1
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Lee CY, Joshi M, Wang A, Myong S. 5'UTR G-quadruplex structure enhances translation in size dependent manner. Nat Commun 2024; 15:3963. [PMID: 38729943 PMCID: PMC11087576 DOI: 10.1038/s41467-024-48247-8] [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: 09/13/2023] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Translation initiation in bacteria is frequently regulated by various structures in the 5' untranslated region (5'UTR). Previously, we demonstrated that G-quadruplex (G4) formation in non-template DNA enhances transcription. In this study, we aim to explore how G4 formation in mRNA (RG4) at 5'UTR impacts translation using a T7-based in vitro translation system and in E. coli. We show that RG4 strongly promotes translation efficiency in a size-dependent manner. Additionally, inserting a hairpin upstream of the RG4 further enhances translation efficiency, reaching up to a 12-fold increase. We find that the RG4-dependent effect is not due to increased ribosome affinity, ribosome binding site accessibility, or mRNA stability. We propose a physical barrier model in which bulky structures in 5'UTR biases ribosome movement toward the downstream start codon, thereby increasing the translation output. This study provides biophysical insights into the regulatory role of 5'UTR structures in in vitro and bacterial translation, highlighting their potential applications in tuning gene expression.
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Affiliation(s)
- Chun-Ying Lee
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Meera Joshi
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Ashley Wang
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, IL, 61801, USA.
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2
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Myong S, Lee CY, Joshi M, Wang A. 5'UTR G-quadruplex structure enhances translation in size dependent manner. RESEARCH SQUARE 2023:rs.3.rs-3352233. [PMID: 37790436 PMCID: PMC10543253 DOI: 10.21203/rs.3.rs-3352233/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Translation initiation in bacteria is frequently regulated by various structures in the 5' untranslated region (5'UTR). Previously, we demonstrated that G-quadruplex (G4) formation in non-template DNA enhances transcription. In this study, we aimed to explore how G4 formation in mRNA (RG4) at 5'UTR impacts translation using a T7-based in vitro translation system and in E. coli. We showed that RG4 strongly promotes translation efficiency in a size-dependent manner. Additionally, inserting a hairpin upstream of the RG4 further enhances translation efficiency, reaching up to a 12-fold increase. We found that the RG4-dependent effect is not due to increased ribosome affinity, ribosome binding site accessibility, or mRNA stability. We proposed a physical barrier model in which bulky structures in 5'UTR prevent ribosome dislodging and thereby increase the translation output. This study provides biophysical insights into the regulatory role of 5'UTR structures in bacterial translation, highlighting their potential applications in tuning gene expression.
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Affiliation(s)
- Sua Myong
- Boston Children's Hospital/Harvard Medical School
| | | | - Meera Joshi
- Boston Children's Hospital/Harvard Medical School
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3
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Maheshwari AJ, Calles J, Waterton SK, Endy D. Engineering tRNA abundances for synthetic cellular systems. Nat Commun 2023; 14:4594. [PMID: 37524714 PMCID: PMC10390467 DOI: 10.1038/s41467-023-40199-9] [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: 12/24/2022] [Accepted: 07/13/2023] [Indexed: 08/02/2023] Open
Abstract
Routinizing the engineering of synthetic cells requires specifying beforehand how many of each molecule are needed. Physics-based tools for estimating desired molecular abundances in whole-cell synthetic biology are missing. Here, we use a colloidal dynamics simulator to make predictions for how tRNA abundances impact protein synthesis rates. We use rational design and direct RNA synthesis to make 21 synthetic tRNA surrogates from scratch. We use evolutionary algorithms within a computer aided design framework to engineer translation systems predicted to work faster or slower depending on tRNA abundance differences. We build and test the so-specified synthetic systems and find qualitative agreement between expected and observed systems. First principles modeling combined with bottom-up experiments can help molecular-to-cellular scale synthetic biology realize design-build-work frameworks that transcend tinker-and-test.
