1
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Zhang C, Chen S, Fu X, Dedkova LM, Hecht SM. Enhancement of N-Methyl Amino Acid Incorporation into Proteins and Peptides Using Modified Bacterial Ribosomes and Elongation Factor P. ACS Chem Biol 2024. [PMID: 38769080 DOI: 10.1021/acschembio.4c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
N-Methylated amino acids are constituents of natural bioactive peptides and proteins. Nα-methylated amino acids appear abundantly in natural cyclic peptides, likely due to their constraint of peptide conformation and contribution to peptide stability. Peptides containing Nα-methylated amino acids have long been prepared by chemical synthesis. While such natural peptides are not produced ribosomally, recent ribosomal strategies have afforded Nα-methylated peptides. Presently, we define new strategies for the ribosomal incorporation of Nα-methylated amino acids into peptides and proteins. First, we identify modified ribosomes capable of facilitating the incorporation of six N-methylated amino acids into antibacterial scorpion peptide IsCT. Also synthesized analogously was a protein domain (RRM1) from hnRNP LL; improved yields were observed for nearly all tested N-methylated amino acids. Computational modeling of the ribosomal assembly illustrated how the distortion imposed by N-methylation could be compensated by altering the nucleotides in key 23S rRNA positions. Finally, it is known that incorporation of multiple prolines (an N-alkylated amino acid) ribosomally can be facilitated by bacterial elongation factor P. We report that supplementing endogenous EF-P during IsCT peptide and RRM1 protein synthesis gave improved yields for most of the N-methylated amino acids studied.
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Affiliation(s)
- Chao Zhang
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Xuan Fu
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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2
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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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3
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Hampton JT, Liu WR. Diversification of Phage-Displayed Peptide Libraries with Noncanonical Amino Acid Mutagenesis and Chemical Modification. Chem Rev 2024; 124:6051-6077. [PMID: 38686960 PMCID: PMC11082904 DOI: 10.1021/acs.chemrev.4c00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Sitting on the interface between biologics and small molecules, peptides represent an emerging class of therapeutics. Numerous techniques have been developed in the past 30 years to take advantage of biological methods to generate and screen peptide libraries for the identification of therapeutic compounds, with phage display being one of the most accessible techniques. Although traditional phage display can generate billions of peptides simultaneously, it is limited to expression of canonical amino acids. Recently, several groups have successfully undergone efforts to apply genetic code expansion to introduce noncanonical amino acids (ncAAs) with novel reactivities and chemistries into phage-displayed peptide libraries. In addition to biological methods, several different chemical approaches have also been used to install noncanonical motifs into phage libraries. This review focuses on these recent advances that have taken advantage of both biological and chemical means for diversification of phage libraries with ncAAs.
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Affiliation(s)
- J. Trae Hampton
- Texas
A&M Drug Discovery Center and Department of Chemistry, College
of Arts and Sciences, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe Ray Liu
- Texas
A&M Drug Discovery Center and Department of Chemistry, College
of Arts and Sciences, Texas A&M University, College Station, Texas 77843, United States
- Institute
of Biosciences and Technology and Department of Translational Medical
Sciences, College of Medicine, Texas A&M
University, Houston, Texas 77030, United States
- Department
of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas 77843, United States
- Department
of Cell Biology and Genetics, College of Medicine, Texas A&M University, College
Station, Texas 77843, United States
- Department
of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas 77843, United States
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4
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Guo QR, Cao YJ. Applications of genetic code expansion technology in eukaryotes. Protein Cell 2024; 15:331-363. [PMID: 37847216 PMCID: PMC11074999 DOI: 10.1093/procel/pwad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/26/2023] [Indexed: 10/18/2023] Open
Abstract
Unnatural amino acids (UAAs) have gained significant attention in protein engineering and drug development owing to their ability to introduce new chemical functionalities to proteins. In eukaryotes, genetic code expansion (GCE) enables the incorporation of UAAs and facilitates posttranscriptional modification (PTM), which is not feasible in prokaryotic systems. GCE is also a powerful tool for cell or animal imaging, the monitoring of protein interactions in target cells, drug development, and switch regulation. Therefore, there is keen interest in utilizing GCE in eukaryotic systems. This review provides an overview of the application of GCE in eukaryotic systems and discusses current challenges that need to be addressed.
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Affiliation(s)
- Qiao-ru Guo
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yu J Cao
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
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5
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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 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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6
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Jewel D, Kelemen RE, Huang RL, Zhu Z, Sundaresh B, Malley K, Pham Q, Loynd C, Huang Z, van Opijnen T, Chatterjee A. Enhanced Directed Evolution in Mammalian Cells Yields a Hyperefficient Pyrrolysyl tRNA for Noncanonical Amino Acid Mutagenesis. Angew Chem Int Ed Engl 2024; 63:e202316428. [PMID: 38279536 PMCID: PMC10922736 DOI: 10.1002/anie.202316428] [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: 11/01/2023] [Indexed: 01/28/2024]
Abstract
Heterologous tRNAs used for noncanonical amino acid (ncAA) mutagenesis in mammalian cells typically show poor activity. We recently introduced a virus-assisted directed evolution strategy (VADER) that can enrich improved tRNA mutants from naïve libraries in mammalian cells. However, VADER was limited to processing only a few thousand mutants; the inability to screen a larger sequence space precluded the identification of highly active variants with distal synergistic mutations. Here, we report VADER2.0, which can process significantly larger mutant libraries. It also employs a novel library design, which maintains base-pairing between distant residues in the stem regions, allowing us to pack a higher density of functional mutants within a fixed sequence space. VADER2.0 enabled simultaneous engineering of the entire acceptor stem of M. mazei pyrrolysyl tRNA (tRNAPyl ), leading to a remarkably improved variant, which facilitates more efficient incorporation of a wider range of ncAAs, and enables facile development of viral vectors and stable cell-lines for ncAA mutagenesis.
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Affiliation(s)
- Delilah Jewel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Rachel E Kelemen
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Rachel L Huang
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Zeyu Zhu
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | | | - Kaitlin Malley
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Quan Pham
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Conor Loynd
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Zeyi Huang
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
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7
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Brown W, Davidson LA, Deiters A. Expanding the Genetic Code of Xenopus laevis Embryos. ACS Chem Biol 2024; 19:516-525. [PMID: 38277773 PMCID: PMC10877573 DOI: 10.1021/acschembio.3c00686] [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: 11/10/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/28/2024]
Abstract
The incorporation of unnatural amino acids into proteins through genetic code expansion has been successfully adapted to African claw-toed frog embryos. Six unique unnatural amino acids are incorporated site-specifically into proteins and demonstrate robust and reliable protein expression. Of these amino acids, several are caged analogues that can be used to establish conditional control over enzymatic activity. Using light or small molecule triggers, we exhibit activation and tunability of protein functions in live embryos. This approach was then applied to optical control over the activity of a RASopathy mutant of NRAS, taking advantage of generating explant cultures from Xenopus. Taken together, genetic code expansion is a robust approach in the Xenopus model to incorporate novel chemical functionalities into proteins of interest to study their function and role in a complex biological setting.
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Affiliation(s)
- Wes Brown
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Lance A. Davidson
- Departments
of Bioengineering, Developmental Biology, and Computational and Systems
Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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8
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Krahn N, Zhang J, Melnikov SV, Tharp JM, Villa A, Patel A, Howard R, Gabir H, Patel T, Stetefeld J, Puglisi J, Söll D. tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut. Nucleic Acids Res 2024; 52:513-524. [PMID: 38100361 PMCID: PMC10810272 DOI: 10.1093/nar/gkad1188] [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: 10/30/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA synthetase (aaRS). These key features are referred to as identity elements. In our study, we investigated the tRNA:aaRS pair that installs the 22nd amino acid, pyrrolysine (tRNAPyl:PylRS). Pyrrolysyl-tRNA synthetases (PylRSs) are naturally encoded in some archaeal and bacterial genomes to acylate tRNAPyl with pyrrolysine. Their large amino acid binding pocket and poor recognition of the tRNA anticodon have been instrumental in incorporating >200 noncanonical amino acids. PylRS enzymes can be divided into three classes based on their genomic structure. Two classes contain both an N-terminal and C-terminal domain, however the third class (ΔpylSn) lacks the N-terminal domain. In this study we explored the tRNA identity elements for a ΔpylSn tRNAPyl from Candidatus Methanomethylophilus alvus which drives the orthogonality seen with its cognate PylRS (MaPylRS). From aminoacylation and translation assays we identified five key elements in ΔpylSn tRNAPyl necessary for MaPylRS activity. The absence of a base (position 8) and a G-U wobble pair (G28:U42) were found to affect the high-resolution structure of the tRNA, while molecular dynamic simulations led us to acknowledge the rigidity imparted from the G-C base pairs (G3:C70 and G5:C68).
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Affiliation(s)
- Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jingji Zhang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sergey V Melnikov
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Jeffery M Tharp
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Alessandra Villa
- PDC-Center for High Performance Computing, KTH-Royal Institute of Technology, Stockholm, SE-100 44, Sweden
| | - Armaan Patel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, SE-171 65, Sweden
| | - Haben Gabir
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Trushar R Patel
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB T1K 2E1, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Joseph Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
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9
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Wang Y, Ji Y, Sun L, Huang Z, Ye S, Xuan W. A Sirtuin-Dependent T7 RNA Polymerase Variant. ACS Synth Biol 2024; 13:54-60. [PMID: 38117980 DOI: 10.1021/acssynbio.3c00607] [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: 12/22/2023]
Abstract
Transcriptional regulation is of great significance for cells to maintain homeostasis and, meanwhile, represents an innovative but less explored means to control biological processes in synthetic biology and bioengineering. Herein we devised a T7 RNA polymerase (T7RNAP) variant through replacing an essential lysine located in the catalytic core (K631) with Nε-acetyl-l-lysine (AcK) via genetic code expansion. This T7RNAP variant requires the deacetylase activity of NAD-dependent sirtuins to recover its enzymatic activities and thereby sustains sirtuin-dependent transcription of the gene of interest in live cells including bacteria and mammalian cells as well as in in vitro systems. This T7RNAP variant could link gene transcription to sirtuin expression and NAD availability, thus holding promise to support some relevant research.
