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Jan 21, 2021
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Abstract
Due to high demand of antibiotics for treatment of increasing bacterial infections there is an urgent need of engineering bacterial strains to get high concentration and meet industrial demands. Different techniques are being used for this purpose: which include over-expression of a gene in its host strain, engineering of different activators and regulators of antibiotic synthesizing gene cluster and expression of antibiotic gene cluster in heterologous host. The emergence of antibiotic resistant pathogens was a huge problem for existing medications and it urges a need or the development of novel antibiotics with high specificity. These can be produced by combinatorial biosynthesis or awakening of silent genes already present in bacteria. These advancements present a bright future of antibiotic production at industrial level.
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This work is licensed under a Creative Commons Attribution 4.0 International License.
How to Cite
Zafar, T., Ahsan, T., & Yuanhua, W. (2023). Genetic engineering of bacteria for the production of antibiotics: A review. Journal of Agriculture and Applied Biology, 4(1), 63-70. https://doi.org/10.11594/jaab.04.01.07
References
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Bilyk, O., & Luzhetskyy, A. (2016). Metabolic engineering of natural product biosynthesis in actinobacteria. Current Opinion in Biotechnology, 42, 98-107. CrossRef
Chen, S., Kinney, W. A., & Van Lanen, S. (2017). Nature’s combinatorial biosynthesis and recently
engineered production of nucleoside antibiotics in Streptomyces. World Journal of Microbiology and Biotechnology, 33(4), 66. CrossRef
Chen, W., Qi, J., Wu, P., Wan, D., Liu, J., Feng, X., & Deng, Z. (2016). Natural and engineered biosynthesis of nucleoside antibiotics in Actinomycetes. Journal of Industrial Microbiology and Biotechnology, 43(2-3), 401-417. CrossRef
Choi, S.-S., Katsuyama, Y., Bai, L., Deng, Z., Ohnishi, Y., & Kim, E.-S. (2018). Genome engineering for microbial natural product discovery. Current Opinion in Microbiology, 45, 53-60. CrossRef
Cochrane, S. A., & Vederas, J. C. (2016). Lipopeptides from Bacillus and Paenibacillus spp.: a gold mine of antibiotic candidates. Medicinal Research Reviews, 36(1), 4-31. CrossRef
d'Aquino, A. E., Kim, D. S., & Jewett, M. C. (2018). Engineered ribosomes for basic science and synthetic biology. Annual Review of Chemical and Biomolecular Engineering, 9, 311-340. CrossRef
Devine, R., Hutchings, M. I., & Holmes, N. A. (2017). Future directions for the discovery of antibiotics from actinomycete bacteria. Emerging Topics in Life Sciences, ETLS20160014. CrossRef
Du, D., Wang, L., Tian, Y., Liu, H., Tan, H., & Niu, G. (2015). Genome engineering and direct cloning of antibiotic gene clusters via phage ϕBT1 integrase-mediated site-specific recombination in Streptomyces. Scientific Reports, 5, 8740. CrossRef
Fields, F. R., Lee, S. W., & McConnell, M. J. (2017). Using bacterial genomes and essential genes for the development of new antibiotics. Biochemical Pharmacology, 134, 74-86. CrossRef
Guzmán-Trampe, S., Ceapa, C. D., Manzo-Ruiz, M., & Sánchez, S. (2017). Synthetic biology era: improving antibiotic’s world. Biochemical Pharmacology, 134, 99-113. CrossRef
Horbal, L., Kobylyanskyy, A., Truman, A. W., Zaburranyi, N., Ostash, B., Luzhetskyy, A., . . . Fedorenko, V. (2014). The pathway-specific regulatory genes, tei15* and tei16*, are the master switches of teicoplanin production in Actinoplanes teichomyceticus. Applied Microbiology and Biotechnology, 98(22), 9295-9309. CrossRef
