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Lin J, Xiao Y, Liu H, Gao D, Duan Y, Zhu X. Combined transcriptomic and pangenomic analyses guide metabolic amelioration to enhance tiancimycins production. Appl Microbiol Biotechnol 2024; 108:18. [PMID: 38170317 DOI: 10.1007/s00253-023-12937-y] [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: 08/03/2023] [Revised: 11/15/2023] [Accepted: 11/26/2023] [Indexed: 01/05/2024]
Abstract
Exploration of high-yield mechanism is important for further titer improvement of valuable antibiotics, but how to achieve this goal is challenging. Tiancimycins (TNMs) are anthraquinone-fused enediynes with promising drug development potentials, but their prospective applications are limited by low titers. This work aimed to explore the intrinsic high-yield mechanism in previously obtained TNMs high-producing strain Streptomyces sp. CB03234-S for the further titer amelioration of TNMs. First, the typical ribosomal RpsL(K43N) mutation in CB03234-S was validated to be merely responsible for the streptomycin resistance but not the titer improvement of TNMs. Subsequently, the combined transcriptomic, pan-genomic and KEGG analyses revealed that the significant changes in the carbon and amino acid metabolisms could reinforce the metabolic fluxes of key CoA precursors, and thus prompted the overproduction of TNMs in CB03234-S. Moreover, fatty acid metabolism was considered to exert adverse effects on the biosynthesis of TNMs by shunting and reducing the accumulation of CoA precursors. Therefore, different combinations of relevant genes were respectively overexpressed in CB03234-S to strengthen fatty acid degradation. The resulting mutants all showed the enhanced production of TNMs. Among them, the overexpression of fadD, a key gene responsible for the first step of fatty acid degradation, achieved the highest 21.7 ± 1.1 mg/L TNMs with a 63.2% titer improvement. Our studies suggested that comprehensive bioinformatic analyses are effective to explore metabolic changes and guide rational metabolic reconstitution for further titer improvement of target products. KEY POINTS: • Comprehensive bioinformatic analyses effectively reveal primary metabolic changes. • Primary metabolic changes cause precursor enrichment to enhance TNMs production. • Strengthening of fatty acid degradation further improves the titer of TNMs.
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Affiliation(s)
- Jing Lin
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Yu Xiao
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Huiming Liu
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Die Gao
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China.
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China.
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
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Buyuklyan JA, Zakalyukina YV, Osterman IA, Biryukov MV. Modern Approaches to the Genome Editing of Antibiotic Biosynthetic Clusters in Actinomycetes. Acta Naturae 2023; 15:4-16. [PMID: 37908767 PMCID: PMC10615194 DOI: 10.32607/actanaturae.23426] [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: 07/13/2023] [Accepted: 08/19/2023] [Indexed: 11/02/2023] Open
Abstract
Representatives of the phylum Actinomycetota are one of the main sources of secondary metabolites, including antibiotics of various classes. Modern studies using high-throughput sequencing techniques enable the detection of dozens of potential antibiotic biosynthetic genome clusters in many actinomycetes; however, under laboratory conditions, production of secondary metabolites amounts to less than 5% of the total coding potential of producer strains. However, many of these antibiotics have already been described. There is a continuous "rediscovery" of known antibiotics, and new molecules become almost invisible against the general background. The established approaches aimed at increasing the production of novel antibiotics include: selection of optimal cultivation conditions by modifying the composition of nutrient media; co-cultivation methods; microfluidics, and the use of various transcription factors to activate silent genes. Unfortunately, these tools are non-universal for various actinomycete strains, stochastic in nature, and therefore do not always lead to success. The use of genetic engineering technologies is much more efficient, because they allow for a directed and controlled change in the production of target metabolites. One example of such technologies is mutagenesis-based genome editing of antibiotic biosynthetic clusters. This targeted approach allows one to alter gene expression, suppressing the production of previously characterized molecules, and thereby promoting the synthesis of other unknown antibiotic variants. In addition, mutagenesis techniques can be successfully applied both to new producer strains and to the genes of known isolates to identify new compounds.
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Affiliation(s)
- J A Buyuklyan
- Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340 Russian Federation
| | - Yu V Zakalyukina
- Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340 Russian Federation
- Lomonosov Moscow State University, Moscow, 119234 Russian Federation
| | - I A Osterman
- Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340 Russian Federation
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, 143025 Russian Federation
| | - M V Biryukov
- Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340 Russian Federation
- Lomonosov Moscow State University, Moscow, 119234 Russian Federation
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Dolya B, Hryhorieva O, Sorochynska K, Lopatniuk M, Ostash I, Tseduliak VM, Sterndorff EB, Jørgensen TS, Gren T, Dacyuk Y, Weber T, Luzhetskyy A, Fedorenko V, Ostash B. Properties of Multidrug-Resistant Mutants Derived from Heterologous Expression Chassis Strain Streptomyces albidoflavus J1074. Microorganisms 2023; 11:1176. [PMID: 37317150 DOI: 10.3390/microorganisms11051176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 03/30/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Streptomyces albidoflavus J1074 is a popular platform to discover novel natural products via the expression of heterologous biosynthetic gene clusters (BGCs). There is keen interest in improving the ability of this platform to overexpress BGCs and, consequently, enable the purification of specialized metabolites. Mutations within gene rpoB for the β-subunit of RNA polymerase are known to increase rifampicin resistance and augment the metabolic capabilities of streptomycetes. Yet, the effects of rpoB mutations on J1074 remained unstudied, and we decided to address this issue. A target collection of strains that we studied carried spontaneous rpoB mutations introduced in the background of the other drug resistance mutations. The antibiotic resistance spectra, growth, and specialized metabolism of the resulting mutants were interrogated using a set of microbiological and analytical approaches. We isolated 14 different rpoB mutants showing various degrees of rifampicin resistance; one of them (S433W) was isolated for the first time in actinomycetes. The rpoB mutations had a major effect on antibiotic production by J1074, as evident from bioassays and LC-MS data. Our data support the idea that rpoB mutations are useful tools to enhance the ability of J1074 to produce specialized metabolites.
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Affiliation(s)
- Borys Dolya
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Olena Hryhorieva
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Khrystyna Sorochynska
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Maria Lopatniuk
- Department of Pharmacy, Saarland University, 66123 Saarbrucken, Germany
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Vasylyna-Marta Tseduliak
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Eva Baggesgaard Sterndorff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Yuriy Dacyuk
- Department of Mineral Geology and Geophysics, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Andriy Luzhetskyy
- Department of Pharmacy, Saarland University, 66123 Saarbrucken, Germany
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
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Baranova AA, Alferova VA, Korshun VA, Tyurin AP. Modern Trends in Natural Antibiotic Discovery. Life (Basel) 2023; 13:life13051073. [PMID: 37240718 DOI: 10.3390/life13051073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/10/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Natural scaffolds remain an important basis for drug development. Therefore, approaches to natural bioactive compound discovery attract significant attention. In this account, we summarize modern and emerging trends in the screening and identification of natural antibiotics. The methods are divided into three large groups: approaches based on microbiology, chemistry, and molecular biology. The scientific potential of the methods is illustrated with the most prominent and recent results.
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Affiliation(s)
- Anna A Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vera A Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Anton P Tyurin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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Iskandaryan M, Blbulyan S, Sahakyan M, Vassilian A, Trchounian K, Poladyan A. L-amino acids affect the hydrogenase activity and growth of Ralstonia eutropha H16. AMB Express 2023; 13:33. [PMID: 36932299 PMCID: PMC10023824 DOI: 10.1186/s13568-023-01535-w] [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: 02/26/2023] [Accepted: 03/04/2023] [Indexed: 03/19/2023] Open
Abstract
Ralstonia eutropha H16 is a chemolithoautotrophic bacterium with O2-tolerant hydrogenase (Hyds) enzymes. Hyds are expressed in the presence of gas mixtures (H2, O2, CO2) or under energy limitation and stress conditions. O2-tolerant Hyds are promising candidates as anode biocatalysts in enzymatic fuel cells (EFCs). Supplementation of 0.5% (w/v) yeast extract to the fructose-nitrogen (FN) growth medium enhanced H2-oxidizing Hyd activity ~ sixfold. Our study aimed to identify key metabolites (L-amino acids (L-AAs) and vitamins) in yeast extract that are necessary for the increased synthesis and activity of Hyds. A decrease in pH and a reduction in ORP (from + 240 ± 5 mV to - 180 mV ± 10 mV values) after 24 h of growth in the presence of AAs were observed. Compared to the FN-medium control, supplementation of 7.0 μmol/ml of the L-AA mixture stimulated the growth of bacteria ~ 1.9 to 2.9 fold, after 72 h. The whole cells' H2-oxidizing Hyd activity was not observed in control samples, whereas the addition of L-AAs, mainly glycine resulted in a maximum of ~ 22 ± 0.5 and 15 ± 0.3 U, g CDW-1 activity after 24 h and 72 h, respectively. Our results suggest a correlation between ORP, pH, and function of Hyds in R. eutropha H16 in the presence of key L-AAs. L-AAs used in small amounts can be proposed as signaling molecules or key components of Hyd maturation. These results are important for the optimization of O2-tolerant Hyds production as anode biocatalysts.
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Affiliation(s)
- Meri Iskandaryan
- Department of Biochemistry, Microbiology, and Biotechnology, Biology Faculty, YSU, Yerevan, Armenia
| | - Syuzanna Blbulyan
- Department of Biochemistry, Microbiology, and Biotechnology, Biology Faculty, YSU, Yerevan, Armenia
| | - Mayramik Sahakyan
- Department of Biochemistry, Microbiology, and Biotechnology, Biology Faculty, YSU, Yerevan, Armenia
| | - Anait Vassilian
- Research Institute of Biology, Biology Faculty, YSU, Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology, and Biotechnology, Biology Faculty, YSU, Yerevan, Armenia.,Research Institute of Biology, Biology Faculty, YSU, Yerevan, Armenia
| | - Anna Poladyan
- Department of Biochemistry, Microbiology, and Biotechnology, Biology Faculty, YSU, Yerevan, Armenia. .,Research Institute of Biology, Biology Faculty, YSU, Yerevan, Armenia.
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Feng NX, Zhang F, Xie Y, Bin H, Xiang L, Li YW, Zhang F, Huang Y, Zhao HM, Cai QY, Mo CH, Li QX. Genome mining-guided activation of two silenced tandem genes in Raoultella ornithinolytica XF201 for complete biodegradation of phthalate acid esters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161013. [PMID: 36549521 DOI: 10.1016/j.scitotenv.2022.161013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
Phthalates (PAEs) are ubiquitous in soils and food products and thus pose a high risk to human health. Herein, genome mining revealed a great diversity of bacteria with PAEs-degrading potential. Mining of the genome of Raoultella ornithinolytica XF201, a novel strain isolated from Dongxiang wild rice rhizosphere, revealed the presence of two silenced tandem genes pcdGH (encoding protocatechuate 3,4-dioxygenase, 3,4-PCD), key aromatic ring-cleaving genes in PAEs biodegradation. Ribosome engineering was successfully utilized to activate the expression of pcdGH genes to produce 3,4-PCD in the mutant XF201-G2U5. The mutant XF201-G2U5 showed high 3,4-PCD activity and could remove 94.5 % of di-n butyl phthalate (DBP) in 72 h. The degradation kinetics obeyed the first-order kinetic model. Strain XF201-G2U5 could also degrade the other PAEs and the main intermediate metabolites, ultimately leading to tricarboxylic acid cycle. Therefore, this strategy facilitates novel bacterial resources discovery for bioremediation of PAEs and other emerging contaminants.
