
- Institute of Pesticides and Environmental Protection, Belgrade, Serbia
| | | | - Biljana Todorović
- Institute of Pesticides and Environmental Protection, Belgrade, Serbia
| | | | - Attila Szűcs
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Lóránt Hatvani
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
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141
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Li W, Ding L, Li J, Wen H, Liu Y, Tan S, Yan X, Shi Y, Lin W, Lin HW, He S. Novel Antimycin Analogues with Agricultural Antifungal Activities from the Sponge-Associated Actinomycete Streptomyces sp. NBU3104. J Agric Food Chem 2022; 70:8309-8316. [PMID: 35773185 DOI: 10.1021/acs.jafc.2c02626] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Phytopathogenic fungi could affect the growth of agricultural products and result in serious economic losses. To develop novel and potent fungicides, secondary metabolites of an oceanic mesophotic zone Streptomyces sp. NBU3104 was isolated by metabolomics and genomics, which led to the discovery of eight novel antimycins I-P (1-8), including antimycin I (1), six rare acetylated actimycins J-N (2-6), P (8), and an unusual deformylated antimycin O (7). The chemical structures of these metabolites were identified using nuclear magnetic resonance (NMR) spectroscopic analysis, high-resolution electrospray ionization mass spectrometry (HRESIMS) data, and the known reported metabolites in the literature. Their absolute configurations were elucidated by comparison of coupling constant and experimental electronic circular dichroism (ECD) spectra. Among them, compound 1 exhibited excellent inhibitory activities against phytopathogenic fungi, such as Candida albicans, Penicillium expansum, Penicillium citrinum, and Botrytis cinerea. Furthermore, compound 1 could effectively control gray mold of apple in vivo (minimum inhibitory concentration (MIC) = 8 μg/mL). The structure-activity relations of antimycins I-P (1-8) suggested that the aldehyde group in 3-formamidosalicylate unit moiety should be the key factor in their antifungal activities.
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Affiliation(s)
- Wenhao Li
- Department of Marine Pharmacy, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Lijian Ding
- Department of Marine Pharmacy, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Juan Li
- Department of Marine Pharmacy, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Huimin Wen
- Department of Marine Pharmacy, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Yang Liu
- Department of Marine Pharmacy, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Shuangling Tan
- Department of Marine Pharmacy, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Xiaojun Yan
- Department of Marine Pharmacy, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Yutong Shi
- Department of Marine Pharmacy, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Wenhan Lin
- Ningbo Institute of Marine Medicine, Peking University, Ningbo 315800, China
| | - Hou-Wen Lin
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Shan He
- Department of Marine Pharmacy, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
- Ningbo Institute of Marine Medicine, Peking University, Ningbo 315800, China
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142
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A Zaki M, A Saleh ES, M Zaki M, S Korayem A, A Amin S. Antibacterial Activity of a New Strain of Streptomyces maritimus MSQ21 against Ralstonia solanacearum. Pak J Biol Sci 2022; 25:642-653. [PMID: 36098171 DOI: 10.3923/pjbs.2022.642.653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
<b>Background and Objective:</b> Actinobacteria represent the most prominent group of microorganisms, which produce a vast number of bioactive compounds especially antibiotics. The present study investigated the antibacterial activity of some actinomycete isolates against <i>Ralstonia solanacearum</i> type 3 biovar 2 (phytopathogenic bacterium that causes tomato wilt disease and brown rot of potatoes). <b>Materials and Methods:</b> The most potent actinomycete isolates in the antibacterial activity was further identified up to species based on its phenotypic and molecular characteristics. Additionally, the most suitable carbon and nitrogen sources for increasing the antibacterial activity were also investigated. <b>Results:</b> Interestingly, <i>Streptomyces </i>isolate MSQ21 achieved the highest antibacterial activity against <i>R. solanacearum</i> with an inhibition zone of 18 mm. 16S rRNA gene analysis suggested that <i>Streptomyces </i>MSQ21 was identified as a strain of <i>S. maritimus</i> Glycerol (2.25%, w/v) and (NH<sub>4</sub>)<sub>2</sub>SO<sub>4</sub> (0.13%, w/v) were the most suitable carbon and nitrogen sources for increasing the antibacterial activity. <b>Conclusion:</b> It could be concluded that the maximum antibacterial activity (30mm) produced by <i>S. maritimus </i>strain MSQ21 against <i>R. solanacearum </i>could be obtained by using the modified starch nitrate medium containing (g L<sup>1</sup>): Glycerol, 25: Ammonium sulphate, 1.6: Dipotassium hydrogen phosphate, 1: Magnesium sulphate, 0.5: Sodium chloride, 0.5: Calcium carbonate, 3: Ferrous sulphate and 0.01: Distilled water up to 1 L and under the following conditions: Temperature 30°C, agitation speed 250 rpm, inoculum size 1-50 mL medium, incubation period 4 days and pH 8.5.
