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Lino BR, Williams SJ, Castor ME, Van Deventer JA. Reaching New Heights in Genetic Code Manipulation with High Throughput Screening. Chem Rev 2024; 124:12145-12175. [PMID: 39418482 PMCID: PMC11879460 DOI: 10.1021/acs.chemrev.4c00329] [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: 10/19/2024]
Abstract
The chemical and physical properties of proteins are limited by the 20 canonical amino acids. Genetic code manipulation allows for the incorporation of noncanonical amino acids (ncAAs) that enhance or alter protein functionality. This review explores advances in the three main strategies for introducing ncAAs into biosynthesized proteins, focusing on the role of high throughput screening in these advancements. The first section discusses engineering aminoacyl-tRNA synthetases (aaRSs) and tRNAs, emphasizing how novel selection methods improve characteristics including ncAA incorporation efficiency and selectivity. The second section examines high-throughput techniques for improving protein translation machinery, enabling accommodation of alternative genetic codes. This includes opportunities to enhance ncAA incorporation through engineering cellular components unrelated to translation. The final section highlights various discovery platforms for high-throughput screening of ncAA-containing proteins, showcasing innovative binding ligands and enzymes that are challenging to create with only canonical amino acids. These advances have led to promising drug leads and biocatalysts. Overall, the ability to discover unexpected functionalities through high-throughput methods significantly influences ncAA incorporation and its applications. Future innovations in experimental techniques, along with advancements in computational protein design and machine learning, are poised to further elevate this field.
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Affiliation(s)
- Briana R. Lino
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Sean J. Williams
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Michelle E. Castor
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
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2
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Harrison K, Mackay AS, Kambanis L, Maxwell JWC, Payne RJ. Synthesis and applications of mirror-image proteins. Nat Rev Chem 2023; 7:383-404. [PMID: 37173596 DOI: 10.1038/s41570-023-00493-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2023] [Indexed: 05/15/2023]
Abstract
The homochirality of biomolecules in nature, such as DNA, RNA, peptides and proteins, has played a critical role in establishing and sustaining life on Earth. This chiral bias has also given synthetic chemists the opportunity to generate molecules with inverted chirality, unlocking valuable new properties and applications. Advances in the field of chemical protein synthesis have underpinned the generation of numerous 'mirror-image' proteins (those comprised entirely of D-amino acids instead of canonical L-amino acids), which cannot be accessed using recombinant expression technologies. This Review seeks to highlight recent work on synthetic mirror-image proteins, with a focus on modern synthetic strategies that have been leveraged to access these complex biomolecules as well as their applications in protein crystallography, drug discovery and the creation of mirror-image life.
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Affiliation(s)
- Katriona Harrison
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Angus S Mackay
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Lucas Kambanis
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Joshua W C Maxwell
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia.
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia.
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Shakya B, Joyner OG, Hartman MCT. Hyperaccurate Ribosomes for Improved Genetic Code Reprogramming. ACS Synth Biol 2022; 11:2193-2201. [PMID: 35549158 PMCID: PMC10100576 DOI: 10.1021/acssynbio.2c00150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reprogramming of the genetic code through the introduction of noncanonical amino acids (ncAAs) has enabled exciting advances in synthetic biology and peptide drug discovery. Ribosomes that function with high efficiency and fidelity are necessary for all of these efforts, but for challenging ncAAs, the competing processes of near-cognate readthrough and peptidyl-tRNA dropoff can be issues. Here we uncover the surprising extent of these competing pathways in the PURE translation system using mRNAs encoding peptides with affinity tags at the N- and C-termini. We also show that hyperaccurate or error restrictive ribosomes with mutations in ribosomal protein S12 lead to significant improvements in yield and fidelity in the context of both canonical AAs and a challenging α,α-disubstituted ncAA. Hyperaccurate ribosomes also improve yields for quadruplet codon readthrough for a tRNA containing an expanded anticodon stem-loop, although they are not able to eliminate triplet codon reading by this tRNA. The impressive improvements in fidelity and the simplicity of introducing this mutation alongside other efforts to engineer the translation apparatus make hyperaccurate ribosomes an important advance for synthetic biology.
