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Magar RT, Pham VTT, Poudel PB, Bridget AF, Sohng JK. A new peucemycin derivative and impacts of peuR and bldA on peucemycin biosynthesis in Streptomyces peucetius. Appl Microbiol Biotechnol 2024; 108:107. [PMID: 38217253 PMCID: PMC10786969 DOI: 10.1007/s00253-023-12923-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/05/2023] [Accepted: 10/30/2023] [Indexed: 01/15/2024]
Abstract
Streptomyces peucetius ATCC 27952 is known to produce a variety of secondary metabolites, including two important antitumor anthracyclines: daunorubicin and doxorubicin. Identification of peucemycin and 25-hydroxy peucemycin (peucemycin A), as well as their biosynthetic pathway, has expanded its biosynthetic potential. In this study, we isolated a new peucemycin derivative and identified it as 19-hydroxy peucemycin (peucemycin B). Its antibacterial activity was lower than those of peucemycin and peucemycin A. On the other hand, this newly identified peucemycin derivative had higher anticancer activity than the other two compounds for MKN45, NCI-H1650, and MDA-MB-231 cancer cell lines with IC50 values of 76.97 µM, 99.68 µM, and 135.2 µM, respectively. Peucemycin biosynthetic gene cluster revealed the presence of a SARP regulator named PeuR whose role was unknown. The presence of the TTA codon in the peuR and the absence of global regulator BldA in S. peucetius reduced its ability to regulate the peucemycin biosynthetic gene cluster. Hence, different mutants harboring these genes were prepared. S. peucetius bldA25 harboring bldA produced 1.75 times and 1.77 times more peucemycin A (11.8 mg/L) and peucemycin B (21.2 mg/L), respectively, than the wild type. On the other hand, S. peucetius R25 harboring peuR produced 1.86 and 1.79 times more peucemycin A (12.5 mg/L) and peucemycin B (21.5 mg/L), respectively, than the wild type. Finally, strain S. peucetius bldAR25 carrying bldA and peuR produced roughly 3.52 and 2.63 times more peucemycin A (23.8 mg/L) and peucemycin B (31.5 mg/L), respectively, than the wild type. KEY POINTS: • This study identifies a new peucemycin derivative, 19-hydroxy peucemycin (peucemycin B). • The SARP regulator (PeuR) acts as a positive regulator of the peucemycin biosynthetic gene cluster. • The overexpression of peuR and heterologous expression of bldA increase the production of peucemycin derivatives.
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Affiliation(s)
- Rubin Thapa Magar
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, 31460, Chungnam, Korea
| | - Van Thuy Thi Pham
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, 31460, Chungnam, Korea
| | - Purna Bahadur Poudel
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, 31460, Chungnam, Korea
| | - Adzemye Fovennso Bridget
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, 31460, Chungnam, Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, 31460, Chungnam, Korea.
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, 31460, Chungnam, Korea.
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2
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Lu L, Liu N, Fan Z, Liu M, Zhang X, Tian J, Yu Y, Lin H, Huang Y, Kong Z. A novel PGPR strain, Streptomyces lasalocidi JCM 3373 T, alleviates salt stress and shapes root architecture in soybean by secreting indole-3-carboxaldehyde. PLANT, CELL & ENVIRONMENT 2024; 47:1941-1956. [PMID: 38369767 DOI: 10.1111/pce.14847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/20/2024]
Abstract
While soybean (Glycine max L.) provides the most important source of vegetable oil and protein, it is sensitive to salinity, which seriously endangers the yield and quality during soybean production. The application of Plant Growth-Promoting Rhizobacteria (PGPR) to improve salt tolerance for plant is currently gaining increasing attention. Streptomycetes are a major group of PGPR. However, to date, few streptomycetes has been successfully developed and applied to promote salt tolerance in soybean. Here, we discovered a novel PGPR strain, Streptomyces lasalocidi JCM 3373T, from 36 strains of streptomycetes via assays of their capacity to alleviate salt stress in soybean. Microscopic observation showed that S. lasalocidi JCM 3373T does not colonise soybean roots. Chemical analysis confirmed that S. lasalocidi JCM 3373T secretes indole-3-carboxaldehyde (ICA1d). Importantly, IAC1d inoculation alleviates salt stress in soybean and modulates its root architecture by regulating the expression of stress-responsive genes GmVSP, GmPHD2 and GmWRKY54 and root growth-related genes GmPIN1a, GmPIN2a, GmYUCCA5 and GmYUCCA6. Taken together, the novel PGPR strain, S. lasalocidi JCM 3373T, alleviates salt stress and improves root architecture in soybean by secreting ICA1d. Our findings provide novel clues for the development of new microbial inoculant and the improvement of crop productivity under salt stress.
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Affiliation(s)
- Liang Lu
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ning Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zihui Fan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Minghao Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaxia Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Juan Tian
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanjun Yu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Honghui Lin
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhaosheng Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Hou-Ji Laboratory in Shanxi province, Academy of Agronomy, Shanxi Agricultural University, Taiyuan, China
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3
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Ngo TE, Ecker A, Ryu B, Guild A, Remmel A, Boudreau PD, Alexander KL, Naman CB, Glukhov E, Avalon NE, Shende VV, Thomas L, Dahesh S, Nizet V, Gerwick L, Gerwick WH. Structure and Biosynthesis of Hectoramide B, a Linear Depsipeptide from Marine Cyanobacterium Moorena producens JHB Discovered via Coculture with Candida albicans. ACS Chem Biol 2024; 19:619-628. [PMID: 38330248 PMCID: PMC10949194 DOI: 10.1021/acschembio.3c00391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
Abstract
The tropical marine cyanobacterium Moorena producens JHB is a prolific source of secondary metabolites with potential biomedical utility. Previous studies on this strain led to the discovery of several novel compounds such as hectochlorins and jamaicamides. However, bioinformatic analyses of its genome indicate the presence of numerous cryptic biosynthetic gene clusters that have yet to be characterized. To potentially stimulate the production of novel compounds from this strain, it was cocultured with Candida albicans. From this experiment, we observed the increased production of a new compound that we characterize here as hectoramide B. Bioinformatic analysis of the M. producens JHB genome enabled the identification of a putative biosynthetic gene cluster responsible for hectoramide B biosynthesis. This work demonstrates that coculture competition experiments can be a valuable method to facilitate the discovery of novel natural products from cyanobacteria.
