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Schaffter SW, Kengmana E, Fern J, Byrne SR, Schulman R. Strategies to Reduce Promoter-Independent Transcription of DNA Nanostructures and Strand Displacement Complexes. ACS Synth Biol 2024. [PMID: 38885464 DOI: 10.1021/acssynbio.3c00726] [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: 06/20/2024]
Abstract
Bacteriophage RNA polymerases, in particular T7 RNA polymerase (RNAP), are well-characterized and popular enzymes for many RNA applications in biotechnology both in vitro and in cellular settings. These monomeric polymerases are relatively inexpensive and have high transcription rates and processivity to quickly produce large quantities of RNA. T7 RNAP also has high promoter-specificity on double-stranded DNA (dsDNA) such that it only initiates transcription downstream of its 17-base promoter site on dsDNA templates. However, there are many promoter-independent T7 RNAP transcription reactions involving transcription initiation in regions of single-stranded DNA (ssDNA) that have been reported and characterized. These promoter-independent transcription reactions are important to consider when using T7 RNAP transcriptional systems for DNA nanotechnology and DNA computing applications, in which ssDNA domains often stabilize, organize, and functionalize DNA nanostructures and facilitate strand displacement reactions. Here we review the existing literature on promoter-independent transcription by bacteriophage RNA polymerases with a specific focus on T7 RNAP, and provide examples of how promoter-independent reactions can disrupt the functionality of DNA strand displacement circuit components and alter the stability and functionality of DNA-based materials. We then highlight design strategies for DNA nanotechnology applications that can mitigate the effects of promoter-independent T7 RNAP transcription. The design strategies we present should have an immediate impact by increasing the rate of success of using T7 RNAP for applications in DNA nanotechnology and DNA computing.
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Affiliation(s)
- Samuel W Schaffter
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Eli Kengmana
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joshua Fern
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Shane R Byrne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Rebecca Schulman
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
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2
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Schumann A, Cohn AR, Gaballa A, Wiedmann M. Escherichia coli B-Strains Are Intrinsically Resistant to Colistin and Not Suitable for Characterization and Identification of mcr Genes. Microbiol Spectr 2023; 11:e0089423. [PMID: 37199645 PMCID: PMC10269513 DOI: 10.1128/spectrum.00894-23] [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: 03/02/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
Antimicrobial resistance is an increasing threat to human and animal health. Due to the rise of multi-, extensive, and pandrug resistance, last resort antibiotics, such as colistin, are extremely important in human medicine. While the distribution of colistin resistance genes can be tracked through sequencing methods, phenotypic characterization of putative antimicrobial resistance (AMR) genes is still important to confirm the phenotype conferred by different genes. While heterologous expression of AMR genes (e.g., in Escherichia coli) is a common approach, so far, no standard methods for heterologous expression and characterization of mcr genes exist. E. coli B-strains, designed for optimum protein expression, are frequently utilized. Here, we report that four E. coli B-strains are intrinsically resistant to colistin (MIC 8-16 μg/mL). The three tested B-strains that encode T7 RNA polymerase show growth defects when transformed with empty or mcr-expressing pET17b plasmids and grown in the presence of IPTG; K-12 or B-strains without T7 RNA polymerase do not show these growth defects. E. coli SHuffle T7 express carrying empty pET17b also skips wells in colistin MIC assays in the presence of IPTG. These phenotypes could explain why B-strains were erroneously reported as colistin susceptible. Analysis of existing genome data identified one nonsynonymous change in each pmrA and pmrB in all four E. coli B-strains; the E121K change in PmrB has previously been linked to intrinsic colistin resistance. We conclude that E. coli B-strains are not appropriate heterologous expression hosts for identification and characterization of mcr genes. IMPORTANCE Given the rise in multidrug, extensive drug, and pandrug resistance in bacteria and the increasing use of colistin to treat human infections, occurrence of mcr genes threatens human health, and characterization of these resistance genes becomes more important. We show that three commonly used heterologous expression strains are intrinsically resistant to colistin. This is important because these strains have previously been used to characterize and identify new mobile colistin resistance (mcr) genes. We also show that expression plasmids (i.e., pET17b) without inserts cause cell viability defects when carried by B-strains with T7 RNA polymerase and grown in the presence of IPTG. Our findings are important as they will facilitate improved selection of heterologous strains and plasmid combinations for characterizing AMR genes, which will be particularly important with a shift to Culture-independent diagnostic tests where bacterial isolates become increasingly less available for characterization.