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Affiliation(s)
- Bipasana Shakya
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23220, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23220, United States
| | - Olivia G. Joyner
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23220, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23220, United States
| | - Matthew C. T. Hartman
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23220, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23220, United States
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Through the looking glass: milestones on the road towards mirroring life. Trends Biochem Sci 2021; 46:931-943. [PMID: 34294544 DOI: 10.1016/j.tibs.2021.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/05/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022]
Abstract
Naturally occurring DNA, RNA, and proteins predominantly exist in only one enantiomeric form (homochirality). Advances in biotechnology and chemical synthesis allow the production of the respective alternate enantiomeric form, enabling access to mirror-image versions of these natural biopolymers. Exploiting the unique properties of such mirror molecules has already led to many applications, such as biostable and nonimmunogenic therapeutics or sensors. However, a 'roadblock' for unlocking the mirror world is the lack of biological systems capable of synthesizing critical building blocks including mirror oligonucleotides and oligopeptides to reducing cost and improve purity. Here, we provide an overview of the current progress, applications, and challenges of the molecular mirror world by identifying milestones towards mirroring life.
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Abstract
The encoded biosynthesis of proteins provides the ultimate paradigm for high-fidelity synthesis of long polymers of defined sequence and composition, but it is limited to polymerizing the canonical amino acids. Recent advances have built on genetic code expansion - which commonly permits the cellular incorporation of one type of non-canonical amino acid into a protein - to enable the encoded incorporation of several distinct non-canonical amino acids. Developments include strategies to read quadruplet codons, use non-natural DNA base pairs, synthesize completely recoded genomes and create orthogonal translational components with reprogrammed specificities. These advances may enable the genetically encoded synthesis of non-canonical biopolymers and provide a platform for transforming the discovery and evolution of new materials and therapeutics.
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Affiliation(s)
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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Abstract
Genetic code expansion is one of the most powerful technologies in protein engineering. In addition to the 20 canonical amino acids, the expanded genetic code is supplemented by unnatural amino acids, which have artificial side chains that can be introduced into target proteins in vitro and in vivo. A wide range of chemical groups have been incorporated co-translationally into proteins in single cells and multicellular organisms by using genetic code expansion. Incorporated unnatural amino acids have been used for novel structure-function relationship studies, bioorthogonal labelling of proteins in cellulo for microscopy and in vivo for tissue-specific proteomics, the introduction of post-translational modifications and optical control of protein function, to name a few examples. In this Minireview, the development of genetic code expansion technology is briefly introduced, then its applications in neurobiology are discussed, with a focus on studies using mammalian cells and mice as model organisms.
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Affiliation(s)
- Ivana Nikić‐Spiegel
- Werner Reichardt Centre for Integrative NeuroscienceUniversity of TübingenOtfried-Müller-Strasse 2572076TübingenGermany
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Unremitting progresses for phosphoprotein synthesis. Curr Opin Chem Biol 2020; 58:96-111. [PMID: 32889414 DOI: 10.1016/j.cbpa.2020.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 02/03/2023]
Abstract
Phosphorylation, one of the important protein post-translational modifications, is involved in many essential cellular processes. Site-specifical and homogeneous phosphoproteins can be used as probes for elucidating the protein phosphorylation network and as potential therapeutics for interfering their involved biological events. However, the generation of phosphoproteins has been challenging owing to the limitation of chemical synthesis and protein expression systems. Despite the pioneering discoveries in phosphoprotein synthesis, over the past decade, great progresses in this field have also been made to promote the biofunctional exploration of protein phosphorylation largely. Therefore, in this review, we mainly summarize recent advances in phosphoprotein synthesis, which includes five sections: 1) synthesis of the nonhydrolyzable phosphorylated amino acid mimetic building blocks, 2) chemical total and semisynthesis strategy, 3) in-cell and in vitro genetic code expansion strategy, 4) the late-stage modification strategy, 5) nonoxygen phosphoprotein synthesis.
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Nagano M, Suga H. Expansion of Modality: Peptides to Pseudo-Natural Macrocyclic Peptides. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo
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Katoh T, Suga H. Ribosomal Elongation of Cyclic γ-Amino Acids using a Reprogrammed Genetic Code. J Am Chem Soc 2020; 142:4965-4969. [PMID: 32129615 DOI: 10.1021/jacs.9b12280] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Because γ-amino acids generally undergo rapid self-cyclization upon esterification on the carboxyl group, for example, γ-aminoacyl-tRNA, there are no reports of the ribosomal elongation of γ-amino acids to the best of our knowledge. To avoid such self-cyclization, we utilized cyclic γ-amino acids and demonstrated their elongation into a peptide chain. Although the incorporation of the cyclic γ-amino acids is intrinsically slow, we here show that the combination of elongation factor P and engineered tRNAs improves cyclic γ-amino acid incorporation efficiency. Via this method, thioether-macrocyclic peptides containing not only cyclic γ-amino acids but also d-α-, N-methyl-α-, and cyclic β-amino acids were expressed under the reprogrammed genetic code. Ribosomally synthesized macrocyclic peptide libraries containing cyclic γ-amino acids should be applicable to in vitro screening methodologies such as mRNA display for discovering novel peptide drugs.
