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Kocabaş P, Çalık G, Çalık P, Özdamar TH. Analyses of extracellular protein production in Bacillus subtilis – II: Responses of reaction network to oxygen transfer at transcriptional level. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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2
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Ma X, Huo YX. The application of microfluidic-based technologies in the cycle of metabolic engineering. Synth Syst Biotechnol 2016; 1:137-142. [PMID: 29062937 PMCID: PMC5640795 DOI: 10.1016/j.synbio.2016.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/15/2016] [Accepted: 09/27/2016] [Indexed: 02/07/2023] Open
Abstract
The process of metabolic engineering consists of multiple cycles of design, build, test and learn, which is typically laborious and time-consuming. To increase the efficiency and the rate of success of strain engineering, novel instrumentation must be applied. Microfluidics, the control of liquid flow in microstructures, has enabled flexible, accurate, automatic, and high-throughput manipulation of cells in liquid at picoliter to nanoliter scale. These attributes hold great promise in advancing metabolic engineering in terms of the phases of design, build, test and learn. To promote the application of microfluidic-based technologies in strain improvement, this review addressed the potentials of microfluidics and the related approaches in DNA assembly, transformation, strain screening, genotyping and phenotyping, and highlighted their adaptations for single-cell analysis. As a result, this facilitates in-depth understanding of the metabolic network, which in turn promote efficient optimization in the following cycles of strain engineering. Taken together, microfluidic-based technologies enable on-chip workflow, and could greatly accelerate the turnaround of metabolic engineering.
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Affiliation(s)
- Xiaoyan Ma
- College of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081, China
| | - Yi-Xin Huo
- College of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081, China
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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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Krivoruchko A, Siewers V, Nielsen J. Opportunities for yeast metabolic engineering: Lessons from synthetic biology. Biotechnol J 2011; 6:262-76. [DOI: 10.1002/biot.201000308] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Revised: 01/06/2011] [Accepted: 01/13/2011] [Indexed: 11/08/2022]
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5
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Shin HS, Kim YJ, Yoo IH, Lee HS, Jin S, Ha UH. Autoinduction of a genetic locus encoding putative acyltransferase in Corynebacterium glutamicum. Biotechnol Lett 2010; 33:97-102. [PMID: 20821248 DOI: 10.1007/s10529-010-0395-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 08/24/2010] [Indexed: 10/19/2022]
Abstract
A genetic locus, encoding putative acyltransferase, was induced by autoinducers in Corynebacterium glutamicum. The autoinducers were maximally produced by the bacterium after 24 h culture. Those molecules are resistant to proteinase K treatment (300 μg ml(-1)) for 30 min at 37°C or at 121°C for 15 min, and remained stable after extensive storage at 4°C. Autoinducers in the cell-free culture fluids from Corynebacterium ammoniagenes and Pseudomonas aeruginosa also induced the expression of acyltransferase in C. glutamicum, suggesting possible cross-recognition of the autoinducers by C. glutamicum. C. glutamicum thus possesses an autoinduction system which secretes autoinducers during growth, triggering the expression of downstream genes, exemplified by the putative acyltransferase gene.
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Affiliation(s)
- Hee-Sung Shin
- Department of Biotechnology and Bioinformatics, Korea University, Yeongi, Chungnam, 339-700, Republic of Korea
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Metabolic engineering for production of biorenewable fuels and chemicals: contributions of synthetic biology. J Biomed Biotechnol 2010; 2010:761042. [PMID: 20414363 PMCID: PMC2857869 DOI: 10.1155/2010/761042] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 12/18/2009] [Accepted: 01/13/2010] [Indexed: 12/18/2022] Open
Abstract
Production of fuels and chemicals through microbial fermentation of plant material is a desirable alternative to petrochemical-based production. Fermentative production of biorenewable fuels and chemicals requires the engineering of biocatalysts that can quickly and efficiently convert sugars to target products at a cost that is competitive with existing petrochemical-based processes. It is also important that biocatalysts be robust to extreme fermentation conditions, biomass-derived inhibitors, and their target products. Traditional metabolic engineering has made great advances in this area, but synthetic biology has contributed and will continue to contribute to this field, particularly with next-generation biofuels. This work reviews the use of metabolic engineering and synthetic biology in biocatalyst engineering for biorenewable fuels and chemicals production, such as ethanol, butanol, acetate, lactate, succinate, alanine, and xylitol. We also examine the existing challenges in this area and discuss strategies for improving biocatalyst tolerance to chemical inhibitors.
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Systems biology of industrial microorganisms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010; 120:51-99. [PMID: 20503029 DOI: 10.1007/10_2009_59] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.
