1
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Tian X, Volkovinskiy A, Marchisio MA. RNAi-based Boolean gates in the yeast Saccharomyces cerevisiae. Front Bioeng Biotechnol 2024; 12:1392967. [PMID: 38895554 PMCID: PMC11184144 DOI: 10.3389/fbioe.2024.1392967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/06/2024] [Indexed: 06/21/2024] Open
Abstract
Boolean gates, the fundamental components of digital circuits, have been widely investigated in synthetic biology because they permit the fabrication of biosensors and facilitate biocomputing. This study was conducted to design and construct Boolean gates in the yeast Saccharomyces cerevisiae, the main component of which was the RNA interference pathway (RNAi) that is naturally absent from the budding yeast cells. We tested different expression cassettes for the siRNA precursor (a giant hairpin sequence, a DNA fragment-flanked by one or two introns-between convergent promoters or transcribed separately in the sense and antisense directions) and placed different components under the control of the circuit inputs (i.e., the siRNA precursor or proteins such as the Dicer and the Argonaute). We found that RNAi-based logic gates are highly sensitive to promoter leakage and, for this reason, challenging to implement in vivo. Convergent-promoter architecture turned out to be the most reliable solution, even though the overall best performance was achieved with the most difficult design based on the siRNA precursor as a giant hairpin.
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Affiliation(s)
- Ximing Tian
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Andrey Volkovinskiy
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
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2
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Cautereels C, Smets J, Bircham P, De Ruysscher D, Zimmermann A, De Rijk P, Steensels J, Gorkovskiy A, Masschelein J, Verstrepen KJ. Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast. Nat Commun 2024; 15:1112. [PMID: 38326309 PMCID: PMC10850122 DOI: 10.1038/s41467-024-44997-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
Microbes are increasingly employed as cell factories to produce biomolecules. This often involves the expression of complex heterologous biosynthesis pathways in host strains. Achieving maximal product yields and avoiding build-up of (toxic) intermediates requires balanced expression of every pathway gene. However, despite progress in metabolic modeling, the optimization of gene expression still heavily relies on trial-and-error. Here, we report an approach for in vivo, multiplexed Gene Expression Modification by LoxPsym-Cre Recombination (GEMbLeR). GEMbLeR exploits orthogonal LoxPsym sites to independently shuffle promoter and terminator modules at distinct genomic loci. This approach facilitates creation of large strain libraries, in which expression of every pathway gene ranges over 120-fold and each strain harbors a unique expression profile. When applied to the biosynthetic pathway of astaxanthin, an industrially relevant antioxidant, a single round of GEMbLeR improved pathway flux and doubled production titers. Together, this shows that GEMbLeR allows rapid and efficient gene expression optimization in heterologous biosynthetic pathways, offering possibilities for enhancing the performance of microbial cell factories.
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Affiliation(s)
- Charlotte Cautereels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Jolien Smets
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Peter Bircham
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Dries De Ruysscher
- Molecular Biotechnology of Plants and Micro-organisms, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, box 2438, Leuven, 3001, Belgium
- Laboratory for Biomolecular Discovery & Engineering, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
| | - Anna Zimmermann
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Peter De Rijk
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, 2610, Belgium
- Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, 2610, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Anton Gorkovskiy
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Joleen Masschelein
- Molecular Biotechnology of Plants and Micro-organisms, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, box 2438, Leuven, 3001, Belgium
- Laboratory for Biomolecular Discovery & Engineering, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium.
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium.
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3
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Zhao Y, Liang F, Xie Y, Duan YT, Andeadelli A, Pateraki I, Makris AM, Pomorski TG, Staerk D, Kampranis SC. Oxetane Ring Formation in Taxol Biosynthesis Is Catalyzed by a Bifunctional Cytochrome P450 Enzyme. J Am Chem Soc 2024; 146:801-810. [PMID: 38129385 DOI: 10.1021/jacs.3c10864] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Taxol is a potent drug used in various cancer treatments. Its complex structure has prompted extensive research into its biosynthesis. However, certain critical steps, such as the formation of the oxetane ring, which is essential for its activity, have remained unclear. Previous proposals suggested that oxetane formation follows the acetylation of taxadien-5α-ol. Here, we proposed that the oxetane ring is formed by cytochrome P450-mediated oxidation events that occur prior to C5 acetylation. To test this hypothesis, we analyzed the genomic and transcriptomic information for Taxus species to identify cytochrome P450 candidates and employed two independent systems, yeast (Saccharomyces cerevisiae) and plant (Nicotiana benthamiana), for their characterization. We revealed that a single enzyme, CYP725A4, catalyzes two successive epoxidation events, leading to the formation of the oxetane ring. We further showed that both taxa-4(5)-11(12)-diene (endotaxadiene) and taxa-4(20)-11(12)-diene (exotaxadiene) are precursors to the key intermediate, taxologenic oxetane, indicating the potential existence of multiple routes in the Taxol pathway. Thus, we unveiled a long-elusive step in Taxol biosynthesis.
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Affiliation(s)
- Yong Zhao
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Feiyan Liang
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Yuman Xie
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Yao-Tao Duan
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Aggeliki Andeadelli
- Institute of Applied Biosciences, Centre for Research & Technology, Hellas (CERTH), Thessaloniki 57001, Greece
- Department of Food Science and Nutrition, University of the Aegean, Myrina 81100, Lemnos, Greece
| | - Irini Pateraki
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Antonios M Makris
- Institute of Applied Biosciences, Centre for Research & Technology, Hellas (CERTH), Thessaloniki 57001, Greece
| | - Thomas G Pomorski
- Transport Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Dan Staerk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, Copenhagen 2100, Denmark
| | - Sotirios C Kampranis
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
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4
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Le Bec M, Pouzet S, Cordier C, Barral S, Scolari V, Sorre B, Banderas A, Hersen P. Optogenetic spatial patterning of cooperation in yeast populations. Nat Commun 2024; 15:75. [PMID: 38168087 PMCID: PMC10761962 DOI: 10.1038/s41467-023-44379-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Microbial communities are shaped by complex metabolic interactions such as cooperation and competition for resources. Methods to control such interactions could lead to major advances in our ability to better engineer microbial consortia for synthetic biology applications. Here, we use optogenetics to control SUC2 invertase production in yeast, thereby shaping spatial assortment of cooperator and cheater cells. Yeast cells behave as cooperators (i.e., transform sucrose into hexose, a public good) upon blue light illumination or cheaters (i.e., consume hexose produced by cooperators to grow) in the dark. We show that cooperators benefit best from the hexoses they produce when their domain size is constrained between two cut-off length-scales. From an engineering point of view, the system behaves as a bandpass filter. The lower limit is the trace of cheaters' competition for hexoses, while the upper limit is defined by cooperators' competition for sucrose. Cooperation mostly occurs at the frontiers with cheater cells, which not only compete for hexoses but also cooperate passively by letting sucrose reach cooperators. We anticipate that this optogenetic method could be applied to shape metabolic interactions in a variety of microbial ecosystems.
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Affiliation(s)
- Matthias Le Bec
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Sylvain Pouzet
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Céline Cordier
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Simon Barral
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Vittore Scolari
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005, Paris, France
| | - Benoit Sorre
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Alvaro Banderas
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France.
| | - Pascal Hersen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France.
