1
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Yang L, Chen C, Xu X, Wang XT, Xing D, Ren N, Lee DJ. Genome and metabolome analysis of Bacillus sp. Hex-HIT36: A newly screened functional microorganism for the degradation of 1-hexadecene in industrial wastewater. ENVIRONMENTAL RESEARCH 2024; 260:119594. [PMID: 39002630 DOI: 10.1016/j.envres.2024.119594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/02/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
1-Hexadecene has been detected at a level of mg/L in both influent and effluent of wastewater treatment plants situated in chemical/pharmaceutical industrial parks, which poses a potential threat to the environment. However, few reports are available on aerobic metabolic pathways and microorganisms involved in 1-Hexadecene degradation. In this study, a new strain of 1-Hexadecene-degrading bacteria, Bacillus sp. Hex-HIT36 (HIT36), was isolated from the activated sludge of a wastewater treatment plants located in an industrial park. The physicochemical properties and degradation efficacy of HIT36 were investigated. HIT36 was cultured on a medium containing 1-Hexadecene as a sole carbon source; it was found to remove ∼67% of total organic carbon as confirmed by mass spectrometric analysis of intermediate metabolites. Metabolomic and genomic analysis showed that HIT36 possesses various enzymes, namely, pyruvate dehydrogenase, dihydropolyhydroxyl dehydrogenase, and 2-oxoglutarate-2-oxoiron oxidoreductase (subunit alpha), which assist in the metabolization of readily available carbon source or long chain hydrocarbons present in the growth medium/vicinity. This suggests that HIT36 has efficient long-chain alkane degradation efficacy, and understanding the alkane degradation mechanism of this strain can help in developing technologies for the degradation of long-chain alkanes present in wastewater, thereby assisting in the bioremediation of environment.
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Affiliation(s)
- Lei Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province, 150090, China
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province, 150090, China
| | - Xijun Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province, 150090, China
| | - Xue-Ting Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province, 150090, China.
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province, 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province, 150090, China
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-li, 32003, Taiwan
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2
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López IL, Sánchez-Costa M, Orrego AH, Zeballos N, Roura Padrosa D, López-Gallego F. Microtiter Plate Immobilization Screening for Prototyping Heterogeneous Enzyme Cascades. Angew Chem Int Ed Engl 2024; 63:e202407411. [PMID: 39037386 DOI: 10.1002/anie.202407411] [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: 04/18/2024] [Indexed: 07/23/2024]
Abstract
Immobilization is a key enabling technology in applied biocatalysis that facilitates the separation, recovery, and reuse of heterogeneous biocatalysts. However, finding a consensus immobilization protocol for several enzymes forming a multi-enzyme system is extremely difficult and relies on a combinatorial trial-and-error approach. Herein, we describe a protocol in which 17 different carriers functionalized with different reactive groups are tested in a 96-well microtiter plate to screen up to 21 immobilization protocols for up to 18 enzymes. This screening includes an activity and stability assay to select the optimal immobilization chemistry to achieve the most active and stable heterogeneous biocatalysts. The information retrieved from the screening can be rationalized using a Python-based application CapiPy. Finally, through scoring the screening results, we find the consensus immobilization protocol to assemble an immobilized four-enzyme system to transform vinyl acetate into (S)-3-hydroxybutyric acid. This methodology opens a path to speed up the prototyping of immobilized multi-enzyme pathways for chemical manufacturing.
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Affiliation(s)
- Idania L López
- Heterogeneous Biocatalysis laboratory Center for Cooperative Research in Biomaterials (CIC biomaGUNE) - Basque, Research and Technology Alliance (BRTA), Paseo de Miramón, 182., 20014, Donostia-San Sebastián, Spain
| | - Mercedes Sánchez-Costa
- Heterogeneous Biocatalysis laboratory Center for Cooperative Research in Biomaterials (CIC biomaGUNE) - Basque, Research and Technology Alliance (BRTA), Paseo de Miramón, 182., 20014, Donostia-San Sebastián, Spain
| | - Alejandro H Orrego
- Heterogeneous Biocatalysis laboratory Center for Cooperative Research in Biomaterials (CIC biomaGUNE) - Basque, Research and Technology Alliance (BRTA), Paseo de Miramón, 182., 20014, Donostia-San Sebastián, Spain
| | - Nicoll Zeballos
- Heterogeneous Biocatalysis laboratory Center for Cooperative Research in Biomaterials (CIC biomaGUNE) - Basque, Research and Technology Alliance (BRTA), Paseo de Miramón, 182., 20014, Donostia-San Sebastián, Spain
| | | | - Fernando López-Gallego
- Heterogeneous Biocatalysis laboratory Center for Cooperative Research in Biomaterials (CIC biomaGUNE) - Basque, Research and Technology Alliance (BRTA), Paseo de Miramón, 182., 20014, Donostia-San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009, Bilbao, Spain
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3
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Clark L, Voigt CA, Jewett MC. Establishing a High-Yield Chloroplast Cell-Free System for Prototyping Genetic Parts. ACS Synth Biol 2024; 13:2402-2411. [PMID: 39023433 DOI: 10.1021/acssynbio.4c00111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Plastid engineering offers the potential to carry multigene traits in plants; however, it requires reliable genetic parts to balance expression. The difficulty of chloroplast transformation and slow plant growth makes it challenging to build plants just to characterize genetic parts. To address these limitations, we developed a high-yield cell-free system from Nicotiana tabacum chloroplast extracts for prototyping genetic parts. Our cell-free system uses combined transcription and translation driven by T7 RNA polymerase and works with plasmid or linear template DNA. To develop our system, we optimized lysis, extract preparation procedures (e.g., runoff reaction, centrifugation, and dialysis), and the physiochemical reaction conditions. Our cell-free system can synthesize 34 ± 1 μg/mL luciferase in batch reactions and 60 ± 4 μg/mL in semicontinuous reactions. We apply our batch reaction system to test a library of 103 ribosome binding site (RBS) variants and rank them based on cell-free gene expression. We observe a 1300-fold dynamic range of luciferase expression when normalized by maximum mRNA expression, as assessed by the malachite green aptamer. We also find that the observed normalized gene expression in chloroplast extracts and the predictions made by the RBS Calculator are correlated. We anticipate that chloroplast cell-free systems will increase the speed and reliability of building genetic systems in plant chloroplasts for diverse applications.
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Affiliation(s)
- Lauren Clark
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Robert H. Lurie Comprehensive Cancer Center, Chicago, Illinois 60611, United States
- Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
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4
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Palma JA, Bunyatov MI, Hulbert SW, Jewett MC, DeLisa MP. Bacterial glycoengineering: Cell-based and cell-free routes for producing biopharmaceuticals with customized glycosylation. Curr Opin Chem Biol 2024; 81:102500. [PMID: 38991462 DOI: 10.1016/j.cbpa.2024.102500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/13/2024]
Abstract
Glycosylation plays a pivotal role in tuning the folding and function of proteins. Because most human therapeutic proteins are glycosylated, understanding and controlling glycosylation is important for the design, optimization, and manufacture of biopharmaceuticals. Unfortunately, natural eukaryotic glycosylation pathways are complex and often produce heterogeneous glycan patterns, making the production of glycoproteins with chemically precise and homogeneous glycan structures difficult. To overcome these limitations, bacterial glycoengineering has emerged as a simple, cost-effective, and scalable approach to produce designer glycoprotein therapeutics and vaccines in which the glycan structures are engineered to reduce heterogeneity and improve biological and biophysical attributes of the protein. Here, we discuss recent advances in bacterial cell-based and cell-free glycoengineering that have enabled the production of biopharmaceutical glycoproteins with customized glycan structures.
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Affiliation(s)
- Jaymee A Palma
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Mehman I Bunyatov
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Sophia W Hulbert
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Michael C Jewett
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Matthew P DeLisa
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA; Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Cornell Institute of Biotechnology, Cornell University, Biotechnology Building, Ithaca, NY 14853, USA.
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5
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DeWinter MA, Wong DA, Fernandez R, Kightlinger W, Thames AH, DeLisa MP, Jewett MC. Establishing a Cell-Free Glycoprotein Synthesis System for Enzymatic N-GlcNAcylation. ACS Chem Biol 2024; 19:1570-1582. [PMID: 38934647 DOI: 10.1021/acschembio.4c00228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
N-linked glycosylation plays a key role in the efficacy of many therapeutic proteins. One limitation to the bacterial glycoengineering of human N-linked glycans is the difficulty of installing a single N-acetylglucosamine (GlcNAc), the reducing end sugar of many human-type glycans, onto asparagine in a single step (N-GlcNAcylation). Here, we develop an in vitro method for N-GlcNAcylating proteins using the oligosaccharyltransferase PglB from Campylobacter jejuni. We use cell-free protein synthesis (CFPS) to test promiscuous PglB variants previously reported in the literature for the ability to produce N-GlcNAc and successfully determine that PglB with an N311V mutation (PglBN311V) exhibits increased GlcNAc transferase activity relative to the wild-type enzyme. We then improve the transfer efficiency by producing CFPS extracts enriched with PglBN311V and further optimize the reaction conditions, achieving a 98.6 ± 0.5% glycosylation efficiency. We anticipate this method will expand the glycoengineering toolbox for therapeutic research and biomanufacturing.
