1
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Dunkelmann DL, Chin JW. Engineering Pyrrolysine Systems for Genetic Code Expansion and Reprogramming. Chem Rev 2024; 124:11008-11062. [PMID: 39235427 PMCID: PMC11467909 DOI: 10.1021/acs.chemrev.4c00243] [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: 04/01/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
Over the past 16 years, genetic code expansion and reprogramming in living organisms has been transformed by advances that leverage the unique properties of pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs. Here we summarize the discovery of the pyrrolysine system and describe the unique properties of PylRS/tRNAPyl pairs that provide a foundation for their transformational role in genetic code expansion and reprogramming. We describe the development of genetic code expansion, from E. coli to all domains of life, using PylRS/tRNAPyl pairs, and the development of systems that biosynthesize and incorporate ncAAs using pyl systems. We review applications that have been uniquely enabled by the development of PylRS/tRNAPyl pairs for incorporating new noncanonical amino acids (ncAAs), and strategies for engineering PylRS/tRNAPyl pairs to add noncanonical monomers, beyond α-L-amino acids, to the genetic code of living organisms. We review rapid progress in the discovery and scalable generation of mutually orthogonal PylRS/tRNAPyl pairs that can be directed to incorporate diverse ncAAs in response to diverse codons, and we review strategies for incorporating multiple distinct ncAAs into proteins using mutually orthogonal PylRS/tRNAPyl pairs. Finally, we review recent advances in the encoded cellular synthesis of noncanonical polymers and macrocycles and discuss future developments for PylRS/tRNAPyl pairs.
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Affiliation(s)
- Daniel L. Dunkelmann
- Medical
Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
- Max
Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jason W. Chin
- Medical
Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
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2
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Pigula ML, Schultz PG. Recent advances in the expanding genetic code. Curr Opin Chem Biol 2024; 83:102537. [PMID: 39366132 DOI: 10.1016/j.cbpa.2024.102537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/20/2024] [Accepted: 09/10/2024] [Indexed: 10/06/2024]
Abstract
For over a billion years, the central dogma of biology has been limited largely to 20 canonical amino acids with relatively simple functionalities. The ability to rationally add new building blocks to the genetic code has enabled the site-specific incorporation of hundreds of noncanonical amino acids (ncAAs) with novel properties into proteins in living organisms. Recent technological advances have enabled high level mammalian expression of proteins containing ncAAs, the use of unique codons to direct ncAA incorporation, extension of this methodology to a range of eukaryotic organisms, and the ability to encode building blocks beyond α-amino acids. These ncAAs have been used to study and control proteins in their native cellular context and to engineer enzymes and biotherapeutics with improved or novel properties. Herein we discuss recent developments in the field and potential future research directions.
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Affiliation(s)
- Michael L Pigula
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Peter G Schultz
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States.
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3
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Kim J, Jeong KJ, Kim GJ, Choi JI. Engineering of Recombinant Human Papillomavirus 16 L1 Protein for Incorporation with para-Azido- L-Phenylalanine. J Microbiol Biotechnol 2024; 34:1926-1932. [PMID: 39155395 PMCID: PMC11473617 DOI: 10.4014/jmb.2407.07033] [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: 07/19/2024] [Revised: 07/30/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024]
Abstract
Human papillomavirus (HPV) L1 capsid protein were produced in several host systems, but few studies have focused on enhancing the properties of the L1 protein. In this study, we aimed to produce recombinant Human papillomavirus (HPV) L1 capsid protein containing para-azido-L-phenylalanine (pAzF) in Escherichia coli. First, we expressed the maltose-binding protein (MBP)-fused HPV16 L1, and 5 residues in HPV16 L1 protein were selected by the in silico modeling for amber codon substitution. Among the variants of the five locations, we identified a candidate that exhibited significant differences in expression with and without pAzF via genetic code expansion (GCE). The expressed recombinant MBP-HPV16L1 protein was confirmed for incorporation of pAzF and the formation of VLPs was tested in vitro.
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Affiliation(s)
- Jinhyeon Kim
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences and Research Center of Ecomimetics, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jong-il Choi
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju 61186, Republic of Korea
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4
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Niu W, Guo J. Cellular Site-Specific Incorporation of Noncanonical Amino Acids in Synthetic Biology. Chem Rev 2024; 124:10577-10617. [PMID: 39207844 PMCID: PMC11470805 DOI: 10.1021/acs.chemrev.3c00938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Over the past two decades, genetic code expansion (GCE)-enabled methods for incorporating noncanonical amino acids (ncAAs) into proteins have significantly advanced the field of synthetic biology while also reaping substantial benefits from it. On one hand, they provide synthetic biologists with a powerful toolkit to enhance and diversify biological designs beyond natural constraints. Conversely, synthetic biology has not only propelled the development of ncAA incorporation through sophisticated tools and innovative strategies but also broadened its potential applications across various fields. This Review delves into the methodological advancements and primary applications of site-specific cellular incorporation of ncAAs in synthetic biology. The topics encompass expanding the genetic code through noncanonical codon addition, creating semiautonomous and autonomous organisms, designing regulatory elements, and manipulating and extending peptide natural product biosynthetic pathways. The Review concludes by examining the ongoing challenges and future prospects of GCE-enabled ncAA incorporation in synthetic biology and highlighting opportunities for further advancements in this rapidly evolving field.
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Affiliation(s)
- Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
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5
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Ding W, Yu W, Chen Y, Lao L, Fang Y, Fang C, Zhao H, Yang B, Lin S. Rare codon recoding for efficient noncanonical amino acid incorporation in mammalian cells. Science 2024; 384:1134-1142. [PMID: 38843324 DOI: 10.1126/science.adm8143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/03/2024] [Indexed: 06/16/2024]
Abstract
The ability to genetically encode noncanonical amino acids (ncAAs) has empowered proteins with improved or previously unknown properties. However, existing strategies in mammalian cells rely on the introduction of a blank codon to incorporate ncAAs, which is inefficient and limits their widespread applications. In this study, we developed a rare codon recoding strategy that takes advantage of the relative rarity of the TCG codon to achieve highly selective and efficient ncAA incorporation through systematic engineering and big data-model predictions. We highlight the broad utility of this strategy for the incorporation of dozens of ncAAs into various functional proteins at the wild-type protein expression levels, as well as the synthesis of proteins with up to six-site ncAAs or four distinct ncAAs in mammalian cells for downstream applications.
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Affiliation(s)
- Wenlong Ding
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Wei Yu
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Yulin Chen
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Lihui Lao
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Yu Fang
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Chengzhu Fang
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Hongxia Zhao
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Bo Yang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Shixian Lin
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
- Department of Medical Oncology, State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
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6
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Tang YD, Yu C, Cai XH. Novel technologies are turning a dream into reality: conditionally replicating viruses as vaccines. Trends Microbiol 2024; 32:292-301. [PMID: 37798168 DOI: 10.1016/j.tim.2023.09.002] [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: 07/18/2023] [Revised: 08/30/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023]
Abstract
Conditionally replicating viruses (CRVs) are a type of virus with one or more essential gene functions that are impaired resulting in the disruption of viral genome replication, protein synthesis, or virus particle assembly. CRVs can replicate only if the deficient essential genes are supplied. CRVs are widely used in biomedical research, particularly as vaccines. Traditionally, CRVs are generated by creating complementary cell lines that provide the impaired genes. With the development of biotechnology, novel techniques have been invented to generate CRVs, such as targeted protein degradation (TPD) technologies and premature termination codon (PTC) read-through technologies. The advantages and disadvantages of these novel technologies are discussed. Finally, we provide perspectives on what challenges need to be overcome for CRVs to reach the market.
