1
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Park H, Jin H, Kim D, Lee J. Cell-Free Systems: Ideal Platforms for Accelerating the Discovery and Production of Peptide-Based Antibiotics. Int J Mol Sci 2024; 25:9109. [PMID: 39201795 PMCID: PMC11354240 DOI: 10.3390/ijms25169109] [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: 07/08/2024] [Revised: 08/12/2024] [Accepted: 08/19/2024] [Indexed: 09/03/2024] Open
Abstract
Peptide-based antibiotics (PBAs), including antimicrobial peptides (AMPs) and their synthetic mimics, have received significant interest due to their diverse and unique bioactivities. The integration of high-throughput sequencing and bioinformatics tools has dramatically enhanced the discovery of enzymes, allowing researchers to identify specific genes and metabolic pathways responsible for producing novel PBAs more precisely. Cell-free systems (CFSs) that allow precise control over transcription and translation in vitro are being adapted, which accelerate the identification, characterization, selection, and production of novel PBAs. Furthermore, these platforms offer an ideal solution for overcoming the limitations of small-molecule antibiotics, which often lack efficacy against a broad spectrum of pathogens and contribute to the development of antibiotic resistance. In this review, we highlight recent examples of how CFSs streamline these processes while expanding our ability to access new antimicrobial agents that are effective against antibiotic-resistant infections.
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Affiliation(s)
- Hyeongwoo Park
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology, Pohang 37673, Republic of Korea;
| | - Haneul Jin
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea; (H.J.); (D.K.)
| | - Dayeong Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea; (H.J.); (D.K.)
| | - Joongoo Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology, Pohang 37673, Republic of Korea;
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea; (H.J.); (D.K.)
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2
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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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3
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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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4
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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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5
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Lehri B, Atkins E, Scott TA, Abouelhadid S, Wren BW, Cuccui J. Investigation into the efficiency of diverse N-linking oligosaccharyltransferases for glycoengineering using a standardised cell-free assay. Microb Biotechnol 2024; 17:e14480. [PMID: 38858807 PMCID: PMC11164674 DOI: 10.1111/1751-7915.14480] [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] [Received: 01/12/2024] [Revised: 03/26/2024] [Accepted: 05/03/2024] [Indexed: 06/12/2024] Open
Abstract
The application of bacterial oligosaccharyltransferases (OSTs) such as the Campylobacter jejuni PglB for glycoengineering has attracted considerable interest in glycoengineering and glycoconjugate vaccine development. However, PglB has limited specificity for glycans that can be transferred to candidate proteins, which along with other factors is dependent on the reducing end sugar of glycans. In this study, we developed a cell-free glycosylation assay that offers the speed and simplicity of a 'yes' or 'no' determination. Using the assay, we tested the activity of eleven PglBs from Campylobacter species and more distantly related bacteria. The following assorted glycans with diverse reducing end sugars were tested for transfer, including Streptococcus pneumoniae capsule serotype 4, Salmonella enterica serovar Typhimurium O antigen (B1), Francisella tularensis O antigen, Escherichia coli O9 antigen and Campylobacter jejuni heptasaccharide. Interestingly, while PglBs from the same genus showed high activity, whereas divergent PglBs differed in their transfer of glycans to an acceptor protein. Notably for glycoengineering purposes, Campylobacter hepaticus and Campylobacter subantarcticus PglBs showed high glycosylation efficiency, with C. hepaticus PglB potentially being useful for glycoconjugate vaccine production. This study demonstrates the versatility of the cell-free assay in rapidly assessing an OST to couple glycan/carrier protein combinations and lays the foundation for future screening of PglBs by linking amino acid similarity to glycosyltransferase activity.
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Affiliation(s)
- Burhan Lehri
- Department of Infection BiologyLondon School of Hygiene and Tropical MedicineLondonUK
| | - Elizabeth Atkins
- Department of Infection BiologyLondon School of Hygiene and Tropical MedicineLondonUK
| | - Timothy A. Scott
- Department of Medicine, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Sherif Abouelhadid
- Department of Infection BiologyLondon School of Hygiene and Tropical MedicineLondonUK
| | - Brendan W. Wren
- Department of Infection BiologyLondon School of Hygiene and Tropical MedicineLondonUK
| | - Jon Cuccui
- Department of Infection BiologyLondon School of Hygiene and Tropical MedicineLondonUK
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6
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Lin L, Kightlinger W, Warfel KF, Jewett MC, Mrksich M. Using High-Throughput Experiments To Screen N-Glycosyltransferases with Altered Specificities. ACS Synth Biol 2024; 13:1290-1302. [PMID: 38526141 DOI: 10.1021/acssynbio.3c00769] [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: 03/26/2024]
Abstract
The important roles that protein glycosylation plays in modulating the activities and efficacies of protein therapeutics have motivated the development of synthetic glycosylation systems in living bacteria and in vitro. A key challenge is the lack of glycosyltransferases that can efficiently and site-specifically glycosylate desired target proteins without the need to alter primary amino acid sequences at the acceptor site. Here, we report an efficient and systematic method to screen a library of glycosyltransferases capable of modifying comprehensive sets of acceptor peptide sequences in parallel. This approach is enabled by cell-free protein synthesis and mass spectrometry of self-assembled monolayers and is used to engineer a recently discovered prokaryotic N-glycosyltransferase (NGT). We screened 26 pools of site-saturated NGT libraries to identify relevant residues that determine polypeptide specificity and then characterized 122 NGT mutants, using 1052 unique peptides and 52,894 unique reaction conditions. We define a panel of 14 NGTs that can modify 93% of all sequences within the canonical X-1-N-X+1-S/T eukaryotic glycosylation sequences as well as another panel for many noncanonical sequences (with 10 of 17 non-S/T amino acids at the X+2 position). We then successfully applied our panel of NGTs to increase the efficiency of glycosylation for three protein therapeutics. Our work promises to significantly expand the substrates amenable to in vitro and bacterial glycoengineering.
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Affiliation(s)
- Liang Lin
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Weston Kightlinger
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Katherine F Warfel
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, California 94305, United States
| | - Milan Mrksich
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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7
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Schachner LF, Mullen C, Phung W, Hinkle JD, Beardsley MI, Bentley T, Day P, Tsai C, Sukumaran S, Baginski T, DiCara D, Agard NJ, Masureel M, Gober J, ElSohly AM, Melani R, Syka JEP, Huguet R, Marty MT, Sandoval W. Exposing the molecular heterogeneity of glycosylated biotherapeutics. Nat Commun 2024; 15:3259. [PMID: 38627419 PMCID: PMC11021452 DOI: 10.1038/s41467-024-47693-8] [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: 07/28/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
The heterogeneity inherent in today's biotherapeutics, especially as a result of heavy glycosylation, can affect a molecule's safety and efficacy. Characterizing this heterogeneity is crucial for drug development and quality assessment, but existing methods are limited in their ability to analyze intact glycoproteins or other heterogeneous biotherapeutics. Here, we present an approach to the molecular assessment of biotherapeutics that uses proton-transfer charge-reduction with gas-phase fractionation to analyze intact heterogeneous and/or glycosylated proteins by mass spectrometry. The method provides a detailed landscape of the intact molecular weights present in biotherapeutic protein preparations in a single experiment. For glycoproteins in particular, the method may offer insights into glycan composition when coupled with a suitable bioinformatic strategy. We tested the approach on various biotherapeutic molecules, including Fc-fusion, VHH-fusion, and peptide-bound MHC class II complexes to demonstrate efficacy in measuring the proteoform-level diversity of biotherapeutics. Notably, we inferred the glycoform distribution for hundreds of molecular weights for the eight-times glycosylated fusion drug IL22-Fc, enabling correlations between glycoform sub-populations and the drug's pharmacological properties. Our method is broadly applicable and provides a powerful tool to assess the molecular heterogeneity of emerging biotherapeutics.