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Affiliation(s)
- Yongan Wang
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Yanli Ji
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Lin Sun
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Zhifen Huang
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Weimin Xuan
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
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10
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Erickson SB, Pham Q, Cao X, Glicksman J, Kelemen RE, Shahraeini SS, Bodkin S, Kiyam Z, Chatterjee A. Precise Manipulation of the Site and Stoichiometry of Capsid Modification Enables Optimization of Functional Adeno-Associated Virus Conjugates. Bioconjug Chem 2024; 35:64-71. [PMID: 38103182 PMCID: PMC10924286 DOI: 10.1021/acs.bioconjchem.3c00411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
The ability to engineer adeno-associated virus (AAV) vectors for targeted transduction of specific cell types is critically important to fully harness their potential for human gene therapy. A promising approach to achieve this objective involves chemically attaching retargeting ligands onto the virus capsid. Site-specific incorporation of a bioorthogonal noncanonical amino acid (ncAA) into the AAV capsid proteins provides a particularly attractive strategy to introduce such modifications with exquisite precision. In this study, we show that using ncAA mutagenesis, it is possible to systematically alter the attachment site of a retargeting ligand (cyclic-RGD) on the AAV capsid to create diverse conjugate architectures and that the site of attachment heavily impacts the retargeting efficiency. We further demonstrate that the performance of these AAV conjugates is highly sensitive to the stoichiometry of capsid labeling (labels per capsid), with an intermediate labeling density providing optimal activity for cRGD-mediated retargeting. Finally, we developed a technology to more precisely control the number of attachment sites per AAV capsid by selectively incorporating an ncAA into the minor capsid proteins with high fidelity and efficiency, such that AAV conjugates with varying stoichiometry can be synthesized. Together, this platform provides unparalleled control over the site and stoichiometry of capsid modification, which will enable the development of next-generation AAV vectors tailored with desirable attributes.
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Affiliation(s)
| | | | - Xiaofu Cao
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Jake Glicksman
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Rachel E. Kelemen
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Seyed S. Shahraeini
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Sebastian Bodkin
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Zainab Kiyam
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
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11
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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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12
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Wright DE, O’Donoghue P. Biosynthesis, Engineering, and Delivery of Selenoproteins. Int J Mol Sci 2023; 25:223. [PMID: 38203392 PMCID: PMC10778597 DOI: 10.3390/ijms25010223] [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: 11/15/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Selenocysteine (Sec) was discovered as the 21st genetically encoded amino acid. In nature, site-directed incorporation of Sec into proteins requires specialized biosynthesis and recoding machinery that evolved distinctly in bacteria compared to archaea and eukaryotes. Many organisms, including higher plants and most fungi, lack the Sec-decoding trait. We review the discovery of Sec and its role in redox enzymes that are essential to human health and important targets in disease. We highlight recent genetic code expansion efforts to engineer site-directed incorporation of Sec in bacteria and yeast. We also review methods to produce selenoproteins with 21 or more amino acids and approaches to delivering recombinant selenoproteins to mammalian cells as new applications for selenoproteins in synthetic biology.
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Affiliation(s)
- David E. Wright
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada;
| | - Patrick O’Donoghue
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada;
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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13
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Ngo PHT, Ishida S, Busogi BB, Do H, Ledesma MA, Kar S, Ellington A. Changes in Coding and Efficiency through Modular Modifications to a One Pot PURE System for In Vitro Transcription and Translation. ACS Synth Biol 2023; 12:3771-3777. [PMID: 38050859 DOI: 10.1021/acssynbio.3c00461] [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: 12/07/2023]
Abstract
The incorporation of unnatural amino acids is an attractive method for improving or bringing new and novel functions in peptides and proteins. Cell-free protein synthesis using the Protein Synthesis Using Recombinant Elements (PURE) system is an attractive platform for efficient unnatural amino acid incorporation. In this work, we further adapted and modified the One Pot PURE to obtain a robust and modular system for enzymatic single-site-specific incorporation of an unnatural amino acid. We demonstrated the flexibility of this system through the introduction of two different orthogonal aminoacyl tRNA synthetase:tRNA pairs that suppressed two distinctive stop codons in separate reaction mixtures.
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Affiliation(s)
- Phuoc H T Ngo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Satoshi Ishida
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Bianca B Busogi
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hannah Do
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Maximiliano A Ledesma
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Shaunak Kar
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
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14
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Liu K, Jiang L, Ma S, Song Z, Wang L, Zhang Q, Xu R, Yang L, Wu J, Yu H. An evolved pyrrolysyl-tRNA synthetase with polysubstrate specificity expands the toolbox for engineering enzymes with incorporation of noncanonical amino acids. BIORESOUR BIOPROCESS 2023; 10:92. [PMID: 38647798 PMCID: PMC10991234 DOI: 10.1186/s40643-023-00712-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/03/2023] [Indexed: 04/25/2024] Open
Abstract
Aminoacyl-tRNA synthetase (aaRS) is a core component for genetic code expansion (GCE), a powerful technique that enables the incorporation of noncanonical amino acids (ncAAs) into a protein. The aaRS with polyspecificity can be exploited in incorporating additional ncAAs into a protein without the evolution of new, orthogonal aaRS/tRNA pair, which hence provides a useful tool for probing the enzyme mechanism or expanding protein function. A variant (N346A/C348A) of pyrrolysyl-tRNA synthetase from Methanosarcina mazei (MmPylRS) exhibited a wide substrate scope of accepting over 40 phenylalanine derivatives. However, for most of the substrates, the incorporation efficiency was low. Here, a MbPylRS (N311A/C313A) variant was constructed that showed higher ncAA incorporation efficiency than its homologous MmPylRS (N346A/C348A). Next, N-terminal of MbPylRS (N311A/C313A) was engineered by a greedy combination of single variants identified previously, resulting in an IPE (N311A/C313A/V31I/T56P/A100E) variant with significantly improved activity against various ncAAs. Activity of IPE was then tested toward 43 novel ncAAs, and 16 of them were identified to be accepted by the variant. The variant hence could incorporate nearly 60 ncAAs in total into proteins. With the utility of this variant, eight various ncAAs were then incorporated into a lanthanide-dependent alcohol dehydrogenase PedH. Incorporation of phenyllactic acid improved the catalytic efficiency of PedH toward methanol by 1.8-fold, indicating the role of modifying protein main chain in enzyme engineering. Incorporation of O-tert-Butyl-L-tyrosine modified the enantioselectivity of PedH by influencing the interactions between substrate and protein. Enzymatic characterization and molecular dynamics simulations revealed the mechanism of ncAAs affecting PedH catalysis. This study provides a PylRS variant with high activity and substrate promiscuity, which increases the utility of GCE in enzyme mechanism illustration and engineering.
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Affiliation(s)
- Ke Liu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Ling Jiang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Shuang Ma
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Zhongdi Song
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou, 310015, Zhejiang, China.
| | - Lun Wang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Qunfeng Zhang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Renhao Xu
- Hangzhou 14th Middle School, Hangzhou, 310006, Zhejiang, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China.
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15
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Abdelkader EH, Qianzhu H, Huber T, Otting G. Genetic Encoding of 7-Aza-l-tryptophan: Isoelectronic Substitution of a Single CH-Group in a Protein for a Nitrogen Atom for Site-Selective Isotope Labeling. ACS Sens 2023; 8:4402-4406. [PMID: 37890165 DOI: 10.1021/acssensors.3c01904] [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: 10/29/2023]
Abstract
Genetic encoding of a noncanonical amino acid (ncAA) in an in vivo expression system requires an aminoacyl-tRNA synthetase that specifically recognizes the ncAA, while the ncAA must not be recognized by the canonical protein expression machinery. We succeeded in genetically encoding 7-aza-tryptophan (7AW), which is isoelectronic with tryptophan. The system is fully orthogonal to protein expression in Escherichia coli, enabling high-yielding site-selective isotope labeling in vivo. 7AW is readily synthesized from serine and 7-aza-indole using a tryptophan synthetase β-subunit (TrpB) mutant, affording easy access to isotope-labeled 7AW. Using labeled 7AW produced from 15N/13C-labeled serine, we produced 7AW mutants of the 25 kDa Zika virus NS2B-NS3 protease. 15N-HSQC spectra display single cross-peaks at chemical shifts near those observed for the wild-type protein labeled with 15N/13C-tryptophan, confirming the structural integrity of the protein and yielding straightforward NMR resonance assignments for site-specific probing.
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Affiliation(s)
- Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Haocheng Qianzhu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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16
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Meineke B, Heimgärtner J, Caridha R, Block MF, Kimler KJ, Pires MF, Landreh M, Elsässer SJ. Dual stop codon suppression in mammalian cells with genomically integrated genetic code expansion machinery. CELL REPORTS METHODS 2023; 3:100626. [PMID: 37935196 PMCID: PMC10694491 DOI: 10.1016/j.crmeth.2023.100626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/22/2023] [Accepted: 10/12/2023] [Indexed: 11/09/2023]
Abstract
Stop codon suppression using dedicated tRNA/aminoacyl-tRNA synthetase (aaRS) pairs allows for genetically encoded, site-specific incorporation of non-canonical amino acids (ncAAs) as chemical handles for protein labeling and modification. Here, we demonstrate that piggyBac-mediated genomic integration of archaeal pyrrolysine tRNA (tRNAPyl)/pyrrolysyl-tRNA synthetase (PylRS) or bacterial tRNA/aaRS pairs, using a modular plasmid design with multi-copy tRNA arrays, allows for homogeneous and efficient genetically encoded ncAA incorporation in diverse mammalian cell lines. We assess opportunities and limitations of using ncAAs for fluorescent labeling applications in stable cell lines. We explore suppression of ochre and opal stop codons and finally incorporate two distinct ncAAs with mutually orthogonal click chemistries for site-specific, dual-fluorophore labeling of a cell surface receptor on live mammalian cells.
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Affiliation(s)
- Birthe Meineke
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, 17165 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, 17165 Stockholm, Sweden.
| | - Johannes Heimgärtner
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, 17165 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Rozina Caridha
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, 17165 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Matthias F Block
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, 17165 Stockholm, Sweden
| | - Kyle J Kimler
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, 17165 Stockholm, Sweden
| | - Maria F Pires
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, 17165 Stockholm, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, 17165 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, 17165 Stockholm, Sweden.
