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García-Santisteban R, Linares-Alba MA, Botello-Bárcenas A, Margay P, Soto C, Fonzar-Furtado J, Brooks D, García D, Sánchez GAG. Subconjunctival liposomal sirolimus vs. cyclosporine or tacrolimus as treatment of keratoconjunctivitis sicca in dogs: A double-blind, randomized study. Vet Ophthalmol 2024. [PMID: 38329299 DOI: 10.1111/vop.13190] [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: 06/27/2023] [Revised: 01/04/2024] [Accepted: 01/24/2024] [Indexed: 02/09/2024]
Abstract
PURPOSE To compare the safety and efficacy of a 100 microgram subconjunctival injection of liposome-encapsulated sirolimus (SCJS) to cyclosporine (CsA) or tacrolimus (CsA/T) for the treatment of keratoconjunctivitis sicca (KCS) in dogs. METHODS Dogs with signs and symptoms of KCS were block-randomized to one of two treatment groups: Biweekly SCJS or conventional treatment (CsA/T). Schirmer tear test 1 (STT-1) scores, conjunctival hyperemia (CH) scores, corneal opacity (CO) scores, and clinical evaluation of potential side effects were recorded every 2 weeks for 14 weeks for both groups. Differences between groups were analyzed using the mixed results ANOVA and U-Mann Whitney tests (p < .05 was considered significant). RESULTS A total of 30 eyes were included in the study, of which 20 eyes completed follow-up. There was no statistically significant interaction between the treatment group and time on STT-1 score (p = .165), and median CH and CO scores showed no statistically significant differences between groups (p = .353 and p = .393, respectively). There were no clinically significant side effects present in any subject at any time. CONCLUSION In this trial, a 1 mg/mL (100 micrograms) SCJS every 2 weeks showed similar safety and efficacy profiles as daily CsA/T in dogs with KS after 14 weeks of treatment. Larger studies should be performed to further assess SCJS as an alternative treatment for KCS.
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Affiliation(s)
| | | | | | - Paola Margay
- Hospital Veterinario Oftalvet, Mexico City, Mexico
| | - Carlos Soto
- Hospital Veterinario Oftalvet, Mexico City, Mexico
| | | | - Dennis Brooks
- University of Florida, Gainesville, Florida, USA
- Brookseyes LLC, Alachua, Florida, USA
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Khan S, Srivastava S, Karnwal A, Malik T. Streptomyces as a promising biological control agents for plant pathogens. Front Microbiol 2023; 14:1285543. [PMID: 38033592 PMCID: PMC10682734 DOI: 10.3389/fmicb.2023.1285543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Plant diseases caused by pathogenic microorganisms in agriculture present a considerable obstacle, resulting in approximately 30-40% crop damage. The use of conventional techniques to manage these microorganisms, i.e., applying chemical pesticides and antimicrobials, has been discovered to have adverse effects on human health and the environment. Furthermore, these methods have contributed to the emergence of resistance among phytopathogens. Consequently, it has become imperative to investigate natural alternatives to address this issue. The Streptomyces genus of gram-positive bacteria is a potentially viable natural alternative that has been extensively researched due to its capacity to generate diverse antimicrobial compounds, such as metabolites and organic compounds. Scientists globally use diverse approaches and methodologies to extract new bioactive compounds from these bacteria. The efficacy of bioactive compounds in mitigating various phytopathogens that pose a significant threat to crops and plants has been demonstrated. Hence, the Streptomyces genus exhibits potential as a biological control agent for combating plant pathogens. This review article aims to provide further insight into the Streptomyces genus as a source of antimicrobial compounds that can potentially be a biological control against plant pathogens. The investigation of various bioactive compounds synthesized by this genus can enhance our comprehension of their prospective utilization in agriculture.
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Affiliation(s)
- Shaista Khan
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Seweta Srivastava
- School of Agriculture, Lovely Professional University, Phagwara, Punjab, India
| | - Arun Karnwal
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Tabarak Malik
- Department of Biomedical sciences, Jimma University, Jimma, Ethiopia
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3
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Gu B, Kim DG, Kim DK, Kim M, Kim HU, Oh MK. Heterologous overproduction of oviedomycin by refactoring biosynthetic gene cluster and metabolic engineering of host strain Streptomyces coelicolor. Microb Cell Fact 2023; 22:212. [PMID: 37838667 PMCID: PMC10576301 DOI: 10.1186/s12934-023-02218-8] [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: 07/09/2023] [Accepted: 09/28/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND Oviedomycin is one among several polyketides known for their potential as anticancer agents. The biosynthetic gene cluster (BGC) for oviedomycin is primarily found in Streptomyces antibioticus. However, because this BGC is usually inactive under normal laboratory conditions, it is necessary to employ systematic metabolic engineering methods, such as heterologous expression, refactoring of BGCs, and optimization of precursor biosynthesis, to allow efficient production of these compounds. RESULTS Oviedomycin BGC was captured from the genome of Streptomyces antibioticus by a newly constructed plasmid, pCBA, and conjugated into the heterologous strain, S. coelicolor M1152. To increase the production of oviedomycin, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system was utilized in an in vitro setting to refactor the native promoters within the ovm BGC. The target promoters of refactoring were selected based on examination of factors such as transcription levels and metabolite profiling. Furthermore, genome-scale metabolic simulation was applied to find overexpression targets that could enhance the biosynthesis of precursors or cofactors related to oviedomycin production. The combined approach led to a significant increase in oviedomycin production, reaching up to 670 mg/L, which is the highest titer reported to date. This demonstrates the potential of the approach undertaken in this study. CONCLUSIONS The metabolic engineering approach used in this study led to the successful production of a valuable polyketide, oviedomycin, via BGC cloning, promoter refactoring, and gene manipulation of host metabolism aided by genome-scale metabolic simulation. This approach can be also useful for the efficient production of other secondary molecules encoded by 'silent' BGCs.