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Affiliation(s)
| | - Jonathan Calles
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Sean K Waterton
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Drew Endy
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
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4
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De Capitani J, Mutschler H. The Long Road to a Synthetic Self-Replicating Central Dogma. Biochemistry 2023; 62:1221-1232. [PMID: 36944355 PMCID: PMC10077596 DOI: 10.1021/acs.biochem.3c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The construction of a biochemical system capable of self-replication is a key objective in bottom-up synthetic biology. Throughout the past two decades, a rapid progression in the design of in vitro cell-free systems has provided valuable insight into the requirements for the development of a minimal system capable of self-replication. The main limitations of current systems can be attributed to their macromolecular composition and how the individual macromolecules use the small molecules necessary to drive RNA and protein synthesis. In this Perspective, we discuss the recent steps that have been taken to generate a minimal cell-free system capable of regenerating its own macromolecular components and maintaining the homeostatic balance between macromolecular biogenesis and consumption of primary building blocks. By following the flow of biological information through the central dogma, we compare the current versions of these systems to date and propose potential alterations aimed at designing a model system for self-replicative synthetic cells.
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Affiliation(s)
- Jacopo De Capitani
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Hannes Mutschler
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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5
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Lavickova B, Grasemann L, Maerkl SJ. Improved Cell-Free Transcription-Translation Reactions in Microfluidic Chemostats Augmented with Hydrogel Membranes for Continuous Small Molecule Dialysis. ACS Synth Biol 2022; 11:4134-4141. [PMID: 36475685 DOI: 10.1021/acssynbio.2c00453] [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: 12/12/2022]
Abstract
Increasing the protein production capacity of the PURE cell-free transcription-translation (TX-TL) system will be key to implementing complex synthetic biological circuits, and to establishing a fully self-regenerating system as a basis for the development of a synthetic cell. Under steady-state conditions, the protein synthesis capacity of the PURE system is likely at least one order of magnitude too low to express sufficient quantities of all PURE protein components. This is in part due to the fact that protein synthesis cannot be sustained during the entire dilution cycle, especially at low dilution rates. We developed a microfluidic chemostat augmented with semipermeable membranes that combines steady-state reactions and continuous dialysis as a possible solution to enhance protein synthesis at steady-state. In batch operation, the continuous dialysis of low molecular weight components via the membranes extended protein synthesis by over an order of magnitude from 2 h to over 30 h, leading to a 7-fold increase in protein yield. In chemostat operation, continuous dialysis enabled sustained protein synthesis during the entire dilution cycle even for low dilution rates, leading to 6-fold higher protein levels at steady state. The possibility to combine and independently manipulate continuous dialysis and chemostat operation renders our dialysis chemostat a promising technological basis for complex cell-free synthetic biology applications that require enhanced protein synthesis capacity.
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Affiliation(s)
- Barbora Lavickova
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Laura Grasemann
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Sebastian J Maerkl
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
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6
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Romantseva E, Alperovich N, Ross D, Lund SP, Strychalski EA. Effects of DNA template preparation on variability in cell-free protein production. Synth Biol (Oxf) 2022; 7:ysac015. [PMID: 36046152 PMCID: PMC9425043 DOI: 10.1093/synbio/ysac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 07/01/2022] [Accepted: 08/12/2022] [Indexed: 08/08/2023] Open
Abstract
DNA templates for protein production remain an unexplored source of variability in the performance of cell-free expression (CFE) systems. To characterize this variability, we investigated the effects of two common DNA extraction methodologies, a postprocessing step and manual versus automated preparation on protein production using CFE. We assess the concentration of the DNA template, the quality of the DNA template in terms of physical damage and the quality of the DNA solution in terms of purity resulting from eight DNA preparation workflows. We measure the variance in protein titer and rate of protein production in CFE reactions associated with the biological replicate of the DNA template, the technical replicate DNA solution prepared with the same workflow and the measurement replicate of nominally identical CFE reactions. We offer practical guidance for preparing and characterizing DNA templates to achieve acceptable variability in CFE performance.