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Affiliation(s)
- Yan-Dong Tang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Research Center for Veterinary Biomedicine, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China.
| | - Changqing Yu
- Engineering Center of Agricultural Biosafety Assessment and Biotechnology, School of Advanced Agricultural Sciences, Yibin Vocational and Technical College, Yibin, China.
| | - Xue-Hui Cai
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Research Center for Veterinary Biomedicine, Harbin, China.
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7
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Chen W, Sullivan MO. Unnatural Amino Acid Engineering for Intracellular Delivery of Protein Therapeutics. Methods Mol Biol 2024; 2720:151-164. [PMID: 37775664 DOI: 10.1007/978-1-0716-3469-1_11] [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: 10/01/2023]
Abstract
Protein drugs are a critically important therapeutic modality due to the sophisticated binding recognition, catalytic properties, and disease relevance of proteins. There is a clear need for new strategies able to improve pharmacokinetics, bioavailability, and/or intracellular delivery of therapeutic proteins, as stability limitations have significantly hindered clinical advancement, and most proteins are membrane impermeable. Bioconjugation strategies able to site-specifically modify proteins with cell binding, and other ligands offer a particularly valuable approach to facilitate protein delivery due to the importance of ligand presentation on protein bioactivity and cellular uptake. We explored unnatural amino acid (UAA) incorporation as a novel strategy to tunably incorporate clustered cell-binding ligands in fluorescent proteins and suicide enzymes, resulting in substantial increases in cell-specific uptake and targeted cell-killing activity. These approaches offer a valuable and versatile method to modify a variety of proteins and enable improved clinical potential.
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Affiliation(s)
- Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
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8
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Butler ND, Kunjapur AM. Selective and Site-Specific Incorporation of Nonstandard Amino Acids Within Proteins for Therapeutic Applications. Methods Mol Biol 2024; 2720:35-53. [PMID: 37775656 DOI: 10.1007/978-1-0716-3469-1_3] [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: 10/01/2023]
Abstract
The incorporation of nonstandard amino acids (nsAAs) within protein sequences has broadened the chemical functionalities available for use in the study, prevention, or treatment of disease. The ability to genetically encode the introduction of nsAAs at precise sites of target recombinant proteins has enabled numerous applications such as bioorthogonal conjugation, thrombin inhibition, intrinsic biological containment of live organisms, and immunochemical termination of self-tolerance. Genetic systems that perform critical steps in enabling nsAA incorporation are known as orthogonal translation systems or orthogonal aminoacyl-tRNA synthetase/tRNA pairs. In Escherichia coli, several of these have been designed to accept novel nsAAs. Certain endogenous proteins, codon context, and standard amino acid concentrations can affect the yield of recombinant protein, the rate of nsAA incorporation within off-target proteins, and the rate of misincorporation due to near-cognate suppression or misacylation of orthogonal tRNA with standard amino acids. As a result, a significant body of work has been performed in engineering the E. coli genome to alleviate these issues. Here, we describe common methods applicable to nsAA incorporation within proteins in E. coli for sufficient purity and characterization for downstream therapeutic applications.
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Affiliation(s)
- Neil D Butler
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Aditya M Kunjapur
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
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9
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Wang TY, Meng FD, Sang GJ, Zhang HL, Tian ZJ, Zheng H, Cai XH, Tang YD. A novel viral vaccine platform based on engineered transfer RNA. Emerg Microbes Infect 2023; 12:2157339. [PMID: 36482724 PMCID: PMC9769134 DOI: 10.1080/22221751.2022.2157339] [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] [Indexed: 12/14/2022]
Abstract
In recent years, an increasing number of emerging and remerging virus outbreaks have occurred and the rapid development of vaccines against these viruses has been crucial. Controlling the replication of premature termination codon (PTC)-containing viruses is a promising approach to generate live but replication-defective viruses that can be used for potent vaccines. Here, we used anticodon-engineered transfer RNAs (ACE-tRNAs) as powerful precision switches to control the replication of PTC-containing viruses. We showed that ACE-tRNAs display higher potency of reading through PTCs than genetic code expansion (GCE) technology. Interestingly, ACE-tRNA has a site preference that may influence its read-through efficacy. We further attempted to use ACE-tRNAs as a novel viral vaccine platform. Using a human immunodeficiency virus type 1 (HIV-1) pseudotyped virus as an RNA virus model, we found that ACE-tRNAs display high potency for read-through viral PTCs and precisely control their production. Pseudorabies virus (PRV), a herpesvirus, was used as a DNA virus model. We found that ACE-tRNAs display high potency for reading through viral PTCs and precisely controlling PTC-containing virus replication. In addition, PTC-engineered PRV completely attenuated and lost virulence in mice in vivo, and immunization with PRV containing a PTC elicited a robust immune response and provided complete protection against wild-type PRV challenge. Overall, replication-controllable PTC-containing viruses based on ACE-tRNAs provide a new strategy to rapidly attenuate virus infection and prime robust immune responses. This technology can be used as a platform for rapidly developing viral vaccines in the future.
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Affiliation(s)
- Tong-Yun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China,Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, People's Republic of China
| | - Fan-Dan Meng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China,Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, People's Republic of China
| | - Guo-Ju Sang
- Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, People's Republic of China
| | - Hong-Liang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Zhi-Jun Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Hao Zheng
- Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China,Hao Zheng Shanghai Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Shanghai150001, People’s Republic of China
| | - Xue-Hui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China,Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, People's Republic of China,Heilongjiang Provincial Research Center for Veterinary Biomedicine, Harbin, People's Republic of China,Xue-Hui Cai State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, People’s Republic of China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin150001, People’s Republic of China
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China,Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, People's Republic of China, Yan-Dong Tang
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10
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Liang M, Yang Y, Zhang J, Sun Y, Peng H, Yi H, Wang Q, Gao X. Use of non-canonical amino acids in genetic code expansion-based therapeutics: Effects on mouse gut microbiota. Microb Biotechnol 2023; 16:2278-2291. [PMID: 37874686 PMCID: PMC10686157 DOI: 10.1111/1751-7915.14358] [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: 06/12/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
Vaccines and cell therapeutics based on genetic code expansion are emerging. A crucial step in these therapeutic technologies is the oral administration of non-canonical amino acids (ncAAs) to control pathogen growth and therapeutic protein levels in vivo. Investigating the toxicity effects of ncAAs can help identify more suitable candidates for developing genetic code expansion-based vaccines and cell therapeutics. In this study, we determined the effects of three ncAAs, namely, 4-acetyl-phenylalanine (pAcF), 4-iodo-phenylalanine (pIoF), and 4-methoxy-phenylalanine (pMeoF), commonly used in genetic code expansion-based vaccines and cell therapeutics, on the main organs, serum biochemical parameters, and gut microbiota in mice. We observed that pIoF and pMeoF significantly altered serum biochemical parameters to some extent. Moreover, the alterations in the mouse gut microbial composition were considerably greater after the oral administration of pIoF and pMeoF than after that of pAcF, compared with that in the control mice. These findings suggest that pAcF is more suitable than pIoF and pMeoF for application in genetic code expansion-based vaccines and cell therapeutics as it disturbs the physiological and gut microecological balance in mice to a lesser extent.
