Single-pot glycoprotein biosynthesis using a cell-free transcription-translation system enriched with glycosylation machinery

Cell-Free Co-Translational Approaches for Producing Mammalian Receptors: Expanding the Cell-Free Expression Toolbox Using Nanolipoproteins

Membranes proteins make up more than 60% of current drug targets and account for approximately 30% or more of the cellular proteome. Access to this important class of proteins has been difficult due to their inherent insolubility and tendency to aggregate in aqueous solutions. Understanding membrane protein structure and function demands novel means of membrane protein production that preserve both their native conformational state as well as function. Over the last decade, cell-free expression systems have emerged as an important complement to cell-based expression of membrane proteins due to their simple and customizable experimental parameters. One approach to overcome the solubility and stability limitations of purified membrane proteins is to support them in stable, native-like states within nanolipoprotein particles (NLPs), aka nanodiscs. This has become common practice to facilitate biochemical and biophysical characterization of proteins of interest. NLP technology can be easily coupled with cell-free systems to achieve functional membrane protein production for this purpose. Our approach involves utilizing cell-free expression systems in the presence of NLPs or using co-translation techniques to perform one-pot expression and self-assembly of membrane protein/NLP complexes. We describe how cell-free reactions can be modified to render control over nanoparticle size and monodispersity in support of membrane protein production. These modifications have been exploited to facilitate co-expression of full-length functional membrane proteins such as G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). In particular, we summarize the state of the art in NLP-assisted cell-free coexpression of these important classes of membrane proteins as well as evaluate the advances in and prospects for this technology that will drive drug discovery against these targets. We conclude with a prospective on the use of NLPs to produce as well as deliver functional mammalian membrane-bound proteins for a range of applications.

Towards On-Demand E. coli-Based Cell-Free Protein Synthesis of Tissue Plasminogen Activator

Stroke is the leading cause of death with over 5 million deaths worldwide each year. About 80% of strokes are ischemic strokes caused by blood clots. Tissue plasminogen activator (tPa) is the only FDA-approved drug to treat ischemic stroke with a wholesale price over $6000. tPa is now off patent although no biosimilar has been developed. The production of tPa is complicated by the 17 disulfide bonds that exist in correctly folded tPA. Here, we present an Escherichia coli-based cell-free protein synthesis platform for tPa expression and report conditions which resulted in the production of active tPa. While the activity is below that of commercially available tPa, this work demonstrates the potential of cell-free expression systems toward the production of future biosimilars. The E. coli-based cell-free system is increasingly becoming an attractive platform for low-cost biosimilar production due to recent developments which enable production from shelf-stable lyophilized reagents, the removal of endotoxins from the reagents to prevent the risk of endotoxic shock, and rapid on-demand production in hours.

Current Advancements in Addressing Key Challenges of Therapeutic Antibody Design, Manufacture, and Formulation

Therapeutic antibody technology heavily dominates the biologics market and continues to present as a significant industrial interest in developing novel and improved antibody treatment strategies. Many noteworthy advancements in the last decades have propelled the success of antibody development; however, there are still opportunities for improvement. In considering such interest to develop antibody therapies, this review summarizes the array of challenges and considerations faced in the design, manufacture, and formulation of therapeutic antibodies, such as stability, bioavailability and immunological engagement. We discuss the advancement of technologies that address these challenges, highlighting key antibody engineered formats that have been adapted. Furthermore, we examine the implication of novel formulation technologies such as nanocarrier delivery systems for the potential to formulate for pulmonary delivery. Finally, we comprehensively discuss developments in computational approaches for the strategic design of antibodies with modulated functions.

BioBits Health: Classroom Activities Exploring Engineering, Biology, and Human Health with Fluorescent Readouts

Recent advances in synthetic biology have resulted in biological technologies with the potential to reshape the way we understand and treat human disease. Educating students about the biology and ethics underpinning these technologies is critical to empower them to make informed future policy decisions regarding their use and to inspire the next generation of synthetic biologists. However, hands-on, educational activities that convey emerging synthetic biology topics can be difficult to implement due to the expensive equipment and expertise required to grow living cells. We present BioBits Health, an educational kit containing lab activities and supporting curricula for teaching antibiotic resistance mechanisms and CRISPR-Cas9 gene editing in high school classrooms. This kit links complex biological concepts to visual, fluorescent readouts in user-friendly freeze-dried cell-free reactions. BioBits Health represents a set of educational resources that promises to encourage teaching of cutting-edge, health-related synthetic biology topics in classrooms and other nonlaboratory settings.

