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Dunkelmann DL, Chin JW. Engineering Pyrrolysine Systems for Genetic Code Expansion and Reprogramming. Chem Rev 2024. [PMID: 39235427 DOI: 10.1021/acs.chemrev.4c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Over the past 16 years, genetic code expansion and reprogramming in living organisms has been transformed by advances that leverage the unique properties of pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs. Here we summarize the discovery of the pyrrolysine system and describe the unique properties of PylRS/tRNAPyl pairs that provide a foundation for their transformational role in genetic code expansion and reprogramming. We describe the development of genetic code expansion, from E. coli to all domains of life, using PylRS/tRNAPyl pairs, and the development of systems that biosynthesize and incorporate ncAAs using pyl systems. We review applications that have been uniquely enabled by the development of PylRS/tRNAPyl pairs for incorporating new noncanonical amino acids (ncAAs), and strategies for engineering PylRS/tRNAPyl pairs to add noncanonical monomers, beyond α-L-amino acids, to the genetic code of living organisms. We review rapid progress in the discovery and scalable generation of mutually orthogonal PylRS/tRNAPyl pairs that can be directed to incorporate diverse ncAAs in response to diverse codons, and we review strategies for incorporating multiple distinct ncAAs into proteins using mutually orthogonal PylRS/tRNAPyl pairs. Finally, we review recent advances in the encoded cellular synthesis of noncanonical polymers and macrocycles and discuss future developments for PylRS/tRNAPyl pairs.
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Affiliation(s)
- Daniel L Dunkelmann
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
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2
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Kim JM, Jung J. Highly chromophoric fluorescent-labeled methionyl-initiator tRNAs applicable in living cells. Biotechnol J 2024; 19:e2300579. [PMID: 38494424 DOI: 10.1002/biot.202300579] [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: 10/25/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 03/19/2024]
Abstract
Fluorescent initiator tRNAs (tRNAi) play a crucial role in studying protein synthesis, yet generating highly fluorescent tRNAi complexes remains challenging. We present an optimized strategy to effectively generate highly fluorescent initiator-tRNA complexes in living cells. Our strategy allows the generation of Fluo-Met-tRNAiMet complexes. These complexes can have highly chromogenic N-terminal labeling. For generating such complexes, we use either purified fluorescent methionine (PFM) or non-purified fluorescently labeled methionine (NPFM). Furthermore, PFM promotes the active generation of endogenous tRNAi in cells, leading to highly efficient Fluo-Met-tRNAiMet complexes. Finally, PFM-tRNAiMet complexes also facilitate the visualization of native fluorescently labeled Tat binding to beads. This demonstrates the potential of our approach to advance precision protein engineering and biotechnology applications.
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Affiliation(s)
- Jung Min Kim
- Ojeong Resilience Institute, Korea University, Seoul, Republic of Korea
| | - Jinho Jung
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
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3
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Ditzel A, Zhao F, Gao X, Phillips GN. Utilizing a cell-free protein synthesis platform for the biosynthesis of a natural product, caffeine. Synth Biol (Oxf) 2023; 8:ysad017. [PMID: 38149044 PMCID: PMC10750991 DOI: 10.1093/synbio/ysad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 10/24/2023] [Accepted: 12/20/2023] [Indexed: 12/28/2023] Open
Abstract
Natural products are a valuable source of pharmaceuticals, providing a majority of the small-molecule drugs in use today. However, their production through organic synthesis or in heterologous hosts can be difficult and time-consuming. Therefore, to allow for easier screening and production of natural products, we demonstrated the use of a cell-free protein synthesis system to partially assemble natural products in vitro using S-Adenosyl Methionine (SAM)-dependent methyltransferase enzyme reactions. The tea caffeine synthase, TCS1, was utilized to synthesize caffeine within a cell-free protein synthesis system. Cell-free systems also provide the benefit of allowing the use of substrates that would normally be toxic in a cellular environment to synthesize novel products. However, TCS1 is unable to utilize a compound like S-adenosyl ethionine as a cofactor to create ethylated caffeine analogs. The automation and reduced metabolic engineering requirements of cell-free protein synthesis systems, in combination with other synthesis methods, may enable the more efficient generation of new compounds. Graphical Abstract.
