1
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Ero R, Leppik M, Reier K, Liiv A, Remme J. Ribosomal RNA modification enzymes stimulate large ribosome subunit assembly in E. coli. Nucleic Acids Res 2024; 52:6614-6628. [PMID: 38554109 PMCID: PMC11194073 DOI: 10.1093/nar/gkae222] [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: 12/07/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
Ribosomal RNA modifications are introduced by specific enzymes during ribosome assembly in bacteria. Deletion of individual modification enzymes has a minor effect on bacterial growth, ribosome biogenesis, and translation, which has complicated the definition of the function of the enzymes and their products. We have constructed an Escherichia coli strain lacking 10 genes encoding enzymes that modify 23S rRNA around the peptidyl-transferase center. This strain exhibits severely compromised growth and ribosome assembly, especially at lower temperatures. Re-introduction of the individual modification enzymes allows for the definition of their functions. The results demonstrate that in addition to previously known RlmE, also RlmB, RlmKL, RlmN and RluC facilitate large ribosome subunit assembly. RlmB and RlmKL have functions in ribosome assembly independent of their modification activities. While the assembly stage specificity of rRNA modification enzymes is well established, this study demonstrates that there is a mutual interdependence between the rRNA modification process and large ribosome subunit assembly.
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MESH Headings
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/metabolism
- Escherichia coli Proteins/genetics
- Methyltransferases/metabolism
- Methyltransferases/genetics
- Ribosome Subunits, Large/metabolism
- Ribosome Subunits, Large/genetics
- Ribosome Subunits, Large, Bacterial/metabolism
- Ribosome Subunits, Large, Bacterial/genetics
- Ribosomes/metabolism
- Ribosomes/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 23S/metabolism
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/chemistry
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Affiliation(s)
- Rya Ero
- IMCB University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Margus Leppik
- IMCB University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Kaspar Reier
- IMCB University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Aivar Liiv
- IMCB University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Jaanus Remme
- IMCB University of Tartu, Riia 23, 51010 Tartu, Estonia
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2
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Gor K, Duss O. Emerging Quantitative Biochemical, Structural, and Biophysical Methods for Studying Ribosome and Protein-RNA Complex Assembly. Biomolecules 2023; 13:biom13050866. [PMID: 37238735 DOI: 10.3390/biom13050866] [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: 04/11/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Ribosome assembly is one of the most fundamental processes of gene expression and has served as a playground for investigating the molecular mechanisms of how protein-RNA complexes (RNPs) assemble. A bacterial ribosome is composed of around 50 ribosomal proteins, several of which are co-transcriptionally assembled on a ~4500-nucleotide-long pre-rRNA transcript that is further processed and modified during transcription, the entire process taking around 2 min in vivo and being assisted by dozens of assembly factors. How this complex molecular process works so efficiently to produce an active ribosome has been investigated over decades, resulting in the development of a plethora of novel approaches that can also be used to study the assembly of other RNPs in prokaryotes and eukaryotes. Here, we review biochemical, structural, and biophysical methods that have been developed and integrated to provide a detailed and quantitative understanding of the complex and intricate molecular process of bacterial ribosome assembly. We also discuss emerging, cutting-edge approaches that could be used in the future to study how transcription, rRNA processing, cellular factors, and the native cellular environment shape ribosome assembly and RNP assembly at large.
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Affiliation(s)
- Kavan Gor
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69117 Heidelberg, Germany
| | - Olivier Duss
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
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3
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De Capitani J, Mutschler H. The Long Road to a Synthetic Self-Replicating Central Dogma. Biochemistry 2023; 62:1221-1232. [PMID: 36944355 PMCID: PMC10077596 DOI: 10.1021/acs.biochem.3c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The construction of a biochemical system capable of self-replication is a key objective in bottom-up synthetic biology. Throughout the past two decades, a rapid progression in the design of in vitro cell-free systems has provided valuable insight into the requirements for the development of a minimal system capable of self-replication. The main limitations of current systems can be attributed to their macromolecular composition and how the individual macromolecules use the small molecules necessary to drive RNA and protein synthesis. In this Perspective, we discuss the recent steps that have been taken to generate a minimal cell-free system capable of regenerating its own macromolecular components and maintaining the homeostatic balance between macromolecular biogenesis and consumption of primary building blocks. By following the flow of biological information through the central dogma, we compare the current versions of these systems to date and propose potential alterations aimed at designing a model system for self-replicative synthetic cells.
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Affiliation(s)
- Jacopo De Capitani
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Hannes Mutschler
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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4
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Krüger A, Watkins AM, Wellington-Oguri R, Romano J, Kofman C, DeFoe A, Kim Y, Anderson-Lee J, Fisker E, Townley J, d'Aquino AE, Das R, Jewett MC. Community science designed ribosomes with beneficial phenotypes. Nat Commun 2023; 14:961. [PMID: 36810740 PMCID: PMC9944925 DOI: 10.1038/s41467-023-35827-3] [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: 04/30/2022] [Accepted: 01/04/2023] [Indexed: 02/23/2023] Open
Abstract
Functional design of ribosomes with mutant ribosomal RNA (rRNA) can expand opportunities for understanding molecular translation, building cells from the bottom-up, and engineering ribosomes with altered capabilities. However, such efforts are hampered by cell viability constraints, an enormous combinatorial sequence space, and limitations on large-scale, 3D design of RNA structures and functions. To address these challenges, we develop an integrated community science and experimental screening approach for rational design of ribosomes. This approach couples Eterna, an online video game that crowdsources RNA sequence design to community scientists in the form of puzzles, with in vitro ribosome synthesis, assembly, and translation in multiple design-build-test-learn cycles. We apply our framework to discover mutant rRNA sequences that improve protein synthesis in vitro and cell growth in vivo, relative to wild type ribosomes, under diverse environmental conditions. This work provides insights into rRNA sequence-function relationships and has implications for synthetic biology.
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Affiliation(s)
- Antje Krüger
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA.,Resilience US Inc, 9310 Athena Circle, La Jolla, CA, 92037, USA
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.,Prescient Design, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Jonathan Romano
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.,Eterna Massive Open Laboratory, Stanford, CA, 94305, USA.,Department of Computer Science and Engineering, State University of New York at Buffalo, Buffalo, NY, 14260, USA
| | - Camila Kofman
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Alysse DeFoe
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Yejun Kim
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | | | - Eli Fisker
- Eterna Massive Open Laboratory, Stanford, CA, 94305, USA
| | - Jill Townley
- Eterna Massive Open Laboratory, Stanford, CA, 94305, USA
| | | | - Anne E d'Aquino
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA. .,Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA.
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA. .,Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA.