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Affiliation(s)
- Boncheol Gu
- Department of Chemical & Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Duck Gyun Kim
- Department of Chemical & Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Do-Kyung Kim
- Department of Chemical & Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Minji Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| | - Min-Kyu Oh
- Department of Chemical & Biological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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Molecular and therapeutic insights of rapamycin: a multi-faceted drug from Streptomyces hygroscopicus. Mol Biol Rep 2023; 50:3815-3833. [PMID: 36696023 PMCID: PMC9875782 DOI: 10.1007/s11033-023-08283-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
The advancement in pharmaceutical research has led to the discovery and development of new combinatorial life-saving drugs. Rapamycin is a macrolide compound produced from Streptomyces hygroscopicus. Rapamycin and its derivatives are one of the promising sources of drug with broad spectrum applications in the medical field. In recent times, rapamycin has gained significant attention as of its activity against cytokine storm in COVID-19 patients. Rapamycin and its derivatives have more potency when compared to other prevailing drugs. Initially, it has been used exclusively as an anti-fungal drug. Currently rapamycin has been widely used as an immunosuppressant. Rapamycin is a multifaceted drug; it has anti-cancer, anti-viral and anti-aging potentials. Rapamycin has its specific action on mTOR signaling pathway. mTOR has been identified as a key regulator of different pathways. There will be an increased demand for rapamycin, because it has lesser adverse effects when compared to steroids. Currently researchers are focused on the production of effective rapamycin derivatives to combat the growing demand of this wonder drug. The main focus of the current review is to explore the origin, development, molecular mechanistic action, and the current therapeutic aspects of rapamycin. Also, this review article revealed the potential of rapamycin and the progress of rapamycin research. This helps in understanding the exact potency of the drug and could facilitate further studies that could fill in the existing knowledge gaps. The study also gathers significant data pertaining to the gene clusters and biosynthetic pathways involved in the synthesis and production of this multi-faceted drug. In addition, an insight into the mechanism of action of the drug and important derivatives of rapamycin has been expounded. The fillings of the current review, aids in understanding the underlying molecular mechanism, strain improvement, optimization and production of rapamycin derivatives.
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Gong X, Yu Y, Hao Y, Wang Q, Ma J, Jiang Y, Lv G, Li L, Qian C. Characterizing corn-straw-degrading actinomycetes and evaluating application efficiency in straw-returning experiments. Front Microbiol 2022; 13:1003157. [PMID: 36545193 PMCID: PMC9760696 DOI: 10.3389/fmicb.2022.1003157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/16/2022] [Indexed: 12/10/2022] Open
Abstract
Corn straw is an abundant lignocellulose resource and by-product of agricultural production. With the continuous increase in agricultural development, the output of corn straw is also increasing significantly. However, the inappropriate disposal of straw results in wasting of resources, and also causes a serious ecological crisis. Screening microorganisms with the capacity to degrade straw and understanding their mechanism of action is an efficient approach to solve such problems. For this purpose, our research group isolated three actinomycete strains with efficient lignocellulose degradation ability from soil in the cold region of China: Streptomyces sp. G1T, Streptomyces sp. G2T and Streptomyces sp. G3T. Their microbial properties and taxonomic status were assessed to improve our understanding of these strains. The three strains showed typical characteristics of the genus Streptomyces, and likely represent three different species. Genome functional annotation indicated that most of their genes were related to functions like carbohydrate transport and metabolism. In addition, a similar phenomenon also appeared in the COG and CAZyme analyses, with a large number of genes encoding carbohydrate-related hydrolases, such as cellulase, glycosidase and endoglucanase, which could effectively destroy the structure of lignocellulose in corn straw. This unambiguously demonstrated the potential of the three microorganisms to hydrolyze macromolecular polysaccharides at the molecular level. In addition, in the straw-returning test, the decomposing consortium composed of the three Streptomyces isolates (G123) effectively destroyed the recalcitrant bonds between the various components of straw, and significantly reduced the content of active components in corn straw. Furthermore, microbial diversity analysis indicated that the relative abundance of Proteobacteria, reportedly associated with soil antibiotic resistance and antibiotic degradation, was significantly improved with straw returning at both tested time points. The microbial diversity of each treatment was also dramatically changed by supplementing with G123. Taken together, G123 has important biological potential and should be further studied, which will provide new insights and strategies for appropriate treatment of corn straw.