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Affiliation(s)
- Luis F Schachner
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Christopher Mullen
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - Wilson Phung
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Joshua D Hinkle
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | | | - Tracy Bentley
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
| | - Peter Day
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
| | - Christina Tsai
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
- Protein Analytical Development, Ascendis Pharma, Palo Alto, CA, USA
| | - Siddharth Sukumaran
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
- Translational Pharmacometrics, Janssen, Horsham, PA, USA
| | - Tomasz Baginski
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
| | - Danielle DiCara
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA, USA
| | - Nicholas J Agard
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA, USA
| | - Matthieu Masureel
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Joshua Gober
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Adel M ElSohly
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Rafael Melani
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - John E P Syka
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - Romain Huguet
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA.
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8
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Levitskaya Z, Ser Z, Koh H, Mei WS, Chee S, Sobota RM, Ghadessy JF. Engineering cell-free systems by chemoproteomic-assisted phenotypic screening. RSC Chem Biol 2024; 5:372-385. [PMID: 38576719 PMCID: PMC10989505 DOI: 10.1039/d4cb00004h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/16/2024] [Indexed: 04/06/2024] Open
Abstract
Phenotypic screening is a valuable tool to both understand and engineer complex biological systems. We demonstrate the functionality of this approach in the development of cell-free protein synthesis (CFPS) technology. Phenotypic screening identified numerous compounds that enhanced protein production in yeast lysate CFPS reactions. Notably, many of these were competitive ATP kinase inhibitors, with the exploitation of their inherent substrate promiscuity redirecting ATP flux towards heterologous protein expression. Chemoproteomic-guided strain engineering partially phenocopied drug effects, with a 30% increase in protein yield observed upon deletion of the ATP-consuming SSA1 component of the HSP70 chaperone. Moreover, drug-mediated metabolic rewiring coupled with template optimization generated the highest protein yields in yeast CFPS to date using a hitherto less efficient, but more cost-effective glucose energy regeneration system. Our approach highlights the utility of target-agnostic phenotypic screening and target identification to deconvolute cell-lysate complexity, adding to the expanding repertoire of strategies for improving CFPS.
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Affiliation(s)
- Zarina Levitskaya
- Protein and Peptide Engineering and Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Zheng Ser
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Hiromi Koh
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Wang Shi Mei
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Sharon Chee
- Protein and Peptide Engineering and Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Radoslaw Mikolaj Sobota
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - John F Ghadessy
- Protein and Peptide Engineering and Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
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9
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Kocalar S, Miller BM, Huang A, Gleason E, Martin K, Foley K, Copeland DS, Jewett MC, Saavedra EA, Kraves S. Validation of Cell-Free Protein Synthesis Aboard the International Space Station. ACS Synth Biol 2024; 13:942-950. [PMID: 38442491 PMCID: PMC10949350 DOI: 10.1021/acssynbio.3c00733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
Cell-free protein synthesis (CFPS) is a rapidly maturing in vitro gene expression platform that can be used to transcribe and translate nucleic acids at the point of need, enabling on-demand synthesis of peptide-based vaccines and biotherapeutics as well as the development of diagnostic tests for environmental contaminants and infectious agents. Unlike traditional cell-based systems, CFPS platforms do not require the maintenance of living cells and can be deployed with minimal equipment; therefore, they hold promise for applications in low-resource contexts, including spaceflight. Here, we evaluate the performance of the cell-free platform BioBits aboard the International Space Station by expressing RNA-based aptamers and fluorescent proteins that can serve as biological indicators. We validate two classes of biological sensors that detect either the small-molecule DFHBI or a specific RNA sequence. Upon detection of their respective analytes, both biological sensors produce fluorescent readouts that are visually confirmed using a hand-held fluorescence viewer and imaged for quantitative analysis. Our findings provide insights into the kinetics of cell-free transcription and translation in a microgravity environment and reveal that both biosensors perform robustly in space. Our findings lay the groundwork for portable, low-cost applications ranging from point-of-care health monitoring to on-demand detection of environmental hazards in low-resource communities both on Earth and beyond.
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Affiliation(s)
- Selin Kocalar
- Leigh
High School, 5210 Leigh
Ave, San Jose, California 95124, United States
- Massachusetts
Institute of Technology, 77 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Bess M. Miller
- Division
of Genetics, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis St, Boston, Massachusetts 02115, United States
| | - Ally Huang
- miniPCR
bio, 1770 Massachusetts
Ave, Cambridge, Massachusetts 02140, United States
| | - Emily Gleason
- miniPCR
bio, 1770 Massachusetts
Ave, Cambridge, Massachusetts 02140, United States
| | - Kathryn Martin
- miniPCR
bio, 1770 Massachusetts
Ave, Cambridge, Massachusetts 02140, United States
| | - Kevin Foley
- Boeing
Defense, Space & Security, 6398 Upper Brandon Dr, Houston, Texas 77058, United States
| | - D. Scott Copeland
- Boeing
Defense, Space & Security, 6398 Upper Brandon Dr, Houston, Texas 77058, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | | | - Sebastian Kraves
- miniPCR
bio, 1770 Massachusetts
Ave, Cambridge, Massachusetts 02140, United States
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10
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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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11
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Hulbert SW, Desai P, Jewett MC, DeLisa MP, Williams AJ. Glycovaccinology: The design and engineering of carbohydrate-based vaccine components. Biotechnol Adv 2023; 68:108234. [PMID: 37558188 DOI: 10.1016/j.biotechadv.2023.108234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/12/2023] [Accepted: 08/05/2023] [Indexed: 08/11/2023]
Abstract
Vaccines remain one of the most important pillars in preventative medicine, providing protection against a wide array of diseases by inducing humoral and/or cellular immunity. Of the many possible candidate antigens for subunit vaccine development, carbohydrates are particularly appealing because of their ubiquitous presence on the surface of all living cells, viruses, and parasites as well as their known interactions with both innate and adaptive immune cells. Indeed, several licensed vaccines leverage bacterial cell-surface carbohydrates as antigens for inducing antigen-specific plasma cells secreting protective antibodies and the development of memory T and B cells. Carbohydrates have also garnered attention in other aspects of vaccine development, for example, as adjuvants that enhance the immune response by either activating innate immune responses or targeting specific immune cells. Additionally, carbohydrates can function as immunomodulators that dampen undesired humoral immune responses to entire protein antigens or specific, conserved regions on antigenic proteins. In this review, we highlight how the interplay between carbohydrates and the adaptive and innate arms of the immune response is guiding the development of glycans as vaccine components that act as antigens, adjuvants, and immunomodulators. We also discuss how advances in the field of synthetic glycobiology are enabling the design, engineering, and production of this new generation of carbohydrate-containing vaccine formulations with the potential to prevent infectious diseases, malignancies, and complex immune disorders.
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Affiliation(s)
- Sophia W Hulbert
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Primit Desai
- 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 F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Cornell Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA.
| | - Asher J Williams
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Department of Chemical Engineering, Columbia University, New York, NY 10027, USA.