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5
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Cho SS, Green AT, Hyeon C, Thirumalai D. TMAO Destabilizes RNA Secondary Structure via Direct Hydrogen Bond Interactions. J Phys Chem B 2023; 127:438-445. [PMID: 36602908 DOI: 10.1021/acs.jpcb.2c05434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Trimethylamine N-oxide (TMAO) is an osmolyte that accumulates in cells in response to osmotic stress. TMAO stabilizes proteins by the entropic stabilization mechanism, which pictures TMAO as a nanocrowder that predominantly destabilizes the unfolded state. However, the mechanism of action of TMAO on RNA is much less understood. Here, we use all-atom molecular dynamics simulations to investigate how TMAO interacts with a 12-nt RNA hairpin with a high melting temperature, and an 8-nt RNA hairpin, which has a relatively fluid native basin in the absence of TMAO. The use of the two hairpins with different free energy of stabilization allows us to probe the origin of the destabilization effect of TMAO on RNA molecules without the possibility of forming tertiary interactions. We generated multiple trajectories using all-atom molecular dynamics (MD) simulations in explicit water by employing AMBER and CHARMM force fields, both in the absence and presence of TMAO. We observed qualitatively similar RNA-TMAO interaction profiles from the simulations using the two force fields. TMAO hydrogen bond interactions are largely depleted around the paired RNA bases and ribose sugars. In contrast, we show that the oxygen atom in TMAO, the hydrogen bond acceptor, preferentially interacts with the hydrogen bond donors in the solvent exposed bases, such as those in the stem-loop and the destabilized base stacks in the unfolded state, especially in the marginally stable 8-nt RNA hairpin. The predicted destabilization mechanism through TMAO-RNA hydrogen bond interactions could be tested using two-dimensional IR spectroscopy. Since TMAO does not significantly interact with the hydroxyl group of the ribose sugars, we predict that similar results must also hold for DNA.
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Affiliation(s)
- Samuel S Cho
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States.,Department of Computer Science, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Adam T Green
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Changbong Hyeon
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - D Thirumalai
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States.,Department of Physics, University of Texas at Austin, Austin, Texas 78712, United States
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6
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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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7
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Choi YN, Cho N, Lee K, Gwon DA, Lee JW, Lee J. Programmable Synthesis of Biobased Materials Using Cell-Free Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2203433. [PMID: 36108274 DOI: 10.1002/adma.202203433] [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: 04/15/2022] [Revised: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Motivated by the intricate mechanisms underlying biomolecule syntheses in cells that chemistry is currently unable to mimic, researchers have harnessed biological systems for manufacturing novel materials. Cell-free systems (CFSs) utilizing the bioactivity of transcriptional and translational machineries in vitro are excellent tools that allow supplementation of exogenous materials for production of innovative materials beyond the capability of natural biological systems. Herein, recent studies that have advanced the ability to expand the scope of biobased materials using CFS are summarized and approaches enabling the production of high-value materials, prototyping of genetic parts and modules, and biofunctionalization are discussed. By extending the reach of chemical and enzymatic reactions complementary to cellular materials, CFSs provide new opportunities at the interface of materials science and synthetic biology.
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Affiliation(s)
- Yun-Nam Choi
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Namjin Cho
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Kanghun Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Da-Ae Gwon
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Joongoo Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
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8
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Ganesh RB, Maerkl SJ. Biochemistry of Aminoacyl tRNA Synthetase and tRNAs and Their Engineering for Cell-Free and Synthetic Cell Applications. Front Bioeng Biotechnol 2022; 10:918659. [PMID: 35845409 PMCID: PMC9283866 DOI: 10.3389/fbioe.2022.918659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-free biology is increasingly utilized for engineering biological systems, incorporating novel functionality, and circumventing many of the complications associated with cells. The central dogma describes the information flow in biology consisting of transcription and translation steps to decode genetic information. Aminoacyl tRNA synthetases (AARSs) and tRNAs are key components involved in translation and thus protein synthesis. This review provides information on AARSs and tRNA biochemistry, their role in the translation process, summarizes progress in cell-free engineering of tRNAs and AARSs, and discusses prospects and challenges lying ahead in cell-free engineering.
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9
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Liljeruhm J, Leppik M, Bao L, Truu T, Calvo-Noriega M, Freyer NS, Liiv A, Wang J, Blanco RC, Ero R, Remme J, Forster AC. Plasticity and conditional essentiality of modification enzymes for domain V of Escherichia coli 23S ribosomal RNA. RNA (NEW YORK, N.Y.) 2022; 28:796-807. [PMID: 35260421 PMCID: PMC9074899 DOI: 10.1261/rna.079096.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/18/2022] [Indexed: 06/03/2023]
Abstract
Escherichia coli rRNAs are post-transcriptionally modified at 36 positions but their modification enzymes are dispensable individually for growth, bringing into question their significance. However, a major growth defect was reported for deletion of the RlmE enzyme, which abolished a 2'O methylation near the peptidyl transferase center (PTC) of the 23S rRNA. Additionally, an adjacent 80-nt "critical region" around the PTC had to be modified to yield significant peptidyl transferase activity in vitro. Surprisingly, we discovered that an absence of just two rRNA modification enzymes is conditionally lethal (at 20°C): RlmE and RluC. At a permissive temperature (37°C), this double knockout was shown to abolish four modifications and be defective in ribosome assembly, though not more so than the RlmE single knockout. However, the double knockout exhibited an even lower rate of tripeptide synthesis than did the single knockout, suggesting an even more defective ribosomal translocation. A combination knockout of the five critical-region-modifying enzymes RluC, RlmKL, RlmN, RlmM, and RluE (not RlmE), which synthesize five of the seven critical-region modifications and 14 rRNA and tRNA modifications altogether, was viable (minor growth defect at 37°C, major at 20°C). This was surprising based on prior in vitro studies. This five-knockout combination had minimal effects on ribosome assembly and frameshifting at 37°C, but greater effects on ribosome assembly and in vitro peptidyl transferase activity at cooler temperatures. These results establish the conditional essentiality of bacterial rRNA modification enzymes and also reveal unexpected plasticity of modification of the PTC region in vivo.
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Affiliation(s)
- Josefine Liljeruhm
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Margus Leppik
- Department of Molecular Biology, University of Tartu, 51010 Tartu, Estonia
| | - Letian Bao
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Triin Truu
- Department of Molecular Biology, University of Tartu, 51010 Tartu, Estonia
| | - Maria Calvo-Noriega
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Nicola S Freyer
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Aivar Liiv
- Department of Molecular Biology, University of Tartu, 51010 Tartu, Estonia
| | - Jinfan Wang
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Rubén Crespo Blanco
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Rya Ero
- Department of Molecular Biology, University of Tartu, 51010 Tartu, Estonia
| | - Jaanus Remme
- Department of Molecular Biology, University of Tartu, 51010 Tartu, Estonia
| | - Anthony C Forster
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
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10
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Aoyama R, Masuda K, Shimojo M, Kanamori T, Ueda T, Shimizu Y. In vitro reconstitution of the Escherichia coli 70S ribosome with a full set of recombinant ribosomal proteins. J Biochem 2021; 171:227-237. [PMID: 34750629 PMCID: PMC8863084 DOI: 10.1093/jb/mvab121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/04/2021] [Indexed: 11/27/2022] Open
Abstract
Many studies of the reconstitution of the Escherichia coli small ribosomal subunit from its individual molecular parts have been reported, but contrastingly, similar studies of the large ribosomal subunit have not been well performed to date. Here, we describe protocols for preparing the 33 ribosomal proteins of the E. coli 50S subunit and demonstrate successful reconstitution of a functionally active 50S particle that can perform protein synthesis in vitro. We also successfully reconstituted both ribosomal subunits (30S and 50S) and 70S ribosomes using a full set of recombinant ribosomal proteins by integrating our developed method with the previously developed fully recombinant-based integrated synthesis, assembly and translation. The approach described here makes a major contribution to the field of ribosome engineering and could be fundamental to the future studies of ribosome assembly processes.