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5
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Aptamers, Riboswitches, and Ribozymes in S. cerevisiae Synthetic Biology. Life (Basel) 2021; 11:life11030248. [PMID: 33802772 PMCID: PMC8002509 DOI: 10.3390/life11030248] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 01/09/2023] Open
Abstract
Among noncoding RNA sequences, riboswitches and ribozymes have attracted the attention of the synthetic biology community as circuit components for translation regulation. When fused to aptamer sequences, ribozymes and riboswitches are enabled to interact with chemicals. Therefore, protein synthesis can be controlled at the mRNA level without the need for transcription factors. Potentially, the use of chemical-responsive ribozymes/riboswitches would drastically simplify the design of genetic circuits. In this review, we describe synthetic RNA structures that have been used so far in the yeast Saccharomyces cerevisiae. We present their interaction mode with different chemicals (e.g., theophylline and antibiotics) or proteins (such as the RNase III) and their recent employment into clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 9 (CRISPR-Cas) systems. Particular attention is paid, throughout the whole paper, to their usage and performance into synthetic gene circuits.
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6
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de Bruijn WJC, Levisson M, Beekwilder J, van Berkel WJH, Vincken JP. Plant Aromatic Prenyltransferases: Tools for Microbial Cell Factories. Trends Biotechnol 2020; 38:917-934. [PMID: 32299631 DOI: 10.1016/j.tibtech.2020.02.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 01/09/2023]
Abstract
In plants, prenylation of aromatic compounds, such as (iso)flavonoids and stilbenoids, by membrane-bound prenyltransferases (PTs), is an essential step in the biosynthesis of many bioactive compounds. Prenylated aromatic compounds have various health-beneficial properties that are interesting for industrial applications, but their exploitation is limited due to their low abundance in nature. Harnessing plant aromatic PTs for prenylation in microbial cell factories may be a sustainable and economically viable alternative. Limitations in prenylated aromatic compound production have been identified, including availability of prenyl donor substrate. In this review, we summarize the current knowledge about plant aromatic PTs and discuss promising strategies towards the optimized production of prenylated aromatic compounds by microbial cell factories.
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Affiliation(s)
- Wouter J C de Bruijn
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, Netherlands
| | - Mark Levisson
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, Netherlands
| | - Jules Beekwilder
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, Netherlands
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, Netherlands
| | - Jean-Paul Vincken
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, Netherlands.
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7
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Rahmat E, Kang Y. Yeast metabolic engineering for the production of pharmaceutically important secondary metabolites. Appl Microbiol Biotechnol 2020; 104:4659-4674. [DOI: 10.1007/s00253-020-10587-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 01/30/2020] [Accepted: 03/24/2020] [Indexed: 11/29/2022]
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8
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Payen C, Thompson D. The renaissance of yeasts as microbial factories in the modern age of biomanufacturing. Yeast 2019; 36:685-700. [DOI: 10.1002/yea.3439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/09/2019] [Accepted: 08/04/2019] [Indexed: 12/18/2022] Open
Affiliation(s)
- Celia Payen
- DuPont Nutrition and Biosciences Wilmington Delaware
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9
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Promoter engineering strategies for the overproduction of valuable metabolites in microbes. Appl Microbiol Biotechnol 2019; 103:8725-8736. [PMID: 31630238 DOI: 10.1007/s00253-019-10172-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 12/16/2022]
Abstract
Promoter engineering is an enabling technology in metabolic engineering and synthetic biology. As an indispensable part of synthetic biology, the promoter is a key factor in regulating genetic circuits and in coordinating multi-gene biosynthetic pathways. In this review, we summarized the recent progresses in promoter engineering in microbes. Specifically, the endogenous promoters are firstly discussed, followed by the statement of the influence of nucleotides exchange on the strength of promoters explored by site-selective mutagenesis. We then introduced the promoter libraries with a wide range of strength, which are constructed focusing on core promoter regions and upstream activating sequences by rational designs. Finally, the application of promoter libraries in the optimization of multi-gene metabolic pathways for high-yield production of metabolites was illustrated with a couple of recent examples.
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10
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Weenink T, van der Hilst J, McKiernan RM, Ellis T. Design of RNA hairpin modules that predictably tune translation in yeast. Synth Biol (Oxf) 2018; 3:ysy019. [PMID: 32995525 PMCID: PMC7445769 DOI: 10.1093/synbio/ysy019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Modular parts for tuning translation are prevalent in prokaryotic synthetic biology but lacking for eukaryotic synthetic biology. Working in Saccharomyces cerevisiae yeast, we here describe how hairpin RNA structures inserted into the 5′ untranslated region (5′UTR) of mRNAs can be used to tune expression levels by 100-fold by inhibiting translation. We determine the relationship between the calculated free energy of folding in the 5′UTR and in vivo protein abundance, and show that this enables rational design of hairpin libraries that give predicted expression outputs. Our approach is modular, working with different promoters and protein coding sequences, and outperforms promoter mutation as a way to predictably generate a library where a protein is induced to express at a range of different levels. With this new tool, computational RNA sequence design can be used to predictably fine-tune protein production for genes expressed in yeast.
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Affiliation(s)
- Tim Weenink
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| | - Jelle van der Hilst
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.,Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Robert M McKiernan
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| | - Tom Ellis
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
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11
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Kobori S, Yokobayashi Y. Analyzing and Tuning Ribozyme Activity by Deep Sequencing To Modulate Gene Expression Level in Mammalian Cells. ACS Synth Biol 2018; 7:371-376. [PMID: 29343061 DOI: 10.1021/acssynbio.7b00367] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Self-cleaving ribozymes, in combination with aptamers and various classes of RNAs, have been heavily engineered to create RNA devices to control gene expression. Although understanding of sequence-function relationships of ribozymes is critical for such efforts, our current knowledge of self-cleaving ribozymes is mostly limited to the results from small scale mutational studies performed under different conditions, or qualitative results of mutate-and-select experiments that may contain experimental biases. Here, we applied our strategy based on deep sequencing to comprehensively assay a large number of mutants to systematically examine the effect of the P4 stem sequence on the activity of an HDV-like ribozyme. We discovered that the ribozyme activity is highly sensitive to the sequence and the apparent stability of the varied positions. Furthermore, we demonstrated that the collection of the ribozyme variants with different activities can be used as a convenient device to fine-tune the level of gene expression in mammalian cells.
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Affiliation(s)
- Shungo Kobori
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
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12
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Huang M, Joensson HN, Nielsen J. High-Throughput Microfluidics for the Screening of Yeast Libraries. Methods Mol Biol 2018; 1671:307-317. [PMID: 29170967 DOI: 10.1007/978-1-4939-7295-1_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Cell factory development is critically important for efficient biological production of chemicals, biofuels, and pharmaceuticals. Many rounds of the Design-Build-Test-Learn cycles may be required before an engineered strain meeting specific metrics required for industrial application. The bioindustry prefer products in secreted form (secreted products or extracellular metabolites) as it can lower the cost of downstream processing, reduce metabolic burden to cell hosts, and allow necessary modification on the final products , such as biopharmaceuticals. Yet, products in secreted form result in the disconnection of phenotype from genotype, which may have limited throughput in the Test step for identification of desired variants from large libraries of mutant strains. In droplet microfluidic screening, single cells are encapsulated in individual droplet and enable high-throughput processing and sorting of single cells or clones. Encapsulation in droplets allows this technology to overcome the throughput limitations present in traditional methods for screening by extracellular phenotypes. In this chapter, we describe a protocol/guideline for high-throughput droplet microfluidics screening of yeast libraries for higher protein secretion . This protocol can be adapted to screening by a range of other extracellular products from yeast or other hosts.