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Affiliation(s)
- Madison A DeWinter
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Derek A Wong
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Regina Fernandez
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Weston Kightlinger
- Cell-free Protein Synthesis and Microbial Process Development, National Resilience Inc.,, Oakland, California 94606, United States
| | - Ariel Helms Thames
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
- Cornell Institute of Biotechnology, Cornell University, Ithaca, New York 14853, United States
| | - Michael C Jewett
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
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6
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Willi JA, Karim AS, Jewett MC. Cell-Free Translation Quantification via a Fluorescent Minihelix. ACS Synth Biol 2024; 13:2253-2259. [PMID: 38979618 DOI: 10.1021/acssynbio.4c00266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Cell-free gene expression systems are used in numerous applications, including medicine making, diagnostics, and educational kits. Accurate quantification of nonfluorescent proteins in these systems remains a challenge. To address this challenge, we report the adaptation and use of an optimized tetra-cysteine minihelix both as a fusion protein and as a standalone reporter with the FlAsH dye. The fluorescent reporter helix is short enough to be encoded on a primer pair to tag any protein of interest via PCR. Both the tagged protein and the standalone reporter can be detected quantitatively in real time or at the end of cell-free expression reactions with standard 96/384-well plate readers, an RT-qPCR system, or gel electrophoresis without the need for staining. The fluorescent signal is stable and correlates linearly with the protein concentration, enabling product quantification. We modified the reporter to study cell-free expression dynamics and engineered ribosome activity. We anticipate that the fluorescent minihelix reporter will facilitate efforts in engineering in vitro transcription and translation systems.
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Affiliation(s)
- Jessica A Willi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
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7
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Wardman JF, Withers SG. Carbohydrate-active enzyme (CAZyme) discovery and engineering via (Ultra)high-throughput screening. RSC Chem Biol 2024; 5:595-616. [PMID: 38966674 PMCID: PMC11221537 DOI: 10.1039/d4cb00024b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/16/2024] [Indexed: 07/06/2024] Open
Abstract
Carbohydrate-active enzymes (CAZymes) constitute a diverse set of enzymes that catalyze the assembly, degradation, and modification of carbohydrates. These enzymes have been fashioned into potent, selective catalysts by millennia of evolution, and yet are also highly adaptable and readily evolved in the laboratory. To identify and engineer CAZymes for different purposes, (ultra)high-throughput screening campaigns have been frequently utilized with great success. This review provides an overview of the different approaches taken in screening for CAZymes and how mechanistic understandings of CAZymes can enable new approaches to screening. Within, we also cover how cutting-edge techniques such as microfluidics, advances in computational approaches and synthetic biology, as well as novel assay designs are leading the field towards more informative and effective screening approaches.
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Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia Vancouver BC V6T 1Z1 Canada
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8
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Xu Z, Pan X, Lu H, Lu Q, Liang Y, He Z, Zhu Y, Yu Y, Wu W, Han X, Pan C. Surface Energy-Assisted Patterning of Vapor Deposited All-Inorganic Perovskite Arrays for Wearable Optoelectronics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402635. [PMID: 38639419 PMCID: PMC11220711 DOI: 10.1002/advs.202402635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Indexed: 04/20/2024]
Abstract
Solution-based methods for fabricating all-inorganic perovskite film arrays often suffer from limited control over nucleation and crystallization, resulting in poor homogeneity and coverage. To improve film quality, advanced vapor deposition techniques are employed for continuous film. Here, the vapor deposition strategy to the all-inorganic perovskite films array, enabling area-selective deposition of perovskite through substrate modulation is expanded. It can yield a high-quality perovskite film array with different pixel shapes, various perovskite compositions, and a high resolution of 423 dpi. The resulting photodetector arrays exhibit remarkable optoelectronic performance with an on/off ratio of 13 887 and responsivity of 47.5 A W-1. The device also displays long-term stability in a damp condition for up to 12 h. Moreover, a pulse monitoring sensor based on the perovskite films array demonstrates stable monitoring for pulse signals after being worn for 12 h and with a low illumination of 0.055 mW cm-2, highlighting the potential application in wearable optoelectronic devices.
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Affiliation(s)
- Zhangsheng Xu
- Beijing Institute of Nanoenergy and NanosystemsChinese Academy of SciencesBeijing101400P. R. China
- School of Nanoscience and EngineeringUniversity of Chinese Academy of SciencesBeijing100049P. R. China
| | - Xiaojun Pan
- Beijing Institute of Nanoenergy and NanosystemsChinese Academy of SciencesBeijing101400P. R. China
| | - Hui Lu
- Beijing Institute of Nanoenergy and NanosystemsChinese Academy of SciencesBeijing101400P. R. China
- School of Nanoscience and EngineeringUniversity of Chinese Academy of SciencesBeijing100049P. R. China
| | - Qiuchun Lu
- Beijing Institute of Nanoenergy and NanosystemsChinese Academy of SciencesBeijing101400P. R. China
| | - Yegang Liang
- Beijing Institute of Nanoenergy and NanosystemsChinese Academy of SciencesBeijing101400P. R. China
| | - Zeping He
- Beijing Institute of Nanoenergy and NanosystemsChinese Academy of SciencesBeijing101400P. R. China
- School of Nanoscience and EngineeringUniversity of Chinese Academy of SciencesBeijing100049P. R. China
| | - Yizhi Zhu
- Beijing Institute of Nanoenergy and NanosystemsChinese Academy of SciencesBeijing101400P. R. China
| | - Yang Yu
- Beijing Institute of Nanoenergy and NanosystemsChinese Academy of SciencesBeijing101400P. R. China
| | - Wenqiang Wu
- Institute of Microscale OptoelectronicsShenzhen UniversityShenzhen518060P. R. China
| | - Xun Han
- Department of Applied PhysicsThe Hong Kong Polytechnic UniversityHong Kong999077P. R. China
| | - Caofeng Pan
- Beijing Institute of Nanoenergy and NanosystemsChinese Academy of SciencesBeijing101400P. R. China
- Institute of Microscale OptoelectronicsShenzhen UniversityShenzhen518060P. R. China
- Institute of Atomic ManufacturingBeihang UniversityBeijing100191P. R. China
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9
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Hao Z, Guo Q, Peng W, Da LT. A kinetic model reveals the critical gating motifs for donor-substrate loading into Actinobacillus pleuropneumoniae N-glycosyltransferase. Phys Chem Chem Phys 2024; 26:13441-13451. [PMID: 38647259 DOI: 10.1039/d3cp06034a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Soluble N-glycosyltransferase from Actinobacillus pleuropneumoniae (ApNGT) catalyzes the glycosylation of asparagine residues, and represents one of the most encouraging biocatalysts for N-glycoprotein production. Since the sugar tolerance of ApNGT is restricted to limited monosaccharides (e.g., Glc, GlcN, Gal, Xyl, and Man), tremendous efforts are devoted to expanding the substrate scope of ApNGT via enzyme engineering. However, rational design of novel NGT variants suffers from an elusive understanding of the substrate-binding process from a dynamic point of view. Here, by employing extensive all-atom molecular dynamics (MD) simulations integrated with a kinetic model, we reveal, at the atomic level, the complete donor-substrate binding process from the bulk solvent to the ApNGT active-site, and the key intermediate states of UDP-Glc during its loading dynamics. We are able to determine the critical transition event that limits the overall binding rate, which guides us to pinpoint the key ApNGT residues dictating the donor-substrate entry. The functional roles of several identified gating residues were evaluated through site-directed mutagenesis and enzymatic assays. Two single-point mutations, N471A and S496A, could profoundly enhance the catalytic activity of ApNGT. Our work provides deep mechanistic insights into the structural dynamics of the donor-substrate loading process for ApNGT, which sets a rational basis for design of novel NGT variants with desired substrate specificity.
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Affiliation(s)
- Zhiqiang Hao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Qiang Guo
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Wenjie Peng
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
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10
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Kofman C, Willi JA, Karim AS, Jewett MC. Ribosome Pool Engineering Increases Protein Biosynthesis Yields. ACS CENTRAL SCIENCE 2024; 10:871-881. [PMID: 38680563 PMCID: PMC11046459 DOI: 10.1021/acscentsci.3c01413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 05/01/2024]
Abstract
The biosynthetic capability of the bacterial ribosome motivates efforts to understand and harness sequence-optimized versions for synthetic biology. However, functional differences between natively occurring ribosomal RNA (rRNA) operon sequences remain poorly characterized. Here, we use an in vitro ribosome synthesis and translation platform to measure protein production capabilities of ribosomes derived from all unique combinations of 16S and 23S rRNAs from seven distinct Escherichia coli rRNA operon sequences. We observe that polymorphisms that distinguish native E. coli rRNA operons lead to significant functional changes in the resulting ribosomes, ranging from negligible or low gene expression to matching the protein production activity of the standard rRNA operon B sequence. We go on to generate strains expressing single rRNA operons and show that not only do some purified in vivo expressed homogeneous ribosome pools outperform the wild-type, heterogeneous ribosome pool but also that a crude cell lysate made from the strain expressing only operon A ribosomes shows significant yield increases for a panel of medically and industrially relevant proteins. We anticipate that ribosome pool engineering can be applied as a tool to increase yields across many protein biomanufacturing systems, as well as improve basic understanding of ribosome heterogeneity and evolution.
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Affiliation(s)
- Camila Kofman
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Jessica A. Willi
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty S. Karim
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Bioengineering, Stanford University, Stanford California 94305, United States
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11
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Azi F, Wang Z, Chen W, Lin D, Xu P. Developing Ganoderma lucidum as a next-generation cell factory for food and nutraceuticals. Trends Biotechnol 2024; 42:197-211. [PMID: 37659953 DOI: 10.1016/j.tibtech.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 09/04/2023]
Abstract
Ganoderma lucidum holds a colossal reservoir of hydrolytic enzymes and therapeutic compounds and can be a sustainable source of proteins and bioactive compounds. Its metabolic versatility, propelled by its rich genome content, provides excellent biosynthetic machinery for innovation-driven pathway engineering. However, robust regulatory networks and low frequency of homologous recombination are critical bottlenecks that limit the development of molecular tools and precise genetic markers for biomanufacturing innovations in this organism. Modern synthetic biology provides tools that could help to accelerate precise multiple gene targeting and editing and untangling the biosynthetic machinery of G. lucidum. This review provides insight into molecular strategies to unwind the regulatory bottlenecks and transform G. lucidum into efficient cell factories for food and nutraceuticals.
