51
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Sinumvayo JP, Zhao C, Tuyishime P. Recent advances and future trends of riboswitches: attractive regulatory tools. World J Microbiol Biotechnol 2018; 34:171. [PMID: 30413889 DOI: 10.1007/s11274-018-2554-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/02/2018] [Indexed: 01/06/2023]
Abstract
Bacterial genomes contain a huge amount of different genes. These genes are spatiotemporally expressed to accomplish some required functions within the organism. Inside the cell, any step of gene expression may be modulated at four possible places such as transcription initiation, translation regulation, mRNA stability and protein stability. To achieve this, there is a necessity of strong regulators either natural or synthetic which can fine-tune gene expression regarding the required function. In recent years, riboswitches as metabolite responsive control elements residing in the untranslated regions of certain messenger RNAs, have been known to control gene expression at transcription or translation level. Importantly, these control elements do not prescribe the involvement of protein factors for metabolite binding. However, they own their particular properties to sense intramolecular metabolites (ligands). Herein, we highlighted current important bacterial riboswitches, their applications to support genetic control, ligand-binding domain mechanisms and current progress in synthetic riboswitches.
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Affiliation(s)
- Jean Paul Sinumvayo
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Chunhua Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Philibert Tuyishime
- University of Chinese Academy of Sciences, Beijing, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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52
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Kim SK, Kim SH, Subhadra B, Woo SG, Rha E, Kim SW, Kim H, Lee DH, Lee SG. A Genetically Encoded Biosensor for Monitoring Isoprene Production in Engineered Escherichia coli. ACS Synth Biol 2018; 7:2379-2390. [PMID: 30261142 DOI: 10.1021/acssynbio.8b00164] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isoprene is a valuable precursor for synthetic rubber and a signature product of terpenoid pathways. Here, we developed an isoprene biosensor by employing a TbuT transcriptional regulator of Ralstonia pickettii to express a fluorescent reporter gene in response to intracellular isoprene in engineered Escherichia coli. The TbuT regulator recognizes isoprene as its less-preferred effector molecule; thus, we amplified the reporter gene expression using a T7 RNA polymerase-mediated transcriptional cascade and iteratively tuned the promoter transcribing tbuT to improve the sensitivity for detecting isoprene. When the engineered E. coli cells expressed heterologous genes for isoprene biosynthesis, the intracellular isoprene was expelled and the tbuT transcription factor was subsequently activated, leading to gfp expression. The chromosomal isoprene biosensor showed a linear correlation between GFP fluorescence and intracellular isoprene concentration. Using this chromosomal isoprene biosensor, we successfully identified the highest isoprene producer among four different E. coli strains producing different amounts of isoprene. The isoprene biosensor presented here can enable high-throughput screening of isoprene synthases and metabolic pathways for efficient and sustainable production of bioisoprene in engineered microbes.
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Affiliation(s)
- Seong Keun Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seo Hyun Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Bindu Subhadra
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seung-Gyun Woo
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Eugene Rha
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seon-Won Kim
- Division of Applied Life Science (BK21 Plus), PMBBRC, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Haseong Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
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53
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Trabelsi H, Koch M, Faulon J. Building a minimal and generalizable model of transcription factor-based biosensors: Showcasing flavonoids. Biotechnol Bioeng 2018; 115:2292-2304. [PMID: 29733444 PMCID: PMC6548992 DOI: 10.1002/bit.26726] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 04/20/2018] [Accepted: 04/30/2018] [Indexed: 01/05/2023]
Abstract
Progress in synthetic biology tools has transformed the way we engineer living cells. Applications of circuit design have reached a new level, offering solutions for metabolic engineering challenges that include developing screening approaches for libraries of pathway variants. The use of transcription-factor-based biosensors for screening has shown promising results, but the quantitative relationship between the sensors and the sensed molecules still needs more rational understanding. Herein, we have successfully developed a novel biosensor to detect pinocembrin based on a transcriptional regulator. The FdeR transcription factor (TF), known to respond to naringenin, was combined with a fluorescent reporter protein. By varying the copy number of its plasmid and the concentration of the biosensor TF through a combinatorial library, different responses have been recorded and modeled. The fitted model provides a tool to understand the impact of these parameters on the biosensor behavior in terms of dose-response and time curves and offers guidelines to build constructs oriented to increased sensitivity and or ability of linear detection at higher titers. Our model, the first to explicitly take into account the impact of plasmid copy number on biosensor sensitivity using Hill-based formalism, is able to explain uncharacterized systems without extensive knowledge of the properties of the TF. Moreover, it can be used to model the response of the biosensor to different compounds (here naringenin and pinocembrin) with minimal parameter refitting.
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Affiliation(s)
- Heykel Trabelsi
- Micalis Institute, INRA, AgroParisTechUniversity of Paris‐SaclayJouy‐en‐JosasFrance
- Systems and Synthetic Biology Lab, CEA, CNRS, UMR 8030, Genomics MetabolicsUniversity Paris‐SaclayÉvryFrance
| | - Mathilde Koch
- Micalis Institute, INRA, AgroParisTechUniversity of Paris‐SaclayJouy‐en‐JosasFrance
| | - Jean‐Loup Faulon
- Micalis Institute, INRA, AgroParisTechUniversity of Paris‐SaclayJouy‐en‐JosasFrance
- Systems and Synthetic Biology Lab, CEA, CNRS, UMR 8030, Genomics MetabolicsUniversity Paris‐SaclayÉvryFrance
- SYNBIOCHEM Center, School of Chemistry, Manchester Institute of BiotechnologyUniversity of ManchesterManchesterUK
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54
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Hammer SK, Avalos JL. Metabolic engineering: Biosensors get the green light. Nat Chem Biol 2018; 12:894-895. [PMID: 27755525 DOI: 10.1038/nchembio.2214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sarah K Hammer
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, the Andlinger Center for Energy and the Environment, and the Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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55
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Halbfeld C, Baumbach JI, Blank LM, Ebert BE. Multi-capillary Column Ion Mobility Spectrometry of Volatile Metabolites for Phenotyping of Microorganisms. Methods Mol Biol 2018; 1671:229-258. [PMID: 29170963 DOI: 10.1007/978-1-4939-7295-1_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Rational strain engineering requires solid testing of phenotypes including productivity and ideally contributes thereby directly to our understanding of the genotype-phenotype relationship. Actually, the test step of the strain engineering cycle becomes the limiting step, as ever advancing tools for generating genetic diversity exist. Here, we briefly define the challenge one faces in quantifying phenotypes and summarize existing analytical techniques that partially overcome this challenge. We argue that the evolution of volatile metabolites can be used as proxy for cellular metabolism. In the simplest case, the product of interest is a volatile (e.g., from bulk alcohols to special fragrances) that is directly quantified over time. But also nonvolatile products (e.g., from bulk long-chain fatty acids to natural products) require major flux rerouting that result potentially in altered volatile production. While alternative techniques for volatile determination exist, rather few can be envisaged for medium to high-throughput analysis required for phenotype testing. Here, we contribute a detailed protocol for an ion mobility spectrometry (IMS) analysis that allows volatile metabolite quantification down to the ppb range. The sensitivity can be exploited for small-scale fermentation monitoring. The insights shared might contribute to a more frequent use of IMS in biotechnology, while the experimental aspects are of general use for researchers interested in volatile monitoring.