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143
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Duhsaki L, Mukherjee S, Rani TS, Madhuprakash J. Genome analysis of Streptomyces sp. UH6 revealed the presence of potential chitinolytic machinery crucial for chitosan production. Environ Microbiol Rep 2022; 14:431-442. [PMID: 34192819 DOI: 10.1111/1758-2229.12986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 06/19/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Chitosan and its derivatives have numerous applications in wastewater treatment as bio-coagulants, flocculants and bio-adsorbents against both particulate and dissolved pollutants. Chitinolytic bacteria secrete an array of enzymes, which play crucial role in chitin to chitosan conversion. Consequently, there is a growing demand for identification and characterization of novel bacterial isolates with potential implications in chitosan production. We describe genomic features of the new isolate Streptomyces sp. UH6. Analysis of the 6.51 Mb genome revealed the GC content as 71.95% and presence of 6990 coding sequences of which 63% were functionally annotated. Further, we identified two possible chitin-utilization pathways, which employ secreted enzymes like lytic polysaccharide monooxygenases and family-18 glycoside hydrolases (GHs). More importantly, the genome has six family-4 polysaccharide deacetylases with probable role in chitin to chitosan conversion, as well as two chitosanases belonging to GH46 and GH75 families. In addition, the gene clusters, dasABC and ngcEFG coding for transporters, which mediate the uptake of N,N'-diacetylchitobiose and N-acetyl-d-glucosamine were identified. Several genes responsible for hydrolysis of other polysaccharides and fermentation of sugars were also identified. Taken together, the phylogenetic and genomic analyses suggest that the isolate Streptomyces sp. UH6 secretes potential chitin-active enzymes responsible for chitin to chitosan conversion.
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Affiliation(s)
- Lal Duhsaki
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, India
| | - Saumashish Mukherjee
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, India
| | | | - Jogi Madhuprakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, India
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Wang Z, Yang FX, Liu C, Wang L, Qi Y, Cao M, Guo X, Li J, Huang X, Yang J, Huang SX. Isolation and Biosynthesis of Phenazine-Polyketide Hybrids from Streptomyces sp. KIB-H483. J Nat Prod 2022; 85:1324-1331. [PMID: 35574837 DOI: 10.1021/acs.jnatprod.2c00067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A phenazine-polyketide hybrid compound, nexphenazine A (1), was isolated from Streptomyces sp. KIB-H483. The bioinformatic analysis of the draft genome of the producing strain and gene inactivation experiments revealed that the biosynthesis of 1 involves a phenazine-polyketide hybrid gene cluster. The abolished production of 1 as well as the accumulation of shunt metabolites 4-7 in mutant strain ΔnpzI revealed the key role of the npzI gene, which encodes an NAD(P)H-dependent ketoreductase, in nexphenazine biosynthesis. The structures and absolute configurations of the isolated intermediates were established on the basis of spectroscopic data analysis, single-crystal X-ray diffraction, chiral chromatography, and chemical conversion experiments. NpzI exhibited stereochemical selectivity in reducing the carbonyl group of 4. Nexphenazine biosynthesis is proposed to involve a condensation of the carboxyl group of phenazine with one molecule of methylmalonyl-CoA by a type I PKS, followed by a ketone reduction by NpzI and an unknown methylation reaction.