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Affiliation(s)
- Anna Schumann
- Department of Food Science, Cornell University, Ithaca, New York, USA
- Graduate Field of Biomedical and Biological Sciences, Cornell University, Ithaca, New York, USA
| | - Alexa R. Cohn
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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3
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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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Liang X, Deng H, Xiong T, Bai Y, Fan TP, Zheng X, Cai Y. Overexpression and biochemical characterization of a carboxyspermidine dehydrogenase from Agrobacterium fabrum str. C58 and its application to carboxyspermidine production. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:3858-3868. [PMID: 34932223 DOI: 10.1002/jsfa.11735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/18/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Carboxyspermidine (C-Spd) is a potentially valuable polyamine carboxylate compound and an excellent building block for spermidine synthesis, which is a critical polyamine with significant implications for human health and longevity. C-Spd can also be used to prepare multivalent cationic lipids and modify nucleoside probes. Because of these positive effects on human health, C-Spd is of considerable interest as a food additive and pharmaceutical target. RESULTS A putative gene afcasdh from Agrobacterium fabrum str. C58, encoding carboxyspermidine dehydrogenase with C-Spd biosynthesis activity, was synthesized and transformed into Escherichia coli BL21 (DE3) for overexpression. The recombinant AfCASDH was purified and fully characterized. The optimum temperature and pH for the recombinant enzyme were 30 °C and 7.5, respectively. The coupled catalytic strategy of AfCASDH and various NADPH regeneration systems were developed to enhance the efficient production of C-Spd compound. Finally, the maximum titer of C-Spd production successfully achieved 1.82 mmol L-1 with a yield of 91% by optimizing the catalytic conditions. CONCLUSION A novel AfCASDH from A. fabrum str. C58 was characterized that could catalyze the formation of C-Spd from putrescine and l-aspartate-β-semialdehyde (L-Asa). A whole-cell catalytic strategy coupled with NADPH regeneration was established successfully for C-Spd biosynthesis for the first time. The coupled system indicated that AfCASDH might provide a feasible method for the industrial production of C-Spd. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Xinxin Liang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Huaxiang Deng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Tianzhen Xiong
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, China
| | - Yujie Cai
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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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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6
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Tarnowski MJ, Gorochowski TE. Massively parallel characterization of engineered transcript isoforms using direct RNA sequencing. Nat Commun 2022; 13:434. [PMID: 35064117 PMCID: PMC8783025 DOI: 10.1038/s41467-022-28074-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 01/07/2022] [Indexed: 12/23/2022] Open
Abstract
Transcriptional terminators signal where transcribing RNA polymerases (RNAPs) should halt and disassociate from DNA. However, because termination is stochastic, two different forms of transcript could be produced: one ending at the terminator and the other reading through. An ability to control the abundance of these transcript isoforms would offer bioengineers a mechanism to regulate multi-gene constructs at the level of transcription. Here, we explore this possibility by repurposing terminators as 'transcriptional valves' that can tune the proportion of RNAP read-through. Using one-pot combinatorial DNA assembly, we iteratively construct 1780 transcriptional valves for T7 RNAP and show how nanopore-based direct RNA sequencing (dRNA-seq) can be used to characterize entire libraries of valves simultaneously at a nucleotide resolution in vitro and unravel genetic design principles to tune and insulate termination. Finally, we engineer valves for multiplexed regulation of CRISPR guide RNAs. This work provides new avenues for controlling transcription and demonstrates the benefits of long-read sequencing for exploring complex sequence-function landscapes.