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Affiliation(s)
- Nai-Xian Feng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Fei Zhang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yunchang Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Hui Bin
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Yunhong Huang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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Shi Y, Zhang J, Ma Z, Zhang Y, Bechthold A, Yu X. Double-reporter-guided targeted activation of the oxytetracycline silent gene cluster in Streptomyces rimosus M527. Biotechnol Bioeng 2023; 120:1411-1422. [PMID: 36775891 DOI: 10.1002/bit.28347] [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: 11/12/2022] [Revised: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
In Streptomyces rimosus M527, the oxytetracycline (OTC) biosynthetic gene cluster is not expressed under laboratory conditions. In this study a reported-guided mutant selection (RGMS) procedure was used to activate the cluster. The double-reporter plasmid pAGT was constructed in which gusA encoding a β-glucuronidase and tsr encoding a thiostrepton resistance methyltransferase were placed under the control of the native promoter of oxyA gene (PoxyA ). Plasmid pAGT was introduced and integrated into the chromosome of S. rimosus M527 by conjugation, yielding initial strain M527-pAGT. Subsequently, mutants of M527-pAGT were generated by using ribosome engineering technology. The mutants harboring activated OTC gene cluster were selected based on visual observation of GUS activity and thiostrepton resistance. Finally, mutant M527-pAGT-R7 was selected producing OTC in a concentration of 235.2 mg/L. In this mutant transcriptional levels of oxysr genes especial oxyAsr gene were increased compared to wild-type strain S. rimosus M527. The mutant M527-pAGT-R7 showed antagonistic activities against Gram-negative and Gram-positive strains. All data indicate that the OTC gene cluster was successfully activated using the RGMS method.
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Affiliation(s)
- Yue Shi
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province, China
| | - Jinyao Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province, China
| | - Zheng Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province, China
| | - Yongyong Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province, China
| | - Andreas Bechthold
- Institute for Pharmaceutical Sciences, Pharmaceutical Biology and Biotechnology, University of Freiburg, Freiburg, Germany
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang Province, China
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Tseduliak VM, Dolia B, Ostash I, Lopatniuk M, Busche T, Ochi K, Kalinowski J, Luzhetskyy A, Fedorenko V, Ostash B. Mutations within gene XNR_2147 for TetR-like protein enhance lincomycin resistance and endogenous specialized metabolism of Streptomyces albus J1074. J Appl Genet 2023; 64:185-195. [PMID: 36417169 DOI: 10.1007/s13353-022-00738-4] [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] [Received: 08/28/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022]
Abstract
Streptomyces albus J1074 is one of the most popular heterologous expression platforms among streptomycetes. Identification of new genes and mutations that influence specialized metabolism in this species is therefore of great applied interest. Here, we describe S. albus KO-1304 that was isolated as a spontaneous lincomycin-resistant variant of double rpsLR94G rsmGR15SG40E mutant KO-1295. Besides altered antibiotic resistance profile, KO-1304 exhibited increased antibiotic activity as compared to its parental strains. KO-1304 genome sequencing revealed mutations within gene XNR_2147 encoding putative TetR-like protein. Gene XNR_2146 for efflux protein is the most likely target of repressing action of Xnr_2147. Our data agree with the scenario where lincomycin resistance phenotype of KO-1304 arose from inability of mutated Xnr_2147 protein to repress XNR_2146. Introduction of additional copy of XNR_2146 into wild type strain increased antibiotic activity of the latter, attesting to the practical value of transporter genes for strain improvement.
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Affiliation(s)
- Vasylyna-Marta Tseduliak
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Borys Dolia
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Maria Lopatniuk
- Helmholtz Institute for Pharmaceutical Research, Saarland Campus, Building C2.3, 66123, Saarbrucken, Germany
| | - Tobias Busche
- Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
| | - Kozo Ochi
- Department of Life Sciences, Hiroshima Institute of Technology, Saeki-Ku, Hiroshima, 731-5193, Japan
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research, Saarland Campus, Building C2.3, 66123, Saarbrucken, Germany
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine.
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Flavacol and Its Novel Derivative 3- β-Hydroxy Flavacol from Streptomyces sp. Pv 4-95 after the Expression of Heterologous AdpA. Microorganisms 2022; 10:microorganisms10122335. [PMID: 36557588 PMCID: PMC9783318 DOI: 10.3390/microorganisms10122335] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Actinomycetes are one of the main producers of biologically active compounds. However, their capabilities have not been fully evaluated due to the presence of many unexpressed silent clusters; moreover, actinomycetes can probably produce new or previously discovered natural products under certain conditions. Overexpressing the adpA gene into streptomycetes strains can unlock silent biosynthetic gene clusters. Herein, we showed that by applying this approach to Streptomyces sp. Pv 4-95 isolated from Phyllostachys viridiglaucescens rhizosphere soil, two new mass peaks were identified. NMR structure analysis identified these compounds as flavacol and a new 3-β-hydroxy flavacol derivative. We suggest that the presence of heterologous AdpA has no direct effect on the synthesis of flavacol and its derivatives in the Pv 4-95 strain. However, AdpA affects the synthesis of precursors by increasing their quantity, which then condenses into the resulting compounds.
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Xiong Z, Tian X, Wang G, Song X, Xia Y, Zhang H, Ai L. Development of a high-throughput screening method for exopolysaccharide-producing Streptococcus thermophilus based on Congo red. Food Res Int 2022; 162:112094. [DOI: 10.1016/j.foodres.2022.112094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/23/2022] [Accepted: 10/28/2022] [Indexed: 11/08/2022]
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Hwang GJ, Jang M, Son S, Kim GS, Lee B, Heo KT, Kim GJ, Choi H, Hur JS, Jang JP, Ko SK, Hong YS, Ahn JS, Jang JH. Ulleungdolin, a Polyketide-Peptide Hybrid Bearing a 2,4-Di- O-methyl-β-d-antiarose from Streptomyces sp. 13F051 Co-cultured with Leohumicola minima 15S071. JOURNAL OF NATURAL PRODUCTS 2022; 85:2445-2453. [PMID: 36197044 DOI: 10.1021/acs.jnatprod.2c00682] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A new secondary metabolite, ulleungdolin (1), was isolated from the co-culture of an actinomycete, Streptomyces sp. 13F051, and a fungus, Leohumicola minima 15S071. Based on the NMR, UV, and MS data, it was deduced that the planar structure of 1 comprised an isoindolinone (IsoID) with an octanoic acid, a tripeptide, and a sugar. The tripeptide has the unprecedented amino acids norcoronamic acid, 3-hydroxy-glutamine, and 4-hydroxy-phenylglycine and is linked by a C-N bond with IsoID. The absolute configurations were determined by chemical derivatization, extensive spectroscopic methods, and electronic circular dichroism calculations and supported by bioinformatic analyses. Bioactivity evaluation studies indicated that 1 had an antimigration effect on MDA-MB-231 breast cancer cells.
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Affiliation(s)
- Gwi Ja Hwang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, South Korea
| | - Mina Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, South Korea
| | - Sangkeun Son
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Gil Soo Kim
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, South Korea
| | - Byeongsan Lee
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
| | - Kyung Taek Heo
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, South Korea
| | - Geum Jin Kim
- College of Pharmacy and Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, South Korea
| | - Hyukjae Choi
- College of Pharmacy and Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, South Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon 57922, South Korea
| | - Jun-Pil Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
| | - Sung-Kyun Ko
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, South Korea
| | - Young-Soo Hong
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, South Korea
| | - Jong Seog Ahn
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, South Korea
| | - Jae-Hyuk Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, South Korea
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12
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Genome Shuffling Mutant of Streptomyces diastatochromogenes for Substantial Improvement of Toyocamycin Production. FERMENTATION 2022. [DOI: 10.3390/fermentation8100535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Toyocamycin, a nucleoside antibiotic, is a fungicide with the potential to control plant pathogens. In this study, three rounds of genome shuffling screening were applied to enhance the toyocamycin production in Streptomyces diastatochromogenes 1628. After three rounds of genome-shuffling screening, the toyocamycin production increased by 10.8-fold that of wild-type, and 2.64-fold of its parental strain. By optimization of its nutrition condition in medium, the highest production of toyocamycin reached 1173.6 mg/L in TY-producing medium. In addition, the mechanism for the improvement of shuffled strains was investigated. Recombinants with increased toyocamycin production exhibited higher transcriptional level of the toy cluster and product resistance. Furthermore, the rise of ATP hydrolysis rate indicated that intracellular ATP exhibit a significant role in tuning the toy cluster by an ATP-binding pathway-specific regulator. In all, we obtained S. diastatochromogenes mutants with enhanced toyocamycin production, and provided a valuable clue for the activation of secondary metabolites.
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13
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Wang J, Chen P, Li S, Zheng X, Zhang C, Zhao W. Mutagenesis of high-efficiency heterotrophic nitrifying-aerobic denitrifying bacterium Rhodococcus sp. strain CPZ 24. BIORESOURCE TECHNOLOGY 2022; 361:127692. [PMID: 35905881 DOI: 10.1016/j.biortech.2022.127692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Breeding high-efficiency heterotrophic nitrifying-aerobic denitrifying (SND) bacteria is important for the removal of biological nitrogen in wastewater treatment. In this study, a high-efficiency SND mutant strain, ΔRhodococcus sp. CPZ 24, was obtained by ultraviolet-diethyl sulfate compound mutagenesis. The maximum nitrification and denitrification rates were 3.77 and 1.37 mg·L-1·h-1, respectively 30.30 % and 17.10 % higher than those of wild bacteria. Biolog technology and network model analysis revealed that ΔCPZ 24 significantly improved the utilisation ability and metabolic activity of organic carbon sources. Furthermore, the expression levels of the nitrogen removal function genes nxrA, nosZ, amoA, and norB in strain ΔCPZ 24 increased significantly. In actual sewage, mutant bacteria ΔCPZ 24 have a 95.05 % ammonia-nitrogen degradation rate and a 96.67 % nitrate-nitrogen degradation rate. These results suggested that UV-DES compound mutation was a successful strategy to improve the nitrogen removal performance of SND bacteria in wastewater treatment.
