1
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Beentjes M, Ortega-Arbulú AS, Löwe H, Pflüger-Grau K, Kremling A. Targeting Transcriptional and Translational Hindrances in a Modular T7RNAP Expression System in Engineered Pseudomonas putida. ACS Synth Biol 2022; 11:3939-3953. [PMID: 36370089 DOI: 10.1021/acssynbio.2c00295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The T7 RNA polymerase is considered one of the most popular tools for heterologous gene expression in the gold standard biotechnological host Escherichia coli. However, the exploitation of this tool in other prospective hosts, such as the biotechnologically relevant bacterium Pseudomonas putida, is still very scarce. The majority of the existing T7-based systems in P. putida show low expression strengths and possess only weak controllability. A fundamental understanding of these systems is necessary in order to design robust and predictable biotechnological processes. To fill this gap, we established and characterized a modular T7 RNA polymerase-based system for heterologous protein production in P. putida, using the enhanced Green Fluorescent Protein (eGFP) as an easy-to-quantify reporter protein. We have effectively targeted the limitations associated with the initial genetic setup of the system, such as slow growth and low protein production rates. By replacing the T7 phage-inherent TΦ terminator downstream of the heterologous gene with the synthetic tZ terminator, growth and protein production rates improved drastically, and the T7 RNA polymerase system reached a productivity level comparable to that of an intrinsic RNA polymerase-based system. Furthermore, we were able to show that the system was saturated with T7 RNA polymerase by applying a T7 RNA polymerase ribosome binding site library to tune heterologous protein production. This saturation indicates an essential role for the ribosome binding sites of the T7 RNA polymerase since, in an oversaturated system, cellular resources are lost to the synthesis of unnecessary T7 RNA polymerase. Eventually, we combined the experimental data into a model that can predict the eGFP production rate with respect to the relative strength of the ribosome binding sites upstream of the T7 gene.
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Affiliation(s)
- Marleen Beentjes
- TUM School of Engineering and Design, Systems Biotechnology, Technical University Munich, 85748Garching, Germany
| | - Ana-Sofia Ortega-Arbulú
- TUM School of Engineering and Design, Systems Biotechnology, Technical University Munich, 85748Garching, Germany
| | - Hannes Löwe
- TUM School of Engineering and Design, Systems Biotechnology, Technical University Munich, 85748Garching, Germany
| | - Katharina Pflüger-Grau
- TUM School of Engineering and Design, Systems Biotechnology, Technical University Munich, 85748Garching, Germany
| | - Andreas Kremling
- TUM School of Engineering and Design, Systems Biotechnology, Technical University Munich, 85748Garching, Germany
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2
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Calvopina-Chavez DG, Gardner MA, Griffitts JS. Engineering efficient termination of bacteriophage T7 RNA polymerase transcription. G3 (BETHESDA, MD.) 2022; 12:jkac070. [PMID: 35348690 PMCID: PMC9157156 DOI: 10.1093/g3journal/jkac070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
The bacteriophage T7 expression system is one of the most prominent transcription systems used in biotechnology and molecular-level research. However, T7 RNA polymerase is prone to read-through transcription due to its high processivity. As a consequence, enforcing efficient transcriptional termination is difficult. The termination hairpin found natively in the T7 genome is adapted to be inefficient, exhibiting 62% termination efficiency in vivo and even lower efficiency in vitro. In this study, we engineered a series of sequences that outperform the efficiency of the native terminator hairpin. By embedding a previously discovered 8-nucleotide T7 polymerase pause sequence within a synthetic hairpin sequence, we observed in vivo termination efficiency of 91%; by joining 2 short sequences into a tandem 2-hairpin structure, termination efficiency was increased to 98% in vivo and 91% in vitro. This study also tests the ability of these engineered sequences to terminate transcription of the Escherichia coli RNA polymerase. Two out of 3 of the most successful T7 polymerase terminators also facilitated termination of the bacterial polymerase with around 99% efficiency.