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Affiliation(s)
- Matthew J Tarnowski
- School of Biological Sciences, University of Bristol, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Thomas E Gorochowski
- School of Biological Sciences, University of Bristol, Tyndall Avenue, Bristol, BS8 1TQ, UK.
- BrisSynBio, University of Bristol, Tyndall Avenue, Bristol, BS8 1TQ, UK.
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7
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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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8
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Tiwari P, Khare T, Shriram V, Bae H, Kumar V. Plant synthetic biology for producing potent phyto-antimicrobials to combat antimicrobial resistance. Biotechnol Adv 2021; 48:107729. [PMID: 33705914 DOI: 10.1016/j.biotechadv.2021.107729] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/22/2021] [Accepted: 03/04/2021] [Indexed: 12/14/2022]
Abstract
Inappropriate and injudicious use of antimicrobial drugs in human health, hygiene, agriculture, animal husbandry and food industries has contributed significantly to rapid emergence and persistence of antimicrobial resistance (AMR), one of the serious global public health threats. The crisis of AMR versus slower discovery of newer antibiotics put forth a daunting task to control these drug-resistant superbugs. Several phyto-antimicrobials have been identified in recent years with direct-killing (bactericidal) and/or drug-resistance reversal (re-sensitization of AMR phenotypes) potencies. Phyto-antimicrobials may hold the key in combating AMR owing to their abilities to target major microbial drug-resistance determinants including cell membrane, drug-efflux pumps, cell communication and biofilms. However, limited distribution, low intracellular concentrations, eco-geographical variations, beside other considerations like dynamic environments, climate change and over-exploitation of plant-resources are major blockades in full potential exploration phyto-antimicrobials. Synthetic biology (SynBio) strategies integrating metabolic engineering, RNA-interference, genome editing/engineering and/or systems biology approaches using plant chassis (as engineerable platforms) offer prospective tools for production of phyto-antimicrobials. With expanding SynBio toolkit, successful attempts towards introduction of entire gene cluster, reconstituting the metabolic pathway or transferring an entire metabolic (or synthetic) pathway into heterologous plant systems highlight the potential of this field. Through this perspective review, we are presenting herein the current situation and options for addressing AMR, emphasizing on the significance of phyto-antimicrobials in this apparently post-antibiotic era, and effective use of plant chassis for phyto-antimicrobial production at industrial scales along with major SynBio tools and useful databases. Current knowledge, recent success stories, associated challenges and prospects of translational success are also discussed.
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Affiliation(s)
- Pragya Tiwari
- Molecular Metabolic Engineering Lab, Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
| | - Tushar Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune 411016, India; Department of Environmental Science, Savitribai Phule Pune University, Pune 411007, India
| | - Varsha Shriram
- Department of Botany, Prof. Ramkrishna More Arts, Commerce and Science College, Savitribai Phule Pune University, Akurdi, Pune 411044, India
| | - Hanhong Bae
- Molecular Metabolic Engineering Lab, Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune 411016, India; Department of Environmental Science, Savitribai Phule Pune University, Pune 411007, India.
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9
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Batista AC, Soudier P, Kushwaha M, Faulon J. Optimising protein synthesis in cell‐free systems, a review. ENGINEERING BIOLOGY 2021; 5:10-19. [PMID: 36968650 PMCID: PMC9996726 DOI: 10.1049/enb2.12004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 12/25/2022] Open
Abstract
Over the last decades, cell-free systems have been extensively used for in vitro protein expression. A vast range of protocols and cellular sources varying from prokaryotes and eukaryotes are now available for cell-free technology. However, exploiting the maximum capacity of cell free systems is not achieved by using traditional protocols. Here, what are the strategies and choices one can apply to optimise cell-free protein synthesis have been reviewed. These strategies provide robust and informative improvements regarding transcription, translation and protein folding which can later be used for the establishment of individual best cell-free reactions per lysate batch.