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Affiliation(s)
- Ryo Aoyama
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka 565-0874, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Keiko Masuda
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka 565-0874, Japan
| | - Masaru Shimojo
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka 565-0874, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | | | - Takuya Ueda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.,Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku, Tokyo 162-8480, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka 565-0874, Japan
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11
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Shimojo M, Amikura K, Masuda K, Kanamori T, Ueda T, Shimizu Y. In vitro reconstitution of functional small ribosomal subunit assembly for comprehensive analysis of ribosomal elements in E. coli. Commun Biol 2020; 3:142. [PMID: 32214223 PMCID: PMC7096426 DOI: 10.1038/s42003-020-0874-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 03/03/2020] [Indexed: 11/25/2022] Open
Abstract
In vitro reconstitution is a powerful tool for investigating ribosome functions and biogenesis, as well as discovering new ribosomal features. In this study, we integrated all of the processes required for Escherichia coli small ribosomal subunit assembly. In our method, termed fully Recombinant-based integrated Synthesis, Assembly, and Translation (R-iSAT), assembly and evaluation of the small ribosomal subunits are coupled with ribosomal RNA (rRNA) synthesis in a reconstituted cell-free protein synthesis system. By changing the components of R-iSAT, including recombinant ribosomal protein composition, we coupled ribosomal assembly with ribosomal protein synthesis, enabling functional synthesis of ribosomal proteins and subsequent subunit assembly. In addition, we assembled and evaluated subunits with mutations in both rRNA and ribosomal proteins. The study demonstrated that our scheme provides new ways to comprehensively analyze any elements of the small ribosomal subunit, with the goal of improving our understanding of ribosomal biogenesis, function, and engineering. Shimojo et al. demonstrate the use of individually purified ribosomal proteins added into iSAT (integrated ribosomal synthesis, assembly, and translation) system to enable assembly of functional 30S subunits. They further show that while some 30S r-proteins must be full synthesized before transcription, others may be co-transcriptionally produced, to enable the assembly of 30S particles.
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Affiliation(s)
- Masaru Shimojo
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, 565-0874, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Kazuaki Amikura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Keiko Masuda
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, 565-0874, Japan
| | | | - Takuya Ueda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.,Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku, Tokyo, 162-8480, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, 565-0874, Japan.
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12
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d’Aquino AE, Azim T, Aleksashin NA, Hockenberry AJ, Krüger A, Jewett MC. Mutational characterization and mapping of the 70S ribosome active site. Nucleic Acids Res 2020; 48:2777-2789. [PMID: 32009164 PMCID: PMC7049736 DOI: 10.1093/nar/gkaa001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 12/06/2019] [Accepted: 01/03/2020] [Indexed: 12/20/2022] Open
Abstract
The synthetic capability of the Escherichia coli ribosome has attracted efforts to repurpose it for novel functions, such as the synthesis of polymers containing non-natural building blocks. However, efforts to repurpose ribosomes are limited by the lack of complete peptidyl transferase center (PTC) active site mutational analyses to inform design. To address this limitation, we leverage an in vitro ribosome synthesis platform to build and test every possible single nucleotide mutation within the PTC-ring, A-loop and P-loop, 180 total point mutations. These mutant ribosomes were characterized by assessing bulk protein synthesis kinetics, readthrough, assembly, and structure mapping. Despite the highly-conserved nature of the PTC, we found that >85% of the PTC nucleotides possess mutational flexibility. Our work represents a comprehensive single-point mutant characterization and mapping of the 70S ribosome's active site. We anticipate that it will facilitate structure-function relationships within the ribosome and make possible new synthetic biology applications.
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Affiliation(s)
- Anne E d’Aquino
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Tasfia Azim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Nikolay A Aleksashin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Adam J Hockenberry
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Michael C Jewett
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
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13
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Hammerling MJ, Fritz BR, Yoesep DJ, Kim DS, Carlson ED, Jewett MC. In vitro ribosome synthesis and evolution through ribosome display. Nat Commun 2020; 11:1108. [PMID: 32111839 PMCID: PMC7048773 DOI: 10.1038/s41467-020-14705-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 01/28/2020] [Indexed: 02/04/2023] Open
Abstract
Directed evolution of the ribosome for expanded substrate incorporation and novel functions is challenging because the requirement of cell viability limits the mutations that can be made. Here we address this challenge by combining cell-free synthesis and assembly of translationally competent ribosomes with ribosome display to develop a fully in vitro methodology for ribosome synthesis and evolution (called RISE). We validate the RISE method by selecting active genotypes from a ~1.7 × 107 member library of ribosomal RNA (rRNA) variants, as well as identifying mutant ribosomes resistant to the antibiotic clindamycin from a library of ~4 × 103 rRNA variants. We further demonstrate the prevalence of positive epistasis in resistant genotypes, highlighting the importance of such interactions in selecting for new function. We anticipate that RISE will facilitate understanding of molecular translation and enable selection of ribosomes with altered properties. Directed evolution of the ribosome is challenging because the requirement of cell viability limits the mutations that can be made. Here the authors develop a platform for in vitro ribosome synthesis and evolution (RISE) to overcome these constraints.
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Affiliation(s)
- Michael J Hammerling
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA
| | - Brian R Fritz
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA
| | - Danielle J Yoesep
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA
| | - Do Soon Kim
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA
| | - Erik D Carlson
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA.,Department of Chemical Engineering, Stanford University, Stanford, California, 94305, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA. .,Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA. .,Simpson Querrey Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA. .,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA. .,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208, USA.
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14
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Hammerling MJ, Krüger A, Jewett MC. Strategies for in vitro engineering of the translation machinery. Nucleic Acids Res 2020; 48:1068-1083. [PMID: 31777928 PMCID: PMC7026604 DOI: 10.1093/nar/gkz1011] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/07/2019] [Accepted: 10/17/2019] [Indexed: 01/06/2023] Open
Abstract
Engineering the process of molecular translation, or protein biosynthesis, has emerged as a major opportunity in synthetic and chemical biology to generate novel biological insights and enable new applications (e.g. designer protein therapeutics). Here, we review methods for engineering the process of translation in vitro. We discuss the advantages and drawbacks of the two major strategies-purified and extract-based systems-and how they may be used to manipulate and study translation. Techniques to engineer each component of the translation machinery are covered in turn, including transfer RNAs, translation factors, and the ribosome. Finally, future directions and enabling technological advances for the field are discussed.
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Affiliation(s)
- Michael J Hammerling
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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15
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Takahashi S, Okura H, Sugimoto N. Bisubstrate Function of RNA Polymerases Triggered by Molecular Crowding Conditions. Biochemistry 2019; 58:1081-1093. [DOI: 10.1021/acs.biochem.8b01204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Hiromichi Okura
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
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16
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Caschera F, Karim AS, Gazzola G, d’Aquino AE, Packard NH, Jewett MC. High-Throughput Optimization Cycle of a Cell-Free Ribosome Assembly and Protein Synthesis System. ACS Synth Biol 2018; 7:2841-2853. [PMID: 30354075 DOI: 10.1021/acssynbio.8b00276] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Building variant ribosomes offers opportunities to reveal fundamental principles underlying ribosome biogenesis and to make ribosomes with altered properties. However, cell viability limits mutations that can be made to the ribosome. To address this limitation, the in vitro integrated synthesis, assembly and translation (iSAT) method for ribosome construction from the bottom up was recently developed. Unfortunately, iSAT is complex, costly, and laborious to researchers, partially due to the high cost of reaction buffer containing over 20 components. In this study, we develop iSAT in Escherichia coli BL21Rosetta2 cell lysates, a commonly used bacterial strain, with a cost-effective poly sugar and nucleotide monophosphate-based metabolic scheme. We achieved a 10-fold increase in protein yield over our base case with an evolutionary design of experiments approach, screening 490 reaction conditions to optimize the reaction buffer. The computationally guided, cell-free, high-throughput technology presented here augments the way we approach multicomponent synthetic biology projects and efforts to repurpose ribosomes.