Huo, L., Hug, J. J., Fu, C., Bian, X., Zhang, Y., & Müller, R. (2019). Heterologous expression of bacterial natural product biosynthetic pathways. Natural Product Reports, 36(10), 1412-1436. CrossRef
Jiang, X., Ellabaan, M. M. H., Charusanti, P., Munck, C., Blin, K., Tong, Y., . . . Lee, S. Y. (2017). Dissemination of
antibiotic resistance genes from antibiotic producers to pathogens. Nature Communications, 8(1), 1-7. CrossRef
Jin, K., Zhou, L., Jiang, H., Sun, S., Fang, Y., Liu, J., . . . He, Y.-W. (2015). Engineering the central biosynthetic and secondary metabolic pathways of Pseudomonas aeruginosa strain PA1201 to improve phenazine-1-carboxylic acid production. Metabolic Engineering, 32, 30-38. CrossRef
Kalkreuter, E., & Williams, G. J. (2018). Engineering enzymatic assembly lines for the production of new antimicrobials. Current Opinion in Microbiology, 45, 140-148. CrossRef
Kealey, C., Creaven, C., Murphy, C., & Brady, C. (2017). New approaches to antibiotic discovery. Biotechnology Letters, 39(6), 805-817. CrossRef
Korp, J., Gurovic, M. S. V., & Nett, M. (2016). Antibiotics from predatory bacteria. Beilstein Journal of Organic Chemistry, 12(1), 594-607. https://doi.org/10.3762/bjoc.12.58
Krishnamurthy, M., Moore, R. T., Rajamani, S., & Panchal, R. G. (2016). Bacterial genome engineering and synthetic biology: combating pathogens. BMC Microbiology, 16(1), 258. CrossRef
Landecker, H. (2016). Antibiotic resistance and the biology of history. Body & Society, 22(4), 19-52. CrossRef
Liu, F., & Myers, A. G. (2016). Development of a platform for the discovery and practical synthesis of new tetracycline antibiotics. Current Opinion in Chemical Biology, 32, 48-57. CrossRef
Liu, K., Hu, H., Wang, W., & Zhang, X. (2016). Genetic engineering of Pseudomonas chlororaphis GP72 for the enhanced production of 2-hydroxyphenazine. Microbial Cell Factories, 15(1), 131. CrossRef
Liu, Q., Lin, Q., Li, X., Ali, M., & He, J. (2020). Construction and application of a “superplasmid” for enhanced production of antibiotics. Applied Microbiology and Biotechnology, 104(4), 1647-1660. CrossRef
MacGowan, A., & Macnaughton, E. (2017). Antibiotic resistance. Medicine, 45(10), 622-628. CrossRef
Niu, G., & Tan, H. (2015). Nucleoside antibiotics: biosynthesis, regulation, and biotechnology. Trends in Microbiology, 23(2), 110-119. CrossRef
Ochi, K., & Hosaka, T. (2013). New strategies for drug discovery: activation of silent or weakly expressed microbial gene clusters. Applied Microbiology and Biotechnology, 97(1), 87-98. CrossRef
Okada, B. K., & Seyedsayamdost, M. R. (2017). Antibiotic dialogues: induction of silent biosynthetic gene clusters by exogenous small molecules. FEMS Microbiology Reviews, 41(1), 19-33. CrossRef
Onaka, H. (2017). Novel antibiotic screening methods to awaken silent or cryptic secondary metabolic pathways in actinomycetes. The Journal of Antibiotics, 70(8), 865-870. CrossRef
Robertsen, H. L., Weber, T., Kim, H. U., & Lee, S. Y. (2018). Toward systems metabolic engineering of streptomycetes for secondary metabolites production. Biotechnology Journal, 13(1), 1700465. CrossRef
Shen, L., Li, F., Jiao, Y., Sun, H., Wang, F., & Wu, Y. (2017). Cloning, expression, and purification of an antiviral protein from Pseudomonas fluorescens CZ and its antagonistic activity against tobacco mosaic virus. Biocontrol Science and Technology, 27(1), 144-148. CrossRef