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Affiliation(s)
- Manyu Liang
- Green Pharmaceutical Technology Key Laboratory of Luzhou, School of PharmacySouthwest Medical UniversityLuzhouChina
| | - Yanhong Yang
- Green Pharmaceutical Technology Key Laboratory of Luzhou, School of PharmacySouthwest Medical UniversityLuzhouChina
| | - Jing Zhang
- Green Pharmaceutical Technology Key Laboratory of Luzhou, School of PharmacySouthwest Medical UniversityLuzhouChina
| | - Yingjie Sun
- Green Pharmaceutical Technology Key Laboratory of Luzhou, School of PharmacySouthwest Medical UniversityLuzhouChina
| | - Haixia Peng
- Green Pharmaceutical Technology Key Laboratory of Luzhou, School of PharmacySouthwest Medical UniversityLuzhouChina
| | - Huawei Yi
- Clinical LaboratoryFirst Affiliated Hospital of Yangtze UniversityJingzhouChina
| | - Qin Wang
- Dazhou Vocational College of Chinese MedicineDazhouChina
| | - Xiaowei Gao
- Green Pharmaceutical Technology Key Laboratory of Luzhou, School of PharmacySouthwest Medical UniversityLuzhouChina
- Dazhou Vocational College of Chinese MedicineDazhouChina
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11
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Zheng Z, Wu X, Wang Y, Yang X, Chen H, Shen Y, Yang Y, Xia Q. Attenuating RNA Viruses with Expanded Genetic Codes to Evoke Adjustable Immune Response in PylRS-tRNACUAPyl Transgenic Mice. Vaccines (Basel) 2023; 11:1606. [PMID: 37897007 PMCID: PMC10610612 DOI: 10.3390/vaccines11101606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/03/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023] Open
Abstract
Ribonucleic acid (RNA) viruses pose heavy burdens on public-health systems. Synthetic biology holds great potential for artificially controlling their replication, a strategy that could be used to attenuate infectious viruses but is still in the exploratory stage. Herein, we used the genetic-code expansion technique to convert Enterovirus 71 (EV71), a prototypical RNA virus, into a controllable EV71 strain carrying the unnatural amino acid (UAA) Nε-2-azidoethyloxycarbonyl-L-lysine (NAEK), which we termed an EV71-NAEK virus. After NAEK supplementation, EV71-NAEK could recapitulate an authentic NAEK time- and dose-dependent infection in vitro, which could serve as a novel method to manipulate virulent viruses in conventional laboratories. We further validated the prophylactic effect of EV71-NAEK in two mouse models. In susceptible parent mice, vaccination with EV71-NAEK elicited a strong immune response and protected their neonatal offspring from lethal challenges similar to that of commercial vaccines. Meanwhile, in transgenic mice harboring a PylRS-tRNACUAPyl pair, substantial elements of genetic-code expansion technology, EV71-NAEK evoked an adjustable neutralizing-antibody response in a strictly external NAEK dose-dependent manner. These findings suggested that EV71-NAEK could be the basis of a feasible immunization program for populations with different levels of immunity. Moreover, we expanded the strategy to generate controllable coxsackieviruses for conceptual verification. In combination, these results could underlie a competent strategy for attenuating viruses and priming the immune system via artificial control, which might be a promising direction for the development of amenable vaccine candidates and be broadly applied to other RNA viruses.
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Affiliation(s)
| | | | | | | | | | | | | | - Qing Xia
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; (Z.Z.); (X.W.); (Y.W.); (X.Y.); (H.C.); (Y.S.); (Y.Y.)
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12
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Chen L, Xin X, Zhang Y, Li S, Zhao X, Li S, Xu Z. Advances in Biosynthesis of Non-Canonical Amino Acids (ncAAs) and the Methods of ncAAs Incorporation into Proteins. Molecules 2023; 28:6745. [PMID: 37764520 PMCID: PMC10534643 DOI: 10.3390/molecules28186745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
The functional pool of canonical amino acids (cAAs) has been enriched through the emergence of non-canonical amino acids (ncAAs). NcAAs play a crucial role in the production of various pharmaceuticals. The biosynthesis of ncAAs has emerged as an alternative to traditional chemical synthesis due to its environmental friendliness and high efficiency. The breakthrough genetic code expansion (GCE) technique developed in recent years has allowed the incorporation of ncAAs into target proteins, giving them special functions and biological activities. The biosynthesis of ncAAs and their incorporation into target proteins within a single microbe has become an enticing application of such molecules. Based on that, in this study, we first review the biosynthesis methods for ncAAs and analyze the difficulties related to biosynthesis. We then summarize the GCE methods and analyze their advantages and disadvantages. Further, we review the application progress of ncAAs and anticipate the challenges and future development directions of ncAAs.
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Affiliation(s)
- Liang Chen
- College of Bioengineering, Beijing Polytechnic, Beijing 100176, China; (X.X.); (Y.Z.); (S.L.); (X.Z.); (S.L.); (Z.X.)
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13
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Xue W, Li T, Gu Y, Li S, Xia N. Molecular engineering tools for the development of vaccines against infectious diseases: current status and future directions. Expert Rev Vaccines 2023. [PMID: 37339445 DOI: 10.1080/14760584.2023.2227699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/16/2023] [Indexed: 06/22/2023]
Abstract
INTRODUCTION The escalating global changes have fostered conditions for the expansion and transmission of diverse biological factors, leading to the rise of emerging and reemerging infectious diseases. Complex viral infections, such as COVID-19, influenza, HIV, and Ebola, continue to surface, necessitating the development of effective vaccine technologies. AREAS COVERED This review article highlights recent advancements in molecular biology, virology, and genomics that have propelled the design and development of innovative molecular tools. These tools have promoted new vaccine research platforms and directly improved vaccine efficacy. The review summarizes the cutting-edge molecular engineering tools used in creating novel vaccines and explores the rapidly expanding molecular tools landscape and potential directions for future vaccine development. EXPERT OPINION The strategic application of advanced molecular engineering tools can address conventional vaccine limitations, enhance the overall efficacy of vaccine products, promote diversification in vaccine platforms, and form the foundation for future vaccine development. Prioritizing safety considerations of these novel molecular tools during vaccine development is crucial.
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Affiliation(s)
- Wenhui Xue
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- Xiang an Biomedicine Laboratory, Xiamen, China
| | - Tingting Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- Xiang an Biomedicine Laboratory, Xiamen, China
| | - Ying Gu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- Xiang an Biomedicine Laboratory, Xiamen, China
| | - Shaowei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- Xiang an Biomedicine Laboratory, Xiamen, China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- Xiang an Biomedicine Laboratory, Xiamen, China
- The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, Xiamen, China
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14
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Zhu X, Zhaoyang Zhang, Bin Jia, Yuan Y. Current advances of biocontainment strategy in synthetic biology. Chin J Chem Eng 2022. [DOI: 10.1016/j.cjche.2022.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Generation of Premature Termination Codon (PTC)-Harboring Pseudorabies Virus (PRV) via Genetic Code Expansion Technology. Viruses 2022; 14:v14030572. [PMID: 35336979 PMCID: PMC8950157 DOI: 10.3390/v14030572] [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: 02/17/2022] [Revised: 02/28/2022] [Accepted: 03/09/2022] [Indexed: 12/27/2022] Open
Abstract
Despite many efforts and diverse approaches, developing an effective herpesvirus vaccine remains a great challenge. Traditional inactivated and live-attenuated vaccines always raise efficacy or safety concerns. This study used Pseudorabies virus (PRV), a swine herpes virus, as a model. We attempted to develop a live but replication-incompetent PRV by genetic code expansion (GCE) technology. Premature termination codon (PTC) harboring PRV was successfully rescued in the presence of orthogonal system MbpylRS/tRNAPyl pair and unnatural amino acids (UAA). However, UAA incorporating efficacy seemed extremely low in our engineered PRV PTC virus. Furthermore, we failed to establish a stable transgenic cell line containing orthogonal translation machinery for PTC virus replication, and we demonstrated that orthogonal tRNAPyl is a key limiting factor. This study is the first to demonstrate that orthogonal translation system-mediated amber codon suppression strategy could precisely control PRV-PTC engineered virus replication. To our knowledge, this is the first reported PTC herpesvirus generated by GCE technology. Our work provides a proof-of-concept for generating UAAs-controlled PRV-PTC virus, which can be used as a safe and effective vaccine.