The Application of Cell-Free Protein Synthesis in Genetic Code Expansion for Post-translational Modifications

The translation system is a sophisticated machinery that synthesizes proteins from 20 canonical amino acids. Recently, the repertoire of such composition has been expanded by the introduction of non-canonical amino acids (ncAAs) with the genetic code expansion strategy, which provides proteins with designed properties and structures for protein studies and engineering. Although the genetic code expansion strategy has been mostly implemented by using living cells as the host, a number of limits such as poor cellular uptake or solubility of specific ncAA substrates and the toxicity of target proteins have hindered the production of certain ncAA-modified proteins. To overcome those challenges, cell-free protein synthesis (CFPS) has been applied as it allows the precise control of reaction components. Several approaches have been recently developed to increase the purity and efficiency of ncAA incorporation in CFPS. Here, we summarized recent development of CFPS with an emphasis on its applications in generating site-specific protein post-translational modifications by the genetic code expansion strategy.

A User's Guide to Cell-Free Protein Synthesis

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.

Application of Cell-Free Protein Synthesis for Faster Biocatalyst Development

Cell-free protein synthesis (CFPS) has become an established tool for rapid protein synthesis in order to accelerate the discovery of new enzymes and the development of proteins with improved characteristics. Over the past years, progress in CFPS system preparation has been made towards simplification, and many applications have been developed with regard to tailor-made solutions for specific purposes. In this review, various preparation methods of CFPS systems are compared and the significance of individual supplements is assessed. The recent applications of CFPS are summarized and the potential for biocatalyst development discussed. One of the central features is the high-throughput synthesis of protein variants, which enables sophisticated approaches for rapid prototyping of enzymes. These applications demonstrate the contribution of CFPS to enhance enzyme functionalities and the complementation to in vivo protein synthesis. However, there are different issues to be addressed, such as the low predictability of CFPS performance and transferability to in vivo protein synthesis. Nevertheless, the usage of CFPS for high-throughput enzyme screening has been proven to be an efficient method to discover novel biocatalysts and improved enzyme variants.

Deconstructing Cell-Free Extract Preparation for in Vitro Activation of Transcriptional Genetic Circuitry

Recent advances in cell-free gene expression (CFE) systems have enabled their use for a host of synthetic biology applications, particularly for rapid prototyping of genetic circuits and biosensors. Despite the proliferation of cell-free protein synthesis platforms, the large number of currently existing protocols for making CFE extracts muddles the collective understanding of how the extract preparation method affects its functionality. A key aspect of extract performance relevant to many applications is the activity of the native host transcriptional machinery that can mediate protein synthesis. However, protein yields from genes transcribed in vitro by the native Escherichia coli RNA polymerase are variable for different extract preparation techniques, and specifically low in some conventional crude extracts originally optimized for expression by the bacteriophage transcriptional machinery. Here, we show that cell-free expression of genes under bacterial σ70 promoters is constrained by the rate of transcription in crude extracts, and that processing the extract with a ribosomal runoff reaction and subsequent dialysis alleviates this constraint. Surprisingly, these processing steps only enhance protein synthesis in genes under native regulation, indicating that the translation rate is unaffected. We further investigate the role of other common extract preparation process variants on extract performance and demonstrate that bacterial transcription is inhibited by including glucose in the growth culture but is unaffected by flash-freezing the cell pellet prior to lysis. Our final streamlined and detailed protocol for preparing extract by sonication generates extract that facilitates expression from a diverse set of sensing modalities including protein and RNA regulators. We anticipate that this work will clarify the methodology for generating CFE extracts that are active for biosensing using native transcriptional machinery and will encourage the further proliferation of cell-free gene expression technology for new applications.

