1
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [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: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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2
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Manghrani A, Rangadurai AK, Szekely O, Liu B, Guseva S, Al-Hashimi HM. Quantitative and systematic NMR measurements of sequence-dependent A-T Hoogsteen dynamics uncovers unique conformational specificity in the DNA double helix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594415. [PMID: 38798635 PMCID: PMC11118333 DOI: 10.1101/2024.05.15.594415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The propensities to form lowly-populated short-lived conformations of DNA could vary with sequence, providing an important source of sequence-specificity in biochemical reactions. However, comprehensively measuring how these dynamics vary with sequence is challenging. Using 1H CEST and 13C R 1 ρ NMR, we measured Watson-Crick to Hoogsteen dynamics for an A-T base pair in thirteen trinucleotide sequence contexts. The Hoogsteen population and exchange rate varied 4-fold and 16-fold, respectively, and were dependent on both the 3'- and 5'-neighbors but only weakly dependent on monovalent ion concentration (25 versus 100 mM NaCl) and pH (6.8 versus 8.0). Flexible TA and CA dinucleotide steps exhibited the highest Hoogsteen populations, and their kinetics rates strongly depended on the 3'-neighbor. In contrast, the stiffer AA and GA steps had the lowest Hoogsteen population, and their kinetics were weakly dependent on the 3'-neighbor. The Hoogsteen lifetime was especially short when G-C neighbors flanked the A-T base pair. The Hoogsteen dynamics had a distinct sequence-dependence compared to duplex stability and minor groove width. Thus, our results uncover a unique source of sequence-specificity hidden within the DNA double helix in the form of A-T Hoogsteen dynamics and establish the utility of 1H CEST to quantitively measure sequence-dependent DNA dynamics.
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Affiliation(s)
- Akanksha Manghrani
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27705, United States
| | - Atul Kaushik Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27705, United States
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada
| | - Or Szekely
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27705, United States
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27705, United States
| | - Serafima Guseva
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
| | - Hashim M. Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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3
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Marín M, López M, Gallego-Yerga L, Álvarez R, Peláez R. Experimental structure based drug design (SBDD) applications for anti-leishmanial drugs: A paradigm shift? Med Res Rev 2024; 44:1055-1120. [PMID: 38142308 DOI: 10.1002/med.22005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
Leishmaniasis is a group of neglected tropical diseases caused by at least 20 species of Leishmania protozoa, which are spread by the bite of infected sandflies. There are three main forms of the disease: cutaneous leishmaniasis (CL, the most common), visceral leishmaniasis (VL, also known as kala-azar, the most serious), and mucocutaneous leishmaniasis. One billion people live in areas endemic to leishmaniasis, with an annual estimation of 30,000 new cases of VL and more than 1 million of CL. New treatments for leishmaniasis are an urgent need, as the existing ones are inefficient, toxic, and/or expensive. We have revised the experimental structure-based drug design (SBDD) efforts applied to the discovery of new drugs against leishmaniasis. We have grouped the explored targets according to the metabolic pathways they belong to, and the key achieved advances are highlighted and evaluated. In most cases, SBDD studies follow high-throughput screening campaigns and are secondary to pharmacokinetic optimization, due to the majoritarian belief that there are few validated targets for SBDD in leishmaniasis. However, some SBDD strategies have significantly contributed to new drug candidates against leishmaniasis and a bigger number holds promise for future development.
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Affiliation(s)
- Miguel Marín
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Marta López
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Laura Gallego-Yerga
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Raquel Álvarez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
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4
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Akiyama N, Ishiguro K, Yokoyama T, Miyauchi K, Nagao A, Shirouzu M, Suzuki T. Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine. Nat Struct Mol Biol 2024; 31:817-825. [PMID: 38538915 DOI: 10.1038/s41594-024-01238-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 01/31/2024] [Indexed: 05/21/2024]
Abstract
The anticodon modifications of transfer RNAs (tRNAs) finetune the codon recognition on the ribosome for accurate translation. Bacteria and archaea utilize the modified cytidines, lysidine (L) and agmatidine (agm2C), respectively, in the anticodon of tRNAIle to decipher AUA codon. L and agm2C contain long side chains with polar termini, but their functions remain elusive. Here we report the cryogenic electron microscopy structures of tRNAsIle recognizing the AUA codon on the ribosome. Both modifications interact with the third adenine of the codon via a unique C-A geometry. The side chains extend toward 3' direction of the mRNA, and the polar termini form hydrogen bonds with 2'-OH of the residue 3'-adjacent to the AUA codon. Biochemical analyses demonstrated that AUA decoding is facilitated by the additional interaction between the polar termini of the modified cytidines and 2'-OH of the fourth mRNA residue. We also visualized cyclic N6-threonylcarbamoyladenosine (ct6A), another tRNA modification, and revealed a molecular basis how ct6A contributes to efficient decoding.
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MESH Headings
- RNA, Transfer, Ile/chemistry
- RNA, Transfer, Ile/metabolism
- RNA, Transfer, Ile/genetics
- Cryoelectron Microscopy
- Anticodon/chemistry
- Anticodon/metabolism
- Ribosomes/metabolism
- Ribosomes/chemistry
- Nucleic Acid Conformation
- Models, Molecular
- Codon/genetics
- Lysine/metabolism
- Lysine/chemistry
- Lysine/analogs & derivatives
- Cytidine/analogs & derivatives
- Cytidine/chemistry
- Cytidine/metabolism
- RNA, Transfer/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- Protein Biosynthesis
- Pyrimidine Nucleosides
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Affiliation(s)
- Naho Akiyama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kensuke Ishiguro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Takeshi Yokoyama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
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5
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Rybak MY, Gagnon MG. Structures of the ribosome bound to EF-Tu-isoleucine tRNA elucidate the mechanism of AUG avoidance. Nat Struct Mol Biol 2024; 31:810-816. [PMID: 38538914 DOI: 10.1038/s41594-024-01236-3] [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: 02/28/2023] [Accepted: 01/31/2024] [Indexed: 04/18/2024]
Abstract
The frequency of errors upon decoding of messenger RNA by the bacterial ribosome is low, with one misreading event per 1 × 104 codons. In the universal genetic code, the AUN codon box specifies two amino acids, isoleucine and methionine. In bacteria and archaea, decoding specificity of the AUA and AUG codons relies on the wobble avoidance strategy that requires modification of C34 in the anticodon loop of isoleucine transfer RNAIleCAU (tRNAIleCAU). Bacterial tRNAIleCAU with 2-lysylcytidine (lysidine) at the wobble position deciphers AUA while avoiding AUG. Here we report cryo-electron microscopy structures of the Escherichia coli 70S ribosome complexed with elongation factor thermo unstable (EF-Tu) and isoleucine-tRNAIleLAU in the process of decoding AUA and AUG. Lysidine in tRNAIleLAU excludes AUG by promoting the formation of an unusual Hoogsteen purine-pyrimidine nucleobase geometry at the third position of the codon, weakening the interactions with the mRNA and destabilizing the EF-Tu ternary complex. Our findings elucidate the molecular mechanism by which tRNAIleLAU specifically decodes AUA over AUG.
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MESH Headings
- Peptide Elongation Factor Tu/metabolism
- Peptide Elongation Factor Tu/chemistry
- Peptide Elongation Factor Tu/genetics
- Cryoelectron Microscopy
- Escherichia coli/metabolism
- Escherichia coli/genetics
- Ribosomes/metabolism
- Ribosomes/ultrastructure
- Ribosomes/chemistry
- RNA, Transfer, Ile/metabolism
- RNA, Transfer, Ile/chemistry
- RNA, Transfer, Ile/genetics
- Models, Molecular
- Codon/metabolism
- Codon/genetics
- Anticodon/chemistry
- Anticodon/metabolism
- Nucleic Acid Conformation
- Isoleucine/metabolism
- Isoleucine/chemistry
- RNA, Messenger/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- Lysine/analogs & derivatives
- Pyrimidine Nucleosides
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Affiliation(s)
- Mariia Yu Rybak
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Matthieu G Gagnon
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
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6
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Fang N, Wu L, Duan S, Li J. The Structural and Molecular Mechanisms of Mycobacterium tuberculosis Translational Elongation Factor Proteins. Molecules 2024; 29:2058. [PMID: 38731549 PMCID: PMC11085428 DOI: 10.3390/molecules29092058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Targeting translation factor proteins holds promise for developing innovative anti-tuberculosis drugs. During protein translation, many factors cause ribosomes to stall at messenger RNA (mRNA). To maintain protein homeostasis, bacteria have evolved various ribosome rescue mechanisms, including the predominant trans-translation process, to release stalled ribosomes and remove aberrant mRNAs. The rescue systems require the participation of translation elongation factor proteins (EFs) and are essential for bacterial physiology and reproduction. However, they disappear during eukaryotic evolution, which makes the essential proteins and translation elongation factors promising antimicrobial drug targets. Here, we review the structural and molecular mechanisms of the translation elongation factors EF-Tu, EF-Ts, and EF-G, which play essential roles in the normal translation and ribosome rescue mechanisms of Mycobacterium tuberculosis (Mtb). We also briefly describe the structure-based, computer-assisted study of anti-tuberculosis drugs.