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Affiliation(s)
| | - Nina Alperovich
- National Institute of Standards and Technology, Gaithersburg, MD USA
| | - David Ross
- National Institute of Standards and Technology, Gaithersburg, MD USA
| | - Steven P Lund
- National Institute of Standards and Technology, Gaithersburg, MD USA
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7
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Berhanu S, Ueda T, Alix JH. The E. coli DnaK chaperone stimulates the α-complementation of β-galactosidase. J Basic Microbiol 2022; 62:669-688. [PMID: 35289419 DOI: 10.1002/jobm.202100487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/11/2022] [Accepted: 02/20/2022] [Indexed: 11/09/2022]
Abstract
pUC18 and pUC19 are well-known high copy-number plasmid vectors routinely used for DNA cloning purposes. We show here that, in E. coli transformed by native pUC18, the α-complementation of β-galactosidase (i.e., mediated by the peptide LacZα18) is intrinsically weak and slow, but is greatly stimulated by the DnaK/DnaJ/GrpE chaperone system. In contrast, the α-complementation mediated by the peptide LacZα19 (in E. coli transformed by the native pUC19) is much more efficient, and therefore does not require the assistance of the DnaK chaperone machinery. The marked difference between these two LacZα peptides is reproduced in cell-free protein expression system coupled with α-complementation. We conclude that: (i) α-complementation of β-galactosidase is DnaK-mediated depending upon the LacZα peptide donor. (ii) DnaK, sensu stricto, is not necessary for α-complementation, but can enhance it to a great extent. (iii) this observation could be used to establish an easy and inexpensive method for screening small molecules libraries in search of DnaK inhibitors and also for deciphering the DnaK-mediated protein quality control mechanism. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Samuel Berhanu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba Prefecture, Japan
| | - Takuya Ueda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba Prefecture, Japan
| | - Jean-Hervé Alix
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba Prefecture, Japan
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8
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Aquino AK, Manzer ZA, Daniel S, DeLisa MP. Glycosylation-on-a-Chip: A Flow-Based Microfluidic System for Cell-Free Glycoprotein Biosynthesis. Front Mol Biosci 2022; 8:782905. [PMID: 35004852 PMCID: PMC8733600 DOI: 10.3389/fmolb.2021.782905] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/06/2021] [Indexed: 12/25/2022] Open
Abstract
In recent years, cell-free synthetic glycobiology technologies have emerged that enable production and remodeling of glycoproteins outside the confines of the cell. However, many of these systems combine multiple synthesis steps into one pot where there can be competing reactions and side products that ultimately lead to low yield of the desired product. In this work, we describe a microfluidic platform that integrates cell-free protein synthesis, glycosylation, and purification of a model glycoprotein in separate compartments where each step can be individually optimized. Microfluidics offer advantages such as reaction compartmentalization, tunable residence time, the ability to tether enzymes for reuse, and the potential for continuous manufacturing. Moreover, it affords an opportunity for spatiotemporal control of glycosylation reactions that is difficult to achieve with existing cell-based and cell-free glycosylation systems. In this work, we demonstrate a flow-based glycoprotein synthesis system that promotes enhanced cell-free protein synthesis, efficient protein glycosylation with an immobilized oligosaccharyltransferase, and enrichment of the protein product from cell-free lysate. Overall, this work represents a first-in-kind glycosylation-on-a-chip prototype that could find use as a laboratory tool for mechanistic dissection of the protein glycosylation process as well as a biomanufacturing platform for small batch, decentralized glycoprotein production.
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Affiliation(s)
- Alicia K Aquino
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Zachary A Manzer
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Susan Daniel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States.,Cornell Institute of Biotechnology, Cornell University, Ithaca, NY, United States
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9
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Romantseva EF, Tack DS, Alperovich N, Ross D, Strychalski EA. Best Practices for DNA Template Preparation Toward Improved Reproducibility in Cell-Free Protein Production. Methods Mol Biol 2022; 2433:3-50. [PMID: 34985735 DOI: 10.1007/978-1-0716-1998-8_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Performance variability is a common challenge in cell-free protein production and hinders a wider adoption of these systems for both research and biomanufacturing. While the inherent stochasticity and complexity of biology likely contributes to variability, other systematic factors may also play a role, including the source and preparation of the cell extract, the composition of the supplemental reaction buffer, the facility at which experiments are conducted, and the human operator (Cole et al. ACS Synth Biol 8:2080-2091, 2019). Variability in protein production could also arise from differences in the DNA template-specifically the amount of functional DNA added to a cell-free reaction and the quality of the DNA preparation in terms of contaminants and strand breakage. Here, we present protocols and suggest best practices optimized for DNA template preparation and quantitation for cell-free systems toward reducing variability in cell-free protein production.