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Affiliation(s)
- Zhiyan Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Feng-Xian Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Chongxi Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Li Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Yuxin Qi
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 418000, People's Republic of China
| | - Minghang Cao
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Xiaowei Guo
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Jie Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xueshuang Huang
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 418000, People's Republic of China
| | - Jing Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Sheng-Xiong Huang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
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Vind K, Maffioli S, Fernandez Ciruelos B, Waschulin V, Brunati C, Simone M, Sosio M, Donadio S. N-Acetyl-Cysteinylated Streptophenazines from Streptomyces. J Nat Prod 2022; 85:1239-1247. [PMID: 35422124 PMCID: PMC9150181 DOI: 10.1021/acs.jnatprod.1c01123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Indexed: 05/29/2023]
Abstract
Here, we describe two N-acetyl-cysteinylated streptophenazines (1 and 2) produced by the soil-derived Streptomyces sp. ID63040 and identified through a metabolomic approach. These metabolites attracted our interest due to their low occurrence frequency in a large library of fermentation broth extracts and their consistent presence in biological replicates of the producer strain. The compounds were found to possess broad-spectrum antibacterial activity while exhibiting low cytotoxicity. The biosynthetic gene cluster from Streptomyces sp. ID63040 was found to be highly similar to the streptophenazine reference cluster in the MIBiG database, which originates from the marine Streptomyces sp. CNB-091. Compounds 1 and 2 were the main streptophenazine products from Streptomyces sp. ID63040 at all cultivation times but were not detected in Streptomyces sp. CNB-091. The lack of obvious candidates for cysteinylation in the Streptomyces sp. ID63040 biosynthetic gene cluster suggests that the N-acetyl-cysteine moiety derives from cellular functions, most likely from mycothiol. Overall, our data represent an interesting example of how to leverage metabolomics for the discovery of new natural products and point out the often-neglected contribution of house-keeping cellular functions to natural product diversification.
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Affiliation(s)
- Kristiina Vind
- NAICONS
Srl, 20139 Milan, Italy
- Host-Microbe
Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands
| | | | | | - Valentin Waschulin
- School
of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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Ravinder P, Manasa M, Roopa D, Bukhari NA, Hatamleh AA, Khan MY, M. S. R, Hameeda B, El Enshasy HA, Hanapi SZ, Sayyed RZ. Biosurfactant producing multifarious Streptomyces puniceus RHPR9 of Coscinium fenestratum rhizosphere promotes plant growth in chilli. PLoS One 2022; 17:e0264975. [PMID: 35290374 PMCID: PMC8923452 DOI: 10.1371/journal.pone.0264975] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/19/2022] [Indexed: 12/29/2022] Open
Abstract
The present study involves isolation of Streptomyces spp. from rhizosphere of Coscinium fenestratum Gaertn, an endangered medicinal plant from Western Ghats of Karnataka, India. Four potential isolates were identified by 16S rRNA sequencing as Streptomyces sp. RHPR3, Streptomyces puniceus RHPR9, Streptomyces sp. RHPR14 and Streptomyces mediolani RHPR25. An enrichment culture method was used for the isolation of Streptomyces spp. for biosurfactant activity. Among four potential Streptomyces spp., S. puniceus RHPR9 showed highest Emulsification index (EI) (78±0.2%) and Emulsification assay (EA) (223±0.2 EU mL-1). Thin layer chromatography, Fourier transform infrared spectroscopy (FTIR) and mass spectrometric analysis revealed that as glycolipid. Further confirmed by presence of fatty acids like hexanoic acid methyl ester, decanoic acid by Gas chromatography mass spectroscopy (GC-MS) analysis. S. puniceus RHPR9 showed a significant IAA production (41μg mL-1), solubilized P (749.1 μg mL-1), growth promotion of chilli (Capsicum annuum L.) was evaluated using paper towel method and greenhouse conditions. S. puniceus RHPR9 showed a significant increase in seed vigor index (2047) and increase in plant biomass (65%) when compared to uninoculated control. To our knowledge, this is the first report on epiphytic S. puniceus RHPR9 isolated from an endangered medicinal plant C. fenestratum Gaertn, for biosurfactant production and plant growth promotion activities.
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Affiliation(s)
- Polapally Ravinder
- Department of Microbiology, University College of Science, Osmania University Hyderabad, Hyderabad, India
| | - M. Manasa
- Department of Microbiology, University College of Science, Osmania University Hyderabad, Hyderabad, India
| | - D. Roopa
- Department of Wildlife and Management, Kuvempu University Shankaraghatta, Karnataka, India
| | - Najat A. Bukhari
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Reddy M. S.