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Affiliation(s)
- Ning Fang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
| | - Lingyun Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
| | - Shuyan Duan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang 277160, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
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7
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Joshi K, Luisi B, Wunderlin G, Saleh S, Lilly A, Okusolubo T, Farabaugh PJ. An evolutionarily conserved phosphoserine-arginine salt bridge in the interface between ribosomal proteins uS4 and uS5 regulates translational accuracy in Saccharomyces cerevisiae. Nucleic Acids Res 2024; 52:3989-4001. [PMID: 38340338 DOI: 10.1093/nar/gkae053] [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: 08/22/2023] [Revised: 01/08/2024] [Accepted: 02/08/2024] [Indexed: 02/12/2024] Open
Abstract
Protein-protein and protein-rRNA interactions at the interface between ribosomal proteins uS4 and uS5 are thought to maintain the accuracy of protein synthesis by increasing selection of cognate aminoacyl-tRNAs. Selection involves a major conformational change-domain closure-that stabilizes aminoacyl-tRNA in the ribosomal acceptor (A) site. This has been thought a constitutive function of the ribosome ensuring consistent accuracy. Recently, the Saccharomyces cerevisiae Ctk1 cyclin-dependent kinase was demonstrated to ensure translational accuracy and Ser238 of uS5 proposed as its target. Surprisingly, Ser238 is outside the uS4-uS5 interface and no obvious mechanism has been proposed to explain its role. We show that the true target of Ctk1 regulation is another uS5 residue, Ser176, which lies in the interface opposite to Arg57 of uS4. Based on site specific mutagenesis, we propose that phospho-Ser176 forms a salt bridge with Arg57, which should increase selectivity by strengthening the interface. Genetic data show that Ctk1 regulates accuracy indirectly; the data suggest that the kinase Ypk2 directly phosphorylates Ser176. A second kinase pathway involving TORC1 and Pkc1 can inhibit this effect. The level of accuracy appears to depend on competitive action of these two pathways to regulate the level of Ser176 phosphorylation.
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Affiliation(s)
- Kartikeya Joshi
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore 21250, USA
| | - Brooke Luisi
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore 21250, USA
| | - Grant Wunderlin
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore 21250, USA
| | - Sima Saleh
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore 21250, USA
| | - Anna Lilly
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore 21250, USA
| | - Temiloluwa Okusolubo
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore 21250, USA
| | - Philip J Farabaugh
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore 21250, USA
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8
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Byju S, Hassan A, Whitford PC. The energy landscape of the ribosome. Biopolymers 2024; 115:e23570. [PMID: 38051695 DOI: 10.1002/bip.23570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/17/2023] [Accepted: 11/08/2023] [Indexed: 12/07/2023]
Abstract
The ribosome is a prototypical assembly that can be used to establish general principles and techniques for the study of biological molecular machines. Motivated by the fact that the dynamics of every biomolecule is governed by an underlying energy landscape, there has been great interest to understand and quantify ribosome energetics. In the present review, we will focus on theoretical and computational strategies for probing the interactions that shape the energy landscape of the ribosome, with an emphasis on more recent studies of the elongation cycle. These efforts include the application of quantum mechanical methods for describing chemical kinetics, as well as classical descriptions to characterize slower (microsecond to millisecond) large-scale (10-100 Å) rearrangements, where motion is described in terms of diffusion across an energy landscape. Together, these studies provide broad insights into the factors that control a diverse range of dynamical processes in this assembly.
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Affiliation(s)
- Sandra Byju
- Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts, USA
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Asem Hassan
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, United States
| | - Paul C Whitford
- Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts, USA
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
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9
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Ali Z, Kukhta T, Trant JF, Sharma P. An Atlas of the base inter-RNA stacks involved in bacterial translation. Biophys Chem 2024; 305:107144. [PMID: 38061282 DOI: 10.1016/j.bpc.2023.107144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
Nucleobase-specific noncovalent interactions play a crucial role in translation. Herein, we provide a comprehensive analysis of the stacks between different RNA components in the crystal structures of the bacterial ribosome caught at different translation stages. Analysis of tRNA||rRNA stacks reveals distinct behaviour; both the A-and E-site tRNAs exhibit unique stacking patterns with 23S rRNA bases, while P-site tRNAs stack with 16S rRNA bases. Furthermore, E-site stacks exhibit diverse face orientations and ring topologies-rare for inter-chain RNA interactions-with higher average interaction energies than A or P-site stacks. This suggests that stacking may be essential for stabilizing tRNA progression through the E-site. Additionally, mRNA||rRNA stacks reveal other geometries, which depend on the tRNA binding site, whereas 16S rRNA||23S rRNA stacks highlight the importance of specific bases in maintaining the integrity of the translational complex by linking the two rRNAs. Furthermore, tRNA||mRNA stacks exhibit distinct geometries and energetics at the E-site, indicating their significance during tRNA translocation and elimination. Overall, both A and E-sites display a more diverse distribution of inter-RNA stacks compared to the P-site. Stacking interactions in the active ribosome are not simply accidental byproducts of biochemistry but are likely invoked to compensate and support the integrity and dynamics of translation.
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MESH Headings
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Ribosomes/chemistry
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/analysis
- RNA, Messenger/metabolism
- Nucleic Acid Conformation
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Affiliation(s)
- Zakir Ali
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Teagan Kukhta
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Ave., Windsor, ON N9B 3P4, Canada
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Ave., Windsor, ON N9B 3P4, Canada; We-Spark Health Institute, 401 Sunset Ave., Windsor, ON N9B 3P4, Canada; Binary Star Research Services, LaSalle, ON N9J 3X8, Canada.
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India; Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Ave., Windsor, ON N9B 3P4, Canada.
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10
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Zhao X, Ma D, Ishiguro K, Saito H, Akichika S, Matsuzawa I, Mito M, Irie T, Ishibashi K, Wakabayashi K, Sakaguchi Y, Yokoyama T, Mishima Y, Shirouzu M, Iwasaki S, Suzuki T, Suzuki T. Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth. Cell 2023; 186:5517-5535.e24. [PMID: 37992713 DOI: 10.1016/j.cell.2023.10.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 08/14/2023] [Accepted: 10/26/2023] [Indexed: 11/24/2023]
Abstract
Transfer RNA (tRNA) modifications are critical for protein synthesis. Queuosine (Q), a 7-deaza-guanosine derivative, is present in tRNA anticodons. In vertebrate tRNAs for Tyr and Asp, Q is further glycosylated with galactose and mannose to generate galQ and manQ, respectively. However, biogenesis and physiological relevance of Q-glycosylation remain poorly understood. Here, we biochemically identified two RNA glycosylases, QTGAL and QTMAN, and successfully reconstituted Q-glycosylation of tRNAs using nucleotide diphosphate sugars. Ribosome profiling of knockout cells revealed that Q-glycosylation slowed down elongation at cognate codons, UAC and GAC (GAU), respectively. We also found that galactosylation of Q suppresses stop codon readthrough. Moreover, protein aggregates increased in cells lacking Q-glycosylation, indicating that Q-glycosylation contributes to proteostasis. Cryo-EM of human ribosome-tRNA complex revealed the molecular basis of codon recognition regulated by Q-glycosylations. Furthermore, zebrafish qtgal and qtman knockout lines displayed shortened body length, implying that Q-glycosylation is required for post-embryonic growth in vertebrates.
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Affiliation(s)
- Xuewei Zhao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Ding Ma
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Kensuke Ishiguro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan; Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Hironori Saito
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Shinichiro Akichika
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Ikuya Matsuzawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Mari Mito
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toru Irie
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Kota Ishibashi
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Kimi Wakabayashi
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Takeshi Yokoyama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Yuichiro Mishima
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Shintaro Iwasaki
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan.
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan.
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11
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Girodat D, Wieden HJ, Blanchard SC, Sanbonmatsu KY. Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding. Nat Commun 2023; 14:5582. [PMID: 37696823 PMCID: PMC10495418 DOI: 10.1038/s41467-023-40404-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 07/27/2023] [Indexed: 09/13/2023] Open
Abstract
Accurate protein synthesis is determined by the two-subunit ribosome's capacity to selectively incorporate cognate aminoacyl-tRNA for each mRNA codon. The molecular basis of tRNA selection accuracy, and how fidelity can be affected by antibiotics, remains incompletely understood. Using molecular simulations, we find that cognate and near-cognate tRNAs delivered to the ribosome by Elongation Factor Tu (EF-Tu) can follow divergent pathways of motion into the ribosome during both initial selection and proofreading. Consequently, cognate aa-tRNAs follow pathways aligned with the catalytic GTPase and peptidyltransferase centers of the large subunit, while near-cognate aa-tRNAs follow pathways that are misaligned. These findings suggest that differences in mRNA codon-tRNA anticodon interactions within the small subunit decoding center, where codon-anticodon interactions occur, are geometrically amplified over distance, as a result of this site's physical separation from the large ribosomal subunit catalytic centers. These insights posit that the physical size of both tRNA and ribosome are key determinants of the tRNA selection fidelity mechanism.
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Affiliation(s)
- Dylan Girodat
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Hans-Joachim Wieden
- Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
- New Mexico Consortium, Los Alamos, NM, 87545, USA.
