1
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Brookwell AW, Gonzalez JL, Martinez AW, Oza JP. Development of Solid-State Storage for Cell-Free Expression Systems. ACS Synth Biol 2023; 12:2561-2577. [PMID: 37490644 DOI: 10.1021/acssynbio.3c00111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The fragility of biological systems during storage, transport, and utilization necessitates reliable cold-chain infrastructure and limits the potential of biotechnological applications. In order to unlock the broad applications of existing and emerging biological technologies, we report the development of a novel solid-state storage platform for complex biologics. The resulting solid-state biologics (SSB) platform meets four key requirements: facile rehydration of solid materials, activation of biochemical activity, ability to support complex downstream applications and functionalities, and compatibility for deployment in a variety of reaction formats and environments. As a model system of biochemical complexity, we utilized crudeEscherichia colicell extracts that retain active cellular metabolism and support robust levels of in vitro transcription and translation. We demonstrate broad versatility and utility of SSB through proof-of-concepts for on-demand in vitro biomanufacturing of proteins at a milliliter scale, the activation of downstream CRISPR activity, as well as deployment on paper-based devices. SSBs unlock a breadth of applications in biomanufacturing, discovery, diagnostics, and education in resource-limited environments on Earth and in space.
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Affiliation(s)
- August W Brookwell
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Jorge L Gonzalez
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Andres W Martinez
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Javin P Oza
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, California 93407, United States
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2
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Fochtman TJ, Oza JP. Established and Emerging Methods for Protecting Linear DNA in Cell-Free Expression Systems. Methods Protoc 2023; 6:mps6020036. [PMID: 37104018 PMCID: PMC10146267 DOI: 10.3390/mps6020036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
Cell-free protein synthesis (CFPS) is a method utilized for producing proteins without the limits of cell viability. The plug-and-play utility of CFPS is a key advantage over traditional plasmid-based expression systems and is foundational to the potential of this biotechnology. A key limitation of CFPS is the varying stability of DNA types, limiting the effectiveness of cell-free protein synthesis reactions. Researchers generally rely on plasmid DNA for its ability to support robust protein expression in vitro. However, the overhead required to clone, propagate, and purify plasmids reduces the potential of CFPS for rapid prototyping. While linear templates overcome the limits of plasmid DNA preparation, linear expression templates (LETs) were under-utilized due to their rapid degradation in extract based CFPS systems, limiting protein synthesis. To reach the potential of CFPS using LETs, researchers have made notable progress toward protection and stabilization of linear templates throughout the reaction. The current advancements range from modular solutions, such as supplementing nuclease inhibitors and genome engineering to produce strains lacking nuclease activity. Effective application of LET protection techniques improves expression yields of target proteins to match that of plasmid-based expression. The outcome of LET utilization in CFPS is rapid design–build–test–learn cycles to support synthetic biology applications. This review describes the various protection mechanisms for linear expression templates, methodological insights for implementation, and proposals for continued efforts that may further advance the field.
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3
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Jew K, Smith PEJ, So B, Kasman J, Oza JP, Black MW. Characterizing and Improving pET Vectors for Cell-free Expression. Front Bioeng Biotechnol 2022; 10:895069. [PMID: 35814024 PMCID: PMC9259831 DOI: 10.3389/fbioe.2022.895069] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 05/26/2022] [Indexed: 11/15/2022] Open
Abstract
Cell-free protein synthesis (CFPS) is an in vitro process that enables diverse applications in research, biomanufacturing, point-of-care diagnostics, therapeutics, and education using minimal laboratory equipment and reagents. One of the major limitations of CFPS implementation is its sensitivity to plasmid type. Specifically, plasmid templates based on commonly used vector backbones such as the pET series of bacterial expression vectors result in the inferior production of proteins. To overcome this limitation, we have evaluated the effect of expression cassette elements present in the pET30 vector on protein production across three different CFPS systems: NEBExpress, PURExpress, and CFAI-based E. coli extracts. Through the systematic elimination of genetic elements within the pET30 vector, we have identified elements that are responsible for the poor performance of pET30 vectors in the various CFPS systems. As a result, we demonstrate that through the removal of the lac operator (lacO) and N-terminal tags included in the vector backbone sequence, a pET vector can support high titers of protein expression when using extract-based CFPS systems. This work provides two key advances for the research community: 1) identification of vector sequence elements that affect robust production of proteins; 2) evaluation of expression across three unique CFPS systems including CFAI extracts, NEBexpress, and PURExpress. We anticipate that this work will improve access to CFPS by enabling researchers to choose the correct expression backbone within the context of their preferred expression system.