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17
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Avila‐Cobian LF, Hoshino H, Horsman ME, Nguyen VT, Qian Y, Feltzer R, Kim C, Hu DD, Champion MM, Fisher JF, Mobashery S. Amber-codon suppression for spatial localization and in vivo photoaffinity capture of the interactome of the Pseudomonas aeruginosa rare lipoprotein A lytic transglycosylase. Protein Sci 2023; 32:e4781. [PMID: 37703013 PMCID: PMC10536563 DOI: 10.1002/pro.4781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/14/2023]
Abstract
The 11 lytic transglycosylases of Pseudomonas aeruginosa have overlapping activities in the turnover of the cell-wall peptidoglycan. Rare lipoprotein A (RlpA) is distinct among the 11 by its use of only peptidoglycan lacking peptide stems. The spatial localization of RlpA and its interactome within P. aeruginosa are unknown. We employed suppression of introduced amber codons at sites in the rlpA gene for the introduction of the unnatural-amino-acids Νζ -[(2-azidoethoxy)carbonyl]-l-lysine (compound 1) and Nζ -[[[3-(3-methyl-3H-diazirin-3-yl)propyl]amino]carbonyl]-l-lysine (compound 2). In live P. aeruginosa, full-length RlpA incorporating compound 1 into its sequence was fluorescently tagged using strained-promoted alkyne-azide cycloaddition and examined by fluorescence microscopy. RlpA is present at low levels along the sidewall length of the bacterium, and at higher levels at the nascent septa of replicating bacteria. In intact P. aeruginosa, UV photolysis of full-length RlpA having compound 2 within its sequence generated a transient reactive carbene, which engaged in photoaffinity capture of neighboring proteins. Thirteen proteins were identified. Three of these proteins-PBP1a, PBP5, and MreB-are members of the bacterial divisome. The use of the complementary methodologies of non-canonical amino-acid incorporation, photoaffinity proximity analysis, and fluorescent microscopy confirm a dominant septal location for the RlpA enzyme of P. aeruginosa, as a divisome-associated activity. This accomplishment adds to the emerging recognition of the value of these methodologies for identification of the intracellular localization of bacterial proteins.
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Affiliation(s)
- Luis F. Avila‐Cobian
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Hidekazu Hoshino
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Mark E. Horsman
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Van T. Nguyen
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Yuanyuan Qian
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Rhona Feltzer
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Choon Kim
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Daniel D. Hu
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Matthew M. Champion
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Jed F. Fisher
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Shahriar Mobashery
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
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18
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Schloßhauer JL, Zemella A, Dondapati SK, Thoring L, Meyer M, Kubick S. Enhancing the performance of a mutant pyrrolysyl-tRNA synthetase to create a highly versatile eukaryotic cell-free protein synthesis tool. Sci Rep 2023; 13:15236. [PMID: 37709815 PMCID: PMC10502014 DOI: 10.1038/s41598-023-42198-8] [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: 04/25/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023] Open
Abstract
Modification of proteins with a broad range of chemical functionalities enables the investigation of protein structure and activity by manipulating polypeptides at single amino acid resolution. Indeed, various functional groups including bulky non-canonical amino acids like strained cyclooctenes could be introduced by the unique features of the binding pocket of the double mutant pyrrolysyl-tRNA synthetase (Y306A, Y384F), but the instable nature of the enzyme limits its application in vivo. Here, we constructed a cell-free protein production system, which increased the overall enzyme stability by combining different reaction compartments. Moreover, a co-expression approach in a one-pot reaction allowed straightforward site-specific fluorescent labeling of the functional complex membrane protein cystic fibrosis transmembrane conductance regulator. Our work provides a versatile platform for introducing various non-canonical amino acids into difficult-to-express proteins for structural and fluorescence based investigation of proteins activity.
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Affiliation(s)
- Jeffrey L Schloßhauer
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Institute of Biotechnology,, Brandenburg University of Technology Cottbus-Senftenberg, Am Mühlenberg, Potsdam, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany.
| | - Srujan K Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Manpreet Meyer
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus -Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
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19
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Goettig P, Koch NG, Budisa N. Non-Canonical Amino Acids in Analyses of Protease Structure and Function. Int J Mol Sci 2023; 24:14035. [PMID: 37762340 PMCID: PMC10531186 DOI: 10.3390/ijms241814035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.
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Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
| | - Nikolaj G. Koch
- Biocatalysis Group, Technische Universität Berlin, 10623 Berlin, Germany;
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
| | - Nediljko Budisa
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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20
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Zhang Q, Zheng W, Song Z, Zhang Q, Yang L, Wu J, Lin J, Xu G, Yu H. Machine Learning Enables Prediction of Pyrrolysyl-tRNA Synthetase Substrate Specificity. ACS Synth Biol 2023; 12:2403-2417. [PMID: 37486975 DOI: 10.1021/acssynbio.3c00225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Knowledge about the substrate scope for a given enzyme is informative for elucidating biochemical pathways and also for expanding applications of the enzyme. However, no general methods are available to accurately predict the substrate specificity of an enzyme. Pyrrolysyl-tRNA synthetase (PylRS) is a powerful tool for incorporating various noncanonical amino acids (NCAAs) into proteins, which enabled us to probe, image, rationally engineer, and evolve protein structure and function. However, the incorporation of a new NCAA typically requires the selection of large libraries of PylRS with randomized mutations at active sites, and this process requires multiple rounds of selection for each new substrate. Therefore, a single aminoacyl-tRNA synthetase with broad substrate promiscuity is ideal to facilitate widespread applications of the genetic NCAA incorporation technique. Herein, machine learning models were developed to predict the substrate specificity of PylRS to accept novel NCAAs that could be incorporated into proteins by three PylRS mutants. The models were built from a training set of 285 unique enzyme-substrate pairs of three PylRS mutants including IFRS, BtaRS, and MFRS against 95 NCAAs. The best BaggingTree (BT) model was then used for virtually screening a NCAAs library containing 1474 phenylalanine, tyrosine, tryptophan, and alanine analogues, and 156 NCAAs were predicted to be accepted by at least one of the three PylRS mutants. Then, 27 NCAAs including 24 positive and 3 negative substrates were experimentally tested for their activities, and 20 of the 24 positive substrates showed weak or strong activity and were accepted by at least one PylRS mutant, among which 11 NCAAs were never reported to be incorporated into proteins before. Three negative substrates did not show any activity. Experimental results suggested that the BT model provides a three-class classification accuracy of 0.69 and a binary classification accuracy of 0.86. This study expanded the substrate scope of three PylRS variants and provided a framework for developing machine learning models to predict substrate specificity of other PylRS variants.
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Affiliation(s)
- Qunfeng Zhang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Wenlong Zheng
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou 311200, Zhejiang, China
| | - Zhongdi Song
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China
| | - Qiang Zhang
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou 311200, Zhejiang, China
- College of Computer Science and Technology, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou 311200, Zhejiang, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou 311200, Zhejiang, China
| | - Jianping Lin
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Gang Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou 311200, Zhejiang, China
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21
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Janosko C, Shade O, Courtney TM, Horst TJ, Liu M, Khare SD, Deiters A. Genetic Encoding of Arylazopyrazole Phenylalanine for Optical Control of Translation. ACS OMEGA 2023; 8:26590-26596. [PMID: 37521667 PMCID: PMC10373180 DOI: 10.1021/acsomega.3c03512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023]
Abstract
An arylazopyrazole was explored for its use as an enhanced photoswitchable amino acid in genetic code expansion. This new unnatural amino acid was successfully incorporated into proteins in both bacterial and mammalian cells. While photocontrol of translation required pulsed irradiations, complete selectivity for the trans-configuration by the pyrrolysyl tRNA synthetase was observed, demonstrating expression of a gene of interest selectively controlled via light exposure.
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Affiliation(s)
- Chasity
P. Janosko
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Olivia Shade
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Taylor M. Courtney
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Trevor J. Horst
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Melinda Liu
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Sagar D. Khare
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Alexander Deiters
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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22
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Hampton JT, Cho CCD, Coleman DD, Geng ZZ, Chen PH, Dubey G, Sylvain L, Xu S, Liu W. An amber-encoding helper phage for more efficient phage display of noncanonical amino acids. Nucleic Acids Res 2023; 51:6566-6577. [PMID: 37293959 PMCID: PMC10359598 DOI: 10.1093/nar/gkad488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/15/2023] [Accepted: 05/24/2023] [Indexed: 06/10/2023] Open
Abstract
Using an amber suppression-based noncanonical amino acid (ncAA) mutagenesis approach, the chemical space in phage display can be significantly expanded for drug discovery. In this work, we demonstrate the development of a novel helper phage, CMa13ile40, for continuous enrichment of amber obligate phage clones and efficient production of ncAA-containing phages. CMa13ile40 was constructed by insertion of a Candidatus Methanomethylophilus alvus pyrrolysyl-tRNA synthetase/PylT gene cassette into a helper phage genome. The novel helper phage allowed for a continuous amber codon enrichment strategy for two different libraries and demonstrated a 100-fold increase in packaging selectivity. CMa13ile40 was then used to create two peptide libraries containing separate ncAAs, Nϵ-tert-butoxycarbonyl-lysine and Nϵ-allyloxycarbonyl-lysine, respectively. These libraries were used to identify peptide ligands that bind to the extracellular domain of ZNRF3. Each selection showed differential enrichment of unique sequences dependent upon the ncAA used. Peptides from both selections were confirmed to have low micromolar affinity for ZNRF3 that was dependent upon the presence of the ncAA used for selection. Our results demonstrate that ncAAs in phages provide unique interactions for identification of unique peptides. As an effective tool for phage display, we believe that CMa13ile40 can be broadly applied to a wide variety of applications.
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Affiliation(s)
- Joshua Trae Hampton
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Chia-Chuan Dean Cho
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Demonta D Coleman
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Zhi Zachary Geng
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Peng-Hsun Chase Chen
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Gopal K Dubey
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Lauralee D Sylvain
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Shiqing Xu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
- Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, TX 77843, USA
| | - Wenshe Ray Liu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Cell Biology and Genetics, College of Medicine, Texas A&M University, College Station, TX 77843, USA
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23
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Seki K, Galindo JL, Karim AS, Jewett MC. A Cell-Free Gene Expression Platform for Discovering and Characterizing Stop Codon Suppressing tRNAs. ACS Chem Biol 2023; 18:1324-1334. [PMID: 37257197 DOI: 10.1021/acschembio.3c00051] [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: 06/02/2023]
Abstract
Non-canonical amino acids (ncAAs) can be incorporated into peptides and proteins to create new properties and functions. Site-specific ncAA incorporation is typically enabled by orthogonal translation systems comprising a stop codon suppressing tRNA (typically UAG), an aminoacyl-tRNA synthetase, and an ncAA of interest. Unfortunately, methods to discover and characterize suppressor tRNAs are limited because of laborious and time-consuming workflows in living cells. In this work, we develop anEscherichia coli crude extract-based cell-free gene expression system to rapidly express and characterize functional suppressor tRNAs. Our approach co-expresses orthogonal tRNAs using endogenous machinery alongside a stop-codon containing superfolder green fluorescent protein (sfGFP) reporter, which can be used as a simple read-out for suppression. As a model, we evaluate the UAG and UAA suppressing activity of several orthogonal tRNAs. Then, we demonstrate that co-transcription of two mutually orthogonal tRNAs can direct the incorporation of two unique ncAAs within a single modified sfGFP. Finally, we show that the cell-free workflow can be used to discover putative UAG-suppressor tRNAs found in metagenomic data, which are nonspecifically recognized by endogenous aminoacyl-tRNA synthetases. We anticipate that our cell-free system will accelerate the development of orthogonal translation systems for synthetic biology.
