1
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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 DOI: 10.1021/acs.chemrev.3c00938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 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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Jann C, Giofré S, Bhattacharjee R, Lemke EA. Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 2024; 124:10281-10362. [PMID: 39120726 DOI: 10.1021/acs.chemrev.3c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.
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Affiliation(s)
- Cosimo Jann
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Sabrina Giofré
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Rajanya Bhattacharjee
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB International PhD Programme (IPP), 55128 Mainz, Germany
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
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3
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Mueller D, Baettig R, Kuenzl T, Rodríguez-Robles E, Roberts TM, Marlière P, Panke S. Characterizing and Tailoring the Substrate Profile of a γ-Glutamyltransferase Variant. ACS Synth Biol 2024; 13:2969-2981. [PMID: 39134057 PMCID: PMC11421214 DOI: 10.1021/acssynbio.4c00364] [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: 05/29/2024] [Revised: 07/11/2024] [Accepted: 07/29/2024] [Indexed: 09/21/2024]
Abstract
Xenobiology is an emerging field that focuses on the extension and redesign of biological systems through the use of laboratory-derived xenomolecules, which are molecules that are new to the metabolism of the cell. Despite the enormous potential of using xenomolecules in living organisms, most noncanonical building blocks still need to be supplied externally, and often poor uptake into cells limits wider applicability. To improve the cytosolic availability of noncanonical molecules, a synthetic transport system based on portage transport was developed, in which molecules of interest "cargo" are linked to a synthetic transport vector that enables piggyback transport through the alkylsulfonate transporter (SsuABC) of Escherichia coli. Upon cytosolic delivery, the vector-cargo conjugate is enzymatically cleaved by GGTxe, leading to the release of the cargo molecule. To deepen our understanding of the synthetic transport system, we focused on the characterization and further development of the enzymatic cargo release step. Hence, the substrate scope of GGTxe was characterized using a library of structurally diverse vector-cargo conjugates and MS/MS-based quantification of hydrolysis products in a kinetic manner. The resulting substrate tolerance characterization revealed that vector-amino acid conjugates were significantly unfavored. To overcome this shortcoming, a selection system based on metabolic auxotrophy complementation and directed evolution of GGTxe was established. In a directed evolution campaign, we improved the enzymatic activity of GGTxe for vector-amino acid conjugates and revealed the importance of residue D386 in the cargo unloading step.
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Affiliation(s)
- David Mueller
- Department
of Biosystems Science and Engineering, ETH
Zürich, 4056 Basel, Switzerland
| | - Remo Baettig
- Department
of Biosystems Science and Engineering, ETH
Zürich, 4056 Basel, Switzerland
| | - Tilmann Kuenzl
- Department
of Biosystems Science and Engineering, ETH
Zürich, 4056 Basel, Switzerland
| | | | | | - Philippe Marlière
- TESSSI,
The European Syndicate of Synthetic Scientists and Industrialists, 75002 Paris, France
| | - Sven Panke
- Department
of Biosystems Science and Engineering, ETH
Zürich, 4056 Basel, Switzerland
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4
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [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: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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5
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Bai J, Zou J, Cao Y, Du Y, Chen T. Recognition of an Unnatural Base Pair by Tool Enzymes from Bacteriophages and Its Application in the Enzymatic Preparation of DNA with an Expanded Genetic Alphabet. ACS Synth Biol 2023; 12:2676-2690. [PMID: 37590442 DOI: 10.1021/acssynbio.3c00250] [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: 08/19/2023]
Abstract
Unnatural base pairs (UBPs) have been developed to expand the genetic alphabet in vitro and in vivo. UBP dNaM-dTPT3 and its analogues have been successfully used to construct the first set of semi-synthetic organisms, which suggested the great potential of UBPs to be used for producing novel synthetic biological parts. Two prerequisites for doing so are the facile manipulation of DNA containing UBPs with common tool enzymes, including DNA polymerases and ligases, and the easy availability of UBP-containing DNA strands. Besides, for the application of UBPs in phage synthetic biology, the recognition of UBPs by phage enzymes is essential. Here, we first explore the recognition of dNaM-dTPT3 by a family B DNA polymerase from bacteriophage, T4 DNA polymerase D219A. Results from primer extension, steady-state kinetics, and gap-filling experiments suggest that T4 DNA polymerase D219A can efficiently and faithfully replicate dNaM-dTPT3, and efficiently fill a gap by inserting dTPT3TP or its analogues opposite dNaM. We then systematically explore the recognition of dNaM-dTPT3 and its analogues by different DNA ligases from bacteriophages and find that these DNA ligases are generally able to efficiently ligate the DNA nick next to dNaM-dTPT3 or its analogues, albeit with slightly different efficiencies. These results suggest more enzymatic tools for the manipulation of dNaM-dTPT3 and indicate the potential use of dNaM-dTPT3 for expanding the genetic alphabet in bacteriophages. Based on these results, we next develop and comprehensively optimize an upgraded method for enzymatic preparation of unnatural nucleobase (UB)-containing DNA oligonucleotides with good simplicity and universality.