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Affiliation(s)
| | - Drew S Tack
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nina Alperovich
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - David Ross
- National Institute of Standards and Technology, Gaithersburg, MD, USA
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10
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Stano P. Gene Expression Inside Liposomes: From Early Studies to Current Protocols. Chemistry 2019; 25:7798-7814. [DOI: 10.1002/chem.201806445] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA)University of Salento, Ecotekne 73100 Lecce Italy
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11
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Doerr A, de Reus E, van Nies P, van der Haar M, Wei K, Kattan J, Wahl A, Danelon C. Modelling cell-free RNA and protein synthesis with minimal systems. Phys Biol 2019; 16:025001. [DOI: 10.1088/1478-3975/aaf33d] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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12
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Jaroentomeechai T, Stark JC, Natarajan A, Glasscock CJ, Yates LE, Hsu KJ, Mrksich M, Jewett MC, DeLisa MP. Single-pot glycoprotein biosynthesis using a cell-free transcription-translation system enriched with glycosylation machinery. Nat Commun 2018; 9:2686. [PMID: 30002445 PMCID: PMC6043479 DOI: 10.1038/s41467-018-05110-x] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 06/06/2018] [Indexed: 12/13/2022] Open
Abstract
The emerging discipline of bacterial glycoengineering has made it possible to produce designer glycans and glycoconjugates for use as vaccines and therapeutics. Unfortunately, cell-based production of homogeneous glycoproteins remains a significant challenge due to cell viability constraints and the inability to control glycosylation components at precise ratios in vivo. To address these challenges, we describe a novel cell-free glycoprotein synthesis (CFGpS) technology that seamlessly integrates protein biosynthesis with asparagine-linked protein glycosylation. This technology leverages a glyco-optimized Escherichia coli strain to source cell extracts that are selectively enriched with glycosylation components, including oligosaccharyltransferases (OSTs) and lipid-linked oligosaccharides (LLOs). The resulting extracts enable a one-pot reaction scheme for efficient and site-specific glycosylation of target proteins. The CFGpS platform is highly modular, allowing the use of multiple distinct OSTs and structurally diverse LLOs. As such, we anticipate CFGpS will facilitate fundamental understanding in glycoscience and make possible applications in on demand biomanufacturing of glycoproteins. The ability to produce homogeneous glycoproteins is expected to advance fundamental understanding in glycoscience, but current in vivo-based production systems have several limitations. Here, the authors develop an E. coli extract-based one-pot system for customized production of N-linked glycoproteins.
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Affiliation(s)
- Thapakorn Jaroentomeechai
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.,Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL, 60208-3120, USA.,Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA
| | - Aravind Natarajan
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Cameron J Glasscock
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Laura E Yates
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Karen J Hsu
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute B224, Evanston, IL, 60208-3120, USA
| | - Milan Mrksich
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA.,Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA.,Department of Cell and Molecular Biology, Northwestern University, Chicago, IL, 60611, USA.,Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA. .,Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL, 60208-3120, USA. .,Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA.
| | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA. .,Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA.
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13
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Guevara-Pantoja PE, Jiménez-Valdés RJ, García-Cordero JL, Caballero-Robledo GA. Pressure-actuated monolithic acrylic microfluidic valves and pumps. LAB ON A CHIP 2018; 18:662-669. [PMID: 29367991 DOI: 10.1039/c7lc01337j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In this article, we describe a microfluidic device with embedded valves and pumps made exclusively of layers of acrylic glass. Flat acrylic sheets are carved out with a micromilling machine and bonded together by solvent bonding. The working principle of the valves is based on a thin flexible membrane (≈100 μm) machined on one acrylic sheet and actuated with pneumatic pressure. A completely closed valve resists a pressure difference of ≈17 kPa (≈2.5 psi), and when open, it can sustain flow rates of up to 100 μL s-1. Pumping is achieved by combining two valves and a pumping chamber in series, which is also based on the bending of a thin acrylic membrane. The maximum flow rate obtained with this pumping mechanism is 20 μL min-1. Acrylic is a popular rigid thermoplastic because it is inexpensive, making it ideal for mass production of disposable devices, and also because it has demonstrated compatibility with different biochemical assays. The physical and optical properties it shares with other thermoplastics could lead to this material being implemented for similar valves and pumps. As a proof-of-concept of our technology, we implemented a controlled cell-staining assay in two parallel incubation chambers integrating four valves and one pump into one device. Our monolithic acrylic valves can enable the mass production of disposable microfluidic devices that require fluid control with pressure-actuated valves and aid in the automation of biochemical assays.