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Affiliation(s)
- Kosuke Seki
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Joey L Galindo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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24
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Fricke R, Swenson CV, Roe LT, Hamlish NX, Shah B, Zhang Z, Ficaretta E, Ad O, Smaga S, Gee CL, Chatterjee A, Schepartz A. Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase enzymes to include non-α-amino acids in vitro and in vivo. Nat Chem 2023:10.1038/s41557-023-01224-y. [PMID: 37264106 DOI: 10.1038/s41557-023-01224-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/28/2023] [Indexed: 06/03/2023]
Abstract
The absence of orthogonal aminoacyl-transfer RNA (tRNA) synthetases that accept non-L-α-amino acids is a primary bottleneck hindering the in vivo translation of sequence-defined hetero-oligomers and biomaterials. Here we report that pyrrolysyl-tRNA synthetase (PylRS) and certain PylRS variants accept α-hydroxy, α-thio and N-formyl-L-α-amino acids, as well as α-carboxy acid monomers that are precursors to polyketide natural products. These monomers are accommodated and accepted by the translation apparatus in vitro; those with reactive nucleophiles are incorporated into proteins in vivo. High-resolution structural analysis of the complex formed between one PylRS enzyme and a m-substituted 2-benzylmalonic acid derivative revealed an active site that discriminates prochiral carboxylates and accommodates the large size and distinct electrostatics of an α-carboxy substituent. This work emphasizes the potential of PylRS-derived enzymes for acylating tRNA with monomers whose α-substituent diverges substantially from the α-amine of proteinogenic amino acids. These enzymes or derivatives thereof could synergize with natural or evolved ribosomes and/or translation factors to generate diverse sequence-defined non-protein heteropolymers.
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Affiliation(s)
- Riley Fricke
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Cameron V Swenson
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Leah Tang Roe
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Noah Xue Hamlish
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Bhavana Shah
- Process Development, Amgen, Thousand Oaks, CA, USA
| | | | - Elise Ficaretta
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Omer Ad
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Sarah Smaga
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Christine L Gee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Abhishek Chatterjee
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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25
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Taylor CJ, Hardy FJ, Burke AJ, Bednar RM, Mehl RA, Green AP, Lovelock SL. Engineering mutually orthogonal PylRS/tRNA pairs for dual encoding of functional histidine analogues. Protein Sci 2023; 32:e4640. [PMID: 37051694 PMCID: PMC10127257 DOI: 10.1002/pro.4640] [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: 01/31/2023] [Revised: 04/06/2023] [Accepted: 04/09/2023] [Indexed: 04/14/2023]
Abstract
The availability of an expanded genetic code opens exciting new opportunities in enzyme design and engineering. In this regard histidine analogues have proven particularly versatile, serving as ligands to augment metalloenzyme function and as catalytic nucleophiles in designed enzymes. The ability to genetically encode multiple functional residues could greatly expand the range of chemistry accessible within enzyme active sites. Here, we develop mutually orthogonal translation components to selectively encode two structurally similar histidine analogues. Transplanting known mutations from a promiscuous Methanosarcina mazei pyrrolysyl-tRNA synthetase (MmPylRSIFGFF ) into a single domain PylRS from Methanomethylophilus alvus (MaPylRSIFGFF ) provided a variant with improved efficiency and specificity for 3-methyl-L-histidine (MeHis) incorporation. The MaPylRSIFGFF clone was further characterized using in vitro biochemical assays and x-ray crystallography. We subsequently engineered the orthogonal MmPylRS for activity and selectivity for 3-(3-pyridyl)-L-alanine (3-Pyr), which was used in combination with MaPylRSIFGFF to produce proteins containing both 3-Pyr and MeHis. Given the versatile roles played by histidine in enzyme mechanisms, we anticipate that the tools developed within this study will underpin the development of enzymes with new and enhanced functions.
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Affiliation(s)
- Christopher J. Taylor
- Manchester Institute of Biotechnology, School of Chemistry, University of ManchesterManchesterUK
| | - Florence J. Hardy
- Manchester Institute of Biotechnology, School of Chemistry, University of ManchesterManchesterUK
| | - Ashleigh J. Burke
- Manchester Institute of Biotechnology, School of Chemistry, University of ManchesterManchesterUK
| | - Riley M. Bednar
- Department of Biochemistry and BiophysicsOregon State UniversityCorvallisOregonUSA
| | - Ryan A. Mehl
- Department of Biochemistry and BiophysicsOregon State UniversityCorvallisOregonUSA
| | - Anthony P. Green
- Manchester Institute of Biotechnology, School of Chemistry, University of ManchesterManchesterUK
| | - Sarah L. Lovelock
- Manchester Institute of Biotechnology, School of Chemistry, University of ManchesterManchesterUK
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26
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Peng T, Das T, Ding K, Hang HC. Functional analysis of protein post-translational modifications using genetic codon expansion. Protein Sci 2023; 32:e4618. [PMID: 36883310 PMCID: PMC10031814 DOI: 10.1002/pro.4618] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Post-translational modifications (PTMs) of proteins not only exponentially increase the diversity of proteoforms, but also contribute to dynamically modulating the localization, stability, activity, and interaction of proteins. Understanding the biological consequences and functions of specific PTMs has been challenging for many reasons, including the dynamic nature of many PTMs and the technical limitations to access homogenously modified proteins. The genetic code expansion technology has emerged to provide unique approaches for studying PTMs. Through site-specific incorporation of unnatural amino acids (UAAs) bearing PTMs or their mimics into proteins, genetic code expansion allows the generation of homogenous proteins with site-specific modifications and atomic resolution both in vitro and in vivo. With this technology, various PTMs and mimics have been precisely introduced into proteins. In this review, we summarize the UAAs and approaches that have been recently developed to site-specifically install PTMs and their mimics into proteins for functional studies of PTMs.
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Affiliation(s)
- Tao Peng
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhenChina
- Institute of Chemical Biology, Shenzhen Bay LaboratoryShenzhenChina
| | - Tandrila Das
- Departments of Immunology and Microbiology and ChemistryScripps ResearchLa JollaCaliforniaUSA
| | - Ke Ding
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhenChina
| | - Howard C. Hang
- Departments of Immunology and Microbiology and ChemistryScripps ResearchLa JollaCaliforniaUSA
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27
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Pavão G, Sfalcin I, Bonatto D. Biocontainment Techniques and Applications for Yeast Biotechnology. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9040341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Biocontainment techniques for genetically modified yeasts (GMYs) are pivotal due to the importance of these organisms for biotechnological processes and also due to the design of new yeast strains by using synthetic biology tools and technologies. Due to the large genetic modifications that many yeast strains display, it is highly desirable to avoid the leakage of GMY cells into natural environments and, consequently, the spread of synthetic genes and circuits by horizontal or vertical gene transfer mechanisms within the microorganisms. Moreover, it is also desirable to avoid patented yeast gene technologies spreading outside the production facility. In this review, the different biocontainment technologies currently available for GMYs were evaluated. Interestingly, uniplex-type biocontainment approaches (UTBAs), which rely on nutrient auxotrophies induced by gene mutation or deletion or the expression of the simple kill switches apparatus, are still the major biocontainment approaches in use with GMY. While bacteria such as Escherichia coli account for advanced biocontainment technologies based on synthetic biology and multiplex-type biocontainment approaches (MTBAs), GMYs are distant from this scenario due to many reasons. Thus, a comparison of different UTBAs and MTBAs applied for GMY and genetically engineered microorganisms (GEMs) was made, indicating the major advances of biocontainment techniques for GMYs.
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28
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Yanagisawa T, Seki E, Tanabe H, Fujii Y, Sakamoto K, Yokoyama S. Crystal Structure of Pyrrolysyl-tRNA Synthetase from a Methanogenic Archaeon ISO4-G1 and Its Structure-Based Engineering for Highly-Productive Cell-Free Genetic Code Expansion with Non-Canonical Amino Acids. Int J Mol Sci 2023; 24:ijms24076256. [PMID: 37047230 PMCID: PMC10094482 DOI: 10.3390/ijms24076256] [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: 02/22/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Pairs of pyrrolysyl-tRNA synthetase (PylRS) and tRNAPyl from Methanosarcina mazei and Methanosarcina barkeri are widely used for site-specific incorporations of non-canonical amino acids into proteins (genetic code expansion). Previously, we achieved full productivity of cell-free protein synthesis for bulky non-canonical amino acids, including Nε-((((E)-cyclooct-2-en-1-yl)oxy)carbonyl)-L-lysine (TCO*Lys), by using Methanomethylophilus alvus PylRS with structure-based mutations in and around the amino acid binding pocket (first-layer and second-layer mutations, respectively). Recently, the PylRS·tRNAPyl pair from a methanogenic archaeon ISO4-G1 was used for genetic code expansion. In the present study, we determined the crystal structure of the methanogenic archaeon ISO4-G1 PylRS (ISO4-G1 PylRS) and compared it with those of structure-known PylRSs. Based on the ISO4-G1 PylRS structure, we attempted the site-specific incorporation of Nε-(p-ethynylbenzyloxycarbonyl)-L-lysine (pEtZLys) into proteins, but it was much less efficient than that of TCO*Lys with M. alvus PylRS mutants. Thus, the first-layer mutations (Y125A and M128L) of ISO4-G1 PylRS, with no additional second-layer mutations, increased the protein productivity with pEtZLys up to 57 ± 8% of that with TCO*Lys at high enzyme concentrations in the cell-free protein synthesis.
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Affiliation(s)
- Tatsuo Yanagisawa
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan;
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan; (E.S.); (H.T.)
- Correspondence: (T.Y.); (S.Y.); Tel.: +81-45-503-9196 (S.Y.)
| | - Eiko Seki
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan; (E.S.); (H.T.)
| | - Hiroaki Tanabe
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan; (E.S.); (H.T.)
| | - Yoshifumi Fujii
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan; (E.S.); (H.T.)
| | - Kensaku Sakamoto
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan;
| | - Shigeyuki Yokoyama
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan; (E.S.); (H.T.)
- Correspondence: (T.Y.); (S.Y.); Tel.: +81-45-503-9196 (S.Y.)