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Affiliation(s)
- Thuan-Ethan Ngo
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Andrew Ecker
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | - Byeol Ryu
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Aurora Guild
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Ariana Remmel
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Paul D. Boudreau
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of BioMolecular Sciences,University of Mississippi,
School of Pharmacy, University, Mississippi 38677, United States
| | - Kelsey L. Alexander
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Chemistry, University of California San
Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - C. Benjamin Naman
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Science and Conservation, San Diego Botanic
Garden, 300 Quail Gardens
Drive, Encinitas, California 92024, United States
| | - Evgenia Glukhov
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Nicole E. Avalon
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Vikram V. Shende
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Lamar Thomas
- Department
of Pediatrics, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
| | - Samira Dahesh
- Department
of Pediatrics, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
| | - Victor Nizet
- Department
of Pediatrics, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Lena Gerwick
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - William H. Gerwick
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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4
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Ngo TE, Ecker A, Guild A, Remmel A, Boudreau PD, Alexander KL, Naman CB, Glukhov E, Avalon NE, Shende VV, Gerwick L, Gerwick WH. Structure and Biosynthesis of Hectoramide B, a Linear Depsipeptide from the Marine Cyanobacterium Moorena producens JHB Discovered via Co-culture with Candida albicans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.547815. [PMID: 37461655 PMCID: PMC10350029 DOI: 10.1101/2023.07.06.547815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
The tropical marine cyanobacterium Moorena producens JHB is a prolific source of secondary metabolites with potential biomedical utility. Previous studies of this strain led to the discovery of several novel compounds such as the hectochlorins and jamaicamides; however, bioinformatic analyses of its genome suggested that there were many more cryptic biosynthetic gene clusters yet to be characterized. To potentially stimulate the production of novel compounds from this strain, it was co-cultured with Candida albicans. From this experiment, we observed the increased production of a new compound that we characterize here as hectoramide B. Bioinformatic analysis of the M. producens JHB genome enabled the identification of a putative biosynthetic gene cluster responsible for hectoramide B biosynthesis. This work demonstrates that co-culture competition experiments can be a valuable method to facilitate the discovery of novel natural products from cyanobacteria.
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Affiliation(s)
- Thuan-Ethan Ngo
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Andrew Ecker
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Aurora Guild
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ariana Remmel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of BioMolecular Sciences, University of Mississippi School of Pharmacy, University, Mississippi 38677, USA
| | - Kelsey L Alexander
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Chemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - C Benjamin Naman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Science and Conservation, San Diego Botanic Garden, 300 Quail Gardens Drive, Encinitas, CA, 92024, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Nicole E Avalon
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Vikram V Shende
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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5
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Kortam YG, Abd El-Rahim WM, Khattab AENA, Rebouh NY, Gurina RR, Barakat OS, Zakaria M, Moawad H. Enhancing the Antibiotic Production by Thermophilic Bacteria Isolated from Hot Spring Waters via Ethyl Methanesulfonate Mutagenesis. Antibiotics (Basel) 2023; 12:1095. [PMID: 37508191 PMCID: PMC10376502 DOI: 10.3390/antibiotics12071095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Antibiotic-resistant bacteria represent a serious public health threat. For that reason, the development of new and effective antibiotics to control pathogens has become necessary. The current study aims to search for new microorganisms expressing antibiotic production capacity. Fifteen sites covering a wide range of harsh environmental conditions in Egypt were investigated. Two hundred and eighty bacterial isolates were obtained and then tested against pathogenic bacteria using the agar disk diffusion technique. Fifty-two (18.6% of the total) of the isolates exhibited antagonistic properties, which affected one or more of the tested pathogens. The isolate 113 was identified as Bacillus licheniformis and isolate 10 was identified as Brevibacillus borstelensis using the 16S rRNA technique. The B. licheniformis strain was stronger in antibiotic production against S. typhi, M. luteus, and P. ariginosa, whereas the strain Br. borstelensis was more efficient against B. cereus, E. coli, and Klebs. sp. The sensitivity of the strains to commercial antibiotics showed that B. licheniformis was highly sensitive to seven commercial antibiotics, whereas Br. borstelensis was sensitive to nine antibiotics. The two strains were subjected to ethyl methanesulfonate (EMS) mutagenesis to obtain mutants with a higher antibiotic production. The total bacterial count was measured after treatment with EMS mutagen and showed a significant gradual increase in the antimicrobial activity, which was achieved via shaking in the presence of EMS for 60 min. High antimicrobial activities were noted with 17 and 14 mutants from the B. licheniformis and Br. borstelensis strains, respectively. The mutant B. licheniformis (M15/Amo) was more active than the parent strain against S. aureus (212.5%), while the mutant Br. borstelensis (B7/Neo) was more effective against S. typhi (83.3%). The present study demonstrates the possibility of obtaining potent antibiotic-producing bacteria in hot spring waters and further improving the indigenous bacterial capacity to produce antibiotics by using EMS mutagenesis.