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Affiliation(s)
- Mingtao Huang
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Haakan N Joensson
- Division of Nanobiotechnology and Proteomics, KTH Royal Institute of Technology, Science for Life Laboratory, Box 1031, SE-17121, Solna, Sweden
- Novo Nordisk Foundation Center for Biosustainability, KTH Royal Institute of Technology, SE-10691, Stockholm, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.
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13
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Vickers CE, Williams TC, Peng B, Cherry J. Recent advances in synthetic biology for engineering isoprenoid production in yeast. Curr Opin Chem Biol 2017. [DOI: 10.1016/j.cbpa.2017.05.017] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Peng B, Plan MR, Chrysanthopoulos P, Hodson MP, Nielsen LK, Vickers CE. A squalene synthase protein degradation method for improved sesquiterpene production in Saccharomyces cerevisiae. Metab Eng 2017; 39:209-219. [DOI: 10.1016/j.ymben.2016.12.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 11/17/2016] [Accepted: 12/07/2016] [Indexed: 10/20/2022]
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15
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Enhancement of protein production via the strong DIT1 terminator and two RNA-binding proteins in Saccharomyces cerevisiae. Sci Rep 2016; 6:36997. [PMID: 27845367 PMCID: PMC5109538 DOI: 10.1038/srep36997] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/20/2016] [Indexed: 11/10/2022] Open
Abstract
Post-transcriptional upregulation is an effective way to increase the expression of transgenes and thus maximize the yields of target chemicals from metabolically engineered organisms. Refractory elements in the 3′ untranslated region (UTR) that increase mRNA half-life might be available. In Saccharomyces cerevisiae, several terminator regions have shown activity in increasing the production of proteins by upstream coding genes; among these terminators the DIT1 terminator has the highest activity. Here, we found in Saccharomyces cerevisiae that two resident trans-acting RNA-binding proteins (Nab6p and Pap1p) enhance the activity of the DIT1 terminator through the cis element GUUCG/U within the 3′-UTR. These two RNA-binding proteins could upregulate a battery of cell-wall–related genes. Mutagenesis of the DIT1 terminator improved its activity by a maximum of 500% of that of the standard PGK1 terminator. Further understanding and improvement of this system will facilitate inexpensive and stable production of complicated organism-derived drugs worldwide.
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16
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Strategies for manipulation of oxygen utilization by the electron transfer chain in microbes for metabolic engineering purposes. J Ind Microbiol Biotechnol 2016; 44:647-658. [PMID: 27800562 DOI: 10.1007/s10295-016-1851-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/06/2016] [Indexed: 12/14/2022]
Abstract
Microaerobic growth is of importance in ecological niches, pathogenic infections and industrial production of chemicals. The use of low levels of oxygen enables the cell to gain energy and grow more robustly in the presence of a carbon source that can be oxidized and provide electrons to the respiratory chain in the membrane. A considerable amount of information is available on the genes and proteins involved in respiratory growth and the regulation of genes involved in aerobic and anaerobic metabolism. The dependence of regulation on sensing systems that respond to reduced quinones (e.g. ArcB) or oxygen levels that affect labile redox components of transcription regulators (Fnr) are key in understanding the regulation. Manipulation of the amount of respiration can be difficult to control in dense cultures or inadequately mixed reactors leading to inhomogeneous cultures that may have lower than optimal performance. Efforts to control respiration through genetic means have been reported and address mutations affecting components of the electron transport chain. In a recent report completion for intermediates of the ubiquinone biosynthetic pathway was used to dial the level of respiration vs lactate formation in an aerobically grown E. coli culture.
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17
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Wadhwa M, Bachhawat A. A genetic screen for increasing metabolic flux in the isoprenoid pathway of Saccharomyces cerevisiae: Isolation of SPT15 mutants using the screen. Metab Eng Commun 2016; 3:164-172. [PMID: 29468122 PMCID: PMC5779727 DOI: 10.1016/j.meteno.2016.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 01/17/2023] Open
Abstract
A genetic screen to identify mutants that can increase flux in the isoprenoid pathway of yeast has been lacking. We describe a carotenoid-based visual screen built with the core carotenogenic enzymes from the red yeast Rhodosporidium toruloides. Enzymes from this yeast displayed the required, higher capacity in the carotenoid pathway. The development also included the identification of the metabolic bottlenecks, primarily phytoene dehydrogenase, that was subjected to a directed evolution strategy to yield more active mutants. To further limit phytoene pools, a less efficient version of GGPP synthase was employed. The screen was validated with a known flux increasing gene, tHMG1. New mutants in the TATA binding protein SPT15 were isolated using this screen that increased the yield of carotenoids, and an alternate isoprenoid, α-Farnesene confirming increase in overall flux. The findings indicate the presence of previously unknown links to the isoprenoid pathway that can be uncovered using this screen.
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18
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Rantasalo A, Czeizler E, Virtanen R, Rousu J, Lähdesmäki H, Penttilä M, Jäntti J, Mojzita D. Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae. PLoS One 2016; 11:e0148320. [PMID: 26901642 PMCID: PMC4762949 DOI: 10.1371/journal.pone.0148320] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 01/15/2016] [Indexed: 12/26/2022] Open
Abstract
This work describes the development and characterization of a modular synthetic expression system that provides a broad range of adjustable and predictable expression levels in S. cerevisiae. The system works as a fixed-gain transcription amplifier, where the input signal is transferred via a synthetic transcription factor (sTF) onto a synthetic promoter, containing a defined core promoter, generating a transcription output signal. The system activation is based on the bacterial LexA-DNA-binding domain, a set of modified, modular LexA-binding sites and a selection of transcription activation domains. We show both experimentally and computationally that the tuning of the system is achieved through the selection of three separate modules, each of which enables an adjustable output signal: 1) the transcription-activation domain of the sTF, 2) the binding-site modules in the output promoter, and 3) the core promoter modules which define the transcription initiation site in the output promoter. The system has a novel bidirectional architecture that enables generation of compact, yet versatile expression modules for multiple genes with highly diversified expression levels ranging from negligible to very strong using one synthetic transcription factor. In contrast to most existing modular gene expression regulation systems, the present system is independent from externally added compounds. Furthermore, the established system was minimally affected by the several tested growth conditions. These features suggest that it can be highly useful in large scale biotechnology applications.
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Affiliation(s)
- Anssi Rantasalo
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Elena Czeizler
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, P.O. Box 15400, FI-00076 Aalto, Espoo, Finland
| | - Riitta Virtanen
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Juho Rousu
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, P.O. Box 15400, FI-00076 Aalto, Espoo, Finland
| | - Harri Lähdesmäki
- Aalto University, Department of Computer Science, P.O. Box 15400, FI-00076 Aalto, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Jussi Jäntti
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Dominik Mojzita
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
- * E-mail:
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19
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Petzold CJ, Chan LJG, Nhan M, Adams PD. Analytics for Metabolic Engineering. Front Bioeng Biotechnol 2015; 3:135. [PMID: 26442249 PMCID: PMC4561385 DOI: 10.3389/fbioe.2015.00135] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/24/2015] [Indexed: 12/20/2022] Open
Abstract
Realizing the promise of metabolic engineering has been slowed by challenges related to moving beyond proof-of-concept examples to robust and economically viable systems. Key to advancing metabolic engineering beyond trial-and-error research is access to parts with well-defined performance metrics that can be readily applied in vastly different contexts with predictable effects. As the field now stands, research depends greatly on analytical tools that assay target molecules, transcripts, proteins, and metabolites across different hosts and pathways. Screening technologies yield specific information for many thousands of strain variants, while deep omics analysis provides a systems-level view of the cell factory. Efforts focused on a combination of these analyses yield quantitative information of dynamic processes between parts and the host chassis that drive the next engineering steps. Overall, the data generated from these types of assays aid better decision-making at the design and strain construction stages to speed progress in metabolic engineering research.