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Affiliation(s)
- Diana G Calvopina-Chavez
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Mikaela A Gardner
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Joel S Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
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3
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Cui W, Lin Q, Hu R, Han L, Cheng Z, Zhang L, Zhou Z. Data-Driven and in Silico-Assisted Design of Broad Host-Range Minimal Intrinsic Terminators Adapted for Bacteria. ACS Synth Biol 2021; 10:1438-1450. [PMID: 34015924 DOI: 10.1021/acssynbio.1c00050] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Efficient transcription termination relying on intrinsic terminators is critical to maintain cell fitness by avoiding unwanted read-through in bacteria. Natural intrinsic terminator (NIT) typically appears in mRNA as a hairpin followed by approximately eight conserved uridines (U-tract) at the 3' terminus. Owing to their simple structure, small size, and protein independence, assorted NITs have been redesigned as robust tools to construct gene circuits. However, most NITs exert functions to adapt to their physiological requirements rather than the demand for building synthetic gene circuits, rendering uncertain working performance when they are constructed intact in synthetic gene circuits. Here, rather than modifying NITs, we established a data-driven and in silico-assisted (DISA) design framework to forward engineer minimal intrinsic terminators (MITs). By comprehensively analyzing 75 natural intrinsic terminators from Bacillus subtilis, we revealed that two pivotal features, the length of the U-tract and the thermodynamics of the terminator hairpin, were involved in the sequence-activity relationship (SAR) of termination efficiency (TE). As per the SAR, we leveraged DISA to fabricate an array of MITs composed of in silico-assisted designed minimal hairpins and fixed U-tracts. Most of these MITs exhibited high TE in diverse Gram-positive and Gram-negative bacteria. In contrast, the TEs of the NITs were highly varied in different hosts. Moreover, TEs of MITs were flexibly tuned over a wide range by modulating the length of the U-tract. Overall, these results demonstrate an efficient framework to forward design functional and broad host-range terminators independent of tedious and iterative screening of mutagenesis libraries of natural terminators.
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Affiliation(s)
- Wenjing Cui
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qiao Lin
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ruichun Hu
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Laichuang Han
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Linpei Zhang
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Jiangnan University (Rugao) Food Biotechnology Research Institute, Rugao, Jiangsu 226500, China
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4
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Abstract
One of the fundamental properties of engineered large-scale complex systems is modularity. In synthetic biology, genetic parts exhibit context-dependent behavior. Here, we describe and quantify a major source of such behavior: retroactivity. In particular, we provide a step-by-step guide for characterizing retroactivity to restore the modular description of genetic modules. Additionally, we also discuss how retroactivity can be leveraged to quantify and maximize robustness to perturbations due to interconnection of genetic modules.
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Affiliation(s)
- Andras Gyorgy
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
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5
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Sim J, Baek MS, Lee KH, Kim DM, Byun JY, Shin YB. A highly sensitive and versatile transcription immunoassay using a DNA-encoding tandem repetitive light-up aptamer. Talanta 2020; 224:121921. [PMID: 33379122 DOI: 10.1016/j.talanta.2020.121921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/19/2020] [Accepted: 11/22/2020] [Indexed: 10/22/2022]
Abstract
Highly sensitive and accurate measurements of protein biomarkers are crucial for early diagnosis and disease monitoring. Here we report a versatile detection platform for sensitive detection of a protein biomarker using a tandem repeat Spinach aptamer DNA-based transcription immunoassay, which is a immunoassay combined with transcription-assisted Spinach RNA aptamer generation. We designed a DNA template encoding spa tandem repetitive Spinach sequence for enhanced generation of an RNA aptamer. The tandem repeated Spinach DNA template is consist of multiple monomeric units which is composed of T7 promoter, Spinach-2 and terminator. After in vitro transcription, the fluorescence signal from the 16R (nR, n = number of repeats) DNA template was enhanced up to ~ 15-fold compared to a single form (1R) DNA template. Using tandem repeat DNA, the proposed transcription immunoassay showed a limit of detection (LOD) of 37 aM, which is 103-fold lower than that of the conventional enzyme-linked immunosorbent assay (ELISA). The results demonstrate substantial promise for the ultrasensitive detection of various biological analytes using simple ELISA techniques. The high sensitivity and reliability of the proposed transcription immunoassay offer great promise for clinical assays.
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Affiliation(s)
- Jieun Sim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, North Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, North Korea; BioNano Health Guard Research Center (H-GUARD), Daejeon, 34141, North Korea
| | - Min-Seok Baek
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 305-764, North Korea
| | - Kyung-Ho Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 305-764, North Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 305-764, North Korea
| | - Ju-Young Byun
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, North Korea.
| | - Yong-Beom Shin
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, North Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, North Korea; BioNano Health Guard Research Center (H-GUARD), Daejeon, 34141, North Korea.