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Affiliation(s)
- Xiujie Gong
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yang Yu
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yubo Hao
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qiuju Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
| | - Juntao Ma
- Institute of Biotechnology, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yubo Jiang
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Guoyi Lv
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Liang Li
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chunrong Qian
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China,*Correspondence: Chunrong Qian,
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Genomic Investigation of Desert Streptomyces huasconensis D23 Reveals Its Environmental Adaptability and Antimicrobial Activity. Microorganisms 2022; 10:microorganisms10122408. [PMID: 36557661 PMCID: PMC9784485 DOI: 10.3390/microorganisms10122408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The harsh climatic conditions of deserts may lead to unique adaptations of microbes, which could serve as potential sources of new metabolites to cope with environmental stresses. However, the mechanisms governing the environmental adaptability and antimicrobial activity of desert Streptomyces remain inadequate, especially in extreme temperature differences, drought conditions, and strong radiation. Here, we isolated a Streptomyces strain from rocks in the Kumtagh Desert in Northwest China and tested its antibacterial activity, resistance to UV-C irradiation, and tolerance to hydrogen peroxide (H2O2). The whole-genome sequencing was carried out to study the mechanisms underlying physiological characteristics and ecological adaptation from a genomic perspective. This strain has a growth inhibitory effect against a variety of indicator bacteria, and the highest antibacterial activity recorded was against Bacillus cereus. Moreover, strain D23 can withstand UV-C irradiation up to 100 J/m2 (D10 = 80 J/m2) and tolerate stress up to 70 mM H2O2. The genome prediction of strain D23 revealed the mechanisms associated with its adaptation to extreme environmental and stressful conditions. In total, 33 biosynthetic gene clusters (BGCs) were predicted based on anti-SMASH. Gene annotation found that S. huasconensis D23 contains several genes and proteins associated with the biosynthesis of factors required to cope with environmental stress of temperature, UV radiation, and osmotic pressure. The results of this study provide information about the genome and BGCs of the strain S. huasconensis D23. The experimental results combined with the genome sequencing data show that antimicrobial activity and stress resistance of S. huasconensis D23 was due to the rich and diverse secondary metabolite production capacity and the induction of stress-responsive genes. The environmental adaptability and antimicrobial activity information presented here will be valuable for subsequent work regarding the isolation of bioactive compounds and provide insight into the ecological adaptation mechanism of microbes to extreme desert environments.
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7
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Chen J, Lan X, Jia R, Hu L, Wang Y. Response Surface Methodology (RSM) Mediated Optimization of Medium Components for Mycelial Growth and Metabolites Production of Streptomyces alfalfae XN-04. Microorganisms 2022; 10:microorganisms10091854. [PMID: 36144456 PMCID: PMC9501596 DOI: 10.3390/microorganisms10091854] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
Streptomyces alfalfae XN-04 has been reported for the production of antifungal metabolites effectively to control Fusarium wilt of cotton, caused by Fusarium oxysporum f. sp. vasinfectum (Fov). In this study, we used integrated statistical experimental design methods to investigate the optimized liquid fermentation medium components of XN-04, which can significantly increase the antifungal activity and biomass of XN-04. Seven variables, including soluble starch, KNO3, soybean cake powder, K2HPO4, MgSO4·7H2O, CaCO3 and FeSO4·7H2O, were identified as the best ingredients based on one-factor-at-a-time (OFAT) method. The results of Plackett–Burman Design (PBD) showed that soluble starch, soybean cake powder and K2HPO4 were the most significant variables among the seven variables. The steepest climbing experiment and response surface methodology (RSM) were performed to determine the interactions among these three variables and fine-tune the concentrations. The optimal compositions of medium were as follows: soluble starch (26.26 g/L), KNO3 (1.00 g/L), soybean cake powder (23.54 g/L), K2HPO4 (0.27 g/L), MgSO4·7H2O (0.50 g/L), CaCO3 (1.00 g/L) and FeSO4·7H2O (0.10 g/L). A verification experiment was then carried out under the optimized conditions, and the results revealed the mycelial dry weight of S. alfalfae XN-04 reaching 6.61 g/L. Compared with the initial medium, a 7.47-fold increase in the biomass was achieved using the optimized medium. Moreover, the active ingredient was purified from the methanol extract of S. alfalfae XN-04 mycelium and then identified as roflamycoin (a polyene macrolide antibiotic). The results may provide new insights into the development of S. alfalfae XN-04 fermentation process and the control of the Fusarium wilt of cotton and other plant diseases.
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Affiliation(s)
| | | | | | | | - Yang Wang
- Correspondence: ; Tel.: +86-187-9280-9011
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8
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Jo HG, Adidjaja JJ, Kim DK, Park BS, Lee N, Cho BK, Kim HU, Oh MK. Comparative genomic analysis of Streptomyces rapamycinicus NRRL 5491 and its mutant overproducing rapamycin. Sci Rep 2022; 12:10302. [PMID: 35717543 PMCID: PMC9206652 DOI: 10.1038/s41598-022-14199-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 06/02/2022] [Indexed: 12/04/2022] Open
Abstract
Streptomyces rapamycinicus NRRL 5491 is a well-known producer of rapamycin, a secondary metabolite with useful bioactivities, including antifungal, antitumor, and immunosuppressive functions. For the enhanced rapamycin production, a rapamycin-overproducing strain SRMK07 was previously obtained as a result of random mutagenesis. To identify genomic changes that allowed the SRMK07 strain’s enhanced rapamycin production, genomes of the NRRL 5491 and SRMK07 strains were newly sequenced in this study. The resulting genome sequences of the wild-type and SRMK07 strains showed the size of 12.47 Mbp and 9.56 Mbp, respectively. Large deletions were observed at both end regions of the SRMK07 strain’s genome, which cover 17 biosynthetic gene clusters (BGCs) encoding secondary metabolites. Also, genes in a genomic region containing the rapamycin BGC were shown to be duplicated. Finally, comparative metabolic network analysis using these two strains’ genome-scale metabolic models revealed biochemical reactions with different metabolic fluxes, which were all associated with NADPH generation. Taken together, the genomic and computational approaches undertaken in this study suggest biological clues for the enhanced rapamycin production of the SRMK07 strain. These clues can also serve as a basis for systematic engineering of a production host for further enhanced rapamycin production.