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Affiliation(s)
| | - Fanglong Zhao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
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Yue K, Chen J, Li Y, Kai L. Advancing synthetic biology through cell-free protein synthesis. Comput Struct Biotechnol J 2023; 21:2899-2908. [PMID: 37216017 PMCID: PMC10196276 DOI: 10.1016/j.csbj.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
The rapid development of synthetic biology has enabled the production of compounds with revolutionary improvements in biotechnology. DNA manipulation tools have expedited the engineering of cellular systems for this purpose. Nonetheless, the inherent constraints of cellular systems persist, imposing an upper limit on mass and energy conversion efficiencies. Cell-free protein synthesis (CFPS) has demonstrated its potential to overcome these inherent constraints and has been instrumental in the further advancement of synthetic biology. Via the removal of the cell membranes and redundant parts of cells, CFPS has provided flexibility in directly dissecting and manipulating the Central Dogma with rapid feedback. This mini-review summarizes recent achievements of the CFPS technique and its application to a wide range of synthetic biology projects, such as minimal cell assembly, metabolic engineering, and recombinant protein production for therapeutics, as well as biosensor development for in vitro diagnostics. In addition, current challenges and future perspectives in developing a generalized cell-free synthetic biology are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Junyu Chen
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
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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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Cell-free protein synthesis systems for vaccine design and production. Curr Opin Biotechnol 2023; 79:102888. [PMID: 36641905 DOI: 10.1016/j.copbio.2022.102888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023]
Abstract
Vaccines are vital for protection against existing and emergent diseases. Current vaccine production strategies are limited by long production times, risky viral material, weak immunogenicity, and poor stability, ultimately restricting the safe or rapid production of vaccines for widespread utilization. Cell-free protein synthesis (CFPS) systems, which use extracted transcriptional and translational machinery from cells, are promising tools for vaccine production because they can rapidly produce proteins without the constraints of living cells, have a highly optimizable open system, and can be used for on-demand biomanufacturing. Here, we review how CFPS systems have been explored for the production of subunit, conjugate, virus-like particle (VLP), and membrane-augmented vaccines and as a tool in vaccine design. We also discuss efforts to address potential limitations with CFPS such as the presence of endotoxins, poor protein folding, reaction stability, and glycosylation to enable promising future vaccine design and production.
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Iskandar SE, Pelton JM, Wick ET, Bolhuis DL, Baldwin AS, Emanuele MJ, Brown NG, Bowers AA. Enabling Genetic Code Expansion and Peptide Macrocyclization in mRNA Display via a Promiscuous Orthogonal Aminoacyl-tRNA Synthetase. J Am Chem Soc 2023; 145:1512-1517. [PMID: 36630539 PMCID: PMC10411329 DOI: 10.1021/jacs.2c11294] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
mRNA display is revolutionizing peptide drug discovery through its ability to quickly identify potent peptide binders of therapeutic protein targets. Methods to expand the chemical diversity of display libraries are continually needed to increase the likelihood of identifying clinically relevant peptide ligands. Orthogonal aminoacyl-tRNA synthetases (ORSs) have proven utility in cellular genetic code expansion, but are relatively underexplored for in vitro translation (IVT) and mRNA display. Herein, we demonstrate that the promiscuous ORS p-CNF-RS can incorporate noncanonical amino acids at amber codons in IVT, including the novel substrate p-cyanopyridylalanine (p-CNpyrA), to enable a pyridine-thiazoline (pyr-thn) macrocyclization in mRNA display. Pyr-thn-based selections against the deubiquitinase USP15 yielded a potent macrocyclic binder that exhibits good selectivity for USP15 and close homologues over other ubiquitin-specific proteases (USPs). Overall, this work exemplifies how promiscuous ORSs can both expand side chain diversity and provide structural novelty in mRNA display libraries through a heterocycle forming macrocyclization.