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Affiliation(s)
- Kara Jew
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Philip E. J. Smith
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Byungcheol So
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Jillian Kasman
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Javin P. Oza
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, CA, United States
- *Correspondence: Javin P. Oza, ; Michael W. Black,
| | - Michael W. Black
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, United States
- *Correspondence: Javin P. Oza, ; Michael W. Black,
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4
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Abstract
Cell-free protein synthesis (CFPS) is a powerful platform for synthetic biology, allowing for the controlled expression of proteins without reliance on living cells. However, the process of producing the cell extract, a key component of cell-free reactions, can be a bottleneck for new users to adopt CFPS as it requires technical knowledge and significant researcher oversight. Here, we provide a detailed method for implementing a simplified cell extract preparation workflow using CFAI media. We also provide a detailed protocol for the alternative, 2x YPTG media-based preparation process, as it represents a useful benchmark within the cell-free community.
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Affiliation(s)
- Alissa C Mullin
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA
| | - Taylor Slouka
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA
| | - Javin P Oza
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA.
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5
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Brookwell A, Oza JP, Caschera F. Biotechnology Applications of Cell-Free Expression Systems. Life (Basel) 2021; 11:life11121367. [PMID: 34947898 PMCID: PMC8705439 DOI: 10.3390/life11121367] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
Cell-free systems are a rapidly expanding platform technology with an important role in the engineering of biological systems. The key advantages that drive their broad adoption are increased efficiency, versatility, and low cost compared to in vivo systems. Traditionally, in vivo platforms have been used to synthesize novel and industrially relevant proteins and serve as a testbed for prototyping numerous biotechnologies such as genetic circuits and biosensors. Although in vivo platforms currently have many applications within biotechnology, they are hindered by time-constraining growth cycles, homeostatic considerations, and limited adaptability in production. Conversely, cell-free platforms are not hindered by constraints for supporting life and are therefore highly adaptable to a broad range of production and testing schemes. The advantages of cell-free platforms are being leveraged more commonly by the biotechnology community, and cell-free applications are expected to grow exponentially in the next decade. In this study, new and emerging applications of cell-free platforms, with a specific focus on cell-free protein synthesis (CFPS), will be examined. The current and near-future role of CFPS within metabolic engineering, prototyping, and biomanufacturing will be investigated as well as how the integration of machine learning is beneficial to these applications.
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Affiliation(s)
- August Brookwell
- Department of Chemistry & Biochemistry, College of Science & Mathematics, California Polytechnic State University, San Luis Obispo, CA 93407, USA;
| | - Javin P. Oza
- Department of Chemistry & Biochemistry, College of Science & Mathematics, California Polytechnic State University, San Luis Obispo, CA 93407, USA;
- Correspondence: (J.P.O.); (F.C.)
| | - Filippo Caschera
- Nuclera Nucleics Ltd., Cambridge CB4 0GD, UK
- Correspondence: (J.P.O.); (F.C.)
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6
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Abstract
Cell-free protein synthesis (CFPS) is a platform biotechnology that has enabled the on-demand synthesis of proteins for a variety of applications. Numerous advances have improved the productivity of the CFPS platform to result in high-yielding reactions; however, many applications remain limited due to long reaction times. To overcome this limitation, we first established the benchmarks reaction times for CFPS across in-house E. coli extracts and commercial kits. We then set out to fine-tune our in-house extract systems to improve reaction times. Through the optimization of reaction composition and titration of low-cost additives, we have identified formulations that reduce reaction times by 30-50% to obtain high protein titers for biomanufacturing applications, and reduce times by more than 50% to reach the sfGFP detection limit for applications in education and diagnostics. Under optimum conditions, we report the visible observation of sfGFP signal in less than 10 min. Altogether, these advances enhance the utility of CFPS as a rapid, user-defined platform.