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Affiliation(s)
- Hee-Geun Jo
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Joshua Julio Adidjaja
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Do-Kyung Kim
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Bu-Soo Park
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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9
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Lee SM, Cho DH, Jung HJ, Kim B, Kim SH, Bhatia SK, Gurav R, Jeon JM, Yoon JJ, Kim W, Choi KY, Yang YH. Finding of novel polyhydroxybutyrate producer Loktanella sp. SM43 capable of balanced utilization of glucose and xylose from lignocellulosic biomass. Int J Biol Macromol 2022; 208:809-818. [PMID: 35364206 DOI: 10.1016/j.ijbiomac.2022.03.155] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/13/2022] [Accepted: 03/23/2022] [Indexed: 11/05/2022]
Abstract
Polyhydroxybutyrate (PHB) is a potential substitute for plastics derived from fossil fuels, owing to its biodegradable and biocompatible properties. Lignocellulosic biomass could be used to reduce PHB production costs; however, the co-utilization of sugars, such as glucose and xylose, without catabolite repression is a difficult problem to be solved. Here, we selected a novel Loktanella sp. SM43 from a marine environment and optimized the conditions for PHB production. Loktanella sp. SM43 showed high PHB production (66.5% content) from glucose. When glucose and xylose were used together, this strain showed high utilization of both substrates compared to other high PHB-producers such as Halomonas sp. and Cupriavidus necator, which showed glucose preference. Loktanella sp. SM43 showed high growth and PHB production with lignocellulosic hydrolysates. When pine tree hydrolysates were used, PHB production was the highest at 3.66 ± 0.01 g/L, followed by Miscanthus (3.46 ± 0.09 g/L) and barley straw hydrolysate (3.36 ± 0.36 g/L). Overall, these results reveal the potential of Loktanella sp. SM43 to produce PHB using various lignocellulosic hydrolysates as feedstock and the first systematic study for PHB production with Loktanella sp. The approach of screening novel strains is a strategy to overcome co-utilization of sugars without genetic engineering.
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Affiliation(s)
- Sun Mi Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Do-Hyun Cho
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Hee Ju Jung
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Byungchan Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Su Hyun Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Ranjit Gurav
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea
| | - Jong-Min Jeon
- Green & Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Republic of Korea
| | - Jeong-Jun Yoon
- Green & Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Republic of Korea
| | - Wooseong Kim
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Kwon-Young Choi
- Department of Environmental and Safety Engineering, College of Engineering, Ajou University, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Republic of Korea.
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Streptomyces gobiensis sp. nov., an antimicrobial producing actinobacterium isolated from soil under black Gobi rocks. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005318] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A novel actinomycete, strain 1_25T, was isolated from soil under a black Gobi rock sample from Shuangta, PR China, and characterized using a polyphasic taxonomic approach. The results of comparative analysis of the 16S rRNA gene sequences indicated the 1_25T represented a member of the genus
Streptomyces
. Chemotaxonomic data revealed that 1_25T possessed MK-9(H8) as the major menaquinone. The cell wall contained ll-diaminopimelic acid (ll-DAP) and the whole-cell sugar pattern consisted of ribose, glucose and galactose. Major fatty acid methyl esters were observed to be iso-C16 : 0 (23.6 %), and anteiso-C15 : 0 (10.4 %). The genomic DNA G+C content of 1_25T was 69 mol %. The results of phylogenetic analysis based on 16S rRNA gene sequence indicated that 1_25T had high sequence similarity with
Streptomyces qinglanensis
172205T (98.1 %),
Streptomyces lycii
TRM 66187T (98 %), and
Streptomyces griseocarneus
JCM4580T (98 %). In addition to the differences in phenotypic characters, the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between 1_25T and closely related species were below the recommended threshold values for assigning strains to the same species. The fermentation product of 1_25T in ISP2 had an inhibitory effect on
Staphylococcus aureus
. On the basis of these genotypic and phenotypic characteristics, strain 1_25T (=JCM 34936T=GDMCC 4.216T) represents a novel species of the genus
Streptomyces
, for which the name Streptomyces gobiensis sp. nov. is proposed.
