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Liu J, Hu Y, Gu W, Lan H, Zhang Z, Jiang L, Xu X. Research progress on the application of cell-free synthesis systems for enzymatic processes. Crit Rev Biotechnol 2023; 43:938-955. [PMID: 35994247 DOI: 10.1080/07388551.2022.2090314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/24/2022] [Accepted: 04/09/2022] [Indexed: 11/03/2022]
Abstract
Cell-free synthesis systems can complete the transcription and translation process in vitro to produce complex proteins that are difficult to be expressed in traditional cell-based systems. Such systems also can be used for the assembly of efficient localized multienzyme cascades to synthesize products that are toxic to cells. Cell-free synthesis systems provide a simpler and faster engineering solution than living cells, allowing unprecedented design freedom. This paper reviews the latest progress on the application of cell-free synthesis systems in the field of enzymatic catalysis, including cell-free protein synthesis and cell-free metabolic engineering. In cell-free protein synthesis: complex proteins, toxic proteins, membrane proteins, and artificial proteins containing non-natural amino acids can be easily synthesized by directly controlling the reaction conditions in the cell-free system. In cell-free metabolic engineering, the synthesis of desired products can be made more specific and efficient by designing metabolic pathways and screening biocatalysts based on purified enzymes or crude extracts. Through the combination of cell-free synthesis systems and emerging technologies, such as: synthetic biology, microfluidic control, cofactor regeneration, and artificial scaffolds, we will be able to build increasingly complex biomolecule systems. In the next few years, these technologies are expected to mature and reach industrialization, providing innovative platforms for a wide range of biotechnological applications.
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Affiliation(s)
- Jie Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yongqi Hu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wanyi Gu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Haiquan Lan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zhidong Zhang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Xian Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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2
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Li J, Tang M, Qi H. Codon-Reduced Protein Synthesis With Manipulating tRNA Components in Cell-Free System. Front Bioeng Biotechnol 2022; 10:891808. [PMID: 35646841 PMCID: PMC9136035 DOI: 10.3389/fbioe.2022.891808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Manipulating transfer RNAs (tRNAs) for emancipating sense codons to simplify genetic codons in a cell-free protein synthesis (CFPS) system can offer more flexibility and controllability. Here, we provide an overview of the tRNA complement protein synthesis system construction in the tRNA-depleted Protein synthesis Using purified Recombinant Elements (PURE) system or S30 extract. These designed polypeptide coding sequences reduce the genetic codon and contain only a single tRNA corresponding to a single amino acid in this presented system. Strategies for removing tRNAs from cell lysates and synthesizing tRNAs in vivo/vitro are summarized and discussed in detail. Furthermore, we point out the trend toward a minimized genetic codon for reducing codon redundancy by manipulating tRNAs in the different proteins. It is hoped that the tRNA complement protein synthesis system can facilitate the construction of minimal cells and expand the biomedical application scope of synthetic biology.
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Affiliation(s)
- Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Mengtong Tang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- *Correspondence: Hao Qi,
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3
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Guo J, Zhu P, Ye Z, Wang M, Yang H, Huang S, Shu Y, Zhang W, Zhou H, Li Q. YRDC Mediates the Resistance of Lenvatinib in Hepatocarcinoma Cells via Modulating the Translation of KRAS. Front Pharmacol 2021; 12:744578. [PMID: 34658879 PMCID: PMC8517968 DOI: 10.3389/fphar.2021.744578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Lenvatinib is the latest and promising agent that has demonstrated a significant improvement of progression-free survival in advanced hepatocellular carcinoma (HCC). However, resistance emerges soon after initial treatment, limiting the clinical benefits of lenvatinib. Therefore, understanding the mechanism of resistance is necessary for improving lenvatinib efficacy. YRDC promotes the proliferation of hepatocarcinoma cells via regulating the activity of the RAS/RAF/MEK/ERK pathway, which was the primary pathway of the anticancer effect of lenvatinib. The purpose of this study is to investigate whether YRDC modulates the sensitivity of lenvatinib in hepatocarcinoma cells. Using the CCK-8 cell viability assay, wound-healing assay and clone formation assay in cell models, and xenograft assay in null mouse, we demonstrated that Huh7 cells with YRDC knockdown showed decreased susceptibility to lenvatinib than their control cells. Furthermore, we found that lenvatinib inhibited the expression of YRDC in a time-dependent manner. This effect may aggravate resistance to lenvatinib in hepatocarcinoma cells and may be an underlying cause of resistance, which emerges soon after lenvatinib initial treatment. To investigate how YRDC modulates the sensitivity of lenvatinib, we assessed the effect of tRNA with different t6A levels on the translation of the KRAS gene by in vitro rabbit reticulocyte translation system and measured the expression levels of the KRAS gene by western blot together with qPCR. We found that YRDC regulates the protein translation of KRAS in cell models, and the tRNA with low t6A modification level reduces the translation of the KRAS in the in vitro translation system. These results suggested that YRDC mediates the resistance of lenvatinib in hepatocarcinoma cells via modulating the translation of the KRAS. In this study, YRDC was confirmed to be a potential novel predictive biomarker of lenvatinib sensitivity in HCC.