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6
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He Z, Duan Y, Zhai W, Zhang X, Shi J, Zhang X, Xu Z. Evaluating Terminator Strength Based on Differentiating Effects on Transcription and Translation. Chembiochem 2020; 21:2067-2072. [PMID: 32180310 DOI: 10.1002/cbic.202000068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/27/2020] [Indexed: 11/05/2022]
Abstract
Transcription terminators play a role in terminating the progress of gene transcription, and are thus essential elements in the gene circuit. Terminators have two main functions: terminating gene transcription and improving the stability of gene transcripts during translation. We therefore considered the detailed characteristics of terminators in relation to their different roles in gene transcription and translation, including transcription shut-down degree (α) and upstream mRNA protection capacity (β), and apparent termination efficiency (η) reflecting the overall regulatory effect of the terminator. Based on a dual-reporter gene system, we constructed three terminator-probe plasmids to investigate each characteristic in Escherichia coli. According to multiple regression analysis, the transcription shut-down degree and the upstream mRNA protection capacity contributed almost equally to the apparent termination efficiency. Sequence analysis of 12 terminators demonstrated that the terminator sequence was dominated by GC bases, and that a high ratio of GC bases in the stem structure of terminators might be associated with a high degree of transcription shut-down. This comprehensive characterization of terminators furthers our understanding of the role of terminators in gene expression and provides a guide for synthetic terminator design.
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Affiliation(s)
- Zhiyun He
- The Key Laboratory of Industrial Biotechnology of Ministry of Education School of Biotechnology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China
| | - Yanting Duan
- The Key Laboratory of Industrial Biotechnology of Ministry of Education School of Biotechnology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China
| | - Weiji Zhai
- The Key Laboratory of Industrial Biotechnology of Ministry of Education School of Biotechnology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China
| | - Xiaomei Zhang
- Jiangsu Engineering Research Center for Bioactive Products Processing Technology, Jiangnan University, No. 1800, Lihu Avenue, Wuxi, 214122, China.,School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China
| | - Jinsong Shi
- Jiangsu Engineering Research Center for Bioactive Products Processing Technology, Jiangnan University, No. 1800, Lihu Avenue, Wuxi, 214122, China.,School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China
| | - Xiaojuan Zhang
- The Key Laboratory of Industrial Biotechnology of Ministry of Education School of Biotechnology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China.,Jiangsu Engineering Research Center for Bioactive Products Processing Technology, Jiangnan University, No. 1800, Lihu Avenue, Wuxi, 214122, China
| | - Zhenghong Xu
- The Key Laboratory of Industrial Biotechnology of Ministry of Education School of Biotechnology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800, Lihu Avenue, Wuxi, 214122, China
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7
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Wang W, Li Y, Wang Y, Shi C, Li C, Li Q, Linhardt RJ. Bacteriophage T7 transcription system: an enabling tool in synthetic biology. Biotechnol Adv 2018; 36:2129-2137. [DOI: 10.1016/j.biotechadv.2018.10.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/30/2018] [Accepted: 10/01/2018] [Indexed: 10/28/2022]
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8
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Shepherd TR, Du L, Liljeruhm J, Samudyata, Wang J, Sjödin MOD, Wetterhall M, Yomo T, Forster AC. De novo design and synthesis of a 30-cistron translation-factor module. Nucleic Acids Res 2017; 45:10895-10905. [PMID: 28977654 PMCID: PMC5737471 DOI: 10.1093/nar/gkx753] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 08/17/2017] [Indexed: 11/17/2022] Open
Abstract
Two of the many goals of synthetic biology are synthesizing large biochemical systems and simplifying their assembly. While several genes have been assembled together by modular idempotent cloning, it is unclear if such simplified strategies scale to very large constructs for expression and purification of whole pathways. Here we synthesize from oligodeoxyribonucleotides a completely de-novo-designed, 58-kb multigene DNA. This BioBrick plasmid insert encodes 30 of the 31 translation factors of the PURE translation system, each His-tagged and in separate transcription cistrons. Dividing the insert between three high-copy expression plasmids enables the bulk purification of the aminoacyl-tRNA synthetases and translation factors necessary for affordable, scalable reconstitution of an in vitro transcription and translation system, PURE 3.0.