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Affiliation(s)
- Jingli Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; Huazhong Agricultural University, Wuhan 430070, China
| | - Peizhen Chen
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
| | - Shaopeng Li
- Tianjin Agricultural University, Tianjin 300392, China
| | - Xiangqun Zheng
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Chunxue Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Wenjie Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
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14
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Liu W, Wang J, Zhang H, Qi X, Du C. Transcriptome analysis of the production enhancement mechanism of antimicrobial lipopeptides of Streptomyces bikiniensis HD-087 by co-culture with Magnaporthe oryzae Guy11. Microb Cell Fact 2022; 21:187. [PMID: 36088378 PMCID: PMC9464393 DOI: 10.1186/s12934-022-01913-2] [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: 06/17/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022] Open
Abstract
The lipopeptides produced by Streptomyces bikiniensis have a significant inhibitory effect on Magnaporthe oryzae, but the low yield limits its application. In this study, the anti-M. oryzae activity of the broth of S. bikiniensis HD-087 co-cultured with M. oryzae Guy11 mycelium has risen by 41.22% compared with pure culture, and under induction conditions of adding Guy11-inducer (cell-free supernatant of M. oryzae Guy11), the activity of strain HD-087 improved 61.76%. The result proved that the enhancement effect of Guy11 on the antimicrobial activity of HD-087 was mainly related to metabolites but mycelium cells. Under optimum induction conditions, NRPS gene expression levels of HD-087 were significantly increased by induction with Guy11-inducer, the biomass of HD-087 had no significant change, but crude extract of lipopeptide (CEL) production was 107.4% higher than pure culture, and TLC result under acid hydrolysis showed that the induced culture has one component more than pure culture. To clarify the regulation mechanism of improving lipopeptide production of HD-087 with Guy11-inducer, transcriptomic analysis was performed using RNAseq to compare the induced culture and pure culture. In the induced culture, 943 genes were up-regulated, while 590 genes were down-regulated in DEGs (differentially expressed genes). KEGG results showed that the expression of genes related to amino acid synthesis, fatty acid metabolism, TCA cycle and pyruvate metabolism pathway were significantly increased. The increased expression of genes related to these metabolic pathways provided sufficient precursors for lipopeptide synthesis. Accordingly, key enzyme genes responsible for the synthesis of lipopeptides Srf and NRPS was significantly increased. Quorum sensing related genes OppA and MppA were significantly up-regulated, and then ComP was activated and promoted lipopeptide synthesis. These results provided a scientific basis for using M. oryzae to induce the increase of the production of Streptomyces lipopeptides, and also laid a foundation for further exploring the co-culture mechanisms among different genera.
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15
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Pang F, Solanki MK, Wang Z. Streptomyces can be an excellent plant growth manager. World J Microbiol Biotechnol 2022; 38:193. [PMID: 35980475 DOI: 10.1007/s11274-022-03380-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/07/2022] [Indexed: 11/27/2022]
Abstract
Streptomyces, the most abundant and arguably the most important genus of actinomycetes, is an important source of biologically active compounds such as antibiotics, and extracellular hydrolytic enzymes. Since Streptomyces can have a beneficial symbiotic relationship with plants they can contribute to nutrition, health and fitness of the latter. This review article summarizes recent research contributions on the ability of Streptomyces to promote plant growth and improve plant tolerance to biotic and abiotic stress responses, as well as on the consequences, on plant health, of the enrichment of rhizospheric soils in Streptomyces species. This review summarizes the most recent reports of the contribution of Streptomyces to plant growth, health and fitness and suggests future research directions to promote the use of these bacteria for the development of a cleaner agriculture.
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Affiliation(s)
- Fei Pang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, College of Biology and Pharmacy, Yulin Normal University, Yulin, 537000, China
| | - Manoj Kumar Solanki
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-701, Katowice, Poland.
| | - Zhen Wang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, College of Biology and Pharmacy, Yulin Normal University, Yulin, 537000, China.
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16
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Syrvatka V, Rabets A, Gromyko O, Luzhetskyy A, Fedorenko V. Scandium-microorganism interactions in new biotechnologies. Trends Biotechnol 2022; 40:1088-1101. [PMID: 35346528 DOI: 10.1016/j.tibtech.2022.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 12/19/2022]
Abstract
Scandium (Sc) plays a special role in high-tech industries because of its wide application in green, space, and defense technologies. However, Sc mining and purification are problematic due to political, technological, and environmental difficulties. The deficit of this element limits global technological development. One sustainable solution to this problem is to use microorganisms to extract Sc from ore and waste, as well as to concentrate and separate it from other elements. Sc also demonstrates attractive metabolic effects on microbes that is of great interest in white biotechnology. Sc increases the production of proteins and secondary metabolites and activates poorly expressed genes. This review offers a comprehensive analysis of current knowledge on the application of Sc-microorganism interactions in promising biotechnologies, its perspectives, and future challenges.
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Affiliation(s)
- Vasyl Syrvatka
- Genetics and Biotechnology Department, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Andrii Rabets
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Oleksandr Gromyko
- Genetics and Biotechnology Department, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Victor Fedorenko
- Genetics and Biotechnology Department, Ivan Franko National University of Lviv, Lviv, Ukraine.
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17
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Shemediuk AL, Dolia BS, Ochi K, Fedorenko VO, Ostash BO. Properties of Spontaneous rpsL Mutant of Streptomyces albus KO-1297. CYTOL GENET+ 2022; 56:31-36. [PMID: 35194265 PMCID: PMC8831875 DOI: 10.3103/s009545272201011x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/28/2021] [Accepted: 11/18/2021] [Indexed: 11/30/2022]
Abstract
The Streptomyces albus J1074 strain remains one of the most popular platforms for the discovery of new natural compounds due to the expression of biosynthetic gene clusters (BGCs) from the microorganisms of the Actinobacteria class. Different methods were tested to provide a maximal expression of heterologous BGCs in this strain. However, there is still no description of the properties of spontaneous J1074 mutants in the rpsL gene encoding a ribosomal protein S12. The interest in such mutations in actinobacteria is due to the fact that they provide a considerable increase in the antibiotic activity. In this work, we describe the isolation and characterization of the S. albus KO-1297 strain, which contains a spontaneous missense mutation in the rpsL gene leading to a Lys88Glu substitution in the protein S12. As compared with the initial strain, this mutant exhibits an increased resistance to streptomycin and higher antibiotic productivity. The KO-1297 strain and genetically engineered rpsLK88E mutant K88E are not identical in their ability to produce antibiotics. KO-1297 also exhibits a certain level of instability of rpsL mutation. The genomes of KO-1297 and its rpsLWT revertant contain the mutations that can cause phenotypic differences between these strains (as well as between them and SAM2 and K88E strains).
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18
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Alam K, Islam MM, Gong K, Abbasi MN, Li R, Zhang Y, Li A. In silico genome mining of potential novel biosynthetic gene clusters for drug discovery from Burkholderia bacteria. Comput Biol Med 2022; 140:105046. [PMID: 34864585 DOI: 10.1016/j.compbiomed.2021.105046] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022]
Abstract
As an emerging resource, Gram-negative Burkholderia bacteria were able to produce a wide range of bioactive secondary metabolites with potential therapeutic and biotechnological applications. Genome mining has emerged as an influential platform for screening and pinpointing natural product diversity with the increasing number of Burkholderia genome sequences. Here, for genome mining of potential biosynthetic gene clusters (BGCs) and prioritizing prolific producing Burkholderia strains, we investigated the relationship between species evolution and distribution of main BGC groups using computational analysis of complete genome sequences of 248 Burkholderia species publicly available. We uncovered significantly differential distribution patterns of BGCs in the Burkholderia phyla, even among strains that are genetically very similar. We found various types of BGCs in Burkholderia, including some representative and most common BGCs for biosynthesis of encrypted or known terpenes, non-ribosomal peptides (NRPs) and some hybrid BGCs for cryptic products. We also observed that Burkholderia contain a lot of unspecified BGCs, representing high potentials to produce novel compounds. Analysis of BGCs for RiPPs (Ribosomally synthesized and posttranslationally modified peptides) and a texobactin-like BGC as examples showed wide classification and diversity of RiPP BGCs in Burkholderia at species level and metabolite predication. In conclusion, as the biggest investigation in silico by far on BGCs of the particular genus Burkholderia, our data implied a great diversity of natural products in Burkholderia and BGC distributions closely related to phylogenetic variation, and suggested different or concurrent strategies used to identify new drug molecules from these microorganisms will be important for the selection of potential BGCs and prolific producing strains for drug discovery.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
| | - Md Mahmudul Islam
- Department of Microbiology, Rajshahi Institute of Biosciences (RIB), Affi. University of Rajshahi, Rajshahi, 6212, Bangladesh.
| | - Kai Gong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
| | - Muhammad Nazeer Abbasi
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
| | - Ruijuan Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
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19
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Unique physiological and genetic features of ofloxacin-resistant Streptomyces mutants. Appl Environ Microbiol 2021; 88:e0232721. [PMID: 34936843 DOI: 10.1128/aem.02327-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
New antimicrobial agents are urgently needed to combat the emergence and spread of multidrug-resistant bacteria. Activating the cryptic biosynthetic gene clusters for actinomycete secondary metabolites can provide essential clues for research into new antimicrobial agents. An effective method for this purpose is based on drug resistance selection. This report describes interesting results for drug resistance selection using antibiotics that target DNA replication can effectively potentiate secondary metabolite production by actinomycetes. Ofloxacin-resistant mutants were isolated from five different streptomycetes. Ofloxacin is an antibiotic that binds to DNA complexes and type II topoisomerase, causing double-stranded breaks in bacterial chromosomes. Physiological and genetic characterization of the mutants revealed that the development of ofloxacin resistance in streptomycetes leads to the emergence of various types of secondary metabolite-overproducing strains. In Streptomyces coelicolor A3(2), ofloxacin-resistant mutants that overproduced actinorhodin, undecylprodigiosin, or carotenoid were identified. Also, an ofloxacin-resistant mutant that overproduces methylenomycin A, whose biosynthetic gene cluster is located on the endogenous plasmid, SCP1, was isolated. These observations indicate that ofloxacin resistance might activate biosynthetic genes on both chromosomes and on endogenous plasmids. We also identified the mutations that are probably involved in the phenotype of ofloxacin resistance and secondary metabolite overproduction in S. coelicolor A3(2). Furthermore, we observed an interesting phenomenon in which several ofloxacin-resistant mutants overproduced antibiotics in the presence of ofloxacin. Based on these results, we present the unique physiological and genetic characteristics of ofloxacin-resistant Streptomyces mutants and discuss the importance and potential development of the new findings. IMPORTANCE The abuse or overuse of antibacterial agents for therapy and animal husbandry has caused an increased population of antimicrobial-resistant bacteria in the environment. Consequently, there are now fewer effective antimicrobials available. Due to the depleted antibiotic pipeline, pandemic outbreaks caused by antimicrobial-resistant bacteria are deeply concerned, and the development of new antibiotics is now an urgent issue. Promising sources of antimicrobial agents include cryptic biosynthetic gene clusters for secondary metabolites in streptomycetes and rare actinomycetes. This study's significance is an unprecedented activation method to accelerate drug discovery research on a global scale. The technique developed in this study could allow for simultaneous drug discovery in different countries, maximizing the world's microbial resources.
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20
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Mutations in the regulatory regions result in increased streptomycin resistance and keratinase synthesis in Bacillus thuringiensis. Arch Microbiol 2021; 203:5387-5396. [PMID: 34390357 DOI: 10.1007/s00203-021-02525-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 12/29/2022]
Abstract
Keratinases are a group of proteases of great industrial significance. To take full advantage of Bacillus species as an inherent superior microbial producer of proteases, we performed the ribosome engineering to improve the keratinase synthesis capacity of the wild-type Bacillus thuringiensis by inducing streptomycin resistance. Mutant Bt(Str-O) was identified as a stable keratinase overproducer. Comparative characterization of the two strains revealed that, although the resistance to Streptomycin increased by eight-fold in MIC, the mutant's resistance to other commonly used antibiotics was not affected. Furthermore, the mutant exhibited an enhanced keratinase synthesis (1.5-fold) when cultured in a liquid LB medium. In the whole feather degradation experiment, the mutant could secret twofold keratinase into the medium, reaching 640 U/mL per 107 CFU. By contrast, no significant differences were found in the scanning electron microscopic analysis and spore formation experiment. To understand the genetic factors causing these phenotypic changes, we cloned and analyzed the rpsL gene. No mutation was observed. We subsequently determined the genome sequences of the two strains. Comparing the rpsL gene revealed that the emergence of streptomycin resistance was not necessarily dependent on the mutation(s) in the generally recognized "hotspot." Genome-wide analysis showed that the phenotypic changes of the mutant were the collective consequence of the genetic variations occurring in the regulatory regions and the non-coding RNA genes. This study demonstrated the importance of genetic changes in regulatory regions and the effectiveness of irrational ribosome engineering in creating prokaryotic microbial mutants without sufficient genetic information.