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29
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Kirchgäßner S, Braun MB, Bartlick N, Koç C, Reinkemeier CD, Lemke EA, Stehle T, Schwarzer D. Synthesis, Biochemical Characterization, and Genetic Encoding of a 1,2,4-Triazole Amino Acid as an Acetyllysine Mimic for Bromodomains of the BET Family. Angew Chem Int Ed Engl 2023; 62:e202215460. [PMID: 36585954 DOI: 10.1002/anie.202215460] [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: 10/20/2022] [Revised: 12/23/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
Lysine acetylation is a charge-neutralizing post-translational modification of proteins bound by bromodomains (Brds). A 1,2,4-triazole amino acid (ApmTri) was established as acetyllysine (Kac) mimic recruiting Brds of the BET family in contrast to glutamine commonly used for simulating this modification. Optimization of triazole substituents and side chain spacing allowed BET Brd recruitment to ApmTri-containing peptides with affinities similar to native substrates. Crystal structures of ApmTri-containing peptides in complex with two BET Brds revealed the binding mode which mirrored that of Kac ligands. ApmTri was genetically encoded and recombinant ApmTri-containing proteins co-enriched BRD3(2) from cellular lysates. This interaction was blocked by BET inhibitor JQ1. With genetically encoded ApmTri, biochemistry is now provided with a stable Kac mimic reflecting charge neutralization and Brd recruitment, allowing new investigations into BET proteins in vitro and in vivo.
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Affiliation(s)
- Sören Kirchgäßner
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Michael B Braun
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Natascha Bartlick
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Cengiz Koç
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany.,Current address: Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, The Medical School, Beech Hill Rd, Sheffield, S10 2RX, UK
| | - Christopher D Reinkemeier
- Biocenter, Johannes Gutenberg University Mainz, 55128, Mainz, Germany.,Institute of Molecular Biology Mainz, 55128, Mainz, Germany.,Current address: Department of Biosystems Science and Engineering Basel, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128, Mainz, Germany.,Institute of Molecular Biology Mainz, 55128, Mainz, Germany
| | - Thilo Stehle
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Dirk Schwarzer
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
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30
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Zhang L, Aragon-Sanabria V, Aditya A, Marelli M, Cao T, Chen F, Yoo B, Ma K, Zhuang L, Cailleau T, Masterson L, Turker MZ, Lee R, DeLeon G, Monette S, Colombo R, Christie RJ, Zanzonico P, Wiesner U, Subramony JA, Bradbury MS. Engineered Ultrasmall Nanoparticle Drug-Immune Conjugates with "Hit and Run" Tumor Delivery to Eradicate Gastric Cancer. ADVANCED THERAPEUTICS 2023; 6:2200209. [PMID: 37007587 PMCID: PMC10061546 DOI: 10.1002/adtp.202370009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Despite advances by recently approved antibody-drug conjugates in treating advanced gastric cancer patients, substantial limitations remain. Here, several key obstacles are overcome by developing a first-in-class ultrasmall (sub-8-nanometer (nm)) anti-human epidermal growth factor receptor 2 (HER2)-targeting drug-immune conjugate nanoparticle therapy. This multivalent fluorescent core-shell silica nanoparticle bears multiple anti-HER2 single-chain variable fragments (scFv), topoisomerase inhibitors, and deferoxamine moieties. Most surprisingly, drawing upon its favorable physicochemical, pharmacokinetic, clearance, and target-specific dual-modality imaging properties in a "hit and run" approach, this conjugate eradicated HER2-expressing gastric tumors without any evidence of tumor regrowth, while exhibiting a wide therapeutic index. Therapeutic response mechanisms are accompanied by the activation of functional markers, as well as pathway-specific inhibition. Results highlight the potential clinical utility of this molecularly engineered particle drug-immune conjugate and underscore the versatility of the base platform as a carrier for conjugating an array of other immune products and payloads.
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Affiliation(s)
- Li Zhang
- Department of Radiology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- MSK-Cornell Center for Translation of Cancer Nanomedicines, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Virginia Aragon-Sanabria
- Department of Radiology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- MSK-Cornell Center for Translation of Cancer Nanomedicines, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Anusha Aditya
- Department of Radiology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- MSK-Cornell Center for Translation of Cancer Nanomedicines, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Marcello Marelli
- AstraZeneca, One MedImmune Way, Gaithersburg, MD 20878, United States
| | - Tianye Cao
- Department of Radiology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- MSK-Cornell Center for Translation of Cancer Nanomedicines, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Feng Chen
- Department of Radiology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- MSK-Cornell Center for Translation of Cancer Nanomedicines, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Barney Yoo
- MSK-Cornell Center for Translation of Cancer Nanomedicines, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Department of Chemistry, Hunter College, New York, NY 10065, USA
| | - Kai Ma
- MSK-Cornell Center for Translation of Cancer Nanomedicines, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Department of Materials Science & Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Li Zhuang
- AstraZeneca, One MedImmune Way, Gaithersburg, MD 20878, United States
| | - Thais Cailleau
- AstraZeneca, Spirogen, QMB Innovation Centre, 42 New Road, London E1 2AX, UK
| | - Luke Masterson
- AstraZeneca, Spirogen, QMB Innovation Centre, 42 New Road, London E1 2AX, UK
| | - Melik Z Turker
- MSK-Cornell Center for Translation of Cancer Nanomedicines, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Department of Materials Science & Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Rachel Lee
- MSK-Cornell Center for Translation of Cancer Nanomedicines, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Department of Materials Science & Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Gabriel DeLeon
- Department of Radiology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- MSK-Cornell Center for Translation of Cancer Nanomedicines, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Sebastien Monette
- Laboratory of Comparative Pathology, Sloan Kettering Institute for Cancer Research, Weill Cornell Medicine, The Rockefeller University, New York, NY 10065, USA
| | - Raffaele Colombo
- AstraZeneca, One MedImmune Way, Gaithersburg, MD 20878, United States
| | - Ronald J Christie
- AstraZeneca, One MedImmune Way, Gaithersburg, MD 20878, United States
| | - Pat Zanzonico
- MSK-Cornell Center for Translation of Cancer Nanomedicines, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Department of Medical Physics, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Ulrich Wiesner
- MSK-Cornell Center for Translation of Cancer Nanomedicines, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Department of Materials Science & Engineering, Cornell University, Ithaca, NY 14853, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853, USA
| | - J Anand Subramony
- AstraZeneca, One MedImmune Way, Gaithersburg, MD 20878, United States
| | - Michelle S Bradbury
- Department of Radiology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- MSK-Cornell Center for Translation of Cancer Nanomedicines, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Molecular Pharmacology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
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31
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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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32
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Jiang HK, Ambrose NL, Chung CZ, Wang YS, Söll D, Tharp JM. Split aminoacyl-tRNA synthetases for proximity-induced stop codon suppression. Proc Natl Acad Sci U S A 2023; 120:e2219758120. [PMID: 36787361 PMCID: PMC9974479 DOI: 10.1073/pnas.2219758120] [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: 11/18/2022] [Accepted: 01/16/2023] [Indexed: 02/15/2023] Open
Abstract
Synthetic biology tools for regulating gene expression have many useful biotechnology and therapeutic applications. Most tools developed for this purpose control gene expression at the level of transcription, and relatively few methods are available for regulating gene expression at the translational level. Here, we design and engineer split orthogonal aminoacyl-tRNA synthetases (o-aaRS) as unique tools to control gene translation in bacteria and mammalian cells. Using chemically induced dimerization domains, we developed split o-aaRSs that mediate gene expression by conditionally suppressing stop codons in the presence of the small molecules rapamycin and abscisic acid. By activating o-aaRSs, these molecular switches induce stop codon suppression, and in their absence stop codon suppression is turned off. We demonstrate, in Escherichia coli and in human cells, that split o-aaRSs function as genetically encoded AND gates where stop codon suppression is controlled by two distinct molecular inputs. In addition, we show that split o-aaRSs can be used as versatile biosensors to detect therapeutically relevant protein-protein interactions, including those involved in cancer, and those that mediate severe acute respiratory syndrome-coronavirus-2 infection.
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Affiliation(s)
- Han-Kai Jiang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
- Institute of Biological Chemistry, Academia Sinica, Taipei11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu100044, Taiwan
| | - Nicole L. Ambrose
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Christina Z. Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Yane-Shih Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei10617, Taiwan
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
- Department of Chemistry, Yale University, New Haven, CT06511
| | - Jeffery M. Tharp
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN46202
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33
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Bridge T, Wegmann U, Crack JC, Orman K, Shaikh SA, Farndon W, Martins C, Saalbach G, Sachdeva A. Site-specific encoding of photoactivity and photoreactivity into antibody fragments. Nat Chem Biol 2023; 19:740-749. [PMID: 36797401 DOI: 10.1038/s41589-022-01251-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 12/21/2022] [Indexed: 02/18/2023]
Abstract
Design of biomolecules that perform two or more distinct functions in response to light remains challenging. Here, we have introduced concurrent photoactivity and photoreactivity into an epidermal growth factor receptor (EGFR)-targeting antibody fragment, 7D12. This was achieved by site-specific incorporation of photocaged tyrosine (pcY) for photoactivity and p-benzoyl-ʟ-phenylalanine (Bpa) for photoreactivity into 7D12. We identified a position for installing Bpa in 7D12 that has minimal effect on 7D12-EGFR binding affinity in the absence of light. Upon exposure to 365-nm light, this Bpa-containing 7D12 mutant forms a covalent bond with EGFR in an antigen-specific manner. We then developed a method for site-specific incorporation of pcY and Bpa at two distinct sites in 7D12. Finally, we demonstrated that in the absence of light, this pcY- and Bpa-containing mutant of 7D12 does not bind to EGFR, but irradiation with 365-nm light activates (1) specific binding and (2) covalent bond formation with EGFR.
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Affiliation(s)
- Thomas Bridge
- School of Chemistry, University of East Anglia, Norwich, UK
| | - Udo Wegmann
- School of Chemistry, University of East Anglia, Norwich, UK
| | - Jason C Crack
- School of Chemistry, University of East Anglia, Norwich, UK
| | - Kate Orman
- School of Chemistry, University of East Anglia, Norwich, UK
| | - Saher A Shaikh
- School of Chemistry, University of East Anglia, Norwich, UK
| | | | - Carlo Martins
- Proteomics Facility, The John Innes Centre, Norwich, UK
| | | | - Amit Sachdeva
- School of Chemistry, University of East Anglia, Norwich, UK.
