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Tian G, Li X, Li XD. Genetically Encoded Epitope Tag for Probing Lysine Acylation-Mediated Protein-Protein Interactions. ACS Chem Biol 2024; 19:1376-1386. [PMID: 38829775 DOI: 10.1021/acschembio.4c00240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Histone lysine acetylation (Kac) and crotonylation (Kcr) marks mediate the recruitment of YEATS domains to chromatin. In this way, YEATS domain-containing proteins such as AF9 participate in the regulation of DNA-templated processes. Our previous study showed that the replacement of Kac/Kcr by a 2-furancarbonyllysine (Kfu) residue led to greatly enhanced affinity toward the AF9 YEATS domain, rendering Kfu-containing peptides useful chemical tools to probe the AF9 YEATS-Kac/Kcr interactions. Here, we report the genetic incorporation of Kfu in Escherichia coli and mammalian cells through the amber codon suppression technology. We develop a Kfu-containing epitope tag, termed RAY-tag, which can robustly and selectively engage with the AF9 YEATS domain in vitro and in cellulo. We further demonstrate that the fusion of RAY-tag to different protein modules, including fluorescent proteins and DNA binding proteins, can facilitate the interrogation of the histone lysine acylation-mediated recruitment of the AF9 YEATS domain in different biological contexts.
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Affiliation(s)
- Gaofei Tian
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong 999077, China
| | - Xin Li
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518107, China
| | - Xiang David Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong 999077, China
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2
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Gan Q, Fan C. Orthogonal Translation for Site-Specific Installation of Post-translational Modifications. Chem Rev 2024; 124:2805-2838. [PMID: 38373737 PMCID: PMC11230630 DOI: 10.1021/acs.chemrev.3c00850] [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: 02/21/2024]
Abstract
Post-translational modifications (PTMs) endow proteins with new properties to respond to environmental changes or growth needs. With the development of advanced proteomics techniques, hundreds of distinct types of PTMs have been observed in a wide range of proteins from bacteria, archaea, and eukarya. To identify the roles of these PTMs, scientists have applied various approaches. However, high dynamics, low stoichiometry, and crosstalk between PTMs make it almost impossible to obtain homogeneously modified proteins for characterization of the site-specific effect of individual PTM on target proteins. To solve this problem, the genetic code expansion (GCE) strategy has been introduced into the field of PTM studies. Instead of modifying proteins after translation, GCE incorporates modified amino acids into proteins during translation, thus generating site-specifically modified proteins at target positions. In this review, we summarize the development of GCE systems for orthogonal translation for site-specific installation of PTMs.
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Affiliation(s)
- Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas 72701, United States
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3
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Rosandić M, Paar V. The Evolution of Life Is a Road Paved with the DNA Quadruplet Symmetry and the Supersymmetry Genetic Code. Int J Mol Sci 2023; 24:12029. [PMID: 37569405 PMCID: PMC10418607 DOI: 10.3390/ijms241512029] [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: 06/13/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Symmetries have not been completely determined and explained from the discovery of the DNA structure in 1953 and the genetic code in 1961. We show, during 10 years of investigation and research, our discovery of the Supersymmetry Genetic Code table in the form of 2 × 8 codon boxes, quadruplet DNA symmetries, and the classification of trinucleotides/codons, all built with the same physiochemical double mirror symmetry and Watson-Crick pairing. We also show that single-stranded RNA had the complete code of life in the form of the Supersymmetry Genetic Code table simultaneously with instructions of codons' relationship as to how to develop the DNA molecule on the principle of Watson-Crick pairing. We show that the same symmetries between the genetic code and DNA quadruplet are highly conserved during the whole evolution even between phylogenetically distant organisms. In this way, decreasing disorder and entropy enabled the evolution of living beings up to sophisticated species with cognitive features. Our hypothesis that all twenty amino acids are necessary for the origin of life on the Earth, which entirely changes our view on evolution, confirms the evidence of organic natural amino acids from the extra-terrestrial asteroid Ryugu, which is nearly as old as our solar system.
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Affiliation(s)
- Marija Rosandić
- Department of Internal Medicine, University Hospital Centre Zagreb, (Ret.), 10000 Zagreb, Croatia
- Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia;
| | - Vladimir Paar
- Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia;
- Physics Department, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
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Niu W, Guo J. Co-translational Installation of Posttranslational Modifications by Non-canonical Amino Acid Mutagenesis. Chembiochem 2023; 24:e202300039. [PMID: 36853967 PMCID: PMC10202221 DOI: 10.1002/cbic.202300039] [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: 01/18/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/02/2023]
Abstract
Protein posttranslational modifications (PTMs) play critical roles in regulating cellular activities. Here we provide a survey of genetic code expansion (GCE) methods that were applied in the co-translational installation and studies of PTMs through noncanonical amino acid (ncAA) mutagenesis. We begin by reviewing types of PTM that have been installed by GCE with a focus on modifications of tyrosine, serine, threonine, lysine, and arginine residues. We also discuss examples of applying these methods in biological studies. Finally, we end the piece with a short discussion on the challenges and the opportunities of the field.