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Affiliation(s)
| | | | - Gianluca Gazzola
- Rutgers Center for Operations Research, Rutgers Business School, 100 Rockafeller Road, Piscataway, New Jersey 08854, United States
| | | | - Norman H. Packard
- ProtoLife, Inc., 57 Post Street Suite 908, San Francisco, California 94104, United States
| | - Michael C. Jewett
- Rutgers Center for Operations Research, Rutgers Business School, 100 Rockafeller Road, Piscataway, New Jersey 08854, United States
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17
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d'Aquino AE, Kim DS, Jewett MC. Engineered Ribosomes for Basic Science and Synthetic Biology. Annu Rev Chem Biomol Eng 2018; 9:311-340. [DOI: 10.1146/annurev-chembioeng-060817-084129] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ribosome is the cell's factory for protein synthesis. With protein synthesis rates of up to 20 amino acids per second and at an accuracy of 99.99%, the extraordinary catalytic capacity of the bacterial translation machinery has attracted extensive efforts to engineer, reconstruct, and repurpose it for biochemical studies and novel functions. Despite these efforts, the potential for harnessing the translation apparatus to manufacture bio-based products beyond natural limits remains underexploited, and fundamental constraints on the chemistry that the ribosome's RNA-based active site can carry out are unknown. This review aims to cover the past and present advances in ribosome design and engineering to understand the fundamental biology of the ribosome to facilitate the construction of synthetic manufacturing machines. The prospects for the development of engineered, or designer, ribosomes for novel polymer synthesis are reviewed, future challenges are considered, and promising advances in a variety of applications are discussed.
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Affiliation(s)
- Anne E. d'Aquino
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
| | - Do Soon Kim
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Michael C. Jewett
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
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18
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Schaefer M, Kapoor U, Jantsch MF. Understanding RNA modifications: the promises and technological bottlenecks of the 'epitranscriptome'. Open Biol 2018; 7:rsob.170077. [PMID: 28566301 PMCID: PMC5451548 DOI: 10.1098/rsob.170077] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/02/2017] [Indexed: 01/08/2023] Open
Abstract
The discovery of mechanisms that alter genetic information via RNA editing or introducing covalent RNA modifications points towards a complexity in gene expression that challenges long-standing concepts. Understanding the biology of RNA modifications represents one of the next frontiers in molecular biology. To this date, over 130 different RNA modifications have been identified, and improved mass spectrometry approaches are still adding to this list. However, only recently has it been possible to map selected RNA modifications at single-nucleotide resolution, which has created a number of exciting hypotheses about the biological function of RNA modifications, culminating in the proposition of the ‘epitranscriptome’. Here, we review some of the technological advances in this rapidly developing field, identify the conceptual challenges and discuss approaches that are needed to rigorously test the biological function of specific RNA modifications.
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Affiliation(s)
- Matthias Schaefer
- Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17-I, 1090 Vienna, Austria
| | - Utkarsh Kapoor
- Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17-I, 1090 Vienna, Austria
| | - Michael F Jantsch
- Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17-I, 1090 Vienna, Austria
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19
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Cell-free protein synthesis in micro compartments: building a minimal cell from biobricks. N Biotechnol 2017; 39:199-205. [DOI: 10.1016/j.nbt.2017.06.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 05/10/2017] [Accepted: 06/30/2017] [Indexed: 12/16/2022]
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20
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Repurposing ribosomes for synthetic biology. Curr Opin Chem Biol 2017; 40:87-94. [PMID: 28869851 DOI: 10.1016/j.cbpa.2017.07.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 11/21/2022]
Abstract
The translation system is the cell's factory for protein biosynthesis, stitching together hundreds to thousands of amino acids into proteins, which are required for the structure, function, and regulation of living systems. The extraordinary synthetic capability of this system, which includes the ribosome and its associated factors required for polymerization, has driven extensive efforts to harness it for societal use in areas as diverse as energy, materials, and medicine. A powerful example is recombinant protein production, which has impacted the lives of patients through the synthesis of biopharmaceuticals such as insulin. In nature, however, only limited sets of monomers are utilized, thereby resulting in limited sets of biopolymers (i.e., proteins). Expanding nature's repertoire of ribosomal monomers could yield new classes of enzymes, therapeutics, materials, and chemicals with diverse, genetically encoded chemistry. Here, we discuss recent progress towards engineering ribosomes both in vivo and in vitro. These fundamental and technical breakthroughs open doors for advanced applications in biotechnology and synthetic biology.
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21
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Fritz BR, Jamil OK, Jewett MC. Implications of macromolecular crowding and reducing conditions for in vitro ribosome construction. Nucleic Acids Res 2015; 43:4774-84. [PMID: 25897121 PMCID: PMC4482083 DOI: 10.1093/nar/gkv329] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/31/2015] [Indexed: 12/11/2022] Open
Abstract
In vitro construction of Escherichia coli ribosomes could elucidate a deeper understanding of these complex molecular machines and make possible the production of synthetic variants with new functions. Toward this goal, we recently developed an integrated synthesis, assembly and translation (iSAT) system that allows for co-activation of ribosomal RNA (rRNA) transcription and ribosome assembly, mRNA transcription and protein translation without intact cells. Here, we discovered that macromolecular crowding and reducing agents increase overall iSAT protein synthesis; the combination of 6% w/v Ficoll 400 and 2 mM DTBA yielded approximately a five-fold increase in overall iSAT protein synthesis activity. By utilizing a fluorescent RNA aptamer, fluorescent reporter proteins and ribosome sedimentation analysis, we showed that crowding agents increase iSAT yields by enhancing translation while reducing agents increase rRNA transcription and ribosome assembly. Finally, we showed that iSAT ribosomes possess ∼70% of the protein synthesis activity of in vivo-assembled E. coli ribosomes. This work improves iSAT protein synthesis through the addition of crowding and reducing agents, provides a thorough understanding of the effect of these additives within the iSAT system and demonstrates how iSAT allows for manipulation and analysis of ribosome biogenesis in the context of an in vitro transcription-translation system.
