1
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Tu H, Niu F, Li X, Gao K, Chen Z, Wang P, Li Z. Nanoarchitectonics of penicillin G acylase with Mn2+ doped β-cyclodextrin/Fe3O4 for enhanced catalytic activity and reusability. MOLECULAR CATALYSIS 2023. [DOI: 10.1016/j.mcat.2022.112838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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2
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Halomonas as a chassis. Essays Biochem 2021; 65:393-403. [PMID: 33885142 PMCID: PMC8314019 DOI: 10.1042/ebc20200159] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 01/04/2023]
Abstract
With the rapid development of systems and synthetic biology, the non-model bacteria, Halomonas spp., have been developed recently to become a cost-competitive platform for producing a variety of products including polyesters, chemicals and proteins owing to their contamination resistance and ability of high cell density growth at alkaline pH and high salt concentration. These salt-loving microbes can partially solve the challenges of current industrial biotechnology (CIB) which requires high energy-consuming sterilization to prevent contamination as CIB is based on traditional chassis, typically, Escherichia coli, Bacillus subtilis, Pseudomonas putida and Corynebacterium glutamicum. The advantages and current status of Halomonas spp. including their molecular biology and metabolic engineering approaches as well as their applications are reviewed here. Moreover, a systematic strain engineering streamline, including product-based host development, genetic parts mining, static and dynamic optimization of modularized pathways and bioprocess-inspired cell engineering are summarized. All of these developments result in the term called next-generation industrial biotechnology (NGIB). Increasing efforts are made to develop their versatile cell factories powered by synthetic biology to demonstrate a new biomanufacturing strategy under open and continuous processes with significant cost-reduction on process complexity, energy, substrates and fresh water consumption.
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Valli M, Bolzani VS. Natural Products: Perspectives and Challenges for use of Brazilian Plant Species in the Bioeconomy. AN ACAD BRAS CIENC 2019; 91:e20190208. [PMID: 31411242 DOI: 10.1590/0001-3765201920190208] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/15/2019] [Indexed: 12/25/2022] Open
Abstract
The development of our society has been based on the use of biodiversity, especially for nutrition, medicines and beauty. Brazil is the nation with the largest biodiversity in the world, with a rich chemical diversity, which is a potential source for bioeconomy. Considering the chemical and biological diversity of the Brazilian territory, we would like to highlight the value of secondary metabolites from Brazilian biodiversity with potential application for new products and technologies and the importance of scientific programs to support the sustainable use of biodiversity.
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Affiliation(s)
- Marilia Valli
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Av. Prof. Francisco Degni, 55, 14800-900 Araraquara, SP, Brazil
| | - Vanderlan S Bolzani
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Av. Prof. Francisco Degni, 55, 14800-900 Araraquara, SP, Brazil
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4
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Yu L, Wu F, Chen G. Next‐Generation Industrial Biotechnology‐Transforming the Current Industrial Biotechnology into Competitive Processes. Biotechnol J 2019; 14:e1800437. [DOI: 10.1002/biot.201800437] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 02/01/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Lin‐Ping Yu
- Ministry of Education Key Laboratory for Bioinformatics, School of Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Center for Synthetic and Systems BiologyTsinghua University New Biology Building 100084 Beijing China
- Tsinghua‐Peking Center for Life SciencesTsinghua University New Biology Building 100084 Beijing China
| | - Fu‐Qing Wu
- Ministry of Education Key Laboratory for Bioinformatics, School of Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Center for Synthetic and Systems BiologyTsinghua University New Biology Building 100084 Beijing China
- Tsinghua‐Peking Center for Life SciencesTsinghua University New Biology Building 100084 Beijing China
| | - Guo‐Qiang Chen
- Ministry of Education Key Laboratory for Bioinformatics, School of Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Center for Synthetic and Systems BiologyTsinghua University New Biology Building 100084 Beijing China
- Tsinghua‐Peking Center for Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Manchester Institute of Biotechnology, Centre for Synthetic BiologyThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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5