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21
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Zong G, Fu J, Zhang P, Zhang W, Xu Y, Cao G, Zhang R. Use of elicitors to enhance or activate the antibiotic production in streptomyces. Crit Rev Biotechnol 2021; 42:1260-1283. [PMID: 34706600 DOI: 10.1080/07388551.2021.1987856] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Streptomyces is the largest and most significant genus of Actinobacteria, comprising 961 species. These Gram-positive bacteria produce many versatile and important bioactive compounds; of these, antibiotics, specifically the enhancement or activation of their production, have received extensive research attention. Recently, various biotic and abiotic elicitors have been reported to modify the antibiotic metabolism of Streptomyces, which promotes the production of new antibiotics and bioactive metabolites for improvement in the yields of endogenous products. However, some elicitors that obviously contribute to secondary metabolite production have not yet received sufficient attention. In this study, we have reviewed the functions and mechanisms of chemicals, novel microbial metabolic elicitors, microbial interactions, enzymes, enzyme inhibitors, environmental factors, and novel combination methods regarding antibiotic production in Streptomyces. This review has aimed to identify potentially valuable elicitors for stimulating the production of latent antibiotics or enhancing the synthesis of subsistent antibiotics in Streptomyces. Future applications and challenges in the discovery of new antibiotics and enhancement of existing antibiotic production using elicitors are discussed.
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Affiliation(s)
- Gongli Zong
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Jiafang Fu
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Peipei Zhang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Wenchi Zhang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Guangxiang Cao
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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22
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Wang Z, Sun R, Li M, Liu L, Duan Y, Huang Y. Yield improvement of enediyne yangpumicins in Micromonospora yangpuensis through ribosome engineering and fermentation optimization. Biotechnol J 2021; 16:e2100250. [PMID: 34473904 DOI: 10.1002/biot.202100250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/22/2022]
Abstract
Yangpumicins (YPMs), for example, YPM A, F, and G, are newly discovered enediynes from Micromonospora yangpuensis DSM 45577, which could be exploited as promising payloads of antibody-drug conjugates. However, the low yield of YPMs in the wild-type strain (∼1 mg L-1 ) significantly hampers their further drug development. In this study, a combined ribosome engineering and fermentation optimization strategy has been used for yield improvement of YPMs. One gentamicin-resistant M. yangpuensis DSM 45577 strain (MY-G-1) showed higher YPMs production (7.4 ± 1.0 mg L-1 ), while it exhibits delayed sporulation and slender mycelium under scanning electron microscopy. Whole genome re-sequencing of MY-G-1 reveals several deletion and single nucleotide polymorphism mutations, which were confirmed by PCR and DNA sequencing. Further Box-Behnken experiment and regression analysis determined that the optimal medium concentrations of soluble starch, D-mannitol, and pharmamedia for YPMs production in shaking flasks (10.0 ± 0.8 mg L-1 ). Finally, the total titer of YPM A/F/G in MY-G-1 reached to 15.0 ± 2.5 mg L-1 in 3 L fermenters, which was about 11-fold higher than the original titer of 1.3 ± 0.3 mg L-1 in wild-type strain. Our study may be instrumental to develop YPMs into a clinical anticancer drug, and inspire the use of these multifaceted strategies for yield improvement in Micromonospora species. GRAPHICAL ABSTRACT LAY SUMMARY: ???
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Affiliation(s)
- Zilong Wang
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China
| | - Runze Sun
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China
| | - Miao Li
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China
| | - Ling Liu
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan, China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan, China
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23
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Facilitating Imaging Mass Spectrometry of Microbial Specialized Metabolites with METASPACE. Metabolites 2021; 11:metabo11080477. [PMID: 34436418 PMCID: PMC8401310 DOI: 10.3390/metabo11080477] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/18/2021] [Accepted: 07/21/2021] [Indexed: 12/17/2022] Open
Abstract
Metabolite annotation from imaging mass spectrometry (imaging MS) data is a difficult undertaking that is extremely resource intensive. Here, we adapted METASPACE, cloud software for imaging MS metabolite annotation and data interpretation, to quickly annotate microbial specialized metabolites from high-resolution and high-mass accuracy imaging MS data. Compared with manual ion image and MS1 annotation, METASPACE is faster and, with the appropriate database, more accurate. We applied it to data from microbial colonies grown on agar containing 10 diverse bacterial species and showed that METASPACE was able to annotate 53 ions corresponding to 32 different microbial metabolites. This demonstrates METASPACE to be a useful tool to annotate the chemistry and metabolic exchange factors found in microbial interactions, thereby elucidating the functions of these molecules.
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24
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Scherlach K, Hertweck C. Mining and unearthing hidden biosynthetic potential. Nat Commun 2021; 12:3864. [PMID: 34162873 PMCID: PMC8222398 DOI: 10.1038/s41467-021-24133-5] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/04/2021] [Indexed: 12/11/2022] Open
Abstract
Genetically encoded small molecules (secondary metabolites) play eminent roles in ecological interactions, as pathogenicity factors and as drug leads. Yet, these chemical mediators often evade detection, and the discovery of novel entities is hampered by low production and high rediscovery rates. These limitations may be addressed by genome mining for biosynthetic gene clusters, thereby unveiling cryptic metabolic potential. The development of sophisticated data mining methods and genetic and analytical tools has enabled the discovery of an impressive array of previously overlooked natural products. This review shows the newest developments in the field, highlighting compound discovery from unconventional sources and microbiomes. Natural products are an important source of bioactive compounds and have versatile applications in different fields, but their discovery is challenging. Here, the authors review the recent developments in genome mining for discovery of natural products, focusing on compounds from unconventional microorganisms and microbiomes.
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Affiliation(s)
- Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
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Menezes RC, Piechulla B, Warber D, Svatoš A, Kai M. Metabolic Profiling of Rhizobacteria Serratia plymuthica and Bacillus subtilis Revealed Intra- and Interspecific Differences and Elicitation of Plipastatins and Short Peptides Due to Co-cultivation. Front Microbiol 2021; 12:685224. [PMID: 34135882 PMCID: PMC8200778 DOI: 10.3389/fmicb.2021.685224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
Rhizobacteria live in diverse and dynamic communities having a high impact on plant growth and development. Due to the complexity of the microbial communities and the difficult accessibility of the rhizosphere, investigations of interactive processes within this bacterial network are challenging. In order to better understand causal relationships between individual members of the microbial community of plants, we started to investigate the inter- and intraspecific interaction potential of three rhizobacteria, the S. plymuthica isolates 4Rx13 and AS9 and B. subtilis B2g, using high resolution mass spectrometry based metabolic profiling of structured, low-diversity model communities. We found that by metabolic profiling we are able to detect metabolite changes during cultivation of all three isolates. The metabolic profile of S. plymuthica 4Rx13 differs interspecifically to B. subtilis B2g and surprisingly intraspecifically to S. plymuthica AS9. Thereby, the release of different secondary metabolites represents one contributing factor of inter- and intraspecific variations in metabolite profiles. Interspecific co-cultivation of S. plymuthica 4Rx13 and B. subtilis B2g showed consistently distinct metabolic profiles compared to mono-cultivated species. Thereby, putative known and new variants of the plipastatin family are increased in the co-cultivation of S. plymuthica 4Rx13 and B. subtilis B2g. Interestingly, intraspecific co-cultivation of S. plymuthica 4Rx13 and S. plymuthica AS9 revealed a distinct interaction zone and showed distinct metabolic profiles compared to mono-cultures. Thereby, several putative short proline-containing peptides are increased in co-cultivation of S. plymuthica 4Rx13 with S. plymuthica AS9 compared to mono-cultivated strains. Our results demonstrate that the release of metabolites by rhizobacteria alters due to growth and induced by social interactions between single members of the microbial community. These results form a basis to elucidate the functional role of such interaction-triggered compounds in establishment and maintenance of microbial communities and can be applied under natural and more realistic conditions, since rhizobacteria also interact with the plant itself and many other members of plant and soil microbiota.
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Affiliation(s)
- Riya C Menezes
- Research Group Mass Spectrometry/Proteomics, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Birgit Piechulla
- Department of Biochemistry, University of Rostock, Institute for Biological Sciences, Rostock, Germany
| | - Dörte Warber
- Department of Biochemistry, University of Rostock, Institute for Biological Sciences, Rostock, Germany
| | - Aleš Svatoš
- Research Group Mass Spectrometry/Proteomics, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Marco Kai
- Research Group Mass Spectrometry/Proteomics, Max-Planck Institute for Chemical Ecology, Jena, Germany.,Department of Biochemistry, University of Rostock, Institute for Biological Sciences, Rostock, Germany
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Wang J, Gao C, Chen X, Liu L. Expanding the lysine industry: biotechnological production of l-lysine and its derivatives. ADVANCES IN APPLIED MICROBIOLOGY 2021; 115:1-33. [PMID: 34140131 DOI: 10.1016/bs.aambs.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
l-lysine is an essential amino acid that contains various functional groups including α-amino, ω-amino, and α-carboxyl groups, exhibiting high reaction potential. The derivatization of these functional groups produces a series of value-added chemicals, such as cadaverine, glutarate, and d-lysine, that are widely applied in the chemical synthesis, cosmetics, food, and pharmaceutical industries. Here, we review recent advances in the biotechnological production of l-lysine and its derivatives and expatiate key technological strategies. Furthermore, we also discuss the existing challenges and potential strategies for more efficient production of these chemicals.
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Affiliation(s)
- Jiaping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.
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27
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de Felício R, Ballone P, Bazzano CF, Alves LFG, Sigrist R, Infante GP, Niero H, Rodrigues-Costa F, Fernandes AZN, Tonon LAC, Paradela LS, Costa RKE, Dias SMG, Dessen A, Telles GP, da Silva MAC, Lima AODS, Trivella DBB. Chemical Elicitors Induce Rare Bioactive Secondary Metabolites in Deep-Sea Bacteria under Laboratory Conditions. Metabolites 2021; 11:metabo11020107. [PMID: 33673148 PMCID: PMC7918856 DOI: 10.3390/metabo11020107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 02/03/2021] [Indexed: 02/06/2023] Open
Abstract
Bacterial genome sequencing has revealed a vast number of novel biosynthetic gene clusters (BGC) with potential to produce bioactive natural products. However, the biosynthesis of secondary metabolites by bacteria is often silenced under laboratory conditions, limiting the controlled expression of natural products. Here we describe an integrated methodology for the construction and screening of an elicited and pre-fractionated library of marine bacteria. In this pilot study, chemical elicitors were evaluated to mimic the natural environment and to induce the expression of cryptic BGCs in deep-sea bacteria. By integrating high-resolution untargeted metabolomics with cheminformatics analyses, it was possible to visualize, mine, identify and map the chemical and biological space of the elicited bacterial metabolites. The results show that elicited bacterial metabolites correspond to ~45% of the compounds produced under laboratory conditions. In addition, the elicited chemical space is novel (~70% of the elicited compounds) or concentrated in the chemical space of drugs. Fractionation of the crude extracts further evidenced minor compounds (~90% of the collection) and the detection of biological activity. This pilot work pinpoints strategies for constructing and evaluating chemically diverse bacterial natural product libraries towards the identification of novel bacterial metabolites in natural product-based drug discovery pipelines.
