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Saito S, Arai MA. Methodology for awakening the potential secondary metabolic capacity in actinomycetes. Beilstein J Org Chem 2024; 20:753-766. [PMID: 38633912 PMCID: PMC11022428 DOI: 10.3762/bjoc.20.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
Secondary metabolites produced by actinomycete strains undoubtedly have great potential for use in applied research areas such as drug discovery. However, it is becoming difficult to obtain novel compounds because of repeated isolation around the world. Therefore, a new strategy for discovering novel secondary metabolites is needed. Many researchers believe that actinomycetes have as yet unanalyzed secondary metabolic activities, and the associated undiscovered secondary metabolite biosynthesis genes are called "silent" genes. This review outlines several approaches to further activate the metabolic potential of actinomycetes.
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Affiliation(s)
- Shun Saito
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Midori A Arai
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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Meißner J, Schramm T, Hoßbach B, Stark K, Link H, Stülke J. How To Deal with Toxic Amino Acids: the Bipartite AzlCD Complex Exports Histidine in Bacillus subtilis. J Bacteriol 2022; 204:e0035322. [PMID: 36377869 DOI: 10.1128/jb.00353-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The Gram-positive model bacterium Bacillus subtilis can use several amino acids as sources of carbon and nitrogen. However, some amino acids inhibit the growth of this bacterium. This amino acid toxicity is often enhanced in strains lacking the second messenger cyclic dimeric adenosine 3',5'-monophosphate (c-di-AMP). We observed that the presence of histidine is also toxic for a B. subtilis strain that lacks all three c-di-AMP synthesizing enzymes. However, suppressor mutants emerged, and whole-genome sequencing revealed mutations in the azlB gene that encode the repressor of the azl operon. This operon encodes an exporter and an importer for branched-chain amino acids. The suppressor mutations result in an overexpression of the azl operon. Deletion of the azlCD genes encoding the branched-chain amino acid exporter restored the toxicity of histidine, indicating that this exporter is required for histidine export and for resistance to otherwise toxic levels of the amino acid. The higher abundance of the amino acid exporter AzlCD increased the extracellular concentration of histidine, thus confirming the new function of AzlCD as a histidine exporter. Unexpectedly, the AzlB-mediated repression of the operon remains active even in the presence of amino acids, suggesting that the expression of the azl operon requires the mutational inactivation of AzlB. IMPORTANCE Amino acids are building blocks for protein biosynthesis in each living cell. However, due to their reactivity and the similarity between several amino acids, they may also be involved in harmful reactions or in noncognate interactions and thus may be toxic. Bacillus subtilis can deal with otherwise toxic histidine by overexpressing the bipartite amino acid exporter AzlCD. Although encoded in an operon that also contains a gene for an amino acid importer, the corresponding genes are not expressed, irrespective of the availability of amino acids in the medium. This suggests that the azl operon is a last resort by which to deal with histidine stress that can be expressed due to the mutational inactivation of the cognate repressor AzlB.
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Deekshit VK, Srikumar S. 'To be, or not to be' - the dilemma of 'silent' antimicrobial resistance genes in bacteria. J Appl Microbiol 2022; 133:2902-2914. [PMID: 35882476 DOI: 10.1111/jam.15738] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022]
Abstract
Antimicrobial resistance is a serious threat to public health that dramatically undermines our ability to treat bacterial infections. Microorganisms exhibit resistance to different drug classes by acquiring resistance determinants through multiple mechanisms including horizontal gene transfer. The presence of drug resistance genotypes is mostly associated with corresponding phenotypic resistance against the particular antibiotic. However, bacterial communities harboring silent antimicrobial resistance genes - genes whose presence is not associated with a corresponding resistant phenotype, do exist. Under suitable conditions, the expression pattern of such genes often revert and regain resistance, and could potentially lead to therapeutic failure. We often miss the presence of silent genes, since the current experimental paradigms are focused on resistant strains. Therefore, the knowledge on the prevalence, importance, and mechanism of silent antibiotic resistance genes in bacterial pathogens is very limited. Silent genes, therefore, provide an additional level of complexity in the war against drug-resistant bacteria, reminding us that not only phenotypically resistant strains but also susceptible strains should be carefully investigated. In this review, we discuss the presence of silent antimicrobial resistance genes in bacteria, their relevance, and their importance in public health.