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Haq SF, Shanbhag AP, Karthikeyan S, Hassan I, Thanukrishnan K, Ashok A, Sukumaran S, Ramaswamy S, Bharatham N, Datta S, Samant S, Katagihallimath N. A strategy to identify a ketoreductase that preferentially synthesizes pharmaceutically relevant (S)-alcohols using whole-cell biotransformation. Microb Cell Fact 2018; 17:192. [PMID: 30509260 PMCID: PMC6276252 DOI: 10.1186/s12934-018-1036-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/21/2018] [Indexed: 01/10/2023] Open
Abstract
Introduction Chemical industries are constantly in search of an expeditious and environmentally benign method for producing chiral synthons. Ketoreductases have been used as catalysts for enantioselective conversion of desired prochiral ketones to their corresponding alcohol. We chose reported promiscuous ketoreductases belonging to different protein families and expressed them in E. coli to evaluate their ability as whole-cell catalysts for obtaining chiral alcohol intermediates of pharmaceutical importance. Apart from establishing a method to produce high value (S)-specific alcohols that have not been evaluated before, we propose an in silico analysis procedure to predict product chirality. Results Six enzymes originating from Sulfolobus sulfotaricus, Zygosaccharomyces rouxii, Hansenula polymorpha, Corynebacterium sp. ST-10, Synechococcus sp. PCC 7942 and Bacillus sp. ECU0013 with reported efficient activity for dissimilar substrates are compared here to arrive at an optimal enzyme for the method. Whole–cell catalysis of ketone intermediates for drugs like Aprepitant, Sitagliptin and Dolastatin using E. coli over-expressing these enzymes yielded (S)-specific chiral alcohols. We explain this chiral specificity for the best-performing enzyme, i.e., Z. rouxii ketoreductase using in silico modelling and MD simulations. This rationale was applied to five additional ketones that are used in the synthesis of Crizotinib, MA-20565 (an antifungal agent), Sulopenem, Rivastigmine, Talampanel and Barnidipine and predicted the yield of (S) enantiomers. Experimental evaluation matched the in silico analysis wherein ~ 95% (S)-specific alcohol with a chemical yield of 23–79% was obtained through biotransformation. Further, the cofactor re-cycling was optimized by switching the carbon source from glucose to sorbitol that improved the chemical yield to 85–99%. Conclusions Here, we present a strategy to synthesize pharmaceutically relevant chiral alcohols by ketoreductases using a cofactor balanced whole-cell catalysis scheme that is useful for the industry. Based on the results obtained in these trials, Zygosaccharomyces rouxii ketoreductase was identified as a proficient enzyme to obtain (S)-specific alcohols from their respective ketones. The whole–cell catalyst when combined with nutrient modulation of using sorbitol as a carbon source helped obtain high enantiomeric and chemical yield. Electronic supplementary material The online version of this article (10.1186/s12934-018-1036-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Anirudh P Shanbhag
- Bugworks Research India, Pvt. Ltd, Bengaluru, India.,Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Subbulakshmi Karthikeyan
- Anthem Biosciences Pvt. Ltd, Bengaluru, India.,Centre for Pharmaceutical Biotechnology, University of Illinois Chicago, Chicago, USA
| | - Imran Hassan
- Anthem Biosciences Pvt. Ltd, Bengaluru, India.,PerkinElmer, Bengaluru, India
| | - Kannan Thanukrishnan
- Anthem Biosciences Pvt. Ltd, Bengaluru, India.,Shasun Research Center, Chennai, India
| | | | | | - S Ramaswamy
- Institute for Stem Cell Biology and Regenerative Medicine, Bengaluru, India
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6
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Valli M, Russo HM, Bolzani VS. The potential contribution of the natural products from Brazilian biodiversity to bioeconomy. AN ACAD BRAS CIENC 2018; 90:763-778. [PMID: 29668803 DOI: 10.1590/0001-3765201820170653] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 09/20/2017] [Indexed: 01/05/2023] Open
Abstract
The development of our society has been based on the use of biodiversity, especially for medicines and nutrition. Brazil is the nation with the largest biodiversity in the world accounting for more than 15% of all living species. The devastation of biodiversity in Brazil is critical and may not only cause the loss of species and genes that encode enzymes involved in the complex metabolism of organisms, but also the loss of a rich chemical diversity, which is a potential source for bioeconomy based on natural products and new synthetic derivatives. Bioeconomy focus on the use of bio-based products, instead of fossil-based ones and could address some of the important challenges faced by society. Considering the chemical and biological diversity of Brazil, this review highlights the Brazilian natural products that were successfully used to develop new products and the value of secondary metabolites from Brazilian biodiversity with potential application for new products and technologies. Additionally, we would like to address the importance of new technologies and scientific programs to support preservation policies, bioeconomy and strategies for the sustainable use of biodiversity.