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Affiliation(s)
- Christoph Halbfeld
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany
| | - Jörg Ingo Baumbach
- Faculty of Applied Chemistry, Reutlingen University, 72762, Reutlingen, Germany
| | - Lars M Blank
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany.
| | - Birgitta E Ebert
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany
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56
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De Paepe B, Maertens J, Vanholme B, De Mey M. Modularization and Response Curve Engineering of a Naringenin-Responsive Transcriptional Biosensor. ACS Synth Biol 2018; 7:1303-1314. [PMID: 29688705 DOI: 10.1021/acssynbio.7b00419] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
To monitor the intra- and extracellular environment of micro-organisms and to adapt their metabolic processes accordingly, scientists are reprogramming nature's myriad of transcriptional regulatory systems into transcriptional biosensors, which are able to detect small molecules and, in response, express specific output signals of choice. However, the naturally occurring response curve, the key characteristic of biosensor circuits, is typically not in line with the requirements for real-life biosensor applications. In this contribution, a natural LysR-type naringenin-responsive biosensor circuit is developed and characterized with Escherichia coli as host organism. Subsequently, this biosensor is dissected into a clearly defined detector and effector module without loss of functionality, and the influence of the expression levels of both modules on the biosensor response characteristics is investigated. Two collections of ten unique synthetic biosensors each are generated. Each collection demonstrates a unique diversity of response curve characteristics spanning a 128-fold change in dynamic and 2.5-fold change in operational ranges and 3-fold change in levels of Noise, fit for a wide range of applications, such as adaptive laboratory evolution, dynamic pathway control and high-throughput screening methods. The established biosensor engineering concepts, and the developed biosensor collections themselves, are of use for the future development and customization of biosensors in general, for the multitude of biosensor applications and as a compelling alternative for the commonly used LacI-, TetR- and AraC-based inducible circuits.
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Affiliation(s)
- Brecht De Paepe
- Centre for Synthetic Biology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Bartel Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, B-9052 Ghent, Belgium
- VIB Center for Plant
Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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57
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A semi-synthetic regulon enables rapid growth of yeast on xylose. Nat Commun 2018; 9:1233. [PMID: 29581426 PMCID: PMC5964326 DOI: 10.1038/s41467-018-03645-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 03/01/2018] [Indexed: 01/27/2023] Open
Abstract
Nutrient assimilation is the first step that allows biological systems to proliferate and produce value-added products. Yet, implementation of heterologous catabolic pathways has so far relied on constitutive gene expression without consideration for global regulatory systems that may enhance nutrient assimilation and cell growth. In contrast, natural systems prefer nutrient-responsive gene regulation (called regulons) that control multiple cellular functions necessary for cell survival and growth. Here, in Saccharomyces cerevisiae, by partially- and fully uncoupling galactose (GAL)-responsive regulation and metabolism, we demonstrate the significant growth benefits conferred by the GAL regulon. Next, by adapting the various aspects of the GAL regulon for a non-native nutrient, xylose, we build a semi-synthetic regulon that exhibits higher growth rate, better nutrient consumption, and improved growth fitness compared to the traditional and ubiquitous constitutive expression strategy. This work provides an elegant paradigm to integrate non-native nutrient catabolism with native, global cellular responses to support fast growth. Efficient assimilation of nutrients is essential for the production of value-added products in microbial fermentation. Here the authors design a semi-synthetic xylose regulon to improve growth characteristics of Saccharomyces cerevisiae on this non-native sugar.
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58
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Cheng F, Tang XL, Kardashliev T. Transcription Factor-Based Biosensors in High-Throughput Screening: Advances and Applications. Biotechnol J 2018; 13:e1700648. [DOI: 10.1002/biot.201700648] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/17/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology; Hangzhou 310014 P. R. China
| | - Xiao-Ling Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology; Hangzhou 310014 P. R. China
| | - Tsvetan Kardashliev
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich; Mattenstrasse 26 4058 Basel Switzerland
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59
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Strategies for microbial synthesis of high-value phytochemicals. Nat Chem 2018; 10:395-404. [DOI: 10.1038/s41557-018-0013-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/25/2018] [Indexed: 01/28/2023]
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Abstract
Current food production faces tremendous challenges from growing human population, maintaining clean resources and food qualities, and protecting climate and environment. Food sustainability is mostly a cooperative effort resulting in technology development supported by both governments and enterprises. Multiple attempts have been promoted in tackling challenges and enhancing drivers in food production. Biosensors and biosensing technologies with their applications, are being widely applied to tackling top challenges in food production and its sustainability. Consequently, a growing demand in biosensing technologies exists in food sustainability. Microfluidics represents a technological system integrating multiple technologies. Nanomaterials, with its technology in biosensing, is thought to be the most promising tool in dealing with health, energy, and environmental issues closely related to world populations. The demand of point of care (POC) technologies in this area focus on rapid, simple, accurate, portable, and low-cost analytical instruments. This review provides current viewpoints from the literature on biosensing in food production, food processing, safety and security, food packaging and supply chain, food waste processing, food quality assurance, and food engineering. The current understanding of progress, solution, and future challenges, as well as the commercialization of biosensors are summarized.