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Affiliation(s)
- Logan R. Burrington
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Katharine R. Watts
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Javin P. Oza
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
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7
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Abstract
Cell-free protein synthesis (CFPS) has grown as a biotechnology platform that captures transcription and translation machinery in vitro. Numerous developments have made the CFPS platform more accessible to new users and have expanded the range of applications. For lysate based CFPS systems, cell extracts can be generated from a variety of organisms, harnessing the unique biochemistry of that host to augment protein synthesis. Within the last 20 years, Escherichia coli (E. coli) has become one of the most widely used organisms for supporting CFPS due to its affordability and versatility. Despite numerous key advances, the workflow for E. coli cell extract preparation has remained a key bottleneck for new users to implement CFPS for their applications. The extract preparation workflow is time-intensive and requires technical expertise to achieve reproducible results. To overcome these barriers, we previously reported the development of a 24 hour cell-free autoinduction (CFAI) workflow that reduces user input and technical expertise required. The CFAI workflow minimizes the labor and technical skill required to generate cell extracts while also increasing the total quantities of cell extracts obtained. Here we describe that workflow in a step-by-step manner to improve access and support the broad implementation of E. coli based CFPS.
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Affiliation(s)
- Philip E J Smith
- Department of Chemistry and Biochemistry, California Polytechnic State University San Luis Obispo; Center for Application in Biotechnology, California Polytechnic State University San Luis Obispo
| | - Taylor Slouka
- Department of Chemistry and Biochemistry, California Polytechnic State University San Luis Obispo; Center for Application in Biotechnology, California Polytechnic State University San Luis Obispo
| | - Javin P Oza
- Department of Chemistry and Biochemistry, California Polytechnic State University San Luis Obispo; Center for Application in Biotechnology, California Polytechnic State University San Luis Obispo;
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8
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Burrington LR, Baryal E, Hui K, Lambert E, Harding ST, Oza JP. The Fold-Illuminator: A low-cost, portable, and disposable incubator-illuminator device. Synth Syst Biotechnol 2021; 6:95-101. [PMID: 33997359 PMCID: PMC8099501 DOI: 10.1016/j.synbio.2021.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 01/08/2023] Open
Abstract
Fluorescent reporters have revolutionized modern applications in the fields of molecular and synthetic biology, enabling applications ranging from education to point-of-care diagnostics. Past advancements in these fields have primarily focused on improving reaction conditions, the development of new applications, and the broad dissemination of these technologies. However, field and classroom-based applications have remained limited in part due to the nature of fluorescent signal detection, which often requires the use of costly lab equipment to observe and quantify fluorescence readouts. Users without access to laboratory equipment rely on qualitative assessments of fluorescence, a process that remains highly variable from user-to-user even within the same classroom. To overcome this challenge, we have developed a foldable illuminator and incubator device to support field-applications of synthetic biology-based biosensors for education and diagnostics. The Fold-Illuminator is an affordable, portable, and recyclable device that allows for the visible detection of fluorescent biomolecules. The Fold-Illuminator's design allows for assembly in under 10 min, a user can then utilize the optional heating element to incubate biochemical reactions and visualize fluorescence outputs in a defined and light-controlled environment. Interchangeable LED strips and light-filtering screens provide modularity to pair with the fluorescence wavelengths of interest. The user can then unfold the device for convenient storage, transport, or even recycling. The cost for the Fold-Illuminator is $5.58 USD and is compatible with an optional heating element for an additional $3.98 cost, with potential for further reductions in cost for larger quantities. Open-source templates for cutting device parts from paper stock are provided for both printing and cutting by hand; cutting can also be achieved with consumer-grade smart cutting machines such as the Cricut®. Combined with the broad applications of fluorescent reporters, the Fold-Illuminator has the potential to improve access to fluorescence visualization and quantification for new users as well as emerging field applications.