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Affiliation(s)
- Marilia Valli
- Núcleo de Bioensaios, Biossíntese e Ecofisiologia de Produtos Naturais (NuBBE), Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista 'Júlio de Mesquita Filho', Av. Prof. Francisco Degni, 55, 14801-970 Araraquara, SP, Brazil
| | - Helena M Russo
- Núcleo de Bioensaios, Biossíntese e Ecofisiologia de Produtos Naturais (NuBBE), Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista 'Júlio de Mesquita Filho', Av. Prof. Francisco Degni, 55, 14801-970 Araraquara, SP, Brazil
| | - Vanderlan S Bolzani
- Núcleo de Bioensaios, Biossíntese e Ecofisiologia de Produtos Naturais (NuBBE), Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista 'Júlio de Mesquita Filho', Av. Prof. Francisco Degni, 55, 14801-970 Araraquara, SP, Brazil
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7
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Nonribosomal biosynthesis of backbone-modified peptides. Nat Chem 2017; 10:282-287. [DOI: 10.1038/nchem.2891] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 10/06/2017] [Indexed: 01/01/2023]
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8
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Lee SQE, Tan TS, Kawamukai M, Chen ES. Cellular factories for coenzyme Q 10 production. Microb Cell Fact 2017; 16:39. [PMID: 28253886 PMCID: PMC5335738 DOI: 10.1186/s12934-017-0646-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/10/2017] [Indexed: 04/20/2023] Open
Abstract
Coenzyme Q10 (CoQ10), a benzoquinone present in most organisms, plays an important role in the electron-transport chain, and its deficiency is associated with various neuropathies and muscular disorders. CoQ10 is the only lipid-soluble antioxidant found in humans, and for this, it is gaining popularity in the cosmetic and healthcare industries. To meet the growing demand for CoQ10, there has been considerable interest in ways to enhance its production, the most effective of which remains microbial fermentation. Previous attempts to increase CoQ10 production to an industrial scale have thus far conformed to the strategies used in typical metabolic engineering endeavors. However, the emergence of new tools in the expanding field of synthetic biology has provided a suite of possibilities that extend beyond the traditional modes of metabolic engineering. In this review, we cover the various strategies currently undertaken to upscale CoQ10 production, and discuss some of the potential novel areas for future research.
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Affiliation(s)
- Sean Qiu En Lee
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Tsu Soo Tan
- School of Chemical & Life Sciences, Nanyang Polytechnic, Singapore, Singapore
| | - Makoto Kawamukai
- Faculty of Life and Environmental Science, Shimane University, Matsue, 690-8504, Japan
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, Singapore, Singapore. .,National University Health System (NUHS), Singapore, Singapore. .,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore. .,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore.
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9
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King JR, Edgar S, Qiao K, Stephanopoulos G. Accessing Nature's diversity through metabolic engineering and synthetic biology. F1000Res 2016; 5. [PMID: 27081481 PMCID: PMC4813638 DOI: 10.12688/f1000research.7311.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/21/2016] [Indexed: 12/31/2022] Open
Abstract
In this perspective, we highlight recent examples and trends in metabolic engineering and synthetic biology that demonstrate the synthetic potential of enzyme and pathway engineering for natural product discovery. In doing so, we introduce natural paradigms of secondary metabolism whereby simple carbon substrates are combined into complex molecules through “scaffold diversification”, and subsequent “derivatization” of these scaffolds is used to synthesize distinct complex natural products. We provide examples in which modern pathway engineering efforts including combinatorial biosynthesis and biological retrosynthesis can be coupled to directed enzyme evolution and rational enzyme engineering to allow access to the “privileged” chemical space of natural products in industry-proven microbes. Finally, we forecast the potential to produce natural product-like discovery platforms in biological systems that are amenable to single-step discovery, validation, and synthesis for streamlined discovery and production of biologically active agents.