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16
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Therapeutic peptides: current applications and future directions. Signal Transduct Target Ther 2022; 7:48. [PMID: 35165272 PMCID: PMC8844085 DOI: 10.1038/s41392-022-00904-4] [Citation(s) in RCA: 516] [Impact Index Per Article: 258.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/08/2023] Open
Abstract
Peptide drug development has made great progress in the last decade thanks to new production, modification, and analytic technologies. Peptides have been produced and modified using both chemical and biological methods, together with novel design and delivery strategies, which have helped to overcome the inherent drawbacks of peptides and have allowed the continued advancement of this field. A wide variety of natural and modified peptides have been obtained and studied, covering multiple therapeutic areas. This review summarizes the efforts and achievements in peptide drug discovery, production, and modification, and their current applications. We also discuss the value and challenges associated with future developments in therapeutic peptides.
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17
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Genetic-code-expanded cell-based therapy for treating diabetes in mice. Nat Chem Biol 2022; 18:47-55. [PMID: 34782743 DOI: 10.1038/s41589-021-00899-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 09/13/2021] [Indexed: 12/13/2022]
Abstract
Inducer-triggered therapeutic protein expression from designer cells is a promising strategy for disease treatment. However, as most inducer systems harness transcriptional machineries, protein expression timeframes are unsuitable for many therapeutic applications. Here, we engineered a genetic code expansion-based therapeutic system, termed noncanonical amino acids (ncAAs)-triggered therapeutic switch (NATS), to achieve fast therapeutic protein expression in response to cognate ncAAs at the translational level. The NATS system showed response within 2 hours of triggering, whereas no signal was detected in a transcription-machinery-based system. Moreover, NATS system is compatible with transcriptional switches for multi-regulatory-layer control. Diabetic mice with microencapsulated cell implants harboring the NATS system could alleviate hyperglycemia within 90 min on oral delivery of ncAA. We also prepared ncAA-containing 'cookies' and achieved long-term glycemic control in diabetic mice implanted with NATS cells. Our proof-of-concept study demonstrates the use of NATS system for the design of next-generation cell-based therapies to achieve fast orally induced protein expression.
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18
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Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nat Commun 2021; 12:7039. [PMID: 34857769 PMCID: PMC8639764 DOI: 10.1038/s41467-021-27399-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 11/16/2021] [Indexed: 01/24/2023] Open
Abstract
Site-specific incorporation of unnatural amino acids (UAAs) with similar incorporation efficiency to that of natural amino acids (NAAs) and low background activity is extremely valuable for efficient synthesis of proteins with diverse new chemical functions and design of various synthetic auxotrophs. However, such efficient translation systems remain largely unknown in the literature. Here, we describe engineered chimeric phenylalanine systems that dramatically increase the yield of proteins bearing UAAs, through systematic engineering of the aminoacyl-tRNA synthetase and its respective cognate tRNA. These engineered synthetase/tRNA pairs allow single-site and multi-site incorporation of UAAs with efficiencies similar to those of NAAs and high fidelity. In addition, using the evolved chimeric phenylalanine system, we construct a series of E. coli strains whose growth is strictly dependent on exogenously supplied of UAAs. We further show that synthetic auxotrophic cells can grow robustly in living mice when UAAs are supplemented.
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19
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Guo J, Niu W. Genetic Code Expansion Through Quadruplet Codon Decoding. J Mol Biol 2021; 434:167346. [PMID: 34762896 PMCID: PMC9018476 DOI: 10.1016/j.jmb.2021.167346] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/25/2021] [Accepted: 10/30/2021] [Indexed: 12/31/2022]
Abstract
Noncanonical amino acid mutagenesis has emerged as a powerful tool for the study of protein structure and function. While triplet nonsense codons, especially the amber codon, have been widely employed, quadruplet codons have attracted attention for the potential of creating additional blank codons for noncanonical amino acids mutagenesis. In this review, we discuss methodologies and applications of quadruplet codon decoding in genetic code expansion both in vitro and in vivo.
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Affiliation(s)
- Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, United States; The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States.
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, United States; The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
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20
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Liu L, Wang B, Li S, Xu F, He Q, Pan C, Gao X, Yao W, Song X. Convenient Genetic Encoding of Phenylalanine Derivatives through Their α-Keto Acid Precursors. Biomolecules 2021; 11:1358. [PMID: 34572570 PMCID: PMC8470325 DOI: 10.3390/biom11091358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 11/16/2022] Open
Abstract
The activity and function of proteins can be improved by incorporation of non-canonical amino acids (ncAAs). To avoid the tedious synthesis of a large number of chiral phenylalanine derivatives, we synthesized the corresponding phenylpyruvic acid precursors. Escherichia coli strain DH10B and strain C321.ΔA.expΔPBAD were selected as hosts for phenylpyruvic acid bioconversion and genetic code expansion using the MmPylRS/pyltRNACUA system. The concentrations of keto acids, PLP and amino donors were optimized in the process. Eight keto acids that can be biotransformed and their coupled genetic code expansions were identified. Finally, the genetic encoded ncAAs were tested for incorporation into fluorescent proteins with keto acids.
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Affiliation(s)
- Li Liu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
| | - Bohao Wang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
| | - Sheng Li
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
| | - Fengyuan Xu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
| | - Qi He
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
| | - Chun Pan
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Southeast University, Nanjing 210009, China;
| | - Xiangdong Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
| | - Wenbing Yao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
| | - Xiaoda Song
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China; (L.L.); (B.W.); (S.L.); (F.X.); (Q.H.)
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21
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Hao R, Ma K, Ru Y, Li D, Song G, Lu B, Liu H, Li Y, Zhang J, Wu C, Zhang G, Hu H, Luo J, Zheng H. Amber codon is genetically unstable in generation of premature termination codon (PTC)-harbouring Foot-and-mouth disease virus (FMDV) via genetic code expansion. RNA Biol 2021; 18:2330-2341. [PMID: 33849391 DOI: 10.1080/15476286.2021.1907055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The foot-and-mouth disease virus (FMDV) is the causative agent of FMD, a highly infectious and devastating viral disease of domestic and wild cloven-hoofed animals. FMD affects livestock and animal products' national and international trade, causing severe economic losses and social consequences. Currently, inactivated vaccines play a vital role in FMD control, but they have several limitations. The genetic code expansion technology provides powerful strategies for generating premature termination codon (PTC)-harbouring virus as a live but replication-incompetent viral vaccine. However, this technology has not been explored for the design and development of new FMD vaccines. In this study, we first expanded the genetic code of the FMDV genome via a transgenic cell line containing an orthogonal translation machinery. We demonstrated that the transgenic cells stably integrated the orthogonal pyltRNA/pylRS pair into the genome and enabled efficient, homogeneous incorporation of unnatural amino acids into target proteins in mammalian cells. Next, we constructed 129 single-PTC FMDV mutants and four dual-PTC FMDV mutants after considering the tolerance, location, and potential functions of those mutated sites. Amber stop codons individually substituted the selected amino acid codons in four viral proteins (3D, L, VP1, and VP4) of FMDV. We successfully rescued PTC-FMDV mutants, but the amber codon unexpectedly showed a highly degree of mutation rate during PTC-FMDV packaging and replication. Our findings highlight that the genetic code expansion technology for the generation of PTC-FMD vaccines needs to be further improved and that the genetic stability of amber codons during the packaging and replication of FMDV is a concern.