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61
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Chen X, Xia X, Lee SY, Qian Z. Engineering tunable biosensors for monitoring putrescine inEscherichia coli. Biotechnol Bioeng 2018; 115:1014-1027. [DOI: 10.1002/bit.26521] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/29/2017] [Accepted: 12/13/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Xue‐Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Xiao‐Xia Xia
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical & Biomolecular Engineering (BK21 Program)BioProcess Engineering Research Center, Bioinformatics Research Center, and Institute for the BioCentury, KAISTYuseong‐guDaejeonRepublic of Korea
| | - Zhi‐Gang Qian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
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62
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Park SY, Yang D, Ha SH, Lee SY. Metabolic Engineering of Microorganisms for the Production of Natural Compounds. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700190] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Seon Young Park
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Dongsoo Yang
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Shin Hee Ha
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
- BioProcess Engineering Research Center; KAIST; Daejeon 34141 Republic of Korea
- BioInformatics Research Center; KAIST; Daejeon 34141 Republic of Korea
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63
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Jang S, Jang S, Xiu Y, Kang TJ, Lee SH, Koffas MAG, Jung GY. Development of Artificial Riboswitches for Monitoring of Naringenin In Vivo. ACS Synth Biol 2017; 6:2077-2085. [PMID: 28749656 DOI: 10.1021/acssynbio.7b00128] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Microbial strains are considered promising hosts for production of flavonoids because of their rapid growth rate and suitability for large-scale manufacturing. However, productivity and titer of current recombinant strains still do not meet the requirements of industrial processes. Genetically encoded biosensors have been applied for high-throughput screening or dynamic regulation of biosynthetic pathways for enhancing the performance of microbial strains that produce valuable chemicals. Currently, few protein sensor-regulators for flavonoids exist. Unlike the protein-based trans-regulating controllers, riboswitches can respond to their ligands faster and eliminate off-target effects. Here, we developed artificial riboswitches that activate gene expression in response to naringenin, an important flavonoid. RNA aptamers for naringenin were developed using SELEX and cloned upstream of a dual selectable marker gene to construct a riboswitch library. Two in vivo selection routes were applied separately to the library by supplementing naringenin at two different concentrations during enrichments to modulate the operational ranges of the riboswitches. The selected riboswitches were responsive to naringenin and activated gene expression up to 2.91-fold. Operational ranges of the riboswitches were distinguished on the basis of their selection route. Additionally, the specificity of the riboswitches was assessed, and their applicability as dynamic regulators was confirmed. Collectively, the naringenin riboswitches reported in this work will be valuable tools in metabolic engineering of microorganisms for the production of flavonoids.
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Affiliation(s)
- Sungho Jang
- Department
of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
| | - Sungyeon Jang
- Department
of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
| | - Yu Xiu
- Department
of Chemical and Biological Engineering, Center for Biotechnology and
Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Key Laboratory of Bioactive Substances and Functional Food, Beijing Union University, Beijing 100191, China
| | - Taek Jin Kang
- Department
of Chemical and Biochemical Engineering, Dongguk University, 30 Pildong-ro 1-gil, Jung-gu, Seoul, 04620, Korea
| | - Sang-Hyeup Lee
- Department
of Life Chemistry, Catholic University of Daegu, Hayang-ro 13-13,
Hayang-eup, Gyeongsan, Gyeongbuk 38430, Korea
| | - Mattheos A. G. Koffas
- Department
of Chemical and Biological Engineering, Center for Biotechnology and
Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Department
of Biological Sciences, Center for Biotechnology and Interdisciplinary
Studies, Rensselaer Polytechnic Institutee, Troy, New York 12180, United States
| | - Gyoo Yeol Jung
- Department
of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
- School
of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
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64
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Siedler S, Khatri NK, Zsohár A, Kjærbølling I, Vogt M, Hammar P, Nielsen CF, Marienhagen J, Sommer MOA, Joensson HN. Development of a Bacterial Biosensor for Rapid Screening of Yeast p-Coumaric Acid Production. ACS Synth Biol 2017; 6:1860-1869. [PMID: 28532147 DOI: 10.1021/acssynbio.7b00009] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Transcription factor-based biosensors are used to identify producer strains, a critical bottleneck in cell factory engineering. Here, we address two challenges with this methodology: transplantation of heterologous transcriptional regulators into new hosts to generate functional biosensors and biosensing of the extracellular product concentration that accurately reflects the effective cell factory production capacity. We describe the effects of different translation initiation rates on the dynamic range of a p-coumaric acid biosensor based on the Bacillus subtilis transcriptional repressor PadR by varying its ribosomal binding site. Furthermore, we demonstrate the functionality of this p-coumaric acid biosensor in Escherichia coli and Corynebacterium glutamicum. Finally, we encapsulate yeast p-coumaric acid-producing cells with E. coli-biosensing cells in picoliter droplets and, in a microfluidic device, rapidly sort droplets containing yeast cells producing high amounts of extracellular p-coumaric acid using the fluorescent E. coli biosensor signal. As additional biosensors become available, such approaches will find broad applications for screening of an extracellular product.