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Affiliation(s)
- Rafael de Felício
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil; (R.d.F.); (P.B.); (C.F.B.); (L.F.G.A.); (R.S.); (G.P.I.); (H.N.); (F.R.-C.); (A.Z.N.F.); (L.A.C.T.); (L.S.P.); (R.K.E.C.); (S.M.G.D.); (A.D.)
| | - Patricia Ballone
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil; (R.d.F.); (P.B.); (C.F.B.); (L.F.G.A.); (R.S.); (G.P.I.); (H.N.); (F.R.-C.); (A.Z.N.F.); (L.A.C.T.); (L.S.P.); (R.K.E.C.); (S.M.G.D.); (A.D.)
- Institute of Biology, University of Campinas (UNICAMP), Campinas 13083-862, SP, Brazil
| | - Cristina Freitas Bazzano
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil; (R.d.F.); (P.B.); (C.F.B.); (L.F.G.A.); (R.S.); (G.P.I.); (H.N.); (F.R.-C.); (A.Z.N.F.); (L.A.C.T.); (L.S.P.); (R.K.E.C.); (S.M.G.D.); (A.D.)
- Institute of Computing (IC), University of Campinas (UNICAMP), Campinas 13083-852, SP, Brazil;
| | - Luiz F. G. Alves
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil; (R.d.F.); (P.B.); (C.F.B.); (L.F.G.A.); (R.S.); (G.P.I.); (H.N.); (F.R.-C.); (A.Z.N.F.); (L.A.C.T.); (L.S.P.); (R.K.E.C.); (S.M.G.D.); (A.D.)
| | - Renata Sigrist
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil; (R.d.F.); (P.B.); (C.F.B.); (L.F.G.A.); (R.S.); (G.P.I.); (H.N.); (F.R.-C.); (A.Z.N.F.); (L.A.C.T.); (L.S.P.); (R.K.E.C.); (S.M.G.D.); (A.D.)
| | - Gina Polo Infante
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil; (R.d.F.); (P.B.); (C.F.B.); (L.F.G.A.); (R.S.); (G.P.I.); (H.N.); (F.R.-C.); (A.Z.N.F.); (L.A.C.T.); (L.S.P.); (R.K.E.C.); (S.M.G.D.); (A.D.)
| | - Henrique Niero
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil; (R.d.F.); (P.B.); (C.F.B.); (L.F.G.A.); (R.S.); (G.P.I.); (H.N.); (F.R.-C.); (A.Z.N.F.); (L.A.C.T.); (L.S.P.); (R.K.E.C.); (S.M.G.D.); (A.D.)
- Institute of Biology, University of Campinas (UNICAMP), Campinas 13083-862, SP, Brazil
| | - Fernanda Rodrigues-Costa
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil; (R.d.F.); (P.B.); (C.F.B.); (L.F.G.A.); (R.S.); (G.P.I.); (H.N.); (F.R.-C.); (A.Z.N.F.); (L.A.C.T.); (L.S.P.); (R.K.E.C.); (S.M.G.D.); (A.D.)
- Institute of Biology, University of Campinas (UNICAMP), Campinas 13083-862, SP, Brazil
| | - Arthur Zanetti Nunes Fernandes
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil; (R.d.F.); (P.B.); (C.F.B.); (L.F.G.A.); (R.S.); (G.P.I.); (H.N.); (F.R.-C.); (A.Z.N.F.); (L.A.C.T.); (L.S.P.); (R.K.E.C.); (S.M.G.D.); (A.D.)
- Institute of Biology, University of Campinas (UNICAMP), Campinas 13083-862, SP, Brazil
| | - Luciane A. C. Tonon
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil; (R.d.F.); (P.B.); (C.F.B.); (L.F.G.A.); (R.S.); (G.P.I.); (H.N.); (F.R.-C.); (A.Z.N.F.); (L.A.C.T.); (L.S.P.); (R.K.E.C.); (S.M.G.D.); (A.D.)
| | - Luciana S. Paradela
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil; (R.d.F.); (P.B.); (C.F.B.); (L.F.G.A.); (R.S.); (G.P.I.); (H.N.); (F.R.-C.); (A.Z.N.F.); (L.A.C.T.); (L.S.P.); (R.K.E.C.); (S.M.G.D.); (A.D.)
| | - Renna Karoline Eloi Costa
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil; (R.d.F.); (P.B.); (C.F.B.); (L.F.G.A.); (R.S.); (G.P.I.); (H.N.); (F.R.-C.); (A.Z.N.F.); (L.A.C.T.); (L.S.P.); (R.K.E.C.); (S.M.G.D.); (A.D.)
| | - Sandra Martha Gomes Dias
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil; (R.d.F.); (P.B.); (C.F.B.); (L.F.G.A.); (R.S.); (G.P.I.); (H.N.); (F.R.-C.); (A.Z.N.F.); (L.A.C.T.); (L.S.P.); (R.K.E.C.); (S.M.G.D.); (A.D.)
| | - Andréa Dessen
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil; (R.d.F.); (P.B.); (C.F.B.); (L.F.G.A.); (R.S.); (G.P.I.); (H.N.); (F.R.-C.); (A.Z.N.F.); (L.A.C.T.); (L.S.P.); (R.K.E.C.); (S.M.G.D.); (A.D.)
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, F-38000 Grenoble, France
| | - Guilherme P. Telles
- Institute of Computing (IC), University of Campinas (UNICAMP), Campinas 13083-852, SP, Brazil;
| | - Marcus Adonai Castro da Silva
- School of Sea, Science and Technology, University of Vale do Itajaí (Univali), Itajaí 88302-202, SC, Brazil; (M.A.C.d.S.); (A.O.d.S.L.)
| | - Andre Oliveira de Souza Lima
- School of Sea, Science and Technology, University of Vale do Itajaí (Univali), Itajaí 88302-202, SC, Brazil; (M.A.C.d.S.); (A.O.d.S.L.)
| | - Daniela Barretto Barbosa Trivella
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil; (R.d.F.); (P.B.); (C.F.B.); (L.F.G.A.); (R.S.); (G.P.I.); (H.N.); (F.R.-C.); (A.Z.N.F.); (L.A.C.T.); (L.S.P.); (R.K.E.C.); (S.M.G.D.); (A.D.)
- Correspondence: ; Tel.: +55-19-3517-5055
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Nicault M, Zaiter A, Dumarcay S, Chaimbault P, Gelhaye E, Leblond P, Bontemps C. Elicitation of Antimicrobial Active Compounds by Streptomyces-Fungus Co-Cultures. Microorganisms 2021; 9:microorganisms9010178. [PMID: 33467607 PMCID: PMC7830452 DOI: 10.3390/microorganisms9010178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/23/2020] [Accepted: 01/12/2021] [Indexed: 02/06/2023] Open
Abstract
The bacteria of the genus Streptomyces and Basidiomycete fungi harbor many biosynthetic gene clusters (BGCs) that are at the origin of many bioactive molecules with medical or industrial interests. Nevertheless, most BGCs do not express in standard lab growth conditions, preventing the full metabolic potential of these organisms from being exploited. Because it generates biotic cues encountered during natural growth conditions, co-culture is a means to elicit such cryptic compounds. In this study, we explored 72 different Streptomyces-fungus interaction zones (SFIZs) generated during the co-culture of eight Streptomyces and nine fungi. Two SFIZs were selected because they showed an elicitation of anti-bacterial activity compared to mono-cultures. The study of these SFIZs showed that co-culture had a strong impact on the metabolic expression of each partner and enabled the expression of specific compounds. These results show that mimicking the biotic interactions present in this ecological niche is a promising avenue of research to explore the metabolic capacities of Streptomyces and fungi.
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Affiliation(s)
- Matthieu Nicault
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France;
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France;
| | - Ali Zaiter
- Université de Lorraine, LCP-A2MC, F-57000 Metz, France; (A.Z.); (P.C.)
| | | | | | - Eric Gelhaye
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France;
| | - Pierre Leblond
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France;
- Correspondence: (P.L.); (C.B.)
| | - Cyril Bontemps
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France;
- Correspondence: (P.L.); (C.B.)
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Zhang Q, Ren JW, Wang W, Zhai J, Yang J, Liu N, Huang Y, Chen Y, Pan G, Fan K. A Versatile Transcription-Translation in One Approach for Activation of Cryptic Biosynthetic Gene Clusters. ACS Chem Biol 2020; 15:2551-2557. [PMID: 32786260 DOI: 10.1021/acschembio.0c00581] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ever-growing drug resistance problem worldwide highlights the urgency to discover and develop new drugs. Microbial natural products are a prolific source of drugs. Genome sequencing has revealed a tremendous amount of uncharacterized natural product biosynthetic gene clusters (BGCs) encoded within microbial genomes, most of which are cryptic or express at very low levels under standard culture conditions. Therefore, developing effective strategies to awaken these cryptic BGCs is of great interest for natural product discovery. In this study, we designed and validated a Transcription-Translation in One (TTO) approach for activation of cryptic BGCs. This approach aims to alter the metabolite profiles of target strains by directly overexpressing exogenous rpsL (encoding ribosomal protein S12) and rpoB (encoding RNA polymerase β subunit) genes containing beneficial mutations for natural product production using a plug-and-play plasmid system. As a result, this approach bypasses the tedious screening work and overcomes the false positive problem in the traditional ribosome engineering approach. In this work, the TTO approach was successfully applied to activating cryptic BGCs in three Streptomyces strains, leading to the discovery of two aromatic polyketide antibiotics, piloquinone and homopiloquinone. We further identified a single BGC responsible for the biosynthesis of both piloquinone and homopiloquinone, which features an unusual starter unit incorporation step. This powerful strategy can be further exploited for BGC activation in strains even beyond streptomycetes, thus facilitating natural product discovery research in the future.
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Affiliation(s)
- Qian Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin-Wei Ren
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji’an Zhai
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Jing Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ning Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guohui Pan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Li Y, Li J, Ye Z, Lu L. Enhancement of angucycline production by combined UV mutagenesis and ribosome engineering and fermentation optimization in Streptomyces dengpaensis XZHG99 T. Prep Biochem Biotechnol 2020; 51:173-182. [PMID: 32815762 DOI: 10.1080/10826068.2020.1805754] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Strain improvement of Streptomyces dengpaensis XZHG99T was performed by combined UV mutagenesis and ribosome engineering, as well as fermentation optimization for enhanced angucycline production (rabelomycin and saquayamycin B1). First, four streptomycin-resistant mutants were obtained after screening of UV mutagenesis and ribosome engineering. Then a rpsL mutant (HTT7) with higher productivity of rabelomycin and saquayamycin B1 was selected according to genetic screening and HPLC/LC-MS analyses, whose maximum titers of rabelomycin and saquayamycin B1 were 3.6 ± 0.02 mg/L and 7.5 ± 0.04 mg/L, respectively, about fourfold higher than those produced by XZHG99T. Next, fermentation optimization of HTT7 was successively carried out by single-factor experiments in shake flasks. The titers of rabelomycin and saquayamycin B1 were increased to 11.2 ± 0.04 mg/L and 20.5 ± 0.02 mg/L after optimization of shake flask fermentation conditions, respectively, which was increased about sixfold compared with those produced by XZHG99T. Finally, the titers of rabelomycin and saquayamycin B1 reached 15.7 ± 0.05 mg/L and 39.9 ± 0.05 mg/L after the scaled-up fermentation, which was 7.8-fold and 11.4-fold higher than those produced by XZHG99T, respectively. These data demonstrate that the combined empirical strain-breeding approaches are still an effective and convenient pathway to improve strain production ability.