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Affiliation(s)
- Wei Niu
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, N-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
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Update of the Pyrrolysyl-tRNA Synthetase/tRNA Pyl Pair and Derivatives for Genetic Code Expansion. J Bacteriol 2023; 205:e0038522. [PMID: 36695595 PMCID: PMC9945579 DOI: 10.1128/jb.00385-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The cotranslational incorporation of pyrrolysine (Pyl), the 22nd proteinogenic amino acid, into proteins in response to the UAG stop codon represents an outstanding example of natural genetic code expansion. Genetic encoding of Pyl is conducted by the pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA, tRNAPyl. Owing to the high tolerance of PylRS toward diverse amino acid substrates and great orthogonality in various model organisms, the PylRS/tRNAPyl-derived pairs are ideal for genetic code expansion to insert noncanonical amino acids (ncAAs) into proteins of interest. Since the discovery of cellular components involved in the biosynthesis and genetic encoding of Pyl, synthetic biologists have been enthusiastic about engineering PylRS/tRNAPyl-derived pairs to rewrite the genetic code of living cells. Recently, considerable progress has been made in understanding the molecular phylogeny, biochemical properties, and structural features of the PylRS/tRNAPyl pair, guiding its further engineering and optimization. In this review, we cover the basic and updated knowledge of the PylRS/tRNAPyl pair's unique characteristics that make it an outstanding tool for reprogramming the genetic code. In addition, we summarize the recent efforts to create efficient and (mutually) orthogonal PylRS/tRNAPyl-derived pairs for incorporation of diverse ncAAs by genome mining, rational design, and advanced directed evolution methods.
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Van Raad D, Huber T. eCell Technology for Cell-Free Protein Synthesis, Biosensing, and Remediation. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:129-146. [PMID: 37306701 DOI: 10.1007/10_2023_225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The eCell technology is a recently introduced, specialized protein production platform with uses in a multitude of biotechnological applications. This chapter summarizes the use of eCell technology in four selected application areas. Firstly, for detecting heavy metal ions, specifically mercury, in an in vitro protein expression system. Results show improved sensitivity and lower limit of detection compared to comparable in vivo systems. Secondly, eCells are semipermeable, stable, and can be stored for extended periods of time, making them a portable and accessible technology for bioremediation of toxicants in extreme environments. Thirdly and fourthly, applications of eCell technology are shown to facilitate expression of correctly folded disulfide-rich proteins and incorporate chemically interesting derivatives of amino acids into proteins which are toxic to in vivo protein expression. Overall, eCell technology presents a cost-effective and efficient method for biosensing, bioremediation, and protein production.
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Affiliation(s)
- Damian Van Raad
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia.
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Allen GL, Grahn AK, Kourentzi K, Willson RC, Waldrop S, Guo J, Kay BK. Expanding the chemical diversity of M13 bacteriophage. Front Microbiol 2022; 13:961093. [PMID: 36003937 PMCID: PMC9393631 DOI: 10.3389/fmicb.2022.961093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/04/2022] [Indexed: 11/21/2022] Open
Abstract
Bacteriophage M13 virions are very stable nanoparticles that can be modified by chemical and genetic methods. The capsid proteins can be functionalized in a variety of chemical reactions without loss of particle integrity. In addition, Genetic Code Expansion (GCE) permits the introduction of non-canonical amino acids (ncAAs) into displayed peptides and proteins. The incorporation of ncAAs into phage libraries has led to the discovery of high-affinity binders with low nanomolar dissociation constant (K D) values that can potentially serve as inhibitors. This article reviews how bioconjugation and the incorporation of ncAAs during translation have expanded the chemistry of peptides and proteins displayed by M13 virions for a variety of purposes.
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Affiliation(s)
| | | | - Katerina Kourentzi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
| | - Richard C. Willson
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
| | - Sean Waldrop
- Department of Chemistry, University of Nebraska at Lincoln, Lincoln, NE, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska at Lincoln, Lincoln, NE, United States
| | - Brian K. Kay
- Tango Biosciences, Inc., Chicago, IL, United States
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Nipun VB, Amin KA. Recent Advances in Protein Kinase CK2, a Potential Therapeutic Target in Cancer. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022; 48:919-931. [DOI: 10.1134/s1068162022050144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- V. B. Nipun
- Cancer Research Center, Shantou University Medical Collage, Shantou, Guangdong, 515041, PR China
- Department of Chemistry, Faculty of Science, University of Imam Abdulrahman Bin Faisal university, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - K. A. Amin
- Department of Chemistry, Faculty of Science, University of Imam Abdulrahman Bin Faisal university, P.O. Box 1982, Dammam, 31441, Saudi Arabia
- Basic and Applied Scientific Research Center, Imam Abdulrahman Bin Faisal university, P.O. Box 1982, Dammam, 31441, Saudi Arabia
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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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Applications of genetic code expansion in studying protein post-translational modification. J Mol Biol 2021; 434:167424. [PMID: 34971673 DOI: 10.1016/j.jmb.2021.167424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 01/18/2023]
Abstract
Various post-translational modifications can naturally occur on proteins, regulating the activity, subcellular localization, interaction, or stability of the proteins. However, it can be challenging to decipher the biological implication or physiological roles of site-specific modifications due to their dynamic and sub-stoichiometric nature. Genetic code expansion method, relying on an orthogonal aminoacyl-tRNA synthetase/tRNA pair, enables site-specific incorporation of non-canonical amino acids. Here we focus on the application of genetic code expansion to study site-specific protein post-translational modification in vitro and in vivo. After a brief introduction, we discuss possibilities of incorporating non-canonical amino acids containing post-translational modifications or their mimics into target proteins. This approach is applicable for Ser/Thr/Tyr phosphorylation, Tyr sulfation and nitration, Lys acetylation and acylation, Lys/His mono-methylation, as well as Arg citrullination. The next section describes the use of a precursor non-canonical amino acid followed by chemical and/or enzymatic reactions to afford the desired modification, such as Cys/Lys acylation, ubiquitin and ubiquitin-like modifications, as well as Lys/Gln methylation. We also discuss means for functional regulation of enzymes involving in post-translational modifications through genetically incorporated non-canonical amino acids. Lastly, the limitations and perspectives of genetic code expansion in studying protein post-translational modification are described.
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