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Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Efficient and robust preparation of tyrosine phosphorylated intrinsically disordered proteins. Biotechniques 2019; 67:16-22. [PMID: 31092000 DOI: 10.2144/btn-2019-0033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are subject to post-translational modifications. This allows the same polypeptide to be involved in different interaction networks with different consequences, ranging from regulatory signalling networks to the formation of membrane-less organelles. We report a robust method for co-expression of modification enzyme and SUMO-tagged IDPs with a subsequent purification procedure that allows for the production of modified IDP. The robustness of our protocol is demonstrated using a challenging system: RNA polymerase II C-terminal domain (CTD); that is, a low-complexity repetitive region with multiple phosphorylation sites. In vitro phosphorylation approaches fail to yield multiple-site phosphorylated CTD, whereas our in vivo protocol allows the rapid production of near homogeneous phosphorylated CTD at a low cost. These samples can be used in functional and structural studies.
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Jin X, Park OJ, Hong SH. Incorporation of non-standard amino acids into proteins: challenges, recent achievements, and emerging applications. Appl Microbiol Biotechnol 2019; 103:2947-2958. [PMID: 30790000 PMCID: PMC6449208 DOI: 10.1007/s00253-019-09690-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 12/19/2022]
Abstract
The natural genetic code only allows for 20 standard amino acids in protein translation, but genetic code reprogramming enables the incorporation of non-standard amino acids (NSAAs). Proteins containing NSAAs provide enhanced or novel properties and open diverse applications. With increased attention to the recent advancements in synthetic biology, various improved and novel methods have been developed to incorporate single and multiple distinct NSAAs into proteins. However, various challenges remain in regard to NSAA incorporation, such as low yield and misincorporation. In this review, we summarize the recent efforts to improve NSAA incorporation by utilizing orthogonal translational system optimization, cell-free protein synthesis, genomically recoded organisms, artificial codon boxes, quadruplet codons, and orthogonal ribosomes, before closing with a discussion of the emerging applications of NSAA incorporation.
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Affiliation(s)
- Xing Jin
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Oh-Jin Park
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
- Department of Biological and Chemical Engineering, Yanbian University of Science and Technology, Yanji, Jilin, People's Republic of China
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA.
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Gerrits M, Budisa N, Merk H. Site-Specific Chemoselective Pyrrolysine Analogues Incorporation Using the Cell-Free Protein Synthesis System. ACS Synth Biol 2019; 8:381-390. [PMID: 30589532 DOI: 10.1021/acssynbio.8b00421] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Cell-free protein synthesis (CFPS) is a fast and convenient way to synthesize proteins for analytical studies and applications. CFPS, when equipped with a suitable orthogonal pair, allows for protein-site-directed labeling with desired functionalities such as fluorescent dyes or therapeutic groups that are needed to tailor proteins for analytical applications. In this context, chemoselective reactive pyrrolysine analogues (CR-OAs) are of particular value, as this class of unnatural amino acids, among other useful properties, covers a wide range of different chemoselective reactions. In this study, we present a flexible approach that facilitates incorporation of CR-OAs in CFPS systems. In particular, a fairly simple addition of two expression plasmids in our cell-free system, one encoding pyrrolysyl-tRNA synthetase and the other one the target protein, enabled ribosomal synthesis of proteins in the half-milligram range with the pre-installed orthogonal reactivity, easily modifiable by using mild, copper-free bioorthogonal chemistry. Our CFPS system allows rapid and highly customizable expression, as shown by several examples of successful site-directed fluorescence labeling. The feasibility of our CFPS system for protein analytics is further proved by demonstrating the functional integrity of a labeled protein by interaction measurements using microscale thermophoresis.
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Affiliation(s)
- Michael Gerrits
- Biocatalysis Group, Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
- biotechrabbit GmbH, 12489 Berlin, Germany
| | - Nediljko Budisa
- Biocatalysis Group, Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
- Chemical Synthetic Biology, Department of Chemistry, University of Manitoba, 144 Dysart Road, R3T 2N2 Winnipeg, MB, Canada
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