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34
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Brown W, Galpin JD, Rosenblum C, Tsang M, Ahern CA, Deiters A. Chemically Acylated tRNAs are Functional in Zebrafish Embryos. J Am Chem Soc 2023; 145:2414-2420. [PMID: 36669466 PMCID: PMC10155198 DOI: 10.1021/jacs.2c11452] [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: 01/21/2023]
Abstract
Genetic code expansion has pushed protein chemistry past the canonical 22 amino acids. The key enzymes that make this possible are engineered aminoacyl tRNA synthetases. However, as the number of genetically encoded amino acids has increased over the years, obvious limits in the type and size of novel side chains that can be accommodated by the synthetase enzyme become apparent. Here, we show that chemically acylating tRNAs allow for robust, site-specific incorporation of unnatural amino acids into proteins in zebrafish embryos, an important model organism for human health and development. We apply this approach to incorporate a unique photocaged histidine analogue for which synthetase engineering efforts have failed. Additionally, we demonstrate optical control over different enzymes in live embryos by installing photocaged histidine into their active sites.
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Affiliation(s)
- Wes Brown
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Carolyn Rosenblum
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael Tsang
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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35
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Andrews J, Gan Q, Fan C. "Not-so-popular" orthogonal pairs in genetic code expansion. Protein Sci 2023; 32:e4559. [PMID: 36585833 PMCID: PMC9850438 DOI: 10.1002/pro.4559] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/16/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
During the past decade, genetic code expansion has been proved to be a powerful tool for protein studies and engineering. As the key part, a series of orthogonal pairs have been developed to site-specifically incorporate hundreds of noncanonical amino acids (ncAAs) into proteins by using bacteria, yeast, mammalian cells, animals, or plants as hosts. Among them, the pair of tyrosyl-tRNA synthetase/tRNATyr from Methanococcus jannaschii and the pair of pyrrolysyl-tRNA synthetase/tRNAPyl from Methanosarcina species are the most popular ones. Recently, other "not-so-popular" orthogonal pairs have started to attract attentions, because they can provide more choices of ncAA candidates and are necessary for simultaneous incorporation of multiple ncAAs into a single protein. Here, we summarize the development and applications of those "not-so-popular" orthogonal pairs, providing guidance for studying and engineering proteins.
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Affiliation(s)
- Joseph Andrews
- Department of Chemistry and BiochemistryUniversity of ArkansasFayettevilleArkansasUSA
| | - Qinglei Gan
- Department of Chemistry and BiochemistryUniversity of ArkansasFayettevilleArkansasUSA
| | - Chenguang Fan
- Department of Chemistry and BiochemistryUniversity of ArkansasFayettevilleArkansasUSA
- Cell and Molecular Biology ProgramUniversity of ArkansasFayettevilleArkansasUSA
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36
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Galles GD, Infield DT, Clark CJ, Hemshorn ML, Manikandan S, Fazan F, Rasouli A, Tajkhorshid E, Galpin JD, Cooley RB, Mehl RA, Ahern CA. Tuning phenylalanine fluorination to assess aromatic contributions to protein function and stability in cells. Nat Commun 2023; 14:59. [PMID: 36599844 PMCID: PMC9813137 DOI: 10.1038/s41467-022-35761-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/27/2022] [Indexed: 01/05/2023] Open
Abstract
The aromatic side-chains of phenylalanine, tyrosine, and tryptophan interact with their environments via both hydrophobic and electrostatic interactions. Determining the extent to which these contribute to protein function and stability is not possible with conventional mutagenesis. Serial fluorination of a given aromatic is a validated method in vitro and in silico to specifically alter electrostatic characteristics, but this approach is restricted to a select few experimental systems. Here, we report a group of pyrrolysine-based aminoacyl-tRNA synthetase/tRNA pairs (tRNA/RS pairs) that enable the site-specific encoding of a varied spectrum of fluorinated phenylalanine amino acids in E. coli and mammalian (HEK 293T) cells. By allowing the cross-kingdom expression of proteins bearing these unnatural amino acids at biochemical scale, these tools may potentially enable the study of biological mechanisms which utilize aromatic interactions in structural and cellular contexts.
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Affiliation(s)
- Grace D Galles
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
- The GCE4All Research Center, Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR, USA
| | - Daniel T Infield
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
| | - Colin J Clark
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
| | - Marcus L Hemshorn
- The GCE4All Research Center, Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR, USA
| | - Shivani Manikandan
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
| | - Frederico Fazan
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
| | - Ali Rasouli
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA
| | - Richard B Cooley
- The GCE4All Research Center, Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR, USA
| | - Ryan A Mehl
- The GCE4All Research Center, Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, IA, USA.
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37
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Jiang HK, Tharp JM. Reprogramming Initiator and Nonsense Codons to Simultaneously Install Three Distinct Noncanonical Amino Acids into Proteins in E. coli. Methods Mol Biol 2023; 2676:101-116. [PMID: 37277627 DOI: 10.1007/978-1-0716-3251-2_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] [Indexed: 06/07/2023]
Abstract
Multiple noncanonical amino acids can be installed into proteins in E. coli using mutually orthogonal aminoacyl-tRNA synthetase and tRNA pairs. Here we describe a protocol for simultaneously installing three distinct noncanonical amino acids into proteins for site-specific bioconjugation at three sites. This method relies on an engineered, UAU-suppressing, initiator tRNA, which is aminoacylated with a noncanonical amino acid by Methanocaldococcus jannaschii tyrosyl-tRNA synthetase. Using this initiator tRNA/aminoacyl-tRNA synthetase pair, together with the pyrrolysyl-tRNA synthetase/tRNAPyl pairs from Methanosarcina mazei and Ca. Methanomethylophilus alvus, three noncanonical amino acids can be installed into proteins in response to the UAU, UAG, and UAA codons.
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Affiliation(s)
- Han-Kai Jiang
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Chemical Biology & Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Jeffery M Tharp
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA.
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38
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Jewel D, Kelemen RE, Huang RL, Zhu Z, Sundaresh B, Cao X, Malley K, Huang Z, Pasha M, Anthony J, van Opijnen T, Chatterjee A. Virus-assisted directed evolution of enhanced suppressor tRNAs in mammalian cells. Nat Methods 2023; 20:95-103. [PMID: 36550276 PMCID: PMC9855281 DOI: 10.1038/s41592-022-01706-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 10/25/2022] [Indexed: 12/24/2022]
Abstract
Site-specific incorporation of unnatural amino acids (Uaas) in living cells relies on engineered aminoacyl-transfer RNA synthetase-tRNA pairs borrowed from a distant domain of life. Such heterologous suppressor tRNAs often have poor intrinsic activity, presumably due to suboptimal interaction with a non-native translation system. This limitation can be addressed in Escherichia coli using directed evolution. However, no suitable selection system is currently available to do the same in mammalian cells. Here we report virus-assisted directed evolution of tRNAs (VADER) in mammalian cells, which uses a double-sieve selection scheme to facilitate single-step enrichment of active yet orthogonal tRNA mutants from naive libraries. Using VADER we developed improved mutants of Methanosarcina mazei pyrrolysyl-tRNA, as well as a bacterial tyrosyl-tRNA. We also show that the higher activity of the most efficient mutant pyrrolysyl-tRNA is specific for mammalian cells, alluding to an improved interaction with the unique mammalian translation apparatus.
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Affiliation(s)
- Delilah Jewel
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | | | - Rachel L Huang
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Zeyu Zhu
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | | | - Xiaofu Cao
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Kaitlin Malley
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Zeyi Huang
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Muhammad Pasha
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Jon Anthony
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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39
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Reinkemeier CD, Lemke EA. Synthetic Organelles for Multiple mRNA Selective Genetic Code Expansions in Eukaryotes. Methods Mol Biol 2023; 2563:341-369. [PMID: 36227482 DOI: 10.1007/978-1-0716-2663-4_17] [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: 06/16/2023]
Abstract
Engineering new functionalities into living eukaryotic systems is one of the main goals of synthetic biology. To this end, often enzyme evolution or de novo protein design is employed, which each have their own advantages and disadvantages. As complimentary tools, we recently developed orthogonally translating and film-like synthetic organelles that allow to create new enzyme functionalities based on spatial separation. We applied this technology to genetic code expansion (GCE) and showed that it is possible to equip eukaryotic cells with multiple orthogonal genetic codes that enable the specific reprogramming of distinct translational machineries, each with single-residue precision.In this protocol, we describe how synthetic organelles can be used to perform mRNA selective GCE and how they can be further developed to allow the simultaneous incorporation of distinct noncanonical amino acids (ncAAs) into selected proteins and how this can be used to label proteins selectively with fluorescent dyes via bioorthogonal chemistry.
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Affiliation(s)
- Christopher D Reinkemeier
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Edward A Lemke
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg University Mainz, Mainz, Germany.
- Institute of Molecular Biology gGmbH, Mainz, Germany.
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40
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Koch NG, Budisa N. Focused Engineering of Pyrrolysyl-tRNA Synthetase-Based Orthogonal Translation Systems for the Incorporation of Various Noncanonical Amino Acids. Methods Mol Biol 2023; 2676:3-19. [PMID: 37277621 DOI: 10.1007/978-1-0716-3251-2_1] [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: 06/07/2023]
Abstract
The expansion of the genetic code has become a valuable tool for molecular biology, biochemistry, and biotechnology. The pyrrolysyl-tRNA synthetase (PylRS) variants with their cognate tRNAPyl derived from methanogenic archaea of the genus Methanosarcina are the most popular tools for ribosomally mediated site-specific and proteome-wide statistical incorporation of noncanonical amino acids (ncAAs) into proteins. The incorporation of ncAAs can be used for numerous biotechnological and even therapeutically relevant applications. Here we present a protocol of engineering PylRS for novel substrates with unique chemical functionalities. These functional groups can act as intrinsic probes, especially in complex biological environments such as mammalian cells, tissues, and even whole animals.
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Affiliation(s)
- Nikolaj G Koch
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Nediljko Budisa
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany.
- Chemical Synthetic Biology, Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada.
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41
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Zheng Z, Xia Q. Noncanonical Amino Acid Incorporation in Mice. Methods Mol Biol 2023; 2676:265-284. [PMID: 37277639 DOI: 10.1007/978-1-0716-3251-2_19] [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: 06/07/2023]
Abstract
Genetic code expansion enables in cellulo biosynthesis of curative proteins with enhanced specificity, improved stability, and even novel functions, due to the incorporation of artificial, designed, noncanonical amino acids (ncAAs). In addition, this orthogonal system also holds great potential for in vivo suppressing nonsense mutations during protein translation, providing an alternative strategy for alleviating inherited diseases caused by premature termination codons (PTCs). Here we describe the approach to explore the therapeutic efficacy and long-term safety of this strategy in transgenic mdx mice with stably expanded genetic codes. Theoretically, this method is applicable to about 11% of monogenic diseases involving nonsense mutations.