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Affiliation(s)
- Solvej Siedler
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, 2970, Denmark
| | - Narendar K. Khatri
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, 2970, Denmark
- Division
of Proteomics and Nanobiotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, 114 28, Sweden
| | - Andrea Zsohár
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, 2970, Denmark
| | - Inge Kjærbølling
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, 2970, Denmark
| | - Michael Vogt
- Institute
of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Petter Hammar
- Division
of Proteomics and Nanobiotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, 114 28, Sweden
| | - Christian F. Nielsen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, 2970, Denmark
| | - Jan Marienhagen
- Institute
of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Morten O. A. Sommer
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, 2970, Denmark
| | - Haakan N. Joensson
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, 2970, Denmark
- Division
of Proteomics and Nanobiotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, 114 28, Sweden
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65
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Demirbas A, Groszman K, Pazmiño‐Hernandez M, Vanegas DC, Welt B, Hondred JA, Garland NT, Claussen JC, McLamore ES. Cryoconcentration of flavonoid extract for enhanced biophotovoltaics and pH sensitive thin films. Biotechnol Prog 2017; 34:206-217. [DOI: 10.1002/btpr.2557] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 08/10/2017] [Indexed: 01/10/2023]
Affiliation(s)
- A. Demirbas
- Agricultural and Biological EngineeringInstitute of Food and Agricultural Sciences, University of FloridaGainesville FL
| | - K. Groszman
- Department of Computational and Applied MathematicsRice UniversityHouston TX
| | - M. Pazmiño‐Hernandez
- Agricultural and Biological EngineeringInstitute of Food and Agricultural Sciences, University of FloridaGainesville FL
| | - D. C. Vanegas
- Food Engineering DepartmentUniversidad del ValleCali Colombia
| | - B. Welt
- Agricultural and Biological EngineeringInstitute of Food and Agricultural Sciences, University of FloridaGainesville FL
| | - J. A. Hondred
- Mechanical Engineering DepartmentIowa State UniversityIowa City IA
| | - N. T. Garland
- Mechanical Engineering DepartmentIowa State UniversityIowa City IA
| | - J. C. Claussen
- Mechanical Engineering DepartmentIowa State UniversityIowa City IA
| | - E. S. McLamore
- Agricultural and Biological EngineeringInstitute of Food and Agricultural Sciences, University of FloridaGainesville FL
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66
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Moses T, Mehrshahi P, Smith AG, Goossens A. Synthetic biology approaches for the production of plant metabolites in unicellular organisms. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4057-4074. [PMID: 28449101 DOI: 10.1093/jxb/erx119] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Synthetic biology is the repurposing of biological systems for novel objectives and applications. Through the co-ordinated and balanced expression of genes, both native and those introduced from other organisms, resources within an industrial chassis can be siphoned for the commercial production of high-value commodities. This developing interdisciplinary field has the potential to revolutionize natural product discovery from higher plants, by providing a diverse array of tools, technologies, and strategies for exploring the large chemically complex space of plant natural products using unicellular organisms. In this review, we emphasize the key features that influence the generation of biorefineries and highlight technologies and strategic solutions that can be used to overcome engineering pitfalls with rational design. Also presented is a succinct guide to assist the selection of unicellular chassis most suited for the engineering and subsequent production of the desired natural product, in order to meet the global demand for plant natural products in a safe and sustainable manner.
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Affiliation(s)
- Tessa Moses
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Payam Mehrshahi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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67
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Lehning CE, Siedler S, Ellabaan MMH, Sommer MOA. Assessing glycolytic flux alterations resulting from genetic perturbations in E. coli using a biosensor. Metab Eng 2017; 42:194-202. [PMID: 28709932 PMCID: PMC5555440 DOI: 10.1016/j.ymben.2017.07.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/11/2017] [Indexed: 11/19/2022]
Abstract
We describe the development of an optimized glycolytic flux biosensor and its application in detecting altered flux in a production strain and in a mutant library. The glycolytic flux biosensor is based on the Cra-regulated ppsA promoter of E. coli controlling fluorescent protein synthesis. We validated the glycolytic flux dependency of the biosensor in a range of different carbon sources in six different E. coli strains and during mevalonate production. Furthermore, we studied the flux-altering effects of genome-wide single gene knock-outs in E. coli in a multiplex FlowSeq experiment. From a library consisting of 2126 knock-out mutants, we identified 3 mutants with high-flux and 95 mutants with low-flux phenotypes that did not have severe growth defects. This approach can improve our understanding of glycolytic flux regulation improving metabolic models and engineering efforts.
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Affiliation(s)
- Christina E Lehning
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800 Lyngby, Denmark
| | - Solvej Siedler
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800 Lyngby, Denmark
| | - Mostafa M H Ellabaan
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800 Lyngby, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800 Lyngby, Denmark.
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68
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Xiu Y, Jang S, Jones JA, Zill NA, Linhardt RJ, Yuan Q, Jung GY, Koffas MAG. Naringenin-responsive riboswitch-based fluorescent biosensor module for Escherichia coli co-cultures. Biotechnol Bioeng 2017; 114:2235-2244. [PMID: 28543037 DOI: 10.1002/bit.26340] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/11/2017] [Accepted: 05/16/2017] [Indexed: 12/29/2022]
Abstract
The ability to design and construct combinatorial synthetic metabolic pathways has far exceeded our capacity for efficient screening and selection of the resulting microbial strains. The need for high-throughput rapid screening techniques is of upmost importance for the future of synthetic biology and metabolic engineering. Here we describe the development of an RNA riboswitch-based biosensor module with dual fluorescent reporters, and demonstrate a high-throughput flow cytometry-based screening method for identification of naringenin over producing Escherichia coli strains in co-culture. Our efforts helped identify a number of key operating parameters that affect biosensor performance, including the selection of promoter and linker elements within the sensor-actuator domain, and the effect of host strain, fermentation time, and growth medium on sensor dynamic range. The resulting biosensor demonstrates a high correlation between specific fluorescence of the biosensor strain and naringenin titer produced by the second member of the synthetic co-culture system. This technique represents a novel application for synthetic microbial co-cultures and can be expanded from naringenin to any metabolite if a suitable riboswitch is identified. The co-culture technique presented here can be applied to a variety of target metabolites in combination with the SELEX approach for aptamer design. Due to the compartmentalization of the two genetic constructs responsible for production and detection into separate cells and application as independent modules of a synthetic microbial co-culture we have subsequently reduced the need for re-optimization of the producer module when the biosensor is replaced or removed. Biotechnol. Bioeng. 2017;114: 2235-2244. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Yu Xiu
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, China.,Beijing Key Laboratory of Bioactive Substances and Functional Food, Beijing Union University, Beijing, China.,Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Sungho Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - J Andrew Jones
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York.,Department of Chemistry, Hamilton College, Clinton, New York
| | - Nicholas A Zill
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Robert J Linhardt
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Mattheos A G Koffas
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
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69
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van Rossum T, Muras A, Baur MJ, Creutzburg SC, van der Oost J, Kengen SW. A growth- and bioluminescence-based bioreporter for the in vivo detection of novel biocatalysts. Microb Biotechnol 2017; 10:625-641. [PMID: 28393499 PMCID: PMC5404197 DOI: 10.1111/1751-7915.12612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/10/2017] [Accepted: 01/13/2017] [Indexed: 11/28/2022] Open
Abstract
The use of bioreporters in high-throughput screening for small molecules is generally laborious and/or expensive. The technology can be simplified by coupling the generation of a desired compound to cell survival, causing only positive cells to stay in the pool of generated variants. Here, a dual selection/screening system was developed for the in vivo detection of novel biocatalysts. The sensor part of the system is based on the transcriptional regulator AraC, which controls expression of both a selection reporter (LeuB or KmR; enabling growth) for rapid reduction of the initially large library size and a screening reporter (LuxCDABE; causing bioluminescence) for further quantification of the positive variants. Of four developed systems, the best system was the medium copy system with KmR as selection reporter. As a proof of principle, the system was tested for the selection of cells expressing an l-arabinose isomerase derived from mesophilic Escherichia coli or thermophilic Geobacillus thermodenitrificans. A more than a millionfold enrichment of cells with l-arabinose isomerase activity was demonstrated by selection and exclusion of false positives by screening. This dual selection/screening system is an important step towards an improved detection method for small molecules, and thereby for finding novel biocatalysts.