Shomar, H., Gontier, S., van den Broek, N. J., Mora, H. T., Noga, M. J., Hagedoorn, P.-L., & Bokinsky, G. (2018). Metabolic engineering of a carbapenem antibiotic synthesis pathway in Escherichia coli. Nature Chemical Biology, 14(8), 794-800. CrossRef
Singh, R., Singh, A. P., Kumar, S., Giri, B. S., & Kim, K.-H. (2019). Antibiotic resistance in major rivers in the world: a systematic review on occurrence, emergence, and management strategies. Journal of Cleaner Production. CrossRef
Sun, H., Liu, Z., Zhao, H., & Ang, E. L. (2015). Recent advances in combinatorial biosynthesis for drug discovery. Drug Design, Development and Therapy, 9, 823. CrossRef
Sun, Y., Feng, Z., Tomura, T., Suzuki, A., Miyano, S., Tsuge, T., . . . Fudou, R. (2016). Heterologous production of the marine myxobacterial antibiotic haliangicin and its unnatural analogues generated by engineering of the biochemical pathway. Scientific Reports, 6(1), 1-11. CrossRef
Sundin, G. W., & Wang, N. (2018). Antibiotic resistance in plant-pathogenic bacteria. Annual Review of Phytopathology, 56, 161-180. CrossRef
Telke, A. A., Ovchinnikov, K. V., Vuoristo, K. S., Mathiesen, G., Thorstensen, T., & Diep, D. B. (2018). Over 2000-fold increased production of the leaderless bacteriocin garvicin KS by genetic engineering and optimization of culture conditions. BioRxiv, 298489. CrossRef
Thaker, M. N., & Wright, G. D. (2015). Opportunities for synthetic biology in antibiotics: expanding glycopeptide chemical diversity. ACS Synthetic Biology, 4(3), 195-206. CrossRef
Van der Meij, A., Worsley, S. F., Hutchings, M. I., & van Wezel, G. P. (2017). Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiology Reviews, 41(3), 392-416. CrossRef
Wang, W., Li, X., Wang, J., Xiang, S., Feng, X., & Yang, K. (2013). An engineered strong promoter for streptomycetes. Applied Environmental Microbiology., 79(14), 4484-4492. CrossRef
Weber, T., Charusanti, P., Musiol-Kroll, E. M., Jiang, X., Tong, Y., Kim, H. U., & Lee, S. Y. (2015). Metabolic engineering of antibiotic factories: new tools for antibiotic production in actinomycetes. Trends in Biotechnology, 33(1), 15-26. CrossRef
Wohlleben, W., Mast, Y., Stegmann, E., & Ziemert, N. (2016). Antibiotic drug discovery. Microbial Biotechnology, 9(5), 541-548. CrossRef
Xu, M., & Wright, G. D. (2019). Heterologous expression-facilitated natural products’ discovery in actinomycetes. Journal of Industrial Microbiology & Biotechnology, 46(3-4), 415-431. CrossRef
Xu, Z., Wang, Y., Chater, K. F., Ou, H.-Y., Xu, H. H., Deng, Z., & Tao, M. (2017). Large-scale transposition mutagenesis of Streptomyces coelicolor identifies hundreds of genes influencing antibiotic biosynthesis. Applied Environmental Microbiology., 83(6), e02889-02816. CrossRef
Yan, Q., & Fong, S. S. (2017). Challenges and advances for genetic engineering of non-model bacteria and uses in consolidated bioprocessing. Frontiers in Microbiology, 8, 2060. CrossRef
Yin, S., Wang, W., Wang, X., Zhu, Y., Jia, X., Li, S., . . . Yang, K. (2015). Identification of a cluster-situated activator of oxytetracycline biosynthesis and manipulation of its expression for improved oxytetracycline production in Streptomyces rimosus. Microbial Cell Factories, 14(1), 46. CrossRef
Yin, S., Wang, X., Shi, M., Yuan, F., Wang, H., Jia, X., . . . Zhang, Y. (2017). Improvement of oxytetracycline production mediated via cooperation of resistance genes in Streptomyces rimosus. Science China Life Sciences, 60(9), 992-999. CrossRef
Zou, X., Wang, L., Li, Z., Luo, J., Wang, Y., Deng, Z., . . . Chen, S. (2018). Genome engineering and modification toward synthetic biology for the production of antibiotics. Medicinal Research Reviews, 38(1), 229-260. CrossRef