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Affiliation(s)
- Christopher J Petzold
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Leanne Jade G Chan
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Melissa Nhan
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Paul D Adams
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA ; Department of Bioengineering, University of California Berkeley , Berkeley, CA , USA
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20
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Ito Y, Yamanishi M, Ikeuchi A, Matsuyama T. A highly tunable system for the simultaneous expression of multiple enzymes in Saccharomyces cerevisiae. ACS Synth Biol 2015; 4:12-6. [PMID: 24927017 DOI: 10.1021/sb500096y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Control of the expression levels of multiple enzymes in transgenic yeasts is essential for the effective production of complex molecules through fermentation. Here, we propose a tunable strategy for the control of expression levels based on the design of terminator regions and other gene-expression control elements in Saccharomyces cerevisiae. Our genome-integrated system, which is capable of producing high expression levels over a wide dynamic range, will broadly enable metabolic engineering and synthetic biology. We demonstrated that the activities of multiple cellulases and the production of ethanol were doubled in a transgenic yeast constructed with our system compared with those achieved with a standard expression system.
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Affiliation(s)
- Yoichiro Ito
- Matsuyama Research Group and ‡Biotechnology Laboratory, Toyota Central Research and Development Laboratories, Inc., 41-1 Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Mamoru Yamanishi
- Matsuyama Research Group and ‡Biotechnology Laboratory, Toyota Central Research and Development Laboratories, Inc., 41-1 Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Akinori Ikeuchi
- Matsuyama Research Group and ‡Biotechnology Laboratory, Toyota Central Research and Development Laboratories, Inc., 41-1 Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Takashi Matsuyama
- Matsuyama Research Group and ‡Biotechnology Laboratory, Toyota Central Research and Development Laboratories, Inc., 41-1 Yokomichi, Nagakute, Aichi 480-1192, Japan
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21
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Tsai CS, Kwak S, Turner TL, Jin YS. Yeast synthetic biology toolbox and applications for biofuel production. FEMS Yeast Res 2015; 15:1-15. [PMID: 25195615 DOI: 10.1111/1567-1364.12206] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/16/2014] [Accepted: 08/31/2014] [Indexed: 01/04/2023] Open
Abstract
Yeasts are efficient biofuel producers with numerous advantages outcompeting bacterial counterparts. While most synthetic biology tools have been developed and customized for bacteria especially for Escherichia coli, yeast synthetic biological tools have been exploited for improving yeast to produce fuels and chemicals from renewable biomass. Here we review the current status of synthetic biological tools and their applications for biofuel production, focusing on the model strain Saccharomyces cerevisiae We describe assembly techniques that have been developed for constructing genes, pathways, and genomes in yeast. Moreover, we discuss synthetic parts for allowing precise control of gene expression at both transcriptional and translational levels. Applications of these synthetic biological approaches have led to identification of effective gene targets that are responsible for desirable traits, such as cellulosic sugar utilization, advanced biofuel production, and enhanced tolerance against toxic products for biofuel production from renewable biomass. Although an array of synthetic biology tools and devices are available, we observed some gaps existing in tool development to achieve industrial utilization. Looking forward, future tool development should focus on industrial cultivation conditions utilizing industrial strains.
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Affiliation(s)
- Ching-Sung Tsai
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Suryang Kwak
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Timothy L Turner
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA .,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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22
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Fidan O, Zhan J. Recent advances in engineering yeast for pharmaceutical protein production. RSC Adv 2015. [DOI: 10.1039/c5ra13003d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Currently available systems and synthetic biology tools can be applied to yeast engineering for improved biopharmaceutical protein production.
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Affiliation(s)
- Ozkan Fidan
- Department of Biological Engineering
- Utah State University
- Logan
- USA
| | - Jixun Zhan
- Department of Biological Engineering
- Utah State University
- Logan
- USA
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23
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Production of Industrially Relevant Isoprenoid Compounds in Engineered Microbes. MICROORGANISMS IN BIOREFINERIES 2015. [DOI: 10.1007/978-3-662-45209-7_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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24
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Shis D, Hussain F, Meinhardt S, Swint-Kruse L, Bennett MR. Modular, multi-input transcriptional logic gating with orthogonal LacI/GalR family chimeras. ACS Synth Biol 2014; 3:645-51. [PMID: 25035932 PMCID: PMC4210161 DOI: 10.1021/sb500262f] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Indexed: 12/22/2022]
Abstract
In prokaryotes, the construction of synthetic, multi-input promoters is constrained by the number of transcription factors that can simultaneously regulate a single promoter. This fundamental engineering constraint is an obstacle to synthetic biologists because it limits the computational capacity of engineered gene circuits. Here, we demonstrate that complex multi-input transcriptional logic gating can be achieved through the use of ligand-inducible chimeric transcription factors assembled from the LacI/GalR family. These modular chimeras each contain a ligand-binding domain and a DNA-binding domain, both of which are chosen from a library of possibilities. When two or more chimeras have the same DNA-binding domain, they independently and simultaneously regulate any promoter containing the appropriate operator site. In this manner, simple transcriptional AND gating is possible through the combination of two chimeras, and multiple-input AND gating is possible with the simultaneous use of three or even four chimeras. Furthermore, we demonstrate that orthogonal DNA-binding domains and their cognate operators allow the coexpression of multiple, orthogonal AND gates. Altogether, this work provides synthetic biologists with novel, ligand-inducible logic gates and greatly expands the possibilities for engineering complex synthetic gene circuits.