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12
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McFeely CAL, Shakya B, Makovsky CA, Haney AK, Ashton Cropp T, Hartman MCT. Extensive breaking of genetic code degeneracy with non-canonical amino acids. Nat Commun 2023; 14:5008. [PMID: 37591858 PMCID: PMC10435567 DOI: 10.1038/s41467-023-40529-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 07/26/2023] [Indexed: 08/19/2023] Open
Abstract
Genetic code expansion (GCE) offers many exciting opportunities for the creation of synthetic organisms and for drug discovery methods that utilize in vitro translation. One type of GCE, sense codon reassignment (SCR), focuses on breaking the degeneracy of the 61 sense codons which encode for only 20 amino acids. SCR has great potential for genetic code expansion, but extensive SCR is limited by the post-transcriptional modifications on tRNAs and wobble reading of these tRNAs by the ribosome. To better understand codon-tRNA pairing, here we develop an assay to evaluate the ability of aminoacyl-tRNAs to compete with each other for a given codon. We then show that hyperaccurate ribosome mutants demonstrate reduced wobble reading, and when paired with unmodified tRNAs lead to extensive and predictable SCR. Together, we encode seven distinct amino acids across nine codons spanning just two codon boxes, thereby demonstrating that the genetic code hosts far more re-assignable space than previously expected, opening the door to extensive genetic code engineering.
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Affiliation(s)
- Clinton A L McFeely
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA
- Massey Cancer Center, Virginia Commonwealth University, 401 College St., Richmond, VA, 23219, USA
| | - Bipasana Shakya
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA
- Massey Cancer Center, Virginia Commonwealth University, 401 College St., Richmond, VA, 23219, USA
| | - Chelsea A Makovsky
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA
- Massey Cancer Center, Virginia Commonwealth University, 401 College St., Richmond, VA, 23219, USA
| | - Aidan K Haney
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA
| | - T Ashton Cropp
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA
| | - Matthew C T Hartman
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA.
- Massey Cancer Center, Virginia Commonwealth University, 401 College St., Richmond, VA, 23219, USA.
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13
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Jain S, Koziej L, Poulis P, Kaczmarczyk I, Gaik M, Rawski M, Ranjan N, Glatt S, Rodnina MV. Modulation of translational decoding by m 6A modification of mRNA. Nat Commun 2023; 14:4784. [PMID: 37553384 PMCID: PMC10409866 DOI: 10.1038/s41467-023-40422-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/27/2023] [Indexed: 08/10/2023] Open
Abstract
N6-methyladenosine (m6A) is an abundant, dynamic mRNA modification that regulates key steps of cellular mRNA metabolism. m6A in the mRNA coding regions inhibits translation elongation. Here, we show how m6A modulates decoding in the bacterial translation system using a combination of rapid kinetics, smFRET and single-particle cryo-EM. We show that, while the modification does not impair the initial binding of aminoacyl-tRNA to the ribosome, in the presence of m6A fewer ribosomes complete the decoding process due to the lower stability of the complexes and enhanced tRNA drop-off. The mRNA codon adopts a π-stacked codon conformation that is remodeled upon aminoacyl-tRNA binding. m6A does not exclude canonical codon-anticodon geometry, but favors alternative more dynamic conformations that are rejected by the ribosome. These results highlight how modifications outside the Watson-Crick edge can still interfere with codon-anticodon base pairing and complex recognition by the ribosome, thereby modulating the translational efficiency of modified mRNAs.
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Affiliation(s)
- Sakshi Jain
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany
| | - Lukasz Koziej
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
| | - Panagiotis Poulis
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany
| | - Igor Kaczmarczyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, 30-387, Poland
| | - Monika Gaik
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
| | - Michal Rawski
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow, 30-387, Poland
| | - Namit Ranjan
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, 30-387, Poland.
| | - Marina V Rodnina
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany.
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14
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Westhof E, Watson ZL, Zirbel CL, Cate JHD. Anionic G•U pairs in bacterial ribosomal rRNAs. RNA (NEW YORK, N.Y.) 2023; 29:1069-1076. [PMID: 37068913 DOI: 10.1261/rna.079583.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/05/2023] [Indexed: 06/18/2023]
Abstract
Wobble GU pairs (or G•U) occur frequently within double-stranded RNA helices interspersed between standard G=C and A-U Watson-Crick pairs. Another type of G•U pair interacting via their Watson-Crick edges has been observed in the A site of ribosome structures between a modified U34 in the tRNA anticodon triplet and G + 3 in the mRNA. In such pairs, the electronic structure of the U is changed with a negative charge on N3(U), resulting in two H-bonds between N1(G)…O4(U) and N2(G)…N3(U). Here, we report that such pairs occur in other highly conserved positions in ribosomal RNAs of bacteria in the absence of U modification. An anionic cis Watson-Crick G•G pair is also observed and well conserved in the small subunit. These pairs are observed in tightly folded regions.
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Affiliation(s)
- Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, F-67084 Strasbourg, France
| | - Zoe L Watson
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA
| | - Craig L Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - Jamie H D Cate
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
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15
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Vila-Sanjurjo A, Mallo N, Atkins JF, Elson JL, Smith PM. Our current understanding of the toxicity of altered mito-ribosomal fidelity during mitochondrial protein synthesis: What can it tell us about human disease? Front Physiol 2023; 14:1082953. [PMID: 37457031 PMCID: PMC10349377 DOI: 10.3389/fphys.2023.1082953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/28/2023] [Indexed: 07/18/2023] Open
Abstract
Altered mito-ribosomal fidelity is an important and insufficiently understood causative agent of mitochondrial dysfunction. Its pathogenic effects are particularly well-known in the case of mitochondrially induced deafness, due to the existence of the, so called, ototoxic variants at positions 847C (m.1494C) and 908A (m.1555A) of 12S mitochondrial (mt-) rRNA. It was shown long ago that the deleterious effects of these variants could remain dormant until an external stimulus triggered their pathogenicity. Yet, the link from the fidelity defect at the mito-ribosomal level to its phenotypic manifestation remained obscure. Recent work with fidelity-impaired mito-ribosomes, carrying error-prone and hyper-accurate mutations in mito-ribosomal proteins, have started to reveal the complexities of the phenotypic manifestation of mito-ribosomal fidelity defects, leading to a new understanding of mtDNA disease. While much needs to be done to arrive to a clear picture of how defects at the level of mito-ribosomal translation eventually result in the complex patterns of disease observed in patients, the current evidence indicates that altered mito-ribosome function, even at very low levels, may become highly pathogenic. The aims of this review are three-fold. First, we compare the molecular details associated with mito-ribosomal fidelity to those of general ribosomal fidelity. Second, we gather information on the cellular and organismal phenotypes associated with defective translational fidelity in order to provide the necessary grounds for an understanding of the phenotypic manifestation of defective mito-ribosomal fidelity. Finally, the results of recent experiments directly tackling mito-ribosomal fidelity are reviewed and future paths of investigation are discussed.
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Affiliation(s)
- Antón Vila-Sanjurjo
- Grupo GIBE, Departamento de Bioloxía e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Natalia Mallo
- Grupo GIBE, Departamento de Bioloxía e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - John F Atkins
- Schools of Biochemistry and Microbiology, University College Cork, Cork, Ireland
| | - Joanna L Elson
- The Bioscience Institute, Newcastle University, Newcastle uponTyne, United Kingdom
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Paul M Smith
- Department of Paediatrics, Raigmore Hospital, Inverness, Scotland, United Kingdom
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16
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Vila-Sanjurjo A, Mallo N, Elson JL, Smith PM, Blakely EL, Taylor RW. Structural analysis of mitochondrial rRNA gene variants identified in patients with deafness. Front Physiol 2023; 14:1163496. [PMID: 37362424 PMCID: PMC10285412 DOI: 10.3389/fphys.2023.1163496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/18/2023] [Indexed: 06/28/2023] Open
Abstract
The last few years have witnessed dramatic advances in our understanding of the structure and function of the mammalian mito-ribosome. At the same time, the first attempts to elucidate the effects of mito-ribosomal fidelity (decoding accuracy) in disease have been made. Hence, the time is right to push an important frontier in our understanding of mitochondrial genetics, that is, the elucidation of the phenotypic effects of mtDNA variants affecting the functioning of the mito-ribosome. Here, we have assessed the structural and functional role of 93 mitochondrial (mt-) rRNA variants thought to be associated with deafness, including those located at non-conserved positions. Our analysis has used the structural description of the human mito-ribosome of the highest quality currently available, together with a new understanding of the phenotypic manifestation of mito-ribosomal-associated variants. Basically, any base change capable of inducing a fidelity phenotype may be considered non-silent. Under this light, out of 92 previously reported mt-rRNA variants thought to be associated with deafness, we found that 49 were potentially non-silent. We also dismissed a large number of reportedly pathogenic mtDNA variants, 41, as polymorphisms. These results drastically update our view on the implication of the primary sequence of mt-rRNA in the etiology of deafness and mitochondrial disease in general. Our data sheds much-needed light on the question of how mt-rRNA variants located at non-conserved positions may lead to mitochondrial disease and, most notably, provide evidence of the effect of haplotype context in the manifestation of some mt-rRNA variants.