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Affiliation(s)
- Jason R King
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven Edgar
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kangjian Qiao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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10
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Murphy AC, Hong H, Vance S, Broadhurst RW, Leadlay PF. Broadening substrate specificity of a chain-extending ketosynthase through a single active-site mutation. Chem Commun (Camb) 2016; 52:8373-6. [DOI: 10.1039/c6cc03501a] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An in vitro model system based on a ketosynthase domain of the erythromycin polyketide synthase was used to probe the apparent substrate tolerance of ketosynthase domains of the mycolactone polyketide synthase.
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Affiliation(s)
- Annabel C. Murphy
- Department of Biochemistry
- University of Cambridge
- Cambridge CB2 1GA
- UK
| | - Hui Hong
- Department of Biochemistry
- University of Cambridge
- Cambridge CB2 1GA
- UK
| | - Steve Vance
- Department of Biochemistry
- University of Cambridge
- Cambridge CB2 1GA
- UK
- Crescendo Biologics Ltd
| | | | - Peter F. Leadlay
- Department of Biochemistry
- University of Cambridge
- Cambridge CB2 1GA
- UK
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11
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White biotechnology: State of the art strategies for the development of biocatalysts for biorefining. Biotechnol Adv 2015; 33:1653-70. [PMID: 26303096 DOI: 10.1016/j.biotechadv.2015.08.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/31/2015] [Accepted: 08/17/2015] [Indexed: 12/31/2022]
Abstract
White biotechnology is a term that is now often used to describe the implementation of biotechnology in the industrial sphere. Biocatalysts (enzymes and microorganisms) are the key tools of white biotechnology, which is considered to be one of the key technological drivers for the growing bioeconomy. Biocatalysts are already present in sectors such as the chemical and agro-food industries, and are used to manufacture products as diverse as antibiotics, paper pulp, bread or advanced polymers. This review proposes an original and global overview of highly complementary fields of biotechnology at both enzyme and microorganism level. A certain number of state of the art approaches that are now being used to improve the industrial fitness of biocatalysts particularly focused on the biorefinery sector are presented. The first part deals with the technologies that underpin the development of industrial biocatalysts, notably the discovery of new enzymes and enzyme improvement using directed evolution techniques. The second part describes the toolbox available by the cell engineer to shape the metabolism of microorganisms. And finally the last part focuses on the 'omic' technologies that are vital for understanding and guide microbial engineering toward more efficient microbial biocatalysts. Altogether, these techniques and strategies will undoubtedly help to achieve the challenging task of developing consolidated bioprocessing (i.e. CBP) readily available for industrial purpose.