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Affiliation(s)
- Zhetao Zheng
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Qing Xia
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China.
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42
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Travis CR, Francis DY, Williams DC, Waters ML. Evaluation of acyllysine isostere interactions with the aromatic pocket of the AF9 YEATS domain. Protein Sci 2023; 32:e4533. [PMID: 36482045 PMCID: PMC9793969 DOI: 10.1002/pro.4533] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/21/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
Amide-π interactions, in which an amide interacts with an aromatic group, are ubiquitous in biology, yet remain understudied relative to other noncovalent interactions. Recently, we demonstrated that an electrostatically tunable amide-π interaction is key to recognition of histone acyllysine by the AF9 YEATS domain, a reader protein which has emerged as a therapeutic target due to its dysregulation in cancer. Amide isosteres are commonly employed in drug discovery, often to prevent degradation by proteases, and have proven valuable in achieving selectivity when targeting epigenetic proteins. However, like amide-π interactions, interactions of amide isosteres with aromatic rings have not been thoroughly studied despite widespread use. Herein, we evaluate the recognition of a series of amide isosteres by the AF9 YEATS domain using genetic code expansion to evaluate the amide isostere-π interaction. We show that compared to the amide-π interaction with the native ligand, each isostere exhibits similar electrostatic tunability with an aromatic residue in the binding pocket, demonstrating that the isosteres maintain similar interactions with the aromatic residue. We identify a urea-containing ligand that binds with enhanced affinity for the AF9 YEATS domain, offering a promising starting point for inhibitor development. Furthermore, we demonstrate that carbamate and urea isosteres of crotonyllysine are resistant to enzymatic removal by SIRT1, a protein that cleaves acyl post-translational modifications, further indicating the potential of amide isosteres in YEATS domain inhibitor development. These results also provide experimental precedent for interactions of these common drug discovery moieties with aromatic rings that can inform computational methods.
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Affiliation(s)
- Christopher R. Travis
- Department of Chemistry, CB 3290University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Denver Y. Francis
- Department of Chemistry, CB 3290University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - David C. Williams
- Department of Pathology and Laboratory Medicine, CB 7525University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
- Lineberger Comprehensive Cancer CenterUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Marcey L. Waters
- Department of Chemistry, CB 3290University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
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43
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Avila-Crump S, Hemshorn ML, Jones CM, Mbengi L, Meyer K, Griffis JA, Jana S, Petrina GE, Pagar VV, Karplus PA, Petersson EJ, Perona JJ, Mehl RA, Cooley RB. Generating Efficient Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetases for Structurally Diverse Non-Canonical Amino Acids. ACS Chem Biol 2022; 17:3458-3469. [PMID: 36383641 PMCID: PMC9833845 DOI: 10.1021/acschembio.2c00639] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Genetic code expansion (GCE) technologies commonly use the pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs from Methanosarcina mazei (Mm) and Methanosarcina barkeri (Mb) for site-specific incorporation of non-canonical amino acids (ncAAs) into proteins. Recently a homologous PylRS/tRNAPyl pair from Candidatus Methanomethylophilus alvus Mx1201 (Ma) was developed that, lacking the N-terminal tRNA-recognition domain of most PylRSs, overcomes insolubility, instability, and proteolysis issues seen with Mb/Mm PylRSs. An open question is how to alter Ma PylRS specificity to encode specific ncAAs with high efficiency. Prior work focused on "transplanting" ncAA substrate specificity by reconstructing the same active site mutations found in functional Mm/Mb PylRSs in Ma PylRS. Here, we found that this strategy produced low-efficiency Ma PylRSs for encoding three structurally diverse ncAAs: acridonyl-alanine (Acd), 3-nitro-tyrosine, and m-methyl-tetrazinyl-phenylalanine (Tet3.0-Me). On the other hand, efficient Ma PylRS variants were generated by a conventional life/death selection process from a large library of active site mutants: for Acd encoding, one variant was highly functional in HEK293T cells at just 10 μM Acd; for nitroY encoding, two variants also encoded 3-chloro, 3-bromo-, and 3-iodo-tyrosine at high efficiency; and for Tet-3.0-Me, all variants were more functional at lower ncAA concentrations. All Ma PylRS variants identified through selection had at least two different active site residues when compared with their Mb PylRS counterparts. We conclude that Ma and Mm/Mb PylRSs are sufficiently different that "active site transplantation" yields suboptimal Ma GCE systems. This work establishes a paradigm for expanding the utility of the promising Ma PylRS/tRNAPyl GCE platform.
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Affiliation(s)
- Savanna Avila-Crump
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Marcus L. Hemshorn
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Chloe M. Jones
- Biochemistry and Molecular Biophysics Graduate Group; University of Pennsylvania; 3700 Hamilton Walk, Philadelphia, PA 19104, USA
| | - Lea Mbengi
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207, USA
| | - Kyle Meyer
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207, USA
| | - Joshua A. Griffis
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Subhashis Jana
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Grace E. Petrina
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Vinayak V. Pagar
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - P. Andrew Karplus
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - E. James Petersson
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - John J. Perona
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207, USA
| | - Ryan A. Mehl
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
| | - Richard B. Cooley
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331, USA
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44
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Rosato F, Pasupuleti R, Tomisch J, Meléndez AV, Kolanovic D, Makshakova ON, Wiltschi B, Römer W. A bispecific, crosslinking lectibody activates cytotoxic T cells and induces cancer cell death. J Transl Med 2022; 20:578. [PMID: 36494671 PMCID: PMC9733292 DOI: 10.1186/s12967-022-03794-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Aberrant glycosylation patterns play a crucial role in the development of cancer cells as they promote tumor growth and aggressiveness. Lectins recognize carbohydrate antigens attached to proteins and lipids on cell surfaces and represent potential tools for application in cancer diagnostics and therapy. Among the emerging cancer therapies, immunotherapy has become a promising treatment modality for various hematological and solid malignancies. Here we present an approach to redirect the immune system into fighting cancer by targeting altered glycans at the surface of malignant cells. We developed a so-called "lectibody", a bispecific construct composed of a lectin linked to an antibody fragment. This lectibody is inspired by bispecific T cell engager (BiTEs) antibodies that recruit cytotoxic T lymphocytes (CTLs) while simultaneously binding to tumor-associated antigens (TAAs) on cancer cells. The tumor-related glycosphingolipid globotriaosylceramide (Gb3) represents the target of this proof-of-concept study. It is recognized with high selectivity by the B-subunit of the pathogen-derived Shiga toxin, presenting opportunities for clinical development. METHODS The lectibody was realized by conjugating an anti-CD3 single-chain antibody fragment to the B-subunit of Shiga toxin to target Gb3+ cancer cells. The reactive non-canonical amino acid azidolysine (AzK) was inserted at predefined single positions in both proteins. The azido groups were functionalized by bioorthogonal conjugation with individual linkers that facilitated selective coupling via an alternative bioorthogonal click chemistry reaction. In vitro cell-based assays were conducted to evaluate the antitumoral activity of the lectibody. CTLs, Burkitt´s lymphoma-derived cells and colorectal adenocarcinoma cell lines were screened in flow cytometry and cytotoxicity assays for activation and lysis, respectively. RESULTS This proof-of-concept study demonstrates that the lectibody activates T cells for their cytotoxic signaling, redirecting CTLs´ cytotoxicity in a highly selective manner and resulting in nearly complete tumor cell lysis-up to 93%-of Gb3+ tumor cells in vitro. CONCLUSIONS This research highlights the potential of lectins in targeting certain tumors, with an opportunity for new cancer treatments. When considering a combinatorial strategy, lectin-based platforms of this type offer the possibility to target glycan epitopes on tumor cells and boost the efficacy of current therapies, providing an additional strategy for tumor eradication and improving patient outcomes.
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Affiliation(s)
- Francesca Rosato
- grid.5963.9Faculty of Biology, University of Freiburg, Freiburg, Germany ,grid.5963.9Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Rajeev Pasupuleti
- grid.432147.70000 0004 0591 4434ACIB - The Austrian Centre of Industrial Biotechnology, Graz, Austria ,grid.410413.30000 0001 2294 748XInstitute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Jana Tomisch
- grid.5963.9Faculty of Biology, University of Freiburg, Freiburg, Germany ,grid.5963.9Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Ana Valeria Meléndez
- grid.5963.9Faculty of Biology, University of Freiburg, Freiburg, Germany ,grid.5963.9Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany ,grid.5963.9Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Dajana Kolanovic
- grid.432147.70000 0004 0591 4434ACIB - The Austrian Centre of Industrial Biotechnology, Graz, Austria ,grid.410413.30000 0001 2294 748XInstitute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Olga N. Makshakova
- grid.5963.9Faculty of Biology, University of Freiburg, Freiburg, Germany ,grid.419733.b0000 0004 0487 3538Kazan Institute for Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russian Federation
| | - Birgit Wiltschi
- grid.432147.70000 0004 0591 4434ACIB - The Austrian Centre of Industrial Biotechnology, Graz, Austria ,grid.410413.30000 0001 2294 748XInstitute of Molecular Biotechnology, Graz University of Technology, Graz, Austria ,grid.5173.00000 0001 2298 5320Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Winfried Römer
- grid.5963.9Faculty of Biology, University of Freiburg, Freiburg, Germany ,grid.5963.9Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany ,grid.5963.9Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
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Morse JS, Sheng YJ, Hampton JT, Sylvain LD, Das S, Alugubelli YR, Chen PC, Yang KS, Xu S, Fierke CA, Liu WR. Phage-assisted, active site-directed ligand evolution of a potent and selective histone deacetylase 8 inhibitor. Protein Sci 2022; 31:e4512. [PMID: 36382882 PMCID: PMC9703592 DOI: 10.1002/pro.4512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/04/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022]
Abstract
Phage-assisted, active site-directed ligand evolution (PADLE) is a recently developed technique that uses an amber codon-encoded noncanonical amino acid (ncAA) as an anchor to direct phage-displayed peptides to a target for an enhanced ligand identification process. 2-Amino-8-oxodecanoic acid (Aoda) is a ketone-containing ncAA residue in the macrocyclic peptide natural product apicidin that is a pan-inhibitor of Zn2+ -dependent histone deacetylases (HDACs). Its ketone serves as an anchoring point to coordinate the catalytic zinc ion in HDACs. Using a previously evolved N𝜀 -acetyl-lysyl-tRNA synthetase in combination with tRNAPyl , we showed that Aoda was efficiently incorporated into proteins in Escherichia coli by amber suppression. By propagating an amber codon-obligate phagemid library in E. coli encoding Aoda, we generated an Aoda-containing phage-displayed peptide library. Using this library to conduct PADLE against HDAC8 revealed a 7-mer peptide GH8P01F1 with Aoda-flanking amino acid residues that matched existing peptide sequences in identified HDAC8 substrates. Switching Aoda in GH8P01F1 to a more Zn2+ -chelating ncAA S-2-amino-8-hydroxyamino-8-oxooctanoic acid (Asuha) led to an extremely potent compound GH8HA01, which has an HDAC8-inhibition Ki value of 0.67 nM. GH8HA01 and its 5-mer truncation analogue Ac-GH8HA01Δ1Δ7 that has an HDAC8-inhibition Ki value of 0.31 nM are two of the most potent HDAC8 inhibitors that have been developed. Furthermore, both are highly selective against HDAC8 compared with other HDACs tested, demonstrating the great potential of using PADLE to identify highly potent and selective ligands for targets with conserved active sites among homologues.