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Zhao S, Cheng M, Lin C, Liu H, Wang Z, Zhang K, Song S, Yang Q. Streptomyces luteolifulvus sp. nov., a novel actinomycete isolated from soil in Nanjing, China. Antonie van Leeuwenhoek 2021; 114:1829-1839. [PMID: 34460021 DOI: 10.1007/s10482-021-01643-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022]
Abstract
During the investigation of exploring potential sources of novel species and natural bioactives, a novel actinomycete, designated strain HIT-DPA4T, was isolated from a soil sample, which was collected from Nanjing, Jiangsu Province, PR China and characterized using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities and the result of phylogenetic analysis, strain HIT-DPA4T was most closely related to Streptomyces cyaneus CGMCC 4.1671 T, and shared the highest sequence similarity of 98.76%. In addition, the cell walls of the species HIT-DPA4T contained LL-diaminopimelic acid as the diagnostic diamino acid and the whole-cell hydrolysates were identified as glucose and ribose, and the principal phospholipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside and phosphatidylmonomethylethanolamine. MK-9(H6) and MK-9(H4) were predominant menaquinones; and C16:0, anteiso-C15:0 and C15:0 as major cellular fatty acids of the organism HIT-DPA4T. Gene Ontology database analysis and antiSMASH server predicted results displayed that strain HIT-DPA4T was a promising classification units, which has various types of functions and contains multiple biosynthetic gene clusters with the similarity more than 80%. Multilocus sequence analysis (MLSA) of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) illustrated that Streptomyces luteolifulvus formed a separate branch in the genus Streptomyces. However, a combination of low level of DNA-DNA relatedness and physiological properties indicated that strain HIT-DPA4T can be distinguished from its phylogenetically related species Streptomyces cyaneus CGMCC 4.1671 T. Moreover, gene synteny research could be further differed organism HIT-DPA4T from similarity species. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces luteolifulvus sp. nov. is proposed. The type strain is HIT-DPA4T (= CGMCC 4.7558 T = TISTR 2751 T).
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Affiliation(s)
- Shanshan Zhao
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China
| | - Ming Cheng
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China
| | - Congyu Lin
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China
| | - He Liu
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China
| | - Zhengran Wang
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China
| | - Kai Zhang
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China
| | - Simin Song
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China
| | - Qian Yang
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China.
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Bibyk MJ, Campbell MJ, Hummon AB. Mass spectrometric investigations of caloric restriction mimetics. Proteomics 2021; 21:e2000121. [PMID: 33460282 PMCID: PMC8262777 DOI: 10.1002/pmic.202000121] [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: 08/15/2020] [Revised: 11/17/2020] [Accepted: 12/07/2020] [Indexed: 11/11/2022]
Abstract
Caloric restriction (CR) is an innovative therapy used in tumor tissue and tumor model studies to promote cell death and decrease cell viability. Caloric restriction mimetics (CRMs) are a class of drugs that induce CR and starvation conditions within a cell. When used simultaneously with other chemotherapy agents, the effects are synergistic and effective at promoting tumor cell death. In this review, we discuss CRMs and their potential as cancer therapeutics. Firstly, we establish an overview of CR and its impacts on healthy and tumor cells. CR and CRM drugs have shown to decrease age-related diseases and can act as an anti-cancer agent. As it can be challenging for an individual to diligently stick to a diet that would induce CR, CRMs are even more desirable. Then, we discuss the drug class by highlighting three CRMs: resveratrol, (-)-hydroxycitric acid, and rapamycin. These CRMs are commonly known for their dietary effects, but the underlying mechanisms that drive cellular metabolic and proteomic changes show promise as a cancer therapeutic. Lastly, we highlight the use of mass spectrometry and proteomic techniques on experiments utilizing CRM drugs to understand the cellular pathways impacted by this drug class, leading to a better understanding of the anti-cancer properties and potentials of CRM.
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Affiliation(s)
- Michael J. Bibyk
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
| | - Melanie J. Campbell
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Amanda B. Hummon
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
- The Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
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13
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Maiti PK, Mandal S. Streptomyces cupreus sp. nov., an antimicrobial producing actinobacterium isolated from Himalayan soil. Arch Microbiol 2021; 203:1601-1609. [PMID: 33415367 DOI: 10.1007/s00203-020-02160-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 11/26/2022]
Abstract
A novel actinobacterium, designated Streptomyces sp strain PSKA01T, was isolated from a soil sample of Kashmir Himalaya, India (latitude:34˚-01'N; longitude:74˚-47'E; altitude: 5328 ft). The taxonomic position of this strain was revealed by a polyphasic approach. Comparative analysis of the 16S rRNA gene sequences indicated that PSKA01T was closely related to the members of the genus Streptomyces, with the highest similarity to Streptomyces venetus CMU-AB225T (99.3%), Streptomyces levis NBRC 15423 T (99.3%), Streptomyces misionensis DSM 40306 T (99.2%), Streptomyces carpinensis NRRL B-16921 T (99.2%), Streptomyces purpurascens NBRC 13077 T (99.2%), and Streptomyces phaeoluteichromatogenes NRRL 5799 T (99.2%). A phylogenomic tree based on genome sequences of the isolated strains, conferred by Type Strain Genome Server (TYGS), separated them from rest of the Streptomyces. The cell wall contained LL-diaminopimelic acid and the whole-cell hydrolysates were xylose and rhamnose. Major fatty acid methyl esters (FAME) were observed as 16:0 iso and 17:0 anteiso. In addition to the differences in phenotypic characters, the average nucleotide identity (ANI), average amino acid identity (AAI), digital DNA-DNA hybridization (dDDH) values, tetranucleotide frequency correlation coefficient (TETRA), and multilocus sequence analysis (MLSA) between PSKA01T and closely related type strains were considerably lower than the recommended threshold value; therefore, this isolate represents a novel Streptomyces species, for which the name Streptomyces cupreus sp. nov. is proposed. The type strain is PSKA01T (= JCM 33752 T = MCC 4182 T).