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Affiliation(s)
- Yumei Li
- School of Bioscience and Biotechnology, University of Jinan, Jinan, China
| | - Jiyu Li
- School of Bioscience and Biotechnology, University of Jinan, Jinan, China
| | - Zhengmao Ye
- School of Materials Science and Engineering, University of Jinan, Jinan, China
| | - Lingchao Lu
- School of Materials Science and Engineering, University of Jinan, Jinan, China
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Mitousis L, Thoma Y, Musiol-Kroll EM. An Update on Molecular Tools for Genetic Engineering of Actinomycetes-The Source of Important Antibiotics and Other Valuable Compounds. Antibiotics (Basel) 2020; 9:E494. [PMID: 32784409 PMCID: PMC7460540 DOI: 10.3390/antibiotics9080494] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 02/06/2023] Open
Abstract
The first antibiotic-producing actinomycete (Streptomyces antibioticus) was described by Waksman and Woodruff in 1940. This discovery initiated the "actinomycetes era", in which several species were identified and demonstrated to be a great source of bioactive compounds. However, the remarkable group of microorganisms and their potential for the production of bioactive agents were only partially exploited. This is caused by the fact that the growth of many actinomycetes cannot be reproduced on artificial media at laboratory conditions. In addition, sequencing, genome mining and bioactivity screening disclosed that numerous biosynthetic gene clusters (BGCs), encoded in actinomycetes genomes are not expressed and thus, the respective potential products remain uncharacterized. Therefore, a lot of effort was put into the development of technologies that facilitate the access to actinomycetes genomes and activation of their biosynthetic pathways. In this review, we mainly focus on molecular tools and methods for genetic engineering of actinomycetes that have emerged in the field in the past five years (2015-2020). In addition, we highlight examples of successful application of the recently developed technologies in genetic engineering of actinomycetes for activation and/or improvement of the biosynthesis of secondary metabolites.
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Affiliation(s)
| | | | - Ewa M. Musiol-Kroll
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (L.M.); (Y.T.)
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Kramer GJ, Pimentel-Elardo S, Nodwell JR. Dual-PKS Cluster for Biosynthesis of a Light-Induced Secondary Metabolite Found from Genome Sequencing of Hyphodiscus hymeniophilus Fungus. Chembiochem 2020; 21:2116-2120. [PMID: 32314858 PMCID: PMC7496686 DOI: 10.1002/cbic.201900689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/17/2020] [Indexed: 11/15/2022]
Abstract
Filamentous fungi are known producers of important secondary metabolites. In spite of this, the majority of these organisms have not been studied at the genome level, leaving many of the bioactive molecules they produce undiscovered. In this study, we explore the secondary metabolite potential of an understudied fungus, Hyphodiscus hymeniophilus. By sequencing and assembling the first genome from this genus, we show that this fungus has genes for at least 20 natural products and that many of these products are likely novel. One of these metabolites is identified: a new, red-pigmented member of the azaphilone class, hyphodiscorubrin. We show that this metabolite is only produced when the fungus is grown in the light. Furthermore, the biosynthetic gene cluster of hyphodiscorubrin is identified though homology to other known azaphilone producing clusters.
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Affiliation(s)
- Glenna J Kramer
- Department of Biochemistry, University of Toronto, MaRS Centre, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Sheila Pimentel-Elardo
- Department of Biochemistry, University of Toronto, MaRS Centre, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Justin R Nodwell
- Department of Biochemistry, University of Toronto, MaRS Centre, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
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Hu D, Sun C, Jin T, Fan G, Mok KM, Li K, Lee SMY. Exploring the Potential of Antibiotic Production From Rare Actinobacteria by Whole-Genome Sequencing and Guided MS/MS Analysis. Front Microbiol 2020; 11:1540. [PMID: 32922368 PMCID: PMC7375171 DOI: 10.3389/fmicb.2020.01540] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/12/2020] [Indexed: 11/26/2022] Open
Abstract
Actinobacteria are well recognized for their production of structurally diverse bioactive secondary metabolites, but the rare actinobacterial genera have been underexploited for such potential. To search for new sources of active compounds, an experiment combining genomic analysis and tandem mass spectrometry (MS/MS) screening was designed to isolate and characterize actinobacterial strains from a mangrove environment in Macau. Fourteen actinobacterial strains were isolated from the collected samples. Partial 16S sequences indicated that they were from six genera, including Brevibacterium, Curtobacterium, Kineococcus, Micromonospora, Mycobacterium, and Streptomyces. The isolate sp.01 showing 99.28% sequence similarity with a reference rare actinobacterial species Micromonospora aurantiaca ATCC 27029T was selected for whole genome sequencing. Organization of its gene clusters for secondary metabolite biosynthesis revealed 21 clusters encoded to antibiotic production, which is higher than other Micromonospora species. Of the genome-predicted antibiotics, kanamycin was found through guided MS/MS analysis producible by the M. aurantiaca strain for the first time. The present study highlighted that genomic analysis combined with MS/MS screening is a promising method to discover potential of antibiotic production from rare actinobacteria.
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Affiliation(s)
- Dini Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Chenghang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Jin
- Beijing Genomics Institute, Shenzhen, China
| | | | - Kai Meng Mok
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Kai Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
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34
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Li ZY, Bu QT, Wang J, Liu Y, Chen XA, Mao XM, Li YQ. Activation of anthrachamycin biosynthesis in Streptomyces chattanoogensis L10 by site-directed mutagenesis of rpoB. J Zhejiang Univ Sci B 2020; 20:983-994. [PMID: 31749345 DOI: 10.1631/jzus.b1900344] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genome sequencing projects revealed massive cryptic gene clusters encoding the undiscovered secondary metabolites in Streptomyces. To investigate the metabolic products of silent gene clusters in Streptomyces chattanoogensis L10 (CGMCC 2644), we used site-directed mutagenesis to generate ten mutants with point mutations in the highly conserved region of rpsL (encoding the ribosomal protein S12) or rpoB (encoding the RNA polymerase β-subunit). Among them, L10/RpoB (H437Y) accumulated a dark pigment on a yeast extract-malt extract-glucose (YMG) plate. This was absent in the wild type. After further investigation, a novel angucycline antibiotic named anthrachamycin was isolated and determined using nuclear magnetic resonance (NMR) spectroscopic techniques. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis and electrophoretic mobility shift assay (EMSA) were performed to investigate the mechanism underlying the activation effect on the anthrachamycin biosynthetic gene cluster. This work indicated that the rpoB-specific missense H437Y mutation had activated anthrachamycin biosynthesis in S. chattanoogensis L10. This may be helpful in the investigation of the pleiotropic regulation system in Streptomyces.
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Affiliation(s)
- Zi-Yue Li
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qing-Ting Bu
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Jue Wang
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yu Liu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xin-Ai Chen
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
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35
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Liu L, Li S, Sun R, Qin X, Ju J, Zhang C, Duan Y, Huang Y. Activation and Characterization of Bohemamine Biosynthetic Gene Cluster from Streptomyces sp. CB02009. Org Lett 2020; 22:4614-4619. [PMID: 32463693 DOI: 10.1021/acs.orglett.0c01224] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bohemamines (BHMs) are bacterial alkaloids containing a pyrrolizidine core with two unusual methyl groups. Herein we report the activation of BHMs biosynthesis using a ribosome engineering approach. Characterization of the bhm gene cluster reveals that nonribosomal peptide synthetase BhmJ and Baeyer-Villiger monooxygenase BhmK are responsible for the formation of the pyrrolizidine core, which is further methylated on C-7 by methyltransferase BhmG. The 9-methyl group of BHMs is instead originated from a nonproteinogenic amino acid (2S,5S)-5-methylproline.
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Affiliation(s)
- Ling Liu
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China
| | - Sainan Li
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China
| | - Runze Sun
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China
| | - Xiangjing Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Jianhua Ju
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, 410011, Hunan, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410011, Hunan, China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410011, Hunan, China
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36
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Fan JX, Song Y, Tang G, Ochi K, Shentu XP, Yu XP. Substantial improvement of tetraene macrolide production in Streptomyces diastatochromogenes by cumulative drug resistance mutations. PLoS One 2020; 15:e0232927. [PMID: 32396566 PMCID: PMC7217443 DOI: 10.1371/journal.pone.0232927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/25/2020] [Indexed: 11/19/2022] Open
Abstract
Tetraene macrolides remain one of the most reliable fungicidal agents as resistance of fungal pathogens to these antibiotics is relatively rare. The modes of action and biosynthesis of polyene macrolides had been the focus of research over the past few years. However, few studies have been carried out on the overproduction of polyene macrolides. In the present study, cumulative drug-resistance mutation was used to obtain a quintuple mutant G5-59 with huge tetraene macrolide overproduction from the starting strain Streptomyces diastatochromogenes 1628. Through DNA sequence analysis, the mutation points in the genes of rsmG, rpsL and rpoB were identified. Additionally, the growth characteristic and expression level of tetrRI gene (belonging to the large ATP binding regulator of LuxR family) involved in the biosynthesis of tetraene macrolides were analyzed. As examined with 5L fermentor, the quintuple mutant G5-59 grew very well and the maximum productivity of tetramycin A, tetramycin P and tetrin B was as high as 1735, 2811 and 1500 mg/L, which was 8.7-, 16- and 25-fold higher than that of the wild-type strain 1628, respectively. The quintuple mutant G5-59 could be useful for further improvement of tetraene macrolides production at industrial level.