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Affiliation(s)
- Tyson R Shepherd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 36, Sweden
| | - Liping Du
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Josefine Liljeruhm
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 36, Sweden
| | - Samudyata
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 36, Sweden
| | - Jinfan Wang
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 36, Sweden
| | - Marcus O D Sjödin
- Department of Physical and Analytical Chemistry, Uppsala University, Uppsala 751 23, Sweden
| | - Magnus Wetterhall
- Department of Physical and Analytical Chemistry, Uppsala University, Uppsala 751 23, Sweden
| | - Tetsuya Yomo
- Institute of Biology and Information Science, School of Computer Science and Software Engineering, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Anthony C Forster
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 36, Sweden.,Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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9
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Promoter and Terminator Discovery and Engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:21-44. [PMID: 27277391 DOI: 10.1007/10_2016_8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Control of gene expression is crucial to optimize metabolic pathways and synthetic gene networks. Promoters and terminators are stretches of DNA upstream and downstream (respectively) of genes that control both the rate at which the gene is transcribed and the rate at which mRNA is degraded. As a result, both of these elements control net protein expression from a synthetic construct. Thus, it is highly important to discover and engineer promoters and terminators with desired characteristics. This chapter highlights various approaches taken to catalogue these important synthetic elements. Specifically, early strategies have focused largely on semi-rational techniques such as saturation mutagenesis to diversify native promoters and terminators. Next, in an effort to reduce the length of the synthetic biology design cycle, efforts in the field have turned towards the rational design of synthetic promoters and terminators. In this vein, we cover recently developed methods such as hybrid engineering, high throughput characterization, and thermodynamic modeling which allow finer control in the rational design of novel promoters and terminators. Emphasis is placed on the methodologies used and this chapter showcases the utility of these methods across multiple host organisms.
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10
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Mairhofer J, Wittwer A, Cserjan-Puschmann M, Striedner G. Preventing T7 RNA polymerase read-through transcription-A synthetic termination signal capable of improving bioprocess stability. ACS Synth Biol 2015; 4:265-73. [PMID: 24847676 DOI: 10.1021/sb5000115] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The phage-derived T7 RNA polymerase is the most prominent orthogonal transcriptions system used in the field of synthetic biology. However, gene expression driven by T7 RNA polymerase is prone to read-through transcription due to contextuality of the T7 terminator. The native T7 terminator has a termination efficiency of approximately 80% and therefore provides insufficient insulation of the expression unit. By using a combination of a synthetic T7 termination signal with two well-known transcriptional terminators (rrnBT1 and T7), we have been able to increase the termination efficiency to 99%. To characterize putative effects of an enhanced termination signal on product yield and process stability, industrial-relevant fed batch cultivations have been performed. Fermentation of a E. coli HMS174(DE3) strain carrying a pET30a derivative containing the improved termination signal showed a significant decrease of plasmid copy number (PCN) and an increase in total protein yield under standard conditions.
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Affiliation(s)
- Juergen Mairhofer
- Department
of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
- Austrian Centre
of Industrial Biotechnology GmbH (ACIB), Petersgasse 14, A-8010 Graz, Austria
| | - Alexander Wittwer
- Department
of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
- Austrian Centre
of Industrial Biotechnology GmbH (ACIB), Petersgasse 14, A-8010 Graz, Austria
| | - Monika Cserjan-Puschmann
- Department
of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
- Austrian Centre
of Industrial Biotechnology GmbH (ACIB), Petersgasse 14, A-8010 Graz, Austria
| | - Gerald Striedner
- Department
of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
- Austrian Centre
of Industrial Biotechnology GmbH (ACIB), Petersgasse 14, A-8010 Graz, Austria
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11
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An amino acid depleted cell-free protein synthesis system for the incorporation of non-canonical amino acid analogs into proteins. J Biotechnol 2014; 178:12-22. [DOI: 10.1016/j.jbiotec.2014.02.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 02/08/2014] [Accepted: 02/14/2014] [Indexed: 11/19/2022]
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12
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Spencer AC, Torre P, Mansy SS. The encapsulation of cell-free transcription and translation machinery in vesicles for the construction of cellular mimics. J Vis Exp 2013:e51304. [PMID: 24192867 PMCID: PMC3948186 DOI: 10.3791/51304] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
As interest shifts from individual molecules to systems of molecules, an increasing number of laboratories have sought to build from the bottom up cellular mimics that better represent the complexity of cellular life. To date there are a number of paths that could be taken to build compartmentalized cellular mimics, including the exploitation of water-in-oil emulsions, microfluidic devices, and vesicles. Each of the available options has specific advantages and disadvantages. For example, water-in-oil emulsions give high encapsulation efficiency but do not mimic well the permeability barrier of living cells. The primary advantage of the methods described herein is that they are all easy and cheap to implement. Transcription-translation machinery is encapsulated inside of phospholipid vesicles through a process that exploits common instrumentation, such as a centrifugal evaporator and an extruder. Reactions are monitored by fluorescence spectroscopy. The protocols can be adapted for recombinant protein expression, the construction of cellular mimics, the exploration of the minimum requirements for cellular life, or the assembly of genetic circuitry.