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12
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Paliya BS, Sharma VK, Tuohy MG, Singh HB, Koffas M, Benhida R, Tiwari BK, Kalaskar DM, Singh BN, Gupta VK. Bacterial glycobiotechnology: A biosynthetic route for the production of biopharmaceutical glycans. Biotechnol Adv 2023; 67:108180. [PMID: 37236328 DOI: 10.1016/j.biotechadv.2023.108180] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/16/2023] [Accepted: 05/21/2023] [Indexed: 05/28/2023]
Abstract
The recent advancement in the human glycome and progress in the development of an inclusive network of glycosylation pathways allow the incorporation of suitable machinery for protein modification in non-natural hosts and explore novel opportunities for constructing next-generation tailored glycans and glycoconjugates. Fortunately, the emerging field of bacterial metabolic engineering has enabled the production of tailored biopolymers by harnessing living microbial factories (prokaryotes) as whole-cell biocatalysts. Microbial catalysts offer sophisticated means to develop a variety of valuable polysaccharides in bulk quantities for practical clinical applications. Glycans production through this technique is highly efficient and cost-effective, as it does not involve expensive initial materials. Metabolic glycoengineering primarily focuses on utilizing small metabolite molecules to alter biosynthetic pathways, optimization of cellular processes for glycan and glycoconjugate production, characteristic to a specific organism to produce interest tailored glycans in microbes, using preferably cheap and simple substrate. However, metabolic engineering faces one of the unique challenges, such as the need for an enzyme to catalyze desired substrate conversion when natural native substrates are already present. So, in metabolic engineering, such challenges are evaluated, and different strategies have been developed to overcome them. The generation of glycans and glycoconjugates via metabolic intermediate pathways can still be supported by glycol modeling achieved through metabolic engineering. It is evident that modern glycans engineering requires adoption of improved strain engineering strategies for creating competent glycoprotein expression platforms in bacterial hosts, in the future. These strategies include logically designing and introducing orthogonal glycosylation pathways, identifying metabolic engineering targets at the genome level, and strategically improving pathway performance (for example, through genetic modification of pathway enzymes). Here, we highlight current strategies, applications, and recent progress in metabolic engineering for producing high-value tailored glycans and their applications in biotherapeutics and diagnostics.
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Affiliation(s)
- Balwant S Paliya
- Herbal Nanobiotechnology Lab, Pharmacology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India
| | - Vivek K Sharma
- Herbal Nanobiotechnology Lab, Pharmacology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India
| | - Maria G Tuohy
- Biochemistry, School of Biological and Chemical Sciences, College of Science & Engineering, University of Galway (Ollscoil na Gaillimhe), University Road, Galway City, Ireland
| | - Harikesh B Singh
- Department of Biotechnology, GLA University, Mathura 281406, Uttar Pradesh, India
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Rachid Benhida
- Institut de Chimie de Nice, UMR7272, Université Côte d'Azur, Nice, France; Mohamed VI Polytechnic University, Lot 660, Hay Moulay Rachid 43150, Benguerir, Morocco
| | | | - Deepak M Kalaskar
- UCL Division of Surgery and Interventional Science, Royal Free Hospital Campus, University College London, Rowland Hill Street, NW3 2PF, UK
| | - Brahma N Singh
- Herbal Nanobiotechnology Lab, Pharmacology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India.
| | - Vijai K Gupta
- Biorefining and Advanced Materials Research Centre, SRUC, Barony Campus, Parkgate, Dumfries DG1 3NE, United Kingdom.
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13
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Liu J, Hu Y, Gu W, Lan H, Zhang Z, Jiang L, Xu X. Research progress on the application of cell-free synthesis systems for enzymatic processes. Crit Rev Biotechnol 2023; 43:938-955. [PMID: 35994247 DOI: 10.1080/07388551.2022.2090314] [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: 10/13/2021] [Revised: 02/24/2022] [Accepted: 04/09/2022] [Indexed: 11/03/2022]
Abstract
Cell-free synthesis systems can complete the transcription and translation process in vitro to produce complex proteins that are difficult to be expressed in traditional cell-based systems. Such systems also can be used for the assembly of efficient localized multienzyme cascades to synthesize products that are toxic to cells. Cell-free synthesis systems provide a simpler and faster engineering solution than living cells, allowing unprecedented design freedom. This paper reviews the latest progress on the application of cell-free synthesis systems in the field of enzymatic catalysis, including cell-free protein synthesis and cell-free metabolic engineering. In cell-free protein synthesis: complex proteins, toxic proteins, membrane proteins, and artificial proteins containing non-natural amino acids can be easily synthesized by directly controlling the reaction conditions in the cell-free system. In cell-free metabolic engineering, the synthesis of desired products can be made more specific and efficient by designing metabolic pathways and screening biocatalysts based on purified enzymes or crude extracts. Through the combination of cell-free synthesis systems and emerging technologies, such as: synthetic biology, microfluidic control, cofactor regeneration, and artificial scaffolds, we will be able to build increasingly complex biomolecule systems. In the next few years, these technologies are expected to mature and reach industrialization, providing innovative platforms for a wide range of biotechnological applications.
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Affiliation(s)
- Jie Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yongqi Hu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wanyi Gu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Haiquan Lan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zhidong Zhang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Xian Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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14
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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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15
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Manzer ZA, Selivanovitch E, Ostwalt AR, Daniel S. Membrane protein synthesis: no cells required. Trends Biochem Sci 2023; 48:642-654. [PMID: 37087310 DOI: 10.1016/j.tibs.2023.03.006] [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: 11/07/2022] [Revised: 02/20/2023] [Accepted: 03/22/2023] [Indexed: 04/24/2023]
Abstract
Despite advances in membrane protein (MP) structural biology and a growing interest in their applications, these proteins remain challenging to study. Progress has been hindered by the complex nature of MPs and innovative methods will be required to circumvent technical hurdles. Cell-free protein synthesis (CFPS) is a burgeoning technique for synthesizing MPs directly into a membrane environment using reconstituted components of the cellular transcription and translation machinery in vitro. We provide an overview of CFPS and how this technique can be applied to the synthesis and study of MPs. We highlight numerous strategies including synthesis methods and folding environments, each with advantages and limitations, to provide a survey of how CFPS techniques can advance the study of MPs.
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Affiliation(s)
- Zachary A Manzer
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Ekaterina Selivanovitch
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Alexis R Ostwalt
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Susan Daniel
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
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16
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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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17
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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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18
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Yue K, Chen J, Li Y, Kai L. Advancing synthetic biology through cell-free protein synthesis. Comput Struct Biotechnol J 2023; 21:2899-2908. [PMID: 37216017 PMCID: PMC10196276 DOI: 10.1016/j.csbj.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
The rapid development of synthetic biology has enabled the production of compounds with revolutionary improvements in biotechnology. DNA manipulation tools have expedited the engineering of cellular systems for this purpose. Nonetheless, the inherent constraints of cellular systems persist, imposing an upper limit on mass and energy conversion efficiencies. Cell-free protein synthesis (CFPS) has demonstrated its potential to overcome these inherent constraints and has been instrumental in the further advancement of synthetic biology. Via the removal of the cell membranes and redundant parts of cells, CFPS has provided flexibility in directly dissecting and manipulating the Central Dogma with rapid feedback. This mini-review summarizes recent achievements of the CFPS technique and its application to a wide range of synthetic biology projects, such as minimal cell assembly, metabolic engineering, and recombinant protein production for therapeutics, as well as biosensor development for in vitro diagnostics. In addition, current challenges and future perspectives in developing a generalized cell-free synthetic biology are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Junyu Chen
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
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19
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Moeller T, Shah SB, Lai K, Lopez-Barbosa N, Desai P, Wang W, Zhong Z, Redmond D, Singh A, DeLisa MP. Profiling Germinal Center-like B Cell Responses to Conjugate Vaccines Using Synthetic Immune Organoids. ACS CENTRAL SCIENCE 2023; 9:787-804. [PMID: 37122450 PMCID: PMC10141597 DOI: 10.1021/acscentsci.2c01473] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Indexed: 05/03/2023]
Abstract
Glycoengineered bacteria have emerged as a cost-effective platform for rapid and controllable biosynthesis of designer conjugate vaccines. However, little is known about the engagement of such conjugates with naïve B cells to induce the formation of germinal centers (GC), a subanatomical microenvironment that converts naïve B cells into antibody-secreting plasma cells. Using a three-dimensional biomaterials-based B-cell follicular organoid system, we demonstrate that conjugates triggered robust expression of hallmark GC markers, B cell receptor clustering, intracellular signaling, and somatic hypermutation. These responses depended on the relative immunogenicity of the conjugate and correlated with the humoral response in vivo. The occurrence of these mechanisms was exploited for the discovery of high-affinity antibodies against components of the conjugate on a time scale that was significantly shorter than for typical animal immunization-based workflows. Collectively, these findings highlight the potential of synthetic organoids for rapidly predicting conjugate vaccine efficacy as well as expediting antigen-specific antibody discovery.