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Affiliation(s)
- Antón Vila-Sanjurjo
- Grupo GIBE. Departamento de Bioloxía e Centro Interdisciplinar de Química e Bioloxía (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Natalia Mallo
- Grupo GIBE. Departamento de Bioloxía e Centro Interdisciplinar de Química e Bioloxía (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Joanna L. Elson
- The Bioscience Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Paul M. Smith
- Department of Paediatrics, Raigmore Hospital, Inverness, United Kingdom
| | - Emma L. Blakely
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
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17
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Holm M, Natchiar SK, Rundlet EJ, Myasnikov AG, Watson ZL, Altman RB, Wang HY, Taunton J, Blanchard SC. mRNA decoding in human is kinetically and structurally distinct from bacteria. Nature 2023; 617:200-207. [PMID: 37020024 PMCID: PMC10156603 DOI: 10.1038/s41586-023-05908-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
In all species, ribosomes synthesize proteins by faithfully decoding messenger RNA (mRNA) nucleotide sequences using aminoacyl-tRNA substrates. Current knowledge of the decoding mechanism derives principally from studies on bacterial systems1. Although key features are conserved across evolution2, eukaryotes achieve higher-fidelity mRNA decoding than bacteria3. In human, changes in decoding fidelity are linked to ageing and disease and represent a potential point of therapeutic intervention in both viral and cancer treatment4-6. Here we combine single-molecule imaging and cryogenic electron microscopy methods to examine the molecular basis of human ribosome fidelity to reveal that the decoding mechanism is both kinetically and structurally distinct from that of bacteria. Although decoding is globally analogous in both species, the reaction coordinate of aminoacyl-tRNA movement is altered on the human ribosome and the process is an order of magnitude slower. These distinctions arise from eukaryote-specific structural elements in the human ribosome and in the elongation factor eukaryotic elongation factor 1A (eEF1A) that together coordinate faithful tRNA incorporation at each mRNA codon. The distinct nature and timing of conformational changes within the ribosome and eEF1A rationalize how increased decoding fidelity is achieved and potentially regulated in eukaryotic species.
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Affiliation(s)
- Mikael Holm
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - S Kundhavai Natchiar
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Emily J Rundlet
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, New York, NY, USA
| | - Alexander G Myasnikov
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
- Dubochet Center for Imaging (DCI), EPFL, Lausanne, Switzerland
| | - Zoe L Watson
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Roger B Altman
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hao-Yuan Wang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Scott C Blanchard
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA.
- Chemical Biology & Therapeutics, St Jude Children's Research Hospital, Memphis, TN, USA.
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18
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Yu T, Jiang J, Yu Q, Li X, Zeng F. Structural Insights into the Distortion of the Ribosomal Small Subunit at Different Magnesium Concentrations. Biomolecules 2023; 13:biom13030566. [PMID: 36979501 PMCID: PMC10046523 DOI: 10.3390/biom13030566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Magnesium ions are abundant and play indispensable functions in the ribosome. A decrease in Mg2+ concentration causes 70S ribosome dissociation and subsequent unfolding. Structural distortion at low Mg2+ concentrations has been observed in an immature pre50S, while the structural changes in mature subunits have not yet been studied. Here, we purified the 30S subunits of E. coli cells under various Mg2+ concentrations and analyzed their structural distortion by cryo-electron microscopy. Upon systematically interrogating the structural heterogeneity within the 1 mM Mg2+ dataset, we observed 30S particles with different levels of structural distortion in the decoding center, h17, and the 30S head. Our model showed that, when the Mg2+ concentration decreases, the decoding center distorts, starting from h44 and followed by the shifting of h18 and h27, as well as the dissociation of ribosomal protein S12. Mg2+ deficiency also eliminates the interactions between h17, h10, h15, and S16, resulting in the movement of h17 towards the tip of h6. More flexible structures were observed in the 30S head and platform, showing high variability in these regions. In summary, the structures resolved here showed several prominent distortion events in the decoding center and h17. The requirement for Mg2+ in ribosomes suggests that the conformational changes reported here are likely shared due to a lack of cellular Mg2+ in all domains of life.
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Affiliation(s)
- Ting Yu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, China
| | - Junyi Jiang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, China
| | - Qianxi Yu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, China
| | - Xin Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, China
| | - Fuxing Zeng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, China
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19
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Nguyen H, Hoffer E, Fagan C, Maehigashi T, Dunham C. Structural basis for reduced ribosomal A-site fidelity in response to P-site codon-anticodon mismatches. J Biol Chem 2023; 299:104608. [PMID: 36924943 PMCID: PMC10140155 DOI: 10.1016/j.jbc.2023.104608] [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: 02/01/2023] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/16/2023] Open
Abstract
Rapid and accurate translation is essential in all organisms to produce properly folded and functional proteins. mRNA codons that define the protein coding sequences are decoded by tRNAs on the ribosome in the aminoacyl (A) binding site. The mRNA codon and the tRNA anticodon interaction is extensively monitored by the ribosome to ensure accuracy in tRNA selection. While other polymerases that synthesize DNA and RNA can correct for misincorporations, the ribosome is unable to correct mistakes. Instead, when a misincorporation occurs, the mismatched tRNA-mRNA pair moves to the peptidyl (P) site and from this location, causes a reduction in the fidelity at the A site, triggering post-peptidyl transfer quality control. This reduced fidelity allows for additional incorrect tRNAs to be accepted and for release factor 2 (RF2) to recognize sense codons, leading to hydrolysis of the aberrant peptide. Here, we present crystal structures of the ribosome containing a tRNALys in the P site with a U•U mismatch with the mRNA codon. We find that when the mismatch occurs in the second position of the P-site codon-anticodon interaction, the first nucleotide of the A-site codon flips from the mRNA path to engage highly conserved 16S rRNA nucleotide A1493 in the decoding center. We propose that this mRNA nucleotide mispositioning leads to reduced fidelity at the A site. Further, this state may provide an opportunity for RF2 to initiate premature termination before erroneous nascent chains disrupt the cellular proteome.
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Affiliation(s)
- HaAn Nguyen
- Department of Chemistry, Emory University, Atlanta, GA USA; Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA
| | - EricD Hoffer
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA; Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, GA USA
| | - CrystalE Fagan
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA; Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, GA USA
| | - Tatsuya Maehigashi
- Department of Chemistry, Emory University, Atlanta, GA USA; Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA
| | - ChristineM Dunham
- Department of Chemistry, Emory University, Atlanta, GA USA; Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA.
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20
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D'Urso G, Guyomar C, Chat S, Giudice E, Gillet R. Insights into the ribosomal trans-translation rescue system: lessons from recent structural studies. FEBS J 2023; 290:1461-1472. [PMID: 35015931 DOI: 10.1111/febs.16349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/27/2021] [Accepted: 01/10/2022] [Indexed: 11/29/2022]
Abstract
The arrest of protein synthesis caused when ribosomes stall on an mRNA lacking a stop codon is a deadly risk for all cells. In bacteria, this situation is remedied by the trans-translation quality control system. Trans-translation occurs because of the synergistic action of two main partners, transfer-messenger RNA (tmRNA) and small protein B (SmpB). These act in complex to monitor protein synthesis, intervening when necessary to rescue stalled ribosomes. During this process, incomplete nascent peptides are tagged for destruction, problematic mRNAs are degraded and the previously stalled ribosomes are recycled. In this 'Structural Snapshot' article, we describe the mechanism at the molecular level, a view updated after the most recent structural studies using cryo-electron microscopy.
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Affiliation(s)
- Gaetano D'Urso
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Charlotte Guyomar
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Sophie Chat
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Emmanuel Giudice
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Reynald Gillet
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
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21
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Nguyen HA, Hoffer ED, Fagan CE, Maehigashi T, Dunham CM. Structural basis for reduced ribosomal A-site fidelity in response to P-site codon-anticodon mismatches. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.28.526049. [PMID: 36747737 PMCID: PMC9900946 DOI: 10.1101/2023.01.28.526049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Rapid and accurate translation is essential in all organisms to produce properly folded and functional proteins. mRNA codons that define the protein coding sequences are decoded by tRNAs on the ribosome in the aminoacyl (A) binding site. The mRNA codon and the tRNA anticodon interaction is extensively monitored by the ribosome to ensure accuracy in tRNA selection. While other polymerases that synthesize DNA and RNA can correct for misincorporations, the ribosome is unable to correct mistakes. Instead, when a misincorporation occurs, the mismatched tRNA-mRNA pair moves to the peptidyl (P) site and from this location, causes a reduction in the fidelity at the A site, triggering post-peptidyl transfer quality control. This reduced fidelity allows for additional incorrect tRNAs to be accepted and for release factor 2 (RF2) to recognize sense codons, leading to hydrolysis of the aberrant peptide. Here, we present crystal structures of the ribosome containing a tRNA Lys in the P site with a U•U mismatch with the mRNA codon. We find that when the mismatch occurs in the second position of the P-site codon-anticodon interaction, the first nucleotide of the A-site codon flips from the mRNA path to engage highly conserved 16S rRNA nucleotide A1493 in the decoding center. We propose that this mRNA nucleotide mispositioning leads to reduced fidelity at the A site. Further, this state may provide an opportunity for RF2 to initiate premature termination before erroneous nascent chains disrupt the cellular proteome.