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Affiliation(s)
- Angelo C. Batista
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
| | - Paul Soudier
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
| | - Manish Kushwaha
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
| | - Jean‐Loup Faulon
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
- SYNBIOCHEM Center School of Chemistry Manchester Institute of Biotechnology The University of Manchester Manchester UK
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10
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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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11
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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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12
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Wang B, Xu J, Gao J, Fu X, Han H, Li Z, Wang L, Tian Y, Peng R, Yao Q. Construction of an Escherichia coli strain to degrade phenol completely with two modified metabolic modules. JOURNAL OF HAZARDOUS MATERIALS 2019; 373:29-38. [PMID: 30901683 DOI: 10.1016/j.jhazmat.2019.03.055] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/01/2019] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
Phenol is a common water pollutant because of its broad industrial applications. Biological method is a promising alternative to conventional physical and chemical methods for removing this toxic pollutant from the environment. In this study, two metabolic modules were introduced into Escherichia coli, the widely used host for various genetic manipulations, to elucidate the metabolic capacity of E. coli for phenol degradation. The first module catalysed the conversion of phenol to catechol, whereas the second module cleaved catechol into the three carboxylic acid circulating intermediates by the ortho-cleavage pathway. Phenol was completely degraded and imported into the tricarboxylic acid cycle by the engineered bacteria. Proteomics analysis showed that all genes in the phenol degradation pathway were over-expressed and affected cell division and energy metabolism of the host cells. Phenol in coking wastewater was degraded powerfully by BL-phe/cat. The engineered E. coli can improve the removal rate and shorten the processing time for phenol removal and has considerable potential in the treatment of toxic and harmful pollutants.
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Affiliation(s)
- Bo Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jing Xu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jianjie Gao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Xiaoyan Fu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Hongjuan Han
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Zhenjun Li
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Lijuan Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Yongsheng Tian
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
| | - Rihe Peng
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
| | - Quanhong Yao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
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13
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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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14
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Kim J, Yoo HW, Kim M, Kim EJ, Sung C, Lee PG, Park BG, Kim BG. Rewiring FadR regulon for the selective production of ω-hydroxy palmitic acid from glucose in Escherichia coli. Metab Eng 2018; 47:414-422. [PMID: 29719215 DOI: 10.1016/j.ymben.2018.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/19/2018] [Accepted: 04/28/2018] [Indexed: 12/28/2022]
Abstract
ω-Hydroxy palmitic acid (ω-HPA) is a valuable compound for an ingredient of artificially synthesized ceramides and an additive for lubricants and adhesives. Production of such a fatty acid derivative is limited by chemical catalysis, but plausible by biocatalysis. However, its low productivity issue, including formations of unsaturated fatty acid (UFA) byproducts in host cells, remains as a hurdle toward industrial biological processes. In this study, to achieve selective and high-level production of ω-HPA from glucose in Escherichia coli, FadR, a native transcriptional regulator of fatty acid metabolism, and its regulon were engineered. First, FadR was co-expressed with a thioesterase with a specificity toward palmitic acid production to enhance palmitic acid production yield, but a considerable quantity of UFAs was also produced. In order to avoid the UFA production caused by fadR overexpression, FadR regulon was rewired by i) mutating FadR consensus binding sites of fabA or fabB, ii) integrating fabZ into fabI operon, and iii) enhancing the strength of fabI promoter. This approach led to dramatic increases in both proportion (48.3-83.0%) and titer (377.8 mg/L to 675.8 mg/L) of palmitic acid, mainly due to the decrease in UFA synthesis. Introducing a fatty acid ω-hydroxylase, CYP153A35, into the engineered strain resulted in a highly selective production of ω-HPA (83.5 mg/L) accounting for 87.5% of total ω-hydroxy fatty acids. Furthermore, strategies, such as i) enhancement in CYP153A35 activity, ii) expression of a fatty acid transporter, iii) supplementation of triton X-100, and iv) separation of the ω-HPA synthetic pathway into two strains for a co-culture system, were applied and resulted in 401.0 mg/L of ω-HPA production. For such selective productions of palmitic acid and ω-HPA, the rewiring of FadR regulation in E. coli is a promising strategy to develop an industrial process with economical downstream processing.