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Affiliation(s)
- Tyler
D. Moeller
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Shivem B. Shah
- Nancy
E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Kristine Lai
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Natalia Lopez-Barbosa
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Primit Desai
- Biochemistry,
Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
| | - Weiyao Wang
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Zhe Zhong
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - David Redmond
- Institute
for Computational Biomedicine, Weill Cornell Medicine, Cornell University, New York, New York 10021, United States
- Department
of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, New York 10021, United States
| | - Ankur Singh
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Matthew P. DeLisa
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
- Nancy
E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
- Biochemistry,
Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
- Cornell
Institute of Biotechnology, Cornell University, Ithaca, New York 14853, United States
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20
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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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21
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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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22
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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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23
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Gupta R, Arora K, Roy SS, Joseph A, Rastogi R, Arora NM, Kundu PK. Platforms, advances, and technical challenges in virus-like particles-based vaccines. Front Immunol 2023; 14:1123805. [PMID: 36845125 PMCID: PMC9947793 DOI: 10.3389/fimmu.2023.1123805] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Viral infectious diseases threaten human health and global stability. Several vaccine platforms, such as DNA, mRNA, recombinant viral vectors, and virus-like particle-based vaccines have been developed to counter these viral infectious diseases. Virus-like particles (VLP) are considered real, present, licensed and successful vaccines against prevalent and emergent diseases due to their non-infectious nature, structural similarity with viruses, and high immunogenicity. However, only a few VLP-based vaccines have been commercialized, and the others are either in the clinical or preclinical phases. Notably, despite success in the preclinical phase, many vaccines are still struggling with small-scale fundamental research owing to technical difficulties. Successful production of VLP-based vaccines on a commercial scale requires a suitable platform and culture mode for large-scale production, optimization of transduction-related parameters, upstream and downstream processing, and monitoring of product quality at each step. In this review article, we focus on the advantages and disadvantages of various VLP-producing platforms, recent advances and technical challenges in VLP production, and the current status of VLP-based vaccine candidates at commercial, preclinical, and clinical levels.
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Affiliation(s)
| | | | | | | | | | | | - Prabuddha K. Kundu
- Department of Research and Development, Premas Biotech Pvt Ltd., Sector IV, Industrial Model Township (IMT), Manesar, Gurgaon, India
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24
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Mariano RMDS, Gonçalves AAM, de Oliveira DS, Ribeiro HS, Pereira DFS, Santos IS, Lair DF, da Silva AV, Galdino AS, Chávez-Fumagalli MA, da Silveira-Lemos D, Dutra WO, Giunchetti RC. A Review of Major Patents on Potential Malaria Vaccine Targets. Pathogens 2023; 12:pathogens12020247. [PMID: 36839519 PMCID: PMC9959516 DOI: 10.3390/pathogens12020247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Malaria is a parasitic infection that is a great public health concern and is responsible for high mortality rates worldwide. Different strategies have been employed to improve disease control, demonstrating the ineffectiveness of controlling vectors, and parasite resistance to antimalarial drugs requires the development of an effective preventive vaccine. There are countless challenges to the development of such a vaccine directly related to the parasite's complex life cycle. After more than four decades of basic research and clinical trials, the World Health Organization (WHO) has recommended the pre-erythrocytic Plasmodium falciparum (RTS, S) malaria vaccine for widespread use among children living in malaria-endemic areas. However, there is a consensus that major improvements are needed to develop a vaccine with a greater epidemiological impact in endemic areas. This review discusses novel strategies for malaria vaccine design taking the target stages within the parasite cycle into account. The design of the multi-component vaccine shows considerable potential, especially as it involves transmission-blocking vaccines (TBVs) that eliminate the parasite's replication towards sporozoite stage parasites during a blood meal of female anopheline mosquitoes. Significant improvements have been made but additional efforts to achieve an efficient vaccine are required to improve control measures. Different strategies have been employed, thus demonstrating the ineffectiveness in controlling vectors, and parasite resistance to antimalarial drugs requires the development of a preventive vaccine. Despite having a vaccine in an advanced stage of development, such as the RTS, S malaria vaccine, the search for an effective vaccine against malaria is far from over. This review discusses novel strategies for malaria vaccine design taking into account the target stages within the parasite's life cycle.
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Affiliation(s)
- Reysla Maria da Silveira Mariano
- Laboratory of Biology of Cell Interactions, Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte CEP 31270-901, MG, Brazil
| | - Ana Alice Maia Gonçalves
- Laboratory of Biology of Cell Interactions, Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte CEP 31270-901, MG, Brazil
| | - Diana Souza de Oliveira
- Laboratory of Biology of Cell Interactions, Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte CEP 31270-901, MG, Brazil
| | - Helen Silva Ribeiro
- Laboratory of Biology of Cell Interactions, Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte CEP 31270-901, MG, Brazil
| | - Diogo Fonseca Soares Pereira
- Laboratory of Biology of Cell Interactions, Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte CEP 31270-901, MG, Brazil
| | - Ingrid Soares Santos
- Laboratory of Biology of Cell Interactions, Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte CEP 31270-901, MG, Brazil
| | - Daniel Ferreira Lair
- Laboratory of Biology of Cell Interactions, Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte CEP 31270-901, MG, Brazil
| | - Augusto Ventura da Silva
- Laboratory of Biology of Cell Interactions, Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte CEP 31270-901, MG, Brazil
| | - Alexsandro Sobreira Galdino
- Laboratory of Biotechnology of Microorganisms, Federal University of São João Del-Rei, Divinópolis CEP 35501-296, MG, Brazil
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Urb. San José S/N, Arequipa 04000, Peru
| | - Denise da Silveira-Lemos
- Campus Jaraguá, University José of Rosário Vellano, UNIFENAS, Belo Horizonte CEP 31270-901, MG, Brazil
| | - Walderez Ornelas Dutra
- Laboratory of Biology of Cell Interactions, Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte CEP 31270-901, MG, Brazil
| | - Rodolfo Cordeiro Giunchetti
- Laboratory of Biology of Cell Interactions, Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte CEP 31270-901, MG, Brazil
- Correspondence: or ; Tel.: +55-31-3409-3003
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25
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Dmitrieva DA, Kotova TV, Safronova NA, Sadova AA, Dashevskii DE, Mishin AV. Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors. BIOCHEMISTRY (MOSCOW) 2023; 88:S192-S226. [PMID: 37069121 DOI: 10.1134/s0006297923140110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.