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Affiliation(s)
- David
L. Shis
- Department
of Biochemistry & Cell Biology, Rice
University, Houston, Texas 77005, United
States
| | - Faiza Hussain
- Department
of Biochemistry & Cell Biology, Rice
University, Houston, Texas 77005, United
States
| | - Sarah Meinhardt
- Department
of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Liskin Swint-Kruse
- Department
of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Matthew R. Bennett
- Department
of Biochemistry & Cell Biology, Rice
University, Houston, Texas 77005, United
States
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25
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Redden H, Morse N, Alper HS. The synthetic biology toolbox for tuning gene expression in yeast. FEMS Yeast Res 2014; 15:1-10. [DOI: 10.1111/1567-1364.12188] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/28/2014] [Accepted: 07/15/2014] [Indexed: 02/04/2023] Open
Affiliation(s)
- Heidi Redden
- Department for Molecular Biosciences; The University of Texas at Austin; Austin TX USA
| | - Nicholas Morse
- McKetta Department of Chemical Engineering; The University of Texas at Austin; Austin TX USA
| | - Hal S. Alper
- Department for Molecular Biosciences; The University of Texas at Austin; Austin TX USA
- McKetta Department of Chemical Engineering; The University of Texas at Austin; Austin TX USA
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26
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Vickers CE, Bongers M, Liu Q, Delatte T, Bouwmeester H. Metabolic engineering of volatile isoprenoids in plants and microbes. PLANT, CELL & ENVIRONMENT 2014; 37:1753-75. [PMID: 24588680 DOI: 10.1111/pce.12316] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 02/18/2014] [Accepted: 02/18/2014] [Indexed: 05/09/2023]
Abstract
The chemical properties and diversity of volatile isoprenoids lends them to a broad variety of biological roles. It also lends them to a host of biotechnological applications, both by taking advantage of their natural functions and by using them as industrial chemicals/chemical feedstocks. Natural functions include roles as insect attractants and repellents, abiotic stress protectants in pathogen defense, etc. Industrial applications include use as pharmaceuticals, flavours, fragrances, fuels, fuel additives, etc. Here we will examine the ways in which researchers have so far found to exploit volatile isoprenoids using biotechnology. Production and/or modification of volatiles using metabolic engineering in both plants and microorganisms are reviewed, including engineering through both mevalonate and methylerythritol diphosphate pathways. Recent advances are illustrated using several case studies (herbivores and bodyguards, isoprene, and monoterpene production in microbes). Systems and synthetic biology tools with particular utility for metabolic engineering are also reviewed. Finally, we discuss the practical realities of various applications in modern biotechnology, explore possible future applications, and examine the challenges of moving these technologies forward so that they can deliver tangible benefits. While this review focuses on volatile isoprenoids, many of the engineering approaches described here are also applicable to non-isoprenoid volatiles and to non-volatile isoprenoids.
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Affiliation(s)
- Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland, 4072, Australia
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27
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Biopharmaceutical protein production bySaccharomyces cerevisiae: current state and future prospects. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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28
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Yamanishi M, Ito Y, Kintaka R, Imamura C, Katahira S, Ikeuchi A, Moriya H, Matsuyama T. A genome-wide activity assessment of terminator regions in Saccharomyces cerevisiae provides a ″terminatome″ toolbox. ACS Synth Biol 2013; 2:337-47. [PMID: 23654277 DOI: 10.1021/sb300116y] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The terminator regions of eukaryotes encode functional elements in the 3' untranslated region (3'-UTR) that influence the 3'-end processing of mRNA, mRNA stability, and translational efficiency, which can modulate protein production. However, the contribution of these terminator regions to gene expression remains unclear, and therefore their utilization in metabolic engineering or synthetic genetic circuits has been limited. Here, we comprehensively evaluated the activity of 5302 terminator regions from a total of 5880 genes in the budding yeast Saccharomyces cerevisiae by inserting each terminator region downstream of the P TDH3 - green fluorescent protein (GFP) reporter gene and measuring the fluorescent intensity of GFP. Terminator region activities relative to that of the PGK1 standard terminator ranged from 0.036 to 2.52, with a mean of 0.87. We thus could isolate the most and least active terminator regions. The activities of the terminator regions showed a positive correlation with mRNA abundance, indicating that the terminator region is a determinant of mRNA abundance. The least active terminator regions tended to encode longer 3'-UTRs, suggesting the existence of active degradation mechanisms for those mRNAs. The terminator regions of ribosomal protein genes tended to be the most active, suggesting the existence of a common regulator of those genes. The ″terminatome″ (the genome-wide set of terminator regions) thus not only provides valuable information to understand the modulatory roles of terminator regions on gene expression but also serves as a useful toolbox for the development of metabolically and genetically engineered yeast.
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Affiliation(s)
| | | | - Reiko Kintaka
- Research Core for Interdisciplinary
Sciences, Okayama University, 3-1-1 Tsushima-Naka,
Kita-ku, Okayama, 700-8530, Japan
| | | | | | | | - Hisao Moriya
- Research Core for Interdisciplinary
Sciences, Okayama University, 3-1-1 Tsushima-Naka,
Kita-ku, Okayama, 700-8530, Japan
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29
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Kim HJ, Turner TL, Jin YS. Combinatorial genetic perturbation to refine metabolic circuits for producing biofuels and biochemicals. Biotechnol Adv 2013; 31:976-85. [PMID: 23562845 DOI: 10.1016/j.biotechadv.2013.03.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 03/18/2013] [Accepted: 03/28/2013] [Indexed: 12/25/2022]
Abstract
Recent advances in metabolic engineering have enabled microbial factories to compete with conventional processes for producing fuels and chemicals. Both rational and combinatorial approaches coupled with synthetic and systematic tools play central roles in metabolic engineering to create and improve a selected microbial phenotype. Compared to knowledge-based rational approaches, combinatorial approaches exploiting biological diversity and high-throughput screening have been demonstrated as more effective tools for improving various phenotypes of interest. In particular, identification of unprecedented targets to rewire metabolic circuits for maximizing yield and productivity of a target chemical has been made possible. This review highlights general principles and the features of the combinatorial approaches using various libraries to implement desired phenotypes for strain improvement. In addition, recent applications that harnessed the combinatorial approaches to produce biofuels and biochemicals will be discussed.
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Affiliation(s)
- Hyo Jin Kim
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 1206 West Gregory Dr., Urbana, IL 61801, USA
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30
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Chen Y, Nielsen J. Advances in metabolic pathway and strain engineering paving the way for sustainable production of chemical building blocks. Curr Opin Biotechnol 2013; 24:965-72. [PMID: 23541505 DOI: 10.1016/j.copbio.2013.03.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 02/27/2013] [Accepted: 03/04/2013] [Indexed: 11/17/2022]
Abstract
Bio-based production of chemical building blocks from renewable resources is an attractive alternative to petroleum-based platform chemicals. Metabolic pathway and strain engineering is the key element in constructing robust microbial chemical factories within the constraints of cost effective production. Here we discuss how the development of computational algorithms, novel modules and methods, omics-based techniques combined with modeling refinement are enabling reduction in development time and thus advance the field of industrial biotechnology. We further discuss how recent technological developments contribute to the development of novel cell factories for the production of the building block chemicals: adipic acid, succinic acid and 3-hydroxypropionic acid.
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Affiliation(s)
- Yun Chen
- Novo Nordisk Foundation Center for Biosustainability, Department of Chemical & Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
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31
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Galanie S, Siddiqui MS, Smolke CD. Molecular tools for chemical biotechnology. Curr Opin Biotechnol 2013; 24:1000-9. [PMID: 23528237 DOI: 10.1016/j.copbio.2013.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 03/03/2013] [Accepted: 03/05/2013] [Indexed: 12/31/2022]
Abstract
Biotechnological production of high value chemical products increasingly involves engineering in vivo multi-enzyme pathways and host metabolism. Recent approaches to these engineering objectives have made use of molecular tools to advance de novo pathway identification, tunable enzyme expression, and rapid pathway construction. Molecular tools also enable optimization of single enzymes and entire genomes through diversity generation and screening, whole cell analytics, and synthetic metabolic control networks. In this review, we focus on advanced molecular tools and their applications to engineered pathways in host organisms, highlighting the degree to which each tool is generalizable.