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Affiliation(s)
- Rongzeng Hao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Kun Ma
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yi Ru
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Dan Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Gaoyuan Song
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Bingzhou Lu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Huanan Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yajun Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jiaoyan Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chunping Wu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Guicai Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Haitao Hu
- Department of Microbiology and Immunology, Sealy Center for Vaccine Development and Institute for Human Infections and Immunity, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
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22
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Fok JA, Mayer C. Genetic-Code-Expansion Strategies for Vaccine Development. Chembiochem 2020; 21:3291-3300. [PMID: 32608153 PMCID: PMC7361271 DOI: 10.1002/cbic.202000343] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/29/2020] [Indexed: 12/16/2022]
Abstract
By providing long-term protection against infectious diseases, vaccinations have significantly reduced death and morbidity worldwide. In the 21st century, (bio)technological advances have paved the way for developing prophylactic vaccines that are safer and more effective as well as enabling the use of vaccines as therapeutics to treat human diseases. Here, we provide a focused review of the utility of genetic code expansion as an emerging tool for the development of vaccines. Specifically, we discuss how the incorporation of immunogenic noncanonical amino acids can aid in eliciting immune responses against adverse self-proteins and highlight the potential of an expanded genetic code for the construction of replication-incompetent viruses. We close the review by discussing the future prospects and remaining challenges for the application of these approaches in the development of both prophylactic and therapeutic vaccines in the near future.
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Affiliation(s)
- Jelle A. Fok
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49474 AGGroningen (TheNetherlands
| | - Clemens Mayer
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49474 AGGroningen (TheNetherlands
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23
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Gang D, Park HS. Noncanonical Amino Acids in Synthetic Biosafety and Post-translational Modification Studies. Chembiochem 2020; 22:460-468. [PMID: 32794239 DOI: 10.1002/cbic.202000437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/11/2020] [Indexed: 11/06/2022]
Abstract
The incorporation of noncanonical amino acids (ncAAs) has been extensively studied because of its broad applicability. In the past decades, various in vitro and in vivo ncAA incorporation approaches have been developed to generate synthetic recombinant proteins. Herein, we discuss the methodologies for ncAA incorporation, and their use in diverse research areas, such as in synthetic biosafety and for studies of post-translational modifications.
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Affiliation(s)
- Donghyeok Gang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Hee-Sung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 341418, Korea
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24
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He X, Chen Y, Beltran DG, Kelly M, Ma B, Lawrie J, Wang F, Dodds E, Zhang L, Guo J, Niu W. Functional genetic encoding of sulfotyrosine in mammalian cells. Nat Commun 2020; 11:4820. [PMID: 32973160 PMCID: PMC7515910 DOI: 10.1038/s41467-020-18629-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022] Open
Abstract
Protein tyrosine O-sulfation (PTS) plays a crucial role in extracellular biomolecular interactions that dictate various cellular processes. It also involves in the development of many human diseases. Regardless of recent progress, our current understanding of PTS is still in its infancy. To promote and facilitate relevant studies, a generally applicable method is needed to enable efficient expression of sulfoproteins with defined sulfation sites in live mammalian cells. Here we report the engineering, in vitro biochemical characterization, structural study, and in vivo functional verification of a tyrosyl-tRNA synthetase mutant for the genetic encoding of sulfotyrosine in mammalian cells. We further apply this chemical biology tool to cell-based studies on the role of a sulfation site in the activation of chemokine receptor CXCR4 by its ligand. Our work will not only facilitate cellular studies of PTS, but also paves the way for economical production of sulfated proteins as therapeutic agents in mammalian systems.
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Affiliation(s)
- Xinyuan He
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Yan Chen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Daisy Guiza Beltran
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Maia Kelly
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Bin Ma
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Justin Lawrie
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Feng Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Eric Dodds
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Limei Zhang
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA.
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA.
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25
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Lieser RM, Yur D, Sullivan MO, Chen W. Site-Specific Bioconjugation Approaches for Enhanced Delivery of Protein Therapeutics and Protein Drug Carriers. Bioconjug Chem 2020; 31:2272-2282. [DOI: 10.1021/acs.bioconjchem.0c00456] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Rachel M. Lieser
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
| | - Daniel Yur
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
| | - Millicent O. Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
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26
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Design of fluorescent protein-based sensors through a general protection-deprotection strategy. Methods Enzymol 2020; 640:63-82. [PMID: 32560806 DOI: 10.1016/bs.mie.2020.04.003] [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: 02/25/2023]
Abstract
Engineered fluorescent proteins have been extensively used in biological research for the study of gene expression, protein function and trafficking, and protein-protein interactions. In addition, fluorescent proteins have also been engineered to act as biosensing agents to detect intracellular signaling molecules and other small-molecule metabolites. Although they have been engineered extensively to achieve novel properties, fluorescent proteins are traditionally modified using the 20 canonical amino acids. This limits the number of functional groups that are available to the design and construction of novel fluorescent proteins. The expansion of the genetic code through the incorporation of noncanonical amino acids presents an opportunity to add new functionalities with the intent of modifying chemical and physical properties of fluorescent proteins. Herein we provide a general procedure for the site-specific incorporation of noncanonical amino acids into fluorescent proteins in live cells. We will also discuss a noncanonical amino acid-containing fluorescent protein sensor that is based on a general protection-deprotection design strategy, for the selective detection and quantification of Hg2+.
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27
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Zhang RR, Ye Q, Li XF, Deng YQ, Xu YP, Huang XY, Xia Q, Qin CF. Construction and characterization of UAA-controlled recombinant Zika virus by genetic code expansion. SCIENCE CHINA-LIFE SCIENCES 2020; 64:171-173. [PMID: 32542514 DOI: 10.1007/s11427-020-1737-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/20/2020] [Indexed: 01/15/2023]
Affiliation(s)
- Rong-Rong Zhang
- Graduate School, Anhui Medical University, Hefei, 230032, China.,Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Qing Ye
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Xiao-Feng Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yong-Qiang Deng
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yan-Peng Xu
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Xing-Yao Huang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Qing Xia
- Department of Chemical Biology, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
| | - Cheng-Feng Qin
- Graduate School, Anhui Medical University, Hefei, 230032, China. .,Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
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28
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Martínez MA, Jordan-Paiz A, Franco S, Nevot M. Synonymous genome recoding: a tool to explore microbial biology and new therapeutic strategies. Nucleic Acids Res 2020; 47:10506-10519. [PMID: 31584076 PMCID: PMC6846928 DOI: 10.1093/nar/gkz831] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/12/2019] [Accepted: 09/30/2019] [Indexed: 12/18/2022] Open
Abstract
Synthetic genome recoding is a new means of generating designed organisms with altered phenotypes. Synonymous mutations introduced into the protein coding region tolerate modifications in DNA or mRNA without modifying the encoded proteins. Synonymous genome-wide recoding has allowed the synthetic generation of different small-genome viruses with modified phenotypes and biological properties. Recently, a decreased cost of chemically synthesizing DNA and improved methods for assembling DNA fragments (e.g. lambda red recombination and CRISPR-based editing) have enabled the construction of an Escherichia coli variant with a 4-Mb synthetic synonymously recoded genome with a reduced number of sense codons (n = 59) encoding the 20 canonical amino acids. Synonymous genome recoding is increasing our knowledge of microbial interactions with innate immune responses, identifying functional genome structures, and strategically ameliorating cis-inhibitory signaling sequences related to splicing, replication (in eukaryotes), and complex microbe functions, unraveling the relevance of codon usage for the temporal regulation of gene expression and the microbe mutant spectrum and adaptability. New biotechnological and therapeutic applications of this methodology can easily be envisaged. In this review, we discuss how synonymous genome recoding may impact our knowledge of microbial biology and the development of new and better therapeutic methodologies.
