1
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Niu W, Guo J. Cellular Site-Specific Incorporation of Noncanonical Amino Acids in Synthetic Biology. Chem Rev 2024. [PMID: 39207844 DOI: 10.1021/acs.chemrev.3c00938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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2
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Choi J, Ahn J, Bae J, Yoon M, Yun H, Koh M. Designing a Novel Temperature- and Noncanonical Amino Acid-Controlled Biological Logic Gate in Escherichia coli. ACS Synth Biol 2024; 13:2587-2599. [PMID: 39110782 DOI: 10.1021/acssynbio.4c00423] [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: 08/17/2024]
Abstract
Genetic code expansion (GCE) is a powerful strategy that expands the genetic code of an organism for incorporating noncanonical amino acids into proteins using engineered tRNAs and aminoacyl-tRNA synthetases (aaRSs). While GCE has opened up new possibilities for synthetic biology, little is known about the potential side effects of exogenous aaRS/tRNA pairs. In this study, we investigated the impact of exogenous aaRS and amber suppressor tRNA on gene expression in Escherichia coli. We discovered that in DH10β ΔcyaA, transformed with the F1RP/F2P two-hybrid system, the high consumption rate of cellular adenosine triphosphate by exogenous aaRS/tRNA at elevated temperatures induces temperature sensitivity in the expression of genes regulated by the cyclic AMP receptor protein (CRP). We harnessed this temperature sensitivity to create a novel biological AND gate in E. coli, responsive to both p-benzoylphenylalanine (BzF) and low temperature, using a BzF-dependent variant of E. coli chorismate mutase and split subunits of Bordetella pertussis adenylate cyclase. Our study provides new insights into the unexpected effects of exogenous aaRS/tRNA pairs and offers a new approach for constructing a biological logic gate.
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Affiliation(s)
- Jongdoo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Jiyeun Ahn
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Jieun Bae
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Moonsang Yoon
- College of Pharmacy and Research Institute for Drug Development, Pusan National University, Busan 46241, Republic of Korea
| | - Hwayoung Yun
- College of Pharmacy and Research Institute for Drug Development, Pusan National University, Busan 46241, Republic of Korea
| | - Minseob Koh
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
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3
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Gómez-Tatay L, Hernández-Andreu JM. Xenobiology for the Biocontainment of Synthetic Organisms: Opportunities and Challenges. Life (Basel) 2024; 14:996. [PMID: 39202738 PMCID: PMC11355180 DOI: 10.3390/life14080996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/07/2024] [Accepted: 08/09/2024] [Indexed: 09/03/2024] Open
Abstract
Since the development of recombinant DNA technologies, the need to establish biosafety and biosecurity measures to control genetically modified organisms has been clear. Auxotrophies, or conditional suicide switches, have been used as firewalls to avoid horizontal or vertical gene transfer, but their efficacy has important limitations. The use of xenobiological systems has been proposed as the ultimate biosafety tool to circumvent biosafety problems in genetically modified organisms. Xenobiology is a subfield of Synthetic Biology that aims to construct orthogonal biological systems based on alternative biochemistries. Establishing true orthogonality in cell-based or cell-free systems promises to improve and assure that we can progress in synthetic biology safely. Although a wide array of strategies for orthogonal genetic systems have been tested, the construction of a host harboring fully orthogonal genetic system, with all parts operating in an orchestrated, integrated, and controlled manner, still poses an extraordinary challenge for researchers. In this study, we have performed a thorough review of the current literature to present the main advances in the use of xenobiology as a strategy for biocontainment, expanding on the opportunities and challenges of this field of research.