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Affiliation(s)
- Amy C Spencer
- Centre for Integrative Biology, University of Trento
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13
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Comparative transcription profiling and in-depth characterization of plasmid-based and plasmid-free Escherichia coli expression systems under production conditions. Appl Environ Microbiol 2013; 79:3802-12. [PMID: 23584782 DOI: 10.1128/aem.00365-13] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plasmid-based Escherichia coli BL21(DE3) expression systems are extensively used for the production of recombinant proteins. However, the combination of a high gene dosage with strong promoters exerts extremely stressful conditions on producing cells, resulting in a multitude of protective reactions and malfunctions in the host cell with a strong impact on yield and quality of the product. Here, we provide in-depth characterization of plasmid-based perturbations in recombinant protein production. A plasmid-free T7 system with a single copy of the gene of interest (GOI) integrated into the genome was used as a reference. Transcriptomics in combination with a variety of process analytics were used to characterize and compare a plasmid-free T7-based expression system to a conventional pET-plasmid-based expression system, with both expressing human superoxide dismutase in fed-batch cultivations. The plasmid-free system showed a moderate stress response on the transcriptional level, with only minor effects on cell growth. In contrast to this finding, comprehensive changes on the transcriptome level were observed in the plasmid-based expression system and cell growth was heavily impaired by recombinant gene expression. Additionally, we found that the T7 terminator is not a sufficient termination signal. Overall, this work reveals that the major metabolic burden in plasmid-based systems is caused at the level of transcription as a result of overtranscription of the multicopy product gene and transcriptional read-through of T7 RNA polymerase. We therefore conclude that the presence of high levels of extrinsic mRNAs, competing for the limited number of ribosomes, leads to the significantly reduced translation of intrinsic mRNAs.
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14
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Frasch HJ, Medema MH, Takano E, Breitling R. Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice. Curr Opin Biotechnol 2013; 24:1144-50. [PMID: 23540422 DOI: 10.1016/j.copbio.2013.03.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/05/2013] [Indexed: 11/18/2022]
Abstract
Synthetic biology is revolutionizing the way in which the biosphere is explored for natural products. Through computational genome mining, thousands of biosynthetic gene clusters are being identified in microbial genomes, which constitute a rich source of potential novel pharmaceuticals. New methods are currently being devised to prioritize these gene clusters in terms of their potential for yielding biochemical novelty. High-potential gene clusters from any biological source can then be activated by 'refactoring' their native regulatory machinery, replacing it by synthetic, orthogonal regulation and optimizing enzyme expression to function effectively in an industry-compatible target host. Various part libraries and assembly technologies have recently been developed which facilitate this process.
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Affiliation(s)
- Hans-Jörg Frasch
- Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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15
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Xu P, Koffas MAG. Assembly of multi-gene pathways and combinatorial pathway libraries through ePathBrick vectors. Methods Mol Biol 2013; 1073:107-129. [PMID: 23996443 DOI: 10.1007/978-1-62703-625-2_10] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
As an emerging discipline, synthetic biology is becoming increasingly important to design, construct, and optimize metabolic pathways leading to desired phenotypes such as overproduction of biofuels and pharmaceuticals in genetically tractable organisms. We have recently developed a versatile gene assembly platform ePathBricks supporting the modular assembly of multi-gene pathway components and combinatorial generation of pathway diversities. In this protocol, we will detail the process to assemble a seven gene flavonoid pathway (~9 kb) on one single ePathBrick vector. We will also demonstrate that a three-gene flavonoid pathway can be easily diversified to 54 pathway equivalents differing in pathway configuration and gene order; coupled with high-throughput screening techniques, we envision that this combinatorial strategy would greatly improve our ability to exploit the full potential of microbial cell factories for recombinant metabolite production.