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Affiliation(s)
- Yasmin G Kortam
- Department of Agricultural Microbiology, National Research Centre, Giza 12622, Egypt
| | - Wafaa M Abd El-Rahim
- Department of Agricultural Microbiology, National Research Centre, Giza 12622, Egypt
| | | | - Nazih Y Rebouh
- Department of Environmental Management, Institute of Environmental Engineering, RUDN University, 6 Miklukho-Maklaya Street, 117198 Moscow, Russia
| | - Regina R Gurina
- Technosphere Security Department, RUDN University, 6 Miklukho-Maklaya Street, 117198 Moscow, Russia
| | - Olfat S Barakat
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Cairo 12613, Egypt
| | - Mohamed Zakaria
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Cairo 12613, Egypt
| | - Hassan Moawad
- Department of Agricultural Microbiology, National Research Centre, Giza 12622, Egypt
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6
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6S-Like scr3559 RNA Affects Development and Antibiotic Production in Streptomyces coelicolor. Microorganisms 2021; 9:microorganisms9102004. [PMID: 34683325 PMCID: PMC8539372 DOI: 10.3390/microorganisms9102004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
Regulatory RNAs control a number of physiological processes in bacterial cells. Here we report on a 6S-like RNA transcript (scr3559) that affects both development and antibiotic production in Streptomyces coelicolor. Its expression is enhanced during the transition to stationary phase. Strains that over-expressed the scr3559 gene region exhibited a shortened exponential growth phase in comparison with a control strain; accelerated aerial mycelium formation and spore maturation; alongside an elevated production of actinorhodin and undecylprodigiosin. These observations were supported by LC-MS analyses of other produced metabolites, including: germicidins, desferrioxamines, and coelimycin. A subsequent microarray differential analysis revealed increased expression of genes associated with the described morphological and physiological changes. Structural and functional similarities between the scr3559 transcript and 6S RNA, and its possible employment in regulating secondary metabolite production are discussed.
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7
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Hindra, Yang D, Luo J, Huang T, Yan X, Adhikari A, Teijaro CN, Ge H, Shen B. Submerged fermentation of Streptomyces uncialis providing a biotechnology platform for uncialamycin biosynthesis, engineering, and production. J Ind Microbiol Biotechnol 2021; 48:6178870. [PMID: 33739406 PMCID: PMC8210685 DOI: 10.1093/jimb/kuab025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/15/2021] [Indexed: 12/19/2022]
Abstract
Uncialamycin (UCM) belongs to the anthraquinone-fused subfamily of 10-membered enediyne natural products that exhibits an extraordinary cytotoxicity against a wide spectrum of human cancer cell lines. Antibody-drug conjugates, utilizing synthetic analogues of UCM as payloads, are in preclinical development. UCM is exclusively produced by Streptomyces uncialis DCA2648 on solid agar medium with low titers (∼0.019 mg/l), limiting its supply by microbial fermentation and hampering its biosynthetic and engineering studies by in vivo pathway manipulation. Here, we report cultivation conditions that enable genetic manipulation of UCM biosynthesis in vivo and allow UCM production, with improved titers, by submerged fermentation of the engineered S. uncialis strains. Specifically, the titer of UCM was improved nearly 58-fold to ∼1.1 mg/l through the combination of deletion of biosynthetic gene clusters encoding unrelated metabolites from the S. uncialis wild-type, chemical mutagenesis and manipulation of pathway-specific regulators to generate the engineered S. uncialis strains, and finally medium optimization of the latter for UCM production. Genetic manipulation of UCM biosynthesis was demonstrated by inactivating selected genes in the engineered S. uncialis strains, one of which afforded a mutant strain accumulating tiancimycin B, a common biosynthetic intermediate known for the anthraquinone-fused subfamily of enediyne natural products. These findings highlight a biotechnology platform for UCM biosynthesis, engineering, and production that should facilitate both its fundamental studies and translational applications.
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Affiliation(s)
| | | | - Jun Luo
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Tingting Huang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ajeeth Adhikari
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Huiming Ge
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ben Shen
- Correspondence to: Ben Shen. Phone: +1-561-228-2456. Fax: +1-561-228-2472. E-mail:
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8
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Pham VTT, Nguyen HT, Nguyen CT, Choi YS, Dhakal D, Kim TS, Jung HJ, Yamaguchi T, Sohng JK. Identification and enhancing production of a novel macrolide compound in engineered Streptomyces peucetius. RSC Adv 2021; 11:3168-3173. [PMID: 35424263 PMCID: PMC8693821 DOI: 10.1039/d0ra06099b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/25/2020] [Indexed: 12/21/2022] Open
Abstract
Streptomyces peucetius produces doxorubicin and daunorubicin, which are important anticancer drugs. In this study, we activate peucemycin, a new antibacterial compound, using an OSMAC strategy. In general, bioactive compounds are produced in a higher amount at room temperature; however, in this study, we have demonstrated that a bioactive novel compound was successfully activated at a low temperature (18 °C) in S. peucetius DM07. Through LC-MS/MS, IR spectroscopy, and NMR analysis, we identified the structure of this compound as a γ-pyrone macrolide. This compound was found to be novel, thus named peucemycin. It is an unusual 14-membered macrocyclic γ-pyrone ring with cyclization. Also, peucemycin exhibits potential antibacterial activity and a suppressive effect on the viability of various cancer cell lines. Activation of peucemycin in S. peucetius DM07 by the OSMAC strategy.![]()
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Affiliation(s)
- Van Thuy Thi Pham
- Department of Life Science and Biochemical Engineering, SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
| | - Hue Thi Nguyen
- Department of Life Science and Biochemical Engineering, SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
| | - Chung Thanh Nguyen
- Department of Life Science and Biochemical Engineering, SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
| | - Ye Seul Choi
- Department of Life Science and Biochemical Engineering, SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
| | - Dipesh Dhakal
- Department of Life Science and Biochemical Engineering, SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
| | - Tae-Su Kim
- Department of Life Science and Biochemical Engineering, SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
| | - Hye Jin Jung
- Department of Life Science and Biochemical Engineering, SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea .,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
| | - Tokutaro Yamaguchi
- Department of Life Science and Biochemical Engineering, SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea .,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
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Rodríguez-García A, Sola-Landa A, Pérez-Redondo R. Coupled Transcriptomics for Differential Expression Analysis and Determination of Transcription Start Sites: Design and Bioinformatics. Methods Mol Biol 2021; 2296:263-278. [PMID: 33977454 DOI: 10.1007/978-1-0716-1358-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The term coupled transcriptomics is coined to describe a design of an RNA-seq experiment intended for both differential expression analysis and genome-wide determination of the transcription start sites (TSS). The minimal requirements for the first analysis are two experimental conditions with at least two biological replicates enabling statistical tests. The second analysis involves the bioinformatics comparison of the data generated from a control RNA-seq library with another library enriched in primary transcripts using Terminator™ 5'-phosphate-dependent exonuclease, in an experiment denominated differential RNA-seq (dRNA-seq). Usually, dRNA-seq is carried out with specific protocols for library construction, different of those used for common differential expression analysis. Our experimental design allows to use the same data for both analyses, reducing the number of libraries to be generated and sequenced. This is a guide for designing a coupled transcriptomics experiment and for the subsequent bioinformatics procedures. The proposed methods can be applied to the detection and study of small RNA genes.