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Affiliation(s)
- Vijaya Kumar Deekshit
- Nitte (Deemed to be University), Nitte University Center for Science Education and Research, Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangaluru - 575018, Karnataka, India
| | - Shabarinath Srikumar
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, UAE
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Stasiak M, Maćkiw E, Kowalska J, Kucharek K, Postupolski J. Silent Genes: Antimicrobial Resistance and Antibiotic Production. Pol J Microbiol 2022; 70:421-429. [PMID: 35003274 PMCID: PMC8702603 DOI: 10.33073/pjm-2021-040] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/15/2021] [Indexed: 11/05/2022] Open
Abstract
Silent genes are DNA sequences that are generally not expressed or expressed at a very low level. These genes become active as a result of mutation, recombination, or insertion. Silent genes can also be activated in laboratory conditions using pleiotropic, targeted genome-wide, or biosynthetic gene cluster approaches. Like every other gene, silent genes can spread through horizontal gene transfer. Most studies have focused on strains with phenotypic resistance, which is the most common subject. However, to fully understand the mechanism behind the spreading of antibiotic resistance, it is reasonable to study the whole resistome, including silent genes.
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Affiliation(s)
- Monika Stasiak
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Elżbieta Maćkiw
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Joanna Kowalska
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Katarzyna Kucharek
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Jacek Postupolski
- Department of Food Safety, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
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Maglangit F, Fang Q, Kyeremeh K, Sternberg JM, Ebel R, Deng H. A Co-Culturing Approach Enables Discovery and Biosynthesis of a Bioactive Indole Alkaloid Metabolite. Molecules 2020; 25:E256. [PMID: 31936318 DOI: 10.3390/molecules25020256] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/26/2019] [Accepted: 01/03/2020] [Indexed: 12/19/2022] Open
Abstract
Whole-genome sequence data of the genus Streptomyces have shown a far greater chemical diversity of metabolites than what have been discovered under typical laboratory fermentation conditions. In our previous natural product discovery efforts on Streptomyces sp. MA37, a bacterium isolated from the rhizosphere soil sample in Legon, Ghana, we discovered a handful of specialised metabolites from this talented strain. However, analysis of the draft genome of MA37 suggested that most of the encoded biosynthetic gene clusters (BGCs) remained cryptic or silent, and only a small fraction of BGCs for the production of specialised metabolites were expressed when cultured in our laboratory conditions. In order to induce the expression of the seemingly silent BGCs, we have carried out a co-culture experiment by growing the MA37 strain with the Gram-negative bacterium Pseudomonas sp. in a co-culture chamber that allows co-fermentation of two microorganisms with no direct contact but allows exchange of nutrients, metabolites, and other chemical cues. This co-culture approach led to the upregulation of several metabolites that were not previously observed in the monocultures of each strain. Moreover, the co-culture induced the expression of the cryptic indole alkaloid BGC in MA37 and led to the characterization of the known indolocarbazole alkaloid, BE-13793C 1. Neither bacterium produced compound 1 when cultured alone. The structure of 1 was elucidated by Nuclear Magnetic Resonance (NMR), mass spectrometry analyses and comparison of experimental with literature data. A putative biosynthetic pathway of 1 was proposed. Furthermore, BE-13793C 1 showed strong anti-proliferative activity against HT-29 (ATCC HTB-38) cells but no toxic effect to normal lung (ATCC CCL-171) cells. To the best of our knowledge, this is the first report for the activity of 1 against HT-29. No significant antimicrobial and anti-trypanosomal activities for 1 were observed. This research provides a solid foundation for the fact that a co-culture approach paves the way for increasing the chemical diversity of strain MA37. Further characterization of other upregulated metabolites in this strain is currently ongoing in our laboratory.
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Ying YM, Li L, Yu HF, Xu YL, Huang L, Mao W, Tong CP, Zhang ZD, Zhan ZJ, Zhang Y. Induced production of a new polyketide in Penicillium sp. HS-11 by chemical epigenetic manipulation. Nat Prod Res 2020; 35:3446-3451. [PMID: 31899961 DOI: 10.1080/14786419.2019.1709190] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Chemical investigation into the culture broth of the plant endophyte Penicillium sp. HS-11 in the modified Martin's medium supplemented with subemylanilide hydroxamic acid (SAHA), a well-known histone deacetylase (HDACs) inhibitor, led to the isolation and identification of two induced products 4-epipenicillone B (1) and (R)-(+)-chrysogine (2). 4-epipenicillone B (1) was obtained as a new compound whose structure was elucidated by comprehensive spectroscopic methods including 1 D/2D NMR, HRESMS, and quantum chemistry calculations including DFT GIAO 13C NMR and ECD calculation. Acquisition of 4-epipenicillone B (1) enriched the chemical diversities of fungal natural products possessing a tricyclo [5.3.1.03,8] undecane skeleton. The cytotoxic activity of 1 was also evaluated.