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Affiliation(s)
- Teunke van Rossum
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Aleksandra Muras
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Marco J.J. Baur
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Sjoerd C.A. Creutzburg
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - John van der Oost
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Servé W.M. Kengen
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
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70
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Genetic biosensors for small-molecule products: Design and applications in high-throughput screening. Front Chem Sci Eng 2017. [DOI: 10.1007/s11705-017-1629-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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71
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Xiong D, Lu S, Wu J, Liang C, Wang W, Wang W, Jin JM, Tang SY. Improving key enzyme activity in phenylpropanoid pathway with a designed biosensor. Metab Eng 2017; 40:115-123. [DOI: 10.1016/j.ymben.2017.01.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/09/2016] [Accepted: 01/18/2017] [Indexed: 01/02/2023]
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72
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Wassem R, Marin AM, Daddaoua A, Monteiro RA, Chubatsu LS, Ramos J, Deakin WJ, Broughton WJ, Pedrosa FO, Souza EM. A NodD-like protein activates transcription of genes involved with naringenin degradation in a flavonoid-dependent manner inHerbaspirillum seropedicae. Environ Microbiol 2017; 19:1030-1040. [DOI: 10.1111/1462-2920.13604] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/16/2016] [Indexed: 11/29/2022]
Affiliation(s)
- R. Wassem
- Departamento de Genética; Universidade Federal do Paraná; Curitiba PR Brazil
| | - A. M. Marin
- Departamento de Bioquímica; Universidade Federal do Paraná; Curitiba PR Brazil
| | - A. Daddaoua
- Department of Environmental Protection; Estación Experimental del Zaídin CSIC; Granada Spain
| | - R. A. Monteiro
- Departamento de Bioquímica; Universidade Federal do Paraná; Curitiba PR Brazil
| | - L. S. Chubatsu
- Departamento de Bioquímica; Universidade Federal do Paraná; Curitiba PR Brazil
| | - J.L. Ramos
- Department of Environmental Protection; Estación Experimental del Zaídin CSIC; Granada Spain
| | - W. J. Deakin
- Laboratoire de Biologie Moléculaire des Plantes Supérieures (LBMPS), Département de Biologie végétale; Sciences III, 30 Quai Ernest-Ansermet, Université de Genève; Genève 4 CH-1211 Switzerland
| | - W. J. Broughton
- Laboratoire de Biologie Moléculaire des Plantes Supérieures (LBMPS), Département de Biologie végétale; Sciences III, 30 Quai Ernest-Ansermet, Université de Genève; Genève 4 CH-1211 Switzerland
| | - F. O. Pedrosa
- Departamento de Bioquímica; Universidade Federal do Paraná; Curitiba PR Brazil
| | - E. M. Souza
- Departamento de Bioquímica; Universidade Federal do Paraná; Curitiba PR Brazil
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73
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Min BE, Hwang HG, Lim HG, Jung GY. Optimization of industrial microorganisms: recent advances in synthetic dynamic regulators. ACTA ACUST UNITED AC 2017; 44:89-98. [DOI: 10.1007/s10295-016-1867-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/04/2016] [Indexed: 12/27/2022]
Abstract
Abstract
Production of biochemicals by industrial fermentation using microorganisms requires maintaining cellular production capacity, because maximal productivity is economically important. High-productivity microbial strains can be developed using static engineering, but these may not maintain maximal productivity throughout the culture period as culture conditions and cell states change dynamically. Additionally, economic reasons limit heterologous protein expression using inducible promoters to prevent metabolic burden for commodity chemical and biofuel production. Recently, synthetic and systems biology has been used to design genetic circuits, precisely controlling gene expression or influencing genetic behavior toward a desired phenotype. Development of dynamic regulators can maintain cellular phenotype in a maximum production state in response to factors including cell concentration, oxygen, temperature, pH, and metabolites. Herein, we introduce dynamic regulators of industrial microorganism optimization and discuss metabolic flux fine control by dynamic regulators in response to metabolites or extracellular stimuli, robust production systems, and auto-induction systems using quorum sensing.