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Affiliation(s)
- Ha An Nguyen
- Department of Chemistry, Emory University, Atlanta, GA USA
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA
| | - Eric D. Hoffer
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, GA USA
| | - Crystal E. Fagan
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, GA USA
| | - Tatsuya Maehigashi
- Department of Chemistry, Emory University, Atlanta, GA USA
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA
| | - Christine M. Dunham
- Department of Chemistry, Emory University, Atlanta, GA USA
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA
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22
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Ali Z, Goyal A, Jhunjhunwala A, Mitra A, Trant JF, Sharma P. Structural and Energetic Features of Base-Base Stacking Contacts in RNA. J Chem Inf Model 2023; 63:655-669. [PMID: 36635230 DOI: 10.1021/acs.jcim.2c01116] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nucleobase π-π stacking is one of the crucial organizing interactions within three-dimensional (3D) RNA architectures. Characterizing the structural variability of these contacts in RNA crystal structures will help delineate their subtleties and their role in determining function. This analysis of different stacking geometries found in RNA X-ray crystal structures is the largest such survey to date; coupled with quantum-mechanical calculations on typical representatives of each possible stacking arrangement, we determined the distribution of stacking interaction energies. A total of 1,735,481 stacking contacts, spanning 359 of the 384 theoretically possible distinct stacking geometries, were identified. Our analysis reveals preferential occurrences of specific consecutive stacking arrangements in certain regions of RNA architectures. Quantum chemical calculations suggest that 88 of the 359 contacts possess intrinsically stable stacking geometries, whereas the remaining stacks require the RNA backbone or surrounding macromolecular environment to force their formation and maintain their stability. Our systematic analysis of π-π stacks in RNA highlights trends in the occurrence and localization of these noncovalent interactions and may help better understand the structural intricacies of functional RNA-based molecular architectures.
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Affiliation(s)
- Zakir Ali
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh160014, India
| | - Ambika Goyal
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh160014, India
| | - Ayush Jhunjhunwala
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, Gachibowli, Hyderabad, Telangana500032, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, Gachibowli, Hyderabad, Telangana500032, India
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, OntarioN9B 3P4, Canada
- Binary Star Research Services, LaSalle, OntarioN9J 3X8, Canada
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh160014, India
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, OntarioN9B 3P4, Canada
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23
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Cozma E, Rao M, Dusick M, Genereaux J, Rodriguez-Mias RA, Villén J, Brandl CJ, Berg MD. Anticodon sequence determines the impact of mistranslating tRNA Ala variants. RNA Biol 2023; 20:791-804. [PMID: 37776539 PMCID: PMC10543346 DOI: 10.1080/15476286.2023.2257471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2023] [Indexed: 10/02/2023] Open
Abstract
Transfer RNAs (tRNAs) maintain translation fidelity through accurate charging by their cognate aminoacyl-tRNA synthetase and codon:anticodon base pairing with the mRNA at the ribosome. Mistranslation occurs when an amino acid not specified by the genetic message is incorporated into proteins and has applications in biotechnology, therapeutics and is relevant to disease. Since the alanyl-tRNA synthetase uniquely recognizes a G3:U70 base pair in tRNAAla and the anticodon plays no role in charging, tRNAAla variants with anticodon mutations have the potential to mis-incorporate alanine. Here, we characterize the impact of the 60 non-alanine tRNAAla anticodon variants on the growth of Saccharomyces cerevisiae. Overall, 36 tRNAAla anticodon variants decreased growth in single- or multi-copy. Mass spectrometry analysis of the cellular proteome revealed that 52 of 57 anticodon variants, not decoding alanine or stop codons, induced mistranslation when on single-copy plasmids. Variants with G/C-rich anticodons resulted in larger growth deficits than A/U-rich variants. In most instances, synonymous anticodon variants impact growth differently, with anticodons containing U at base 34 being the least impactful. For anticodons generating the same amino acid substitution, reduced growth generally correlated with the abundance of detected mistranslation events. Differences in decoding specificity, even between synonymous anticodons, resulted in each tRNAAla variant mistranslating unique sets of peptides and proteins. We suggest that these differences in decoding specificity are also important in determining the impact of tRNAAla anticodon variants.
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Affiliation(s)
- Ecaterina Cozma
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Megha Rao
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Madison Dusick
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christopher J. Brandl
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Matthew D. Berg
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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24
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Fages‐Lartaud M, Hundvin K, Hohmann‐Marriott MF. Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:919-945. [PMID: 36071273 PMCID: PMC9828097 DOI: 10.1111/tpj.15970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 05/30/2023]
Abstract
Chloroplasts possess a considerably reduced genome that is decoded via an almost minimal set of tRNAs. These features make an excellent platform for gaining insights into fundamental mechanisms that govern protein expression. Here, we present a comprehensive and revised perspective of the mechanisms that drive codon selection in the chloroplast of Chlamydomonas reinhardtii and the functional consequences for protein expression. In order to extract this information, we applied several codon usage descriptors to genes with different expression levels. We show that highly expressed genes strongly favor translationally optimal codons, while genes with lower functional importance are rather affected by directional mutational bias. We demonstrate that codon optimality can be deduced from codon-anticodon pairing affinity and, for a small number of amino acids (leucine, arginine, serine, and isoleucine), tRNA concentrations. Finally, we review, analyze, and expand on the impact of codon usage on protein yield, secondary structures of mRNA, translation initiation and termination, and amino acid composition of proteins, as well as cotranslational protein folding. The comprehensive analysis of codon choice provides crucial insights into heterologous gene expression in the chloroplast of C. reinhardtii, which may also be applicable to other chloroplast-containing organisms and bacteria.
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Affiliation(s)
- Maxime Fages‐Lartaud
- Department of BiotechnologyNorwegian University of Science and TechnologyTrondheimN‐7491Norway
| | - Kristoffer Hundvin
- Department of BiotechnologyNorwegian University of Science and TechnologyTrondheimN‐7491Norway
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25
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Christie M, Friesen Westley J, Suresh B, Baiazitov Ramil Y, Wu D, Karloff Diane B, Chang-Sun L, Young-Choon M, Hongyu R, Jairo S, Yuki T, Priya V, Welch Ellen M, Xiaojiao X, Jin Z. Guanidino Quinazolines and Pyrimidines Promote Readthrough of Premature Termination Codons in Cells with Native Nonsense Mutations. Bioorg Med Chem Lett 2022; 76:128989. [PMID: 36150638 DOI: 10.1016/j.bmcl.2022.128989] [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: 08/02/2022] [Revised: 08/26/2022] [Accepted: 09/09/2022] [Indexed: 11/25/2022]
Abstract
Using small molecules to induce readthrough of premature termination codons is a promising therapeutic approach to treating genetic diseases and cancers caused by nonsense mutations, as evidenced by the widespread use of ataluren to treat nonsense mutation Duchene muscular dystrophy. Herein we describe a series of novel guanidino quinazoline and pyrimidine scaffolds that induce readthrough in both HDQ-P1 mammary carcinoma cells and mdx myotubes. Linkage of basic, tertiary amines with aliphatic, hydrophobic substituents to the terminal guanidine nitrogen of these scaffolds led to significant potency increases. Further potency gains were achieved by flanking the pyrimidine ring with hydrophobic substituents, inducing readthrough at concentrations as low as 120 nM and demonstrating the potential of these compounds to be used either in combination with ataluren or as stand-alone therapeutics.
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Affiliation(s)
- Morrill Christie
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, 07080, USA
| | - J Friesen Westley
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, 07080, USA
| | - Babu Suresh
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, 07080, USA
| | - Y Baiazitov Ramil
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, 07080, USA
| | - Du Wu
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, 07080, USA
| | - B Karloff Diane
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, 07080, USA
| | - Lee Chang-Sun
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, 07080, USA
| | - Moon Young-Choon
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, 07080, USA
| | - Ren Hongyu
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, 07080, USA
| | - Sierra Jairo
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, 07080, USA
| | - Tomizawa Yuki
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, 07080, USA
| | - Vazirani Priya
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, 07080, USA
| | - M Welch Ellen
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, 07080, USA
| | - Xue Xiaojiao
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, 07080, USA
| | - Zhuo Jin
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, 07080, USA
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26
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Taiwo KM, Nam H, LeBlanc RM, Longhini AP, Dayie TK. Cross-correlated relaxation rates provide facile exchange signature in selectively labeled RNA. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 342:107245. [PMID: 35908529 DOI: 10.1016/j.jmr.2022.107245] [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: 01/30/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Gerhard Wagner has made numerous contributions to NMR spectroscopy, particularly his developments in the field of spin-relaxation stand out in directly mapping the spectral density functions of proteins. He and his group developed experimental techniques to reveal the importance of dynamics to protein biological function and drug discovery. On his 75th birthday, we take this opportunity to highlight how some of those seminal ideas developed for proteins are being extended to RNAs. The role of dynamics in the structure and function of RNA has been a major interest in drug design and therapeutics. Here we present the use of cross-correlated relaxation rates (ηxy) from anti-TROSY (R2α) and TROSY (R2β) to rapidly obtain qualitative information about the chemical exchange taking place within the bacterial and human A-site RNA system while reducing the sets of relaxation experiments required to map dynamics. We show that ηxy correlates with the order parameter which gives information on how flexible or rigid a residue is. We further show R2β/ηxy can rapidly be used to probe chemical exchange as seen from its agreement with Rex. In addition, we report the ability of R2β/ηxy to determine chemical exchange taking place within the bacterial A-site RNA during structural transitions at pH 6.2 and 6.5. Finally, comparison of the R2β/ηxy ratios indicates bacterial A-site has greater R2β/ηxy values for G19 (1.34 s-1), A20 (1.38 s-1), U23 (1.63 s-1) and C24 (1.51 s-1) than human A-site [A19 (0.76 s-1), A20 (1.01 s-1), U23 (0.74 s-1) and C24 (0.71 s-1)]. Taken together, we have shown that the chemical exchange can quickly be analyzed for RNA systems from cross-correlated relaxation rates.