Establishing a High-Yielding Cell-Free Protein Synthesis Platform Derived from Vibrio natriegens

A new wave of interest in cell-free protein synthesis (CFPS) systems has shown their utility for producing proteins at high titers, establishing genetic regulatory element libraries ( e.g., promoters, ribosome binding sites) in nonmodel organisms, optimizing biosynthetic pathways before implementation in cells, and sensing biomarkers for diagnostic applications. Unfortunately, most previous efforts have focused on a select few model systems, such as Escherichia coli. Broadening the spectrum of organisms used for CFPS promises to better mimic host cell processes in prototyping applications and open up new areas of research. Here, we describe the development and characterization of a facile CFPS platform based on lysates derived from the fast-growing bacterium Vibrio natriegens, which is an emerging host organism for biotechnology. We demonstrate robust preparation of highly active extracts using sonication, without specialized and costly equipment. After optimizing the extract preparation procedure and cell-free reaction conditions, we show synthesis of 1.6 ± 0.05 g/L of superfolder green fluorescent protein in batch mode CFPS, making it competitive with existing E. coli CFPS platforms. To showcase the flexibility of the system, we demonstrate that it can be lyophilized and retain biosynthesis capability, that it is capable of producing antimicrobial peptides, and that our extract preparation procedure can be coupled with the recently described Vmax Express strain in a one-pot system. Finally, to further increase system productivity, we explore a knockout library in which putative negative effectors of CFPS are genetically removed from the source strain. Our V. natriegens-derived CFPS platform is versatile and simple to prepare and use. We expect it will facilitate expansion of CFPS systems into new laboratories and fields for compelling applications in synthetic biology.

Metabolic engineering of glycoprotein biosynthesis in bacteria

The demonstration more than a decade ago that glycoproteins could be produced in Escherichia coli cells equipped with the N-linked protein glycosylation machinery from Campylobacter jejuni opened the door to using simple bacteria for the expression and engineering of complex glycoproteins. Since that time, metabolic engineering has played an increasingly important role in developing and optimizing microbial cell glyco-factories for the production of diverse glycoproteins and other glycoconjugates. It is becoming clear that future progress in creating efficient glycoprotein expression platforms in bacteria will depend on the adoption of advanced strain engineering strategies such as rational design and assembly of orthogonal glycosylation pathways, genome-wide identification of metabolic engineering targets, and evolutionary engineering of pathway performance. Here, we highlight recent advances in the deployment of metabolic engineering tools and strategies to develop microbial cell glyco-factories for the production of high-value glycoprotein targets with applications in research and medicine.

BioBits™ Bright: A fluorescent synthetic biology education kit

Synthetic biology offers opportunities for experiential educational activities at the intersection of the life sciences, engineering, and design. However, implementation of hands-on biology activities in classrooms is challenging because of the need for specialized equipment and expertise to grow living cells. We present BioBits™ Bright, a shelf-stable, just-add-water synthetic biology education kit with easy visual outputs enabled by expression of fluorescent proteins in freeze-dried, cell-free reactions. We introduce activities and supporting curricula for teaching the central dogma, tunable protein expression, and design-build-test cycles and report data generated by K-12 teachers and students. We also develop inexpensive incubators and imagers, resulting in a comprehensive kit costing Collapse

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MESH Headings

• Biosensing Techniques/methods
• Cell Physiological Phenomena
• Genes, Synthetic
• Luminescent Proteins/metabolism
• Synthetic Biology/education
• Teaching

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Grants

• National Science Foundation
• David and Lucile Packard Foundation
• Air Force Office of Scientific Research
• Army Research Office
• Wyss institute
• Paul G. Allen Frontiers Group
• Defense Threat Reduction Agency
• Camille Dreyfus Teacher-Scholar Program
• Air Force Research Laboratory Center of Excellence
• Natural Sciences and Engineering Council of Canada

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Affiliation(s)