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Affiliation(s)
- Brian R Fritz
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Osman K Jamil
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA Interdisciplinary Biological Sciences Graduate Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA Northwestern Institute on Complex Systems, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA Simpson Querrey Institute, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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22
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Liu Y, Fritz BR, Anderson MJ, Schoborg JA, Jewett MC. Characterizing and alleviating substrate limitations for improved in vitro ribosome construction. ACS Synth Biol 2015; 4:454-62. [PMID: 25079899 DOI: 10.1021/sb5002467] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Complete cell-free synthesis of ribosomes could make possible minimal cell projects and the construction of variant ribosomes with new functions. Recently, we reported the development of an integrated synthesis, assembly, and translation (iSAT) method for in vitro construction of Escherichia coli ribosomes. iSAT allows simultaneous rRNA synthesis, ribosome assembly, and reporter protein expression as a measure of ribosome activity. Here, we explore causes of iSAT reaction termination to improve efficiency and yields. We discovered that phosphoenolpyruvate (PEP), the secondary energy substrate, and nucleoside triphosphates (NTPs) were rapidly degraded during iSAT reactions. In turn, we observed a significant drop in the adenylate energy charge and termination of protein synthesis. Furthermore, we identified that the accumulation of inorganic phosphate is inhibitory to iSAT. Fed-batch replenishment of PEP and magnesium glutamate (to offset the inhibitory effects of accumulating phosphate by repeated additions of PEP) prior to energy depletion prolonged the reaction duration 2-fold and increased superfolder green fluorescent protein (sfGFP) yield by ~75%. By adopting a semi-continuous method, where passive diffusion enables substrate replenishment and byproduct removal, we prolonged iSAT reaction duration 5-fold and increased sfGFP yield 7-fold to 7.5 ± 0.7 μmol L(-1). This protein yield is the highest ever reported for iSAT reactions. Our results underscore the critical role energy substrates play in iSAT and highlight the importance of understanding metabolic processes that influence substrate depletion for cell-free synthetic biology.
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Affiliation(s)
- Yi Liu
- Interdepartmental Biological Sciences Graduate
Program, ‡Chemistry of Life
Processes Institute, §Department of Chemical and Biological Engineering, ∥Member, Robert H. Lurie Comprehensive
Cancer Center, ⊥Affiliate Member, Institute for Bionanotechnology in Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Brian R. Fritz
- Interdepartmental Biological Sciences Graduate
Program, ‡Chemistry of Life
Processes Institute, §Department of Chemical and Biological Engineering, ∥Member, Robert H. Lurie Comprehensive
Cancer Center, ⊥Affiliate Member, Institute for Bionanotechnology in Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Mark J. Anderson
- Interdepartmental Biological Sciences Graduate
Program, ‡Chemistry of Life
Processes Institute, §Department of Chemical and Biological Engineering, ∥Member, Robert H. Lurie Comprehensive
Cancer Center, ⊥Affiliate Member, Institute for Bionanotechnology in Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Jennifer A. Schoborg
- Interdepartmental Biological Sciences Graduate
Program, ‡Chemistry of Life
Processes Institute, §Department of Chemical and Biological Engineering, ∥Member, Robert H. Lurie Comprehensive
Cancer Center, ⊥Affiliate Member, Institute for Bionanotechnology in Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Interdepartmental Biological Sciences Graduate
Program, ‡Chemistry of Life
Processes Institute, §Department of Chemical and Biological Engineering, ∥Member, Robert H. Lurie Comprehensive
Cancer Center, ⊥Affiliate Member, Institute for Bionanotechnology in Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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23
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Gopanenko AV, Malygin AA, Karpova GG. Exploring human 40S ribosomal proteins binding to the 18S rRNA fragment containing major 3'-terminal domain. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:101-9. [PMID: 25462191 DOI: 10.1016/j.bbapap.2014.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 10/10/2014] [Accepted: 11/04/2014] [Indexed: 10/24/2022]
Abstract
Association of ribosomal proteins with rRNA during assembly of ribosomal subunits is an intricate process, which is strictly regulated in vivo. As for the assembly in vitro, it was reported so far only for prokaryotic subunits. Bacterial ribosomal proteins are capable of selective binding to 16S rRNA as well as to its separate morphological domains. In this work, we explored binding of total protein of human 40S ribosomal subunit to the RNA transcript corresponding to the major 3'-domain of 18S rRNA. We showed that the resulting ribonucleoprotein particles contained almost all of the expected ribosomal proteins, whose binding sites are located in this 18S rRNA domain in the 40S subunit, together with several nonspecific proteins. The binding in solution was accompanied with aggregation of the RNA-protein complexes. Ribosomal proteins bound to the RNA transcript protected from chemical modification mostly those 18S rRNA nucleotides that are known to be involved in binding with the proteins in the 40S subunit and thereby demonstrated their ability to selectively bind to the rRNA in vitro. The possible implication of unstructured extensions of eukaryotic ribosomal proteins in their nonspecific binding with rRNA and in subsequent aggregation of the resulting complexes is discussed.
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Affiliation(s)
- Alexander V Gopanenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia.
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24
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Fritz BR, Jewett MC. The impact of transcriptional tuning on in vitro integrated rRNA transcription and ribosome construction. Nucleic Acids Res 2014; 42:6774-85. [PMID: 24792158 PMCID: PMC4041470 DOI: 10.1093/nar/gku307] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In vitro ribosome construction could enable studies of ribosome assembly and function, provide a route toward constructing minimal cells for synthetic biology, and permit the construction of ribosome variants with new functions. Toward these long-term goals, we recently reported on an integrated, one-pot ribosomal RNA synthesis (rRNA), ribosome assembly, and translation technology (termed iSAT) for the construction of Escherichia coli ribosomes in crude ribosome-free S150 extracts. Here, we aimed to improve the activity of iSAT through transcriptional tuning. Specifically, we increased transcriptional efficiency through 3′ modifications to the rRNA gene sequences, optimized plasmid and polymerase concentrations, and demonstrated the use of a T7-promoted rRNA operon for stoichiometrically balanced rRNA synthesis and native rRNA processing. Our modifications produced a 45-fold improvement in iSAT protein synthesis activity, enabling synthesis of 429 ± 15 nmol/l green fluorescent protein in 6 h batch reactions. Further, we show that the translational activity of ribosomes purified from iSAT reactions is about 20% the activity of native ribosomes purified directly from E. coli cells. Looking forward, we believe iSAT will enable unique studies to unravel the systems biology of ribosome biogenesis and open the way to new methods for making and studying ribosomal variants.
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Affiliation(s)
- Brian R Fritz
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA Interdepartmental Program in Biological Sciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA Northwestern Institute on Complex Systems, Northwestern University, 600 Foster Street, Evanston, IL 60208, USA Institute for Bionanotechnology in Medicine, Northwestern University, 303 E. Superior, Chicago, IL 60611, USA Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA
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25
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Sugimoto N. Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:205-73. [PMID: 24380597 DOI: 10.1016/b978-0-12-800046-5.00008-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
How does molecular crowding affect the stability of nucleic acid structures inside cells? Water is the major solvent component in living cells, and the properties of water in the highly crowded media inside cells differ from that in buffered solution. As it is difficult to measure the thermodynamic behavior of nucleic acids in cells directly and quantitatively, we recently developed a cell-mimicking system using cosolutes as crowding reagents. The influences of molecular crowding on the structures and thermodynamics of various nucleic acid sequences have been reported. In this chapter, we discuss how the structures and thermodynamic properties of nucleic acids differ under various conditions such as highly crowded environments, compartment environments, and in the presence of ionic liquids, and the major determinants of the crowding effects on nucleic acids are discussed. The effects of molecular crowding on the activities of ribozymes and riboswitches on noncanonical structures of DNA- and RNA-like quadruplexes that play important roles in transcription and translation are also described.
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Affiliation(s)
- Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan.