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Affiliation(s)
- Fidelis Azi
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong 515063, China; Technion-Israel Institute of Technology, Haifa 3200002, Israel
| | - Zhe Wang
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Wenhao Chen
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong 515063, China; Technion-Israel Institute of Technology, Haifa 3200002, Israel
| | - Dewei Lin
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong 515063, China; Technion-Israel Institute of Technology, Haifa 3200002, Israel
| | - Peng Xu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong 515063, China; Technion-Israel Institute of Technology, Haifa 3200002, Israel; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, GTIIT, Shantou, Guangdong 515063, China.
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12
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Bidstrup EJ, Kwon YH, Kim K, Bandi CK, Aw R, Jewett MC, DeLisa MP. Cell-Free Systems for the Production of Glycoproteins. Methods Mol Biol 2024; 2762:309-328. [PMID: 38315374 DOI: 10.1007/978-1-0716-3666-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Cell-free protein synthesis (CFPS), whereby cell lysates are used to produce proteins from a genetic template, has matured as an attractive alternative to standard biomanufacturing modalities due to its high volumetric productivity contained within a distributable platform. Initially, cell-free lysates produced from Escherichia coli, which are both simple to produce and cost-effective for the production of a wide variety of proteins, were unable to produce glycosylated proteins as E. coli lacks native glycosylation machinery. With many important therapeutic proteins possessing asparagine-linked glycans that are critical for structure and function, this gap in CFPS production capabilities was addressed with the development of cell-free expression of glycoproteins (glycoCFE), which uses the supplementation of extracted lipid-linked oligosaccharides and purified oligosaccharyltransferases to enable glycoprotein production in the CFPS reaction environment. In this chapter, we highlight the basic methods for the preparation of reagents for glycoCFE and the protocol for expression and glycosylation of a model protein using a more productive, yet simplified, glycoCFE setup. Beyond this initial protocol, we also highlight how this protocol can be extended to a wide range of alternative glycan structures, oligosaccharyltransferases, and acceptor proteins as well as to a one-pot cell-free glycoprotein synthesis reaction.
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Affiliation(s)
- Erik J Bidstrup
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Yong Hyun Kwon
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Keehun Kim
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Chandra Kanth Bandi
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Rochelle Aw
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Matthew P DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA.
- Cornell Institute of Biotechnology, Cornell University, Ithaca, NY, USA.
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13
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Yi X, Rasor BJ, Boadi N, Louie K, Northen TR, Karim AS, Jewett MC, Alper HS. Establishing a versatile toolkit of flux enhanced strains and cell extracts for pathway prototyping. Metab Eng 2023; 80:241-253. [PMID: 37890611 DOI: 10.1016/j.ymben.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/07/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023]
Abstract
Building and optimizing biosynthetic pathways in engineered cells holds promise to address societal needs in energy, materials, and medicine, but it is often time-consuming. Cell-free synthetic biology has emerged as a powerful tool to accelerate design-build-test-learn cycles for pathway engineering with increased tolerance to toxic compounds. However, most cell-free pathway prototyping to date has been performed in extracts from wildtype cells which often do not have sufficient flux towards the pathways of interest, which can be enhanced by engineering. Here, to address this gap, we create a set of engineered Escherichia coli and Saccharomyces cerevisiae strains rewired via CRISPR-dCas9 to achieve high-flux toward key metabolic precursors; namely, acetyl-CoA, shikimate, triose-phosphate, oxaloacetate, α-ketoglutarate, and glucose-6-phosphate. Cell-free extracts generated from these strains are used for targeted enzyme screening in vitro. As model systems, we assess in vivo and in vitro production of triacetic acid lactone from acetyl-CoA and muconic acid from the shikimate pathway. The need for these platforms is exemplified by the fact that muconic acid cannot be detected in wildtype extracts provided with the same biosynthetic enzymes. We also perform metabolomic comparison to understand biochemical differences between the cellular and cell-free muconic acid synthesis systems (E. coli and S. cerevisiae cells and cell extracts with and without metabolic rewiring). While any given pathway has different interfaces with metabolism, we anticipate that this set of pre-optimized, flux enhanced cell extracts will enable prototyping efforts for new biosynthetic pathways and the discovery of biochemical functions of enzymes.
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Affiliation(s)
- Xiunan Yi
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA; McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Blake J Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Nathalie Boadi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Katherine Louie
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trent R Northen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, 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, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA; Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA; McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA.
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14
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Jung JK, Rasor BJ, Rybnicky GA, Silverman AD, Standeven J, Kuhn R, Granito T, Ekas HM, Wang BM, Karim AS, Lucks JB, Jewett MC. At-Home, Cell-Free Synthetic Biology Education Modules for Transcriptional Regulation and Environmental Water Quality Monitoring. ACS Synth Biol 2023; 12:2909-2921. [PMID: 37699423 DOI: 10.1021/acssynbio.3c00223] [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] [Indexed: 09/14/2023]
Abstract
As the field of synthetic biology expands, the need to grow and train science, technology, engineering, and math (STEM) practitioners is essential. However, the lack of access to hands-on demonstrations has led to inequalities of opportunity and practice. In addition, there is a gap in providing content that enables students to make their own bioengineered systems. To address these challenges, we develop four shelf-stable cell-free biosensing educational modules that work by simply adding water and DNA to freeze-dried crude extracts of non-pathogenic Escherichia coli. We introduce activities and supporting curricula to teach the structure and function of the lac operon, dose-responsive behavior, considerations for biosensor outputs, and a "build-your-own" activity for monitoring environmental contaminants in water. We piloted these modules with K-12 teachers and 130 high-school students in their classrooms─and at home─without professional laboratory equipment. This work promises to catalyze access to interactive synthetic biology education opportunities.
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Affiliation(s)
- Jaeyoung K Jung
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Center for Water Research, Northwestern University, Evanston, Illinois 60208, United States
| | - Blake J Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Grant A Rybnicky
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Adam D Silverman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Center for Water Research, Northwestern University, Evanston, Illinois 60208, United States
| | | | - Robert Kuhn
- Centennial High School, Roswell, Georgia 30076, United States
- Innovation Academy STEM High School, Alpharetta, Georgia 30009, United States
| | - Teresa Granito
- Evanston Township High School, Evanston, Illinois 60201, United States
| | - Holly M Ekas
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Brenda M Wang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Center for Water Research, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, United States
- Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
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15
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Hussnaetter KP, Palm P, Pich A, Franzreb M, Rapp E, Elling L. Strategies for Automated Enzymatic Glycan Synthesis (AEGS). Biotechnol Adv 2023; 67:108208. [PMID: 37437855 DOI: 10.1016/j.biotechadv.2023.108208] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
Glycans are the most abundant biopolymers on earth and are constituents of glycoproteins, glycolipids, and proteoglycans with multiple biological functions. The availability of different complex glycan structures is of major interest in biotechnology and basic research of biological systems. High complexity, establishment of general and ubiquitous synthesis techniques, as well as sophisticated analytics, are major challenges in the development of glycan synthesis strategies. Enzymatic glycan synthesis with Leloir-glycosyltransferases is an attractive alternative to chemical synthesis as it can achieve quantitative regio- and stereoselective glycosylation in a single step. Various strategies for synthesis of a wide variety of different glycan structures has already be established and will exemplarily be discussed in the scope of this review. However, the application of enzymatic glycan synthesis in an automated system has high demands on the equipment, techniques, and methods. Different automation approaches have already been shown. However, while these techniques have been applied for several glycans, only a few strategies are able to conserve the full potential of enzymatic glycan synthesis during the process - economical and enzyme technological recycling of enzymes is still rare. In this review, we show the major challenges towards Automated Enzymatic Glycan Synthesis (AEGS). First, we discuss examples for immobilization of glycans or glycosyltransferases as an important prerequisite for the embedment and implementation in an enzyme reactor. Next, improvement of bioreactors towards automation will be described. Finally, analysis and monitoring of the synthesis process are discussed. Furthermore, automation processes and cycle design are highlighted. Accordingly, the transition of recent approaches towards a universal automated glycan synthesis platform will be projected. To this end, this review aims to describe essential key features for AEGS, evaluate the current state-of-the-art and give thought- encouraging impulses towards future full automated enzymatic glycan synthesis.
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Affiliation(s)
- Kai Philip Hussnaetter
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, D-52074 Aachen, Germany
| | - Philip Palm
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, D-52074 Aachen, Germany
| | - Andrij Pich
- Functional and Interactive Polymers, Institute of Technical and Macromolecular Chemistry and DWI Leibniz-Institute for Interactive Materials e.V., RWTH Aachen University, Forckenbeckstr. 50, 52074 Aachen, Germany
| | - Matthias Franzreb
- Karlsruher Institute of Technology (KIT), Institute of Functional Interfaces, Hermann v. Helmholtz, Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Erdmann Rapp
- glyXera GmbH, Brenneckestrasse 20 * ZENIT, 39120 Magdeburg, Germany; Max Planck Institute for Dynamics of Complex Technical System, Bioprocess Engineering, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Lothar Elling
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, D-52074 Aachen, Germany.