Jessica C. Stark Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL 60208–3120, USA Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208–3120, USA Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL 60208–3120, USA
Ally Huang Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
Peter Q. Nguyen Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
Rachel S. Dubner Department of Biological Sciences, Northwestern University, 2205 Tech Drive, Hogan Hall 2144, Evanston, IL 60208, USA
Karen J. Hsu Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute B224, Evanston, IL 60208–3120, USA
Thomas C. Ferrante Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
Mary Anderson Glenbard East High School, 1014 South Main Street, Lombard, IL 60148–3938, USA
Ada Kanapskyte Amos Alonzo Stagg High School, 8015 West 111th Street, Palos Hills, IL 60465–2203, USA
Quinn Mucha Glenbard East High School, 1014 South Main Street, Lombard, IL 60148–3938, USA
Jessica S. Packett Amos Alonzo Stagg High School, 8015 West 111th Street, Palos Hills, IL 60465–2203, USA
Palak Patel Glenbard East High School, 1014 South Main Street, Lombard, IL 60148–3938, USA
Richa Patel Glenbard East High School, 1014 South Main Street, Lombard, IL 60148–3938, USA
Deema Qaq Glenbard East High School, 1014 South Main Street, Lombard, IL 60148–3938, USA
Tyler Zondor Glenbard East High School, 1014 South Main Street, Lombard, IL 60148–3938, USA
Julie Burke Grover Cleveland Elementary School, 3121 West Byron Street, Chicago, IL 60618–3403, USA
Thomas Martinez Glenbard East High School, 1014 South Main Street, Lombard, IL 60148–3938, USA
Ashlee Miller-Berry Evanston Township High School, 1600 Dodge Avenue, Evanston, IL 60201–3449, USA
Aparna Puppala Glenbrook South High School, 4000 West Lake Avenue, Glenview, IL 60026–1239, USA
Kara Reichert Jones College Prep High School, 700 South State Street, Chicago, IL 60605–2109, USA
Miriam Schmid Gwendolyn Brooks College Preparatory Academy, 250 East 111th Street, Chicago, IL 60628–4324, USA
Lance Brand Delta High School, 3400 East SR 28, Muncie, IN 47303, USA
Lander R. Hill ASPIRA Business and Finance High School, 2989 North Milwaukee Avenue, Chicago, IL 60618–7347, USA
Jemima F. Chellaswamy Aptakisic-Tripp School District 102, 850 Highland Grove Drive, Buffalo Grove, IL 60089, USA
Nuhie Faheem Oak Lawn Hometown Middle School, 5345 West 99th Street, Oak Lawn, IL 60453–3815, USA
Suzanne Fetherling Hoffman Estates High School, 1100 West Higgins Road, Hoffman Estates, IL 60169–4050, USA
Elissa Gong Vernon Hills High School, 145 Lakeview Parkway, Vernon Hills, IL 60061–1566, USA
Eddie Marie Gonzalzles Morgan Park High School, 1744 West Pryor Avenue, Chicago, IL 60643–3497, USA
Teresa Granito Evanston Township High School, 1600 Dodge Avenue, Evanston, IL 60201–3449, USA
Jenna Koritsaris Evanston Township High School, 1600 Dodge Avenue, Evanston, IL 60201–3449, USA
Binh Nguyen Northside College Prep High School, 5501 North Kedzie Avenue, Chicago, IL 60625–3923, USA
Sujud Ottman Aqsa School, 7361 West 92nd Street, Bridgeview, IL 60455–2133, USA
Christina Palffy Adlai E. Stevenson High School, 1 Stevenson Drive, Lincolnshire, IL 60069–2824, USA
Angela Patel Lyons Township High School, 100 South Brainard Avenue, La Grange, IL 60525–2101, USA
Sheila Skweres Evanston Township High School, 1600 Dodge Avenue, Evanston, IL 60201–3449, USA
Adriane Slaton Evanston Township High School, 1600 Dodge Avenue, Evanston, IL 60201–3449, USA
TaRhonda Woods Evanston Township High School, 1600 Dodge Avenue, Evanston, IL 60201–3449, USA
Nina Donghia Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
Keith Pardee Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
James J. Collins Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA Synthetic Biology Center, MIT, Cambridge, MA 02139, USA Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Michael C. Jewett Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL 60208–3120, USA Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208–3120, USA Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL 60208–3120, USA Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 North Saint Clair Street, Suite 1200, Chicago, IL 60611–3068, USA Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Suite 11-131, Chicago, IL 60611–2875, USA

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