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Affiliation(s)
| | - Alberto Sola-Landa
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, León, Spain
| | - Rosario Pérez-Redondo
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, León, Spain
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10
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Mechanism of CuO nano-particles on stimulating production of actinorhodin in Streptomyces coelicolor by transcriptional analysis. Sci Rep 2019; 9:11253. [PMID: 31375702 PMCID: PMC6677739 DOI: 10.1038/s41598-019-46833-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/05/2019] [Indexed: 11/18/2022] Open
Abstract
In this research, antibiotic-producing bacteria, Streptomyces coelicolor (S. coelicolor) M145, was exposed to copper oxide (CuO) particles to investigate the effects of nano-particles (NPs) on antibiotic production. Results showed that a higher yield of antibiotics was obtained with smaller particle sizes of CuO NPs. When exposed to 10 mg/L of 40 nm CuO NPs, the maximum amount of actinorhodin (ACT) obtained was 2.6 mg/L after 144 h, which was 2.0-fold greater than that of control. However, the process was inhibited when the concentration of CuO NPs was increased to higher than 20 mg/L. Transcriptome analysis showed that all the genes involved in the ACT cluster were significantly up-regulated after exposure to 10 mg/L NPs, which could be the direct cause of the increase of ACT production. Additionally, some genes related to the generation of acetyl-coA were up-regulated. In this way, CuO NPs led to an increase of secondary metabolites. The mechanism related to these changes indicated that nano-particle‒induced ROS and Cu2+ played synergetic roles in promoting ACT biosynthesis. This is a first report suggesting that CuO NPs had a significant effect on antibiotic production, which will be helpful in understanding the mechanism of antibiotic production in nature.
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Liu X, Tang J, Wang L, Giesy JP. Al 2O 3 nanoparticles promote secretion of antibiotics in Streptomyces coelicolor by regulating gene expression through the nano effect. CHEMOSPHERE 2019; 226:687-695. [PMID: 30959453 DOI: 10.1016/j.chemosphere.2019.03.156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/12/2019] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
Toxic effects of nanoparticles (NPs) on microorganisms have attracted substantial attention; however, there are few reports on whether NPs can affect the secondary metabolism of microbes. To investigate the toxic effects of Al2O3 NPs on cell growth and antibiotic secretion, Streptomyces coelicolor M145 was exposed to Al2O3 NPs with diameters of 30 and 80 nm and bulk Al2O3 at concentrations up to 1000 mg/L. The results indicated that differences in the toxicity of Al2O3 NPs were related to the particle size. In treatment with Al2O3 NPs, the maximum yields of undecylprodigiosin (RED) and actinorhodin (ACT) were 3.7- and 4.6-fold greater than that of the control, respectively, and the initial time of antibiotic production was much shorter. ROS quenching experiment by N-acetylcysteine (NAC) confirmed that ROS were responsible for the increased RED production. From 0 to 72 h, ROS had a significant impact on ACT production; however, after 72 h, the ROS content began to decrease until it disappeared. During ongoing exposure (0-144 h), ACT production continued to increase, indicating that in addition to ROS, nano effect of Al2O3 NPs also played roles in this process. Transcriptional analysis demonstrated that Al2O3 NPs could increase the expression levels of antibiotic biosynthetic genes and two-component systems (TCSs) and inhibit the expression levels of primary metabolic pathways. This study provides a new perspective for understanding the mechanisms of antibiotic production in nature and reveals important implications for exploring other uses of NPs in biomedical applications or regulation of antibiotics in nature.
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Affiliation(s)
- Xiaomei Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Jingchun Tang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.
| | - Lan Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Bhatia SK, Lee BR, Sathiyanarayanan G, Song HS, Kim J, Jeon JM, Kim JH, Park SH, Yu JH, Park K, Yang YH. Medium engineering for enhanced production of undecylprodigiosin antibiotic in Streptomyces coelicolor using oil palm biomass hydrolysate as a carbon source. BIORESOURCE TECHNOLOGY 2016; 217:141-149. [PMID: 26951741 DOI: 10.1016/j.biortech.2016.02.055] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/01/2016] [Accepted: 02/16/2016] [Indexed: 06/05/2023]
Abstract
In this study, a biosugar obtained from empty fruit bunch (EFB) of oil palm by hot water treatment and subsequent enzymatic saccharification was used for undecylprodigiosin production, using Streptomyces coelicolor. Furfural is a major inhibitor present in EFB hydrolysate (EFBH), having a minimum inhibitory concentration (MIC) of 1.9mM, and it reduces utilization of glucose (27%), xylose (59%), inhibits mycelium formation, and affects antibiotic production. Interestingly, furfural was found to be a good activator of undecylprodigiosin production in S. coelicolor, which enhanced undecylprodigiosin production by up to 52%. Optimization by mixture analysis resulted in a synthetic medium containing glucose:furfural:ACN:DMSO (1%, 2mM, 0.2% and 0.3%, respectively). Finally, S. coelicolor was cultured in a fermenter in minimal medium with EFBH as a carbon source and addition of the components described above. This yielded 4.2μg/mgdcw undecylprodigiosin, which was 3.2-fold higher compared to that in un-optimized medium.