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Kocabaş P, Çalık P, Çalık G, Özdamar TH. Microarray Studies inBacillus subtilis. Biotechnol J 2009; 4:1012-27. [DOI: 10.1002/biot.200800330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Otero JM, Panagiotou G, Olsson L. Fueling industrial biotechnology growth with bioethanol. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2007; 108:1-40. [PMID: 17684710 DOI: 10.1007/10_2007_071] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Industrial biotechnology is the conversion of biomass via biocatalysis, microbial fermentation, or cell culture to produce chemicals, materials, and/or energy. Industrial biotechnology processes aim to be cost-competitive, environmentally favorable, and self-sustaining compared to their petrochemical equivalents. Common to all processes for the production of energy, commodity, added value, or fine chemicals is that raw materials comprise the most significant cost fraction, particularly as operating efficiencies increase through practice and improving technologies. Today, crude petroleum represents the dominant raw material for the energy and chemical sectors worldwide. Within the last 5 years petroleum prices, stability, and supply have increased, decreased, and been threatened, respectively, driving a renewed interest across academic, government, and corporate centers to utilize biomass as an alternative raw material. Specifically, bio-based ethanol as an alternative biofuel has emerged as the single largest biotechnology commodity, with close to 46 billion L produced worldwide in 2005. Bioethanol is a leading example of how systems biology tools have significantly enhanced metabolic engineering, inverse metabolic engineering, and protein and enzyme engineering strategies. This enhancement stems from method development for measurement, analysis, and data integration of functional genomics, including the transcriptome, proteome, metabolome, and fluxome. This review will show that future industrial biotechnology process development will benefit tremendously from the precedent set by bioethanol - that enabling technologies (e.g., systems biology tools) coupled with favorable economic and socio-political driving forces do yield profitable, sustainable, and environmentally responsible processes. Biofuel will continue to be the keystone of any industrial biotechnology-based economy whereby biorefineries leverage common raw materials and unit operations to integrate diverse processes to produce demand-driven product portfolios.
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Affiliation(s)
- José Manuel Otero
- Center for Microbial Biotechnology, BioCentrum, Technical University of Denmark, BioCentrum-DTU, 2800, Kgs. Lyngby, Denmark
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Gupta P, Lee KH. Genomics and proteomics in process development: opportunities and challenges. Trends Biotechnol 2007; 25:324-30. [PMID: 17475353 DOI: 10.1016/j.tibtech.2007.04.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 03/19/2007] [Accepted: 04/19/2007] [Indexed: 02/05/2023]
Abstract
Global gene expression profiling by genomic and proteomic analyses has changed the face of drug discovery and biological research in the past few years. The benefit of these technologies in the area of process development for recombinant protein production has been increasingly realized. This review discusses the application of genome-wide expression profiling tools in the design and optimization of bioprocesses, with the emphasis on the effect on process development of mammalian cell culture. Despite the lack of genome sequence information for most of the relevant mammalian cell lines used, these technologies can be applied during various process development steps. Although there are only a few examples in the literature that present a major improvement in productivity based on genomics and proteomics, further advances in analytical tools and genome sequencing technologies will greatly increase our knowledge at the molecular level and will drive the design of future bioprocesses.
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Affiliation(s)
- Prateek Gupta
- School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY 14853, USA
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Wendisch VF, Bott M, Eikmanns BJ. Metabolic engineering of Escherichia coli and Corynebacterium glutamicum for biotechnological production of organic acids and amino acids. Curr Opin Microbiol 2006; 9:268-74. [PMID: 16617034 DOI: 10.1016/j.mib.2006.03.001] [Citation(s) in RCA: 216] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Accepted: 03/24/2006] [Indexed: 11/22/2022]
Abstract
Industrial microorganisms have been developed as biocatalysts to provide new or to optimize existing processes for the biotechnological production of chemicals from renewable plant biomass. Rational strain development by metabolic engineering is crucial to successful processes, and is based on efficient genetic tools and detailed knowledge of metabolic pathways and their regulation. This review summarizes recent advances in metabolic engineering of the industrial model bacteria Escherichia coli and Corynebacterium glutamicum that led to efficient recombinant biocatalysts for the production of acetate, pyruvate, ethanol, d- and l-lactate, succinate, l-lysine and l-serine.
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Affiliation(s)
- Volker F Wendisch
- Institute of Molecular Microbiology and Biotechnology, Westfalian Wilhelms University Münster, 48149 Münster, Germany.
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Lee SY, Lee DY, Kim TY. Systems biotechnology for strain improvement. Trends Biotechnol 2005; 23:349-58. [PMID: 15923052 DOI: 10.1016/j.tibtech.2005.05.003] [Citation(s) in RCA: 182] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2005] [Revised: 02/28/2005] [Accepted: 05/06/2005] [Indexed: 10/25/2022]
Abstract
Various high-throughput experimental techniques are routinely used for generating large amounts of omics data. In parallel, in silico modelling and simulation approaches are being developed for quantitatively analyzing cellular metabolism at the systems level. Thus informative high-throughput analysis and predictive computational modelling or simulation can be combined to generate new knowledge through iterative modification of an in silico model and experimental design. On the basis of such global cellular information we can design cells that have improved metabolic properties for industrial applications. This article highlights the recent developments in these systems approaches, which we call systems biotechnology, and discusses future prospects.
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Affiliation(s)
- Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory and Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea.
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Koffas M, Stephanopoulos G. Strain improvement by metabolic engineering: lysine production as a case study for systems biology. Curr Opin Biotechnol 2005; 16:361-6. [PMID: 15961038 DOI: 10.1016/j.copbio.2005.04.010] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Revised: 03/15/2005] [Accepted: 04/28/2005] [Indexed: 11/22/2022]
Abstract
A central goal of systems biology is the elucidation of cell function and physiology through the integrated use of broad based genomic and physiological data. Such systemic approaches have been employed extensively in the past, as they are a central element of metabolic flux analysis, the distribution of kinetic control in pathways, and the key differentiating characteristic of metabolic engineering. In one case study, these tools have been applied to the improvement of lysine-producing strains of Corynebacterium glutamicum. The systematic study of the physiology of this organism allowed the identification of specific metabolic targets and subsequently led to significant improvements in product yield and productivity. This case study can serve as a guide for the development of systems biology tools for the utilization of large volumes of cell- and genome-wide transcriptional and physiological data.
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Affiliation(s)
- Mattheos Koffas
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, 904 Furnas Hall, Buffalo, New York 14260, USA.
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15
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447519 DOI: 10.1002/cfg.420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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