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26
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Jewett MC, Fritz BR, Timmerman LE, Church GM. In vitro integration of ribosomal RNA synthesis, ribosome assembly, and translation. Mol Syst Biol 2013; 9:678. [PMID: 23799452 PMCID: PMC3964315 DOI: 10.1038/msb.2013.31] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Accepted: 05/12/2013] [Indexed: 01/22/2023] Open
Abstract
This report describes an integrated method for in vitro construction of Escherichia coli ribosomes under near-physiological conditions. This method enables coupling of ribosome synthesis and assembly in a single, integrated system. ![]()
An integrated synthesis, assembly, and translation technology (termed iSAT) was developed to construct ribosomes in vitro. iSAT mimics co-transcription of rRNA and ribosome assembly as it occurs in vivo. iSAT makes possible the in vitro construction of modified ribosomes. iSAT is expected to aid studies of ribosome assembly and open new avenues for making ribosomes with altered capabilities.
Purely in vitro ribosome synthesis could provide a critical step towards unraveling the systems biology of ribosome biogenesis, constructing minimal cells from defined components, and engineering ribosomes with new functions. Here, as an initial step towards this goal, we report a method for constructing Escherichia coli ribosomes in crude S150 E. coli extracts. While conventional methods for E. coli ribosome reconstitution are non-physiological, our approach attempts to mimic chemical conditions in the cytoplasm, thus permitting several biological processes to occur simultaneously. Specifically, our integrated synthesis, assembly, and translation (iSAT) technology enables one-step co-activation of rRNA transcription, assembly of transcribed rRNA with native ribosomal proteins into functional ribosomes, and synthesis of active protein by these ribosomes in the same compartment. We show that iSAT makes possible the in vitro construction of modified ribosomes by introducing a 23S rRNA mutation that mediates resistance against clindamycin. We anticipate that iSAT will aid studies of ribosome assembly and open new avenues for making ribosomes with altered properties.
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Affiliation(s)
- Michael C Jewett
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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27
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Miyoshi D, Fujimoto T, Sugimoto N. Molecular Crowding and Hydration Regulating of G-Quadruplex Formation. Top Curr Chem (Cham) 2012; 330:87-110. [DOI: 10.1007/128_2012_335] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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28
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Giessing AMB, Kirpekar F. Mass spectrometry in the biology of RNA and its modifications. J Proteomics 2012; 75:3434-49. [PMID: 22348820 DOI: 10.1016/j.jprot.2012.01.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 01/20/2012] [Accepted: 01/26/2012] [Indexed: 01/31/2023]
Abstract
Many powerful analytical techniques for investigation of nucleic acids exist in the average modern molecular biology lab. The current review will focus on questions in RNA biology that have been answered by the use of mass spectrometry, which means that new biological information is the purpose and outcome of most of the studies we refer to. The review begins with a brief account of the subject "MS in the biology of RNA" and an overview of the prevalent RNA modifications identified to date. Fundamental considerations about mass spectrometric analysis of RNA are presented with the aim of detailing the analytical possibilities and challenges relating to the unique chemical nature of nucleic acids. The main biological topics covered are RNA modifications and the enzymes that perform the modifications. Modifications of RNA are essential in biology, and it is a field where mass spectrometry clearly adds knowledge of biological importance compared to traditional methods used in nucleic acid research. The biological applications are divided into analyses exclusively performed at the building block (mainly nucleoside) level and investigations involving mass spectrometry at the oligonucleotide level. We conclude the review discussing aspects of RNA identification and quantifications, which are upcoming fields for MS in RNA research. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.
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Affiliation(s)
- Anders M B Giessing
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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29
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Havelund JF, Giessing AMB, Hansen T, Rasmussen A, Scott LG, Kirpekar F. Identification of 5-hydroxycytidine at position 2501 concludes characterization of modified nucleotides in E. coli 23S rRNA. J Mol Biol 2011; 411:529-36. [PMID: 21723290 DOI: 10.1016/j.jmb.2011.06.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/17/2011] [Accepted: 06/20/2011] [Indexed: 10/18/2022]
Abstract
Complete characterization of a biomolecule's chemical structure is crucial in the full understanding of the relations between their structure and function. The dominating components in ribosomes are ribosomal RNAs (rRNAs), and the entire rRNA-but a single modified nucleoside at position 2501 in 23S rRNA-has previously been characterized in the bacterium Escherichia coli. Despite a first report nearly 20 years ago, the chemical nature of the modification at position 2501 has remained elusive, and attempts to isolate it have so far been unsuccessful. We unambiguously identify this last unknown modification as 5-hydroxycytidine-a novel modification in RNA. Identification of 5-hydroxycytidine was completed by liquid chromatography under nonoxidizing conditions using a graphitized carbon stationary phase in combination with ion trap tandem mass spectrometry and by comparing the fragmentation behavior of the natural nucleoside with that of a chemically synthesized ditto. Furthermore, we show that 5-hydroxycytidine is also present in the equivalent position of 23S rRNA from the bacterium Deinococcus radiodurans. Given the unstable nature of 5-hydroxycytidine, this modification might be found in other RNAs when applying the proper analytical conditions as described here.
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Affiliation(s)
- Jesper Foged Havelund
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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30
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Graf D, Haselow K, Münks I, Bode JG, Häussinger D. Inhibition of interferon-α-induced signaling by hyperosmolarity and hydrophobic bile acids. Biol Chem 2011; 391:1175-87. [PMID: 21028968 DOI: 10.1515/bc.2010.108] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Apart from viral conditions, host factors such as elevated bile acid concentrations are determinants of successful interferon-α (IFN-α) treatment in patients with chronic hepatitis C or B. The present study demonstrates that hydrophobic bile acids inhibit Jak1- and Tyk2-phosphorylation, which lead to blockade of STAT1-mediated IFN-α-signaling in the sodium-taurocholate cotransporting peptide (NTCP)-transfected human hepatoma cell line HepG2, resulting in a decreased mRNA and protein expression of IFN-stimulated genes such as myxovirus resistance protein A (MxA) or dsRNA-activated protein kinase (PKR). In addition, hyperosmotic stress leads to an inhibition of IFN-α-induced Jak1- and Tyk2-phosphorylation, and STAT1/STAT2-phosphorylation and gene expression. This inhibitory effect of hydrophobic bile acids or hyperosmolarity is not due to caspase-mediated cleavage or lysosomal degradation of the cognate receptors or to the generation of oxidative stress, activation of p38- or Erk-mediated MAPK pathways or phosphatase activity. Preincubation with the organic osmolyte betaine blocked the inhibitory effect of bile acids or hyperosmolarity on MxA protein expression, but had no effect on transcript levels or activation of STAT1, suggesting that betaine mediates its effects on MxA expression at a translational or post-translational level. Our findings could provide a rationale for betaine use in cholestatic HBV/HCV patients undergoing interferon therapy.
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Affiliation(s)
- Dirk Graf
- Department of Gastroenterology, Hepatology and Infectiology, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany.