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Affiliation(s)
- Jing-Xuan Fan
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Yang Song
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Gu Tang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Kozo Ochi
- Department of Life Science, Hiroshima Institute of Technology, Hiroshima, Japan
| | - Xu-Ping Shentu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
- * E-mail: (XPS); (XPY)
| | - Xiao-Ping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
- * E-mail: (XPS); (XPY)
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37
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Genome shuffling based on different types of ribosome engineering mutants for enhanced production of 10-membered enediyne tiancimycin-A. Appl Microbiol Biotechnol 2020; 104:4359-4369. [PMID: 32236679 DOI: 10.1007/s00253-020-10583-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/15/2020] [Accepted: 03/23/2020] [Indexed: 12/21/2022]
Abstract
Tiancimycin-A (TNM-A) is an anthraquinone-fused ten-membered enediyne produced by Streptomyces sp. CB03234, which is very promising for the development of anticancer antibody-drug conjugates (ADCs). To improve the titer of TNM-A, we have generated high-producing mutants CB03234-S and CB03234-R through ribosome engineering, but still not sufficient for pilot production of TNM-A. As the follow-up work, gentamycin-induced ribosome engineering was further adopted here to generate the mutant CB03234-G, which produced similar level of TNM-A as in CB03234-S and CB03234-R. Benefiting from the distinct antibiotic resistances of three ribosome engineering mutants, genome shuffling between any two of them was respectively carried out, and finally obtained the recombinant CB03234-GS26. Under optimal conditions, CB03234-GS26 produced 40.6 ± 1.0 mg/L TNM-A in shaking flasks and 20.8 ± 0.4 mg/L in a scaled-up 30-L fermentor. Comparing with the parental high-producing mutants, the over 1.6-fold titer improvement of CB03234-GS26 in fermentor was more promising for pilot production of TNM-A. Besides the distinctive morphological features, genetic characterization revealed that CB03234-GS26 possessed 1.8 kb rsmG related deletion just the same as CB03234-S, but no mutation was found in rpsL. Subsequent knockouts proved that rsmG was unrelated to titer improvement of TNM-A, which implied other genomic variations and mechanisms rather than ribosome engineering to enhance the biosynthesis of TNM-A. Therefore, CB03234-GS26 provided a basis to locate potential novel genetic targets, and explore the interactions between complex metabolic network and TNM biosynthetic pathway, which shall promote future construction of high-yielding systems for TNM-A and other anthraquinone-fused enediynes.Key Points •United genome shuffling and ribosome engineering help further strain improvement. •CB03234-GS26 with improved titer is practical for the pilot production of TNM-A. •Enhanced TNM-A production should attribute to novel genetic features/mechanisms.
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38
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Xia H, Li X, Li Z, Zhan X, Mao X, Li Y. The Application of Regulatory Cascades in Streptomyces: Yield Enhancement and Metabolite Mining. Front Microbiol 2020; 11:406. [PMID: 32265866 PMCID: PMC7105598 DOI: 10.3389/fmicb.2020.00406] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Streptomyces is taken as an important resource for producing the most abundant antibiotics and other bio-active natural products, which have been widely used in pharmaceutical and agricultural areas. Usually they are biosynthesized through secondary metabolic pathways encoded by cluster situated genes. And these gene clusters are stringently regulated by interweaved transcriptional regulatory cascades. In the past decades, great advances have been made to elucidate the regulatory mechanisms involved in antibiotic production in Streptomyces. In this review, we summarized the recent advances on the regulatory cascades of antibiotic production in Streptomyces from the following four levels: the signals triggering the biosynthesis, the global regulators, the pathway-specific regulators and the feedback regulation. The production of antibiotic can be largely enhanced by rewiring the regulatory networks, such as overexpression of positive regulators, inactivation of repressors, fine-tuning of the feedback and ribosomal engineering in Streptomyces. The enormous amount of genomic sequencing data implies that the Streptomyces has potential to produce much more antibiotics for the great diversities and wide distributions of biosynthetic gene clusters in Streptomyces genomes. Most of these gene clusters are defined cryptic for unknown or undetectable natural products. In the synthetic biology era, activation of the cryptic gene clusters has been successfully achieved by manipulation of the regulatory genes. Chemical elicitors, rewiring regulatory gene and ribosomal engineering have been employed to crack the potential of cryptic gene clusters. These have been proposed as the most promising strategy to discover new antibiotics. For the complex of regulatory network in Streptomyces, we proposed that the discovery of new antibiotics and the optimization of industrial strains would be greatly promoted by further understanding the regulatory mechanism of antibiotic production.
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Affiliation(s)
- Haiyang Xia
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xiaofang Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Zhangqun Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xinqiao Zhan
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xuming Mao
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China.,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongquan Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China.,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
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39
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A putative mechanism underlying secondary metabolite overproduction by Streptomyces strains with a 23S rRNA mutation conferring erythromycin resistance. Appl Microbiol Biotechnol 2020; 104:2193-2203. [PMID: 31925486 DOI: 10.1007/s00253-019-10288-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 02/07/2023]
Abstract
Mutations in rrn encoding ribosomal RNA (rRNA) and rRNA modification often confer resistance to ribosome-targeting antibiotics by altering the site of their interaction with the small (30S) and large (50S) subunits of the bacterial ribosome. The highly conserved central loop of domain V of 23S rRNA (nucleotides 2042-2628 in Escherichia coli; the exact position varies by species) of the 50S subunit, which is implicated in peptidyl transferase activity, is known to be important in macrolide interactions and resistance. In this study, we identified an A2302T mutation in the rrnA-23S rRNA gene and an A2281G mutation in the rrnC-23S rRNA gene that were responsible for resistance to erythromycin in the model actinomycete Streptomyces coelicolor A3(2) and its close relative Streptomyces lividans 66, respectively. Interestingly, genetic and phenotypic characterization of the erythromycin-resistant mutants indicated a possibility that under coexistence of the 23S rRNA mutation and mutations in other genes, S. coelicolor A3(2) and S. lividans 66 can produce abundant amounts of the pigmented antibiotics actinorhodin and undecylprodigiosin depending on the combinations of mutations. Herein, we report the unique phenomenon occurring by unexpected characteristics of the 23S rRNA mutations that can affect the emergence of additional mutations probably with an upswing in spontaneous mutations and enrichment in their variations in Streptomyces strains. Further, we discuss a putative mechanism underlying secondary metabolite overproduction by Streptomyces strains with a 23S rRNA mutation conferring erythromycin resistance.
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40
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Li ZY, Bu QT, Wang J, Liu Y, Chen XA, Mao XM, Li YQ. Activation of anthrachamycin biosynthesis in Streptomyces chattanoogensis L10 by site-directed mutagenesis of rpoB. J Zhejiang Univ Sci B 2019. [PMID: 31749345 PMCID: PMC6885405 DOI: 10.1631/jzus.b191900344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Genome sequencing projects revealed massive cryptic gene clusters encoding the undiscovered secondary metabolites in Streptomyces. To investigate the metabolic products of silent gene clusters in Streptomyces chattanoogensis L10 (CGMCC 2644), we used site-directed mutagenesis to generate ten mutants with point mutations in the highly conserved region of rpsL (encoding the ribosomal protein S12) or rpoB (encoding the RNA polymerase β-subunit). Among them, L10/RpoB (H437Y) accumulated a dark pigment on a yeast extract-malt extract-glucose (YMG) plate. This was absent in the wild type. After further investigation, a novel angucycline antibiotic named anthrachamycin was isolated and determined using nuclear magnetic resonance (NMR) spectroscopic techniques. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis and electrophoretic mobility shift assay (EMSA) were performed to investigate the mechanism underlying the activation effect on the anthrachamycin biosynthetic gene cluster. This work indicated that the rpoB-specific missense H437Y mutation had activated anthrachamycin biosynthesis in S. chattanoogensis L10. This may be helpful in the investigation of the pleiotropic regulation system in Streptomyces.
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Affiliation(s)
- Zi-yue Li
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qing-ting Bu
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Jue Wang
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yu Liu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xin-ai Chen
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Xu-ming Mao
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China,†E-mail:
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41
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Musiol-Kroll EM, Tocchetti A, Sosio M, Stegmann E. Challenges and advances in genetic manipulation of filamentous actinomycetes - the remarkable producers of specialized metabolites. Nat Prod Rep 2019; 36:1351-1369. [PMID: 31517370 DOI: 10.1039/c9np00029a] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: up to February 2019Actinomycetes are Gram positive bacteria of the phylum Actinobacteria. These organisms are one of the most important sources of structurally diverse, clinically used antibiotics and other valuable bioactive products, as well as biotechnologically relevant enzymes. Most strains were discovered by their ability to produce a given molecule and were often poorly characterized, physiologically and genetically. The development of genetic methods for Streptomyces and related filamentous actinomycetes has led to the successful manipulation of antibiotic biosynthesis to attain structural modification of microbial metabolites that would have been inaccessible by chemical means and improved production yields. Moreover, genome mining reveals that actinomycete genomes contain multiple biosynthetic gene clusters (BGCs), however only a few of them are expressed under standard laboratory conditions, leading to the production of the respective compound(s). Thus, to access and activate the so-called "silent" BGCs, to improve their biosynthetic potential and to discover novel natural products methodologies for genetic manipulation are required. Although different methods have been applied for many actinomycete strains, genetic engineering is still remaining very challenging for some "underexplored" and poorly characterized actinomycetes. This review summarizes the strategies developed to overcome the obstacles to genetic manipulation of actinomycetes and allowing thereby rational genetic engineering of this industrially relevant group of microorganisms. At the end of this review we give some tips to researchers with limited or no previous experience in genetic manipulation of actinomycetes. The article covers the most relevant literature published until February 2019.
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Affiliation(s)
- Ewa M Musiol-Kroll
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, Auf der Morgenstelle 28, Tübingen, 72076, Germany.
| | | | | | - Evi Stegmann
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, Auf der Morgenstelle 28, Tübingen, 72076, Germany.
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42
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The Application of Ribosome Engineering to Natural Product Discovery and Yield Improvement in Streptomyces. Antibiotics (Basel) 2019; 8:antibiotics8030133. [PMID: 31480298 PMCID: PMC6784132 DOI: 10.3390/antibiotics8030133] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/10/2019] [Accepted: 08/27/2019] [Indexed: 12/23/2022] Open
Abstract
Microbial natural product drug discovery and development has entered a new era, driven by microbial genomics and synthetic biology. Genome sequencing has revealed the vast potential to produce valuable secondary metabolites in bacteria and fungi. However, many of the biosynthetic gene clusters are silent under standard fermentation conditions. By rational screening for mutations in bacterial ribosomal proteins or RNA polymerases, ribosome engineering is a versatile approach to obtain mutants with improved titers for microbial product formation or new natural products through activating silent biosynthetic gene clusters. In this review, we discuss the mechanism of ribosome engineering and its application to natural product discovery and yield improvement in Streptomyces. Our analysis suggests that ribosome engineering is a rapid and cost-effective approach and could be adapted to speed up the discovery and development of natural product drug leads in the post-genomic era.
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Hautbergue T, Jamin EL, Debrauwer L, Puel O, Oswald IP. From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites. Nat Prod Rep 2019; 35:147-173. [PMID: 29384544 DOI: 10.1039/c7np00032d] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fungal secondary metabolites are defined by bioactive properties that ensure adaptation of the fungus to its environment. Although some of these natural products are promising sources of new lead compounds especially for the pharmaceutical industry, others pose risks to human and animal health. The identification of secondary metabolites is critical to assessing both the utility and risks of these compounds. Since fungi present biological specificities different from other microorganisms, this review covers the different strategies specifically used in fungal studies to perform this critical identification. Strategies focused on the direct detection of the secondary metabolites are firstly reported. Particularly, advances in high-throughput untargeted metabolomics have led to the generation of large datasets whose exploitation and interpretation generally require bioinformatics tools. Then, the genome-based methods used to study the entire fungal metabolic potential are reported. Transcriptomic and proteomic tools used in the discovery of fungal secondary metabolites are presented as links between genomic methods and metabolomic experiments. Finally, the influence of the culture environment on the synthesis of secondary metabolites by fungi is highlighted as a major factor to consider in research on fungal secondary metabolites. Through this review, we seek to emphasize that the discovery of natural products should integrate all of these valuable tools. Attention is also drawn to emerging technologies that will certainly revolutionize fungal research and to the use of computational tools that are necessary but whose results should be interpreted carefully.
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Affiliation(s)
- T Hautbergue
- Toxalim (Research Centre in Food Toxicology) Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, F-31027 Toulouse, France.