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Affiliation(s)
- Joonwon Kim
- School of Chemical and Biological Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Hee-Wang Yoo
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea; Interdisciplinary Program of Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Minsuk Kim
- Institute of Engineering Research, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun-Jung Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea; Bio-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Changmin Sung
- Doping Control Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Pyung-Gang Lee
- School of Chemical and Biological Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Beom Gi Park
- School of Chemical and Biological Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea; Interdisciplinary Program of Bioengineering, Seoul National University, Seoul 08826, Republic of Korea; Institute of Engineering Research, Seoul National University, Seoul 08826, Republic of Korea.
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15
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van Nies P, Westerlaken I, Blanken D, Salas M, Mencía M, Danelon C. Self-replication of DNA by its encoded proteins in liposome-based synthetic cells. Nat Commun 2018; 9:1583. [PMID: 29679002 PMCID: PMC5910420 DOI: 10.1038/s41467-018-03926-1] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/22/2018] [Indexed: 12/31/2022] Open
Abstract
Replication of DNA-encoded information and its conversion into functional proteins are universal properties of life. In an effort toward the construction of a synthetic minimal cell, we implement here the DNA replication machinery of the Φ29 virus in a cell-free gene expression system. Amplification of a linear DNA template by self-encoded, de novo synthesized Φ29 proteins is demonstrated. Complete information transfer is confirmed as the copied DNA can serve as a functional template for gene expression, which can be seen as an autocatalytic DNA replication cycle. These results show how the central dogma of molecular biology can be reconstituted and form a cycle in vitro. Finally, coupled DNA replication and gene expression is compartmentalized inside phospholipid vesicles providing the chassis for evolving functions in a prospective synthetic cell relying on the extant biology.
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Affiliation(s)
- Pauline van Nies
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Ilja Westerlaken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Duco Blanken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Margarita Salas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, 28049, Spain
| | - Mario Mencía
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, 28049, Spain
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, Delft, 2629 HZ, The Netherlands.
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16
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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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17
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Takemori N, Takemori A, Tanaka Y, Endo Y, Hurst JL, Gómez-Baena G, Harman VM, Beynon RJ. MEERCAT: Multiplexed Efficient Cell Free Expression of Recombinant QconCATs For Large Scale Absolute Proteome Quantification. Mol Cell Proteomics 2017; 16:2169-2183. [PMID: 29055021 PMCID: PMC5724179 DOI: 10.1074/mcp.ra117.000284] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/15/2017] [Indexed: 01/25/2023] Open
Abstract
A major challenge in proteomics is the absolute accurate quantification of large numbers of proteins. QconCATs, artificial proteins that are concatenations of multiple standard peptides, are well established as an efficient means to generate standards for proteome quantification. Previously, QconCATs have been expressed in bacteria, but we now describe QconCAT expression in a robust, cell-free system. The new expression approach rescues QconCATs that previously were unable to be expressed in bacteria and can reduce the incidence of proteolytic damage to QconCATs. Moreover, it is possible to cosynthesize QconCATs in a highly-multiplexed translation reaction, coexpressing tens or hundreds of QconCATs simultaneously. By obviating bacterial culture and through the gain of high level multiplexing, it is now possible to generate tens of thousands of standard peptides in a matter of weeks, rendering absolute quantification of a complex proteome highly achievable in a reproducible, broadly deployable system.