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Affiliation(s)
- Sabrina E. Iskandar
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jarrett M. Pelton
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Elizaveta T. Wick
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Derek L. Bolhuis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Albert S. Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Michael J. Emanuele
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Nicholas G. Brown
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Yue K, Li Y, Cao M, Shen L, Gu J, Kai L. Bottom-Up Synthetic Biology Using Cell-Free Protein Synthesis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:1-20. [PMID: 37526707 DOI: 10.1007/10_2023_232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Technical advances in biotechnology have greatly accelerated the development of bottom-up synthetic biology. Unlike top-down approaches, bottom-up synthetic biology focuses on the construction of a minimal cell from scratch and the application of these principles to solve challenges. Cell-free protein synthesis (CFPS) systems provide minimal machinery for transcription and translation, from either a fractionated cell lysate or individual purified protein elements, thus speeding up the development of synthetic cell projects. In this review, we trace the history of the cell-free technique back to the first in vitro fermentation experiment using yeast cell lysate. Furthermore, we summarized progresses of individual cell mimicry modules, such as compartmentalization, gene expression regulation, energy regeneration and metabolism, growth and division, communication, and motility. Finally, current challenges and future perspectives on the field are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Mengjiao Cao
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lulu Shen
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingsheng Gu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China.
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9
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Wright DE, Siddika T, Heinemann IU, O’Donoghue P. Delivery of the selenoprotein thioredoxin reductase 1 to mammalian cells. Front Mol Biosci 2022; 9:1031756. [PMID: 36304926 PMCID: PMC9595596 DOI: 10.3389/fmolb.2022.1031756] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Over-expression of genetically encoded thioredoxin reductase 1 (TrxR1) TrxR1 can be toxic to cells due to the formation of a truncated version of the enzyme. We developed a new mammalian cell-based model to investigate TrxR1 activity. Fusion of the HIV-derived cell penetrating peptide (TAT) enabled efficient cellular uptake of purified TrxR1 containing 21 genetically encoded amino acids, including selenocysteine. The TAT peptide did not significantly alter the catalytic activity of TrxR1 in vitro. We monitored TrxR1-dependent redox activity in human cells using a TrxR1-specific red fluorescent live-cell reporter. Using programmed selenocysteine incorporation in Escherichia coli, our approach allowed efficient production of active recombinant human selenoprotein TrxR1 for delivery to the homologous context of the mammalian cell. The delivered TAT-TrxR1 showed robust activity in live cells and provided a novel platform to study TrxR1 biology in human cells.
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Nagappa LK, Sato W, Alam F, Chengan K, Smales CM, Von Der Haar T, Polizzi KM, Adamala KP, Moore SJ. A ubiquitous amino acid source for prokaryotic and eukaryotic cell-free transcription-translation systems. Front Bioeng Biotechnol 2022; 10:992708. [PMID: 36185432 PMCID: PMC9524191 DOI: 10.3389/fbioe.2022.992708] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022] Open
Abstract
Cell-free gene expression (CFE) systems are an attractive tool for engineering within synthetic biology and for industrial production of high-value recombinant proteins. CFE reactions require a cell extract, energy system, amino acids, and DNA, to catalyse mRNA transcription and protein synthesis. To provide an amino acid source, CFE systems typically use a commercial standard, which is often proprietary. Herein we show that a range of common microbiology rich media (i.e., tryptone, peptone, yeast extract and casamino acids) unexpectedly provide an effective and low-cost amino acid source. We show that this approach is generalisable, by comparing batch variability and protein production in the following range of CFE systems: Escherichia coli (Rosetta™ 2 (DE3), BL21(DE3)), Streptomyces venezuelae and Pichia pastoris. In all CFE systems, we show equivalent or increased protein synthesis capacity upon replacement of the commercial amino acid source. In conclusion, we suggest rich microbiology media provides a new amino acid source for CFE systems with potential broad use in synthetic biology and industrial biotechnology applications.
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Affiliation(s)
| | - Wakana Sato
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States
| | - Farzana Alam
- Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | | | | | | | - Karen M Polizzi
- Centre for Synthetic Biology, Imperial College London, London, United Kingdom
- Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States
| | - Simon J Moore
- School of Biosciences, University of Kent, Canterbury, United Kingdom
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