Aparicio, J. F., Barreales, E. G., Payero, T. D., Vicente, C. M., de Pedro, A., & Santos-Aberturas, J. (2016). Biotechnological production and application of the antibiotic pimaricin: biosynthesis and its regulation. Applied Microbiology and Biotechnology, 100(1), 61-78. CrossRef
Baltz, R. H. (2018). Synthetic biology, genome mining, and combinatorial biosynthesis of NRPS-derived antibiotics: a perspective. Journal of Industrial Microbiology & Biotechnology, 45(7), 635-649. CrossRef
Bekiesch, P., Basitta, P., & Apel, A. K. (2016). Challenges in the heterologous production of antibiotics in Streptomyces. Archiv der Pharmazie, 349(8), 594-601. CrossRef
Bhatia, S. K., Lee, B.-R., Sathiyanarayanan, G., Song, H.-S., Kim, J., Jeon, J.-M., . . . Park, K. (2016). Medium engineering for enhanced production of undecylprodigiosin antibiotic in Streptomyces coelicolor using oil palm biomass hydrolysate as a carbon source. Bioresource Technology, 217, 141-149. CrossRef
Bilal, M., Guo, S., Iqbal, H. M., Hu, H., Wang, W., & Zhang, X. (2017). Engineering Pseudomonas for phenazine biosynthesis, regulation, and biotechnological applications: a review. World Journal of Microbiology and Biotechnology, 33(10), 191. CrossRef
Bilyk, O., & Luzhetskyy, A. (2016). Metabolic engineering of natural product biosynthesis in actinobacteria. Current Opinion in Biotechnology, 42, 98-107. CrossRef
Chen, S., Kinney, W. A., & Van Lanen, S. (2017). Nature’s combinatorial biosynthesis and recently
engineered production of nucleoside antibiotics in Streptomyces. World Journal of Microbiology and Biotechnology, 33(4), 66. CrossRef
Chen, W., Qi, J., Wu, P., Wan, D., Liu, J., Feng, X., & Deng, Z. (2016). Natural and engineered biosynthesis of nucleoside antibiotics in Actinomycetes. Journal of Industrial Microbiology and Biotechnology, 43(2-3), 401-417. CrossRef
Choi, S.-S., Katsuyama, Y., Bai, L., Deng, Z., Ohnishi, Y., & Kim, E.-S. (2018). Genome engineering for microbial natural product discovery. Current Opinion in Microbiology, 45, 53-60. CrossRef
Cochrane, S. A., & Vederas, J. C. (2016). Lipopeptides from Bacillus and Paenibacillus spp.: a gold mine of antibiotic candidates. Medicinal Research Reviews, 36(1), 4-31. CrossRef
d'Aquino, A. E., Kim, D. S., & Jewett, M. C. (2018). Engineered ribosomes for basic science and synthetic biology. Annual Review of Chemical and Biomolecular Engineering, 9, 311-340. CrossRef
Devine, R., Hutchings, M. I., & Holmes, N. A. (2017). Future directions for the discovery of antibiotics from actinomycete bacteria. Emerging Topics in Life Sciences, ETLS20160014. CrossRef
Du, D., Wang, L., Tian, Y., Liu, H., Tan, H., & Niu, G. (2015). Genome engineering and direct cloning of antibiotic gene clusters via phage ϕBT1 integrase-mediated site-specific recombination in Streptomyces. Scientific Reports, 5, 8740. CrossRef
Fields, F. R., Lee, S. W., & McConnell, M. J. (2017). Using bacterial genomes and essential genes for the development of new antibiotics. Biochemical Pharmacology, 134, 74-86. CrossRef
Guzmán-Trampe, S., Ceapa, C. D., Manzo-Ruiz, M., & Sánchez, S. (2017). Synthetic biology era: improving antibiotic’s world. Biochemical Pharmacology, 134, 99-113. CrossRef
Horbal, L., Kobylyanskyy, A., Truman, A. W., Zaburranyi, N., Ostash, B., Luzhetskyy, A., . . . Fedorenko, V. (2014). The pathway-specific regulatory genes, tei15* and tei16*, are the master switches of teicoplanin production in Actinoplanes teichomyceticus. Applied Microbiology and Biotechnology, 98(22), 9295-9309. CrossRef