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Affiliation(s)
- Jun Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Peng Zhu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Zhi Ye
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China
| | - Mengke Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Haijun Yang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Shiqiong Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Yan Shu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China.,Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland at Baltimore, Baltimore, MD, United States
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Qing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
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4
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Abstract
The intergenic IRES of Cricket Paralysis Virus (CrPV-IRES) forms a tight complex with 80S ribosomes capable of initiating the cell-free synthesis of complete proteins in the absence of initiation factors. Such synthesis raises the question of what effect the necessary IRES dissociation from the tRNA binding sites, and ultimately from all of the ribosome, has on the rates of initial peptide elongation steps as nascent peptide is formed. Here we report the first results measuring rates of reaction for the initial cycles of IRES-dependent elongation. Our results demonstrate that 1) the first two cycles of elongation proceed much more slowly than subsequent cycles, 2) these reduced rates arise from slow pseudo-translocation and translocation steps, and 3) the retarding effect of ribosome-bound IRES on protein synthesis is largely overcome following translocation of tripeptidyl-tRNA. Our results also provide a straightforward approach to detailed mechanistic characterization of many aspects of eukaryotic polypeptide elongation.
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Affiliation(s)
- Haibo Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Martin Y Ng
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Yuanwei Chen
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
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5
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Quast RB, Mrusek D, Hoffmeister C, Sonnabend A, Kubick S. Cotranslational incorporation of non-standard amino acids using cell-free protein synthesis. FEBS Lett 2015; 589:1703-12. [PMID: 25937125 DOI: 10.1016/j.febslet.2015.04.041] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 11/30/2022]
Abstract
Over the last years protein engineering using non-standard amino acids has gained increasing attention. As a result, improved methods are now available, enabling the efficient and directed cotranslational incorporation of various non-standard amino acids to equip proteins with desired characteristics. In this context, the utilization of cell-free protein synthesis is particularly useful due to the direct accessibility of the translational machinery and synthesized proteins without having to maintain a vital cellular host. We review prominent methods for the incorporation of non-standard amino acids into proteins using cell-free protein synthesis. Furthermore, a list of non-standard amino acids that have been successfully incorporated into proteins in cell-free systems together with selected applications is provided.
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Affiliation(s)
- Robert B Quast
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Devid Mrusek
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Christian Hoffmeister
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Andrei Sonnabend
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany.
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6
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Abstract
Genetic code expansion is a key objective of synthetic biology and protein engineering. Most efforts in this direction are focused on reassigning termination or decoding quadruplet codons. While the redundancy of genetic code provides a large number of potentially reassignable codons, their utility is diminished by the inevitable interaction with cognate aminoacyl-tRNAs. To address this problem, we sought to establish an in vitro protein synthesis system with a simplified synthetic tRNA complement, thereby orthogonalizing some of the sense codons. This quantitative in vitro peptide synthesis assay allowed us to analyze the ability of synthetic tRNAs to decode all of 61 sense codons. We observed that, with the exception of isoacceptors for Asn, Glu, and Ile, the majority of 48 synthetic Escherichia coli tRNAs could support protein translation in the cell-free system. We purified to homogeneity functional Asn, Glu, and Ile tRNAs from the native E. coli tRNA mixture, and by combining them with synthetic tRNAs, we formulated a semisynthetic tRNA complement for all 20 amino acids. We further demonstrated that this tRNA complement could restore the protein translation activity of tRNA-depleted E. coli lysate to a level comparable to that of total native tRNA. To confirm that the developed system could efficiently synthesize long polypeptides, we expressed three different sequences coding for superfolder GFP. This novel semisynthetic translation system is a powerful tool for tRNA engineering and potentially enables the reassignment of at least 9 sense codons coding for Ser, Arg, Leu, Pro, Thr, and Gly.