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Affiliation(s)
- Miguel Angel Martínez
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Ana Jordan-Paiz
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Sandra Franco
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Maria Nevot
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
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29
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Nödling AR, Spear LA, Williams TL, Luk LYP, Tsai YH. Using genetically incorporated unnatural amino acids to control protein functions in mammalian cells. Essays Biochem 2019; 63:237-266. [PMID: 31092687 PMCID: PMC6610526 DOI: 10.1042/ebc20180042] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023]
Abstract
Genetic code expansion allows unnatural (non-canonical) amino acid incorporation into proteins of interest by repurposing the cellular translation machinery. The development of this technique has enabled site-specific incorporation of many structurally and chemically diverse amino acids, facilitating a plethora of applications, including protein imaging, engineering, mechanistic and structural investigations, and functional regulation. Particularly, genetic code expansion provides great tools to study mammalian proteins, of which dysregulations often have important implications in health. In recent years, a series of methods has been developed to modulate protein function through genetically incorporated unnatural amino acids. In this review, we will first discuss the basic concept of genetic code expansion and give an up-to-date list of amino acids that can be incorporated into proteins in mammalian cells. We then focus on the use of unnatural amino acids to activate, inhibit, or reversibly modulate protein function by translational, optical or chemical control. The features of each approach will also be highlighted.
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Affiliation(s)
| | - Luke A Spear
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Thomas L Williams
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
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30
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Venkat S, Chen H, Gan Q, Fan C. The Application of Cell-Free Protein Synthesis in Genetic Code Expansion for Post-translational Modifications. Front Pharmacol 2019; 10:248. [PMID: 30949051 PMCID: PMC6436179 DOI: 10.3389/fphar.2019.00248] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 02/26/2019] [Indexed: 02/04/2023] Open
Abstract
The translation system is a sophisticated machinery that synthesizes proteins from 20 canonical amino acids. Recently, the repertoire of such composition has been expanded by the introduction of non-canonical amino acids (ncAAs) with the genetic code expansion strategy, which provides proteins with designed properties and structures for protein studies and engineering. Although the genetic code expansion strategy has been mostly implemented by using living cells as the host, a number of limits such as poor cellular uptake or solubility of specific ncAA substrates and the toxicity of target proteins have hindered the production of certain ncAA-modified proteins. To overcome those challenges, cell-free protein synthesis (CFPS) has been applied as it allows the precise control of reaction components. Several approaches have been recently developed to increase the purity and efficiency of ncAA incorporation in CFPS. Here, we summarized recent development of CFPS with an emphasis on its applications in generating site-specific protein post-translational modifications by the genetic code expansion strategy.
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Affiliation(s)
- Sumana Venkat
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | - Hao Chen
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States.,Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
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31
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Mayer C. Selection, Addiction and Catalysis: Emerging Trends for the Incorporation of Noncanonical Amino Acids into Peptides and Proteins in Vivo. Chembiochem 2019; 20:1357-1364. [PMID: 30618145 PMCID: PMC6563710 DOI: 10.1002/cbic.201800733] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 12/22/2022]
Abstract
Expanding the genetic code of organisms by incorporating noncanonical amino acids (ncAAs) into target proteins through the suppression of stop codons in vivo has profoundly impacted how we perform protein modification or detect proteins and their interaction partners in their native environment. Yet, with genetic code expansion strategies maturing over the past 15 years, new applications that make use—or indeed repurpose—these techniques are beginning to emerge. This Concept article highlights three of these developments: 1) The incorporation of ncAAs for the biosynthesis and selection of bioactive macrocyclic peptides with novel ring architectures, 2) synthetic biocontainment strategies based on the addiction of microorganisms to ncAAs, and 3) enzyme design strategies, in which ncAAs with unique functionalities enable the catalysis of new‐to‐nature reactions. Key advances in all three areas are presented and potential future applications discussed.
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Affiliation(s)
- Clemens Mayer
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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32
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Lieser RM, Chen W, Sullivan MO. Controlled Epidermal Growth Factor Receptor Ligand Display on Cancer Suicide Enzymes via Unnatural Amino Acid Engineering for Enhanced Intracellular Delivery in Breast Cancer Cells. Bioconjug Chem 2019; 30:432-442. [PMID: 30615416 DOI: 10.1021/acs.bioconjchem.8b00783] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Proteins are ideal candidates for disease treatment because of their high specificity and potency. Despite this potential, delivery of proteins remains a significant challenge due to the intrinsic size, charge, and stability of proteins. Attempts to overcome these challenges have most commonly relied on direct conjugation of polymers and peptides to proteins via reactive groups on naturally occurring residues. While such approaches have shown some success, they allow limited control of the spacing and number of moieties coupled to proteins, which can hinder bioactivity and delivery capabilities of the therapeutic. Here, we describe a strategy to site-specifically conjugate delivery moieties to therapeutic proteins through unnatural amino acid (UAA) incorporation, in order to explore the effect of epidermal growth factor receptor (EGFR)-targeted ligand valency and spacing on internalization of proteins in EGFR-overexpressing inflammatory breast cancer (IBC) cells. Our results demonstrate the ability to enhance targeted protein delivery by tuning a small number of EGFR ligands per protein and clustering these ligands to promote multivalent ligand-receptor interactions. Furthermore, the tailorability of this simple approach was demonstrated through IBC-targeted cell death via the delivery of yeast cytosine deaminase (yCD), a prodrug converting enzyme.
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Affiliation(s)
- Rachel M Lieser
- Department of Chemical and Biomolecular Engineering , University of Delaware , 150 Academy Street , Newark , Delaware 19716 , United States
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering , University of Delaware , 150 Academy Street , Newark , Delaware 19716 , United States
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering , University of Delaware , 150 Academy Street , Newark , Delaware 19716 , United States
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33
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Kato Y. Translational Control using an Expanded Genetic Code. Int J Mol Sci 2019; 20:ijms20040887. [PMID: 30781713 PMCID: PMC6412442 DOI: 10.3390/ijms20040887] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 11/16/2022] Open
Abstract
A bio-orthogonal and unnatural substance, such as an unnatural amino acid (Uaa), is an ideal regulator to control target gene expression in a synthetic gene circuit. Genetic code expansion technology has achieved Uaa incorporation into ribosomal synthesized proteins in vivo at specific sites designated by UAG stop codons. This site-specific Uaa incorporation can be used as a controller of target gene expression at the translational level by conditional read-through of internal UAG stop codons. Recent advances in optimization of site-specific Uaa incorporation for translational regulation have enabled more precise control over a wide range of novel important applications, such as Uaa-auxotrophy-based biological containment, live-attenuated vaccine, and high-yield zero-leakage expression systems, in which Uaa translational control is exclusively used as an essential genetic element. This review summarizes the history and recent advance of the translational control by conditional stop codon read-through, especially focusing on the methods using the site-specific Uaa incorporation.
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Affiliation(s)
- Yusuke Kato
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Oowashi 1-2, Tsukuba, Ibaraki 305-8634, Japan.