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Affiliation(s)
- Nobuaki Takemori
- From the ‡Proteo-Science Center, Ehime University, Ehime, 791-0295, Japan; .,§Advanced Research Support Center, Ehime University, Ehime, 791-0295, Japan
| | - Ayako Takemori
- From the ‡Proteo-Science Center, Ehime University, Ehime, 791-0295, Japan.,¶The United Graduate School of Agricultural Sciences, Ehime University, Ehime, 790-8566, Japan
| | - Yuki Tanaka
- §Advanced Research Support Center, Ehime University, Ehime, 791-0295, Japan
| | - Yaeta Endo
- From the ‡Proteo-Science Center, Ehime University, Ehime, 791-0295, Japan
| | - Jane L Hurst
- **Mammalian Behaviour and Evolution Group, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston CH64 7TE
| | - Guadalupe Gómez-Baena
- ‖Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Victoria M Harman
- ‖Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Robert J Beynon
- ‖Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK;
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18
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Li J, Zhang C, Huang P, Kuru E, Forster-Benson ETC, Li T, Church GM. Dissecting limiting factors of the Protein synthesis Using Recombinant Elements (PURE) system. TRANSLATION (AUSTIN, TEX.) 2017; 5:e1327006. [PMID: 28702280 PMCID: PMC5501384 DOI: 10.1080/21690731.2017.1327006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/14/2017] [Accepted: 04/28/2017] [Indexed: 01/10/2023]
Abstract
Reconstituted cell-free protein synthesis systems such as the Protein synthesis Using Recombinant Elements (PURE) system give high-throughput and controlled access to in vitro protein synthesis. Here we show that compared with the commercial S30 crude extract based RTS 100 E. coli HY system, the PURE system has less mRNA degradation and produces up to ∼6-fold full-length proteins. However the majority of polypeptides PURE produces are partially translated or inactive since the signal from firefly luciferase (Fluc) translated in PURE is only ∼2/3rd of that measured using the RTS 100 E. coli HY S30 system. Both of the 2 batch systems suffer from low ribosome recycling efficiency when translating proteins from 82 kD to 224 kD. A systematic fed-batch analysis of PURE shows replenishment of 6 small molecule substrates individually or in combination before energy depletion increased Fluc protein yield by ∼1.5 to ∼2-fold, while creatine phosphate and magnesium have synergistic effects when added to the PURE system. Additionally, while adding EF-P to PURE reduced full-length protein translated, it increased the fraction of functional protein and reduced partially translated protein probably by slowing down the translation process. Finally, ArfA, rather than YaeJ or PrfH, helped reduce ribosome stalling when translating Fluc and improved system productivity in a template-dependent fashion.
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Affiliation(s)
- Jun Li
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Harvard Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Chi Zhang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Poyi Huang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Erkin Kuru
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Taibo Li
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Harvard Institute of Biologically Inspired Engineering, Boston, MA, USA
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19
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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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20
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Xenobiotic Life. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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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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22
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Chizzolini F, Forlin M, Cecchi D, Mansy SS. Gene position more strongly influences cell-free protein expression from operons than T7 transcriptional promoter strength. ACS Synth Biol 2014; 3:363-71. [PMID: 24283192 DOI: 10.1021/sb4000977] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cell-free transcription-translation of multiple proteins typically exploits genes placed behind strong transcriptional promoters that reside on separate pieces of DNA so that protein levels can be easily controlled by changing DNA template concentration. However, such systems are not amenable to the construction of artificial cells with a synthetic genome. Herein, we evaluated the activity of a series of T7 transcriptional promoters by monitoring the fluorescence arising from a genetically encoded Spinach aptamer. Subsequently the influences of transcriptional promoter strength on fluorescent protein synthesis from one, two, and three gene operons were assessed. It was found that transcriptional promoter strength was more effective at controlling RNA synthesis than protein synthesis in vitro with the PURE system. Conversely, the gene position within the operon strongly influenced protein synthesis but not RNA synthesis.
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Affiliation(s)
- Fabio Chizzolini
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello, Italy
| | - Michele Forlin
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello, Italy
| | - Dario Cecchi
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello, Italy
| | - Sheref S. Mansy
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello, Italy
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23
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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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24
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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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25
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Whittaker JW. Cell-free protein synthesis: the state of the art. Biotechnol Lett 2013; 35:143-52. [PMID: 23086573 PMCID: PMC3553302 DOI: 10.1007/s10529-012-1075-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 10/10/2012] [Indexed: 10/27/2022]
Abstract
Cell-free protein synthesis harnesses the synthetic power of biology, programming the ribosomal translational machinery of the cell to create macromolecular products. Like PCR, which uses cellular replication machinery to create a DNA amplifier, cell-free protein synthesis is emerging as a transformative technology with broad applications in protein engineering, biopharmaceutical development, and post-genomic research. By breaking free from the constraints of cell-based systems, it takes the next step towards synthetic biology. Recent advances in reconstituted cell-free protein synthesis (Protein synthesis Using Recombinant Elements expression systems) are creating new opportunities to tailor the reactions for specialized applications including in vitro protein evolution, printing protein microarrays, isotopic labeling, and incorporating nonnatural amino acids.