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Affiliation(s)
- Lucía Gómez-Tatay
- Institute of Life Sciences, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain;
| | - José Miguel Hernández-Andreu
- Grupo de Investigación en Medicina Molecular y Mitocondrial, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain
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4
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Pigula M, Lai YC, Koh M, Diercks CS, Rogers TF, Dik DA, Schultz PG. An unnatural amino acid dependent, conditional Pseudomonas vaccine prevents bacterial infection. Nat Commun 2024; 15:6766. [PMID: 39117651 PMCID: PMC11310302 DOI: 10.1038/s41467-024-50843-7] [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: 02/14/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Live vaccines are ideal for inducing immunity but suffer from the need to attenuate their pathogenicity or replication to preclude the possibility of escape. Unnatural amino acids (UAAs) provide a strategy to engineer stringent auxotrophies, yielding conditionally replication incompetent live bacteria with excellent safety profiles. Here, we engineer Pseudomonas aeruginosa to maintain auxotrophy for the UAA p-benzoyl-L-phenylalanine (BzF) through its incorporation into the essential protein DnaN. In vivo evolution using an Escherichia coli-based two-hybrid selection system enabled engineering of a mutant DnaN homodimeric interface completely dependent on a BzF-specific interaction. This engineered strain, Pa Vaccine, exhibits undetectable escape frequency (<10-11) and shows excellent safety in naïve mice. Animals vaccinated via intranasal or intraperitoneal routes are protected from lethal challenge with pathogenic P. aeruginosa PA14. These results establish UAA-auxotrophic bacteria as promising candidates for bacterial vaccine therapy and outline a platform for expanding this technology to diverse bacterial pathogens.
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Affiliation(s)
- Michael Pigula
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Yen-Chung Lai
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Minseob Koh
- Department of Chemistry, Pusan National University, Busan, Korea
| | | | - Thomas F Rogers
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - David A Dik
- Department of Biology, Calibr-Skaggs Institute for Innovative Medicines, Scripps Research, La Jolla, CA, USA.
| | - Peter G Schultz
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
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5
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Jansen S, Mayer C. A Robust Growth-Based Selection Platform to Evolve an Enzyme via Dependency on Noncanonical Tyrosine Analogues. JACS AU 2024; 4:1583-1590. [PMID: 38665651 PMCID: PMC11040555 DOI: 10.1021/jacsau.4c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 04/28/2024]
Abstract
Growth-based selections evaluate the fitness of individual organisms at a population level. In enzyme engineering, such growth selections allow for the rapid and straightforward identification of highly efficient biocatalysts from extensive libraries. However, selection-based improvement of (synthetically useful) biocatalysts is challenging, as they require highly dependable strategies that artificially link their activities to host survival. Here, we showcase a robust and scalable growth-based selection platform centered around the complementation of noncanonical amino acid-dependent bacteria. Specifically, we demonstrate how serial passaging of populations featuring millions of carbamoylase variants autonomously selects biocatalysts with up to 90,000-fold higher initial rates. Notably, selection of replicate populations enriched diverse biocatalysts, which feature distinct amino acid motifs that drastically boost carbamoylase activity. As beneficial substitutions also originated from unintended copying errors during library preparation or cell division, we anticipate that our growth-based selection platform will be applicable to the continuous, autonomous evolution of diverse biocatalysts in the future.
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Affiliation(s)
- Suzanne
C. Jansen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Clemens Mayer
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
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6
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Chang T, Ding W, Yan S, Wang Y, Zhang H, Zhang Y, Ping Z, Zhang H, Huang Y, Zhang J, Wang D, Zhang W, Xu X, Shen Y, Fu X. A robust yeast biocontainment system with two-layered regulation switch dependent on unnatural amino acid. Nat Commun 2023; 14:6487. [PMID: 37838746 PMCID: PMC10576815 DOI: 10.1038/s41467-023-42358-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023] Open
Abstract
Synthetic auxotrophy in which cell viability depends on the presence of an unnatural amino acid (unAA) provides a powerful strategy to restrict unwanted propagation of genetically modified organisms (GMOs) in open environments and potentially prevent industrial espionage. Here, we describe a generic approach for robust biocontainment of budding yeast dependent on unAA. By understanding escape mechanisms, we specifically optimize our strategies by introducing designed "immunity" to the generation of amber-suppressor tRNAs and developing the transcriptional- and translational-based biocontainment switch. We further develop a fitness-oriented screening method to easily obtain multiplex safeguard strains that exhibit robust growth and undetectable escape frequency (<~10-9) on solid media for 14 days. Finally, we show that employing our multiplex safeguard system could restrict the proliferation of strains of interest in a real fermentation scenario, highlighting the great potential of our yeast biocontainment strategy to protect the industrial proprietary strains.
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Affiliation(s)
- Tiantian Chang
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, Shenzhen, 518083, China
| | - Weichao Ding
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Shirui Yan
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Yun Wang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Haoling Zhang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Yu Zhang
- BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Zhi Ping
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Huiming Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, Shenzhen, 518083, China
| | - Yijian Huang
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, Shenzhen, 518083, China
| | - Jiahui Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, Shenzhen, 518083, China
| | - Dan Wang
- Guangdong Provincial Key Laboratory of Interdisciplinary Research and Application for Data Science, BNU-HKBU United International College, Zhuhai, 519087, China
- BNU-HKBU United International College, Zhuhai, 519087, China
| | - Wenwei Zhang
- BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Xun Xu
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Yue Shen
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China.