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44
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Improvement of ε-poly-L-lysine production of Streptomyces albulus by continuous introduction of streptomycin resistance. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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45
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Fernández‐Cabezón L, Cros A, Nikel PI. Evolutionary Approaches for Engineering Industrially Relevant Phenotypes in Bacterial Cell Factories. Biotechnol J 2019; 14:e1800439. [DOI: 10.1002/biot.201800439] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/08/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Lorena Fernández‐Cabezón
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
| | - Antonin Cros
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
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46
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Jahanshah G, Yan Q, Gerhardt H, Pataj Z, Lämmerhofer M, Pianet I, Josten M, Sahl HG, Silby MW, Loper JE, Gross H. Discovery of the Cyclic Lipopeptide Gacamide A by Genome Mining and Repair of the Defective GacA Regulator in Pseudomonas fluorescens Pf0-1. JOURNAL OF NATURAL PRODUCTS 2019; 82:301-308. [PMID: 30666877 DOI: 10.1021/acs.jnatprod.8b00747] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Genome mining of the Gram-negative bacterium Pseudomonas fluorescens Pf0-1 showed that the strain possesses a silent NRPS-based biosynthetic gene cluster encoding a new lipopeptide; its activation required the repair of the global regulator system. In this paper, we describe the genomics-driven discovery and characterization of the associated secondary metabolite gacamide A, a lipodepsipeptide that forms a new family of Pseudomonas lipopeptides. The compound has a moderate, narrow-spectrum antibiotic activity and facilitates bacterial surface motility.
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Affiliation(s)
- Gahzaleh Jahanshah
- Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , 72076 Tübingen , Germany
- German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
| | - Qing Yan
- Department of Botany and Plant Pathology , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Heike Gerhardt
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis , University of Tübingen , 72076 Tübingen , Germany
- UMR 5060, IRAMAT-CRP2A, Esplanade des Antilles , F-33600 Pessac , France
| | - Zoltán Pataj
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis , University of Tübingen , 72076 Tübingen , Germany
- UMR 5060, IRAMAT-CRP2A, Esplanade des Antilles , F-33600 Pessac , France
| | - Michael Lämmerhofer
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis , University of Tübingen , 72076 Tübingen , Germany
- UMR 5060, IRAMAT-CRP2A, Esplanade des Antilles , F-33600 Pessac , France
| | - Isabelle Pianet
- CESAMO-ISM, UMR 5255, CNRS , Université Bordeaux I , 351 Cours de la Libération , F-33405 Talence , France
| | - Michaele Josten
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology Unit , University of Bonn , 53115 Bonn , Germany
- German Centre for Infection Research (DZIF) , partner site Bonn-Cologne , 53115 Bonn , Germany
| | - Hans-Georg Sahl
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology Unit , University of Bonn , 53115 Bonn , Germany
- German Centre for Infection Research (DZIF) , partner site Bonn-Cologne , 53115 Bonn , Germany
| | - Mark W Silby
- Department of Biology , University of Massachusetts Dartmouth , North Dartmouth , Massachusetts 02747 , United States
| | - Joyce E Loper
- Department of Botany and Plant Pathology , Oregon State University , Corvallis , Oregon 97331 , United States
- Agricultural Research Service , U.S. Department of Agriculture , Corvallis , Oregon 97331 , United States
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , 72076 Tübingen , Germany
- German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
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47
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Li X, Li X, Zhu J, Wang H, Lu C. Carbamothioic S-acid derivative and kigamicins, the activated production of silent metabolites in Amycolatopsis alba DSM 44262Δ abm9 elicited by N-acetyl-D-glucosamine. Nat Prod Res 2019; 34:3514-3521. [PMID: 30784305 DOI: 10.1080/14786419.2019.1574783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
One new carbamothioic S-acid derivative (1) and five known kigamicin derivatives (2-6) were isolated from the fermentation extract of Amycolatopsis alba DSM 44262Δabm9 elicited by N-acetyl-D-glucosamine. HPLC-DAD-UV analyses indicated that the DSM 44262Δabm9 strain did not produce these metabolites originally and the production of 1-6 was induced by adding 25 mM N-acetyl-D-glucosamine in the culture medium. The structures of 1-6 were identified on the basis of NMR spectroscopic data and high-resolution ESIMS. These results highlight that addition of N-acetyl-D-glucosamine in the microbial culture medium could activate cryptic gene expression, induce and increase the production of new or known secondary metabolites.
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Affiliation(s)
- Xiaomei Li
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, China
| | - Xiaoman Li
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, China
| | - Jing Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Haoxin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Chunhua Lu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, China
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48
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Zhuang Z, Jiang C, Zhang F, Huang R, Yi L, Huang Y, Yan X, Duan Y, Zhu X. Streptomycin-induced ribosome engineering complemented with fermentation optimization for enhanced production of 10-membered enediynes tiancimycin-A and tiancimycin-D. Biotechnol Bioeng 2019; 116:1304-1314. [PMID: 30712262 DOI: 10.1002/bit.26944] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/18/2019] [Accepted: 01/30/2019] [Indexed: 01/01/2023]
Abstract
Tiancimycins (TNMs) are a group of 10-membered anthraquinone-fused enediynes, newly discovered from Streptomyces sp. CB03234. Among them, TNM-A and TNM-D have exhibited excellent antitumor performances and could be exploited as very promising warheads for the development of anticancer antibody-drug conjugates (ADCs). However, their low titers, especially TNM-D, have severely limited following progress. Therefore, the streptomycin-induced ribosome engineering was adopted in this work for strain improvement of CB03234, and a TNMs high producer S. sp. CB03234-S with the K43N mutation at 30S ribosomal protein S12 was successfully screened out. Subsequent media optimization revealed the essential effects of iodide and copper ion on the production of TNMs, while the substitution of nitrogen source could evidently promote the accumulation of TNM-D, and the ratio of produced TNM-A and TNM-D was responsive to the change of carbon and nitrogen ratio in the medium. Further amelioration of the pH control in scaled up 25 L fermentation increased the average titers of TNM-A and TNM-D up to 13.7 ± 0.3 and 19.2 ± 0.4 mg/L, respectively. The achieved over 45-fold titer improvement of TNM-A, and 109-fold total titer improvement of TNM-A and TNM-D enabled the efficient purification of over 200 mg of each target molecule from 25 L fermentation. Our efforts have demonstrated a practical strategy for titer improvement of anthraquinone-fused enediynes and set up a solid base for the pilot scale production and preclinical studies of TNMs to expedite the future development of anticancer ADC drugs.
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Affiliation(s)
- Zhoukang Zhuang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China
| | - Chengzhou Jiang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China
| | - Fan Zhang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China
| | - Rong Huang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China
| | - Liwei Yi
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, China
| | - Xiaohui Yan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, China
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, China
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49
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Zhao Y, Song Z, Ma Z, Bechthold A, Yu X. Sequential improvement of rimocidin production in Streptomyces rimosus M527 by introduction of cumulative drug-resistance mutations. J Ind Microbiol Biotechnol 2019; 46:697-708. [PMID: 30697650 DOI: 10.1007/s10295-019-02146-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/24/2019] [Indexed: 12/01/2022]
Abstract
Rimocidin is a polyene macrolide that exhibits a strong inhibitory activity against a broad range of plant-pathogenic fungi. In this study, fermentation optimization and ribosome engineering technology were employed to enhance rimocidin production in Streptomyces rimosus M527. After the optimization of fermentation, rimocidin production in S. rimosus M527 increased from 0.11 ± 0.01 to 0.23 ± 0.02 g/L during shake-flask experiments and reached 0.41 ± 0.05 g/L using 5-L fermentor. Fermentation optimization was followed by the generation of mutants of S. rimosus M527 through treatment of the strain with different concentrations of gentamycin (Gen) or rifamycin. One Genr mutant named S. rimosus M527-G37 and one Rifr mutant named S. rimosus M527-R5 showed increased rimocidin production. Double-resistant (Genr and Rifr) mutants were selected using S. rimosus M527-G37 and S. rimosus M527-R5, and subsequently tested. One mutant, S. rimosus M527-GR7, which was derived from M527-G37, achieved the greatest cumulative improvement in rimocidin production. In the 5-L fermentor, the maximum rimocidin production achieved by S. rimosus M527-GR7 was 25.36% and 62.89% greater than those achieved by S. rimosus M527-G37 and the wild-type strain S. rimosus M527, respectively. Moreover, in the mutants S. rimosus M527-G37 and S. rimosus M527-GR7 the transcriptional levels of ten genes (rimAsr to rimKsr) located in the gene cluster involved in rimocidin biosynthesis were all higher than those in the parental strain M527 to varying degrees. In addition, after expression of the single rimocidin biosynthetic genes in S. rimosus M527 a few recombinants showed an increase in rimocidin production. Expression of rimE led to the highest production.
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Affiliation(s)
- Yanfang Zhao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang, People's Republic of China
| | - Zhangqing Song
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang, People's Republic of China
| | - Zheng Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang, People's Republic of China.
| | - Andreas Bechthold
- Institute for Pharmaceutical Sciences, Pharmaceutical Biology and Biotechnology, University of Freiburg, 79104, Freiburg, Germany
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang, People's Republic of China.
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50
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Prajapati D, Kumari N, Dave K, Chatupale V, Pohnerkar J. Chromomycin, an antibiotic produced by Streptomyces flaviscleroticus might play a role in the resistance to oxidative stress and is essential for viability in stationary phase. Environ Microbiol 2019; 21:814-826. [PMID: 30585380 DOI: 10.1111/1462-2920.14515] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/13/2018] [Accepted: 12/20/2018] [Indexed: 12/14/2022]
Abstract
The well-known role of antibiotics in killing sensitive organisms has been challenged by the effects they exert at subinhibitory concentrations. Unfortunately, there are very few published reports on the advantages these molecules may confer to their producers. This study describes the construction of a genetically verified deletion mutant of Streptomyces flaviscleroticus unable to synthesize chromomycin. This mutant was characterized by a rapid loss of viability in stationary phase that was correlated with high oxidative stress and altered antioxidant defences. Altered levels of key metabolites in the mutant signalled a redistribution of the glycolytic flux toward the PPP to generate NADPH to fight oxidative stress as well as reduction of ATP-phosphofructokinase and Krebs cycle enzymes activities. These changes were correlated with a shift in the preference for carbon utilization from glucose to amino acids. Remarkably, chromomycin at subinhibitory concentration increased longevity of the non-producer and restored most of the phenotypic features' characteristic of the wild type strain. Altogether these observations suggest that chromomycin may have antioxidant properties that would explain, at least in part, some of the phenotypes of the mutant. Our observations warrant reconsideration of the secondary metabolite definition and raise the possibility of crucial roles for their producers.
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Affiliation(s)
- Divya Prajapati
- Department of Bio-Chemistry, The Maharaja Sayajirao University of Baroda, Baroda, 390003, Gujarat, India
| | - Namita Kumari
- Center for Sickle Cell Disease, Howard University, Washington, DC, 20059
| | - Keyur Dave
- Cellcys Labs Pvt. Ltd., Mumbai, 400104, India
| | - Vaidehi Chatupale
- Department of Bio-Chemistry, The Maharaja Sayajirao University of Baroda, Baroda, 390003, Gujarat, India
| | - Jayashree Pohnerkar
- Department of Bio-Chemistry, The Maharaja Sayajirao University of Baroda, Baroda, 390003, Gujarat, India
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