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Affiliation(s)
- Jingsi Bai
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jinrong Zou
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yijun Cao
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
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6
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Cao Y, Bai J, Zou J, Du Y, Chen T. One-Pot Enzymatic Preparation of Oligonucleotides with an Expanded Genetic Alphabet via Controlled Pause and Restart of Primer Extension: Making Unnatural Out of Natural. ACS Synth Biol 2023; 12:2691-2706. [PMID: 37672623 DOI: 10.1021/acssynbio.3c00258] [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: 09/08/2023]
Abstract
The genetic alphabet of life has been dramatically expanded via the development of unnatural base pairs (UBPs) that work as efficiently as natural base pairs in the storage and retrieval of genetic information. Among the most predominant UBPs, dNaM-dTPT3 and its analogues have been successfully employed to build semisynthetic cells with a functional six-letter genome. With the rapidly growing applications of UBPs in vitro and in vivo, there is an ever-increasing demand for DNA oligonucleotides containing unnatural bases (UBs) at desired positions. Conventional solid-phase synthesis of oligonucleotides has intrinsic limitations and needs to use unstable unnatural phosphoramidites and a DNA synthesizer, so it does not meet the daily urgent requirement for a few UB-containing DNA oligonucleotides in the laboratory. In this work, we develop a one-pot enzymatic method for preparing dNaM- or dTPT3-containing DNA oligonucleotides via controlled pause and restart of primer extension mediated by Klenow fragment (exo-). By systematic optimization of the reaction conditions, high efficiencies and product purities have been achieved. The universality of this method for preparing DNA oligonucleotides containing dNaM or dTPT3 in different sequence contexts is also demonstrated. This method allows convenient production of an arbitrary UB-containing DNA oligonucleotide in a single test tube with only two natural DNA oligonucleotides, stable nucleoside triphosphates, Klenow fragment (exo-), and other common reagents in the laboratory, providing the lowest cost and the highest simplicity for the enzymatic preparation of UB-containing oligonucleotides. Clearly, this method has great potential to facilitate the in vitro and in vivo applications of the UBPs.
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Affiliation(s)
- Yijun Cao
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jingsi Bai
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jinrong Zou
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
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7
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Richards NGJ, Bearne SL, Goto Y, Parker EJ. Reactivity and mechanism in chemical and synthetic biology. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220023. [PMID: 36633278 PMCID: PMC9835593 DOI: 10.1098/rstb.2022.0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 01/13/2023] Open
Abstract
Physical organic chemistry and mechanistic thinking provide a strong intellectual framework for understanding the chemical logic of evolvable informational macromolecules and metabolic transformations in living organisms. These concepts have also led to numerous successes in designing and applying tools to delineate biological function in health and disease, chemical ecology and possible alternative chemistries employed by extraterrestrial life. A symposium at the 2020 Pacifichem meeting was scheduled in December 2020 to discuss designing and exploiting expanded genetic alphabets, methods to understand the biosynthesis of natural products and re-engineering primary metabolism in bacteria. The COVID-19 pandemic led to postponement of in-person discussions, with the symposium eventually being held on 20-21 December 2021 as an online event. This issue is a written record of work presented on biosynthetic pathways and enzyme catalysis, engineering microorganisms with new metabolic capabilities, and the synthesis of non-canonical, nucleobases for medical applications and for studies of alternate chemistries for living organisms. The variety of opinion pieces, reviews and original research articles provide a starting point for innovations that clarify how complex biological systems emerge from the rules of chemical reactivity and mechanism. This article is part of the themed issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Nigel G. J. Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
- Foundation for Advanced Molecular Evolution, 13709 Progress Boulevard, Alachua, FL 32615, USA
| | - Stephen L. Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, Canada B3H 4R2
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia, Canada B3H 4R2
| | - Yuki Goto
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Emily J. Parker
- Department of Chemistry, Victoria University of Wellington, Kelburn Parade, Wellington 6012, New Zealand
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8
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Wang G, He C, Zou J, Liu J, Du Y, Chen T. Enzymatic Synthesis of DNA with an Expanded Genetic Alphabet Using Terminal Deoxynucleotidyl Transferase. ACS Synth Biol 2022; 11:4142-4155. [PMID: 36455255 DOI: 10.1021/acssynbio.2c00456] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Development of unnatural base pairs (UBPs) has significantly expanded the genetic alphabet both in vitro and in vivo and led to numerous potential applications in the biotechnology and biopharmaceutical industry. Efficient synthesis of oligonucleotides containing unnatural nucleobases is undoubtedly an essential prerequisite for making full use of the UBPs, and de novo synthesis of oligonucleotides with terminal deoxynucleotidyl transferases (TdTs) has emerged as a method of great potential to overcome limitations of traditional solid-phase synthesis. Herein, we report the efficient template-independent incorporation of nucleotides of unnatural nucleobases dTPT3 and dNaM, which have been designed to make one of the most successful UBPs to date, dTPT3-dNaM, into DNA oligonucleotides with a TdT enzyme under optimized conditions. We also demonstrate the efficient TdT incorporation of dTPT3 derivatives with different functional linkers into oligonucleotides for orthogonal labeling of nucleic acids and applications thereof. The development of a method for the daily laboratory preparation of DNAs with UBPs at arbitrary sites with the assistance of TdT is also described.