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16
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Su T, Chua WZ, Liu Y, Fan J, Tan SY, Yang DW, Sham LT. Rewiring the pneumococcal capsule pathway for investigating glycosyltransferase specificity and genetic glycoengineering. SCIENCE ADVANCES 2023; 9:eadi8157. [PMID: 37672581 PMCID: PMC10482335 DOI: 10.1126/sciadv.adi8157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
Virtually all living cells are covered with glycans. Their structures are primarily controlled by the specificities of glycosyltransferases (GTs). GTs typically adopt one of the three folds, namely, GT-A, GT-B, and GT-C. However, what defines their specificities remain poorly understood. Here, we developed a genetic glycoengineering platform by reprogramming the capsular polysaccharide pathways in Streptococcus pneumoniae to interrogate GT specificity and manipulate glycan structures. Our findings suggest that the central cleft of GT-B enzymes is important for determining acceptor specificity. The constraint of the glycoengineering platform was partially alleviated when the specificity of the precursor transporter was reduced, indicating that the transporter contributes to the overall fidelity of glycan synthesis. We also modified the pneumococcal capsule to produce several medically important mammalian glycans, as well as demonstrated the importance of regiochemistry in a glycosidic linkage on binding lung epithelial cells. Our work provided mechanistic insights into GT specificity and an approach for investigating glycan functions.
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Affiliation(s)
- Tong Su
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Wan-Zhen Chua
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Yao Liu
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Jingsong Fan
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117545, Singapore
| | - Si-Yin Tan
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Dai-wen Yang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117545, Singapore
| | - Lok-To Sham
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
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17
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Misorin AK, Chernyshova DO, Karbyshev MS. State-of-the-Art Approaches to Heterologous Expression of Bispecific Antibodies Targeting Solid Tumors. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1215-1231. [PMID: 37770390 DOI: 10.1134/s0006297923090031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/09/2023] [Accepted: 08/23/2023] [Indexed: 09/30/2023]
Abstract
Bispecific antibodies (bsAbs) are some of the most promising biotherapeutics due to the versatility provided by their structure and functional features. bsAbs simultaneously bind two antigens or two epitopes on the same antigen. Moreover, they are capable of directing immune effector cells to cancer cells and delivering various compounds (radionuclides, toxins, and immunologic agents) to the target cells, thus offering a broad spectrum of clinical applications. Current review is focused on the technologies used in bsAb engineering, current progress and prospects of these antibodies, and selection of various heterologous expression systems for bsAb production. We also discuss the platforms development of bsAbs for the therapy of solid tumors.
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18
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Hao Z, Guo Q, Feng Y, Zhang Z, Li T, Tian Z, Zheng J, Da LT, Peng W. Investigation of the Catalytic Mechanism of a Soluble N-glycosyltransferase Allows Synthesis of N-glycans at Noncanonical Sequons. JACS AU 2023; 3:2144-2155. [PMID: 37654596 PMCID: PMC10466321 DOI: 10.1021/jacsau.3c00214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 09/02/2023]
Abstract
The soluble N-glycosyltransferase from Actinobacillus pleuropneumoniae (ApNGT) can establish an N-glycosidic bond at the asparagine residue in the Asn-Xaa-Ser/Thr consensus sequon and is one of the most promising tools for N-glycoprotein production. Here, by integrating computational and experimental strategies, we revealed the molecular mechanism of the substrate recognition and following catalysis of ApNGT. These findings allowed us to pinpoint a key structural motif (215DVYM218) in ApNGT responsible for the peptide substrate recognition. Moreover, Y222 and H371 of ApNGT were found to participate in activating the acceptor Asn. The constructed models were supported by further crystallographic studies and the functional roles of the identified residues were validated by measuring the glycosylation activity of various mutants against a library of synthetic peptides. Intriguingly, with particular mutants, site-selective N-glycosylation of canonical or noncanonical sequons within natural polypeptides from the SARS-CoV-2 spike protein could be achieved, which were used to investigate the biological roles of the N-glycosylation in membrane fusion during virus entry. Our study thus provides in-depth molecular mechanisms underlying the substrate recognition and catalysis for ApNGT, leading to the synthesis of previously unknown chemically defined N-glycoproteins for exploring the biological importance of the N-glycosylation at a specific site.
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Affiliation(s)
- Zhiqiang Hao
- Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai
Center for Systems Biomedicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Qiang Guo
- Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai
Center for Systems Biomedicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Yuanyuan Feng
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zihan Zhang
- Shanghai
Key Laboratory of Chemical Assessment and Sustainability, School of
Chemical Science & Engineering, Tongji
University, Shanghai 200092, China
| | - Tiantian Li
- Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai
Center for Systems Biomedicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Zhixin Tian
- Shanghai
Key Laboratory of Chemical Assessment and Sustainability, School of
Chemical Science & Engineering, Tongji
University, Shanghai 200092, China
| | - Jianting Zheng
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin-Tai Da
- Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai
Center for Systems Biomedicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Wenjie Peng
- Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai
Center for Systems Biomedicine, Shanghai
Jiao Tong University, Shanghai 200240, China
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19
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Thames AH, Rische CH, Cao Y, Krier-Burris RA, Kuang FL, Hamilton RG, Bronzert C, Bochner BS, Jewett MC. A Cell-Free Protein Synthesis Platform to Produce a Clinically Relevant Allergen Panel. ACS Synth Biol 2023; 12:2252-2261. [PMID: 37553068 PMCID: PMC10768853 DOI: 10.1021/acssynbio.3c00269] [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] [Indexed: 08/10/2023]
Abstract
Allergens are used in the clinical diagnosis (e.g., skin tests) and treatment (e.g., immunotherapy) of allergic diseases. With growing interest in molecular allergy diagnostics and precision therapies, new tools are needed for producing allergen-based reagents. As a step to address this need, we demonstrate a cell-free protein synthesis approach for allergen production of a clinically relevant allergen panel composed of common allergens spanning a wide range of phylogenetic kingdoms. We show that allergens produced with this approach can be recognized by allergen-specific immunoglobulin E (IgE), either monoclonals or in patient sera. We also show that a cell-free expressed allergen can activate human cells such as peripheral blood basophils and CD34+ progenitor-derived mast cells in an IgE-dependent manner. We anticipate that this cell-free platform for allergen production will enable diagnostic and therapeutic technologies, providing useful tools and treatments for both the allergist and allergic patient.
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Affiliation(s)
- Ariel Helms Thames
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Clayton H Rische
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
- Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
| | - Yun Cao
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Rebecca A Krier-Burris
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Fei Li Kuang
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Robert G Hamilton
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21224, United States
| | - Charles Bronzert
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21224, United States
| | - Bruce S Bochner
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Michael C Jewett
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
- Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
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20
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Stark JC, Jaroentomeechai T, Warfel KF, Hershewe JM, DeLisa MP, Jewett MC. Rapid biosynthesis of glycoprotein therapeutics and vaccines from freeze-dried bacterial cell lysates. Nat Protoc 2023:10.1038/s41596-022-00799-z. [PMID: 37328605 DOI: 10.1038/s41596-022-00799-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 11/22/2022] [Indexed: 06/18/2023]
Abstract
The advent of distributed biomanufacturing platforms promises to increase agility in biologic production and expand access by reducing reliance on refrigerated supply chains. However, such platforms are not capable of robustly producing glycoproteins, which represent the majority of biologics approved or in development. To address this limitation, we developed cell-free technologies that enable rapid, modular production of glycoprotein therapeutics and vaccines from freeze-dried Escherichia coli cell lysates. Here, we describe a protocol for generation of cell-free lysates and freeze-dried reactions for on-demand synthesis of desired glycoproteins. The protocol includes construction and culture of the bacterial chassis strain, cell-free lysate production, assembly of freeze-dried reactions, cell-free glycoprotein synthesis, and glycoprotein characterization, all of which can be completed in one week or less. We anticipate that cell-free technologies, along with this comprehensive user manual, will help accelerate development and distribution of glycoprotein therapeutics and vaccines.
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Affiliation(s)
- Jessica C Stark
- Department of Chemistry & Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| | - Thapakorn Jaroentomeechai
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Katherine F Warfel
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Jasmine M Hershewe
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA.
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
- Simpson-Querrey Institute, Northwestern University, Chicago, IL, USA.
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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21
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Seki K, Galindo JL, Karim AS, Jewett MC. A Cell-Free Gene Expression Platform for Discovering and Characterizing Stop Codon Suppressing tRNAs. ACS Chem Biol 2023; 18:1324-1334. [PMID: 37257197 DOI: 10.1021/acschembio.3c00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Non-canonical amino acids (ncAAs) can be incorporated into peptides and proteins to create new properties and functions. Site-specific ncAA incorporation is typically enabled by orthogonal translation systems comprising a stop codon suppressing tRNA (typically UAG), an aminoacyl-tRNA synthetase, and an ncAA of interest. Unfortunately, methods to discover and characterize suppressor tRNAs are limited because of laborious and time-consuming workflows in living cells. In this work, we develop anEscherichia coli crude extract-based cell-free gene expression system to rapidly express and characterize functional suppressor tRNAs. Our approach co-expresses orthogonal tRNAs using endogenous machinery alongside a stop-codon containing superfolder green fluorescent protein (sfGFP) reporter, which can be used as a simple read-out for suppression. As a model, we evaluate the UAG and UAA suppressing activity of several orthogonal tRNAs. Then, we demonstrate that co-transcription of two mutually orthogonal tRNAs can direct the incorporation of two unique ncAAs within a single modified sfGFP. Finally, we show that the cell-free workflow can be used to discover putative UAG-suppressor tRNAs found in metagenomic data, which are nonspecifically recognized by endogenous aminoacyl-tRNA synthetases. We anticipate that our cell-free system will accelerate the development of orthogonal translation systems for synthetic biology.