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Affiliation(s)
- Kehinde M Taiwo
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States.
| | - Hyeyeon Nam
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States
| | - Regan M LeBlanc
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States
| | - Andrew P Longhini
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States
| | - Theodore K Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States.
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27
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Lombardi S, Testa MF, Pinotti M, Branchini A. Translation termination codons in protein synthesis and disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:1-48. [PMID: 36088072 DOI: 10.1016/bs.apcsb.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Fidelity of protein synthesis, a process shaped by several mechanisms involving specialized ribosome regions and external factors, ensures the precise reading of sense as well as stop codons (UGA, UAG, UAA), which are usually localized at the 3' of mRNA and drive the release of the polypeptide chain. However, either natural (NTCs) or premature (PTCs) termination codons, the latter arising from nucleotide changes, can undergo a recoding process named ribosome or translational readthrough, which insert specific amino acids (NTCs) or subset(s) depending on the stop codon type (PTCs). This process is particularly relevant for nonsense mutations, a relatively frequent cause of genetic disorders, which impair gene expression at different levels by potentially leading to mRNA degradation and/or synthesis of truncated proteins. As a matter of fact, many efforts have been made to develop efficient and safe readthrough-inducing compounds, which have been challenged in several models of human disease to provide with a therapy. In this view, the dissection of the molecular determinants shaping the outcome of readthrough, namely nucleotide and protein contexts as well as their interplay and impact on protein structure/function, is crucial to identify responsive nonsense mutations resulting in functional full-length proteins. The interpretation of experimental and mechanistic findings is also important to define a possibly clear picture of potential readthrough-favorable features useful to achieve rescue profiles compatible with therapeutic thresholds typical of each targeted disorder, which is of primary importance for the potential translatability of readthrough into a personalized and mutation-specific, and thus patient-oriented, therapeutic strategy.
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Affiliation(s)
- Silvia Lombardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Maria Francesca Testa
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
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28
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Brown ZP, Abaeva IS, De S, Hellen CUT, Pestova TV, Frank J. Molecular architecture of 40S translation initiation complexes on the hepatitis C virus IRES. EMBO J 2022; 41:e110581. [PMID: 35822879 DOI: 10.15252/embj.2022110581] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 02/05/2023] Open
Abstract
Hepatitis C virus mRNA contains an internal ribosome entry site (IRES) that mediates end-independent translation initiation, requiring a subset of eukaryotic initiation factors (eIFs). Biochemical studies revealed that direct binding of the IRES to the 40S ribosomal subunit places the initiation codon into the P site, where it base pairs with eIF2-bound Met-tRNAiMet forming a 48S initiation complex. Subsequently, eIF5 and eIF5B mediate subunit joining, yielding an elongation-competent 80S ribosome. Initiation can also proceed without eIF2, in which case Met-tRNAiMet is recruited directly by eIF5B. However, the structures of initiation complexes assembled on the HCV IRES, the transitions between different states, and the accompanying conformational changes have remained unknown. To fill these gaps, we now obtained cryo-EM structures of IRES initiation complexes, at resolutions up to 3.5 Å, that cover all major stages from the initial ribosomal association, through eIF2-containing 48S initiation complexes, to eIF5B-containing complexes immediately prior to subunit joining. These structures provide insights into the dynamic network of 40S/IRES contacts, highlight the role of IRES domain II, and reveal conformational changes that occur during the transition from eIF2- to eIF5B-containing 48S complexes and prepare them for subunit joining.
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Affiliation(s)
- Zuben P Brown
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Irina S Abaeva
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Swastik De
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Department of Biological Sciences, Columbia University, New York, NY, USA
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29
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Kimoto M, Hirao I. Genetic Code Engineering by Natural and Unnatural Base Pair Systems for the Site-Specific Incorporation of Non-Standard Amino Acids Into Proteins. Front Mol Biosci 2022; 9:851646. [PMID: 35685243 PMCID: PMC9171071 DOI: 10.3389/fmolb.2022.851646] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/25/2022] [Indexed: 12/21/2022] Open
Abstract
Amino acid sequences of proteins are encoded in nucleic acids composed of four letters, A, G, C, and T(U). However, this four-letter alphabet coding system limits further functionalities of proteins by the twenty letters of amino acids. If we expand the genetic code or develop alternative codes, we could create novel biological systems and biotechnologies by the site-specific incorporation of non-standard amino acids (or unnatural amino acids, unAAs) into proteins. To this end, new codons and their complementary anticodons are required for unAAs. In this review, we introduce the current status of methods to incorporate new amino acids into proteins by in vitro and in vivo translation systems, by focusing on the creation of new codon-anticodon interactions, including unnatural base pair systems for genetic alphabet expansion.
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Affiliation(s)
| | - Ichiro Hirao
- *Correspondence: Michiko Kimoto, ; Ichiro Hirao,
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30
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Shakya B, Joyner OG, Hartman MCT. Hyperaccurate Ribosomes for Improved Genetic Code Reprogramming. ACS Synth Biol 2022; 11:2193-2201. [PMID: 35549158 PMCID: PMC10100576 DOI: 10.1021/acssynbio.2c00150] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reprogramming of the genetic code through the introduction of noncanonical amino acids (ncAAs) has enabled exciting advances in synthetic biology and peptide drug discovery. Ribosomes that function with high efficiency and fidelity are necessary for all of these efforts, but for challenging ncAAs, the competing processes of near-cognate readthrough and peptidyl-tRNA dropoff can be issues. Here we uncover the surprising extent of these competing pathways in the PURE translation system using mRNAs encoding peptides with affinity tags at the N- and C-termini. We also show that hyperaccurate or error restrictive ribosomes with mutations in ribosomal protein S12 lead to significant improvements in yield and fidelity in the context of both canonical AAs and a challenging α,α-disubstituted ncAA. Hyperaccurate ribosomes also improve yields for quadruplet codon readthrough for a tRNA containing an expanded anticodon stem-loop, although they are not able to eliminate triplet codon reading by this tRNA. The impressive improvements in fidelity and the simplicity of introducing this mutation alongside other efforts to engineer the translation apparatus make hyperaccurate ribosomes an important advance for synthetic biology.
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Affiliation(s)
- Bipasana Shakya
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23220, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23220, United States
| | - Olivia G. Joyner
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23220, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23220, United States
| | - Matthew C. T. Hartman
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23220, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23220, United States
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31
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Ye S, Lehmann J. Genetic code degeneracy is established by the decoding center of the ribosome. Nucleic Acids Res 2022; 50:4113-4126. [PMID: 35325219 PMCID: PMC9023292 DOI: 10.1093/nar/gkac171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 02/10/2022] [Accepted: 03/23/2022] [Indexed: 11/21/2022] Open
Abstract
The degeneracy of the genetic code confers a wide array of properties to coding sequences. Yet, its origin is still unclear. A structural analysis has shown that the stability of the Watson–Crick base pair at the second position of the anticodon–codon interaction is a critical parameter controlling the extent of non-specific pairings accepted at the third position by the ribosome, a flexibility at the root of degeneracy. Based on recent cryo-EM analyses, the present work shows that residue A1493 of the decoding center provides a significant contribution to the stability of this base pair, revealing that the ribosome is directly involved in the establishment of degeneracy. Building on existing evolutionary models, we show the evidence that the early appearance of A1493 and A1492 established the basis of degeneracy when an elementary kinetic scheme of translation was prevailing. Logical considerations on the expansion of this kinetic scheme indicate that the acquisition of the peptidyl transferase center was the next major evolutionary step, while the induced-fit mechanism, that enables a sharp selection of the tRNAs, necessarily arose later when G530 was acquired by the decoding center.
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Affiliation(s)
- Shixin Ye
- INSERM U1195 unit, University of Paris-Saclay, 94276 Le Kremlin Bicêtre, France
| | - Jean Lehmann
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Saclay, 91198 Gif-sur-Yvette, France
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32
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Overview of tRNA Modifications in Chloroplasts. Microorganisms 2022; 10:microorganisms10020226. [PMID: 35208681 PMCID: PMC8877259 DOI: 10.3390/microorganisms10020226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/16/2022] [Accepted: 01/18/2022] [Indexed: 11/29/2022] Open
Abstract
The chloroplast is a promising platform for biotechnological innovation due to its compact translation machinery. Nucleotide modifications within a minimal set of tRNAs modulate codon–anticodon interactions that are crucial for translation efficiency. However, a comprehensive assessment of these modifications does not presently exist in chloroplasts. Here, we synthesize all available information concerning tRNA modifications in the chloroplast and assign translation efficiency for each modified anticodon–codon pair. In addition, we perform a bioinformatics analysis that links enzymes to tRNA modifications and aminoacylation in the chloroplast of Chlamydomonas reinhardtii. This work provides the first comprehensive analysis of codon and anticodon interactions of chloroplasts and its implication for translation efficiency.