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Affiliation(s)
- Guangyuan Wang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Chuanping He
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jinrong Zou
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jiayun Liu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
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9
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Sun L, Ma X, Zhang B, Qin Y, Ma J, Du Y, Chen T. From polymerase engineering to semi-synthetic life: artificial expansion of the central dogma. RSC Chem Biol 2022; 3:1173-1197. [PMID: 36320892 PMCID: PMC9533422 DOI: 10.1039/d2cb00116k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Nucleic acids have been extensively modified in different moieties to expand the scope of genetic materials in the past few decades. While the development of unnatural base pairs (UBPs) has expanded the genetic information capacity of nucleic acids, the production of synthetic alternatives of DNA and RNA has increased the types of genetic information carriers and introduced novel properties and functionalities into nucleic acids. Moreover, the efforts of tailoring DNA polymerases (DNAPs) and RNA polymerases (RNAPs) to be efficient unnatural nucleic acid polymerases have enabled broad application of these unnatural nucleic acids, ranging from production of stable aptamers to evolution of novel catalysts. The introduction of unnatural nucleic acids into living organisms has also started expanding the central dogma in vivo. In this article, we first summarize the development of unnatural nucleic acids with modifications or alterations in different moieties. The strategies for engineering DNAPs and RNAPs are then extensively reviewed, followed by summarization of predominant polymerase mutants with good activities for synthesizing, reverse transcribing, or even amplifying unnatural nucleic acids. Some recent application examples of unnatural nucleic acids with their polymerases are then introduced. At the end, the approaches of introducing UBPs and synthetic genetic polymers into living organisms for the creation of semi-synthetic organisms are reviewed and discussed.
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Affiliation(s)
- Leping Sun
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Xingyun Ma
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Binliang Zhang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Yanjia Qin
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Jiezhao Ma
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
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10
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Kimoto M, Hirao I. Genetic Code Engineering by Natural and Unnatural Base Pair Systems for the Site-Specific Incorporation of Non-Standard Amino Acids Into Proteins. Front Mol Biosci 2022; 9:851646. [PMID: 35685243 PMCID: PMC9171071 DOI: 10.3389/fmolb.2022.851646] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/25/2022] [Indexed: 12/21/2022] Open
Abstract
Amino acid sequences of proteins are encoded in nucleic acids composed of four letters, A, G, C, and T(U). However, this four-letter alphabet coding system limits further functionalities of proteins by the twenty letters of amino acids. If we expand the genetic code or develop alternative codes, we could create novel biological systems and biotechnologies by the site-specific incorporation of non-standard amino acids (or unnatural amino acids, unAAs) into proteins. To this end, new codons and their complementary anticodons are required for unAAs. In this review, we introduce the current status of methods to incorporate new amino acids into proteins by in vitro and in vivo translation systems, by focusing on the creation of new codon-anticodon interactions, including unnatural base pair systems for genetic alphabet expansion.
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Affiliation(s)
| | - Ichiro Hirao
- *Correspondence: Michiko Kimoto, ; Ichiro Hirao,
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11
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Liu T. Recent advances in Genetic Code Expansion: from cell engineering to protein design. J Mol Biol 2022; 434:167565. [PMID: 35341745 DOI: 10.1016/j.jmb.2022.167565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
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