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Affiliation(s)
- Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Kotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nadezda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexandra A Sadova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
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26
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Yue K, Li Y, Cao M, Shen L, Gu J, Kai L. Bottom-Up Synthetic Biology Using Cell-Free Protein Synthesis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:1-20. [PMID: 37526707 DOI: 10.1007/10_2023_232] [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: 08/02/2023]
Abstract
Technical advances in biotechnology have greatly accelerated the development of bottom-up synthetic biology. Unlike top-down approaches, bottom-up synthetic biology focuses on the construction of a minimal cell from scratch and the application of these principles to solve challenges. Cell-free protein synthesis (CFPS) systems provide minimal machinery for transcription and translation, from either a fractionated cell lysate or individual purified protein elements, thus speeding up the development of synthetic cell projects. In this review, we trace the history of the cell-free technique back to the first in vitro fermentation experiment using yeast cell lysate. Furthermore, we summarized progresses of individual cell mimicry modules, such as compartmentalization, gene expression regulation, energy regeneration and metabolism, growth and division, communication, and motility. Finally, current challenges and future perspectives on the field are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Mengjiao Cao
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lulu Shen
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingsheng Gu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China.
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27
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Williams AJ, Warfel KF, Desai P, Li J, Lee JJ, Wong DA, Nguyen PM, Qin Y, Sobol SE, Jewett MC, Chang YF, DeLisa MP. A low-cost recombinant glycoconjugate vaccine confers immunogenicity and protection against enterotoxigenic Escherichia coli infections in mice. Front Mol Biosci 2023; 10:1085887. [PMID: 36936989 PMCID: PMC10018396 DOI: 10.3389/fmolb.2023.1085887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) is the primary etiologic agent of traveler's diarrhea and a major cause of diarrheal disease and death worldwide, especially in infants and young children. Despite significant efforts over the past several decades, an affordable vaccine that appreciably decreases mortality and morbidity associated with ETEC infection among children under the age of 5 years remains an unmet aspirational goal. Here, we describe robust, cost-effective biosynthetic routes that leverage glycoengineered strains of non-pathogenic E. coli or their cell-free extracts for producing conjugate vaccine candidates against two of the most prevalent O serogroups of ETEC, O148 and O78. Specifically, we demonstrate site-specific installation of O-antigen polysaccharides (O-PS) corresponding to these serogroups onto licensed carrier proteins using the oligosaccharyltransferase PglB from Campylobacter jejuni. The resulting conjugates stimulate strong O-PS-specific humoral responses in mice and elicit IgG antibodies that possess bactericidal activity against the cognate pathogens. We also show that one of the prototype conjugates decorated with serogroup O148 O-PS reduces ETEC colonization in mice, providing evidence of vaccine-induced mucosal protection. We anticipate that our bacterial cell-based and cell-free platforms will enable creation of multivalent formulations with the potential for broad ETEC serogroup protection and increased access through low-cost biomanufacturing.
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Affiliation(s)
- Asher J. Williams
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Katherine F. Warfel
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute, Evanston, IL, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, United States
- Center for Synthetic Biology, Northwestern University, Technological Institute, Evanston, IL, United States
| | - Primit Desai
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY, United States
| | - Jie Li
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Jen-Jie Lee
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Derek A. Wong
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute, Evanston, IL, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, United States
- Center for Synthetic Biology, Northwestern University, Technological Institute, Evanston, IL, United States
| | - Phuong M. Nguyen
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Yufan Qin
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Sarah E. Sobol
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute, Evanston, IL, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, United States
- Center for Synthetic Biology, Northwestern University, Technological Institute, Evanston, IL, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute, Evanston, IL, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, United States
- Center for Synthetic Biology, Northwestern University, Technological Institute, Evanston, IL, United States
- Department of Bioengineering, Stanford University, Stanford, CA, United States
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Matthew P. DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY, United States
- Cornell Institute of Biotechnology, Cornell University, Ithaca, NY, United States
- *Correspondence: Matthew P. DeLisa,
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28
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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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29
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Chung SS, Bidstrup EJ, Hershewe JM, Warfel KF, Jewett MC, DeLisa MP. Ribosome Stalling of N-Linked Glycoproteins in Cell-Free Extracts. ACS Synth Biol 2022; 11:3892-3899. [PMID: 36399685 PMCID: PMC9764415 DOI: 10.1021/acssynbio.2c00311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Indexed: 11/21/2022]
Abstract
Ribosome display is a powerful in vitro method for selection and directed evolution of proteins expressed from combinatorial libraries. However, the ability to display proteins with complex post-translational modifications such as glycosylation is limited. To address this gap, we developed a set of complementary methods for producing stalled ribosome complexes that displayed asparagine-linked (N-linked) glycoproteins in conformations amenable to downstream functional and glycostructural interrogation. The ability to generate glycosylated ribosome-nascent chain (glycoRNC) complexes was enabled by integrating SecM-mediated translation arrest with methods for cell-free N-glycoprotein synthesis. This integration enabled a first-in-kind method for ribosome stalling of target proteins modified efficiently and site-specifically with different N-glycan structures. Moreover, the observation that encoding mRNAs remained stably attached to ribosomes provides evidence of a genotype-glycophenotype link between an arrested glycoprotein and its RNA message. We anticipate that our method will enable selection and evolution of N-glycoproteins with advantageous biological and biophysical properties.
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Affiliation(s)
- Sean S. Chung
- Biochemistry,
Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
| | - Erik J. Bidstrup
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Jasmine M. Hershewe
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road Technological Institute E136, Evanston, Illinois 60208-3120, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road Technological
Institute E136, Evanston, Illinois 60208-3120, United States
- Chemistry
of Life Processes Institute, Northwestern
University, 2170 Campus
Drive, Evanston, Illinois 60208-3120, United States
| | - Katherine F. Warfel
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road Technological Institute E136, Evanston, Illinois 60208-3120, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road Technological
Institute E136, Evanston, Illinois 60208-3120, United States
- Chemistry
of Life Processes Institute, Northwestern
University, 2170 Campus
Drive, Evanston, Illinois 60208-3120, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road Technological Institute E136, Evanston, Illinois 60208-3120, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road Technological
Institute E136, Evanston, Illinois 60208-3120, United States
- Chemistry
of Life Processes Institute, Northwestern
University, 2170 Campus
Drive, Evanston, Illinois 60208-3120, United States
| | - Matthew P. DeLisa
- Biochemistry,
Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
- Robert
F. 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
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30
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Ullrich J, Göhmann PJ, Zemella A, Kubick S. Oligomerization of the heteromeric γ-aminobutyric acid receptor GABA B in a eukaryotic cell-free system. Sci Rep 2022; 12:20742. [PMID: 36456667 PMCID: PMC9715706 DOI: 10.1038/s41598-022-24885-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
Understanding the assembly mechanism and function of membrane proteins is a fundamental problem in biochemical research. Among the membrane proteins, G protein-coupled receptors (GPCRs) represent the largest class in the human body and have long been considered to function as monomers. Nowadays, the oligomeric assembly of GPCRs is widely accepted, although the functional importance and therapeutic intervention remain largely unexplored. This is partly due to difficulties in the heterologous production of membrane proteins. Cell-free protein synthesis (CFPS) with its endogenous endoplasmic reticulum-derived structures has proven as a technique to address this issue. In this study, we investigate for the first time the conceptual CFPS of a heteromeric GPCR, the γ-aminobutyric acid receptor type B (GABAB), from its protomers BR1 and BR2 using a eukaryotic cell-free lysate. Using a fluorescence-based proximity ligation assay, we provide evidence for colocalization and thus suggesting heterodimerization. We prove the heterodimeric assembly by a bioluminescence resonance energy transfer saturation assay providing the manufacturability of a heterodimeric GPCR by CFPS. Additionally, we show the binding of a fluorescent orthosteric antagonist, demonstrating the feasibility of combining the CFPS of GPCRs with pharmacological applications. These results provide a simple and powerful experimental platform for the synthesis of heteromeric GPCRs and open new perspectives for the modelling of protein-protein interactions. Accordingly, the presented technology enables the targeting of protein assemblies as a new interface for pharmacological intervention in disease-relevant dimers.