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12
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Przybylski D, Rohwerder T, Dilßner C, Maskow T, Harms H, Müller RH. Exploiting mixtures of H2, CO2, and O2 for improved production of methacrylate precursor 2-hydroxyisobutyric acid by engineered Cupriavidus necator strains. Appl Microbiol Biotechnol 2014; 99:2131-45. [DOI: 10.1007/s00253-014-6266-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/23/2014] [Accepted: 11/24/2014] [Indexed: 12/23/2022]
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13
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Yu H, Tang H, Xu P. Green strategy from waste to value-added-chemical production: efficient biosynthesis of 6-hydroxy-3-succinoyl-pyridine by an engineered biocatalyst. Sci Rep 2014; 4:5397. [PMID: 24953905 PMCID: PMC4066252 DOI: 10.1038/srep05397] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 06/03/2014] [Indexed: 12/04/2022] Open
Abstract
Value-added intermediates produced by microorganisms during the catabolism of N-heterocycles are potential building blocks for agrochemical synthesis and pharmaceutical production. 6-Hydroxy-3-succinoyl-pyridine (HSP), an intermediate in nicotine degradation, is an important precursor for the synthesis of drugs and compounds with biological activities. In the present study, we show that an engineered biocatalyst, Pseudomonas putida P-HSP, efficiently produced HSP from the renewable raw material of tobacco-waste that contains a high concentration of nicotine. The genetically constructed strain P-HSP realized a high accumulation of HSP, and HSP production was 3.7-fold higher than the non-engineered strain S16. Under optimal conditions, HSP was produced at high concentrations of 6.8 g l(-1) and 16.3 g l(-1) from tobacco-waste and nicotine, respectively. This work demonstrates a green strategy to block the catabolic pathway of N-heterocycles, which is a promising approach for the mutasynthesis of valuable compounds.
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Affiliation(s)
- Hao Yu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
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14
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Korman TP, Sahachartsiri B, Li D, Vinokur JM, Eisenberg D, Bowie JU. A synthetic biochemistry system for the in vitro production of isoprene from glycolysis intermediates. Protein Sci 2014; 23:576-85. [PMID: 24623472 DOI: 10.1002/pro.2436] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 01/30/2014] [Accepted: 01/30/2014] [Indexed: 02/04/2023]
Abstract
The high yields required for the economical production of chemicals and fuels using microbes can be difficult to achieve due to the complexities of cellular metabolism. An alternative to performing biochemical transformations in microbes is to build biochemical pathways in vitro, an approach we call synthetic biochemistry. Here we test whether the full mevalonate pathway can be reconstituted in vitro and used to produce the commodity chemical isoprene. We construct an in vitro synthetic biochemical pathway that uses the carbon and ATP produced from the glycolysis intermediate phosphoenolpyruvate to run the mevalonate pathway. The system involves 12 enzymes to perform the complex transformation, while providing and balancing the ATP, NADPH, and acetyl-CoA cofactors. The optimized system produces isoprene from phosphoenolpyruvate in ∼100% molar yield. Thus, by inserting the isoprene pathway into previously developed glycolysis modules it may be possible to produce isoprene and other acetyl-CoA derived isoprenoids from glucose in vitro.
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Affiliation(s)
- Tyler P Korman
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, California
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15
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Jensen TØ, Kvist T, Mikkelsen MJ, Westermann P. Rapid and reliable method for identification of associated endonuclease cleavage and recognition sites. Lett Appl Microbiol 2014; 58:576-81. [PMID: 24698368 DOI: 10.1111/lam.12238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/22/2014] [Accepted: 02/04/2014] [Indexed: 11/30/2022]
Abstract
UNLABELLED One barrier to cross during genetic engineering is the restriction-modification system found in many bacteria. In this study, we developed a fast and reliable method for mapping the recognition and cleavage site of the restriction endonucleases. Clostridium pasteurianum, a model organism for the study of nitrogen fixation, has been found to harbour at least two restriction-modification systems including the restriction endonucleases CpaPI, which is an isoschizomer of MboI and CpaAI. Dam-methylated DNA was used to isolate the activity of CpaAI. Exposing freshly prepared cell lysate to known nucleotide fragments and directly sequencing the pool of digested nucleotide fragments enabled identification of the cleavage sites in the fragments. By aligning the sequences adjacent to the cleavage site, it was possible to identify the recognition sequence. Using this method, we successfully located all CpaAI recognition and cleavage sites within the template sequence. By modifying DNA with both Dam and CpG methylases (M.SssI) and thereby preventing digestion by CpaPI and CpaAI, no further endonuclease activity was detected. SIGNIFICANCE AND IMPACT OF THE STUDY Restriction-modification systems are important barriers to successful genetic modification in many bacterial species. In this study, we demonstrate an efficient and general applicable method for identifying endonuclease recognition and cleavage sites. For the study and the trails, the model organism for nitrogen fixation Clostridium pasteurianum was used. The method was proven to be reliable, and by modifying DNA at the identified sites, it is possible to prevent digestion.
