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Süntar I, Çetinkaya S, Haydaroğlu ÜS, Habtemariam S. Bioproduction process of natural products and biopharmaceuticals: Biotechnological aspects. Biotechnol Adv 2021; 50:107768. [PMID: 33974980 DOI: 10.1016/j.biotechadv.2021.107768] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 02/07/2023]
Abstract
Decades of research have been put in place for developing sustainable routes of bioproduction of high commercial value natural products (NPs) on the global market. In the last few years alone, we have witnessed significant advances in the biotechnological production of NPs. The development of new methodologies has resulted in a better understanding of the metabolic flux within the organisms, which have driven manipulations to improve production of the target product. This was further realised due to the recent advances in the omics technologies such as genomics, transcriptomics, proteomics, metabolomics and secretomics, as well as systems and synthetic biology. Additionally, the combined application of novel engineering strategies has made possible avenues for enhancing the yield of these products in an efficient and economical way. Invention of high-throughput technologies such as next generation sequencing (NGS) and toolkits for genome editing Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated 9 (CRISPR/Cas9) have been the game changers and provided unprecedented opportunities to generate rationally designed synthetic circuits which can produce complex molecules. This review covers recent advances in the engineering of various hosts for the production of bioactive NPs and biopharmaceuticals. It also highlights general approaches and strategies to improve their biosynthesis with higher yields in a perspective of plants and microbes (bacteria, yeast and filamentous fungi). Although there are numerous reviews covering this topic on a selected species at a time, our approach herein is to give a comprehensive understanding about state-of-art technologies in different platforms of organisms.
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Affiliation(s)
- Ipek Süntar
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, 06330 Etiler, Ankara, Turkey.
| | - Sümeyra Çetinkaya
- Biotechnology Research Center of Ministry of Agriculture and Forestry, 06330 Yenimahalle, Ankara, Turkey
| | - Ülkü Selcen Haydaroğlu
- Biotechnology Research Center of Ministry of Agriculture and Forestry, 06330 Yenimahalle, Ankara, Turkey
| | - Solomon Habtemariam
- Pharmacognosy Research Laboratories & Herbal Analysis Services UK, University of Greenwich, Chatham-Maritime, Kent ME4 4TB, United Kingdom
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Fu L, Zhang J, Si T. Recent advances in high-throughput mass spectrometry that accelerates enzyme engineering for biofuel research. ACTA ACUST UNITED AC 2020. [DOI: 10.1186/s42500-020-0011-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractEnzymes play indispensable roles in producing biofuels, a sustainable and renewable source of transportation fuels. Lacking rational design rules, the development of industrially relevant enzyme catalysts relies heavily on high-throughput screening. However, few universal methods exist to rapidly characterize large-scale enzyme libraries. Therefore, assay development is necessary on an ad hoc basis to link enzyme properties to spectrophotometric signals and often requires the use of surrogate, optically active substrates. On the other hand, mass spectrometry (MS) performs label-free enzyme assays that utilize native substrates and is therefore generally applicable. But the analytical speed of MS is considered rate limiting, mainly due to the use of time-consuming chromatographic separation in traditional MS analysis. Thanks to new instrumentation and sample preparation methods, direct analyte introduction into a mass spectrometer without a prior chromatographic step can be achieved by laser, microfluidics, and acoustics, so that each sample can be analyzed within seconds. Here we review recent advances in MS platforms that improve the throughput of enzyme library screening and discuss how these advances can potentially facilitate biofuel research by providing high sensitivity, selectivity and quantitation that are difficult to obtain using traditional assays. We also highlight the limitations of current MS assays in studying biofuel-related enzymes and propose possible solutions.