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Affiliation(s)
- Kosuke Seki
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Joey L Galindo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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22
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Toul M, Slonkova V, Mican J, Urminsky A, Tomkova M, Sedlak E, Bednar D, Damborsky J, Hernychova L, Prokop Z. Identification, characterization, and engineering of glycosylation in thrombolyticsa. Biotechnol Adv 2023; 66:108174. [PMID: 37182613 DOI: 10.1016/j.biotechadv.2023.108174] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/09/2023] [Accepted: 05/09/2023] [Indexed: 05/16/2023]
Abstract
Cardiovascular diseases, such as myocardial infarction, ischemic stroke, and pulmonary embolism, are the most common causes of disability and death worldwide. Blood clot hydrolysis by thrombolytic enzymes and thrombectomy are key clinical interventions. The most widely used thrombolytic enzyme is alteplase, which has been used in clinical practice since 1986. Another clinically used thrombolytic protein is tenecteplase, which has modified epitopes and engineered glycosylation sites, suggesting that carbohydrate modification in thrombolytic enzymes is a viable strategy for their improvement. This comprehensive review summarizes current knowledge on computational and experimental identification of glycosylation sites and glycan identity, together with methods used for their reengineering. Practical examples from previous studies focus on modification of glycosylations in thrombolytics, e.g., alteplase, tenecteplase, reteplase, urokinase, saruplase, and desmoteplase. Collected clinical data on these glycoproteins demonstrate the great potential of this engineering strategy. Outstanding combinatorics originating from multiple glycosylation sites and the vast variety of covalently attached glycan species can be addressed by directed evolution or rational design. Directed evolution pipelines would benefit from more efficient cell-free expression and high-throughput screening assays, while rational design must employ structure prediction by machine learning and in silico characterization by supercomputing. Perspectives on challenges and opportunities for improvement of thrombolytic enzymes by engineering and evolution of protein glycosylation are provided.
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Affiliation(s)
- Martin Toul
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Veronika Slonkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jan Mican
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Adam Urminsky
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - Maria Tomkova
- Center for Interdisciplinary Biosciences, P. J. Safarik University in Kosice, Jesenna 5, 04154 Kosice, Slovakia
| | - Erik Sedlak
- Center for Interdisciplinary Biosciences, P. J. Safarik University in Kosice, Jesenna 5, 04154 Kosice, Slovakia
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Lenka Hernychova
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic.
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23
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Li X, Du Y, Chen X, Liu C. Emerging roles of O-glycosylation in regulating protein aggregation, phase separation, and functions. Curr Opin Chem Biol 2023; 75:102314. [PMID: 37156204 DOI: 10.1016/j.cbpa.2023.102314] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/28/2023] [Accepted: 04/02/2023] [Indexed: 05/10/2023]
Abstract
Protein O-glycosylation is widely identified in various proteins involved in diverse biological processes. Recent studies have demonstrated that O-glycosylation plays crucial and multifaceted roles in modulating protein amyloid aggregation and liquid-liquid phase separation (LLPS) under physiological conditions. Dysregulation of these processes is closely associated with human diseases such as neurodegenerative diseases (NDs) and cancers. In this review, we first summarize the distinct roles of O-glycosylation in regulating pathological aggregation of different amyloid proteins related to NDs and elaborate the underlying mechanisms of how O-glycosylation modulates protein aggregation kinetics, induces new aggregated structures, and mediates the pathogenesis of amyloid aggregates under diseased conditions. Furthermore, we introduce recent discoveries on O-GlcNAc-mediated regulation of synaptic LLPS and phase separation potency of low-complexity domain-enriched proteins. Finally, we identify challenges in future research and highlight the potential for developing new therapeutic strategies of NDs by targeting protein O-glycosylation.
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Affiliation(s)
- Xiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Yifei Du
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Synthetic and Functional Biomolecules Center, Peking University, Beijing, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China.
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.
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24
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Thames AH, Moons SJ, Wong DA, Boltje TJ, Bochner BS, Jewett MC. GlycoCAP: A Cell-Free, Bacterial Glycosylation Platform for Building Clickable Azido-Sialoglycoproteins. ACS Synth Biol 2023; 12:1264-1274. [PMID: 37040463 PMCID: PMC10758250 DOI: 10.1021/acssynbio.3c00017] [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] [Indexed: 04/13/2023]
Abstract
Glycan-binding receptors known as lectins represent a class of potential therapeutic targets. Yet, the therapeutic potential of targeting lectins remains largely untapped due in part to limitations in tools for building glycan-based drugs. One group of desirable structures is proteins with noncanonical glycans. Cell-free protein synthesis systems have matured as a promising approach for making glycoproteins that may overcome current limitations and enable new glycoprotein medicines. Yet, this approach has not been applied to the construction of proteins with noncanonical glycans. To address this limitation, we develop a cell-free glycoprotein synthesis platform for building noncanonical glycans and, specifically, clickable azido-sialoglycoproteins (called GlycoCAP). The GlycoCAP platform uses an Escherichia coli-based cell-free protein synthesis system for the site-specific installation of noncanonical glycans onto proteins with a high degree of homogeneity and efficiency. As a model, we construct four noncanonical glycans onto a dust mite allergen (Der p 2): α2,3 C5-azido-sialyllactose, α2,3 C9-azido-sialyllactose, α2,6 C5-azido-sialyllactose, and α2,6 C9-azido-sialyllactose. Through a series of optimizations, we achieve more than 60% sialylation efficiency with a noncanonical azido-sialic acid. We then show that the azide click handle can be conjugated with a model fluorophore using both strain-promoted and copper-catalyzed click chemistry. We anticipate that GlycoCAP will facilitate the development and discovery of glycan-based drugs by granting access to a wider variety of possible noncanonical glycan structures and also provide an approach for functionalizing glycoproteins by click chemistry conjugation.
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Affiliation(s)
- Ariel Helms Thames
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Sam J Moons
- Synvenio B.V., Mercator 3, Nijmegen 6525ED, The Netherlands
| | - Derek A Wong
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Thomas J Boltje
- Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen 6525AJ, The Netherlands
| | - Bruce S Bochner
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Michael C Jewett
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
- Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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25
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DeWinter MA, Thames AH, Guerrero L, Kightlinger W, Karim AS, Jewett MC. Point-of-Care Peptide Hormone Production Enabled by Cell-Free Protein Synthesis. ACS Synth Biol 2023; 12:1216-1226. [PMID: 36940255 DOI: 10.1021/acssynbio.2c00680] [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: 03/22/2023]
Abstract
In resource-limited settings, it can be difficult to safely deliver sensitive biologic medicines to patients due to cold chain and infrastructure constraints. Point-of-care drug manufacturing could circumvent these challenges since medicines could be produced locally and used on-demand. Toward this vision, we combine cell-free protein synthesis (CFPS) and a 2-in-1 affinity purification and enzymatic cleavage scheme to develop a platform for point-of-care drug manufacturing. As a model, we use this platform to synthesize a panel of peptide hormones, an important class of medications that can be used to treat a wide variety of diseases including diabetes, osteoporosis, and growth disorders. With this approach, temperature-stable lyophilized CFPS reaction components can be rehydrated with DNA encoding a SUMOylated peptide hormone of interest when needed. Strep-Tactin affinity purification and on-bead SUMO protease cleavage yield peptide hormones in their native form that are recognized by ELISA antibodies and that can bind their respective receptors. With further development to ensure proper biologic activity and patient safety, we envision that this platform could be used to manufacture valuable peptide hormone drugs in a decentralized way.
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Affiliation(s)
- Madison A DeWinter
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Ariel Helms Thames
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Laura Guerrero
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Weston Kightlinger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, United States
- Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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26
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Rasor BJ, Chirania P, Rybnicky GA, Giannone RJ, Engle NL, Tschaplinski TJ, Karim AS, Hettich RL, Jewett MC. Mechanistic Insights into Cell-Free Gene Expression through an Integrated -Omics Analysis of Extract Processing Methods. ACS Synth Biol 2023; 12:405-418. [PMID: 36700560 DOI: 10.1021/acssynbio.2c00339] [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: 01/27/2023]
Abstract
Cell-free systems derived from crude cell extracts have developed into tools for gene expression, with applications in prototyping, biosensing, and protein production. Key to the development of these systems is optimization of cell extract preparation methods. However, the applied nature of these optimizations often limits investigation into the complex nature of the extracts themselves, which contain thousands of proteins and reaction networks with hundreds of metabolites. Here, we sought to uncover the black box of proteins and metabolites in Escherichia coli cell-free reactions based on different extract preparation methods. We assess changes in transcription and translation activity from σ70 promoters in extracts prepared with acetate or glutamate buffer and the common post-lysis processing steps of a runoff incubation and dialysis. We then utilize proteomic and metabolomic analyses to uncover potential mechanisms behind these changes in gene expression, highlighting the impact of cold shock-like proteins and the role of buffer composition.
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Affiliation(s)
- Blake J Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Payal Chirania
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Grant A Rybnicky
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard J Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, United States.,Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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27
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Tang C, Wang L, Zang L, Wang Q, Qi D, Dai Z. On-demand biomanufacturing through synthetic biology approach. Mater Today Bio 2023; 18:100518. [PMID: 36636637 PMCID: PMC9830231 DOI: 10.1016/j.mtbio.2022.100518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
Biopharmaceuticals including protein therapeutics, engineered protein-based vaccines and monoclonal antibodies, are currently the mainstay products of the biotechnology industry. However, the need for specialized equipment and refrigeration during production and distribution poses challenges for the delivery of these technologies to the field and low-resource area. With the development of synthetic biology, multiple studies rewire the cell-free system or living cells to impact the portable, on-site and on-demand manufacturing of biomolecules. Here, we review these efforts and suggest future directions.