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Affiliation(s)
- Shashi Kant Bhatia
- Department of Microbial Engineering, College of Engineering, Konkuk University, Seoul 143-701, South Korea
| | - Bo-Rahm Lee
- Department of Microbial Engineering, College of Engineering, Konkuk University, Seoul 143-701, South Korea
| | - Ganesan Sathiyanarayanan
- Department of Microbial Engineering, College of Engineering, Konkuk University, Seoul 143-701, South Korea
| | - Hun-Seok Song
- Department of Microbial Engineering, College of Engineering, Konkuk University, Seoul 143-701, South Korea
| | - Junyoung Kim
- Department of Microbial Engineering, College of Engineering, Konkuk University, Seoul 143-701, South Korea
| | - Jong-Min Jeon
- Department of Microbial Engineering, College of Engineering, Konkuk University, Seoul 143-701, South Korea
| | - Jung-Ho Kim
- Department of Microbial Engineering, College of Engineering, Konkuk University, Seoul 143-701, South Korea
| | - Sung-Hee Park
- Food Ingredients Center, Foods R&D, CheilJedang, Guro-dong, Guro-Gu, Seoul 152-051, South Korea
| | - Ju-Hyun Yu
- Center for Industrial Chemical Biotechnology, Ulsan Chemical R&BD Division, Korea Research Institute of Chemical Technology, P.O. Box 107, 141 Gajeong-ro, Yuseong-gu, Daejeon 305-600, South Korea
| | - Kyungmoon Park
- Department of Biological and Chemical Engineering, Hongik University, Sejong Ro 2639, Jochiwon, Sejong City 339-701, South Korea
| | - Yung-Hun Yang
- Department of Microbial Engineering, College of Engineering, Konkuk University, Seoul 143-701, South Korea; Department of Biological and Chemical Engineering, Hongik University, Sejong Ro 2639, Jochiwon, Sejong City 339-701, South Korea; Microbial Carbohydrate Resource Bank, Konkuk University, Seoul 143-701, South Korea; Institute for Ubiquitous Information Technology and Applications (CBRU), Konkuk University, Seoul 143-701, South Korea.
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Zacchetti B, Willemse J, Recter B, van Dissel D, van Wezel GP, Wösten HAB, Claessen D. Aggregation of germlings is a major contributing factor towards mycelial heterogeneity of Streptomyces. Sci Rep 2016; 6:27045. [PMID: 27244565 PMCID: PMC4886682 DOI: 10.1038/srep27045] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/13/2016] [Indexed: 12/22/2022] Open
Abstract
Streptomycetes are filamentous bacteria that produce numerous valuable compounds, including the majority of clinically used antibiotics. At an industrial scale, most of these compounds are produced in bioreactors. Growth of streptomycetes under these conditions is characterized by the formation of complex mycelial particles, whose sizes follow a bimodal distribution. Given the correlation between specific productivity and morphology, this size heterogeneity poses a potential drawback in industry. Recent work indicates that mycelial morphology is controlled by a number of genes that encode proteins required for the synthesis of cell surface-associated glycans. Using a quantifiable system based on fluorescent markers, we here show that these glycans mediate aggregation between germlings and young mycelia, yielding mycelial particles that originate from many different individuals. We also demonstrate that at later time points aggregation between distinct particles is no longer detectable. Notably, the absence of the corresponding glycan synthases yields mycelia that are homogeneous in size, identifying mycelial aggregation as a driving factor towards size heterogeneity. Given that aggregation is widespread within streptomycetes and can also occur between different Streptomyces strains, our work paves the way to improve Streptomyces as a cell factory for the production of known metabolites, but possibly also to discover new ones.
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Affiliation(s)
- Boris Zacchetti
- Microbial Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Joost Willemse
- Microbial Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Brand Recter
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dino van Dissel
- Microbial Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Gilles P. van Wezel
- Microbial Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - H. A. B. Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dennis Claessen
- Microbial Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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14
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15
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Reen FJ, Romano S, Dobson ADW, O'Gara F. The Sound of Silence: Activating Silent Biosynthetic Gene Clusters in Marine Microorganisms. Mar Drugs 2015; 13:4754-83. [PMID: 26264003 PMCID: PMC4557003 DOI: 10.3390/md13084754] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 06/05/2015] [Accepted: 07/27/2015] [Indexed: 12/14/2022] Open
Abstract
Unlocking the rich harvest of marine microbial ecosystems has the potential to both safeguard the existence of our species for the future, while also presenting significant lifestyle benefits for commercial gain. However, while significant advances have been made in the field of marine biodiscovery, leading to the introduction of new classes of therapeutics for clinical medicine, cosmetics and industrial products, much of what this natural ecosystem has to offer is locked in, and essentially hidden from our screening methods. Releasing this silent potential represents a significant technological challenge, the key to which is a comprehensive understanding of what controls these systems. Heterologous expression systems have been successful in awakening a number of these cryptic marine biosynthetic gene clusters (BGCs). However, this approach is limited by the typically large size of the encoding sequences. More recently, focus has shifted to the regulatory proteins associated with each BGC, many of which are signal responsive raising the possibility of exogenous activation. Abundant among these are the LysR-type family of transcriptional regulators, which are known to control production of microbial aromatic systems. Although the environmental signals that activate these regulatory systems remain unknown, it offers the exciting possibility of evoking mimic molecules and synthetic expression systems to drive production of potentially novel natural products in microorganisms. Success in this field has the potential to provide a quantum leap forward in medical and industrial bio-product development. To achieve these new endpoints, it is clear that the integrated efforts of bioinformaticians and natural product chemists will be required as we strive to uncover new and potentially unique structures from silent or cryptic marine gene clusters.
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Affiliation(s)
- F Jerry Reen
- BIOMERIT Research Centre, School of Microbiology, University College Cork-National University of Ireland, Cork, Ireland.
| | - Stefano Romano
- BIOMERIT Research Centre, School of Microbiology, University College Cork-National University of Ireland, Cork, Ireland.
| | - Alan D W Dobson
- School of Microbiology, University College Cork-National University of Ireland, Cork, Ireland.
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork-National University of Ireland, Cork, Ireland.
