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Gilman J, Walls L, Bandiera L, Menolascina F. Statistical Design of Experiments for Synthetic Biology. ACS Synth Biol 2021; 10:1-18. [PMID: 33406821 DOI: 10.1021/acssynbio.0c00385] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The design and optimization of biological systems is an inherently complex undertaking that requires careful balancing of myriad synergistic and antagonistic variables. However, despite this complexity, much synthetic biology research is predicated on One Factor at A Time (OFAT) experimentation; the genetic and environmental variables affecting the activity of a system of interest are sequentially altered while all other variables are held constant. Beyond being time and resource intensive, OFAT experimentation crucially ignores the effect of interactions between factors. Given the ubiquity of interacting genetic and environmental factors in biology this failure to account for interaction effects in OFAT experimentation can result in the development of suboptimal systems. To address these limitations, an increasing number of studies have turned to Design of Experiments (DoE), a suite of methods that enable efficient, systematic exploration and exploitation of complex design spaces. This review provides an overview of DoE for synthetic biologists. Key concepts and commonly used experimental designs are introduced, and we discuss the advantages of DoE as compared to OFAT experimentation. We dissect the applicability of DoE in the context of synthetic biology and review studies which have successfully employed these methods, illustrating the potential of statistical experimental design to guide the design, characterization, and optimization of biological protocols, pathways, and processes.
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Affiliation(s)
- James Gilman
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9YL, U.K
| | - Laura Walls
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9YL, U.K
| | - Lucia Bandiera
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9YL, U.K
| | - Filippo Menolascina
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9YL, U.K
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Stepwise optimization of recombinant protein production in Escherichia coli utilizing computational and experimental approaches. Appl Microbiol Biotechnol 2020; 104:3253-3266. [DOI: 10.1007/s00253-020-10454-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/28/2020] [Accepted: 02/07/2020] [Indexed: 12/14/2022]
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Zhou J, Yin L, Wu C, Wu S, Lu J, Fang H, Qian Y. Screening of an Alkaline CMCase-Producing Strain and the Optimization of its Fermentation Condition. Curr Pharm Biotechnol 2020; 21:1304-1315. [PMID: 31995003 DOI: 10.2174/1389201021666200129123818] [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: 06/03/2019] [Revised: 07/02/2019] [Accepted: 07/18/2019] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Alkaline Carboxymethyl Cellulase (CMCase) is an attractive enzyme for the textile, laundry, pulp, and paper industries; however, commercial preparations with sufficient activity at alkaline conditions are scarce. METHODS High CMCase-producing bacterial isolate, SX9-4, was screened out from soil bacteria, which was identified as Flavobacterium sp. on the basis of 16S rDNA sequencing. RESULTS The optimum pH and temperature for CMCase reaction were 8.0 and 55°C, respectively. Alkaline CMCase was stable over wide pH (3.0-10.6) and temperature (25-55°C) ranges. Enzyme activity was significantly inhibited by the bivalent cations Mn2+ and Cu2+, and was activated by Fe2+. To improve the alkaline CMCase production of SX9-4, fermentation parameters were selected through onefactor- at-a-time and further carried out by response surface methodologies based on a central composite design. CONCLUSION High CMCase production (57.18 U/mL) was achieved under the optimal conditions: 10.53 g/L carboxymethylcellulose sodium, 7.74 g/L glucose, 13.71 g/L peptone, and 5.27 g/L ammonium oxalate.