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Affiliation(s)
- Chenwang Tang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage; National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Lin Wang
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Lei Zang
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Qing Wang
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Dianpeng Qi
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage; National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Zhuojun Dai
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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28
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Ouadhi S, López DMV, Mohideen FI, Kwan DH. Engineering the enzyme toolbox to tailor glycosylation in small molecule natural products and protein biologics. Protein Eng Des Sel 2023; 36:gzac010. [PMID: 36444941 DOI: 10.1093/protein/gzac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/11/2022] [Accepted: 10/04/2022] [Indexed: 12/03/2022] Open
Abstract
Many glycosylated small molecule natural products and glycoprotein biologics are important in a broad range of therapeutic and industrial applications. The sugar moieties that decorate these compounds often show a profound impact on their biological functions, thus biocatalytic methods for controlling their glycosylation are valuable. Enzymes from nature are useful tools to tailor bioproduct glycosylation but these sometimes have limitations in their catalytic efficiency, substrate specificity, regiospecificity, stereospecificity, or stability. Enzyme engineering strategies such as directed evolution or semi-rational and rational design have addressed some of the challenges presented by these limitations. In this review, we highlight some of the recent research on engineering enzymes to tailor the glycosylation of small molecule natural products (including alkaloids, terpenoids, polyketides, and peptides), as well as the glycosylation of protein biologics (including hormones, enzyme-replacement therapies, enzyme inhibitors, vaccines, and antibodies).
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Affiliation(s)
- Sara Ouadhi
- Centre for Applied Synthetic Biology, Concordia University, Montreal, QC H4B 2A6, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
| | - Dulce María Valdez López
- Centre for Applied Synthetic Biology, Concordia University, Montreal, QC H4B 2A6, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
| | - F Ifthiha Mohideen
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - David H Kwan
- Centre for Applied Synthetic Biology, Concordia University, Montreal, QC H4B 2A6, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
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29
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Jung KJ, Rasor BJ, Rybnicky GA, Silverman AD, Standeven J, Kuhn R, Granito T, Ekas HM, Wang BM, Karim AS, Lucks JB, Jewett MC. At-home, cell-free synthetic biology education modules for transcriptional regulation and environmental water quality monitoring. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523248. [PMID: 36711593 PMCID: PMC9881948 DOI: 10.1101/2023.01.09.523248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
As the field of synthetic biology expands, the need to grow and train science, technology, engineering, and math (STEM) practitioners is essential. However, the lack of access to hands-on demonstrations has led to inequalities of opportunity and practice. In addition, there is a gap in providing content that enables students to make their own bioengineered systems. To address these challenges, we develop four shelf-stable cell-free biosensing educational modules that work by just-adding-water and DNA to freeze-dried crude extracts of Escherichia coli . We introduce activities and supporting curricula to teach the structure and function of the lac operon, dose-responsive behavior, considerations for biosensor outputs, and a 'build-your-own' activity for monitoring environmental contaminants in water. We piloted these modules with K-12 teachers and 130 high school students in their classrooms - and at home - without professional laboratory equipment or researcher oversight. This work promises to catalyze access to interactive synthetic biology education opportunities.
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Affiliation(s)
- Kirsten J. Jung
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Center for Water Research, Northwestern University, Evanston, IL 60208, USA
| | - Blake J. Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Grant A. Rybnicky
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, 60208, USA
| | - Adam D. Silverman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Center for Water Research, Northwestern University, Evanston, IL 60208, USA
| | | | - Robert Kuhn
- Centennial High School, Roswell, GA 30076, USA
- Fulton County Schools Innovation Academy, Alpharetta, GA 30009, USA
| | | | - Holly M. Ekas
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Brenda M. Wang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Ashty S. Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Center for Water Research, 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, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305
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30
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Choi YN, Cho N, Lee K, Gwon DA, Lee JW, Lee J. Programmable Synthesis of Biobased Materials Using Cell-Free Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2203433. [PMID: 36108274 DOI: 10.1002/adma.202203433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Motivated by the intricate mechanisms underlying biomolecule syntheses in cells that chemistry is currently unable to mimic, researchers have harnessed biological systems for manufacturing novel materials. Cell-free systems (CFSs) utilizing the bioactivity of transcriptional and translational machineries in vitro are excellent tools that allow supplementation of exogenous materials for production of innovative materials beyond the capability of natural biological systems. Herein, recent studies that have advanced the ability to expand the scope of biobased materials using CFS are summarized and approaches enabling the production of high-value materials, prototyping of genetic parts and modules, and biofunctionalization are discussed. By extending the reach of chemical and enzymatic reactions complementary to cellular materials, CFSs provide new opportunities at the interface of materials science and synthetic biology.
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Affiliation(s)
- Yun-Nam Choi
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Namjin Cho
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Kanghun Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Da-Ae Gwon
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Joongoo Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
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31
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Gonzales DT, Suraritdechachai S, Tang TYD. Compartmentalized Cell-Free Expression Systems for Building Synthetic Cells. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:77-101. [PMID: 37306700 DOI: 10.1007/10_2023_221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
One of the grand challenges in bottom-up synthetic biology is the design and construction of synthetic cellular systems. One strategy toward this goal is the systematic reconstitution of biological processes using purified or non-living molecular components to recreate specific cellular functions such as metabolism, intercellular communication, signal transduction, and growth and division. Cell-free expression systems (CFES) are in vitro reconstitutions of the transcription and translation machinery found in cells and are a key technology for bottom-up synthetic biology. The open and simplified reaction environment of CFES has helped researchers discover fundamental concepts in the molecular biology of the cell. In recent decades, there has been a drive to encapsulate CFES reactions into cell-like compartments with the aim of building synthetic cells and multicellular systems. In this chapter, we discuss recent progress in compartmentalizing CFES to build simple and minimal models of biological processes that can help provide a better understanding of the process of self-assembly in molecularly complex systems.
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Affiliation(s)
- David T Gonzales
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | | | - T -Y Dora Tang
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology Dresden, Dresden, Germany.
- Physics of Life, Cluster of Excellence, TU Dresden, Dresden, Germany.
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32
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Jaroentomeechai T, Kwon YH, Liu Y, Young O, Bhawal R, Wilson JD, Li M, Chapla DG, Moremen KW, Jewett MC, Mizrachi D, DeLisa MP. A universal glycoenzyme biosynthesis pipeline that enables efficient cell-free remodeling of glycans. Nat Commun 2022; 13:6325. [PMID: 36280670 PMCID: PMC9592599 DOI: 10.1038/s41467-022-34029-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 10/11/2022] [Indexed: 12/25/2022] Open
Abstract
The ability to reconstitute natural glycosylation pathways or prototype entirely new ones from scratch is hampered by the limited availability of functional glycoenzymes, many of which are membrane proteins that fail to express in heterologous hosts. Here, we describe a strategy for topologically converting membrane-bound glycosyltransferases (GTs) into water soluble biocatalysts, which are expressed at high levels in the cytoplasm of living cells with retention of biological activity. We demonstrate the universality of the approach through facile production of 98 difficult-to-express GTs, predominantly of human origin, across several commonly used expression platforms. Using a subset of these water-soluble enzymes, we perform structural remodeling of both free and protein-linked glycans including those found on the monoclonal antibody therapeutic trastuzumab. Overall, our strategy for rationally redesigning GTs provides an effective and versatile biosynthetic route to large quantities of diverse, enzymatically active GTs, which should find use in structure-function studies as well as in biochemical and biomedical applications involving complex glycomolecules.
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Affiliation(s)
- Thapakorn Jaroentomeechai
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY, 14853, USA
| | - Yong Hyun Kwon
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY, 14853, USA
| | - Yiwen Liu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY, 14853, USA
| | - Olivia Young
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY, 14853, USA
| | - Ruchika Bhawal
- Cornell Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Joshua D Wilson
- Glycobia, Inc., 33 Thornwood Drive, Suite 104, Ithaca, NY, 14850, USA
| | - Mingji Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY, 14853, USA
| | - Digantkumar G Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL, 60208-3120, USA
| | - Dario Mizrachi
- Department of Physiology & Developmental Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Matthew P DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY, 14853, USA.
- Cornell Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA.
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33
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Copeland CE, Kim J, Copeland PL, Heitmeier CJ, Kwon YC. Characterizing a New Fluorescent Protein for a Low Limit of Detection Sensing in the Cell-Free System. ACS Synth Biol 2022; 11:2800-2810. [PMID: 35850511 PMCID: PMC9396652 DOI: 10.1021/acssynbio.2c00180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cell-free protein synthesis-based biosensors have been developed as highly accurate, low-cost biosensors. However, since most biomarkers exist at low concentrations in various types of biopsies, the biosensor's dynamic range must be increased in the system to achieve low limits of detection necessary while deciphering from higher background signals. Many attempts to increase the dynamic range have relied on amplifying the input signal from the analyte, which can lead to complications of false positives. In this study, we aimed to increase the protein synthesis capability of the cell-free protein synthesis system and the output signal of the reporter protein to achieve a lower limit of detection. We utilized a new fluorescent protein, mNeonGreen, which produces a higher output than those commonly used in cell-free biosensors. Optimizations of DNA sequence and the subsequent cell-free protein synthesis reaction conditions allowed characterizing protein expression variability by given DNA template types, reaction environment, and storage additives that cause the greatest time constraint on designing the cell-free biosensor. Finally, we characterized the fluorescence kinetics of mNeonGreen compared to the commonly used reporter protein, superfolder green fluorescent protein. We expect that this finely tuned cell-free protein synthesis platform with the new reporter protein can be used with sophisticated synthetic gene circuitry networks to increase the dynamic range of a cell-free biosensor to reach lower detection limits and reduce the false-positive proportion.