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Affiliation(s)
- Logan R Burrington
- Chemistry and Biochemistry Department, College of Science and Math, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Emran Baryal
- Mechanical Engineering Department, College of Engineering, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Katherine Hui
- Mechanical Engineering Department, College of Engineering, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Emmett Lambert
- Mechanical Engineering Department, College of Engineering, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Sarah T Harding
- Mechanical Engineering Department, College of Engineering, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Javin P Oza
- Chemistry and Biochemistry Department, College of Science and Math, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
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9
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Levine MZ, So B, Mullin AC, Fanter R, Dillard K, Watts KR, La Frano MR, Oza JP. Activation of Energy Metabolism through Growth Media Reformulation Enables a 24-Hour Workflow for Cell-Free Expression. ACS Synth Biol 2020; 9:2765-2774. [PMID: 32835484 DOI: 10.1021/acssynbio.0c00283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cell-free protein synthesis (CFPS) platforms have undergone numerous workflow improvements to enable diverse applications in research, biomanufacturing, and education. The Escherichia coli cell extract-based platform has been broadly adopted due to its affordability and versatility. The upstream processing of cells to generate crude cell lysate remains time-intensive and technically nuanced, representing one of the largest sources of cost associated with the biotechnology. To overcome these limitations, we have improved the processes by developing a long-lasting autoinduction media formulation for CFPS that obviates human intervention between inoculation and harvest. The cell-free autoinduction (CFAI) media supports the production of robust cell extracts from high cell density cultures nearing the stationary phase of growth. As a result, the total mass of cells and the resulting extract volume obtained increases by 400% while maintaining robust reaction yields of reporter protein, sfGFP (>1 mg/mL). Notably, the CFAI workflow allows users to go from cells on a streak plate to completing CFPS reactions within 24 h. The CFAI workflow uniquely enabled us to elucidate the metabolic limits in CFPS associated with cells grown to stationary phase in the traditional 2× YTPG media. Metabolomics analysis demonstrates that CFAI-based extracts overcome these limits due to improved energy metabolism and redox balance. The advances reported here shed new light on the metabolism associated with highly active CFPS reactions and inform future efforts to tune the metabolism in CFPS systems. Additionally, we anticipate that the improvements in the time and cost-efficiency of CFPS will increase the simplicity and reproducibility, reducing the barriers for new researchers interested in implementing CFPS.
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Affiliation(s)
- Max Z. Levine
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Application in Biotechnology, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Byungcheol So
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Application in Biotechnology, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Alissa C. Mullin
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Application in Biotechnology, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Rob Fanter
- College of Agriculture, Food and Environmental Sciences, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Kayla Dillard
- Department of Food Science and Nutrition, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Katharine R. Watts
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Application in Biotechnology, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Michael R. La Frano
- Department of Food Science and Nutrition, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Health Research, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Javin P. Oza
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Application in Biotechnology, California Polytechnic State University, San Luis Obispo, California 93407, United States
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10
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Williams LC, Gregorio NE, So B, Kao WY, Kiste AL, Patel PA, Watts KR, Oza JP. The Genetic Code Kit: An Open-Source Cell-Free Platform for Biochemical and Biotechnology Education. Front Bioeng Biotechnol 2020; 8:941. [PMID: 32974303 PMCID: PMC7466673 DOI: 10.3389/fbioe.2020.00941] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/21/2020] [Indexed: 01/06/2023] Open
Abstract
Teaching the processes of transcription and translation is challenging due to the intangibility of these concepts and a lack of instructional, laboratory-based, active learning modules. Harnessing the genetic code in vitro with cell-free protein synthesis (CFPS) provides an open platform that allows for the direct manipulation of reaction conditions and biological machinery to enable inquiry-based learning. Here, we report our efforts to transform the research-based CFPS biotechnology into a hands-on module called the “Genetic Code Kit” for implementation into teaching laboratories. The Genetic Code Kit includes all reagents necessary for CFPS, as well as a laboratory manual, student worksheet, and augmented reality activity. This module allows students to actively explore transcription and translation while gaining exposure to an emerging research technology. In our testing of this module, undergraduate students who used the Genetic Code Kit in a teaching laboratory showed significant score increases on transcription and translation questions in a post-lab questionnaire compared with students who did not participate in the activity. Students also demonstrated an increase in self-reported confidence in laboratory methods and comfort with CFPS, indicating that this module helps prepare students for careers in laboratory research. Importantly, the Genetic Code Kit can accommodate a variety of learning objectives beyond transcription and translation and enables hypothesis-driven science. This opens the possibility of developing Course-Based Undergraduate Research Experiences (CUREs) based on the Genetic Code Kit, as well as supporting next-generation science standards in 8–12th grade science courses.