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Affiliation(s)
- Stephanie Galanie
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States; Department of Bioengineering, Stanford University, 473 Via Ortega, MC 4201, Stanford, CA 94305, United States
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32
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Zelcbuch L, Antonovsky N, Bar-Even A, Levin-Karp A, Barenholz U, Dayagi M, Liebermeister W, Flamholz A, Noor E, Amram S, Brandis A, Bareia T, Yofe I, Jubran H, Milo R. Spanning high-dimensional expression space using ribosome-binding site combinatorics. Nucleic Acids Res 2013; 41:e98. [PMID: 23470993 PMCID: PMC3643573 DOI: 10.1093/nar/gkt151] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Protein levels are a dominant factor shaping natural and synthetic biological systems. Although proper functioning of metabolic pathways relies on precise control of enzyme levels, the experimental ability to balance the levels of many genes in parallel is a major outstanding challenge. Here, we introduce a rapid and modular method to span the expression space of several proteins in parallel. By combinatorially pairing genes with a compact set of ribosome-binding sites, we modulate protein abundance by several orders of magnitude. We demonstrate our strategy by using a synthetic operon containing fluorescent proteins to span a 3D color space. Using the same approach, we modulate a recombinant carotenoid biosynthesis pathway in Escherichia coli to reveal a diversity of phenotypes, each characterized by a distinct carotenoid accumulation profile. In a single combinatorial assembly, we achieve a yield of the industrially valuable compound astaxanthin 4-fold higher than previously reported. The methodology presented here provides an efficient tool for exploring a high-dimensional expression space to locate desirable phenotypes.
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Affiliation(s)
- Lior Zelcbuch
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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33
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Furukawa K, Hohmann S. Synthetic biology: lessons from engineering yeast MAPK signalling pathways. Mol Microbiol 2013; 88:5-19. [PMID: 23461595 DOI: 10.1111/mmi.12174] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2013] [Indexed: 02/04/2023]
Abstract
All living cells respond to external stimuli and execute specific physiological responses through signal transduction pathways. Understanding the mechanisms controlling signalling pathways is important for diagnosing and treating diseases and for reprogramming cells with desired functions. Although many of the signalling components in the budding yeast Saccharomyces cerevisiae have been identified by genetic studies, many features concerning the dynamic control of pathway activity, cross-talk, cell-to-cell variability or robustness against perturbation are still incompletely understood. Comparing the behaviour of engineered and natural signalling pathways offers insight complementary to that achievable with standard genetic and molecular studies. Here, we review studies that aim at a deeper understanding of signalling design principles and generation of novel signalling properties by engineering the yeast mitogen-activated protein kinase (MAPK) pathways. The underlying approaches can be applied to other organisms including mammalian cells and offer opportunities for building synthetic pathways and functionalities useful in medicine and biotechnology.
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Affiliation(s)
- Kentaro Furukawa
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
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34
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Wang YH, Wei KY, Smolke CD. Synthetic biology: advancing the design of diverse genetic systems. Annu Rev Chem Biomol Eng 2013; 4:69-102. [PMID: 23413816 DOI: 10.1146/annurev-chembioeng-061312-103351] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A major objective of synthetic biology is to make the process of designing genetically encoded biological systems more systematic, predictable, robust, scalable, and efficient. Examples of genetic systems in the field vary widely in terms of operating hosts, compositional approaches, and network complexity, ranging from simple genetic switches to search-and-destroy systems. While significant advances in DNA synthesis capabilities support the construction of pathway- and genome-scale programs, several design challenges currently restrict the scale of systems that can be reasonably designed and implemented. Thus, while synthetic biology offers much promise in developing systems to address challenges faced in the fields of manufacturing, environment and sustainability, and health and medicine, the realization of this potential is currently limited by the diversity of available parts and effective design frameworks. As researchers make progress in bridging this design gap, advances in the field hint at ever more diverse applications for biological systems.
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Affiliation(s)
- Yen-Hsiang Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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35
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Wei KY, Chen YY, Smolke CD. A yeast-based rapid prototype platform for gene control elements in mammalian cells. Biotechnol Bioeng 2013. [DOI: 10.1002/bit.24792] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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36
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Identification and treatment of heme depletion attributed to overexpression of a lineage of evolved P450 monooxygenases. Proc Natl Acad Sci U S A 2012; 109:19504-9. [PMID: 23129650 DOI: 10.1073/pnas.1212287109] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Recent advances in metabolic engineering have demonstrated that microbial biosynthesis can provide a viable alternative to chemical synthesis for the production of bulk and fine chemicals. Introduction of a new biosynthetic pathway typically requires the expression of multiple heterologous enzymes in the production host, which can impose stress on the host cell and, thereby, limit performance of the pathway. Unfortunately, analysis and treatment of the host stress response can be difficult, because there are many sources of stress that may interact in complex ways. We use a systems biological approach to analyze the stress imposed by expressing different enzyme variants from a lineage of soluble P450 monooxygenases, previously evolved for heterologous activity in Saccharomyces cerevisiae. Our analysis identifies patterns of stress imposed on the host by heterologous enzyme overexpression that are consistent across the evolutionary lineage, ultimately implicating heme depletion as the major stress. We show that the monooxygenase evolution, starting from conditions of either high or low stress, caused the cellular stress to converge to a common level. Overexpression of rate-limiting enzymes in the endogenous heme biosynthetic pathway alleviates the stress imposed by expression of the P450 monooxygenases and increases the enzymatic activity of the final evolved P450 by an additional 2.3-fold. Heme overexpression also increases the total activity of an endogenous cytosolic heme-containing catalase but not a heterologous P450 that is membrane-associated. This work demonstrates the utility of combining systems and synthetic biology to analyze and optimize heterologous enzyme expression.
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37
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Kampranis SC, Makris AM. Developing a yeast cell factory for the production of terpenoids. Comput Struct Biotechnol J 2012; 3:e201210006. [PMID: 24688666 PMCID: PMC3962098 DOI: 10.5936/csbj.201210006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/25/2012] [Accepted: 10/25/2012] [Indexed: 12/21/2022] Open
Abstract
Technological developments over the past century have made microbes the work-horses of large scale industrial production processes. Current efforts focus on the metabolic engineering of microbial strains to produce high levels of desirable end-products. The arsenal of the contemporary metabolic engineer contains tools that allow either targeted rational interventions or global screens that combine classical approaches with –omics technologies. Production of terpenoids in S. cerevisiae presents a characteristic example of contemporary biotechnology that integrates all the variety of novel approaches used in metabolic engineering. Terpenoids have attracted significant interest as pharmaceuticals, flavour and fragrance additives, and, more recently, biofuels. The ongoing metabolic engineering efforts, combined with the continuously increasing number of terpene biosynthetic enzymes discovered will enable the economical and environmentally friendly production of a wide range of compounds.
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Affiliation(s)
| | - Antonios M Makris
- Institute of Applied Biosciences/ CERTH, P.O. Box 60361, Thermi 57001, Thessaloniki, Greece
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38
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Innovation at the intersection of synthetic and systems biology. Curr Opin Biotechnol 2012; 23:712-7. [DOI: 10.1016/j.copbio.2011.12.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 12/20/2011] [Indexed: 01/06/2023]
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39
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Abstract
The parameters in a complex synthetic gene network must be extensively tuned before the network functions as designed. Here, we introduce a simple and general approach to rapidly tune gene networks in Escherichia coli using hypermutable simple sequence repeats embedded in the spacer region of the ribosome binding site. By varying repeat length, we generated expression libraries that incrementally and predictably sample gene expression levels over a 1,000-fold range. We demonstrate the utility of the approach by creating a bistable switch library that programmatically samples the expression space to balance the two states of the switch, and we illustrate the need for tuning by showing that the switch's behavior is sensitive to host context. Further, we show that mutation rates of the repeats are controllable in vivo for stability or for targeted mutagenesis--suggesting a new approach to optimizing gene networks via directed evolution. This tuning methodology should accelerate the process of engineering functionally complex gene networks.