- School of Biomedical Sciences, Curtin University, Perth WA 6845, Australia.
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16
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Paired-termini antisense RNA mediated inhibition of DoxR in Streptomyces peucetius ATCC 27952. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0810-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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17
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Romero-Rodríguez A, Robledo-Casados I, Sánchez S. An overview on transcriptional regulators in Streptomyces. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1017-39. [PMID: 26093238 DOI: 10.1016/j.bbagrm.2015.06.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/09/2015] [Accepted: 06/12/2015] [Indexed: 12/19/2022]
Abstract
Streptomyces are Gram-positive microorganisms able to adapt and respond to different environmental conditions. It is the largest genus of Actinobacteria comprising over 900 species. During their lifetime, these microorganisms are able to differentiate, produce aerial mycelia and secondary metabolites. All of these processes are controlled by subtle and precise regulatory systems. Regulation at the transcriptional initiation level is probably the most common for metabolic adaptation in bacteria. In this mechanism, the major players are proteins named transcription factors (TFs), capable of binding DNA in order to repress or activate the transcription of specific genes. Some of the TFs exert their action just like activators or repressors, whereas others can function in both manners, depending on the target promoter. Generally, TFs achieve their effects by using one- or two-component systems, linking a specific type of environmental stimulus to a transcriptional response. After DNA sequencing, many streptomycetes have been found to have chromosomes ranging between 6 and 12Mb in size, with high GC content (around 70%). They encode for approximately 7000 to 10,000 genes, 50 to 100 pseudogenes and a large set (around 12% of the total chromosome) of regulatory genes, organized in networks, controlling gene expression in these bacteria. Among the sequenced streptomycetes reported up to now, the number of transcription factors ranges from 471 to 1101. Among these, 315 to 691 correspond to transcriptional regulators and 31 to 76 are sigma factors. The aim of this work is to give a state of the art overview on transcription factors in the genus Streptomyces.
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Affiliation(s)
- Alba Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico
| | - Ivonne Robledo-Casados
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico.
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18
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Development, antibiotic production, and ribosome assembly in Streptomyces venezuelae are impacted by RNase J and RNase III deletion. J Bacteriol 2014; 196:4253-67. [PMID: 25266378 DOI: 10.1128/jb.02205-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA metabolism is a critical but frequently overlooked control element affecting virtually every cellular process in bacteria. RNA processing and degradation is mediated by a suite of ribonucleases having distinct cleavage and substrate specificity. Here, we probe the role of two ribonucleases (RNase III and RNase J) in the emerging model system Streptomyces venezuelae. We show that each enzyme makes a unique contribution to the growth and development of S. venezuelae and further affects the secondary metabolism and antibiotic production of this bacterium. We demonstrate a connection between the action of these ribonucleases and translation, with both enzymes being required for the formation of functional ribosomes. RNase III mutants in particular fail to properly process 23S rRNA, form fewer 70S ribosomes, and show reduced translational processivity. The loss of either RNase III or RNase J additionally led to the appearance of a new ribosomal species (the 100S ribosome dimer) during exponential growth and dramatically sensitized these mutants to a range of antibiotics.
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19
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Complex intra-operonic dynamics mediated by a small RNA in Streptomyces coelicolor. PLoS One 2014; 9:e85856. [PMID: 24465751 PMCID: PMC3896431 DOI: 10.1371/journal.pone.0085856] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 12/03/2013] [Indexed: 11/18/2022] Open
Abstract
Streptomyces are predominantly soil-dwelling bacteria that are best known for their multicellular life cycle and their prodigious metabolic capabilities. They are also renowned for their regulatory capacity and flexibility, with each species encoding >60 sigma factors, a multitude of transcription factors, and an increasing number of small regulatory RNAs. Here, we describe our characterization of a conserved small RNA (sRNA), scr4677. In the model species Streptomyces coelicolor, this sRNA is located in the intergenic region separating SCO4677 (an anti-sigma factor-encoding gene) and SCO4676 (a putative regulatory protein-encoding gene), close to the SCO4676 translation start site in an antisense orientation. There appears to be considerable genetic interplay between these different gene products, with wild type expression of scr4677 requiring function of the anti-sigma factor SCO4677, and scr4677 in turn influencing the abundance of SCO4676-associated transcripts. The scr4677-mediated effects were independent of RNase III (a double stranded RNA-specific nuclease), with RNase III having an unexpectedly positive influence on the level of SCO4676-associated transcripts. We have shown that both SCO4676 and SCO4677 affect the production of the blue-pigmented antibiotic actinorhodin under specific growth conditions, and that this activity appears to be independent of scr4677.
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20
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Sidebottom AM, Johnson AR, Karty JA, Trader DJ, Carlson EE. Integrated metabolomics approach facilitates discovery of an unpredicted natural product suite from Streptomyces coelicolor M145. ACS Chem Biol 2013; 8:2009-16. [PMID: 23777274 DOI: 10.1021/cb4002798] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Natural products exhibit a broad range of biological properties and have been a crucial source of therapeutic agents and novel scaffolds. Although bacterial secondary metabolomes are widely explored, they remain incompletely cataloged by current isolation and characterization strategies. To identify metabolites residing in unexplored chemical space, we have developed an integrated discovery approach that combines bacterial growth perturbation, accurate mass spectrometry, comparative mass spectra data analysis, and fragmentation spectra clustering for the identification of low-abundant, novel compounds from complex biological matrices. In this investigation, we analyzed the secreted metabolome of the extensively studied Actinomycete, Streptomyces coelicolor M145, and discovered a low-abundant suite of 15 trihydroxamate, amphiphilic siderophores. Compounds in this class have primarily been observed in marine microorganisms making their detection in the soil-dwelling S. coelicolor M145 significant. At least 10 of these ferrioxamine-based molecules are not known to be produced by any organism, and none have previously been detected from S. coelicolor M145. In addition, we confirmed the production of ferrioxamine D1, a relatively hydrophilic family member that has not been shown to be biosynthesized by this organism. The identified molecules are part of only a small list of secondary metabolites that have been discovered since sequencing of S. coelicolor M145 revealed that it possessed numerous putative secondary metabolite-producing gene clusters with no known metabolites. Thus, the identified siderophores represent the unexplored metabolic potential of both well-studied and new organisms that could be uncovered with our sensitive and robust approach.