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Affiliation(s)
- Jessica Ullrich
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
- Institute of Biotechnology, Technische Universität Berlin, Straße Des 17. Juni 135, 10623, Berlin, Germany
| | - Philip Jonas Göhmann
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
- Institute of Biotechnology, Technische Universität Berlin, Straße Des 17. Juni 135, 10623, Berlin, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.
- Institute of Chemistry and Biochemistry-Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany.
- Faculty of Health Science, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany.
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Yin X, Li X, Mu L, Bai H, Yang Y, Chen N, Wu L, Fu S, Li J, Ying W, Ye J. Affinity-Driven Site-Specific High Mannose Modification Determines the Structural Polymerization and Function of Tetrameric IgM in a Primitive Vertebrate. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:593-605. [PMID: 35868636 DOI: 10.4049/jimmunol.2100921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/21/2022] [Indexed: 10/17/2023]
Abstract
Teleost tetramer IgM is the predominant Ig in the immune system and plays essential roles in host defense against microbial infection. Due to variable disulfide polymerization of the monomeric subunits, tetrameric IgM possesses considerable structural diversity. Previous work indicated that the teleost IgM H chain was fully occupied with complex-type N-glycans. However, after challenge with trinitrophenyl (TNP) Ag, the complex N-glycans in the Asn-509 site of Oreochromis niloticus IgM H chain transformed into high mannose. This study, therefore, was conducted to examine the functional roles of the affinity-related high-mannose modification in tilapia IgM. The TNP-specific IgM Ab affinity maturation was revealed in tilapia over the response. A positive correlation between TNP-specific IgM affinity and its disulfide polymerization level of isomeric structure was demonstrated. Mass spectrometric analysis indicated that the relationship between IgM affinity and disulfide polymerization was associated with the Asn-509 site-specific high-mannose modification. Furthermore, the increase of high mannose content promoted the combination of IgM and mannose receptor (MR) on the surface of phagocytes. Moreover, the increased interaction of IgM and MR amplified the phagocytic ability of phagocytes to Streptococcus agalactiae. To our knowledge, this study demonstrates that site-specific high-mannose modification associates with IgM Ab affinity and its structural disulfide polymerization and amplifies the phagocytosis of phagocytes by the combination of IgM and MR. The present study provides evidence for understanding the association of IgM structure and function during the evolution of the immune system.
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Affiliation(s)
- Xiaoxue Yin
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
| | - Xiaoyu Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Life Omics, Beijing, People's Republic of China
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, People's Republic of China
| | - Liangliang Mu
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
| | - Hao Bai
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
| | - Yanjian Yang
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
| | - Nuo Chen
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
| | - Liting Wu
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
| | - Shengli Fu
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
| | - Jun Li
- School of Science and Medicine, Lake Superior State University, Sault Ste. Marie, MI; and
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Life Omics, Beijing, People's Republic of China
| | - Jianmin Ye
- School of Life Sciences, South China Normal University, Institute of Modern Aquaculture Science and Engineering, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, People's Republic of China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou, People's Republic of China
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32
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Cell-free production of personalized therapeutic phages targeting multidrug-resistant bacteria. Cell Chem Biol 2022; 29:1434-1445.e7. [PMID: 35820417 DOI: 10.1016/j.chembiol.2022.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 03/11/2022] [Accepted: 06/16/2022] [Indexed: 12/26/2022]
Abstract
Bacteriophages are potent therapeutics against biohazardous bacteria, which rapidly develop multidrug resistance. However, routine administration of phage therapy is hampered by a lack of rapid production, safe bioengineering, and detailed characterization of phages. Thus, we demonstrate a comprehensive cell-free platform for personalized production, transient engineering, and proteomic characterization of a broad spectrum of phages. Using mass spectrometry, we validated hypothetical and non-structural proteins and could also monitor the protein expression during phage assembly. Notably, a few microliters of a one-pot reaction produced effective doses of phages against enteroaggregative Escherichia coli (EAEC), Yersinia pestis, and Klebsiella pneumoniae. By co-expressing suitable host factors, we could extend the range of cell-free production to phages targeting gram-positive bacteria. We further introduce a non-genomic phage engineering method, which adds functionalities for only one replication cycle. In summary, we expect this cell-free methodology to foster reverse and forward phage engineering and customized production of clinical-grade bacteriophages.
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33
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Li J, Tang M, Qi H. Codon-Reduced Protein Synthesis With Manipulating tRNA Components in Cell-Free System. Front Bioeng Biotechnol 2022; 10:891808. [PMID: 35646841 PMCID: PMC9136035 DOI: 10.3389/fbioe.2022.891808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Manipulating transfer RNAs (tRNAs) for emancipating sense codons to simplify genetic codons in a cell-free protein synthesis (CFPS) system can offer more flexibility and controllability. Here, we provide an overview of the tRNA complement protein synthesis system construction in the tRNA-depleted Protein synthesis Using purified Recombinant Elements (PURE) system or S30 extract. These designed polypeptide coding sequences reduce the genetic codon and contain only a single tRNA corresponding to a single amino acid in this presented system. Strategies for removing tRNAs from cell lysates and synthesizing tRNAs in vivo/vitro are summarized and discussed in detail. Furthermore, we point out the trend toward a minimized genetic codon for reducing codon redundancy by manipulating tRNAs in the different proteins. It is hoped that the tRNA complement protein synthesis system can facilitate the construction of minimal cells and expand the biomedical application scope of synthetic biology.
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Affiliation(s)
- Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Mengtong Tang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- *Correspondence: Hao Qi,
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34
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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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35
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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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36
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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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37
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Sato W, Zajkowski T, Moser F, Adamala KP. Synthetic cells in biomedical applications. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1761. [PMID: 34725945 PMCID: PMC8918002 DOI: 10.1002/wnan.1761] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 08/23/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Synthetic cells are engineered vesicles that can mimic one or more salient features of life. These features include directed localization, sense-and-respond behavior, gene expression, metabolism, and high stability. In nanomedicine, many of these features are desirable capabilities of drug delivery vehicles but are difficult to engineer. In this focus article, we discuss where synthetic cells offer unique advantages over nanoparticle and living cell therapies. We review progress in the engineering of the above life-like behaviors and how they are deployed in nanomedicine. Finally, we assess key challenges synthetic cells face before being deployed as drugs and suggest ways to overcome these challenges. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Biology-Inspired Nanomaterials > Lipid-Based Structures.