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Affiliation(s)
- T Ø Jensen
- Section for Sustainable Biotechnology, Aalborg University Copenhagen, Copenhagen, Denmark
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16
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Falls KC, Williams AL, Bryksin AV, Matsumura I. Escherichia coli deletion mutants illuminate trade-offs between growth rate and flux through a foreign anabolic pathway. PLoS One 2014; 9:e88159. [PMID: 24505410 PMCID: PMC3913754 DOI: 10.1371/journal.pone.0088159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 01/04/2014] [Indexed: 11/18/2022] Open
Abstract
Metabolic engineers strive to improve the production yields of microbial fermentations, sometimes by mutating the genomes of production strains. Some mutations are detrimental to the health of the organism, so a quantitative and mechanistic understanding of the trade-offs could inform better designs. We employed the bacterial luciferase operon (luxABCDE), which uses ubiquitous energetic cofactors (NADPH, ATP, FMNH2, acetyl-CoA) from the host cell, as a proxy for a novel anabolic pathway. The strains in the Escherichia coli Keio collection, each of which contains a single deletion of a non-essential gene, represent mutational choices that an engineer might make to optimize fermentation yields. The Keio strains and the parental BW25113 strain were transformed with a luxABCDE expression vector. Each transformant was propagated in defined M9 medium at 37°C for 48 hours; the cell density (optical density at 600 nanometers, OD600) and luminescence were measured every 30 minutes. The trade-offs were visualized by plotting the maximum growth rate and luminescence/OD600 of each transformant across a “production possibility frontier”. Our results show that some loss-of-function mutations enhance growth in vitro or light production, but that improvement in one trait generally comes at the expense of the other.
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Affiliation(s)
- Kelly C. Falls
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Aimee L. Williams
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Anton V. Bryksin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Ichiro Matsumura
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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17
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Barrales Cureño HJ, Ramírez Sepúlveda MF. Una revisión sobre la producción de taxoides anticancerígenos en cultivos in vitro de callos y células de Taxus spp. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2013. [DOI: 10.15446/rev.colomb.biote.v15n2.41743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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18
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Boehm CR, Freemont PS, Ces O. Design of a prototype flow microreactor for synthetic biology in vitro. LAB ON A CHIP 2013; 13:3426-3432. [PMID: 23842984 DOI: 10.1039/c3lc50231g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
As a reference platform for in vitro synthetic biology, we have developed a prototype flow microreactor for enzymatic biosynthesis. We report the design, implementation, and computer-aided optimisation of a three-step model pathway within a microfluidic reactor. A packed bed format was shown to be optimal for enzyme compartmentalisation after experimental evaluation of several approaches. The specific substrate conversion efficiency could significantly be improved by an optimised parameter set obtained by computational modelling. Our microreactor design provides a platform to explore new in vitro synthetic biology solutions for industrial biosynthesis.
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Affiliation(s)
- Christian R Boehm
- Institute of Chemical Biology, Imperial College London, Exhibition Road, London, UK SW7 2AZ.
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Jang YS, Kim B, Shin JH, Choi YJ, Choi S, Song CW, Lee J, Park HG, Lee SY. Bio-based production of C2-C6 platform chemicals. Biotechnol Bioeng 2012; 109:2437-59. [DOI: 10.1002/bit.24599] [Citation(s) in RCA: 299] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 06/26/2012] [Accepted: 06/26/2012] [Indexed: 12/20/2022]
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20
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Abstract
Microorganisms have been used for decades as sources of antibiotics, vitamins and enzymes and for the production of fermented foods and chemicals. In the 21st century microorganisms will play a vital role in addressing some of the problems faced by mankind. In this article three of the current applications in which microbes have a significant role to play are highlighted: the discovery of new antibiotics, manufacture of biofuels and bioplastics, and production of fine chemicals via biotransformation.
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Affiliation(s)
- Cormac D Murphy
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, Ardmore House, University College Dublin, Dublin 4, Ireland.
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