Huo, L., Hug, J. J., Fu, C., Bian, X., Zhang, Y., & Müller, R. (2019). Heterologous expression of bacterial natural product biosynthetic pathways. Natural Product Reports, 36(10), 1412-1436. CrossRef
Jiang, X., Ellabaan, M. M. H., Charusanti, P., Munck, C., Blin, K., Tong, Y., . . . Lee, S. Y. (2017). Dissemination of
antibiotic resistance genes from antibiotic producers to pathogens. Nature Communications, 8(1), 1-7. CrossRef
Jin, K., Zhou, L., Jiang, H., Sun, S., Fang, Y., Liu, J., . . . He, Y.-W. (2015). Engineering the central biosynthetic and secondary metabolic pathways of Pseudomonas aeruginosa strain PA1201 to improve phenazine-1-carboxylic acid production. Metabolic Engineering, 32, 30-38. CrossRef
Kalkreuter, E., & Williams, G. J. (2018). Engineering enzymatic assembly lines for the production of new antimicrobials. Current Opinion in Microbiology, 45, 140-148. CrossRef
Kealey, C., Creaven, C., Murphy, C., & Brady, C. (2017). New approaches to antibiotic discovery. Biotechnology Letters, 39(6), 805-817. CrossRef
Korp, J., Gurovic, M. S. V., & Nett, M. (2016). Antibiotics from predatory bacteria. Beilstein Journal of Organic Chemistry, 12(1), 594-607. https://doi.org/10.3762/bjoc.12.58
Krishnamurthy, M., Moore, R. T., Rajamani, S., & Panchal, R. G. (2016). Bacterial genome engineering and synthetic biology: combating pathogens. BMC Microbiology, 16(1), 258. CrossRef
Landecker, H. (2016). Antibiotic resistance and the biology of history. Body & Society, 22(4), 19-52. CrossRef
Liu, F., & Myers, A. G. (2016). Development of a platform for the discovery and practical synthesis of new tetracycline antibiotics. Current Opinion in Chemical Biology, 32, 48-57. CrossRef
Liu, K., Hu, H., Wang, W., & Zhang, X. (2016). Genetic engineering of Pseudomonas chlororaphis GP72 for the enhanced production of 2-hydroxyphenazine. Microbial Cell Factories, 15(1), 131. CrossRef
Liu, Q., Lin, Q., Li, X., Ali, M., & He, J. (2020). Construction and application of a “superplasmid” for enhanced production of antibiotics. Applied Microbiology and Biotechnology, 104(4), 1647-1660. CrossRef
MacGowan, A., & Macnaughton, E. (2017). Antibiotic resistance. Medicine, 45(10), 622-628. CrossRef
Niu, G., & Tan, H. (2015). Nucleoside antibiotics: biosynthesis, regulation, and biotechnology. Trends in Microbiology, 23(2), 110-119. CrossRef
Ochi, K., & Hosaka, T. (2013). New strategies for drug discovery: activation of silent or weakly expressed microbial gene clusters. Applied Microbiology and Biotechnology, 97(1), 87-98. CrossRef
Okada, B. K., & Seyedsayamdost, M. R. (2017). Antibiotic dialogues: induction of silent biosynthetic gene clusters by exogenous small molecules. FEMS Microbiology Reviews, 41(1), 19-33. CrossRef
Onaka, H. (2017). Novel antibiotic screening methods to awaken silent or cryptic secondary metabolic pathways in actinomycetes. The Journal of Antibiotics, 70(8), 865-870. CrossRef
Robertsen, H. L., Weber, T., Kim, H. U., & Lee, S. Y. (2018). Toward systems metabolic engineering of streptomycetes for secondary metabolites production. Biotechnology Journal, 13(1), 1700465. CrossRef
Shen, L., Li, F., Jiao, Y., Sun, H., Wang, F., & Wu, Y. (2017). Cloning, expression, and purification of an antiviral protein from Pseudomonas fluorescens CZ and its antagonistic activity against tobacco mosaic virus. Biocontrol Science and Technology, 27(1), 144-148. CrossRef
Shomar, H., Gontier, S., van den Broek, N. J., Mora, H. T., Noga, M. J., Hagedoorn, P.-L., & Bokinsky, G. (2018). Metabolic engineering of a carbapenem antibiotic synthesis pathway in Escherichia coli. Nature Chemical Biology, 14(8), 794-800. CrossRef