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Affiliation(s)
- Zhenling Cui
- Institute for Molecular Bioscience and the Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Viktor Stein
- Institute for Molecular Bioscience and the Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Zakir Tnimov
- Institute for Molecular Bioscience and the Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Sergey Mureev
- Institute for Molecular Bioscience and the Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Kirill Alexandrov
- Institute for Molecular Bioscience and the Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
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7
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Rosenblum G, Cooperman BS. Engine out of the chassis: cell-free protein synthesis and its uses. FEBS Lett 2013; 588:261-8. [PMID: 24161673 DOI: 10.1016/j.febslet.2013.10.016] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/14/2013] [Accepted: 10/15/2013] [Indexed: 12/15/2022]
Abstract
The translation machinery is the engine of life. Extracting the cytoplasmic milieu from a cell affords a lysate capable of producing proteins in concentrations reaching to tens of micromolar. Such lysates, derivable from a variety of cells, allow the facile addition and subtraction of components that are directly or indirectly related to the translation machinery and/or the over-expressed protein. The flexible nature of such cell-free expression systems, when coupled with high throughput monitoring, can be especially suitable for protein engineering studies, allowing one to bypass multiple steps typically required using conventional in vivo protein expression.
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Affiliation(s)
- Gabriel Rosenblum
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States.
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States
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8
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Lee KH, Kim DM. Applications of cell-free protein synthesis in synthetic biology: Interfacing bio-machinery with synthetic environments. Biotechnol J 2013; 8:1292-300. [DOI: 10.1002/biot.201200385] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 08/16/2013] [Accepted: 09/12/2013] [Indexed: 11/08/2022]
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9
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Brandmayr C, Wagner M, Brückl T, Globisch D, Pearson D, Kneuttinger AC, Reiter V, Hienzsch A, Koch S, Thoma I, Thumbs P, Michalakis S, Müller M, Biel M, Carell T. Isotope-based analysis of modified tRNA nucleosides correlates modification density with translational efficiency. Angew Chem Int Ed Engl 2012; 51:11162-5. [PMID: 23037940 PMCID: PMC3533783 DOI: 10.1002/anie.201203769] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 07/26/2012] [Indexed: 11/09/2022]
Abstract
Useful diversity: Quantification of modified tRNA nucleobases in different murine and porcine tissues reveals a tissue-specific overall modification content. The modification content correlates with rates of protein synthesis in vitro, suggesting a direct link between tRNA modification levels and tissue-specific translational efficiency.
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Affiliation(s)
- Caterina Brandmayr
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Mirko Wagner
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Tobias Brückl
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Daniel Globisch
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - David Pearson
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Andrea Christa Kneuttinger
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Veronika Reiter
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Antje Hienzsch
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Susanne Koch
- Center for Integrated Protein Science at the Department of Pharmacy, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany)
| | - Ines Thoma
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Peter Thumbs
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Stylianos Michalakis
- Center for Integrated Protein Science at the Department of Pharmacy, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany)
| | - Markus Müller
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Martin Biel
- Center for Integrated Protein Science at the Department of Pharmacy, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany)
| | - Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
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10
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Brandmayr C, Wagner M, Brückl T, Globisch D, Pearson D, Kneuttinger AC, Reiter V, Hienzsch A, Koch S, Thoma I, Thumbs P, Michalakis S, Müller M, Biel M, Carell T. Eine isotopenbasierte Analyse modifizierter tRNA-Nukleoside korreliert die Modifikationsdichte mit der Translationseffizienz. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203769] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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11
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Starck SR, Jiang V, Pavon-Eternod M, Prasad S, McCarthy B, Pan T, Shastri N. Leucine-tRNA initiates at CUG start codons for protein synthesis and presentation by MHC class I. Science 2012; 336:1719-23. [PMID: 22745432 DOI: 10.1126/science.1220270] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Effective immune surveillance by cytotoxic T cells requires newly synthesized polypeptides for presentation by major histocompatibility complex (MHC) class I molecules. These polypeptides are produced not only from conventional AUG-initiated, but also from cryptic non-AUG-initiated, reading frames by distinct translational mechanisms. Biochemical analysis of ribosomal initiation complexes at CUG versus AUG initiation codons revealed that cells use an elongator leucine-bound transfer RNA (Leu-tRNA) to initiate translation at cryptic CUG start codons. CUG/Leu-tRNA initiation was independent of the canonical initiator tRNA (AUG/Met-tRNA(i)(Met)) pathway but required expression of eukaryotic initiation factor 2A. Thus, a tRNA-based translation initiation mechanism allows non-AUG-initiated protein synthesis and supplies peptides for presentation by MHC class I molecules.