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34
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Kang M, Lu Y, Chen S, Tian F. Harnessing the power of an expanded genetic code toward next-generation biopharmaceuticals. Curr Opin Chem Biol 2018; 46:123-129. [DOI: 10.1016/j.cbpa.2018.07.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/30/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
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35
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Huang Y, Liu T. Therapeutic applications of genetic code expansion. Synth Syst Biotechnol 2018; 3:150-158. [PMID: 30345400 PMCID: PMC6190509 DOI: 10.1016/j.synbio.2018.09.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/16/2018] [Accepted: 09/18/2018] [Indexed: 12/05/2022] Open
Abstract
In nature, a limited, conservative set of amino acids are utilized to synthesize proteins. Genetic code expansion technique reassigns codons and incorporates noncanonical amino acids (ncAAs) through orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pairs. The past decade has witnessed the rapid growth in diversity and scope for therapeutic applications of this technology. Here, we provided an update on the recent progress using genetic code expansion in the following areas: antibody-drug conjugates (ADCs), bispecific antibodies (BsAb), immunotherapies, long-lasting protein therapeutics, biosynthesized peptides, engineered viruses and cells, as well as other therapeutic related applications, where the technique was used to elucidate the mechanisms of biotherapeutics and drug targets.
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Affiliation(s)
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
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36
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Kato Y. Tight Translational Control Using Site-Specific Unnatural Amino Acid Incorporation with Positive Feedback Gene Circuits. ACS Synth Biol 2018; 7:1956-1963. [PMID: 29979867 DOI: 10.1021/acssynbio.8b00204] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tight regulatory system for gene expression, which is ideally controlled by unnatural and bio-orthogonal substances, is a keystone for successful construction of synthetic gene circuits. Here, we present a widely applicable approach to construct tight protein translational switches using site-specific unnatural amino acid (Uaa) incorporation systems. As a key mechanism to obtain excellent tightness, we installed gene circuits for positive feedback derepression. This mechanism dramatically suppressed leakage translation in the absence of the Uaa. In a translational switch with the feedback circuit in Escherichia coli, a 1.4 × 103 ON/OFF ratio was achieved which was 3 × 102-fold greater than that of the parent system and was comparable to that of the well-known tight expression system using the araBAD promoter and the araC regulator. This method offers an avenue for generation of novel tight genetic switches from over a hundred site-specific unnatural amino acid incorporation systems which have already been established. These tight translational switches will facilitate the development of fine gene control systems in synthetic biology, especially for Uaa-auxotrophy-based biological containments and live attenuated vaccines.
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Affiliation(s)
- Yusuke Kato
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Oowashi 1-2, Tsukuba, Ibaraki 305-8634, Japan
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37
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Kelemen RE, Erickson SB, Chatterjee A. Synthesis at the interface of virology and genetic code expansion. Curr Opin Chem Biol 2018; 46:164-171. [PMID: 30086446 DOI: 10.1016/j.cbpa.2018.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 05/18/2018] [Accepted: 07/13/2018] [Indexed: 01/24/2023]
Abstract
How a virus efficiently invades its host cell and masterfully engineers its properties provides valuable lessons and resources for the emerging discipline of synthetic biology, which seeks to create engineered biological systems with novel functions. Recently, the toolbox of synthetic biology has also been enriched by the genetic code expansion technology, which has provided access to a large assortment of unnatural amino acids with novel chemical functionalities that can be site-specifically incorporated into proteins in living cells. The synergistic interplay of these two disciplines holds much promise to advance their individual progress, while creating new paradigms for synthetic biology. In this review we seek to provide an account of the recent advances at the interface of these two research areas.
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Affiliation(s)
- Rachel E Kelemen
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA 02467, United States
| | - Sarah B Erickson
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA 02467, United States
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA 02467, United States.
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38
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Chen Y, Wan Y, Wang N, Yuan Z, Niu W, Li Q, Guo J. Controlling the Replication of a Genomically Recoded HIV-1 with a Functional Quadruplet Codon in Mammalian Cells. ACS Synth Biol 2018; 7:1612-1617. [PMID: 29787233 DOI: 10.1021/acssynbio.8b00096] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Large efforts have been devoted to genetic code engineering in the past decade, aiming for unnatural amino acid mutagenesis. Recently, an increasing number of studies were reported to employ quadruplet codons to encode unnatural amino acids. We and others have demonstrated that the quadruplet decoding efficiency could be significantly enhanced by an extensive engineering of tRNAs bearing an extra nucleotide in their anticodon loops. In this work, we report the identification of tRNA mutants derived from directed evolution to efficiently decode a UAGA quadruplet codon in mammalian cells. Intriguingly, the trend of quadruplet codon decoding efficiency among the tested tRNA variants in mammalian cells was largely the same as that in E. coli. We subsequently demonstrate the utility of quadruplet codon decoding by the construction of the first HIV-1 mutant that lacks any in-frame amber nonsense codons and can be precisely activated by the decoding of a genomically embedded UAGA codon with an unnatural amino acid. Such conditionally activatable HIV-1 mutant can likely facilitate both fundamental investigations of HIV-1 as well as vaccine developments. The use of quadruplet codon, instead of an amber nonsense codon, to control HIV-1 replication has the advantage in that the correction of a frameshift caused by a quadruplet codon is much less likely than the reversion of an amber codon back into a sense codon in HIV-1.
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39
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Abstract
Our understanding of the complex molecular processes of living organisms at the molecular level is growing exponentially. This knowledge, together with a powerful arsenal of tools for manipulating the structures of macromolecules, is allowing chemists to to harness and reprogram the cellular machinery in ways previously unimaged. Here we review one example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins with unprecedented precision.
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Affiliation(s)
- Douglas D. Young
- Department of Chemistry, College of William & Mary,
P.O. Box 8795, Williamsburg, VA 23187 (USA)
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute,
La Jolla, CA 92037 (USA),
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40
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Chin JW. Expanding and reprogramming the genetic code. Nature 2017; 550:53-60. [PMID: 28980641 DOI: 10.1038/nature24031] [Citation(s) in RCA: 513] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022]
Abstract
Nature uses a limited, conservative set of amino acids to synthesize proteins. The ability to genetically encode an expanded set of building blocks with new chemical and physical properties is transforming the study, manipulation and evolution of proteins, and is enabling diverse applications, including approaches to probe, image and control protein function, and to precisely engineer therapeutics. Underpinning this transformation are strategies to engineer and rewire translation. Emerging strategies aim to reprogram the genetic code so that noncanonical biopolymers can be synthesized and evolved, and to test the limits of our ability to engineer the translational machinery and systematically recode genomes.
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Affiliation(s)
- Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.,Department of Chemistry, Cambridge University, Cambridge CB2 1EW, UK
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41
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Xuan W, Schultz PG. A Strategy for Creating Organisms Dependent on Noncanonical Amino Acids. Angew Chem Int Ed Engl 2017; 56:9170-9173. [PMID: 28593724 PMCID: PMC5580492 DOI: 10.1002/anie.201703553] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Indexed: 11/11/2022]
Abstract
The use of noncanonical amino acids (ncAAs) to control the viability of an organism provides a strategy for the development of conditional "kill switches" for live vaccines or engineered human cells. We report an approach inspired by the posttranslational acetylation/deacetylation of lysine residues, in which a protein encoded by a gene with an in-frame nonsense codon at an essential lysine can be expressed in its native state only upon genetic incorporation of N-ϵ-acetyl-l-Lys (AcK), and subsequent enzymatic deacetylation in the host cell. We applied this strategy to two essential E. coli enzymes: the branched-chain aminotransferase BCAT and the DNA replication initiator protein DnaA. We also devised a barnase-based conditional suicide switch to further lower the escape frequency of the host cells. This strategy offers a number of attractive features for controlling host viability, including a single small-molecule-based kill switch, low escape frequency, and unaffected protein function.