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Affiliation(s)
- Pulak Kumar Maiti
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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14
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Piroozmand F, Mohammadipanah F, Faridbod F. Emerging biosensors in detection of natural products. Synth Syst Biotechnol 2020; 5:293-303. [PMID: 32954023 PMCID: PMC7484522 DOI: 10.1016/j.synbio.2020.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 01/10/2023] Open
Abstract
Natural products (NPs) are a valuable source in the food, pharmaceutical, agricultural, environmental, and many other industrial sectors. Their beneficial properties along with their potential toxicities make the detection, determination or quantification of NPs essential for their application. The advanced instrumental methods require time-consuming sample preparation and analysis. In contrast, biosensors allow rapid detection of NPs, especially in complex media, and are the preferred choice of detection when speed and high throughput are intended. Here, we review diverse biosensors reported for the detection of NPs. The emerging approaches for improving the efficiency of biosensors, such as microfluidics, nanotechnology, and magnetic beads, are also discussed. The simultaneous use of two detection techniques is suggested as a robust strategy for precise detection of a specific NP with structural complexity in complicated matrices. The parallel detection of a variety of NPs structures or biological activities in a mixture of extract in a single detection phase is among the anticipated future advancements in this field which can be achieved using multisystem biosensors applying multiple flow cells, sensing elements, and detection mechanisms on miniaturized folded chips.
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Affiliation(s)
- Firoozeh Piroozmand
- Pharmaceutical Biotechnology Lab, Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455, Tehran, Iran
| | - Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology Lab, Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455, Tehran, Iran
| | - Farnoush Faridbod
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
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15
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Han YH, Choi TR, Park YL, Park JY, Song HS, Kim HJ, Lee SM, Park SL, Lee HS, Bhatia SK, Gurav R, Yang YH. Enhancement of pipecolic acid production by the expression of multiple lysine cyclodeaminase in the Escherichia coli whole-cell system. Enzyme Microb Technol 2020; 140:109643. [DOI: 10.1016/j.enzmictec.2020.109643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/06/2020] [Accepted: 08/04/2020] [Indexed: 12/14/2022]
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16
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Pham JV, Yilma MA, Feliz A, Majid MT, Maffetone N, Walker JR, Kim E, Cho HJ, Reynolds JM, Song MC, Park SR, Yoon YJ. A Review of the Microbial Production of Bioactive Natural Products and Biologics. Front Microbiol 2019; 10:1404. [PMID: 31281299 PMCID: PMC6596283 DOI: 10.3389/fmicb.2019.01404] [Citation(s) in RCA: 233] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/04/2019] [Indexed: 12/24/2022] Open
Abstract
A variety of organisms, such as bacteria, fungi, and plants, produce secondary metabolites, also known as natural products. Natural products have been a prolific source and an inspiration for numerous medical agents with widely divergent chemical structures and biological activities, including antimicrobial, immunosuppressive, anticancer, and anti-inflammatory activities, many of which have been developed as treatments and have potential therapeutic applications for human diseases. Aside from natural products, the recent development of recombinant DNA technology has sparked the development of a wide array of biopharmaceutical products, such as recombinant proteins, offering significant advances in treating a broad spectrum of medical illnesses and conditions. Herein, we will introduce the structures and diverse biological activities of natural products and recombinant proteins that have been exploited as valuable molecules in medicine, agriculture and insect control. In addition, we will explore past and ongoing efforts along with achievements in the development of robust and promising microorganisms as cell factories to produce biologically active molecules. Furthermore, we will review multi-disciplinary and comprehensive engineering approaches directed at improving yields of microbial production of natural products and proteins and generating novel molecules. Throughout this article, we will suggest ways in which microbial-derived biologically active molecular entities and their analogs could continue to inspire the development of new therapeutic agents in academia and industry.
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Affiliation(s)
- Janette V. Pham
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Mariamawit A. Yilma
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Adriana Feliz
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Murtadha T. Majid
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Nicholas Maffetone
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Jorge R. Walker
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Eunji Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, South Korea
| | - Hyo Je Cho
- School of Life Sciences and Biotechnology, Kyungpook National University, Daegu, South Korea
| | - Jared M. Reynolds
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Myoung Chong Song
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, South Korea
| | - Sung Ryeol Park
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
- Natural Products Discovery Institute, Doylestown, PA, United States
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, South Korea
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Djinni I, Defant A, Djoudi W, Chaabane Chaouch F, Souagui S, Kecha M, Mancini I. Modeling improved production of the chemotherapeutic polypeptide actinomycin D by a novel Streptomyces sp. strain from a Saharan soil. Heliyon 2019; 5:e01695. [PMID: 31193702 PMCID: PMC6538969 DOI: 10.1016/j.heliyon.2019.e01695] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 03/30/2019] [Accepted: 05/07/2019] [Indexed: 12/21/2022] Open
Abstract
The novel bioactive actinobacterial strain GSBNT10 obtained from a Saharan soil, was taxonomically characterized using a polyphasic approach. 16S rRNA gene sequence analysis supported the classification of the isolate within the genus Streptomyces indicating it as a novel species. The major metabolite responsible of the bioactivity was purified and structurally characterized as actinomycin D (act-D) by mass spectrometric and nuclear magnetic resonance analyses Plackett-Burman design (PBD) and response surface methodology (RSM) were applied in order to optimize the medium formulation for the production of this bioactive metabolite. By PBD experiments, NaNO3, K2HPO4 and initial pH value were selected as significant variables affecting the metabolite production. Central Composite Design (CCD) showed that adjustment of the fermentative medium at pH 8.25, K2HPO4 at 0.2 gL-1 and NaNO3 at 3.76 gL-1 were the values suiting the production of act-D. Moreover, the results obtained by the statistical approach were confirmed by act-D detection using the HPLC equipped with a diode array detector and coupled online with electrospray-mass spectrometry (ESIMS) technique. act-D production was highly stimulated, obtaining a good yield (656.46 mgL-1) which corresponds to a 58.56% increase compared with the non-optimized conditions and data from LC-ESIMS technique efficiently confirmed the forecast from RSM.