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Affiliation(s)
- Ashley M. Sidebottom
- Department of Chemistry and ‡Department of Molecular
and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Andrew R. Johnson
- Department of Chemistry and ‡Department of Molecular
and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jonathan A. Karty
- Department of Chemistry and ‡Department of Molecular
and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Darci J. Trader
- Department of Chemistry and ‡Department of Molecular
and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Erin E. Carlson
- Department of Chemistry and ‡Department of Molecular
and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
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21
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Synthetic RNA Silencing of Actinorhodin Biosynthesis in Streptomyces coelicolor A3(2). PLoS One 2013; 8:e67509. [PMID: 23826310 PMCID: PMC3694883 DOI: 10.1371/journal.pone.0067509] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 05/24/2013] [Indexed: 01/15/2023] Open
Abstract
We demonstrate the first application of synthetic RNA gene silencers in Streptomyces coelicolor A3(2). Peptide nucleic acid and expressed antisense RNA silencers successfully inhibited actinorhodin production. Synthetic RNA silencing was target-specific and is a new tool for gene regulation and metabolic engineering studies in Streptomyces.
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22
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Craney A, Ahmed S, Nodwell J. Towards a new science of secondary metabolism. J Antibiot (Tokyo) 2013; 66:387-400. [PMID: 23612726 DOI: 10.1038/ja.2013.25] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/12/2013] [Accepted: 02/12/2013] [Indexed: 12/20/2022]
Abstract
Secondary metabolites are a reliable and very important source of medicinal compounds. While these molecules have been mined extensively, genome sequencing has suggested that there is a great deal of chemical diversity and bioactivity that remains to be discovered and characterized. A central challenge to the field is that many of the novel or poorly understood molecules are expressed at low levels in the laboratory-such molecules are often described as the 'cryptic' secondary metabolites. In this review, we will discuss evidence that research in this field has provided us with sufficient knowledge and tools to express and purify any secondary metabolite of interest. We will describe 'unselective' strategies that bring about global changes in secondary metabolite output as well as 'selective' strategies where a specific biosynthetic gene cluster of interest is manipulated to enhance the yield of a single product.
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Affiliation(s)
- Arryn Craney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Michael Degroote Institute for Infectious Diseases Research, Hamilton, Ontario, Canada
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23
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Swiercz JP, Nanji T, Gloyd M, Guarné A, Elliot MA. A novel nucleoid-associated protein specific to the actinobacteria. Nucleic Acids Res 2013; 41:4171-84. [PMID: 23427309 PMCID: PMC3627587 DOI: 10.1093/nar/gkt095] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Effective chromosome organization is central to the functioning of any cell. In bacteria, this organization is achieved through the concerted activity of multiple nucleoid-associated proteins. These proteins are not, however, universally conserved, and different groups of bacteria have distinct subsets that contribute to chromosome architecture. Here, we describe the characterization of a novel actinobacterial-specific protein in Streptomyces coelicolor. We show that sIHF (SCO1480) associates with the nucleoid and makes important contributions to chromosome condensation and chromosome segregation during Streptomyces sporulation. It also affects antibiotic production, suggesting an additional role in gene regulation. In vitro, sIHF binds DNA in a length-dependent but sequence-independent manner, without any obvious structural preferences. It does, however, impact the activity of topoisomerase, significantly altering DNA topology. The sIHF–DNA co-crystal structure reveals sIHF to be composed of two domains: a long N-terminal helix and a C-terminal helix-two turns-helix domain with two separate DNA interaction sites, suggesting a potential role in bridging DNA molecules.
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Affiliation(s)
- Julia P Swiercz
- Department of Biology and Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada
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24
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Marcellin E, Mercer TR, Licona-Cassani C, Palfreyman RW, Dinger ME, Steen JA, Mattick JS, Nielsen LK. Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch. BMC Genomics 2013; 14:15. [PMID: 23324121 PMCID: PMC3610266 DOI: 10.1186/1471-2164-14-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/20/2012] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Actinobacteria form a major bacterial phylum that includes numerous human pathogens. Actinobacteria are primary contributors to carbon cycling and also represent a primary source of industrial high value products such as antibiotics and biopesticides. Consistent with other members of the actinobacterial phylum, Saccharopolyspora erythraea undergo a transitional switch. This switch is characterized by numerous metabolic and morphological changes. RESULTS We performed RNA sequencing to analyze the transcriptional changes that occur during growth of Saccharopolyspora erythraea in batch culture. By sequencing RNA across the fermentation time course, at a mean coverage of 4000X, we found the vast majority of genes to be prominently expressed, showing that we attained close to saturating sequencing coverage of the transcriptome. During the metabolic switch, global changes in gene expression influence the metabolic machinery of Saccharopolyspora erythraea, resetting an entirely novel gene expression program. After the switch, global changes include the broad repression of half the genes regulated by complex transcriptional mechanisms. Paralogous transposon clusters, delineate these transcriptional programs. The new transcriptional program is orchestrated by a bottleneck event during which mRNA levels are severely restricted by targeted mRNA degradation. CONCLUSIONS Our results, which attained close to saturating sequencing coverage of the transcriptome, revealed unanticipated transcriptional complexity with almost one third of transcriptional content originating from un-annotated sequences. We showed that the metabolic switch is a sophisticated mechanism of transcriptional regulation capable of resetting and re-synchronizing gene expression programs at extraordinary speed and scale.