Singh, R., Singh, A. P., Kumar, S., Giri, B. S., & Kim, K.-H. (2019). Antibiotic resistance in major rivers in the world: a systematic review on occurrence, emergence, and management strategies. Journal of Cleaner Production. CrossRef
Sun, H., Liu, Z., Zhao, H., & Ang, E. L. (2015). Recent advances in combinatorial biosynthesis for drug discovery. Drug Design, Development and Therapy, 9, 823. CrossRef
Sun, Y., Feng, Z., Tomura, T., Suzuki, A., Miyano, S., Tsuge, T., . . . Fudou, R. (2016). Heterologous production of the marine myxobacterial antibiotic haliangicin and its unnatural analogues generated by engineering of the biochemical pathway. Scientific Reports, 6(1), 1-11. CrossRef
Sundin, G. W., & Wang, N. (2018). Antibiotic resistance in plant-pathogenic bacteria. Annual Review of Phytopathology, 56, 161-180. CrossRef
Telke, A. A., Ovchinnikov, K. V., Vuoristo, K. S., Mathiesen, G., Thorstensen, T., & Diep, D. B. (2018). Over 2000-fold increased production of the leaderless bacteriocin garvicin KS by genetic engineering and optimization of culture conditions. BioRxiv, 298489. CrossRef
Thaker, M. N., & Wright, G. D. (2015). Opportunities for synthetic biology in antibiotics: expanding glycopeptide chemical diversity. ACS Synthetic Biology, 4(3), 195-206. CrossRef
Van der Meij, A., Worsley, S. F., Hutchings, M. I., & van Wezel, G. P. (2017). Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiology Reviews, 41(3), 392-416. CrossRef
Wang, W., Li, X., Wang, J., Xiang, S., Feng, X., & Yang, K. (2013). An engineered strong promoter for streptomycetes. Applied Environmental Microbiology., 79(14), 4484-4492. CrossRef
Weber, T., Charusanti, P., Musiol-Kroll, E. M., Jiang, X., Tong, Y., Kim, H. U., & Lee, S. Y. (2015). Metabolic engineering of antibiotic factories: new tools for antibiotic production in actinomycetes. Trends in Biotechnology, 33(1), 15-26. CrossRef
Wohlleben, W., Mast, Y., Stegmann, E., & Ziemert, N. (2016). Antibiotic drug discovery. Microbial Biotechnology, 9(5), 541-548. CrossRef
Xu, M., & Wright, G. D. (2019). Heterologous expression-facilitated natural products’ discovery in actinomycetes. Journal of Industrial Microbiology & Biotechnology, 46(3-4), 415-431. CrossRef
Xu, Z., Wang, Y., Chater, K. F., Ou, H.-Y., Xu, H. H., Deng, Z., & Tao, M. (2017). Large-scale transposition mutagenesis of Streptomyces coelicolor identifies hundreds of genes influencing antibiotic biosynthesis. Applied Environmental Microbiology., 83(6), e02889-02816. CrossRef
Yan, Q., & Fong, S. S. (2017). Challenges and advances for genetic engineering of non-model bacteria and uses in consolidated bioprocessing. Frontiers in Microbiology, 8, 2060. CrossRef
Yin, S., Wang, W., Wang, X., Zhu, Y., Jia, X., Li, S., . . . Yang, K. (2015). Identification of a cluster-situated activator of oxytetracycline biosynthesis and manipulation of its expression for improved oxytetracycline production in Streptomyces rimosus. Microbial Cell Factories, 14(1), 46. CrossRef
Yin, S., Wang, X., Shi, M., Yuan, F., Wang, H., Jia, X., . . . Zhang, Y. (2017). Improvement of oxytetracycline production mediated via cooperation of resistance genes in Streptomyces rimosus. Science China Life Sciences, 60(9), 992-999. CrossRef
Zou, X., Wang, L., Li, Z., Luo, J., Wang, Y., Deng, Z., . . . Chen, S. (2018). Genome engineering and modification toward synthetic biology for the production of antibiotics. Medicinal Research Reviews, 38(1), 229-260. CrossRef