- BGI Research, Shenzhen, 518083, China.
- BGI Research, Changzhou, 213299, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China.
| | - Xian Fu
- BGI Research, Shenzhen, 518083, China.
- BGI Research, Changzhou, 213299, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China.
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7
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Elastin-like polypeptide-based micelles as a promising platform in nanomedicine. J Control Release 2023; 353:713-726. [PMID: 36526018 DOI: 10.1016/j.jconrel.2022.12.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
New and improved nanomaterials are constantly being developed for biomedical purposes. Nanomaterials based on elastin-like polypeptides (ELPs) have increasingly shown potential over the past two decades. These polymers are artificial proteins of which the design is based on human tropoelastin. Due to this similarity, ELP-based nanomaterials are biodegradable and therefore well suited to drug delivery. The assembly of ELP molecules into nanoparticles spontaneously occurs at temperatures above a transition temperature (Tt). The ELP sequence influences both the Tt and the physicochemical properties of the assembled nanomaterial. Nanoparticles with desired properties can hence be designed by choosing the appropriate sequence. A promising class of ELP nanoparticles are micelles assembled from amphiphilic ELP diblock copolymers. Such micelles are generally uniform and well defined. Furthermore, site-specific attachment of cargo to the hydrophobic block results in micelles with the cargo shielded inside their core, while conjugation to the hydrophilic block causes the cargo to reside in the corona where it is available for interactions. Such control over particle design is one of the main contributing factors for the potential of ELP-based micelles as a drug delivery system. Additionally, the micelles are easily loaded with protein or peptide-based cargo by expressing it as a fusion protein. Small molecule drugs and other cargo types can be either covalently conjugated to ELP domains or physically entrapped inside the micelle core. This review aims to give an overview of ELP-based micelles and their applications in nanomedicine.
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8
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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: 8] [Impact Index Per Article: 2.7] [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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9
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Tang H, Zhang P, Luo X. Recent Technologies for Genetic Code Expansion and their Implications on Synthetic Biology Applications. J Mol Biol 2021; 434:167382. [PMID: 34863778 DOI: 10.1016/j.jmb.2021.167382] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/18/2021] [Accepted: 11/24/2021] [Indexed: 02/03/2023]
Abstract
Genetic code expansion (GCE) enables the site-specific incorporation of non-canonical amino acids as novel building blocks for the investigation and manipulation of proteins. The advancement of genetic code expansion has been benefited from the development of synthetic biology, while genetic code expansion also helps to create more synthetic biology tools. In this review, we summarize recent advances in genetic code expansion brought by synthetic biology progresses, including engineering of the translation machinery, genome-wide codon reassignment, and the biosynthesis of non-canonical amino acids. We highlight the emerging application of this technology in construction of new synthetic biology parts, circuits, chassis, and products.
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Affiliation(s)
- Hongting Tang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Pan Zhang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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10
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Abstract
The maturation of chemical synthesis during the 20th century has elevated the discipline from a largely empirical into a rational science. This ability to purposefully craft matter at the molecular level has put chemists in a privileged position to contribute to progress in neighboring natural sciences. Recently, we have witnessed another major advance in the field in which chemists use chemical and biological "synthetic" methods together to alter the structures and properties of biological macromolecules in ways heretofore unimagined. This interdisciplinary approach to synthesis has even allowed us to expand upon the defining characteristics of living organisms at the molecular level. In this perspective, we present a case study for the successful addition of new chemistries to the fundamental processes of the central dogma of molecular biology, exemplified by the expansion of the genetic code.