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Affiliation(s)
- Layne C Williams
- Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, United States.,Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Nicole E Gregorio
- Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, United States.,Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Byungcheol So
- Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, United States.,Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Wesley Y Kao
- Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, United States.,Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Alan L Kiste
- Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Pratish A Patel
- Department of Finance, Orfalea College of Business, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Katharine R Watts
- Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, United States.,Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Javin P Oza
- Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, United States.,Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA, United States
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11
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Gregorio NE, Kao WY, Williams LC, Patel PA, Watts KR, Oza JP. Identification of additive formulations for enhanced shelf‐life and productivity of
E. coli
cell‐free protein synthesis extracts. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.00102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Pratish A. Patel
- Orfalea College of BusinessCalifornia Polytechnic State University
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12
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Gregorio NE, Kao WY, Williams LC, Hight CM, Patel P, Watts KR, Oza JP. Unlocking Applications of Cell-Free Biotechnology through Enhanced Shelf Life and Productivity of E. coli Extracts. ACS Synth Biol 2020; 9:766-778. [PMID: 32083847 DOI: 10.1021/acssynbio.9b00433] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell-free protein synthesis (CFPS) is a platform biotechnology that enables a breadth of applications. However, field applications remain limited due to the poor shelf-stability of aqueous cell extracts required for CFPS. Lyophilization of E. coli extracts improves shelf life but remains insufficient for extended storage at room temperature. To address this limitation, we mapped the chemical space of ten low-cost additives with four distinct mechanisms of action in a combinatorial manner to identify formulations capable of stabilizing lyophilized cell extract. We report three key findings: (1) unique additive formulations that maintain full productivity of cell extracts stored at 4 °C and 23 °C; (2) additive formulations that enhance extract productivity by nearly 2-fold; (3) a machine learning algorithm that provides predictive capacity for the stabilizing effects of additive formulations that were not tested experimentally. These findings provide a simple and low-cost advance toward making CFPS field-ready and cost-competitive for biomanufacturing.
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Affiliation(s)
- Nicole E. Gregorio
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Wesley Y. Kao
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Layne C. Williams
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Christopher M. Hight
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Pratish Patel
- Department of Finance, Orfalea College of Business, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Katharine R. Watts
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Javin P. Oza
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
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13
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Smith PEJ, Burrington LR, Levine MZ, Watts KR, Oza JP. Optimization of Cell‐Free Protein Synthesis Through Identification of Rate‐Limiting Factors. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.05823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Max Z. Levine
- California Polytechnic State University, San Luis Obispo
| | | | - Javin P. Oza
- California Polytechnic State University, San Luis Obispo
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14
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Reilly Q, Mulllin AC, Oza JP. Optimization of Click Chemistry for Bioconjugation. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.06602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Quinn Reilly
- California Polytechnic State University, San Luis Obispo
| | | | - Javin P. Oza
- California Polytechnic State University, San Luis Obispo
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15
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Gregorio NE, Kao WY, Williams LC, Oza JP. Improvements to Simplicity and Stability of the Cell‐Free Protein Synthesis Platform to Enable Applications in the Field and the Classroom. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.461.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nicole E. Gregorio
- Chemistry and BiochemistryCalifornia Polytechnic State UniversitySan Luis ObispoCA