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Affiliation(s)
- Ibtissem Djinni
- Laboratoire de Microbiologie Appliquée, Faculté des Sciences de la Nature et de la Vie, Département de Microbiologie, Université de Bejaia, 06000, Algeria.,Bioorganic Chemistry Laboratory, Department of Physics, University of Trento, via Sommarive 14, Povo, I-38123, Trento, Italy
| | - Andrea Defant
- Bioorganic Chemistry Laboratory, Department of Physics, University of Trento, via Sommarive 14, Povo, I-38123, Trento, Italy
| | - Warda Djoudi
- Laboratoire de Microbiologie Appliquée, Faculté des Sciences de la Nature et de la Vie, Département de Microbiologie, Université de Bejaia, 06000, Algeria
| | - Faouzia Chaabane Chaouch
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Alger, Algeria
| | - Samiha Souagui
- Bioorganic Chemistry Laboratory, Department of Physics, University of Trento, via Sommarive 14, Povo, I-38123, Trento, Italy
| | - Mouloud Kecha
- Laboratoire de Microbiologie Appliquée, Faculté des Sciences de la Nature et de la Vie, Département de Microbiologie, Université de Bejaia, 06000, Algeria
| | - Ines Mancini
- Bioorganic Chemistry Laboratory, Department of Physics, University of Trento, via Sommarive 14, Povo, I-38123, Trento, Italy
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Insights into the metabolic mechanism of rapamycin overproduction in the shikimate-resistant Streptomyces hygroscopicus strain UV-II using comparative metabolomics. World J Microbiol Biotechnol 2017; 33:101. [DOI: 10.1007/s11274-017-2266-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/12/2017] [Indexed: 01/27/2023]
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19
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Dutta S, Basak B, Bhunia B, Sinha A, Dey A. Approaches towards the enhanced production of Rapamycin by Streptomyces hygroscopicus MTCC 4003 through mutagenesis and optimization of process parameters by Taguchi orthogonal array methodology. World J Microbiol Biotechnol 2017; 33:90. [PMID: 28390015 DOI: 10.1007/s11274-017-2260-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 04/01/2017] [Indexed: 11/28/2022]
Abstract
The present research was conducted to define the approaches for enhanced production of rapamycin (Rap) by Streptomyces hygroscopicus microbial type culture collection (MTCC) 4003. Both physical mutagenesis by ultraviolet ray (UV) and chemical mutagenesis by N-methyl-N-nitro-N-nitrosoguanidine (NTG) have been applied successfully for the improvement of Rap production. Enhancing Rap yield by novel sequential UV mutagenesis technique followed by fermentation gives a significant difference in getting economically scalable amount of this industrially important macrolide compound. Mutant obtained through NTG mutagenesis (NTG-30-27) was found to be superior to others as it initially produced 67% higher Rap than wild type. Statistical optimization of nutritional and physiochemical parameters was carried out to find out most influential factors responsible for enhanced Rap yield by NTG-30-27 which was performed using Taguchi orthogonal array approach. Around 72% enhanced production was achieved with nutritional factors at their assigned level at 23 °C, 120 rpm and pH 7.6. Results were analysed in triplicate basis where validation and purification was carried out using high performance liquid chromatography. Stability study and potency of extracted Rap was supported by turbidimetric assay taking Candida albicans MTCC 227 as test organism.
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Affiliation(s)
- Subhasish Dutta
- Department of Biotechnology, National Institute of Technology Durgapur, Mahatma Gandhi Avenue, Durgapur, 713209, India
| | - Bikram Basak
- Energy Research and Technology Group, CSIR-Central Mechanical Engineering Research Institute, Mahatma Gandhi Avenue, Durgapur, 713209, India
| | - Biswanath Bhunia
- Department of Bioengineering, National Institute of Technology Agartala, Barjala, Tripura, 799055, India
| | - Ankan Sinha
- Department of Biotechnology, National Institute of Technology Durgapur, Mahatma Gandhi Avenue, Durgapur, 713209, India.,Bioprocess Development Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Apurba Dey
- Department of Biotechnology, National Institute of Technology Durgapur, Mahatma Gandhi Avenue, Durgapur, 713209, India.