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Affiliation(s)
- James W Whittaker
- Division of Environmental and Biomolecular Systems, Institute for Environmental Health, Oregon Health and Science University, 20000 N.W. Walker Road, Beaverton, OR 97006-8921, USA.
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26
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27
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Liu M, Yu H. Cocktail production of an endo-β-xylanase and a β-glucosidase from Trichoderma reesei QM 9414 in Escherichia coli. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2012.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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28
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Hockenberry AJ, Jewett MC. Synthetic in vitro circuits. Curr Opin Chem Biol 2012; 16:253-9. [PMID: 22676890 PMCID: PMC3424401 DOI: 10.1016/j.cbpa.2012.05.179] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 04/17/2012] [Accepted: 05/04/2012] [Indexed: 11/19/2022]
Abstract
Inspired by advances in the ability to construct programmable circuits in living organisms, in vitro circuits are emerging as a viable platform for designing, understanding, and exploiting dynamic biochemical circuitry. In vitro systems allow researchers to directly access and manipulate biomolecular parts without the unwieldy complexity and intertwined dependencies that often exist in vivo. Experimental and computational foundations in DNA, DNA/RNA, and DNA/RNA/protein based circuitry have given rise to systems with more than 100 programmed molecular constituents. Functionally, they have diverse capabilities including: complex mathematical calculations, associative memory tasks, and sensing of small molecules. Progress in this field is showing that cell-free synthetic biology is a versatile testing ground for understanding native biological circuits and engineering novel functionality.
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Affiliation(s)
- Adam J. Hockenberry
- Interdepartmental Biological Sciences Graduate Program, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA
| | - Michael C. Jewett
- Interdepartmental Biological Sciences Graduate Program, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Northwestern University, 303 E. Superior, Chicago, IL 60611, USA
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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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Karig DK, Iyer S, Simpson ML, Doktycz MJ. Expression optimization and synthetic gene networks in cell-free systems. Nucleic Acids Res 2011; 40:3763-74. [PMID: 22180537 PMCID: PMC3333853 DOI: 10.1093/nar/gkr1191] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Synthetic biology offers great promise to a variety of applications through the forward engineering of biological function. Most efforts in this field have focused on employing living cells, yet cell-free approaches offer simpler and more flexible contexts. Here, we evaluate cell-free regulatory systems based on T7 promoter-driven expression by characterizing variants of TetR and LacI repressible T7 promoters in a cell-free context and examining sequence elements that determine expression efficiency. Using the resulting constructs, we then explore different approaches for composing regulatory systems, leading to the implementation of inducible negative feedback in Escherichia coli extracts and in the minimal PURE system, which consists of purified proteins necessary for transcription and translation. Despite the fact that negative feedback motifs are common and essential to many natural and engineered systems, this simple building block has not previously been implemented in a cell-free context. As a final step, we then demonstrate that the feedback systems developed using our cell-free approach can be implemented in live E. coli as well, illustrating the potential for using cell-free expression to fast track the development of live cell systems in synthetic biology. Our quantitative cell-free component characterizations and demonstration of negative feedback embody important steps on the path to harnessing biological function in a bottom-up fashion.