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Affiliation(s)
- Byung Eun Min
- grid.49100.3c 0000000107424007 Department of Chemical Engineering Pohang University of Science and Technology 77 Cheongam-ro, Nam-gu 37673 Pohang Gyeongbuk Korea
| | - Hyun Gyu Hwang
- grid.49100.3c 0000000107424007 School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology 77 Cheongam-ro, Nam-gu 37673 Pohang Gyeongbuk Korea
| | - Hyun Gyu Lim
- grid.49100.3c 0000000107424007 Department of Chemical Engineering Pohang University of Science and Technology 77 Cheongam-ro, Nam-gu 37673 Pohang Gyeongbuk Korea
| | - Gyoo Yeol Jung
- grid.49100.3c 0000000107424007 Department of Chemical Engineering Pohang University of Science and Technology 77 Cheongam-ro, Nam-gu 37673 Pohang Gyeongbuk Korea
- grid.49100.3c 0000000107424007 School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology 77 Cheongam-ro, Nam-gu 37673 Pohang Gyeongbuk Korea
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74
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75
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Qian S, Cirino PC. Using metabolite-responsive gene regulators to improve microbial biosynthesis. Curr Opin Chem Eng 2016. [DOI: 10.1016/j.coche.2016.08.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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76
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Skjoedt ML, Snoek T, Kildegaard KR, Arsovska D, Eichenberger M, Goedecke TJ, Rajkumar AS, Zhang J, Kristensen M, Lehka BJ, Siedler S, Borodina I, Jensen MK, Keasling JD. Engineering prokaryotic transcriptional activators as metabolite biosensors in yeast. Nat Chem Biol 2016; 12:951-958. [DOI: 10.1038/nchembio.2177] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 06/30/2016] [Indexed: 01/30/2023]
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77
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Pandey RP, Parajuli P, Koffas MA, Sohng JK. Microbial production of natural and non-natural flavonoids: Pathway engineering, directed evolution and systems/synthetic biology. Biotechnol Adv 2016; 34:634-662. [DOI: 10.1016/j.biotechadv.2016.02.012] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 02/24/2016] [Accepted: 02/29/2016] [Indexed: 12/18/2022]
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78
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Libis V, Delépine B, Faulon JL. Sensing new chemicals with bacterial transcription factors. Curr Opin Microbiol 2016; 33:105-112. [PMID: 27472026 DOI: 10.1016/j.mib.2016.07.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/15/2016] [Accepted: 07/06/2016] [Indexed: 11/30/2022]
Abstract
Bacteria rely on allosteric transcription factors (aTFs) to sense a wide range of chemicals. The variety of effectors has contributed in making aTFs the most used input system in synthetic biological circuits. Considering their enabling role in biotechnology, an important question concerns the size of the chemical space that can potentially be detected by these biosensors. From digging into the ever changing repertoire of natural regulatory circuits, to advances in aTF engineering, we review here different strategies that are pushing the boundaries of this chemical space. We also review natural and synthetic cases of indirect sensing, where aTFs work in combination with metabolism to enable detection of new molecules.
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Affiliation(s)
- Vincent Libis
- iSSB, Genopole, CNRS, UEVE, Université Paris Saclay, 91000 Évry, France; Micalis Institute, INRA, AgroParisTech, Université Paris Saclay, 78350 Jouy-en-Josas, France
| | - Baudoin Delépine
- iSSB, Genopole, CNRS, UEVE, Université Paris Saclay, 91000 Évry, France; Micalis Institute, INRA, AgroParisTech, Université Paris Saclay, 78350 Jouy-en-Josas, France
| | - Jean-Loup Faulon
- iSSB, Genopole, CNRS, UEVE, Université Paris Saclay, 91000 Évry, France; Micalis Institute, INRA, AgroParisTech, Université Paris Saclay, 78350 Jouy-en-Josas, France; SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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79
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Wang Z, Cirino PC. New and improved tools and methods for enhanced biosynthesis of natural products in microorganisms. Curr Opin Biotechnol 2016; 42:159-168. [PMID: 27284635 DOI: 10.1016/j.copbio.2016.05.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 12/28/2022]
Abstract
Engineering efficient biosynthesis of natural products in microorganisms requires optimizing gene expression levels to balance metabolite flux distributions and to minimize accumulation of toxic intermediates. Such metabolic optimization is challenged with identifying the right gene targets, and then determining and achieving appropriate gene expression levels. After decades of having a relatively limited set of gene regulation tools available, metabolic engineers are recently enjoying an ever-growing repertoire of more precise and tunable gene expression platforms. Here we review recent applications of natural and designed transcriptional and translational regulatory machinery for engineering biosynthesis of natural products in microorganisms. Customized trans-acting RNAs (sgRNA, asRNA and sRNA), along with appropriate accessory proteins, are allowing for unparalleled tuning of gene expression. Meanwhile metabolite-responsive transcription factors and riboswitches have been implemented in strain screening and evolution, and in dynamic gene regulation. Further refinements and expansions on these platform technologies will circumvent many long-term obstacles in natural products biosynthesis.
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Affiliation(s)
- Zhiqing Wang
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Patrick C Cirino
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA.
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80
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Mahr R, von Boeselager RF, Wiechert J, Frunzke J. Screening of an Escherichia coli promoter library for a phenylalanine biosensor. Appl Microbiol Biotechnol 2016; 100:6739-6753. [PMID: 27170323 DOI: 10.1007/s00253-016-7575-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/14/2016] [Accepted: 04/21/2016] [Indexed: 02/06/2023]
Abstract
In recent years, the application of transcription factor-based biosensors for the engineering of microbial production strains opened up new opportunities for industrial biotechnology. However, the design of synthetic regulatory circuits depends on the selection of suitable transcription factor-promoter pairs to convert the concentration of effector molecules into a measureable output. Here, we present an efficient strategy to screen promoter libraries for appropriate parts for biosensor design. To this end, we pooled the strains of the Alon library containing about 2000 different Escherichia coli promoter-gfpmut2 fusions, and enriched galactose- and L-phenylalanine-responsive promoters by toggled rounds of positive and negative selection using fluorescence-activated cell sorting (FACS). For both effectors, responsive promoters were isolated and verified by cultivation in microtiter plates. The promoter of mtr, encoding an L-tryptophan-specific transporter, was identified as suitable part for the construction of an L-phenylalanine biosensor. In the following, we performed a comparative analysis of different biosensor constructs based on the mtr promoter. The obtained data revealed a strong influence of the biosensor architecture on the performance characteristics. For proof-of-principle, the mtr sensor was applied in a FACS high-throughput screening of an E. coli MG1655 mutant library for the isolation of L-phenylalanine producers. These results emphasize the developed screening approach as a convenient strategy for the identification of effector-responsive promoters for the design of novel biosensors.
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Affiliation(s)
- Regina Mahr
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | | | - Johanna Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany.