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Affiliation(s)
- Wakana Sato
- 1 Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN US
| | - Tomasz Zajkowski
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
- USRA at NASA Ames Research Center, Mountain View, CA 94035
- Blue Marble Space Institute of Science, 600 1st Avenue, Seattle WA 98104
| | - Felix Moser
- Synlife, Inc., One Kendall Square Suite B4401, Cambridge, MA 20139
| | - Katarzyna P. Adamala
- 1 Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN US
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38
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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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39
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Terra VS, Mauri M, Sannasiddappa TH, Smith AA, Stevens MP, Grant AJ, Wren BW, Cuccui J. PglB function and glycosylation efficiency is temperature dependent when the pgl locus is integrated in the Escherichia coli chromosome. Microb Cell Fact 2022; 21:6. [PMID: 34986868 PMCID: PMC8728485 DOI: 10.1186/s12934-021-01728-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
Background Campylobacter is an animal and zoonotic pathogen of global importance, and a pressing need exists for effective vaccines, including those that make use of conserved polysaccharide antigens. To this end, we adapted Protein Glycan Coupling Technology (PGCT) to develop a versatile Escherichia coli strain capable of generating multiple glycoconjugate vaccine candidates against Campylobacter jejuni. Results We generated a glycoengineering E. coli strain containing the conserved C. jejuni heptasaccharide coding region integrated in its chromosome as a model glycan. This methodology confers three advantages: (i) reduction of plasmids and antibiotic markers used for PGCT, (ii) swift generation of many glycan-protein combinations and consequent rapid identification of the most antigenic proteins or peptides, and (iii) increased genetic stability of the polysaccharide coding-region. In this study, by using the model glycan expressing strain, we were able to test proteins from C. jejuni, Pseudomonas aeruginosa (both Gram-negative), and Clostridium perfringens (Gram-positive) as acceptors. Using this pgl integrant E. coli strain, four glycoconjugates were readily generated. Two glycoconjugates, where both protein and glycan are from C. jejuni (double-hit vaccines), and two glycoconjugates, where the glycan antigen is conjugated to a detoxified toxin from a different pathogen (single-hit vaccines). Because the downstream application of Live Attenuated Vaccine Strains (LAVS) against C. jejuni is to be used in poultry, which have a higher body temperature of 42 °C, we investigated the effect of temperature on protein expression and glycosylation in the E. coli pgl integrant strain. Conclusions We determined that glycosylation is temperature dependent and that for the combination of heptasaccharide and carriers used in this study, the level of PglB available for glycosylation is a step limiting factor in the glycosylation reaction. We also demonstrated that temperature affects the ability of PglB to glycosylate its substrates in an in vitro glycosylation assay independent of its transcriptional level. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01728-7.
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Affiliation(s)
- Vanessa S Terra
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E7HT, UK
| | - Marta Mauri
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E7HT, UK
| | - Thippeswamy H Sannasiddappa
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, Cambridgeshire, UK
| | - Alexander A Smith
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, Cambridgeshire, UK
| | - Mark P Stevens
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Andrew J Grant
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, Cambridgeshire, UK
| | - Brendan W Wren
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E7HT, UK.
| | - Jon Cuccui
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E7HT, UK.
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40
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Buntru M, Vogel S, Finnern R, Schillberg S. Plant-Based Cell-Free Transcription and Translation of Recombinant Proteins. Methods Mol Biol 2022; 2480:113-124. [PMID: 35616861 DOI: 10.1007/978-1-0716-2241-4_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant cell-free lysates contain all the cellular components of the protein biosynthesis machinery, providing an alternative to intact plant cells, tissues, and whole plants for the production of recombinant proteins. Cell-free lysates achieve rapid protein production (within hours or days) and allow the synthesis of proteins that are cytotoxic or unstable in living cells. The open nature of cell-free lysates and their homogeneous and reproducible performance is ideal for protein production, especially for screening applications, allowing the direct addition of nucleic acid templates encoding proteins of interest, as well as other components such as enzyme substrates, chaperones, artificial amino acids, or labeling molecules. Here we describe procedures for the production of recombinant proteins in the ALiCE (Almost Living Cell-free Expression) system, a lysate derived from tobacco cell suspension cultures that can be used to manufacture protein products for molecular and biochemical analysis as well as applications in the pharmaceutical industry.
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Affiliation(s)
- Matthias Buntru
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Simon Vogel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | | | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany.
- Department of Phytopathology, Justus-Liebig-University Giessen, Giessen, Germany.
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41
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42
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Pratama F, Linton D, Dixon N. Genetic and process engineering strategies for enhanced recombinant N-glycoprotein production in bacteria. Microb Cell Fact 2021; 20:198. [PMID: 34649588 PMCID: PMC8518210 DOI: 10.1186/s12934-021-01689-x] [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] [Received: 07/19/2021] [Accepted: 09/25/2021] [Indexed: 11/28/2022] Open
Abstract
Background The production of N-linked glycoproteins in genetically amenable bacterial hosts offers great potential for reduced cost, faster/simpler bioprocesses, greater customisation, and utility for distributed manufacturing of glycoconjugate vaccines and glycoprotein therapeutics. Efforts to optimize production hosts have included heterologous expression of glycosylation enzymes, metabolic engineering, use of alternative secretion pathways, and attenuation of gene expression. However, a major bottleneck to enhance glycosylation efficiency, which limits the utility of the other improvements, is the impact of target protein sequon accessibility during glycosylation. Results Here, we explore a series of genetic and process engineering strategies to increase recombinant N-linked glycosylation, mediated by the Campylobacter-derived PglB oligosaccharyltransferase in Escherichia coli. Strategies include increasing membrane residency time of the target protein by modifying the cleavage site of its secretion signal, and modulating protein folding in the periplasm by use of oxygen limitation or strains with compromised oxidoreductase or disulphide-bond isomerase activity. These approaches achieve up to twofold improvement in glycosylation efficiency. Furthermore, we also demonstrate that supplementation with the chemical oxidant cystine enhances the titre of glycoprotein in an oxidoreductase knockout strain by improving total protein production and cell fitness, while at the same time maintaining higher levels of glycosylation efficiency. Conclusions In this study, we demonstrate that improved protein glycosylation in the heterologous host could be achieved by mimicking the coordination between protein translocation, folding and glycosylation observed in native host such as Campylobacter jejuni and mammalian cells. Furthermore, it provides insight into strain engineering and bioprocess strategies, to improve glycoprotein yield and titre, and to avoid physiological burden of unfolded protein stress upon cell growth. The process and genetic strategies identified herein will inform further optimisation and scale-up of heterologous recombinant N-glycoprotein production. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01689-x.
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Affiliation(s)
- Fenryco Pratama
- Manchester Institute of Biotechnology (MIB), The University of Manchester, Manchester, M1 7DN, UK.,Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.,Microbial Biotechnology Research Group, School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Dennis Linton
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M1 7DN, UK
| | - Neil Dixon
- Manchester Institute of Biotechnology (MIB), The University of Manchester, Manchester, M1 7DN, UK. .,Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
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43
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Ferdous S, Dopp JL, Reuel NF. Optimization of E. Coli Tip-Sonication for High-Yield Cell-Free Extract using Finite Element Modeling. AIChE J 2021; 67:e17389. [PMID: 35663841 PMCID: PMC9161774 DOI: 10.1002/aic.17389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/17/2021] [Indexed: 12/23/2022]
Abstract
Optimal tip sonication settings, namely tip position, input power, and pulse durations, are necessary for temperature sensitive procedures like preparation of viable cell extract. In this paper, the optimum tip immersion depth (20-30% height below the liquid surface) is estimated which ensures maximum mixing thereby enhancing thermal dissipation of local cavitation hotspots. A finite element (FE) heat transfer model is presented, validated experimentally with (R2 > 97%) and used to observe the effect of temperature rise on cell extract performance of E. coli BL21 DE3 star strain and estimate the temperature threshold. Relative yields in the top 10% are observed for solution temperatures maintained below 32°C; this reduces below 50% relative yield at temperatures above 47°C. A generalized workflow for direct simulation using the COMSOL code as well as master plots for estimation of sonication parameters (power input and pulse settings) is also presented.