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33
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Xu B, Liu L, Song G. Functions and Regulation of Translation Elongation Factors. Front Mol Biosci 2022; 8:816398. [PMID: 35127825 PMCID: PMC8807479 DOI: 10.3389/fmolb.2021.816398] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Translation elongation is a key step of protein synthesis, during which the nascent polypeptide chain extends by one amino acid residue during one elongation cycle. More and more data revealed that the elongation is a key regulatory node for translational control in health and disease. During elongation, elongation factor Tu (EF-Tu, eEF1A in eukaryotes) is used to deliver aminoacyl-tRNA (aa-tRNA) to the A-site of the ribosome, and elongation factor G (EF-G, EF2 in eukaryotes and archaea) is used to facilitate the translocation of the tRNA2-mRNA complex on the ribosome. Other elongation factors, such as EF-Ts/eEF1B, EF-P/eIF5A, EF4, eEF3, SelB/EFsec, TetO/Tet(M), RelA and BipA, have been found to affect the overall rate of elongation. Here, we made a systematic review on the canonical and non-canonical functions and regulation of these elongation factors. In particular, we discussed the close link between translational factors and human diseases, and clarified how post-translational modifications control the activity of translational factors in tumors.
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Affiliation(s)
- Benjin Xu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
| | - Ling Liu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
| | - Guangtao Song
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
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34
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Kazantsev A, Ignatova Z. Constraints on error rate revealed by computational study of G•U tautomerization in translation. Nucleic Acids Res 2021; 49:11823-11833. [PMID: 34669948 PMCID: PMC8599798 DOI: 10.1093/nar/gkab947] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 11/18/2022] Open
Abstract
In translation, G•U mismatch in codon-anticodon decoding is an error hotspot likely due to transition of G•U from wobble (wb) to Watson-Crick (WC) geometry, which is governed by keto/enol tautomerization (wb-WC reaction). Yet, effects of the ribosome on the wb-WC reaction and its implications for decoding mechanism remain unclear. Employing quantum-mechanical/molecular-mechanical umbrella sampling simulations using models of the ribosomal decoding site (A site) we determined that the wb-WC reaction is endoergic in the open, but weakly exoergic in the closed A-site state. We extended the classical ‘induced-fit’ model of initial selection by incorporating wb-WC reaction parameters in open and closed states. For predicted parameters, the non-equilibrium exoergic wb-WC reaction is kinetically limited by the decoding rates. The model explains early observations of the WC geometry of G•U from equilibrium structural studies and reveals discrimination capacity for the working ribosome operating at non-equilibrium conditions. The equilibration of the exoergic wb-WC reaction counteracts the equilibration of the open-closed transition of the A site, constraining the decoding accuracy and potentially explaining the persistence of the G•U as an error hotspot. Our results unify structural and mechanistic views of codon-anticodon decoding and generalize the ‘induced-fit’ model for flexible substrates.
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Affiliation(s)
- Andriy Kazantsev
- Institute of Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
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35
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Martinez-Miguel VE, Lujan C, Espie-Caullet T, Martinez-Martinez D, Moore S, Backes C, Gonzalez S, Galimov ER, Brown AEX, Halic M, Tomita K, Rallis C, von der Haar T, Cabreiro F, Bjedov I. Increased fidelity of protein synthesis extends lifespan. Cell Metab 2021; 33:2288-2300.e12. [PMID: 34525330 PMCID: PMC8570412 DOI: 10.1016/j.cmet.2021.08.017] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 05/06/2021] [Accepted: 08/30/2021] [Indexed: 12/20/2022]
Abstract
Loss of proteostasis is a fundamental process driving aging. Proteostasis is affected by the accuracy of translation, yet the physiological consequence of having fewer protein synthesis errors during multi-cellular organismal aging is poorly understood. Our phylogenetic analysis of RPS23, a key protein in the ribosomal decoding center, uncovered a lysine residue almost universally conserved across all domains of life, which is replaced by an arginine in a small number of hyperthermophilic archaea. When introduced into eukaryotic RPS23 homologs, this mutation leads to accurate translation, as well as heat shock resistance and longer life, in yeast, worms, and flies. Furthermore, we show that anti-aging drugs such as rapamycin, Torin1, and trametinib reduce translation errors, and that rapamycin extends further organismal longevity in RPS23 hyperaccuracy mutants. This implies a unified mode of action for diverse pharmacological anti-aging therapies. These findings pave the way for identifying novel translation accuracy interventions to improve aging.
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Affiliation(s)
| | - Celia Lujan
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Tristan Espie-Caullet
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Daniel Martinez-Martinez
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Saul Moore
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Cassandra Backes
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Suam Gonzalez
- School of Health, Sport and Bioscience, University of East London, Water Lane, London E15 4LZ, UK
| | - Evgeniy R Galimov
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - André E X Brown
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Mario Halic
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Kazunori Tomita
- Centre for Genome Engineering and Maintenance, College of Health, Medicine and Life Sciences, Brunel University London, London UB8 3PH, UK
| | - Charalampos Rallis
- School of Health, Sport and Bioscience, University of East London, Water Lane, London E15 4LZ, UK
| | - Tobias von der Haar
- Kent Fungal Group, School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Filipe Cabreiro
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931 Cologne, Germany.
| | - Ivana Bjedov
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London WC1E 6DD, UK; Department of Medical Physics and Biomedical Engineering, University College London, Malet Place Engineering Building, Gower Street, London WC1E 6BT, UK.
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36
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Berg MD, Zhu Y, Ruiz BY, Loll-Krippleber R, Isaacson J, San Luis BJ, Genereaux J, Boone C, Villén J, Brown GW, Brandl CJ. The amino acid substitution affects cellular response to mistranslation. G3-GENES GENOMES GENETICS 2021; 11:6310018. [PMID: 34568909 PMCID: PMC8473984 DOI: 10.1093/g3journal/jkab218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/17/2021] [Indexed: 01/24/2023]
Abstract
Mistranslation, the misincorporation of an amino acid not specified by the "standard" genetic code, occurs in all organisms. tRNA variants that increase mistranslation arise spontaneously and engineered tRNAs can achieve mistranslation frequencies approaching 10% in yeast and bacteria. Interestingly, human genomes contain tRNA variants with the potential to mistranslate. Cells cope with increased mistranslation through multiple mechanisms, though high levels cause proteotoxic stress. The goal of this study was to compare the genetic interactions and the impact on transcriptome and cellular growth of two tRNA variants that mistranslate at a similar frequency but create different amino acid substitutions in Saccharomyces cerevisiae. One tRNA variant inserts alanine at proline codons whereas the other inserts serine for arginine. Both tRNAs decreased growth rate, with the effect being greater for arginine to serine than for proline to alanine. The tRNA that substituted serine for arginine resulted in a heat shock response. In contrast, heat shock response was minimal for proline to alanine substitution. Further demonstrating the significance of the amino acid substitution, transcriptome analysis identified unique up- and down-regulated genes in response to each mistranslating tRNA. Number and extent of negative synthetic genetic interactions also differed depending upon type of mistranslation. Based on the unique responses observed for these mistranslating tRNAs, we predict that the potential of mistranslation to exacerbate diseases caused by proteotoxic stress depends on the tRNA variant. Furthermore, based on their unique transcriptomes and genetic interactions, different naturally occurring mistranslating tRNAs have the potential to negatively influence specific diseases.
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Affiliation(s)
- Matthew D Berg
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 3K7, Canada.,Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Yanrui Zhu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Bianca Y Ruiz
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Raphaël Loll-Krippleber
- Department of Biochemistry, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S, Canada
| | - Joshua Isaacson
- Department of Biology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Bryan-Joseph San Luis
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S, Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Charles Boone
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S, Canada
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Grant W Brown
- Department of Biochemistry, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S, Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 3K7, Canada
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37
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Bulygin KN, Timofeev IO, Malygin AA, Graifer DM, Meschaninova MI, Venyaminova AG, Krumkacheva OA, Fedin MV, Yu Frolova L, Karpova GG, Bagryanskaya EG. Two alternative conformations of mRNA in the human ribosome during elongation and termination of translation as revealed by EPR spectroscopy. Comput Struct Biotechnol J 2021; 19:4702-4710. [PMID: 34504663 PMCID: PMC8390954 DOI: 10.1016/j.csbj.2021.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 11/29/2022] Open
Abstract
DEER reveals the conformational variability of mRNA at the certain translation steps. Elongation and termination complexes exist in 2 conformations in dynamic equilibrium. The conformations of mRNA in 40S channel undergo no major change during termination.
The conformation of mRNA in the region of the human 80S ribosome decoding site was monitored using 11-mer mRNA analogues that bore nitroxide spin labels attached to the terminal nucleotide bases. Intramolecular spin–spin distances were measured by DEER/PELDOR spectroscopy in model complexes mimicking different states of the 80S ribosome during elongation and termination of translation. The measurements revealed that in all studied complexes, mRNA exists in two alternative conformations, whose ratios are different in post-translocation, pre-translocation and termination complexes. We found that the presence of a tRNA molecule at the ribosomal A site decreases the relative share of the more extended mRNA conformation, whereas the binding of eRF1 (alone or in a complex with eRF3) results in the opposite effect. In the termination complexes, the ratios of mRNA conformations are practically the same, indicating that a part of mRNA bound in the ribosome channel does not undergo significant structural alterations in the course of completion of the translation. Our results contribute to the understanding of mRNA molecular dynamics in the mammalian ribosome channel during translation.