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Geng F, Ma CW, Zeng AP. Reengineering substrate specificity of E. coli glutamate dehydrogenase using a position-based prediction method. Biotechnol Lett 2017; 39:599-605. [DOI: 10.1007/s10529-017-2297-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/10/2016] [Indexed: 01/11/2023]
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Jang E, Shim HW, Ryu BH, An DR, Yoo WK, Kim KK, Kim DW, Kim TD. Preparation of cobalt nanoparticles from polymorphic bacterial templates: A novel platform for biocatalysis. Int J Biol Macromol 2015; 81:747-53. [PMID: 26358553 DOI: 10.1016/j.ijbiomac.2015.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 08/31/2015] [Accepted: 09/04/2015] [Indexed: 12/20/2022]
Abstract
Nanoparticles have gathered significant research attention as materials for enzyme immobilization due to their advantageous properties such as low diffusion rates, ease of manipulation, and large surface areas. Here, polymorphic cobalt nanoparticles of varied sizes and shapes were prepared using Micrococcus lylae, Bacillus subtilis, Escherichia coli, Paracoccus sp., and Haloarcula vallismortis as bacterial templates. Furthermore, nine lipases/carboxylesterases were successfully immobilized on these cobalt nanoparticles. Especially, immobilized forms of Est-Y29, LmH, and Sm23 were characterized in more detail for potential industrial applications. Immobilization of enzymes onto cobalt oxide nanoparticles prepared from polymorphic bacterial templates may have potential for efficient hydrolysis on an industrial-scale, with several advantages such as high retention of enzymatic activity, increased stability, and strong reusability.
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Affiliation(s)
- Eunjin Jang
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 140-742, Republic of Korea
| | - Hyun-Woo Shim
- School of Civil, Environmental, and Architectural Engineering, Korea University, Seoul 136-713, Republic of Korea
| | - Bum Han Ryu
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 140-742, Republic of Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, SungKyunKwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Deu Rae An
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 140-742, Republic of Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, SungKyunKwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Wan Ki Yoo
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 140-742, Republic of Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, SungKyunKwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, SungKyunKwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Dong-Wan Kim
- School of Civil, Environmental, and Architectural Engineering, Korea University, Seoul 136-713, Republic of Korea
| | - T Doohun Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 140-742, Republic of Korea.
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Hosford J, Shepherd SA, Micklefield J, Wong LS. A high-throughput assay for arylamine halogenation based on a peroxidase-mediated quinone-amine coupling with applications in the screening of enzymatic halogenations. Chemistry 2014; 20:16759-63. [PMID: 25319801 PMCID: PMC4291110 DOI: 10.1002/chem.201403953] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Indexed: 02/04/2023]
Abstract
Arylhalides are important building blocks in many fine chemicals, pharmaceuticals and agrochemicals, and there has been increasing interest in the development of more "green" halogenation methods based on enzyme catalysis. However, the screening and development of new enzymes for biohalogenation has been hampered by a lack of high-throughput screening methods. Described herein is the development of a colorimetric assay for detecting both chemical and enzymatic arylamine halogenation reactions in an aqueous environment. The assay is based on the unique UV/Vis spectrum created by the formation of an ortho-benzoquinone-amine adduct, which is produced by the peroxidase-catalysed benzoquinone generation, followed by Michael addition of either a halogenated or non-halogenated arylamine. This assay is sensitive, rapid and amenable to high-throughput screening platforms. We have also shown this assay to be easily coupled to a flavin-dependent halogenase, which currently lacks any convenient colorimetric assay, in a "one-pot" workflow.
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Affiliation(s)
- Joseph Hosford
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN (UK)
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Recent advances in engineering proteins for biocatalysis. Biotechnol Bioeng 2014; 111:1273-87. [DOI: 10.1002/bit.25240] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 02/10/2014] [Accepted: 03/19/2014] [Indexed: 01/14/2023]
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Van Dien S. From the first drop to the first truckload: commercialization of microbial processes for renewable chemicals. Curr Opin Biotechnol 2013; 24:1061-8. [PMID: 23537815 DOI: 10.1016/j.copbio.2013.03.002] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 02/27/2013] [Accepted: 03/05/2013] [Indexed: 01/24/2023]
Abstract
Fermentation of carbohydrate substrates by microorganisms represents an attractive route for the manufacture of industrial chemicals from renewable resources. The technology to manipulate metabolism of bacteria and yeast, including the introduction of heterologous chemical pathways, has accelerated research in this field. However, the public literature contains very few examples of strains achieving the production metrics required for commercialization. This article presents the challenges in reaching commercial titer, yield, and productivity targets, along with other necessary strain and process characteristics. It then reviews various methods in systems biology, synthetic biology, enzyme engineering, and fermentation engineering which can be applied to strain improvement, and presents a strategy for using these tools to overcome the major hurdles on the path to commercialization.
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Affiliation(s)
- Stephen Van Dien
- Genomatica, Inc., 10520 Wateridge Circle, San Diego, CA 92121, United States.
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