- Center for Applications in BiotechnologySan Luis ObispoCA
| | - Wesley Y. Kao
- Chemistry and BiochemistryCalifornia Polytechnic State UniversitySan Luis ObispoCA
- Center for Applications in BiotechnologySan Luis ObispoCA
| | - Layne C. Williams
- Chemistry and BiochemistryCalifornia Polytechnic State UniversitySan Luis ObispoCA
- Center for Applications in BiotechnologySan Luis ObispoCA
| | - Javin P. Oza
- Chemistry and BiochemistryCalifornia Polytechnic State UniversitySan Luis ObispoCA
- Center for Applications in BiotechnologySan Luis ObispoCA
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16
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Sabsay KR, Lee RT, Ravatt LM, Oza JP, McDonald AR. Computational Models for Activated Human MEK1: Identification of Key Active Site Residues and Interactions. J Chem Inf Model 2019; 59:2383-2393. [DOI: 10.1021/acs.jcim.8b00989] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kimberly R. Sabsay
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Rebecca T. Lee
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Leandre M. Ravatt
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Javin P. Oza
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Ashley Ringer McDonald
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, California 93407, United States
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17
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Abstract
Cell-free protein synthesis (CFPS) is a platform technology that provides new opportunities for protein expression, metabolic engineering, therapeutic development, education, and more. The advantages of CFPS over in vivo protein expression include its open system, the elimination of reliance on living cells, and the ability to focus all system energy on production of the protein of interest. Over the last 60 years, the CFPS platform has grown and diversified greatly, and it continues to evolve today. Both new applications and new types of extracts based on a variety of organisms are current areas of development. However, new users interested in CFPS may find it challenging to implement a cell-free platform in their laboratory due to the technical and functional considerations involved in choosing and executing a platform that best suits their needs. Here we hope to reduce this barrier to implementing CFPS by clarifying the similarities and differences amongst cell-free platforms, highlighting the various applications that have been accomplished in each of them, and detailing the main methodological and instrumental requirement for their preparation. Additionally, this review will help to contextualize the landscape of work that has been done using CFPS and showcase the diversity of applications that it enables.
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Affiliation(s)
- Nicole E Gregorio
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| | - Max Z Levine
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| | - Javin P Oza
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
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18
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Levine MZ, Gregorio NE, Jewett MC, Watts KR, Oza JP. Escherichia coli-Based Cell-Free Protein Synthesis: Protocols for a robust, flexible, and accessible platform technology. J Vis Exp 2019. [DOI: 10.3791/58882] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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19
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Lee RT, Ravatt LM, Runco CE, Oza JP. Elucidating structure‐function relationships of the human protein kinase MEK1. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.662.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rebecca T. Lee
- Chemistry & Biochemistry DepartmentCalifornia Polytechnic State UniversitySan Luis ObispoCA
| | - Leandre M. Ravatt
- Chemistry & Biochemistry DepartmentCalifornia Polytechnic State UniversitySan Luis ObispoCA
| | - Caroline E. Runco
- Chemistry & Biochemistry DepartmentCalifornia Polytechnic State UniversitySan Luis ObispoCA
| | - Javin P. Oza
- Chemistry & Biochemistry DepartmentCalifornia Polytechnic State UniversitySan Luis ObispoCA
- Center for Applications in BiotechnologyCalifornia Polytechnic State UniversitySan Luis ObispoCA
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20
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Kao WY, Gregorio NE, Oza JP. Cell‐Free Protein Synthesis: A Platform Technology for Education. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.663.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Wesley Y. Kao
- Chemistry & Biochemistry DepartmentCalifornia Polytechnic State UniversitySan Luis ObispoCA
| | - Nicole E. Gregorio
- Chemistry & Biochemistry DepartmentCalifornia Polytechnic State UniversitySan Luis ObispoCA
| | - Javin P. Oza
- Chemistry & Biochemistry DepartmentCalifornia Polytechnic State UniversitySan Luis ObispoCA
- Center for Applications in BiotechnologyCalifornia Polytechnic State UniversitySan Luis ObispoCA
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21