- Asian PGPR Society for Sustainable Agriculture, Auburn University, Auburn, Alabama, United States of America
| | - Bee Hameeda
- Department of Microbiology, University College of Science, Osmania University Hyderabad, Hyderabad, India
- * E-mail: ,
| | - Hesham Ali El Enshasy
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), Skudai, Johor, Malaysia
- School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia (UTM), Skudai, Johor, Malaysia
- City of Scientific Research and Technology Applications (SRTA), New Burg Al Arab, Alexandria, Egypt
| | - Siti Zulaiha Hanapi
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), Skudai, Johor, Malaysia
| | - R. Z. Sayyed
- Department of Microbiology, PSGVP Mandal’s, S I Patil Arts, G B Patel Science & STKVS Commerce College, Shahada, India
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147
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Bradley NP, Wahl KL, Steenwyk JL, Rokas A, Eichman BF. Resistance-Guided Mining of Bacterial Genotoxins Defines a Family of DNA Glycosylases. mBio 2022; 13:e0329721. [PMID: 35311535 PMCID: PMC9040887 DOI: 10.1128/mbio.03297-21] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/22/2022] [Indexed: 11/20/2022] Open
Abstract
Unique DNA repair enzymes that provide self-resistance against therapeutically important, genotoxic natural products have been discovered in bacterial biosynthetic gene clusters (BGCs). Among these, the DNA glycosylase AlkZ is essential for azinomycin B production and belongs to the HTH_42 superfamily of uncharacterized proteins. Despite their widespread existence in antibiotic producers and pathogens, the roles of these proteins in production of other natural products are unknown. Here, we determine the evolutionary relationship and genomic distribution of all HTH_42 proteins from Streptomyces and use a resistance-based genome mining approach to identify homologs associated with known and uncharacterized BGCs. We find that AlkZ-like (AZL) proteins constitute one distinct HTH_42 subfamily and are highly enriched in BGCs and variable in sequence, suggesting each has evolved to protect against a specific secondary metabolite. As a validation of the approach, we show that the AZL protein, HedH4, associated with biosynthesis of the alkylating agent hedamycin, excises hedamycin-DNA adducts with exquisite specificity and provides resistance to the natural product in cells. We also identify a second, phylogenetically and functionally distinct subfamily whose proteins are never associated with BGCs, are highly conserved with respect to sequence and genomic neighborhood, and repair DNA lesions not associated with a particular natural product. This work delineates two related families of DNA repair enzymes-one specific for complex alkyl-DNA lesions and involved in self-resistance to antimicrobials and the other likely involved in protection against an array of genotoxins-and provides a framework for targeted discovery of new genotoxic compounds with therapeutic potential. IMPORTANCE Bacteria are rich sources of secondary metabolites that include DNA-damaging genotoxins with antitumor/antibiotic properties. Although Streptomyces produce a diverse number of therapeutic genotoxins, efforts toward targeted discovery of biosynthetic gene clusters (BGCs) producing DNA-damaging agents is lacking. Moreover, work on toxin-resistance genes has lagged behind our understanding of those involved in natural product synthesis. Here, we identified over 70 uncharacterized BGCs producing potentially novel genotoxins through resistance-based genome mining using the azinomycin B-resistance DNA glycosylase AlkZ. We validate our analysis by characterizing the enzymatic activity and cellular resistance of one AlkZ ortholog in the BGC of hedamycin, a potent DNA alkylating agent. Moreover, we uncover a second, phylogenetically distinct family of proteins related to Escherichia coli YcaQ, a DNA glycosylase capable of unhooking interstrand DNA cross-links, which differs from the AlkZ-like family in sequence, genomic location, proximity to BGCs, and substrate specificity. This work defines two families of DNA glycosylase for specialized repair of complex genotoxic natural products and generalized repair of a broad range of alkyl-DNA adducts and provides a framework for targeted discovery of new compounds with therapeutic potential.
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Affiliation(s)
- Noah P. Bradley
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Katherine L. Wahl
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Brandt F. Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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148
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Kresna IDM, Wuisan ZG, Pohl JM, Mettal U, Otoya VL, Gand M, Marner M, Otoya LL, Böhringer N, Vilcinskas A, Schäberle TF. Genome-Mining-Guided Discovery and Characterization of the PKS-NRPS-Hybrid Polyoxyperuin Produced by a Marine-Derived Streptomycete. J Nat Prod 2022; 85:888-898. [PMID: 35239335 DOI: 10.1021/acs.jnatprod.1c01018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The azinothricin family comprises several cyclic hexadepsipeptides with diverse pharmacological bioactivities, including antimicrobial, antitumoral, and apoptosis induction. In this work, using a genome mining approach, a biosynthetic gene cluster encoding an azinothricin-like compound was identified from the Streptomyces sp. s120 genome sequence (pop BGC). Comparative MS analysis of extracts from the native producer and a knockout mutant led to the identification of metabolites corresponding to the pop BGC. Furthermore, regulatory elements of the BGC were identified. By overexpression of an LmbU-like transcriptional activator, the production yield of 1 and 2 was increased, enabling isolation and structure elucidation of polyoxyperuin A seco acid (1) and polyoxyperuin A (2) using high-resolution mass spectrometry and NMR spectroscopy. Compound 1 exhibited a low antibiotic effect against Micrococcus luteus, while 2 showed a strong Gram-positive antibiotic effect in a micro-broth-dilution assay.