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14
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Li J, Haas W, Jackson K, Kuru E, Jewett MC, Fan ZH, Gygi S, Church GM. Cogenerating Synthetic Parts toward a Self-Replicating System. ACS Synth Biol 2017; 6:1327-1336. [PMID: 28330337 DOI: 10.1021/acssynbio.6b00342] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To build replicating systems with new functions, the engineering of existing biological machineries requires a sensible strategy. Protein synthesis Using Recombinant Elements (PURE) system consists of the desired components for transcription, translation, aminoacylation and energy regeneration. PURE might be the basis for a radically alterable, lifelike system after optimization. Here, we regenerated 54 E. coli ribosomal (r-) proteins individually from DNA templates in the PURE system. We show that using stable isotope labeling with amino acids, mass spectrometry based quantitative proteomics could detect 26 of the 33 50S and 20 of the 21 30S subunit r-proteins when coexpressed in batch format PURE system. By optimizing DNA template concentrations and adapting a miniaturized Fluid Array Device with optimized feeding solution, we were able to cogenerate and detect at least 29 of the 33 50S and all of the 21 30S subunit r-proteins in one pot. The boost on yield of a single r-protein in coexpression pool varied from ∼1.5 to 5-fold compared to the batch mode, with up to ∼2.4 μM yield for a single r-protein. Reconstituted ribosomes under physiological condition from PURE system synthesized 30S r-proteins and native 16S rRNA showed ∼13% activity of native 70S ribosomes, which increased to 21% when supplemented with GroEL/ES. This work also points to what is still needed to obtain self-replicating synthetic ribosomes in situ in the PURE system.
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Affiliation(s)
- Jun Li
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Wyss Harvard Institute of Biologically Inspired Engineering, 3 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center;
Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Kirsten Jackson
- J. Crayton
Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, Florida 32611, United States
| | - Erkin Kuru
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Wyss Harvard Institute of Biologically Inspired Engineering, 3 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Z. Hugh Fan
- J. Crayton
Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, Florida 32611, United States
- Department of Mechanical and Aerospace
Engineering, University of Florida, P.O. Box 116250, Gainesville, Florida 32611, United States
| | - Steven Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - George M. Church
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Wyss Harvard Institute of Biologically Inspired Engineering, 3 Blackfan Circle, Boston, Massachusetts 02115, United States
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15
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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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Peñalber-Johnstone C, Ge X, Tran K, Selock N, Sardesai N, Gurramkonda C, Pilli M, Tolosa M, Tolosa L, Kostov Y, Frey DD, Rao G. Optimizing cell-free protein expression in CHO: Assessing small molecule mass transfer effects in various reactor configurations. Biotechnol Bioeng 2017; 114:1478-1486. [PMID: 28266026 DOI: 10.1002/bit.26282] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/11/2017] [Accepted: 03/01/2017] [Indexed: 01/12/2023]
Abstract
Cell-free protein synthesis (CFPS) is an ideal platform for rapid and convenient protein production. However, bioreactor design remains a critical consideration in optimizing protein expression. Using turbo green fluorescent protein (tGFP) as a model, we tracked small molecule components in a Chinese Hamster Ovary (CHO) CFPS system to optimize protein production. Here, three bioreactors in continuous-exchange cell-free (CECF) format were characterized. A GFP optical sensor was built to monitor the product in real-time. Mass transfer of important substrate and by-product components such as nucleoside triphosphates (NTPs), creatine, and inorganic phosphate (Pi) across a 10-kDa MWCO cellulose membrane was calculated. The highest efficiency measured by tGFP yields were found in a microdialysis device configuration; while a negative effect on yield was observed due to limited mass transfer of NTPs in a dialysis cup configuration. In 24-well plate high-throughput CECF format, addition of up to 40 mM creatine phosphate in the system increased yields by up to ∼60% relative to controls. Direct ATP addition, as opposed to creatine phosphate addition, negatively affected the expression. Pi addition of up to 30 mM to the expression significantly reduced yields by over ∼40% relative to controls. Overall, data presented in this report serves as a valuable reference to optimize the CHO CFPS system for next-generation bioprocessing. Biotechnol. Bioeng. 2017;114: 1478-1486. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Chariz Peñalber-Johnstone
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | | | - Kevin Tran
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Nicholas Selock
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Neha Sardesai
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Chandrasekhar Gurramkonda
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Manohar Pilli
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Michael Tolosa
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Leah Tolosa
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Yordan Kostov
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Douglas D Frey
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Govind Rao
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
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17
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Perez JG, Stark JC, Jewett MC. Cell-Free Synthetic Biology: Engineering Beyond the Cell. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023853. [PMID: 27742731 DOI: 10.1101/cshperspect.a023853] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell-free protein synthesis (CFPS) technologies have enabled inexpensive and rapid recombinant protein expression. Numerous highly active CFPS platforms are now available and have recently been used for synthetic biology applications. In this review, we focus on the ability of CFPS to expand our understanding of biological systems and its applications in the synthetic biology field. First, we outline a variety of CFPS platforms that provide alternative and complementary methods for expressing proteins from different organisms, compared with in vivo approaches. Next, we review the types of proteins, protein complexes, and protein modifications that have been achieved using CFPS systems. Finally, we introduce recent work on genetic networks in cell-free systems and the use of cell-free systems for rapid prototyping of in vivo networks. Given the flexibility of cell-free systems, CFPS holds promise to be a powerful tool for synthetic biology as well as a protein production technology in years to come.