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Affiliation(s)
- Shelley R Starck
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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12
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Wild T, Horvath P, Wyler E, Widmann B, Badertscher L, Zemp I, Kozak K, Csucs G, Lund E, Kutay U. A protein inventory of human ribosome biogenesis reveals an essential function of exportin 5 in 60S subunit export. PLoS Biol 2010; 8:e1000522. [PMID: 21048991 PMCID: PMC2964341 DOI: 10.1371/journal.pbio.1000522] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 09/03/2010] [Indexed: 12/20/2022] Open
Abstract
The assembly of ribosomal subunits in eukaryotes is a complex, multistep process so far mostly studied in yeast. In S. cerevisiae, more than 200 factors including ribosomal proteins and trans-acting factors are required for the ordered assembly of 40S and 60S ribosomal subunits. To date, only few human homologs of these yeast ribosome synthesis factors have been characterized. Here, we used a systematic RNA interference (RNAi) approach to analyze the contribution of 464 candidate factors to ribosomal subunit biogenesis in human cells. The screen was based on visual readouts, using inducible, fluorescent ribosomal proteins as reporters. By performing computer-based image analysis utilizing supervised machine-learning techniques, we obtained evidence for a functional link of 153 human proteins to ribosome synthesis. Our data show that core features of ribosome assembly are conserved from yeast to human, but differences exist for instance with respect to 60S subunit export. Unexpectedly, our RNAi screen uncovered a requirement for the export receptor Exportin 5 (Exp5) in nuclear export of 60S subunits in human cells. We show that Exp5, like the known 60S exportin Crm1, binds to pre-60S particles in a RanGTP-dependent manner. Interference with either Exp5 or Crm1 function blocks 60S export in both human cells and frog oocytes, whereas 40S export is compromised only upon inhibition of Crm1. Thus, 60S subunit export is dependent on at least two RanGTP-binding exportins in vertebrate cells.
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Affiliation(s)
- Thomas Wild
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Molecular Life Science Ph.D. Program, Zurich, Switzerland
| | - Peter Horvath
- Light Microscopy Center, RISC, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Emanuel Wyler
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Molecular Life Science Ph.D. Program, Zurich, Switzerland
| | - Barbara Widmann
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Molecular Life Science Ph.D. Program, Zurich, Switzerland
| | - Lukas Badertscher
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Molecular Life Science Ph.D. Program, Zurich, Switzerland
| | - Ivo Zemp
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Karol Kozak
- Light Microscopy Center, RISC, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Gabor Csucs
- Light Microscopy Center, RISC, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Elsebet Lund
- University of Wisconsin, Madison, Wisconsin, United States of America
| | - Ulrike Kutay
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- * E-mail:
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13
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Songe-Møller L, van den Born E, Leihne V, Vågbø CB, Kristoffersen T, Krokan HE, Kirpekar F, Falnes PØ, Klungland A. Mammalian ALKBH8 possesses tRNA methyltransferase activity required for the biogenesis of multiple wobble uridine modifications implicated in translational decoding. Mol Cell Biol 2010; 30:1814-27. [PMID: 20123966 DOI: 10.1128/MCB.01602-09] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Uridines in the wobble position of tRNA are almost invariably modified. Modifications can increase the efficiency of codon reading, but they also prevent mistranslation by limiting wobbling. In mammals, several tRNAs have 5-methoxycarbonylmethyluridine (mcm5U) or derivatives thereof in the wobble position. Through analysis of tRNA from Alkbh8-/- mice, we show here that ALKBH8 is a tRNA methyltransferase required for the final step in the biogenesis of mcm5U. We also demonstrate that the interaction of ALKBH8 with a small accessory protein, TRM112, is required to form a functional tRNA methyltransferase. Furthermore, prior ALKBH8-mediated methylation is a prerequisite for the thiolation and 2'-O-ribose methylation that form 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) and 5-methoxycarbonylmethyl-2'-O-methyluridine (mcm5Um), respectively. Despite the complete loss of all of these uridine modifications, Alkbh8-/- mice appear normal. However, the selenocysteine-specific tRNA (tRNASec) is aberrantly modified in the Alkbh8-/- mice, and for the selenoprotein Gpx1, we indeed observed reduced recoding of the UGA stop codon to selenocysteine.