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Oza JP, Soye BD, Jewett MC. An engineered
E. coli
ribosome with tunable translation rates enhances recombinant protein expression. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.793.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Javin P. Oza
- Chemistry & Biochemistry DepartmentCalifornia Polytechnic State UniversitySan Luis ObispoCA
- Center for Applications in BiotechnologyCalifornia Polytechnic State UniversitySan Luis ObispoCA
| | - Ben Des Soye
- Department of Chemical and Biological EngineeringNorthwestern UniversityEvanstonIL
| | - Michael C. Jewett
- Department of Chemical and Biological EngineeringNorthwestern UniversityEvanstonIL
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22
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Abstract
Hydrogenotrophic methanogens possessing the hydrogen-dependent dehydrogenase Hmd also encode paralogs of this protein whose function is poorly understood. Here we present biochemical evidence that the two inactive Hmd paralogs of Methanocaldococcus jannaschii, HmdII and HmdIII, form binary and ternary complexes with several components of the protein translation apparatus. HmdII and HmdIII, but not the active dehydrogenase Hmd, bind with micromolar binding affinities to a number of tRNAs and form ternary complexes with tRNA(Pro) and prolyl-tRNA synthetase (ProRS). Fluorescence spectroscopy experiments also suggest that binding of HmdII and ProRS involves distinct binding determinants on the tRNA. These biochemical data suggest the possibility of a regulatory link between energy production and protein translation pathways that may allow a rapid cellular response to altered environmental conditions.
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Affiliation(s)
- Javin P Oza
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, California 93106-9510, United States
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23
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Wu H, Lippmann JE, Oza JP, Zeng M, Fives-Taylor P, Reich NO. Inactivation of DNA adenine methyltransferase alters virulence factors in Actinobacillus actinomycetemcomitans. ACTA ACUST UNITED AC 2006; 21:238-44. [PMID: 16842508 DOI: 10.1111/j.1399-302x.2006.00284.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA adenine methyltransferase (DAM) plays critical roles in diverse biological pathways in gram-negative bacteria, and specifically in regulating the expression of virulence genes in several organisms. Actinobacillus actinomycetemcomitans plays an important role in the pathogenesis of juvenile and adult periodontal disease, yet little is known about its mechanisms of gene regulation. DAM is shown here to directly or indirectly affect well-known A. actinomycetemcomitans virulence factors. A mutant A. actinomycetemcomitans strain lacking the dam gene was created by homologous recombination and shows normal growth phenotypes when grown exponentially. This mutant strain has four sixfold increased levels of extracellular leukotoxin, altered cellular levels of leukotoxin, and significant changes in bacterial invasion of KB oral epithelial cells. These results provide a basis for further characterization of regulatory mechanisms that control A. actinomycetemcomitans virulence.
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Affiliation(s)
- H Wu
- Department of Pediatric Dentistry, School of Dentistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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24
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Oza JP, Yeh JB, Reich NO. DNA methylation modulates Salmonella enterica serovar Typhimurium virulence in Caenorhabditis elegans. FEMS Microbiol Lett 2005; 245:53-9. [PMID: 15796979 DOI: 10.1016/j.femsle.2005.02.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2004] [Revised: 02/15/2005] [Accepted: 02/16/2005] [Indexed: 11/26/2022] Open
Abstract
Salmonella enterica serovar Typhimurium was previously shown to be virulent in Caenorhabditis elegans. Here we demonstrate that DNA adenine methyltransferase (DAM) modulates Salmonella virulence in the nematode, as it does in mice. After 5 days of continual exposure to bacteria, twice as many worms died when exposed to the wild-type than the dam-mutant strain of Salmonella. Similar trends in virulence were observed when worms were exposed to Salmonella strains for 5 h and transferred to the avirulent Escherichia coli OP50. While a 10-fold attenuation was observed in the absence of DAM, the dam-strain was still able to infect and persist in the host worm. Our results further support the use of C. elegans as an accessible and readily studied animal model of bacterial pathogenesis. However, our results suggest that crucial host responses differ between the murine and nematode models. Additionally, we carried out preliminary liquid culture based experiments with the long term goal of developing high throughput animal based screens of DAM inhibitors.
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Affiliation(s)
- Javin P Oza
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
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