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Affiliation(s)
- Christian S. Diercks
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- These authors contributed equally
| | - David A. Dik
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- These authors contributed equally
| | - Peter G. Schultz
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Lead contact
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11
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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: 7] [Impact Index Per Article: 2.3] [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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12
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Parker MT, Kunjapur AM. Deployment of Engineered Microbes: Contributions to the Bioeconomy and Considerations for Biosecurity. Health Secur 2021; 18:278-296. [PMID: 32816583 DOI: 10.1089/hs.2020.0010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Engineering at microscopic scales has an immense effect on the modern bioeconomy. Microbes contribute to such disparate markets as chemical manufacturing, fuel production, crop optimization, and pharmaceutical synthesis, to name a few. Due to new and emerging synthetic biology technologies, and the sophistication and control afforded by them, we are on the brink of deploying engineered microbes to not only enhance traditional applications but also to introduce these microbes to sectors, contexts, and formats not previously attempted. In microbially managed medicine, microbial engineering holds promise for increasing efficacy, improving tissue penetration, and sustaining treatment. In the environment, the most effective areas for deployment are in the management of crops and protection of ecosystems. However, caution is warranted before introducing engineered organisms to new environments where they may proliferate without control and could cause unforeseen effects. We summarize ideas and data that can inform identification and assessment of the risks that these tools present to ensure that realistic hazards are described and unrealistic ones do not hinder advancement. Further, because modes of containment are crucial complements to deployment, we describe the state of the art in microbial biocontainment strategies, current gaps, and how these gaps might be addressed through technological advances in synthetic engineering. Collectively, this work highlights engineered microbes as a foundational and expanding facet of the bioeconomy, projects their utility in upcoming deployments outside the laboratory, and identifies knowns and unknowns that will be necessary considerations and points of focus in this endeavor.
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Affiliation(s)
- Michael T Parker
- Michael T. Parker, PhD, is an Assistant Dean, Office of the Dean, Georgetown University, Washington, DC. Aditya M. Kunjapur, PhD, is an Assistant Professor, Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
| | - Aditya M Kunjapur
- Michael T. Parker, PhD, is an Assistant Dean, Office of the Dean, Georgetown University, Washington, DC. Aditya M. Kunjapur, PhD, is an Assistant Professor, Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
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13
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Abstract
![]()
Biocontainment is an essential feature
when deploying genetically
modified organisms (GMOs) in open system applications, as variants
escaping their intended operating environments could negatively impact
ecosystems and human health. To avoid breaches resulting from metabolic
cross-feeding, horizontal gene transfer, and/or genetic mutations,
synthetic auxotrophs have been engineered to become dependent on exogenously
supplied xenobiotics, such as noncanonical amino acids (ncAAs). The
incorporation of these abiological building blocks into essential
proteins constitutes a first step toward constructing xenobiological
barriers between GMOs and their environments. To transition synthetic
auxotrophs further away from familiar biology, we demonstrate how
bacterial growth can be confined by transition-metal complexes that
catalyze the formation of an essential ncAA through new-to-nature
reactions. Specifically, using a homogeneous ruthenium complex enabled
us to localize bacterial growth on solid media, while heterogeneous
palladium nanoparticles could be recycled and deployed up to five
consecutive times to ensure the survival of synthetic auxotrophs in
liquid cultures.
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Affiliation(s)
- Rudy Rubini
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Clemens Mayer
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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14
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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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15
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Conibear AC. Deciphering protein post-translational modifications using chemical biology tools. Nat Rev Chem 2020; 4:674-695. [PMID: 37127974 DOI: 10.1038/s41570-020-00223-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2020] [Indexed: 02/06/2023]
Abstract
Proteins carry out a wide variety of catalytic, regulatory, signalling and structural functions in living systems. Following their assembly on ribosomes and throughout their lifetimes, most eukaryotic proteins are modified by post-translational modifications; small functional groups and complex biomolecules are conjugated to amino acid side chains or termini, and the protein backbone is cleaved, spliced or cyclized, to name just a few examples. These modifications modulate protein activity, structure, location and interactions, and, thereby, control many core biological processes. Aberrant post-translational modifications are markers of cellular stress or malfunction and are implicated in several diseases. Therefore, gaining an understanding of which proteins are modified, at which sites and the resulting biological consequences is an important but complex challenge requiring interdisciplinary approaches. One of the key challenges is accessing precisely modified proteins to assign functional consequences to specific modifications. Chemical biologists have developed a versatile set of tools for accessing specifically modified proteins by applying robust chemistries to biological molecules and developing strategies for synthesizing and ligating proteins. This Review provides an overview of these tools, with selected recent examples of how they have been applied to decipher the roles of a variety of protein post-translational modifications. Relative advantages and disadvantages of each of the techniques are discussed, highlighting examples where they are used in combination and have the potential to address new frontiers in understanding complex biological processes.
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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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