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Affiliation(s)
- Caroline E Copeland
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Jeehye Kim
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Pearce L Copeland
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Chloe J Heitmeier
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Yong-Chan Kwon
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States.,Louisiana State University Agricultural Center, Baton Rouge, Louisiana 70803, United States
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34
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Toward modular construction of cell-free multienzyme systems. CHINESE JOURNAL OF CATALYSIS 2022. [DOI: 10.1016/s1872-2067(21)64002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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35
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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] [Abstract] [Key Words] [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
| | - Michael W. Black
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, United States
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36
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GAN R, Cabezas MD, Pan M, Zhang H, Hu G, Clark LG, Jewett MC, Nicol R. High-Throughput Regulatory Part Prototyping and Analysis by Cell-Free Protein Synthesis and Droplet Microfluidics. ACS Synth Biol 2022; 11:2108-2120. [PMID: 35549070 DOI: 10.1021/acssynbio.2c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Engineering regulatory parts for improved performance in genetic programs has played a pivotal role in the development of the synthetic biology cell programming toolbox. Here, we report the development of a novel high-throughput platform for regulatory part prototyping and analysis that leverages the advantages of engineered DNA libraries, cell-free protein synthesis (CFPS), high-throughput emulsion droplet microfluidics, standard flow sorting adapted to screen droplet reactions, and next-generation sequencing (NGS). With this integrated platform, we screened the activity of millions of genetic parts within hours, followed by NGS retrieval of the improved designs. This in vitro platform is particularly valuable for engineering regulatory parts of nonmodel organisms, where in vivo high-throughput screening methods are not readily available. The platform can be extended to multipart screening of complete genetic programs to optimize yield and stability.
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Affiliation(s)
- Rui GAN
- Broad Institute of MIT and Harvard, Cambridge, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Maria D. Cabezas
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3120, United States
| | - Ming Pan
- Broad Institute of MIT and Harvard, Cambridge, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Huaibin Zhang
- Broad Institute of MIT and Harvard, Cambridge, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Gang Hu
- Broad Institute of MIT and Harvard, Cambridge, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Lauren G. Clark
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3120, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3120, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3120, United States
- Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3120, United States
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3120, United States
| | - Robert Nicol
- Broad Institute of MIT and Harvard, Cambridge, 415 Main Street, Cambridge, Massachusetts 02142, United States
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37
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Wu Q, Dong W, Miao H, Wang Q, Dong S, Xuan W. Site‐Specific Protein Modification with Reducing Carbohydrates. Angew Chem Int Ed Engl 2022; 61:e202116545. [DOI: 10.1002/anie.202116545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Indexed: 01/13/2023]
Affiliation(s)
- Qifan Wu
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Weidong Dong
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Hui Miao
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Weimin Xuan
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
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38
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Perez JG, Carlson ED, Weisser O, Kofman C, Seki K, Des Soye BJ, Karim AS, Jewett MC. Improving genomically recoded Escherichia coli to produce proteins containing non-canonical amino acids. Biotechnol J 2022; 17:e2100330. [PMID: 34894206 DOI: 10.1002/biot.202100330] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022]
Abstract
A genomically recoded Escherichia coli strain that lacks all amber codons and release factor 1 (C321.∆A) enables efficient genetic encoding of chemically diverse non-canonical amino acids (ncAAs) into proteins. While C321.∆A has opened new opportunities in chemical and synthetic biology, this strain has not been optimized for protein production, limiting its utility in widespread industrial and academic applications. To address this limitation, the construction of a series of genomically recoded organisms that are optimized for cellular protein production is described. It is demonstrated that the functional deactivation of nucleases (e.g., rne, endA) and proteases (e.g., lon) increases production of wild-type superfolder green fluorescent protein (sfGFP) and sfGFP containing two ncAAs up to ≈5-fold. Additionally, a genomic IPTG-inducible T7 RNA polymerase (T7RNAP) cassette into these strains is introduced. Using an optimized platform, the ability to introduce two identical N6 -(propargyloxycarbonyl)-L -Lysine residues site specifically into sfGFP with a 17-fold improvement in production relative to the parent strain is demonstrated. The authors envision that their library of organisms will provide the community with multiple options for increased expression of proteins with new and diverse chemistries.
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Affiliation(s)
- Jessica G Perez
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Erik D Carlson
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Oliver Weisser
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Camila Kofman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Kosuke Seki
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Benjamin J Des Soye
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
- Simpson Querrey Institute, Northwestern University, Chicago, Illinois, USA
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39
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Wu Q, Dong W, Miao H, Wang Q, Dong S, Xuan W. Site‐Specific Protein Modification with Reducing Carbohydrates. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Qifan Wu
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Weidong Dong
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Hui Miao
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Weimin Xuan
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
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40
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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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41
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Monck C, Elani Y, Ceroni F. Cell-free protein synthesis: biomedical applications and future perspectives. Chem Eng Res Des 2022. [DOI: 10.1016/j.cherd.2021.11.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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42
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Wang C, Yang J, Lu Y. Modularize and Unite: Toward Creating a Functional Artificial Cell. Front Mol Biosci 2021; 8:781986. [PMID: 34912849 PMCID: PMC8667554 DOI: 10.3389/fmolb.2021.781986] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
An artificial cell is a simplified model of a living system, bringing breakthroughs into both basic life science and applied research. The bottom-up strategy instructs the construction of an artificial cell from nonliving materials, which could be complicated and interdisciplinary considering the inherent complexity of living cells. Although significant progress has been achieved in the past 2 decades, the area is still facing some problems, such as poor compatibility with complex bio-systems, instability, and low standardization of the construction method. In this review, we propose creating artificial cells through the integration of different functional modules. Furthermore, we divide the function requirements of an artificial cell into four essential parts (metabolism, energy supplement, proliferation, and communication) and discuss the present researches. Then we propose that the compartment and the reestablishment of the communication system would be essential for the reasonable integration of functional modules. Although enormous challenges remain, the modular construction would facilitate the simplification and standardization of an artificial cell toward a natural living system. This function-based strategy would also broaden the application of artificial cells and represent the steps of imitating and surpassing nature.
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Affiliation(s)
- Chen Wang
- Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
| | - Junzhu Yang
- Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
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43
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44
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Cellular and Molecular Engineering of Glycan Sialylation in Heterologous Systems. Molecules 2021; 26:molecules26195950. [PMID: 34641494 PMCID: PMC8512710 DOI: 10.3390/molecules26195950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 02/05/2023] Open
Abstract
Glycans have been shown to play a key role in many biological processes, such as signal transduction, immunogenicity, and disease progression. Among the various glycosylation modifications found on cell surfaces and in biomolecules, sialylation is especially important, because sialic acids are typically found at the terminus of glycans and have unique negatively charged moieties associated with cellular and molecular interactions. Sialic acids are also crucial for glycosylated biopharmaceutics, where they promote stability and activity. In this regard, heterogenous sialylation may produce variability in efficacy and limit therapeutic applications. Homogenous sialylation may be achieved through cellular and molecular engineering, both of which have gained traction in recent years. In this paper, we describe the engineering of intracellular glycosylation pathways through targeted disruption and the introduction of carbohydrate active enzyme genes. The focus of this review is on sialic acid-related genes and efforts to achieve homogenous, humanlike sialylation in model hosts. We also discuss the molecular engineering of sialyltransferases and their application in chemoenzymatic sialylation and sialic acid visualization on cell surfaces. The integration of these complementary engineering strategies will be useful for glycoscience to explore the biological significance of sialic acids on cell surfaces as well as the future development of advanced biopharmaceuticals.
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45
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Shotgun scanning glycomutagenesis: A simple and efficient strategy for constructing and characterizing neoglycoproteins. Proc Natl Acad Sci U S A 2021; 118:2107440118. [PMID: 34551980 PMCID: PMC8488656 DOI: 10.1073/pnas.2107440118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2021] [Indexed: 11/18/2022] Open
Abstract
Asparagine-linked (N-linked) protein glycosylation—the covalent attachment of complex sugars to the nitrogen atom in asparagine side chains—is the most widespread posttranslational modification to proteins and also the most complex. N-glycosylation affects a significant number of cellular proteins and can have profound effects on their most important attributes such as biological activity, chemical solubility, folding and stability, immunogenicity, and serum half-life. Accordingly, the strategic installation of glycans at naïve sites has become an attractive means for endowing proteins with advantageous biological and/or biophysical properties. Here, we describe a glycoprotein engineering strategy that enables systematic investigation of the structural and functional consequences of glycan installation at every position along a protein backbone and provides a new route to bespoke glycoproteins. As a common protein modification, asparagine-linked (N-linked) glycosylation has the capacity to greatly influence the biological and biophysical properties of proteins. However, the routine use of glycosylation as a strategy for engineering proteins with advantageous properties is limited by our inability to construct and screen large collections of glycoproteins for cataloguing the consequences of glycan installation. To address this challenge, we describe a combinatorial strategy termed shotgun scanning glycomutagenesis in which DNA libraries encoding all possible glycosylation site variants of a given protein are constructed and subsequently expressed in glycosylation-competent bacteria, thereby enabling rapid determination of glycosylatable sites in the protein. The resulting neoglycoproteins can be readily subjected to available high-throughput assays, making it possible to systematically investigate the structural and functional consequences of glycan conjugation along a protein backbone. The utility of this approach was demonstrated with three different acceptor proteins, namely bacterial immunity protein Im7, bovine pancreatic ribonuclease A, and human anti-HER2 single-chain Fv antibody, all of which were found to tolerate N-glycan attachment at a large number of positions and with relatively high efficiency. The stability and activity of many glycovariants was measurably altered by N-linked glycans in a manner that critically depended on the precise location of the modification. Structural models suggested that affinity was improved by creating novel interfacial contacts with a glycan at the periphery of a protein–protein interface. Importantly, we anticipate that our glycomutagenesis workflow should provide access to unexplored regions of glycoprotein structural space and to custom-made neoglycoproteins with desirable properties.