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Affiliation(s)
- I Dewa M Kresna
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
| | - Zerlina G Wuisan
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
- German Center of Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392 Giessen, Germany
| | - Jean-Marie Pohl
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
| | - Ute Mettal
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
| | - Virginia Linares Otoya
- Unidad de Posgrado en Farmacia y Bioquímica, Facultad de Farmacia y Bioquímica, Universidad Nacional de Trujillo, 13011. Trujillo, Peru
| | - Martin Gand
- Institute of Food Chemistry and Food Biotechnology, Faculty of Biology and Chemistry, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Michael Marner
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
| | - Luis Linares Otoya
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Nils Böhringer
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
- German Center of Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392 Giessen, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
- German Center of Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392 Giessen, Germany
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149
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Song F, Hu J, Zhang X, Xu W, Yang J, Li S, Xu X. Unique Cyclized Thiolopyrrolones from the Marine-Derived Streptomyces sp. BTBU20218885. Mar Drugs 2022; 20:md20030214. [PMID: 35323513 PMCID: PMC8953990 DOI: 10.3390/md20030214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 12/04/2022] Open
Abstract
Two new cyclized thiolopyrrolone derivatives, namely, thiolopyrrolone A (1) and 2,2-dioxidothiolutin (2), together with the kn own compound, thiolutin (3) were identified from a marine-derived Streptomyces sp. BTBU20218885, which was isolated from a mud sample collected from the coastal region of Xiamen, China. Their chemical structures were determined using spectroscopic data, including HRESIMS, 1D and 2D NMR techniques. 1 possessed a unique unsymmetrical sulfur-containing thiolopyrrolone structure. All the compounds were tested for bioactivities against Staphylococcus aureus, Escherichia coli, Bacille Calmette–Guérin (BCG), Mycobacterium tuberculosis, and Candida albicans. 1 displayed antibacterial activities against BCG, M. tuberculosis, and S. aureus with minimum inhibitory concentration (MIC) values of 10, 10, and 100 μg/mL, respectively. Thiolutin (3) showed antibacterial activities against E. coli, BCG, M. tuberculosis, and S. aureus with MIC values of 6.25, 0.3125, 0.625, and 3.125 μg/mL, respectively.
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Affiliation(s)
- Fuhang Song
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China;
| | - Jiansen Hu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
| | - Xinwan Zhang
- School of Ocean Sciences, China University of Geosciences, Beijing 100083, China; (X.Z.); (W.X.); (J.Y.)
| | - Wei Xu
- School of Ocean Sciences, China University of Geosciences, Beijing 100083, China; (X.Z.); (W.X.); (J.Y.)
| | - Jinpeng Yang
- School of Ocean Sciences, China University of Geosciences, Beijing 100083, China; (X.Z.); (W.X.); (J.Y.)
| | - Shaoyong Li
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China;
| | - Xiuli Xu
- School of Ocean Sciences, China University of Geosciences, Beijing 100083, China; (X.Z.); (W.X.); (J.Y.)
- Correspondence:
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150
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Abstract
Streptomyces are soil- and marine-dwelling microbes that need to survive dramatic fluctuations in nutrient levels and environmental conditions. Here, we explore the advances made in understanding how Streptomyces bacteria can thrive in their natural environments. We examine their classical developmental cycle, and the intricate regulatory cascades that govern it. We discuss alternative growth strategies and behaviors, like the rapid expansion and colonization properties associated with exploratory growth, the release of membrane vesicles and S-cells from hyphal tips, and the acquisition of exogenous DNA along the lateral walls. We further investigate Streptomyces interactions with other organisms through the release of volatile compounds that impact nutrient levels, microbial growth, and insect behavior. Finally, we explore the increasingly diverse strategies employed by Streptomyces species in escaping and thwarting phage infections.
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Affiliation(s)
- Matthew P Zambri
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Michelle A Williams
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Marie A Elliot
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
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