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Affiliation(s)
- David K Karig
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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Du L, Villarreal S, Forster AC. Multigene expression in vivo: supremacy of large versus small terminators for T7 RNA polymerase. Biotechnol Bioeng 2011; 109:1043-50. [PMID: 22094962 DOI: 10.1002/bit.24379] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 11/05/2011] [Accepted: 11/11/2011] [Indexed: 01/22/2023]
Abstract
Designing and building multigene constructs is commonplace in synthetic biology. Yet functional successes at first attempts are rare because the genetic parts are not fully modular. In order to improve the modularity of transcription, we previously showed that transcription termination in vitro by bacteriophage T7 RNA polymerase could be made more efficient by substituting the standard, single, TΦ large (class I) terminator with adjacent copies of the vesicular stomatitis virus (VSV) small (class II) terminator. However, in vitro termination at the downstream VSV terminator was less efficient than at the upstream VSV terminator, and multigene overexpression in vivo was complicated by unexpectedly inefficient VSV termination within Escherichia coli cells. Here, we address hypotheses raised in that study by showing that VSV or preproparathyroid hormone (PTH) small terminators spaced further apart can work independently (i.e., more efficiently) in vitro, and that VSV and PTH terminations are severely inhibited in vivo. Surprisingly, the difference between class II terminator function in vivo versus in vitro is not due to differences in plasmid supercoiling, as supercoiling had a minimal effect on termination in vitro. We therefore turned to TΦ terminators for "BioBrick" synthesis of a pentameric gene construct suitable for overexpression in vivo. This indeed enabled coordinated overexpression and copurification of five His-tagged proteins using the first construct attempted, indicating that this strategy is more modular than other strategies. An application of this multigene overexpression and protein copurification method is demonstrated by supplying five of the six E. coli translation factors required for reconstitution of translation from a single cell line via copurification, greatly simplifying the reconstitution.
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Affiliation(s)
- Liping Du
- Department of Pharmacology, Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, 2222 Pierce Avenue, Nashville, Tennessee 37232, USA
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Caschera F, Bedau MA, Buchanan A, Cawse J, de Lucrezia D, Gazzola G, Hanczyc MM, Packard NH. Coping with complexity: Machine learning optimization of cell-free protein synthesis. Biotechnol Bioeng 2011; 108:2218-28. [DOI: 10.1002/bit.23178] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 03/29/2011] [Accepted: 04/04/2011] [Indexed: 11/12/2022]
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Shetty R, Lizarazo M, Rettberg R, Knight TF. Assembly of BioBrick Standard Biological Parts Using Three Antibiotic Assembly. Methods Enzymol 2011; 498:311-26. [DOI: 10.1016/b978-0-12-385120-8.00013-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Jewett MC, Forster AC. Update on designing and building minimal cells. Curr Opin Biotechnol 2010; 21:697-703. [PMID: 20638265 DOI: 10.1016/j.copbio.2010.06.008] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 06/18/2010] [Indexed: 12/11/2022]
Abstract
Minimal cells comprise only the genes and biomolecular machinery necessary for basic life. Synthesizing minimal and minimized cells will improve understanding of core biology, enhance development of biotechnology strains of bacteria, and enable evolutionary optimization of natural and unnatural biopolymers. Design and construction of minimal cells is proceeding in two different directions: 'top-down' reduction of bacterial genomes in vivo and 'bottom-up' integration of DNA/RNA/protein/membrane syntheses in vitro. Major progress in the past 5 years has occurred in synthetic genomics, minimization of the Escherichia coli genome, sequencing of minimal bacterial endosymbionts, identification of essential genes, and integration of biochemical systems.
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Affiliation(s)
- Michael C Jewett
- Department of Chemical and Biological Engineering and Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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Toward engineering synthetic microbial metabolism. J Biomed Biotechnol 2009; 2010:459760. [PMID: 20037734 PMCID: PMC2796345 DOI: 10.1155/2010/459760] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2009] [Accepted: 10/09/2009] [Indexed: 11/18/2022] Open
Abstract
The generation of well-characterized parts and the formulation of biological design principles in synthetic biology are laying the foundation for more complex and advanced microbial metabolic engineering. Improvements in de novo DNA synthesis and codon-optimization alone are already contributing to the manufacturing of pathway enzymes with improved or novel function. Further development of analytical and computer-aided design tools should accelerate the forward engineering of precisely regulated synthetic pathways by providing a standard framework for the predictable design of biological systems from well-characterized parts. In this review we discuss the current state of synthetic biology within a four-stage framework (design, modeling, synthesis, analysis) and highlight areas requiring further advancement to facilitate true engineering of synthetic microbial metabolism.
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