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Affiliation(s)
- Sakib Ferdous
- Department of Chemical and Biological Engineering, Iowa State University
| | - Jared L. Dopp
- Department of Chemical and Biological Engineering, Iowa State University
| | - Nigel F. Reuel
- Department of Chemical and Biological Engineering, Iowa State University
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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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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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Lehr FX, Kuzembayeva A, Bailey ME, Kleindienst W, Kabisch J, Koeppl H. Functionalizing Cell-Free Systems with CRISPR-Associated Proteins: Application to RNA-Based Circuit Engineering. ACS Synth Biol 2021; 10:2138-2150. [PMID: 34383464 DOI: 10.1021/acssynbio.0c00386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell-free systems have become a compelling choice for the prototyping of synthetic circuits. Many robust protocols for preparing cell-free systems are now available along with toolboxes designed for a variety of applications. Thus far, the production of cell-free extracts has often been decoupled from the production of functionalized proteins. Here, we leveraged a recent protocol for producing an E. coli-based cell-free expression system with two CRISPR-associated proteins, Csy4 and dCas9, expressed prior to harvest. We found that pre-expression did not affect the resulting extract performance, and the final concentrations of the endonucleases matched the level required for synthetic circuit prototyping. We demonstrated the benefits and versatility of dCas9 and Csy4 through the use of RNA circuitry based on a combination of single guide RNAs, small transcriptional activator RNAs, and toehold switches. For instance, we show that Csy4 processing increased 4-fold the dynamic range of a previously published AND-logic gate. Additionally, blending the CRISPR-enhanced extracts enabled us to reduce leakage in a multiple inputs gate, and to extend the type of Boolean functions available for RNA-based circuits, such as NAND-logic. Finally, we reported the use of simultaneous transcriptional and translational reporters in our RNA-based circuits. In particular, the AND-gate mRNA and protein levels were able to be independently monitored in response to transcriptional and translational activators. We hope this work will facilitate the adoption of advanced processing tools for RNA-based circuit prototyping in a cell-free environment.
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Affiliation(s)
- François-Xavier Lehr
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, Darmstadt 64283, Germany
| | - Alina Kuzembayeva
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, Darmstadt 64283, Germany
| | - Megan E Bailey
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, Darmstadt 64283, Germany
| | - Werner Kleindienst
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
| | - Johannes Kabisch
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
| | - Heinz Koeppl
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, Darmstadt 64283, Germany
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Makrydaki E, Marshall O, Heide C, Buldum G, Kontoravdi C, Polizzi KM. Cell-free protein synthesis using Chinese hamster ovary cells. Methods Enzymol 2021; 659:411-435. [PMID: 34752298 DOI: 10.1016/bs.mie.2021.08.004] [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: 01/04/2023]
Abstract
Cell-free protein synthesis (CFPS) platforms can be used for rapid and flexible expression of proteins. The use of CFPS platforms from mammalian, specifically Chinese hamster ovary (CHO) cells, offers the possibility of a rapid prototyping platform for recombinant protein production with the capabilities of post-translational modifications. In this chapter, we discuss a refined CFPS system based on CHO cells, including: extract preparation, reaction mix composition, and accessory protein supplementation to enhance expression. Specifically, when the CHO cell extract is combined with a truncated version of GADD34 and K3L, stress-induced eIF2 phosphorylation is reduced and inhibition of translation initiation is relieved, increasing yields. A brief summary of the protocol for running the CFPS reactions is also described. Overall, the method is reliable and leads to a highly reproducible expression system. Finally, the advantages and disadvantages of the platform, in addition to expected outcomes, are also discussed.
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Affiliation(s)
- Elli Makrydaki
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Oscar Marshall
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Chiara Heide
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Gizem Buldum
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Cleo Kontoravdi
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom.
| | - Karen M Polizzi
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom.
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A Metabolomic Analysis of the Sex-Dependent Hispanic Paradox. Metabolites 2021; 11:metabo11080552. [PMID: 34436492 PMCID: PMC8401672 DOI: 10.3390/metabo11080552] [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: 05/17/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/14/2022] Open
Abstract
In Mexican Americans, metabolic conditions, such as obesity and type 2 diabetes (T2DM), are not necessarily associated with an increase in mortality; this is the so-called Hispanic paradox. In this cross-sectional analysis, we used a metabolomic analysis to look at the mechanisms behind the Hispanic paradox. To do this, we examined dietary intake and body mass index (BMI; kg/m2) in men and women and their effects on serum metabolomic fingerprints in 70 Mexican Americans (26 men, 44 women). Although having different BMI values, the participants had many similar anthropometric and biochemical parameters, such as systolic and diastolic blood pressure, total cholesterol, and LDL cholesterol, which supported the paradox in these subjects. Plasma metabolomic phenotypes were measured using liquid chromatography tandem mass spectrometry (LC-MS/MS). A two-way ANOVA assessing sex, BMI, and the metabolome revealed 23 significant metabolites, such as 2-pyrrolidinone (p = 0.007), TMAO (p = 0.014), 2-aminoadipic acid (p = 0.019), and kynurenine (p = 0.032). Pathway and enrichment analyses discovered several significant metabolic pathways between men and women, including lysine degradation, tyrosine metabolism, and branch-chained amino acid (BCAA) degradation and biosynthesis. A log-transformed OPLS-DA model was employed and demonstrated a difference due to BMI in the metabolomes of both sexes. When stratified for caloric intake (<2200 kcal/d vs. >2200 kcal/d), a separate OPLS-DA model showed clear separation in men, while females remained relatively unchanged. After accounting for caloric intake and BMI status, the female metabolome showed substantial resistance to alteration. Therefore, we provide a better understanding of the Mexican-American metabolome, which may help demonstrate how this population—particularly women—possesses a longer life expectancy despite several comorbidities, and reveal the underlying mechanisms of the Hispanic paradox.
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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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Nomura K, Maki Y, Okamoto R, Satoh A, Kajihara Y. Glycoprotein Semisynthesis by Chemical Insertion of Glycosyl Asparagine Using a Bifunctional Thioacid-Mediated Strategy. J Am Chem Soc 2021; 143:10157-10167. [PMID: 34189908 DOI: 10.1021/jacs.1c02601] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Glycosylation is a major modification of secreted and cell surface proteins, and the resultant glycans show considerable heterogeneity in their structures. To understand the biological processes arising from each glycoform, the preparation of homogeneous glycoproteins is essential for extensive biological experiments. To establish a more robust and rapid synthetic route for the synthesis of homogeneous glycoproteins, we studied several key reactions based on amino thioacids. We found that diacyl disulfide coupling (DDC) formed with glycosyl asparagine thioacid and peptide thioacid yielded glycopeptides. This efficient coupling reaction enabled us to develop a new glycoprotein synthesis method, such as the bifunctional thioacid-mediated strategy, which can couple two peptides with the N- and C-termini of glycosyl asparagine thioacid. Previous glycoprotein synthesis methods required valuable glycosyl asparagine in the early stage and subsequent multiple glycoprotein synthesis routes, whereas the developed concept can generate glycoproteins within a few steps from peptide and glycosyl asparagine thioacid. Herein, we report the characterization of the DDC of amino thioacids and the efficient ability of glycosyl asparagine thioacid to be used for robust glycoprotein semisynthesis.
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Affiliation(s)
| | | | | | - Ayano Satoh
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1, Tsushimanaka, Okayama 700-0082, Japan
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