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Dudley QM, Cai YM, Kallam K, Debreyne H, Carrasco Lopez JA, Patron NJ. Biofoundry-assisted expression and characterization of plant proteins. Synth Biol (Oxf) 2021; 6:ysab029. [PMID: 34693026 PMCID: PMC8529701 DOI: 10.1093/synbio/ysab029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/25/2021] [Accepted: 09/09/2021] [Indexed: 12/29/2022] Open
Abstract
Many goals in synthetic biology, including the elucidation and refactoring of biosynthetic pathways and the engineering of regulatory circuits and networks, require knowledge of protein function. In plants, the prevalence of large gene families means it can be particularly challenging to link specific functions to individual proteins. However, protein characterization has remained a technical bottleneck, often requiring significant effort to optimize expression and purification protocols. To leverage the ability of biofoundries to accelerate design-built-test-learn cycles, we present a workflow for automated DNA assembly and cell-free expression of plant proteins that accelerates optimization and enables rapid screening of enzyme activity. First, we developed a phytobrick-compatible Golden Gate DNA assembly toolbox containing plasmid acceptors for cell-free expression using Escherichia coli or wheat germ lysates as well as a set of N- and C-terminal tag parts for detection, purification and improved expression/folding. We next optimized automated assembly of miniaturized cell-free reactions using an acoustic liquid handling platform and then compared tag configurations to identify those that increase expression. We additionally developed a luciferase-based system for rapid quantification that requires a minimal 11-amino acid tag and demonstrate facile removal of tags following synthesis. Finally, we show that several functional assays can be performed with cell-free protein synthesis reactions without the need for protein purification. Together, the combination of automated assembly of DNA parts and cell-free expression reactions should significantly increase the throughput of experiments to test and understand plant protein function and enable the direct reuse of DNA parts in downstream plant engineering workflows.
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Affiliation(s)
- Quentin M Dudley
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk UK
| | - Yao-Min Cai
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk UK
| | - Kalyani Kallam
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk UK
| | - Hubert Debreyne
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk UK
| | | | - Nicola J Patron
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk UK
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Fostering "Education": Do Extracellular Vesicles Exploit Their Own Delivery Code? Cells 2021; 10:cells10071741. [PMID: 34359911 PMCID: PMC8305232 DOI: 10.3390/cells10071741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 12/15/2022] Open
Abstract
Extracellular vesicles (EVs), comprising large microvesicles (MVs) and exosomes (EXs), play a key role in intercellular communication, both in physiological and in a wide variety of pathological conditions. However, the education of EV target cells has so far mainly been investigated as a function of EX cargo, while few studies have focused on the characterization of EV surface membrane molecules and the mechanisms that mediate the addressability of specific EVs to different cell types and tissues. Identifying these mechanisms will help fulfill the diagnostic, prognostic, and therapeutic promises fueled by our growing knowledge of EVs. In this review, we first discuss published studies on the presumed EV “delivery code” and on the combinations of the hypothesized EV surface membrane “sender” and “recipient” molecules that may mediate EV targeting in intercellular communication. Then we briefly review the main experimental approaches and techniques, and the bioinformatic tools that can be used to identify and characterize the structure and functional role of EV surface membrane molecules. In the final part, we present innovative techniques and directions for future research that would improve and deepen our understandings of EV-cell targeting.
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Choi YN, Shin YR, Park JM, Lee JW. Cell-Free Transcription-Coupled CRISPR/Cas12a Assay for Prototyping Cyanobacterial Promoters. ACS Synth Biol 2021; 10:1300-1307. [PMID: 34015913 DOI: 10.1021/acssynbio.1c00148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cyanobacteria are promising microbial hosts for the production of diverse biofuels and biochemicals. However, compared to other model microbial hosts such as Escherichia coli and yeast, it takes a long time to genetically modify cyanobacteria. One way to efficiently engineer cyanobacteria while minimizing genetic engineering would be to develop a fast, high-throughput prototyping tool for cyanobacteria. In this study, we developed a CRISPR/Cas12a-based assay coupled with cyanobacteria cell-free systems to rapidly prototype promoter characteristics. Using this newly developed assay, we demonstrated cyanobacteria cell-free transcription for the first time and confirmed a positive correlation between the in vitro and in vivo transcription performance. Furthermore, we generated a synthetic promoter library and evaluated the characteristics of promoter subregions by using the assay. Varied promoter strength derived from random mutations were rapidly and effectively measured in a high-throughput way. We believe that this study offers an easily applicable and rapid prototyping platform to characterize promoters for cyanobacterial engineering.
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Affiliation(s)
- Yun-Nam Choi
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Ye Rim Shin
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Jong Moon Park
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
- School of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
- Division of Advanced Nuclear Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
- School of Integrated Technology, Yonsei University (POSTECH-Yonsei Open Campus), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk, 37673, Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
- School of Integrated Technology, Yonsei University (POSTECH-Yonsei Open Campus), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk, 37673, Korea
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Meyer C, Nakamura Y, Rasor BJ, Karim AS, Jewett MC, Tan C. Analysis of the Innovation Trend in Cell-Free Synthetic Biology. Life (Basel) 2021; 11:551. [PMID: 34208358 PMCID: PMC8231175 DOI: 10.3390/life11060551] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/05/2021] [Accepted: 06/08/2021] [Indexed: 01/21/2023] Open
Abstract
Cell-free synthetic biology is a maturing field that aims to assemble biomolecular reactions outside cells for compelling applications in drug discovery, metabolic engineering, biomanufacturing, diagnostics, and education. Cell-free systems have several key features. They circumvent mechanisms that have evolved to facilitate species survival, bypass limitations on molecular transport across the cell wall, enable high-yielding and rapid synthesis of proteins without creating recombinant cells, and provide high tolerance towards toxic substrates or products. Here, we analyze ~750 published patents and ~2000 peer-reviewed manuscripts in the field of cell-free systems. Three hallmarks emerged. First, we found that both patent filings and manuscript publications per year are significantly increasing (five-fold and 1.5-fold over the last decade, respectively). Second, we observed that the innovation landscape has changed. Patent applications were dominated by Japan in the early 2000s before shifting to China and the USA in recent years. Finally, we discovered an increasing prevalence of biotechnology companies using cell-free systems. Our analysis has broad implications on the future development of cell-free synthetic biology for commercial and industrial applications.
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Affiliation(s)
- Conary Meyer
- Department of Biomedical Engineering, University of California, Davis, CA 95618, USA; (C.M.); (Y.N.)
| | - Yusuke Nakamura
- Department of Biomedical Engineering, University of California, Davis, CA 95618, USA; (C.M.); (Y.N.)
| | - Blake J. Rasor
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; (B.J.R.); (A.S.K.); (M.C.J.)
| | - Ashty S. Karim
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; (B.J.R.); (A.S.K.); (M.C.J.)
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; (B.J.R.); (A.S.K.); (M.C.J.)
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California, Davis, CA 95618, USA; (C.M.); (Y.N.)
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Hershewe JM, Warfel KF, Iyer SM, Peruzzi JA, Sullivan CJ, Roth EW, DeLisa MP, Kamat NP, Jewett MC. Improving cell-free glycoprotein synthesis by characterizing and enriching native membrane vesicles. Nat Commun 2021; 12:2363. [PMID: 33888690 PMCID: PMC8062659 DOI: 10.1038/s41467-021-22329-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 03/08/2021] [Indexed: 02/02/2023] Open
Abstract
Cell-free gene expression (CFE) systems from crude cellular extracts have attracted much attention for biomanufacturing and synthetic biology. However, activating membrane-dependent functionality of cell-derived vesicles in bacterial CFE systems has been limited. Here, we address this limitation by characterizing native membrane vesicles in Escherichia coli-based CFE extracts and describing methods to enrich vesicles with heterologous, membrane-bound machinery. As a model, we focus on bacterial glycoengineering. We first use multiple, orthogonal techniques to characterize vesicles and show how extract processing methods can be used to increase concentrations of membrane vesicles in CFE systems. Then, we show that extracts enriched in vesicle number also display enhanced concentrations of heterologous membrane protein cargo. Finally, we apply our methods to enrich membrane-bound oligosaccharyltransferases and lipid-linked oligosaccharides for improving cell-free N-linked and O-linked glycoprotein synthesis. We anticipate that these methods will facilitate on-demand glycoprotein production and enable new CFE systems with membrane-associated activities.
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Affiliation(s)
- Jasmine M Hershewe
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
| | - Katherine F Warfel
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
| | - Shaelyn M Iyer
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
| | - Justin A Peruzzi
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
| | - Claretta J Sullivan
- Air Force Research Laboratory, Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
| | - Eric W Roth
- Northwestern University Atomic and Nanoscale Characterization and Experimentation (NUANCE) Center, Tech Institute A/B Wing A173, Evanston, IL, 60208, USA
| | - Matthew P DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
- Biomedical and Biological Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Neha P Kamat
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Technological Institute E310, Evanston, IL, 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.
- Center for Synthetic Biology, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA.
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