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Ahn JH, Hwang MY, Oh IS, Park KM, Hahn GH, Choi CY, Kim DM. Preparation method forEscherichia coli S30 extracts completely dependent upon tRNA addition to catalyze cell-free protein synthesis. BIOTECHNOL BIOPROC E 2006. [DOI: 10.1007/bf02932309] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
Conventional display libraries are generally limited to the 20 naturally occurring amino acids. Here, we demonstrate that novel unnatural amide-linked oligomers can be constructed and encoded in an attached RNA for the purpose of mRNA display library design. To do this, we translated templates of various lengths in a protein synthesis system modified to promote sense codon suppression. Unnatural residues were escorted to the ribosome as chemically acylated tRNAs added to the translation mixture. Our experiments reveal that unnatural peptide oligomers ("encodamers") consisting of an N-substituted amino acid are readily generated as mRNA-peptide fusions with excellent stepwise efficiency. The N-substituted polyamides have strikingly improved proteolytic stability relative to their naturally encoded counterparts. Overall, our work indicates that the ribosome can be used as a synthesis platform to generate encoded combinatorial chemistry outside the universal genetic code.
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Affiliation(s)
- Adam Frankel
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 147-75, Pasadena, CA 91125, USA
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Abstract
Combinatorial peptide and protein libraries have now been developed to accommodate unnatural amino acids in a genetically encoded format via in vitro nonsense and sense suppression. General translation features and specific regioselective and stereoselective properties of the ribosome endow these libraries with a broad chemical diversity. Alternatively, amino acid residues can be chemically derivatized post-translationally to add preferred functionality to the encoded peptide. All of these efforts are advancing combinatorial peptide and protein libraries for enhanced ligands against biological targets of interest.
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Affiliation(s)
- Adam Frankel
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Napthine S, Vidakovic M, Girnary R, Namy O, Brierley I. Prokaryotic-style frameshifting in a plant translation system: conservation of an unusual single-tRNA slippage event. EMBO J 2003; 22:3941-50. [PMID: 12881428 PMCID: PMC169038 DOI: 10.1093/emboj/cdg365] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2003] [Revised: 05/22/2003] [Accepted: 06/20/2003] [Indexed: 11/28/2022] Open
Abstract
Ribosomal frameshifting signals are found in mobile genetic elements, viruses and cellular genes of prokaryotes and eukaryotes. Typically they comprise a slippery sequence, X XXY YYZ, where the frameshift occurs, and a stimulatory mRNA element. Here we studied the influence of host translational environment and the identity of slippery sequence-decoding tRNAs on the frameshift mechanism. By expressing candidate signals in Escherichia coli, and in wheatgerm extracts depleted of endogenous tRNAs and supplemented with prokaryotic or eukaryotic tRNA populations, we show that when decoding AAG in the ribosomal A-site, E.coli tRNA(Lys) promotes a highly unusual single-tRNA slippage event in both prokaryotic and eukaryotic ribosomes. This event does not appear to require slippage of the adjacent P-site tRNA, although its identity is influential. Conversely, asparaginyl-tRNA promoted a dual slippage event in either system. Thus, the tRNAs themselves are the main determinants in the selection of single- or dual-tRNA slippage mechanisms. We also show for the first time that prokaryotic tRNA(Asn) is not inherently 'unslippery' and induces efficient frameshifting when in the context of a eukaryotic translation system.
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Affiliation(s)
- Sawsan Napthine
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
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Abstract
The universal genetic code links the 20 naturally occurring amino acids to the 61 sense codons. Previously, the UAG amber stop codon (a nonsense codon) has been used as a blank in the code to insert natural and unnatural amino acids via nonsense suppression. We have developed a selection methodology to investigate whether the unnatural amino acid biocytin could be incorporated into an mRNA display library at sense codons. In these experiments we probed a single randomized NNN codon with a library of 16 orthogonal, biocytin-acylated tRNAs. In vitro selection for efficient incorporation of the unnatural amino acid resulted in templates containing the GUA codon at the randomized position. This sense suppression occurs via Watson-Crick pairing with similar efficiency to UAG-mediated nonsense suppression. These experiments suggest that sense codon suppression is a viable means to expand the chemical and functional diversity of the genetic code.
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Affiliation(s)
- Adam Frankel
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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