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81
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Synthetic Evolution of Metabolic Productivity Using Biosensors. Trends Biotechnol 2016; 34:371-381. [DOI: 10.1016/j.tibtech.2016.02.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 02/01/2016] [Accepted: 02/01/2016] [Indexed: 11/23/2022]
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82
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Jones JA, Koffas MAG. Optimizing Metabolic Pathways for the Improved Production of Natural Products. Methods Enzymol 2016; 575:179-93. [PMID: 27417929 DOI: 10.1016/bs.mie.2016.02.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metabolic engineering strives to develop microbial strains that are capable of high-titer production of a variety of industrially significant pharmaceuticals, nutraceuticals, commodity, and high-value compounds. Despite extensive success with many proof-of-concept systems there is still the need for optimization to achieve industrially relevant titers, yields, and productivities. The field of metabolic pathway optimization and balancing has formed to address this need using a scientific and systematic approach. In this chapter, we aim to outline various pathway optimization and system balancing strategies while giving insights and tips into the systems and procedures that have demonstrated recent success in the peer-reviewed literature.
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Affiliation(s)
- J A Jones
- Rensselaer Polytechnic Institute, Troy, NY, United States; Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - M A G Koffas
- Rensselaer Polytechnic Institute, Troy, NY, United States; Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States.
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83
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Intermediate-sensor assisted push–pull strategy and its application in heterologous deoxyviolacein production in Escherichia coli. Metab Eng 2016; 33:41-51. [DOI: 10.1016/j.ymben.2015.10.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 09/22/2015] [Accepted: 10/15/2015] [Indexed: 01/29/2023]
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84
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Ma CW, Zhou LB, Zeng AP. Engineering Biomolecular Switches for Dynamic Metabolic Control. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:45-76. [DOI: 10.1007/10_2016_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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85
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Li S, Si T, Wang M, Zhao H. Development of a Synthetic Malonyl-CoA Sensor in Saccharomyces cerevisiae for Intracellular Metabolite Monitoring and Genetic Screening. ACS Synth Biol 2015; 4:1308-15. [PMID: 26149896 DOI: 10.1021/acssynbio.5b00069] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Genetic sensors capable of converting key metabolite levels to fluorescence signals enable the monitoring of intracellular compound concentrations in living cells, and emerge as an efficient tool in high-throughput genetic screening. However, the development of genetic sensors in yeasts lags far behind their development in bacteria. Here we report the design of a malonyl-CoA sensor in Saccharomyces cerevisiae using an adapted bacterial transcription factor FapR and its corresponding operator fapO to gauge intracellular malonyl-CoA levels. By combining this sensor with a genome-wide overexpression library, we identified two novel gene targets that improved intracellular malonyl-CoA concentration. We further utilized the resulting recombinant yeast strain to produce a valuable compound, 3-hydroxypropionic acid, from malonyl-CoA and enhanced its titer by 120%. Such a genetic sensor provides a powerful approach for genome-wide screening and could further improve the synthesis of a large range of chemicals derived from malonyl-CoA in yeast.
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Affiliation(s)
- Sijin Li
- Energy Biosciences Institute, ‡Institute for Genomic Biology, §Department of Chemical
and Biomolecular Engineering, and ∥Departments of Chemistry, Biochemistry, and
Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Tong Si
- Energy Biosciences Institute, ‡Institute for Genomic Biology, §Department of Chemical
and Biomolecular Engineering, and ∥Departments of Chemistry, Biochemistry, and
Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Meng Wang
- Energy Biosciences Institute, ‡Institute for Genomic Biology, §Department of Chemical
and Biomolecular Engineering, and ∥Departments of Chemistry, Biochemistry, and
Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Energy Biosciences Institute, ‡Institute for Genomic Biology, §Department of Chemical
and Biomolecular Engineering, and ∥Departments of Chemistry, Biochemistry, and
Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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86
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Mahr R, Gätgens C, Gätgens J, Polen T, Kalinowski J, Frunzke J. Biosensor-driven adaptive laboratory evolution of l-valine production in Corynebacterium glutamicum. Metab Eng 2015; 32:184-194. [DOI: 10.1016/j.ymben.2015.09.017] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/01/2015] [Accepted: 09/21/2015] [Indexed: 11/25/2022]
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87
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Mahr R, Frunzke J. Transcription factor-based biosensors in biotechnology: current state and future prospects. Appl Microbiol Biotechnol 2015; 100:79-90. [PMID: 26521244 PMCID: PMC4700088 DOI: 10.1007/s00253-015-7090-3] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 01/01/2023]
Abstract
Living organisms have evolved a plethora of sensing systems for the intra- and extracellular detection of small molecules, ions or physical parameters. Several recent studies have demonstrated that these principles can be exploited to devise synthetic regulatory circuits for metabolic engineering strategies. In this context, transcription factors (TFs) controlling microbial physiology at the level of transcription play a major role in biosensor design, since they can be implemented in synthetic circuits controlling gene expression in dependency of, for example, small molecule production. Here, we review recent progress on the utilization of TF-based biosensors in microbial biotechnology highlighting different areas of application. Recent advances in metabolic engineering reveal TF-based sensors to be versatile tools for strain and enzyme development using high-throughput (HT) screening strategies and adaptive laboratory evolution, the optimization of heterologous pathways via the implementation of dynamic control circuits and for the monitoring of single-cell productivity in live cell imaging studies. These examples underline the immense potential of TF-based biosensor circuits but also identify limitations and room for further optimization.