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Affiliation(s)
- Weimin Xuan
- Department of Chemistry, the Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter G Schultz
- Department of Chemistry, the Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
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42
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Xuan W, Schultz PG. A Strategy for Creating Organisms Dependent on Noncanonical Amino Acids. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703553] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Weimin Xuan
- Department of Chemistry; the Scripps Research Institute; 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Peter G. Schultz
- Department of Chemistry; the Scripps Research Institute; 10550 N. Torrey Pines Road La Jolla CA 92037 USA
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43
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Yuan Z, Wang N, Kang G, Niu W, Li Q, Guo J. Controlling Multicycle Replication of Live-Attenuated HIV-1 Using an Unnatural Genetic Switch. ACS Synth Biol 2017; 6:721-731. [PMID: 28106981 DOI: 10.1021/acssynbio.6b00373] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A safe and effective human immunodeficiency virus type 1 (HIV-1) vaccine is urgently needed, but remains elusive. While HIV-1 live-attenuated vaccine can provide potent protection as demonstrated in rhesus macaque-simian immunodeficiency virus model, the potential pathogenic consequences associated with the uncontrolled virus replication preclude such vaccine from clinical applications. We investigated a novel approach to address this problem by controlling live-attenuated HIV-1 replication through an unnatural genetic switch that was based on the amber suppression strategy. Here we report the construction of all-in-one live-attenuated HIV-1 mutants that contain genomic copy of the amber suppression system. This genetic modification resulted in viruses that were capable of multicycle replication in vitro and could be switched on and off using an unnatural amino acid as the cue. This stand-alone, replication-controllable attenuated HIV-1 virus represents an important step toward the generation of a safe and efficacious live-attenuated HIV-1 vaccine. The strategy reported in this work can be adopted for the development of other live-attenuated vaccines.
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Affiliation(s)
- Zhe Yuan
- Nebraska Center for Virology & School of Biological Sciences, University of Nebraska−Lincoln, Lincoln, Nebraska 68583, United States
| | - Nanxi Wang
- Department
of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Guobin Kang
- Nebraska Center for Virology & School of Biological Sciences, University of Nebraska−Lincoln, Lincoln, Nebraska 68583, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Qingsheng Li
- Nebraska Center for Virology & School of Biological Sciences, University of Nebraska−Lincoln, Lincoln, Nebraska 68583, United States
| | - Jiantao Guo
- Department
of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
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44
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Koh M, Nasertorabi F, Han GW, Stevens RC, Schultz PG. Generation of an Orthogonal Protein–Protein Interface with a Noncanonical Amino Acid. J Am Chem Soc 2017; 139:5728-5731. [DOI: 10.1021/jacs.7b02273] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Minseob Koh
- Department
of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - Fariborz Nasertorabi
- Department
of Biological Sciences, Bridge Institute, University of Southern California, 3430 S Vermont Avenue, Los
Angeles, California 90089, United States
| | - Gye Won Han
- Department
of Biological Sciences, Bridge Institute, University of Southern California, 3430 S Vermont Avenue, Los
Angeles, California 90089, United States
| | - Raymond C. Stevens
- Department
of Biological Sciences, Bridge Institute, University of Southern California, 3430 S Vermont Avenue, Los
Angeles, California 90089, United States
| | - Peter G. Schultz
- Department
of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
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45
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Guo D. A novel strategy to generate virus vaccines with expanded genetic codes. SCIENCE CHINA-LIFE SCIENCES 2017; 60:555-557. [PMID: 28299577 PMCID: PMC7092380 DOI: 10.1007/s11427-016-9010-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 01/17/2017] [Indexed: 12/01/2022]
Affiliation(s)
- Deyin Guo
- School of Basic Medicine (Shenzhen), Sun Yat-sen University, Guangdong, 510080, China. .,School of Basic Medical Sciences, Wuhan University, Wuhan, 430072, China.
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46
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Wang N, Yuan Z, Niu W, Li Q, Guo J. Synthetic biology approach for the development of conditionally replicating HIV-1 vaccine. JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY (OXFORD, OXFORDSHIRE : 1986) 2017; 92:455-462. [PMID: 28983143 PMCID: PMC5624719 DOI: 10.1002/jctb.5174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
While the combined antiretroviral therapy has resulted in a significant decrease in HIV-1 related morbidity and mortality, the HIV-1 pandemic has not been substantially averted. To curtail the 2.4 million new infections each year, a prophylactic HIV-1 vaccine is urgently needed. This review first summarizes four major completed clinical efficacy trials of prophylactic HIV-1 vaccine and their outcomes. Next, it discusses several other approaches that have not yet advanced to clinical efficacy trials, but provided valuable insights into vaccine design. Among them, live-attenuated vaccines (LAVs) provided excellent protection in a non-human primate model. However, safety concerns have precluded the current version of LAVs from clinical application. As the major component of this review, two synthetic biology approaches for improving the safety of HIV-1 LAVs through controlling HIV-1 replication are discussed. Particular focus is on a novel approach that uses unnatural amino acid-mediated suppression of amber nonsense codon to generate conditionally replicating HIV-1 variants. The objective is to attract more attention towards this promising research field and to provoke creative designs and innovative utilization of the two control strategies.
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Affiliation(s)
- Nanxi Wang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Zhe Yuan
- Nebraska Center for Virology & School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Wei Niu
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Qingsheng Li
- Nebraska Center for Virology & School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
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47
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Si L, Xu H, Zhou X, Zhang Z, Tian Z, Wang Y, Wu Y, Zhang B, Niu Z, Zhang C, Fu G, Xiao S, Xia Q, Zhang L, Zhou D. Generation of influenza A viruses as live but replication-incompetent virus vaccines. Science 2016; 354:1170-1173. [DOI: 10.1126/science.aah5869] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/08/2016] [Indexed: 01/16/2023]
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48
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Xiao H, Schultz PG. At the Interface of Chemical and Biological Synthesis: An Expanded Genetic Code. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023945. [PMID: 27413101 DOI: 10.1101/cshperspect.a023945] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The ability to site-specifically incorporate noncanonical amino acids (ncAAs) with novel structures into proteins in living cells affords a powerful tool to investigate and manipulate protein structure and function. More than 200 ncAAs with diverse biological, chemical, and physical properties have been genetically encoded in response to nonsense or frameshift codons in both prokaryotic and eukaryotic organisms with high fidelity and efficiency. In this review, recent advances in the technology and its application to problems in protein biochemistry, cellular biology, and medicine are highlighted.
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Affiliation(s)
- Han Xiao
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Peter G Schultz
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037 California Institute for Biomedical Research, La Jolla, California 92037
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49
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Recent advances in the molecular design of synthetic vaccines. Nat Chem 2015; 7:952-60. [DOI: 10.1038/nchem.2396] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 10/13/2015] [Indexed: 01/07/2023]
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Wang N, Ju T, Niu W, Guo J. Fine-tuning interaction between aminoacyl-tRNA synthetase and tRNA for efficient synthesis of proteins containing unnatural amino acids. ACS Synth Biol 2015; 4:207-12. [PMID: 24847685 PMCID: PMC4384836 DOI: 10.1021/sb500195w] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
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By
using a directed evolution approach, we have identified aminoacyl-tRNA
synthetase variants with significantly enhanced activity for the incorporation
of unnatural amino acids into proteins in response to the amber nonsense
codon in bacteria. We demonstrated that the optimization of anticodon
recognition of tRNA by aminoacyl-tRNA synthetase led to improved incorporation
efficiency that is unnatural amino acid-specific. The findings will
facilitate the creation of an optimized system for the genetic incorporation
of unnatural amino acids in bacteria.
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Affiliation(s)
- Nanxi Wang
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Tong Ju
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Wei Niu
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Jiantao Guo
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| |
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