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Affiliation(s)
- Peng Xu
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
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16
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Engineering plant metabolism into microbes: from systems biology to synthetic biology. Curr Opin Biotechnol 2012; 24:291-9. [PMID: 22985679 DOI: 10.1016/j.copbio.2012.08.010] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 08/21/2012] [Accepted: 08/27/2012] [Indexed: 12/11/2022]
Abstract
Plant metabolism represents an enormous repository of compounds that are of pharmaceutical and biotechnological importance. Engineering plant metabolism into microbes will provide sustainable solutions to produce pharmaceutical and fuel molecules that could one day replace substantial portions of the current fossil-fuel based economy. Metabolic engineering entails targeted manipulation of biosynthetic pathways to maximize yields of desired products. Recent advances in Systems Biology and the emergence of Synthetic Biology have accelerated our ability to design, construct and optimize cell factories for metabolic engineering applications. Progress in predicting and modeling genome-scale metabolic networks, versatile gene assembly platforms and delicate synthetic pathway optimization strategies has provided us exciting opportunities to exploit the full potential of cell metabolism. In this review, we will discuss how systems and synthetic biology tools can be integrated to create tailor-made cell factories for efficient production of natural products and fuel molecules in microorganisms.
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17
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Forster AC. Synthetic biology challenges long-held hypotheses in translation, codon bias and transcription. Biotechnol J 2012; 7:835-45. [DOI: 10.1002/biot.201200002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 04/28/2012] [Accepted: 05/08/2012] [Indexed: 11/09/2022]
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Cardinale S, Arkin AP. Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems. Biotechnol J 2012; 7:856-66. [PMID: 22649052 PMCID: PMC3440575 DOI: 10.1002/biot.201200085] [Citation(s) in RCA: 250] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/12/2012] [Accepted: 05/04/2012] [Indexed: 12/19/2022]
Abstract
Despite the efforts that bioengineers have exerted in designing and constructing biological processes that function according to a predetermined set of rules, their operation remains fundamentally circumstantial. The contextual situation in which molecules and single-celled or multi-cellular organisms find themselves shapes the way they interact, respond to the environment and process external information. Since the birth of the field, synthetic biologists have had to grapple with contextual issues, particularly when the molecular and genetic devices inexplicably fail to function as designed when tested in vivo. In this review, we set out to identify and classify the sources of the unexpected divergences between design and actual function of synthetic systems and analyze possible methodologies aimed at controlling, if not preventing, unwanted contextual issues.
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Affiliation(s)
- Stefano Cardinale
- Physical Biosciences Division, LBNL, Department of Bioengineering, University of California, Berkeley, CA, USA
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Wang HH, Huang PY, Xu G, Haas W, Marblestone A, Li J, Gygi SP, Forster AC, Jewett MC, Church GM. Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis. ACS Synth Biol 2012; 1:43-52. [PMID: 22737598 DOI: 10.1021/sb3000029] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein pathways are dynamic and highly coordinated spatially and temporally, capable of performing a diverse range of complex chemistries and enzymatic reactions with precision and at high efficiency. Biotechnology aims to harvest these natural systems to construct more advanced in vitro reactions, capable of new chemistries and operating at high yield. Here, we present an efficient Multiplex Automated Genome Engineering (MAGE) strategy to simultaneously modify and co-purify large protein complexes and pathways from the model organism Escherichia coli to reconstitute functional synthetic proteomes in vitro. By application of over 110 MAGE cycles, we successfully inserted hexa-histidine sequences into 38 essential genes in vivo that encode for the entire translation machinery. Streamlined co-purification and reconstitution of the translation protein complex enabled protein synthesis in vitro. Our approach can be applied to a growing area of applications in in vitro one-pot multienzyme catalysis (MEC) to manipulate or enhance in vitro pathways such as natural product or carbohydrate biosynthesis.
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Affiliation(s)
| | | | - George Xu
- Program in
Medical Engineering
Medical Physics, Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts 02139, United
States
| | | | | | | | | | - Anthony C. Forster
- Department of Cell
and Molecular
Biology, Uppsala University, Uppsala 75124,
Sweden
| | - Michael C. Jewett
- Department of Chemical
and Biological
Engineering and Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208,
United States
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