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40
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Krumpe K, Frumkin I, Herzig Y, Rimon N, Özbalci C, Brügger B, Rapaport D, Schuldiner M. Ergosterol content specifies targeting of tail-anchored proteins to mitochondrial outer membranes. Mol Biol Cell 2012; 23:3927-35. [PMID: 22918956 PMCID: PMC3469509 DOI: 10.1091/mbc.e11-12-0994] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial outer membrane tail-anchored proteins are a unique class of membrane proteins with unknown targeting mechanism. Using two high-throughput microscopy screens, we demonstrate that the inherent differences in membrane composition between organelle membranes is enough to determine membrane integration specificity in a living cell. Tail-anchored (TA) proteins have a single C-terminal transmembrane domain, making their biogenesis dependent on posttranslational translocation. Despite their importance, no dedicated insertion machinery has been uncovered for mitochondrial outer membrane (MOM) TA proteins. To decipher the molecular mechanisms guiding MOM TA protein insertion, we performed two independent systematic microscopic screens in which we visualized the localization of model MOM TA proteins on the background of mutants in all yeast genes. We could find no mutant in which insertion was completely blocked. However, both screens demonstrated that MOM TA proteins were partially localized to the endoplasmic reticulum (ER) in ∆spf1 cells. Spf1, an ER ATPase with unknown function, is the first protein shown to affect MOM TA protein insertion. We found that ER membranes in ∆spf1 cells become similar in their ergosterol content to mitochondrial membranes. Indeed, when we visualized MOM TA protein distribution in yeast strains with reduced ergosterol content, they phenocopied the loss of Spf1. We therefore suggest that the inherent differences in membrane composition between organelle membranes are sufficient to determine membrane integration specificity in a eukaryotic cell.
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Affiliation(s)
- Katrin Krumpe
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
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41
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Blazeck J, Alper HS. Promoter engineering: Recent advances in controlling transcription at the most fundamental level. Biotechnol J 2012; 8:46-58. [DOI: 10.1002/biot.201200120] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/25/2012] [Accepted: 07/17/2012] [Indexed: 12/25/2022]
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42
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Sasson V, Shachrai I, Bren A, Dekel E, Alon U. Mode of regulation and the insulation of bacterial gene expression. Mol Cell 2012; 46:399-407. [PMID: 22633488 DOI: 10.1016/j.molcel.2012.04.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 04/16/2012] [Accepted: 04/27/2012] [Indexed: 10/28/2022]
Abstract
A gene can be said to be insulated from environmental variations if its expression level depends only on its cognate inducers, and not on variations in conditions. We tested the insulation of the lac promoter of E. coli and of synthetic constructs in which the transcription factor CRP acts as either an activator or a repressor, by measuring their input function-their expression as a function of inducers-in different growth conditions. We find that the promoter activities show sizable variation across conditions of 10%-100% (SD/mean). When the promoter is bound to its cognate regulator(s), variation across conditions is smaller than when it is unbound. Thus, mode of regulation affects insulation: activators seem to show better insulation at high expression levels, and repressors at low expression levels. This may explain the Savageau demand rule, in which E. coli genes needed often in the natural environment tend to be regulated by activators, and rarely needed genes by repressors. The present approach can be used to study insulation in other genes and organisms.
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Affiliation(s)
- Vered Sasson
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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43
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Liang JC, Chang AL, Kennedy AB, Smolke CD. A high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity. Nucleic Acids Res 2012; 40:e154. [PMID: 22810204 PMCID: PMC3488204 DOI: 10.1093/nar/gks636] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recent advances have demonstrated the use of RNA-based control devices to program sophisticated cellular functions; however, the efficiency with which these devices can be quantitatively tailored has limited their broader implementation in cellular networks. Here, we developed a high-efficiency, high-throughput and quantitative two-color fluorescence-activated cell sorting-based screening strategy to support the rapid generation of ribozyme-based control devices with user-specified regulatory activities. The high-efficiency of this screening strategy enabled the isolation of a single functional sequence from a library of over 106 variants within two sorting cycles. We demonstrated the versatility of our approach by screening large libraries generated from randomizing individual components within the ribozyme device platform to efficiently isolate new device sequences that exhibit increased in vitro cleavage rates up to 10.5-fold and increased in vivo activation ratios up to 2-fold. We also identified a titratable window within which in vitro cleavage rates and in vivo gene-regulatory activities are correlated, supporting the importance of optimizing RNA device activity directly in the cellular environment. Our two-color fluorescence-activated cell sorting-based screen provides a generalizable strategy for quantitatively tailoring genetic control elements for broader integration within biological networks.
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Affiliation(s)
- Joe C. Liang
- Division of Chemistry and Chemical Engineering, 1200 E. California Blvd., MC 210-41, California Institute of Technology, Pasadena, CA 91125, Department of Chemistry, Stanford University and Department of Bioengineering, 473 Via Ortega, MC 4201, Stanford University, Stanford, CA 94305, USA
| | - Andrew L. Chang
- Division of Chemistry and Chemical Engineering, 1200 E. California Blvd., MC 210-41, California Institute of Technology, Pasadena, CA 91125, Department of Chemistry, Stanford University and Department of Bioengineering, 473 Via Ortega, MC 4201, Stanford University, Stanford, CA 94305, USA
| | - Andrew B. Kennedy
- Division of Chemistry and Chemical Engineering, 1200 E. California Blvd., MC 210-41, California Institute of Technology, Pasadena, CA 91125, Department of Chemistry, Stanford University and Department of Bioengineering, 473 Via Ortega, MC 4201, Stanford University, Stanford, CA 94305, USA
| | - Christina D. Smolke
- Division of Chemistry and Chemical Engineering, 1200 E. California Blvd., MC 210-41, California Institute of Technology, Pasadena, CA 91125, Department of Chemistry, Stanford University and Department of Bioengineering, 473 Via Ortega, MC 4201, Stanford University, Stanford, CA 94305, USA
- *To whom correspondence should be addressed. Tel: +1 650 721 6371; Fax: +1 650 721 6602;
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44
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Kittleson JT, Wu GC, Anderson JC. Successes and failures in modular genetic engineering. Curr Opin Chem Biol 2012; 16:329-36. [PMID: 22818777 DOI: 10.1016/j.cbpa.2012.06.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Revised: 05/15/2012] [Accepted: 06/20/2012] [Indexed: 11/19/2022]
Abstract
Synthetic biology relies on engineering concepts such as abstraction, standardization, and decoupling to develop systems that address environmental, clinical, and industrial needs. Recent advances in applying modular design to system development have enabled creation of increasingly complex systems. However, several challenges to module and system development remain, including syntactic errors, semantic errors, parameter mismatches, contextual sensitivity, noise and evolution, and load and stress. To combat these challenges, researchers should develop a framework for describing and reasoning about biological information, design systems with modularity in mind, and investigate how to predictively describe the diverse sources and consequences of metabolic load and stress.