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Affiliation(s)
- You-Min Ying
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Ling Li
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Hang-Fei Yu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yi-Lian Xu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Lu Huang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, P. R. China.,Department of Quality Management, Hangzhou Zhongmeihuadong China Pharmaceutical Co., Ltd, Hangzhou, P. R. China
| | - Wei Mao
- Department of Quality Management, Hangzhou Zhongmeihuadong China Pharmaceutical Co., Ltd, Hangzhou, P. R. China
| | - Cui-Ping Tong
- Department of Quality Management, Hangzhou Zhongmeihuadong China Pharmaceutical Co., Ltd, Hangzhou, P. R. China
| | - Zhi-Dong Zhang
- Xinjiang Laboratory of Special Environmental Microbiology, Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, P. R. China
| | - Zha-Jun Zhan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yun Zhang
- Department of Quality Management, Hangzhou Zhongmeihuadong China Pharmaceutical Co., Ltd, Hangzhou, P. R. China
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Teng T, Xie L, Xie J. [Development of new anti-tuberculosis drugs: the strategy of unconventional microbial culture and silencing gene activation]. Sheng Wu Gong Cheng Xue Bao 2018; 34:1306-1315. [PMID: 30152216 DOI: 10.13345/j.cjb.170534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, has become a major human infectious disease. The existing first-line and second-line TB drugs have poor treatment outcomes in patients with MDR-TB and XDR-TB. There is an urgent need for new and better drugs to treat tuberculosis due to lengthy and complex treatment regimens and a rising problem of drug resistance. Microbial-derived natural products have revealed enormous reservoirs of as yet untapped lead compounds. In this review, we discuss the strategies that have been developed in bacteria and fungi to isolation of non-culturable microorganisms and activation of silent biosynthetic gene clusters involved in the study of microbial-derived natural products. This review also highlights recent advances in microbial-derived natural products with anti-tuberculosis activity using these methods.
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Affiliation(s)
- Tieshan Teng
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, Henan, China.,State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Longxiang Xie
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, Henan, China.,State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jianping Xie
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing 400715, China
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Funane K, Tanaka Y, Hosaka T, Murakami K, Miyazaki T, Shiwa Y, Gibu S, Inaoka T, Kasahara K, Fujita N, Yoshikawa H, Hiraga Y, Ochi K. Combined Drug Resistance Mutations Substantially Enhance Enzyme Production in Paenibacillus agaridevorans. J Bacteriol 2018; 200:e00188-18. [PMID: 29866810 DOI: 10.1128/JB.00188-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/29/2018] [Indexed: 11/20/2022] Open
Abstract
This study shows that sequential introduction of drug resistance mutations substantially increased enzyme production in Paenibacillus agaridevorans The triple mutant YT478 (rsmG Gln225→stop codon, rpsL K56R, and rpoB R485H), generated by screening for resistance to streptomycin and rifampin, expressed a 1,100-fold-larger amount of the extracellular enzyme cycloisomaltooligosaccharide glucanotransferase (CITase) than the wild-type strain. These mutants were characterized by higher intracellular S-adenosylmethionine concentrations during exponential phase and enhanced protein synthesis activity during stationary phase. Surprisingly, the maximal expression of CITase mRNA was similar in the wild-type and triple mutant strains, but the mutant showed greater CITase mRNA expression throughout the growth curve, resulting in enzyme overproduction. A metabolome analysis showed that the triple mutant YT478 had higher levels of nucleic acids and glycolysis metabolites than the wild type, indicating that YT478 mutant cells were activated. The production of CITase by the triple mutant was further enhanced by introducing a mutation conferring resistance to the rare earth element, scandium. This combined drug resistance mutation method also effectively enhanced the production of amylases, proteases, and agarases by P. agaridevorans and Streptomyces coelicolor This method also activated the silent or weak expression of the P. agaridevorans CITase gene, as shown by comparisons of the CITase gene loci of P. agaridevorans T-3040 and another cycloisomaltooligosaccharide-producing bacterium, Paenibacillus sp. strain 598K. The simplicity and wide applicability of this method should facilitate not only industrial enzyme production but also the identification of dormant enzymes by activating the expression of silent or weakly expressed genes.IMPORTANCE Enzyme use has become more widespread in industry. This study evaluated the molecular basis and effectiveness of ribosome engineering in markedly enhancing enzyme production (>1,000-fold). This method, due to its simplicity, wide applicability, and scalability for large-scale production, should facilitate not only industrial enzyme production but also the identification of novel enzymes, because microorganisms contain many silent or weakly expressed genes which encode novel antibiotics or enzymes. Furthermore, this study provides a new mechanism for strain improvement, with a consistent rather than transient high expression of the key gene(s) involved in enzyme production.
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