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Affiliation(s)
- Jared S. Morse
- Texas A&M Drug Discovery Laboratory, Department of ChemistryTexas A&M UniversityTexasUSA
| | - Yan J. Sheng
- Texas A&M Drug Discovery Laboratory, Department of ChemistryTexas A&M UniversityTexasUSA
| | - Joshua Trae Hampton
- Texas A&M Drug Discovery Laboratory, Department of ChemistryTexas A&M UniversityTexasUSA
| | - Lauralee D. Sylvain
- Texas A&M Drug Discovery Laboratory, Department of ChemistryTexas A&M UniversityTexasUSA
| | - Sukant Das
- Texas A&M Drug Discovery Laboratory, Department of ChemistryTexas A&M UniversityTexasUSA
| | - Yugendar R. Alugubelli
- Texas A&M Drug Discovery Laboratory, Department of ChemistryTexas A&M UniversityTexasUSA
| | - Peng‐Hsun Chase Chen
- Texas A&M Drug Discovery Laboratory, Department of ChemistryTexas A&M UniversityTexasUSA
| | - Kai S. Yang
- Texas A&M Drug Discovery Laboratory, Department of ChemistryTexas A&M UniversityTexasUSA
| | - Shiqing Xu
- Texas A&M Drug Discovery Laboratory, Department of ChemistryTexas A&M UniversityTexasUSA
| | - Carol A. Fierke
- Department of BiochemistryBrandeis UniversityWalthamMassachusettsUSA
| | - Wenshe Ray Liu
- Texas A&M Drug Discovery Laboratory, Department of ChemistryTexas A&M UniversityTexasUSA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of MedicineTexas A&M UniversityHoustonTexasUSA
- Department of Biochemistry and BiophysicsTexas A&M UniversityTexasUSA
- Department of Molecular and Cellular Medicine, College of MedicineTexas A&M UniversityTexasUSA
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46
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Zackin MT, Stieglitz JT, Van Deventer JA. Genome-Wide Screen for Enhanced Noncanonical Amino Acid Incorporation in Yeast. ACS Synth Biol 2022; 11:3669-3680. [PMID: 36346914 PMCID: PMC10065164 DOI: 10.1021/acssynbio.2c00267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Numerous applications of noncanonical amino acids (ncAAs) in basic biology and therapeutic development require efficient protein biosynthesis using an expanded genetic code. However, achieving such incorporation at repurposed stop codons in cells is generally inefficient and limited by complex cellular processes that preserve the fidelity of protein synthesis. A more comprehensive understanding of the processes that contribute to ncAA incorporation would aid in the development of genomic engineering strategies for augmenting genetic code manipulation. In this work, we used a series of fluorescent reporters to screen a pooled Saccharomyces cerevisiae molecular barcoded yeast knockout (YKO) collection. Fluorescence-activated cell sorting enabled isolation of strains encoding single-gene deletions exhibiting improved ncAA incorporation efficiency in response to the amber (TAG) stop codon; 55 unique candidate deletions were identified. The deleted genes encoded for proteins that participate in diverse cellular processes, including many genes that have no known connection with protein translation. We then verified that two knockouts, yil014c-aΔ and alo1Δ, exhibited improved ncAA incorporation efficiency starting from independently acquired strains possessing the knockouts. Using additional orthogonal translation systems and ncAAs, we determined that yil014c-aΔ and alo1Δ enhance ncAA incorporation efficiency without loss of fidelity over a wide range of conditions. Our findings highlight opportunities for further modulating gene expression with genetic, genomic, and synthetic biology approaches to improve ncAA incorporation efficiency. In addition, these discoveries have the potential to enhance our fundamental understanding of protein translation. Ultimately, cells that efficiently biosynthesize ncAA-containing proteins will streamline the realization of applications utilizing expanded genetic codes ranging from basic biology to drug discovery.
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Affiliation(s)
- Matthew T. Zackin
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
| | - Jessica T. Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
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47
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Koch NG, Baumann T, Nickling JH, Dziegielewski A, Budisa N. Engineered bacterial host for genetic encoding of physiologically stable protein nitration. Front Mol Biosci 2022; 9:992748. [PMID: 36353730 PMCID: PMC9638147 DOI: 10.3389/fmolb.2022.992748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/16/2022] [Indexed: 11/23/2022] Open
Abstract
Across scales, many biological phenomena, such as protein folding or bioadhesion and cohesion, rely on synergistic effects of different amino acid side chains at multiple positions in the protein sequence. These are often fine-tuned by post-translational modifications that introduce additional chemical properties. Several PTMs can now be genetically encoded and precisely installed at single and multiple sites by genetic code expansion. Protein nitration is a PTM of particular interest because it has been associated with several diseases. However, even when these nitro groups are directly incorporated into proteins, they are often physiologically reduced during or shortly after protein production. We have solved this problem by using an engineered Escherichia coli host strain. Six genes that are associated with nitroreductase activity were removed from the genome in a simple and robust manner. The result is a bacterial expression host that can stably produce proteins and peptides containing nitro groups, especially when these are amenable to modification. To demonstrate the applicability of this strain, we used this host for several applications. One of these was the multisite incorporation of a photocaged 3,4-dihydroxyphenylalanine derivative into Elastin-Like Polypeptides. For this non-canonical amino acid and several other photocaged ncAAs, the nitro group is critical for photocleavability. Accordingly, our approach also enhances the production of biomolecules containing photocaged tyrosine in the form of ortho-nitrobenzyl-tyrosine. We envision our engineered host as an efficient tool for the production of custom designed proteins, peptides or biomaterials for various applications ranging from research in cell biology to large-scale production in biotechnology.
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Affiliation(s)
- Nikolaj G. Koch
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Tobias Baumann
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Jessica H. Nickling
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Anna Dziegielewski
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Nediljko Budisa
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
- Chemical Synthetic Biology Group, Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
- *Correspondence: Nediljko Budisa,
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48
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Lee J, Yang M, Song WJ. The expanded landscape of metalloproteins by genetic incorporation of noncanonical amino acids. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jaehee Lee
- Department of Chemistry Seoul National University Seoul South Korea
| | - Minwoo Yang
- Department of Chemistry Seoul National University Seoul South Korea
| | - Woon Ju Song
- Department of Chemistry Seoul National University Seoul South Korea
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49
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Wu K, Moore JA, Miller MD, Chen Y, Lee C, Xu W, Peng Z, Duan Q, Phillips GN, Uribe RA, Xiao H. Expanding the eukaryotic genetic code with a biosynthesized 21st amino acid. Protein Sci 2022; 31:e4443. [PMID: 36173166 PMCID: PMC9601876 DOI: 10.1002/pro.4443] [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: 06/18/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 01/31/2023]
Abstract
Genetic code expansion technology allows for the use of noncanonical amino acids (ncAAs) to create semisynthetic organisms for both biochemical and biomedical applications. However, exogenous feeding of chemically synthesized ncAAs at high concentrations is required to compensate for the inefficient cellular uptake and incorporation of these components into proteins, especially in the case of eukaryotic cells and multicellular organisms. To generate organisms capable of autonomously biosynthesizing an ncAA and incorporating it into proteins, we have engineered a metabolic pathway for the synthesis of O-methyltyrosine (OMeY). Specifically, we endowed organisms with a marformycins biosynthetic pathway-derived methyltransferase that efficiently converts tyrosine to OMeY in the presence of the co-factor S-adenosylmethionine. The resulting cells can produce and site-specifically incorporate OMeY into proteins at much higher levels than cells exogenously fed OMeY. To understand the structural basis for the substrate selectivity of the transferase, we solved the X-ray crystal structures of the ligand-free and tyrosine-bound enzymes. Most importantly, we have extended this OMeY biosynthetic system to both mammalian cells and the zebrafish model to enhance the utility of genetic code expansion. The creation of autonomous eukaryotes using a 21st amino acid will make genetic code expansion technology more applicable to multicellular organisms, providing valuable vertebrate models for biological and biomedical research.
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Affiliation(s)
- Kuan‐Lin Wu
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Joshua A. Moore
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Biochemistry and Cell Biology ProgramRice UniversityHoustonTexasUSA
| | | | - Yuda Chen
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Catherine Lee
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Weijun Xu
- Department of BiosciencesRice UniversityHoustonTexasUSA
| | - Zane Peng
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Qinghui Duan
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - George N. Phillips
- Department of ChemistryRice UniversityHoustonTexasUSA
- Department of BiosciencesRice UniversityHoustonTexasUSA
| | - Rosa A. Uribe
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Biochemistry and Cell Biology ProgramRice UniversityHoustonTexasUSA
| | - Han Xiao
- Department of ChemistryRice UniversityHoustonTexasUSA
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of BioengineeringRice UniversityHoustonTexasUSA
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50
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Meng K, Chung CZ, Söll D, Krahn N. Unconventional genetic code systems in archaea. Front Microbiol 2022; 13:1007832. [PMID: 36160229 PMCID: PMC9499178 DOI: 10.3389/fmicb.2022.1007832] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Archaea constitute the third domain of life, distinct from bacteria and eukaryotes given their ability to tolerate extreme environments. To survive these harsh conditions, certain archaeal lineages possess unique genetic code systems to encode either selenocysteine or pyrrolysine, rare amino acids not found in all organisms. Furthermore, archaea utilize alternate tRNA-dependent pathways to biosynthesize and incorporate members of the 20 canonical amino acids. Recent discoveries of new archaeal species have revealed the co-occurrence of these genetic code systems within a single lineage. This review discusses the diverse genetic code systems of archaea, while detailing the associated biochemical elements and molecular mechanisms.
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Affiliation(s)
- Kexin Meng
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
| | - Christina Z. Chung
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Natalie Krahn
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
- *Correspondence: Natalie Krahn,
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