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31
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Hase Y, Yokoyama S, Muto A, Himeno H. Removal of a ribosome small subunit-dependent GTPase confers salt resistance on Escherichia coli cells. RNA (NEW YORK, N.Y.) 2009; 15:1766-1774. [PMID: 19620234 PMCID: PMC2743055 DOI: 10.1261/rna.1687309] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2009] [Accepted: 06/03/2009] [Indexed: 05/28/2023]
Abstract
RsgA is a unique GTP hydrolytic protein in which GTPase activity is significantly enhanced by the small ribosomal subunit. Deletion of RsgA causes slow cell growth as well as defects in subunit assembly of the ribosome and 16S rRNA processing, suggesting its involvement in maturation of the small subunit. In this study, we found that removal of RsgA or inactivation of its ribosome small subunit-dependent GTPase activity provides Escherichia coli cells with resistance to high salt stress. Salt stress suppressed the defects in subunit assembly of the ribosome and processing of 16S rRNA as well as truncation of the 3' end of 16S rRNA in RsgA-deletion cells. In contrast, salt stress transiently impaired subunit assembly of the ribosome and processing of 16S rRNA and induced 3' truncation of 16S rRNA in wild-type cells. These results suggest that the action of RsgA on the ribosome, which usually facilitates maturation of the small subunit, disturbs it under a salt stress condition. Consistently, there was a drastic but transient decrease in the intracellular amount of RsgA after salt shock. Salt shock would make the pathway of maturation of the ribosome small subunit RsgA independent.
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Affiliation(s)
- Yoichi Hase
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
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32
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Abstract
The assembly of bacterial ribosomes is viewed with increasing interest as a potential target for new antibiotics. The in vivo synthesis and assembly of ribosomes are briefly reviewed here, highlighting the many ways in which assembly can be perturbed. The process is compared with the model in vitro process from which much of our knowledge is derived. The coordinate synthesis of the ribosomal components is essential for their ordered and efficient assembly; antibiotics interfere with this coordination and therefore affect assembly. It has also been claimed that the binding of antibiotics to nascent ribosomes prevents their assembly. These two contrasting models of antibiotic action are compared and evaluated. Finally, the suitability and tractability of assembly as a drug target are assessed.
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33
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Kurz M. Compatible solute influence on nucleic acids: many questions but few answers. SALINE SYSTEMS 2008; 4:6. [PMID: 18522725 PMCID: PMC2430576 DOI: 10.1186/1746-1448-4-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Accepted: 06/03/2008] [Indexed: 12/21/2022]
Abstract
Compatible solutes are small organic osmolytes including but not limited to sugars, polyols, amino acids, and their derivatives. They are compatible with cell metabolism even at molar concentrations. A variety of organisms synthesize or take up compatible solutes for adaptation to extreme environments. In addition to their protective action on whole cells, compatible solutes display significant effects on biomolecules in vitro. These include stabilization of native protein and nucleic acid structures. They are used as additives in polymerase chain reactions to increase product yield and specificity, but also in other nucleic acid and protein applications. Interactions of compatible solutes with nucleic acids and protein-nucleic acid complexes are much less understood than the corresponding interactions of compatible solutes with proteins. Although we may begin to understand solute/nucleic acid interactions there are only few answers to the many questions we have. I summarize here the current state of knowledge and discuss possible molecular mechanisms and thermodynamics.
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Affiliation(s)
- Matthias Kurz
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich Wilhelms-Universität Bonn, Bonn, Germany.
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34
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Lambert D, Draper DE. Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions. J Mol Biol 2007; 370:993-1005. [PMID: 17555763 PMCID: PMC1995082 DOI: 10.1016/j.jmb.2007.03.080] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Accepted: 03/19/2007] [Indexed: 01/21/2023]
Abstract
Osmolytes are small organic molecules accumulated by cells in response to osmotic stress. Although their effects on protein stability have been studied, there has been no systematic documentation of their influence on RNA. Here, the effects of nine osmolytes on the secondary and tertiary structure stabilities of six RNA structures of differing complexity and stability have been surveyed. Using thermal melting analysis, m-values (change in DeltaG degrees of RNA folding per molal concentration of osmolyte) have been measured. All the osmolytes destabilize RNA secondary structure, although to different extents, probably because they favor solubilization of base surfaces. Osmolyte effects on tertiary structure, however, can be either stabilizing or destabilizing. We hypothesize that the stabilizing osmolytes have unfavorable interactions with the RNA backbone, which becomes less accessible to solvent in most tertiary structures. Finally, it was found that as a larger fraction of the negative charge of an RNA tertiary structure is neutralized by hydrated Mg(2+), the RNA becomes less responsive to stabilizing osmolytes and may even be destabilized. The natural selection of osmolytes as protective agents must have been influenced by their effects on the stabilities of functional RNA structures, though in general, the effects of osmolytes on RNA and protein stabilities do not parallel each other. Our results also suggest that some osmolytes can be useful tools for studying intrinsically unstable RNA folds and assessing the mechanisms of Mg(2+)-induced RNA stabilization.
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Affiliation(s)
- Dominic Lambert
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
| | - David E. Draper
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
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35
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Abstract
Advances in the in vitro synthesis and evolution of DNA, RNA, and polypeptides are accelerating the construction of biopolymers, pathways, and organisms with novel functions. Known functions are being integrated and debugged with the aim of synthesizing life-like systems. The goals are knowledge, tools, smart materials, and therapies.
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Affiliation(s)
- Anthony C Forster
- Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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36
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Abstract
Construction of a chemical system capable of replication and evolution, fed only by small molecule nutrients, is now conceivable. This could be achieved by stepwise integration of decades of work on the reconstitution of DNA, RNA and protein syntheses from pure components. Such a minimal cell project would initially define the components sufficient for each subsystem, allow detailed kinetic analyses and lead to improved in vitro methods for synthesis of biopolymers, therapeutics and biosensors. Completion would yield a functionally and structurally understood self-replicating biosystem. Safety concerns for synthetic life will be alleviated by extreme dependence on elaborate laboratory reagents and conditions for viability. Our proposed minimal genome is 113 kbp long and contains 151 genes. We detail building blocks already in place and major hurdles to overcome for completion.
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Affiliation(s)
- Anthony C Forster
- Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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37
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Abstract
RNA is structurally very flexible, which provides the basis for its functional diversity. An RNA molecule can often adopt different conformations, which enables the regulation of its function through folding. Proteins help RNAs reach their functionally active conformation by increasing their structural stability or by chaperoning the folding process. Large, dynamic RNA-protein complexes, such as the ribosome or the spliceosome, require numerous proteins that coordinate conformational switches of the RNA components during assembly and during their respective activities.
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Affiliation(s)
- Renée Schroeder
- Max F. Perutz Laboratories, Department of Microbiology and Genetics, University of Vienna, Austria.
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38
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Hesslein AE, Katunin VI, Beringer M, Kosek AB, Rodnina MV, Strobel SA. Exploration of the conserved A+C wobble pair within the ribosomal peptidyl transferase center using affinity purified mutant ribosomes. Nucleic Acids Res 2004; 32:3760-70. [PMID: 15256541 PMCID: PMC484164 DOI: 10.1093/nar/gkh672] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Protein synthesis in the ribosome's large subunit occurs within an active site comprised exclusively of RNA. Mutational studies of rRNA active site residues could provide valuable insight into the mechanism of peptide bond formation, but many of these mutations cause a dominant lethal phenotype, which prevents production of the homogeneous mutant ribosomes needed for analysis. We report a general method to affinity purify in vivo assembled 50S ribosomal subunits containing lethal active site mutations via a U1A protein-binding tag inserted onto the 23S rRNA. The expected pH-dependent formation of the A2450+C2063 wobble pair has made it a potential candidate for the pH-dependent conformational change that occurs within the ribosomal active site. Using this approach, the active site A2450+C2063 pair was mutated to the isosteric, but pH-independent, G2450*U2063 wobble pair, and 50S subunits containing the mutations were affinity purified. The G*U mutation caused the adjacent A2451 to become hyper-reactive to dimethylsulfate (DMS) modification in a pH-independent manner. Furthermore, the G*U mutation decreased both the rate of peptide bond formation and the affinity of the post-translocation complex for puromycin. The reaction rate (k(pep)) was reduced approximately 200-fold for both puromycin and the natural aminoacyl-tRNA A-site substrate. The mutations also substantially altered the pH dependence of the reaction. Mutation of this base pair has significant deleterious effects upon peptidyl transferase activity, but because G*U mutation disrupts several tertiary contacts with the wobble pair, the assignment of A2450 as the active site residue with the neutral pK(a) important for the peptidyl transferase reaction cannot be fully supported or excluded based upon these data.