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Affiliation(s)
- Regina Mahr
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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88
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Bott M. Need for speed - finding productive mutations using transcription factor-based biosensors, fluorescence-activated cell sorting and recombineering. Microb Biotechnol 2015; 8:8-10. [PMID: 25627839 PMCID: PMC4321356 DOI: 10.1111/1751-7915.12248] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, D-52428, Germany
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89
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Assembly of a novel biosynthetic pathway for production of the plant flavonoid fisetin in Escherichia coli. Metab Eng 2015; 31:84-93. [PMID: 26192693 DOI: 10.1016/j.ymben.2015.07.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/29/2015] [Accepted: 07/09/2015] [Indexed: 01/13/2023]
Abstract
Plant secondary metabolites are an underutilized pool of bioactive molecules for applications in the food, pharma and nutritional industries. One such molecule is fisetin, which is present in many fruits and vegetables and has several potential health benefits, including anti-cancer, anti-viral and anti-aging activity. Moreover, fisetin has recently been shown to prevent Alzheimer's disease in mice and to prevent complications associated with diabetes type I. Thus far the biosynthetic pathway of fisetin in plants remains elusive. Here, we present the heterologous assembly of a novel fisetin pathway in Escherichia coli. We propose a novel biosynthetic pathway from the amino acid, tyrosine, utilizing nine heterologous enzymes. The pathway proceeds via the synthesis of two flavanones never produced in microorganisms before--garbanzol and resokaempferol. We show for the first time a functional biosynthetic pathway and establish E. coli as a microbial platform strain for the production of fisetin and related flavonols.
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90
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Hirooka K. Transcriptional response machineries of Bacillus subtilis conducive to plant growth promotion. Biosci Biotechnol Biochem 2015; 78:1471-84. [PMID: 25209494 DOI: 10.1080/09168451.2014.943689] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Bacillus subtilis collectively inhabits the rhizosphere, where it contributes to the promotion of plant growth, although it does not have a direct symbiotic relationship to plants as observed in the case of rhizobia between leguminous plants. As rhizobia sense the flavonoids released from their host roots through the NodD transcriptional factor, which triggers transcription of the nod genes involved in the symbiotic processes, we supposed that B. subtilis utilizes certain flavonoids as signaling molecules to perceive and adapt to the rhizospheric environment that it is in. Our approaches to identify the flavonoid-responsive transcriptional regulatory system from B. subtilis resulted in the findings that three transcriptional factors (LmrA/QdoR, YetL, and Fur) are responsive to flavonoids, with the modes of action being different from each other. We also revealed a unique regulatory system by two transcriptional factors, YcnK and CsoR, for copper homeostasis in B. subtilis. In this review, we summarize the molecular mechanisms of these regulatory systems with the relevant information and discuss their physiological significances in the mutually beneficial interaction between B. subtilis and plants, considering the possibility of their application for plant cultivation.
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Affiliation(s)
- Kazutake Hirooka
- a Department of Biotechnology, Faculty of Life Science and Biotechnology , Fukuyama University , Fukuyama , Hiroshima , Japan
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91
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Fehér T, Libis V, Carbonell P, Faulon JL. A Sense of Balance: Experimental Investigation and Modeling of a Malonyl-CoA Sensor in Escherichia coli. Front Bioeng Biotechnol 2015; 3:46. [PMID: 25905101 PMCID: PMC4389729 DOI: 10.3389/fbioe.2015.00046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 03/23/2015] [Indexed: 01/26/2023] Open
Abstract
Production of value-added chemicals in microorganisms is regarded as a viable alternative to chemical synthesis. In the past decade, several engineered pathways producing such chemicals, including plant secondary metabolites in microorganisms have been reported; upscaling their production yields, however, was often challenging. Here, we analyze a modular device designed for sensing malonyl-CoA, a common precursor for both fatty acid and flavonoid biosynthesis. The sensor can be used either for high-throughput pathway screening in synthetic biology applications or for introducing a feedback circuit to regulate production of the desired chemical. Here, we used the sensor to compare the performance of several predicted malonyl-CoA-producing pathways, and validated the utility of malonyl-CoA reductase and malonate-CoA transferase for malonyl-CoA biosynthesis. We generated a second-order dynamic linear model describing the relation of the fluorescence generated by the sensor to the biomass of the host cell representing a filter/amplifier with a gain that correlates with the level of induction. We found the time constants describing filter dynamics to be independent of the level of induction but distinctively clustered for each of the production pathways, indicating the robustness of the sensor. Moreover, by monitoring the effect of the copy-number of the production plasmid on the dose–response curve of the sensor, we managed to coarse-tune the level of pathway expression to maximize malonyl-CoA synthesis. In addition, we provide an example of the sensor’s use in analyzing the effect of inducer or substrate concentrations on production levels. The rational development of models describing sensors, supplemented with the power of high-throughput optimization provide a promising potential for engineering feedback loops regulating enzyme levels to maximize productivity yields of synthetic metabolic pathways.
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Affiliation(s)
- Tamás Fehér
- Institute of Systems and Synthetic Biology, University of Evry Val d'Essonne , Evry , France ; Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences , Szeged , Hungary
| | - Vincent Libis
- Institute of Systems and Synthetic Biology, University of Evry Val d'Essonne , Evry , France ; Paris Diderot University , Paris , France
| | - Pablo Carbonell
- Institute of Systems and Synthetic Biology, University of Evry Val d'Essonne , Evry , France ; Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra , Barcelona , Spain ; SYNBIOCHEM Center, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester , Manchester , UK
| | - Jean-Loup Faulon
- Institute of Systems and Synthetic Biology, University of Evry Val d'Essonne , Evry , France ; SYNBIOCHEM Center, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester , Manchester , UK
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92
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Liu W, Jiang R. Combinatorial and high-throughput screening approaches for strain engineering. Appl Microbiol Biotechnol 2015; 99:2093-104. [DOI: 10.1007/s00253-015-6400-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/09/2015] [Accepted: 01/10/2015] [Indexed: 12/31/2022]
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93
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Novel screening methods--biosensors. Curr Opin Biotechnol 2015; 35:30-6. [PMID: 25578902 DOI: 10.1016/j.copbio.2014.12.021] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 02/06/2023]
Abstract
Biosensors offer exciting possibilities for improving cells or enzymes as biocatalysts for the synthesis of small molecules. We here review recent progress in the development and the screening applications of transcription-factor-based biosensors. An example is a cofactor-dependent biosensor which provides a generalizable screen for NADPH-dependent enzymes. Another example is the use of a biosensor in combination with recombineering for strain development, thereby expanding the genome engineering techniques to deliver directly bacteria producing small molecules of interest. Biosensor-based techniques in combination with fluorescence-activated cell sorting demonstrate that the gap regarding throughput capabilities of existing methods for the generation of genetic diversity and methods for the subsequent screening can be closed.
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