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Affiliation(s)
- Junmei Zhou
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Lianghong Yin
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Chenbin Wu
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Sijia Wu
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Jidong Lu
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Hailing Fang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Yongchang Qian
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
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Uhoraningoga A, Kinsella GK, Henehan GT, Ryan BJ. The Goldilocks Approach: A Review of Employing Design of Experiments in Prokaryotic Recombinant Protein Production. Bioengineering (Basel) 2018; 5:E89. [PMID: 30347746 PMCID: PMC6316313 DOI: 10.3390/bioengineering5040089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/09/2018] [Accepted: 10/12/2018] [Indexed: 02/06/2023] Open
Abstract
The production of high yields of soluble recombinant protein is one of the main objectives of protein biotechnology. Several factors, such as expression system, vector, host, media composition and induction conditions can influence recombinant protein yield. Identifying the most important factors for optimum protein expression may involve significant investment of time and considerable cost. To address this problem, statistical models such as Design of Experiments (DoE) have been used to optimise recombinant protein production. This review examines the application of DoE in the production of recombinant proteins in prokaryotic expression systems with specific emphasis on media composition and culture conditions. The review examines the most commonly used DoE screening and optimisation designs. It provides examples of DoE applied to optimisation of media and culture conditions.
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Affiliation(s)
| | | | - Gary T Henehan
- Dublin Institute of Technology, Dublin D01 HV58, Ireland.
| | - Barry J Ryan
- Dublin Institute of Technology, Dublin D01 HV58, Ireland.
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Kim MH, Gao W, Chung CH, Lee JW. Comparison of optimal conditions for mass production of carboxymethylcellulase by Escherichia coli JM109/A-68 with other recombinants in pilot-scale bioreactor. BIOTECHNOL BIOPROC E 2017. [DOI: 10.1007/s12257-017-0035-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Construction of a recombinant Escherichia coli JM109/A-68 for production of carboxymethylcellulase and comparison of its production with its wild type, Bacillus velezensis A-68 in a pilot-scale bioreactor. BIOTECHNOL BIOPROC E 2016. [DOI: 10.1007/s12257-016-0468-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Gao W, Chung CH, Li J, Lee JW. Enhanced production of cellobiase by marine bacterium Cellulophaga lytica LBH-14 from rice bran under optimized conditions involved in dissolved oxygen. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0486-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Enhanced production of carboxymethylcellulase of Bacillus subtilis subsp. subtilis A-53 by a recombinant Escherichia coli JM109/A-53 with pH and temperature shifts. KOREAN J CHEM ENG 2014. [DOI: 10.1007/s11814-014-0160-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Gao W, Kim HJ, Chung CH, Lee JW. Enhanced Production of carboxymethylcellulase by a marine bacterium, Bacillus velezensis A-68, by using rice hulls in pilot-scale bioreactor under optimized conditions for dissolved oxygen. J Microbiol 2014; 52:755-61. [DOI: 10.1007/s12275-014-4156-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/07/2014] [Accepted: 06/02/2014] [Indexed: 11/29/2022]
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Kazemi A, Rasoul-Amini S, Shahbazi M, Safari A, Ghasemi Y. Isolation, identification, and media optimization of high-level cellulase production by Bacillus sp. BCCS A3, in a fermentation system using response surface methodology. Prep Biochem Biotechnol 2014; 44:107-18. [PMID: 24152098 DOI: 10.1080/10826068.2013.792276] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cellulases are important glycosyl hydrolase enzymes, which break down cellulose to β-glucose. They have been used widely in biotechnological processing such as bioethanol production. In this work we studied maximizing cellulase production by Bacillus sp. BCCS A3 using response surface methodology (RSM). A good result was attained with these conditions (% w/v): tryptone 0.1, Na₂PO₄ 0.25, (NH₄)₂SO₄ 0.2, MgSO₄ · 7H₂O 0.005, CaCl₂ 0.005, KH₂PO₄ 0.1, NaCl 0.1, sodium carboxymethylcellulose (CMC) 0.75, and pH 9. The cellulase activity in optimized medium was 49.80 U/ml. Moreover, high level of enzyme production was obtained by using fermentor system (50.30 U/ml). Thus, according to the obtained results, this statistical method provided quick identification and integration of key medium details for Bacillus sp. BCCS A3, leading to more cellulase production.