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Affiliation(s)
- Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Qld 4072, Australia
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Abstract
Cyclic AMP receptor protein (Crp) is a transcription regulator controlling diverse cellular processes in many bacteria. In Streptomyces coelicolor, it is well established that Crp plays a critical role in spore germination and colony development. Here, we demonstrate that Crp is a key regulator of secondary metabolism and antibiotic production in S. coelicolor and show that it may additionally coordinate precursor flux from primary to secondary metabolism. We found that crp deletion adversely affected the synthesis of three well-characterized antibiotics in S. coelicolor: actinorhodin (Act), undecylprodigiosin (Red), and calcium-dependent antibiotic (CDA). Using chromatin immunoprecipitation-microarray (ChIP-chip) assays, we determined that eight (out of 22) secondary metabolic clusters encoded by S. coelicolor contained Crp-associated sites. We followed the effect of Crp induction using transcription profiling analyses and found secondary metabolic genes to be significantly affected: included in this Crp-dependent group were genes from six of the clusters identified in the ChIP-chip experiments. Overexpressing Crp in a panel of Streptomyces species led to enhanced antibiotic synthesis and new metabolite production, suggesting that Crp control over secondary metabolism is broadly conserved in the streptomycetes and that Crp overexpression could serve as a powerful tool for unlocking the chemical potential of these organisms. Streptomyces produces a remarkably diverse array of secondary metabolites, including many antibiotics. In recent years, genome sequencing has revealed that these products represent only a small proportion of the total secondary metabolite potential of Streptomyces. There is, therefore, considerable interest in discovering ways to stimulate the production of new metabolites. Here, we show that Crp (the classical regulator of carbon catabolite repression in Escherichia coli) is a master regulator of secondary metabolism in Streptomyces. It binds to eight of 22 secondary metabolic gene clusters in the Streptomyces coelicolor genome and directly affects the expression of six of these. Deletion of crp in S. coelicolor leads to dramatic reductions in antibiotic levels, while Crp overexpression enhances antibiotic production. We find that the antibiotic-stimulatory capacity of Crp extends to other streptomycetes, where its overexpression activates the production of “cryptic” metabolites that are not otherwise seen in the corresponding wild-type strain.
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Jung J, Yu KO, Ramzi AB, Choe SH, Kim SW, Han SO. Improvement of surfactin production in Bacillus subtilis using synthetic wastewater by overexpression of specific extracellular signaling peptides, comX and phrC. Biotechnol Bioeng 2012; 109:2349-56. [DOI: 10.1002/bit.24524] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 03/12/2012] [Accepted: 04/04/2012] [Indexed: 11/07/2022]
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Duong A, Capstick DS, Di Berardo C, Findlay KC, Hesketh A, Hong HJ, Elliot MA. Aerial development in Streptomyces coelicolor requires sortase activity. Mol Microbiol 2012; 83:992-1005. [PMID: 22296345 DOI: 10.1111/j.1365-2958.2012.07983.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Streptomyces coelicolor is a multicellular bacterium whose life cycle encompasses three differentiated states: vegetative hyphae, aerial hyphae and spores. Among the factors required for aerial development are the 'chaplins', a family of eight secreted proteins that coat the surface of aerial hyphae. Three chaplins (the 'long' chaplins, ChpA, B and C) possess an LAXTG-containing C-terminal sorting signal and are predicted sortase substrates. The five remaining 'short' chaplins are presumed to be associated with the cell surface through interactions with the long chaplins. We show here that two sortase enzymes, SrtE1 and SrtE2, cleave LAXTG-containing peptides at two distinct positions in vitro, and are required for cell wall anchoring of ChpC in vivo. srtE1/E2 double mutants are delayed in aerial hyphae formation, do not sporulate and fail to display all short chaplins on their aerial surfaces. Surprisingly, these mutant characteristics were not shared by a long chaplin mutant, which exhibited only modest delays in aerial development, leading us to revise the current model of chaplin-mediated aerial development. The sortase mutant phenotype, instead, appears to stem from an inability to transcribe aerial hyphae-specific genes, whose products have diverse functions. This suggests that sortase activity triggers an important, and previously unknown, developmental checkpoint.
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Affiliation(s)
- Andrew Duong
- Department of Biology and Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada
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Nah JH, Park SH, Yoon HM, Choi SS, Lee CH, Kim ES. Identification and characterization of wblA-dependent tmcT regulation during tautomycetin biosynthesis in Streptomyces sp. CK4412. Biotechnol Adv 2011; 30:202-9. [PMID: 21624452 DOI: 10.1016/j.biotechadv.2011.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 05/04/2011] [Accepted: 05/08/2011] [Indexed: 11/19/2022]
Abstract
Tautomycetin (TMC) is an unusual linear polyketide compound esterified with a cyclic anhydride. It exhibits novel activated T cell-specific immunosuppressant as well as anti-cancer activities. Previously, we isolated and characterized the entire TMC biosynthetic gene cluster from Streptomyces sp. CK4412, including a TMC pathway-specific gene, tmcN, the over-expression of which led to a significant increase in TMC productivity. In addition, we also reported that WblA acts as a global down-regulator of antibiotic biosynthesis through pathway-specific regulation in Streptomyces species. Here, we confirm that TmcT acts as another TMC pathway-specific regulator within the TMC biosynthetic cluster. Specifically, tmcT deletion resulted in the complete loss of TMC production, whereas complementation with a tmcT-carrying integrative plasmid significantly restored TMC biosynthesis. We also identified a 0.39kb wblA ortholog (named wblA(tmc)) from Streptomyces sp. CK4412 via genomic DNA library screening that showed 96% amino acid identity compared to a previously-known S. coelicolor wblA. Targeted gene disruption of wblA(tmc) in Streptomyces sp. CK4412 exhibited approximately 3-fold higher TMC productivity than that in the wild-type strain. Moreover, transcription analyses of the TMC biosynthetic and regulatory genes revealed that the expression of tmcT was strongly down-regulated by wblA(tmc). These results imply that the TMC biosynthetic regulation network is controlled by two pathway-specific positive regulator, WblA(tmc)-dependent TmcT as well as WblA(tmc)-independent TmcN in Streptomyces sp. CK4412.
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Affiliation(s)
- Ji-Hye Nah
- Department of Biological Engineering, Inha University, Incheon, Republic of Korea
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