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Affiliation(s)
- Ashley Eversole Hesslein
- Yale University, Department of Molecular Biophysics and Biochemistry, 260 Whitney Avenue, New Haven, CT 06520 8114, USA
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39
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Liu B, Fournier MJ. Interference probing of rRNA with snoRNPs: a novel approach for functional mapping of RNA in vivo. RNA (NEW YORK, N.Y.) 2004; 10:1130-41. [PMID: 15208448 PMCID: PMC1370603 DOI: 10.1261/rna.7190104] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Synthesis of eukaryotic ribosomal RNAs (rRNAs) includes methylation of scores of nucleotides at the 2'-O-ribose position (Nm) by small nucleolar RNP complexes (snoRNPs). Sequence specificity is provided by the snoRNA component through base-pairing of a guide sequence with rRNA. Here, we report that methylation snoRNPs can be targeted to many new sites in yeast rRNA, by providing the snoRNA with a novel guide sequence, and that in some cases growth and translation activity are strongly impaired. Novel snoRNAs can be expressed individually or by a unique library strategy that yields guide sequences specific for a large target region. Interference effects were observed for sites in both the small and large subunits, including the reaction center region. Targeting guide RNAs to nucleotides flanking the sensitive sites caused little or no defect, indicating that methylation is responsible for the interference rather than a simple antisense effect or misguided chaperone function. To our knowledge, this is the only approach that has been used to mutagenize the backbone of rRNA in vivo.
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Affiliation(s)
- Ben Liu
- Department of Biochemistry and Molecular Biology, Lederle Graduate Research Center, University of Massachusetts, Amherst, MA 01003, USA
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40
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Cochella L, Green R. Isolation of antibiotic resistance mutations in the rRNA by using an in vitro selection system. Proc Natl Acad Sci U S A 2004; 101:3786-91. [PMID: 15001709 PMCID: PMC374322 DOI: 10.1073/pnas.0307596101] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetic, biochemical, and structural data support an essential role for the ribosomal RNA in all steps of the translation process. Although in vivo genetic selection techniques have been used to identify mutations in the rRNAs that result in various miscoding phenotypes and resistance to known ribosome-targeted antibiotics, these are limited because the resulting mutant ribosomes must be only marginally disabled if they are able to support growth of the cell. Furthermore, in vivo, it is not possible to control the environment in precise ways that might allow for the isolation of certain types of rRNA variants. To overcome these limitations, we have developed an in vitro selection system for the isolation of functionally competent ribosomal particles from populations containing variant rRNAs. Here, we describe this system and present an example of its application to the selection of antibiotic resistance mutations. From a pool of 4,096 23S rRNA variants, a double mutant (A2058U/A2062G) was isolated after iteration of the selection process. This mutant was highly resistant to clindamycin in in vitro translation reactions and yet was not viable in Escherichia coli. These data establish that this system has the potential to identify mutations in the rRNA not readily accessed by comparable in vivo systems, thus allowing for more exhaustive ribosomal genetic screens.
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Affiliation(s)
- Luisa Cochella
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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41
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Alix JH, Nierhaus KH. DnaK-facilitated ribosome assembly in Escherichia coli revisited. RNA (NEW YORK, N.Y.) 2003; 9:787-793. [PMID: 12810912 PMCID: PMC1370445 DOI: 10.1261/rna.5360203] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2003] [Accepted: 03/28/2003] [Indexed: 05/24/2023]
Abstract
Assembly helpers exist for the formation of ribosomal subunits. Such a function has been suggested for the DnaK system of chaperones (DnaK, DnaJ, GrpE). Here we show that 50S and 30S ribosomal subunits from an Escherichia coli dnaK-null mutant (containing a disrupted dnaK gene) grown at 30 degrees C are physically and functionally identical to wild-type ribosomes. Furthermore, ribosomal components derived from mutant 30S and 50S subunits are fully competent for in vitro reconstitution of active ribosomal subunits. On the other hand, the DnaK chaperone system cannot circumvent the necessary heat-dependent activation step for the in vitro reconstitution of fully active 30S ribosomal subunits. It is therefore questionable whether the requirement for DnaK observed during in vivo ribosome assembly above 37 degrees C implicates a direct or indirect role for DnaK in this process.
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Affiliation(s)
- Jean-Hervé Alix
- Institut de Biologie Physico-Chimique, UPR 9073 du CNRS, F-75005 Paris, France.
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42
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Kim DF, Semrad K, Green R. Analysis of the active site of the ribosome by site-directed mutagenesis. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 66:119-26. [PMID: 12762014 DOI: 10.1101/sqb.2001.66.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- D F Kim
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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43
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Gluick TC, Yadav S. Trimethylamine N-oxide stabilizes RNA tertiary structure and attenuates the denaturating effects of urea. J Am Chem Soc 2003; 125:4418-9. [PMID: 12683801 DOI: 10.1021/ja0292997] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Trimethylamine N-oxide (TMAO) and urea are osmolytes. Osmolytes allow cells to remain viable in harsh or extreme environments. Both TMAO and urea are found in shark and rays at approximate molar ratios of 1:2, respectively. At this ratio TMAO nearly completely counteracts the destabilizing effects that urea has on proteins. We ask whether RNA, which is denatured by urea, is stabilized by TMAO in a manner similar to that seen for proteins. We found that TMAO stabilizes Escherichia coli tRNAfmet tertiary structure and counteracts the denaturing effects of urea at the same ratios found for proteins. Cation binding usually drives RNA tertiary structure formation. These results suggest that tertiary structure stability is not only sensitive to cations but also to the aqueous composition and properties of the solvent. We propose that tertiary structure folding is driven by unfavorable interactions between TMAO and the phosphodiester backbone.
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Affiliation(s)
- Thomas C Gluick
- Department of Chemistry and Biochemistry, P.O. Box 19065, The University of Texas at Arlington, Arlington, TX 76019, USA.
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44
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Williamson JR. After the ribosome structures: how are the subunits assembled? RNA (NEW YORK, N.Y.) 2003; 9:165-7. [PMID: 12554857 PMCID: PMC1370380 DOI: 10.1261/rna.2164903] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The recent structures of the ribosome and the ribosomal subunits only heighten the intrigue of trying to understand how the ribosome is assembled. Biochemical and mechanistic studies have mapped out the basic series of protein binding events that occur, but we do not yet have a clear picture of the RNA conformational changes that must accompany the protein binding. Recent studies point to roles of protein folding chaperones and RNA helicases as facilitators of ribosome assembly, but the basic process of assembly seems to be encoded in the RNA sequences and can occur for the most part spontaneously in vitro, and quite possibly in vivo as well.
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Affiliation(s)
- James R Williamson
- Departments of Molecular Biology and Chemistry, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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