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Affiliation(s)
- Jessica G Perez
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611-3068.,Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611-2875
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18
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Zhang L, Tripathi A. Archaeal RNA ligase from thermoccocus kodakarensis for template dependent ligation. RNA Biol 2016; 14:36-44. [PMID: 27715457 DOI: 10.1080/15476286.2016.1239688] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Nicking-sealing RNA ligases play a significant biological role in host defense and cellular repair, and have become an important molecular tool in biomedical engineering. Due to the propensity for RNA to form secondary structures, RNA modifying enzymes with elevated optimum temperatures are highly desired. Current characterized double stranded RNA ligases, such as the bacteriophage T4 RNA ligase 2, while possessing good template dependency, are not active at elevated temperatures. The few characterized RNA ligases from thermophiles exhibit high template independency. We synthesize and characterize here, KOD RNA ligase (KOD1Rnl), a thermostable and template dependent RNA ligase from the archaeon, Thermoccocus Kodakarensis. We disclose that a 13 time reduction in template independent ligation can be achieved with the addition of a single stranded DNase, such as RecJ. We also elucidate the effects of the presence of blood proteins on the activity of KOD1Rnl. Template dependent and thermostable RNA ligases, such as KOD RNA ligase, can be utilized in RNA detection, modification and sequencing.
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Affiliation(s)
- Lei Zhang
- a Center for Biomedical Engineering, School of Engineering, Brown University , Providence , RI , USA
| | - Anubhav Tripathi
- a Center for Biomedical Engineering, School of Engineering, Brown University , Providence , RI , USA
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19
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Jackson K, Jin S, Fan ZH. Optimization of a miniaturized fluid array device for cell-free protein synthesis. Biotechnol Bioeng 2015; 112:2459-67. [PMID: 26037852 DOI: 10.1002/bit.25668] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/18/2015] [Accepted: 05/28/2015] [Indexed: 11/06/2022]
Abstract
Cell-free protein synthesis (CFPS), which entails synthesizing proteins outside of intact cells, is conducted in several formats with the continuous-exchange cell-free (CECF) format generally having the greatest protein expression yields. With this format, continuous chemical exchange occurs through a dialysis membrane separating a reaction solution from a feeding solution containing supplemental nutrient/energy molecules. Here, we describe the optimization of the miniaturized fluid array device (µFAD) by studying the effects of structural and experimental parameters responsible for the heightened chemical exchange across the dialysis membranes and enhanced protein expression capabilities of the high-throughput device. The interface area and number between the reaction and feeding solutions have a direct impact on protein expression, with a 1.6% enhancement in protein expression yield with each square millimeter increase in area and a 20% decrease with each additional interface. For nutrient/energy availability, an increasing solution volume ratio and height difference increase protein expression yield until the expression yield plateaus at a volume ratio of 20 to 1 (feeding to reaction solution) and a solution height difference of 2 mm. This yield can be further increased by 7% every 30 min with feeding solution replacement. Of the studied experimental factors (feeding solution stirring, device shaking, and temperature increase), feeding solution stirring has a significant effect on protein expression in this device. In the optimized system, green fluorescent protein (GFP), ß-glucuronidase (GUS), ß-galactosidase (LacZ), luciferase, and tissue plasminogen activator (tPA) expression increased 77.8-, 212-, 3.66-, 463-, and 5.43-fold, respectively, compared to the conventional batch format in a standard microplate. These results highlight the significance of structural/experimental conditions on the productive expression of proteins in the CECF format.
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Affiliation(s)
- Kirsten Jackson
- J.Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, 32611, Florida
| | - Shouguang Jin
- Department of Molecular Genetics and Microbiology, University of Florida, P.O. Box 100266, Gainesville, 32610, Florida
| | - Z Hugh Fan
- J.Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, 32611, Florida. .,Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, 32611, Florida. .,Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, 32611, Florida.
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