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45
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Ceroni F, Furini S, Stefan A, Hochkoeppler A, Giordano E. A synthetic post-transcriptional controller to explore the modular design of gene circuits. ACS Synth Biol 2012; 1:163-71. [PMID: 23651154 DOI: 10.1021/sb200021s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The assembly from modular parts is an efficient approach for creating new devices in Synthetic Biology. In the "bottom-up" designing strategy, modular parts are characterized in advance, and then mathematical modeling is used to predict the outcome of the final device. A prerequisite for bottom-up design is that the biological parts behave in a modular way when assembled together. We designed a new synthetic device for post-transcriptional regulation of gene expression and tested if the outcome of the device could be described from the features of its components. Modular parts showed unpredictable behavior when assembled in different complex circuits. This prevented a modular description of the device that was possible only under specific conditions. Our findings shed doubts into the feasibility of a pure bottom-up approach in synthetic biology, highlighting the urgency for new strategies for the rational design of synthetic devices.
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Affiliation(s)
- Francesca Ceroni
- Laboratory of Cellular and Molecular Engineering, University of Bologna, I-47521 Cesena, Italy
| | - Simone Furini
- Department of Medical Surgery and Bioengineering, University of Siena, I-53100 Siena, Italy
| | - Alessandra Stefan
- Department of Industrial Chemistry, University of Bologna, Viale Risorgimento 4, I-40136
Bologna, Italy
- CSGI, University of Firenze, Via della Lastruccia 3, I-50019
Sesto Fiorentino, Italy
| | - Alejandro Hochkoeppler
- Department of Industrial Chemistry, University of Bologna, Viale Risorgimento 4, I-40136
Bologna, Italy
- CSGI, University of Firenze, Via della Lastruccia 3, I-50019
Sesto Fiorentino, Italy
| | - Emanuele Giordano
- Laboratory of Cellular and Molecular Engineering, University of Bologna, I-47521 Cesena, Italy
- Department of Biochemistry “G. Moruzzi”, University of Bologna, I-40126 Bologna, Italy
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46
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Blazeck J, Garg R, Reed B, Alper HS. Controlling promoter strength and regulation inSaccharomyces cerevisiaeusing synthetic hybrid promoters. Biotechnol Bioeng 2012; 109:2884-95. [DOI: 10.1002/bit.24552] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Revised: 04/20/2012] [Accepted: 04/26/2012] [Indexed: 11/10/2022]
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47
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Abstract
Over the past decade, synthetic biology has emerged as an engineering discipline for biological systems. Compared with other substrates, biology poses a unique set of engineering challenges resulting from an incomplete understanding of natural biological systems and tools for manipulating them. To address these challenges, synthetic biology is advancing from developing proof-of-concept designs to focusing on core platforms for rational and high-throughput biological engineering. These platforms span the entire biological design cycle, including DNA construction, parts libraries, computational design tools, and interfaces for manipulating and probing synthetic circuits. The development of these enabling technologies requires an engineering mindset to be applied to biology, with an emphasis on generalizable techniques in addition to application-specific designs. This review aims to discuss the progress and challenges in synthetic biology and to illustrate areas where synthetic biology may impact biomedical engineering and human health.
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Affiliation(s)
- Allen A Cheng
- Synthetic Biology Group, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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48
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Thompson KE, Bashor CJ, Lim WA, Keating AE. SYNZIP protein interaction toolbox: in vitro and in vivo specifications of heterospecific coiled-coil interaction domains. ACS Synth Biol 2012; 1:118-29. [PMID: 22558529 PMCID: PMC3339576 DOI: 10.1021/sb200015u] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Indexed: 12/20/2022]
Abstract
![]()
The synthetic biology toolkit contains a growing number
of parts
for regulating transcription and translation, but very few that can
be used to control protein association. Here we report characterization
of 22 previously published heterospecific synthetic coiled-coil peptides
called SYNZIPs. We present biophysical analysis of the oligomerization
states, helix orientations, and affinities of 27 SYNZIP pairs. SYNZIP
pairs were also tested for interaction in two cell-based assays. In
a yeast two-hybrid screen, >85% of 253 comparable interactions
were
consistent with prior in vitro measurements made
using coiled-coil microarrays. In a yeast-signaling assay controlled
by coiled-coil mediated scaffolding, 12 SYNZIP pairs were successfully
used to down-regulate the expression of a reporter gene following
treatment with α-factor. Characterization of these interaction
modules dramatically increases the number of available protein interaction
parts for synthetic biology and should facilitate a wide range of
molecular engineering applications. Summary characteristics of 27
SYNZIP peptide pairs are reported in specification sheets available
in the Supporting Information and at the SYNZIP Web site [http://keatingweb.mit.edu/SYNZIP/].
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Affiliation(s)
- Kenneth Evan Thompson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | | | | | - Amy E. Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
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49
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Rationally designed families of orthogonal RNA regulators of translation. Nat Chem Biol 2012; 8:447-54. [DOI: 10.1038/nchembio.919] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 01/27/2012] [Indexed: 12/19/2022]
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50
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Stapleton JA, Endo K, Fujita Y, Hayashi K, Takinoue M, Saito H, Inoue T. Feedback control of protein expression in mammalian cells by tunable synthetic translational inhibition. ACS Synth Biol 2012; 1:83-8. [PMID: 23651072 PMCID: PMC4165468 DOI: 10.1021/sb200005w] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
Feedback regulation plays a crucial role in dynamic gene
expression
in nature, but synthetic translational feedback systems have yet to
be demonstrated. Here we use an RNA/protein interaction-based synthetic
translational switch to create a feedback system that tightly controls
the expression of proteins of interest in mammalian cells. Feedback
is mediated by modified ribosomal L7Ae proteins, which bind a set
of RNA motifs with a range of affinities. We designed these motifs
into L7Ae-encoding mRNA. Newly translated L7Ae binds its own mRNA,
inhibiting further translation. This inhibition tightly feedback-regulates
the concentration of L7Ae and any fusion partner of interest. A mathematical
model predicts system behavior as a function of RNA/protein affinity.
We further demonstrate that the L7Ae protein can simultaneously and
tunably regulate the expression of multiple proteins of interest by
binding RNA control motifs built into each mRNA, allowing control
over the coordinated expression of protein networks.
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Affiliation(s)
- James A. Stapleton
- Laboratory of Gene
Biodynamics,
Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kei Endo
- International Cooperative Research
Project, Japan Science and Technology Agency, 5 Sanban-cho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Yoshihiko Fujita
- Laboratory of Gene
Biodynamics,
Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
- International Cooperative Research
Project, Japan Science and Technology Agency, 5 Sanban-cho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Karin Hayashi
- International Cooperative Research
Project, Japan Science and Technology Agency, 5 Sanban-cho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Masahiro Takinoue
- Department of Computational Intelligence
and Systems Science, Interdisciplinary Graduate School of Science
and Engineering, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Hirohide Saito
- International Cooperative Research
Project, Japan Science and Technology Agency, 5 Sanban-cho, Chiyoda-ku, Tokyo 102-0075, Japan
- The Hakubi Center, Kyoto University, Oiwake-cho,
Kitashirakawa, Sakyo-ku,
Kyoto 606-8502, Japan
- Center
for iPS Cell Research
and Application, Kyoto University, 53 Kawahara-cho,
Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Tan Inoue
- Laboratory of Gene
Biodynamics,
Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
- International Cooperative Research
Project, Japan Science and Technology Agency, 5 Sanban-cho, Chiyoda-ku, Tokyo 102-0075, Japan
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