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20
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Dang L, Liu J, Wang C, Liu H, Wen J. Enhancement of rapamycin production by metabolic engineering in Streptomyces hygroscopicus based on genome-scale metabolic model. ACTA ACUST UNITED AC 2017; 44:259-270. [DOI: 10.1007/s10295-016-1880-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/26/2016] [Indexed: 12/18/2022]
Abstract
Abstract
Rapamycin, as a macrocyclic polyketide with immunosuppressive, antifungal, and anti-tumor activity produced by Streptomyces hygroscopicus, is receiving considerable attention for its significant contribution in medical field. However, the production capacity of the wild strain is very low. Hereby, a computational guided engineering approach was proposed to improve the capability of rapamycin production. First, a genome-scale metabolic model of Streptomyces hygroscopicus ATCC 29253 was constructed based on its annotated genome and biochemical information. The model consists of 1003 reactions, 711 metabolites after manual refinement. Subsequently, several potential genetic targets that likely guaranteed an improved yield of rapamycin were identified by flux balance analysis and minimization of metabolic adjustment algorithm. Furthermore, according to the results of model prediction, target gene pfk (encoding 6-phosphofructokinase) was knocked out, and target genes dahP (encoding 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase) and rapK (encoding chorismatase) were overexpressed in the parent strain ATCC 29253. The yield of rapamycin increased by 30.8% by knocking out gene pfk and increased by 36.2 and 44.8% by overexpression of rapK and dahP, respectively, compared with parent strain. Finally, the combined effect of the genetic modifications was evaluated. The titer of rapamycin reached 250.8 mg/l by knockout of pfk and co-expression of genes dahP and rapK, corresponding to a 142.3% increase relative to that of the parent strain. The relationship between model prediction and experimental results demonstrates the validity and rationality of this approach for target identification and rapamycin production improvement.
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Affiliation(s)
- Lanqing Dang
- grid.419897.a 0000 0004 0369 313X Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
| | - Jiao Liu
- grid.419897.a 0000 0004 0369 313X Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
| | - Cheng Wang
- grid.419897.a 0000 0004 0369 313X Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
| | - Huanhuan Liu
- grid.419897.a 0000 0004 0369 313X Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
| | - Jianping Wen
- grid.419897.a 0000 0004 0369 313X Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
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21
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Streptomyces gamaensis sp. nov., a novel actinomycete with antifungal activity isolated from soil in Gama, Chad. Antonie van Leeuwenhoek 2016; 110:471-477. [PMID: 28005217 DOI: 10.1007/s10482-016-0816-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/05/2016] [Indexed: 10/20/2022]
Abstract
During an investigation exploring potential sources of novel species and natural products, a novel actinomycete with antifungal activity, designated strain NEAU-Gz11T, was isolated from a soil sample, which was collected from Gama, Chad. The isolate was found to have morphological and chemotaxonomic characteristics typical of members of the genus Streptomyces. 16S rRNA gene sequence similarity studies showed that strain NEAU-Gz11T belongs to the genus Streptomyces with high sequence similarity to Streptomyces hiroshimensis JCM 4098T (98.0 %). Similarities to other type strains of the genus Streptomyces were lower than 98.0 %. However, the physiological and biochemical characteristics and low levels of DNA-DNA relatedness could differentiate the isolate genotypically and phenotypically from S. hiroshimensis JCM 4098T. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces gamaensis sp. nov. is proposed. The type strain is NEAU-Gz11T (=CGMCC 4.7304T=DSM 101531T).
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Bennur T, Ravi Kumar A, Zinjarde S, Javdekar V. Nocardiopsis
species: a potential source of bioactive compounds. J Appl Microbiol 2015; 120:1-16. [DOI: 10.1111/jam.12950] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/16/2015] [Accepted: 07/07/2015] [Indexed: 12/12/2022]
Affiliation(s)
- T. Bennur
- Institute of Bioinformatics and Biotechnology; Savitribai Phule Pune University; Pune India
| | - A. Ravi Kumar
- Institute of Bioinformatics and Biotechnology; Savitribai Phule Pune University; Pune India
| | - S.S. Zinjarde
- Institute of Bioinformatics and Biotechnology; Savitribai Phule Pune University; Pune India
| | - V. Javdekar
- Department of Biotechnology; Abasaheb Garware College; Pune India
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Comparative metabolic profiling reveals the key role of amino acids metabolism in the rapamycin overproduction by Streptomyces hygroscopicus. ACTA ACUST UNITED AC 2015; 42:949-63. [DOI: 10.1007/s10295-015-1611-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 03/23/2015] [Indexed: 01/06/2023]
Abstract
Abstract
Rapamycin is an important natural macrolide antibiotic with antifungal, immunosuppressive and anticancer activity produced by Streptomyces hygroscopicus. In this study, a mutant strain obtained by ultraviolet mutagenesis displayed higher rapamycin production capacity compared to the wild-type S. hygroscopicus ATCC 29253. To gain insights into the mechanism of rapamycin overproduction, comparative metabolic profiling between the wild-type and mutant strain was performed. A total of 86 metabolites were identified by gas chromatography–mass spectrometry. Pattern recognition methods, including principal component analysis, partial least squares and partial least squares discriminant analysis, were employed to determine the key biomarkers. The results showed that 22 potential biomarkers were closely associated with the increase of rapamycin production and the tremendous metabolic difference was observed between the two strains. Furthermore, metabolic pathway analysis revealed that amino acids metabolism played an important role in the synthesis of rapamycin, especially lysine, valine, tryptophan, isoleucine, glutamate, arginine and ornithine. The inadequate supply of amino acids, or namely “nitrogen starvation” occurred in the mutant strain. Subsequently, the exogenous addition of amino acids into the fermentation medium of the mutant strain confirmed the above conclusion, and rapamycin production of the mutant strain increased to 426.7 mg/L after adding lysine, approximately 5.8-fold of that in the wild-type strain. Finally, the results of real-time PCR and enzyme activity assays demonstrated that dihydrodipicolinate synthase involved with lysine metabolism played vital role in the biosynthesis of rapamycin. These findings will provide a theoretical basis for further improving production of rapamycin.
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