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Affiliation(s)
- Aboozar Kazemi
- a Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences , Shiraz , Iran
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Zhong J, Zhang X, Ren Y, Yang J, Tan H, Zhou J. Optimization of Bacillus subtilis cell growth effecting jiean-peptide production in fed batch fermentation using central composite design. ELECTRON J BIOTECHN 2014. [DOI: 10.1016/j.ejbt.2014.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Merrylin J, Kaliappan S, Kumar SA, Yeom IT, Banu JR. Enhancing aerobic digestion potential of municipal waste-activated sludge through removal of extracellular polymeric substance. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:1112-1123. [PMID: 23872893 DOI: 10.1007/s11356-013-1976-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 07/02/2013] [Indexed: 06/02/2023]
Abstract
A protease-secreting bacteria was used to pretreat municipal sewage sludge to enhance aerobic digestion. To enhance the accessibility of the sludge to the enzyme, extracellular polymeric substances were removed using citric acid thereby removing the flocs in the sludge. The conditions for the bacterial pretreatment were optimized using response surface methodology. The results of the bacterial pretreatment indicated that the suspended solids reduction was 18% in sludge treated with citric acid and 10% in sludge not treated with citric acid whereas in raw sludge, suspended solids reduction was 5.3%. Solubilization was 10.9% in the sludge with extracellular polymeric substances removed in contrast to that of the sludge with extracellular polymeric substances, which was 7.2%, and that of the raw sludge, which was just 4.8%. The suspended solids reduction in the aerobic reactor containing pretreated sludge was 52.4% whereas that in the control reactor was 15.3%. Thus, pretreatment with the protease-secreting bacteria after the removal of extracellular polymeric substances is a cost-effective and environmentally friendly method.
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Affiliation(s)
- J Merrylin
- Department of Civil Engineering, Anna University of Technology Tirunelveli, Tirunelveli, 627007, Tamil Nadu, India
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Garvey M, Klose H, Fischer R, Lambertz C, Commandeur U. Cellulases for biomass degradation: comparing recombinant cellulase expression platforms. Trends Biotechnol 2013; 31:581-93. [DOI: 10.1016/j.tibtech.2013.06.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/21/2013] [Accepted: 06/24/2013] [Indexed: 10/26/2022]
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Kim BK, Kim HJ, Lee JW. Rapid Statistical Optimization of Cultural Conditions for Mass Production of Carboxymethylcellulase by a Newly Isolated Marine Bacterium, Bacillus velezensis A-68 from Rice Hulls. ACTA ACUST UNITED AC 2013. [DOI: 10.5352/jls.2013.23.6.757] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Cao W, Kim HW, Li J, Lee JW. Enhanced Production of Cellobiase by a Marine Bacterium, Cellulophaga lytica LBH-14, in Pilot-Scaled Bioreactor Using Rice Bran. ACTA ACUST UNITED AC 2013. [DOI: 10.5352/jls.2013.23.4.542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Jung DY, Son CW, Kim SK, Gao W, Lee JW. Enhanced production of heteropolysaccharide-7 by Beijerinckia indica HS-2001 in pilot-scaled bioreactor under optimized conditions involved in dissolved oxygen using sucrose-based medium. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-012-0520-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Cao W, Lee SU, Li J, Lee JW. Enhanced production of carboxymethylcellulase by Cellulophaga lytica LBH-14 in pilot-scale bioreactor under optimized conditions involved in dissolved oxygen. KOREAN J CHEM ENG 2013. [DOI: 10.1007/s11814-012-0219-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Enhanced production of carboxymethylcellulase of a marine microorganism, Bacillus subtilis subsp. subtilis A-53 in a pilot-scaled bioreactor by a recombinant Escherichia coli JM109/A-53 from rice bran. Mol Biol Rep 2013; 40:3609-21. [DOI: 10.1007/s11033-012-2435-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 12/18/2012] [Indexed: 11/25/2022]
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Kim YJ, Cao W, Lee YJ, Lee SU, Jeong JH, Lee JW. Enhanced Production of Carboxymethylcellulase by a Newly Isolated Marine Microorganism Bacillus atrophaeus LBH-18 Using Rice Bran, a Byproduct from the Rice Processing Industry. ACTA ACUST UNITED AC 2012. [DOI: 10.5352/jls.2012.22.10.1295] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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