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Affiliation(s)
- Konstantin N Bulygin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia
| | - Ivan O Timofeev
- International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
| | - Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia
| | - Dmitri M Graifer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia
| | - Maria I Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia
| | - Olesya A Krumkacheva
- International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
| | - Matvey V Fedin
- International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
| | - Ludmila Yu Frolova
- Engelhardt Institute of Molecular Biology RAS, Vavilova Str. 32, Moscow 119991, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, pr. Lavrentjeva 9, Novosibirsk 630090, Russia
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38
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Structures of tmRNA and SmpB as they transit through the ribosome. Nat Commun 2021; 12:4909. [PMID: 34389707 PMCID: PMC8363625 DOI: 10.1038/s41467-021-24881-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/13/2021] [Indexed: 01/01/2023] Open
Abstract
In bacteria, trans-translation is the main rescue system, freeing ribosomes stalled on defective messenger RNAs. This mechanism is driven by small protein B (SmpB) and transfer-messenger RNA (tmRNA), a hybrid RNA known to have both a tRNA-like and an mRNA-like domain. Here we present four cryo-EM structures of the ribosome during trans-translation at resolutions from 3.0 to 3.4 Å. These include the high-resolution structure of the whole pre-accommodated state, as well as structures of the accommodated state, the translocated state, and a translocation intermediate. Together, they shed light on the movements of the tmRNA-SmpB complex in the ribosome, from its delivery by the elongation factor EF-Tu to its passage through the ribosomal A and P sites after the opening of the B1 bridges. Additionally, we describe the interactions between the tmRNA-SmpB complex and the ribosome. These explain why the process does not interfere with canonical translation.
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39
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Giannerini S, Gonzalez DL, Goracci G, Danielli A. A role for circular code properties in translation. Sci Rep 2021; 11:9218. [PMID: 33911089 PMCID: PMC8080828 DOI: 10.1038/s41598-021-87534-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/23/2021] [Indexed: 11/19/2022] Open
Abstract
Circular codes represent a form of coding allowing detection/correction of frame-shift errors. Building on recent theoretical advances on circular codes, we provide evidence that protein coding sequences exhibit in-frame circular code marks, that are absent in introns and are intimately linked to the keto-amino transformation of codon bases. These properties strongly correlate with translation speed, codon influence and protein synthesis levels. Strikingly, circular code marks are absent at the beginning of coding sequences, but stably occur 40 codons after the initiator codon, hinting at the translation elongation process. Finally, we use the lens of circular codes to show that codon influence on translation correlates with the strong-weak dichotomy of the first two bases of the codon. The results can lead to defining new universal tools for sequence indicators and sequence optimization for bioinformatics and biotechnological applications, and can shed light on the molecular mechanisms behind the decoding process.
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Affiliation(s)
- Simone Giannerini
- Department of Statistical Sciences, University of Bologna, Bologna, 40126, Italy.
| | - Diego Luis Gonzalez
- Department of Statistical Sciences, University of Bologna, Bologna, 40126, Italy.,Institute for Microelectronics and Microsystems - Bologna Unit, CNR, Bologna, 40129, Italy
| | - Greta Goracci
- Department of Statistical Sciences, University of Bologna, Bologna, 40126, Italy
| | - Alberto Danielli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
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40
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Müller C, Crowe-McAuliffe C, Wilson DN. Ribosome Rescue Pathways in Bacteria. Front Microbiol 2021; 12:652980. [PMID: 33815344 PMCID: PMC8012679 DOI: 10.3389/fmicb.2021.652980] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Ribosomes that become stalled on truncated or damaged mRNAs during protein synthesis must be rescued for the cell to survive. Bacteria have evolved a diverse array of rescue pathways to remove the stalled ribosomes from the aberrant mRNA and return them to the free pool of actively translating ribosomes. In addition, some of these pathways target the damaged mRNA and the incomplete nascent polypeptide chain for degradation. This review highlights the recent developments in our mechanistic understanding of bacterial ribosomal rescue systems, including drop-off, trans-translation mediated by transfer-messenger RNA and small protein B, ribosome rescue by the alternative rescue factors ArfA and ArfB, as well as Bacillus ribosome rescue factor A, an additional rescue system found in some Gram-positive bacteria, such as Bacillus subtilis. Finally, we discuss the recent findings of ribosome-associated quality control in particular bacterial lineages mediated by RqcH and RqcP. The importance of rescue pathways for bacterial survival suggests they may represent novel targets for the development of new antimicrobial agents against multi-drug resistant pathogenic bacteria.
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Affiliation(s)
| | | | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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41
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The expanding world of tRNA modifications and their disease relevance. Nat Rev Mol Cell Biol 2021; 22:375-392. [PMID: 33658722 DOI: 10.1038/s41580-021-00342-0] [Citation(s) in RCA: 271] [Impact Index Per Article: 90.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2021] [Indexed: 02/08/2023]
Abstract
Transfer RNA (tRNA) is an adapter molecule that links a specific codon in mRNA with its corresponding amino acid during protein synthesis. tRNAs are enzymatically modified post-transcriptionally. A wide variety of tRNA modifications are found in the tRNA anticodon, which are crucial for precise codon recognition and reading frame maintenance, thereby ensuring accurate and efficient protein synthesis. In addition, tRNA-body regions are also frequently modified and thus stabilized in the cell. Over the past two decades, 16 novel tRNA modifications were discovered in various organisms, and the chemical space of tRNA modification continues to expand. Recent studies have revealed that tRNA modifications can be dynamically altered in response to levels of cellular metabolites and environmental stresses. Importantly, we now understand that deficiencies in tRNA modification can have pathological consequences, which are termed 'RNA modopathies'. Dysregulation of tRNA modification is involved in mitochondrial diseases, neurological disorders and cancer.
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42
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Berg MD, Brandl CJ. Transfer RNAs: diversity in form and function. RNA Biol 2021; 18:316-339. [PMID: 32900285 PMCID: PMC7954030 DOI: 10.1080/15476286.2020.1809197] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/08/2020] [Indexed: 12/11/2022] Open
Abstract
As the adaptor that decodes mRNA sequence into protein, the basic aspects of tRNA structure and function are central to all studies of biology. Yet the complexities of their properties and cellular roles go beyond the view of tRNAs as static participants in protein synthesis. Detailed analyses through more than 60 years of study have revealed tRNAs to be a fascinatingly diverse group of molecules in form and function, impacting cell biology, physiology, disease and synthetic biology. This review analyzes tRNA structure, biosynthesis and function, and includes topics that demonstrate their diversity and growing importance.
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Affiliation(s)
- Matthew D. Berg
- Department of Biochemistry, The University of Western Ontario, London, Canada
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43
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Bennett RK, Gregory GJ, Gonzalez JE, Har JRG, Antoniewicz MR, Papoutsakis ET. Improving the Methanol Tolerance of an Escherichia coli Methylotroph via Adaptive Laboratory Evolution Enhances Synthetic Methanol Utilization. Front Microbiol 2021; 12:638426. [PMID: 33643274 PMCID: PMC7904680 DOI: 10.3389/fmicb.2021.638426] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 01/21/2021] [Indexed: 02/05/2023] Open
Abstract
There is great interest in developing synthetic methylotrophs that harbor methane and methanol utilization pathways in heterologous hosts such as Escherichia coli for industrial bioconversion of one-carbon compounds. While there are recent reports that describe the successful engineering of synthetic methylotrophs, additional efforts are required to achieve the robust methylotrophic phenotypes required for industrial realization. Here, we address an important issue of synthetic methylotrophy in E. coli: methanol toxicity. Both methanol, and its oxidation product, formaldehyde, are cytotoxic to cells. Methanol alters the fluidity and biological properties of cellular membranes while formaldehyde reacts readily with proteins and nucleic acids. Thus, efforts to enhance the methanol tolerance of synthetic methylotrophs are important. Here, adaptive laboratory evolution was performed to improve the methanol tolerance of several E. coli strains, both methylotrophic and non-methylotrophic. Serial batch passaging in rich medium containing toxic methanol concentrations yielded clones exhibiting improved methanol tolerance. In several cases, these evolved clones exhibited a > 50% improvement in growth rate and biomass yield in the presence of high methanol concentrations compared to the respective parental strains. Importantly, one evolved clone exhibited a two to threefold improvement in the methanol utilization phenotype, as determined via 13C-labeling, at non-toxic, industrially relevant methanol concentrations compared to the respective parental strain. Whole genome sequencing was performed to identify causative mutations contributing to methanol tolerance. Common mutations were identified in 30S ribosomal subunit proteins, which increased translational accuracy and provided insight into a novel methanol tolerance mechanism. This study addresses an important issue of synthetic methylotrophy in E. coli and provides insight as to how methanol toxicity can be alleviated via enhancing methanol tolerance. Coupled improvement of methanol tolerance and synthetic methanol utilization is an important advancement for the field of synthetic methylotrophy.
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Affiliation(s)
- R Kyle Bennett
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States.,Molecular Biotechnology Laboratory, The Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
| | - Gwendolyn J Gregory
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States.,Molecular Biotechnology Laboratory, The Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
| | - Jacqueline E Gonzalez
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States
| | - Jie Ren Gerald Har
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States.,Molecular Biotechnology Laboratory, The Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
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44
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Scopino K, Dalgarno C, Nachmanoff C, Krizanc D, Thayer KM, Weir MP. Arginine Methylation Regulates Ribosome CAR Function. Int J Mol Sci 2021; 22:ijms22031335. [PMID: 33572867 PMCID: PMC7866298 DOI: 10.3390/ijms22031335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/16/2022] Open
Abstract
The ribosome CAR interaction surface is hypothesized to provide a layer of translation regulation through hydrogen-bonding to the +1 mRNA codon that is next to enter the ribosome A site during translocation. The CAR surface consists of three residues, 16S/18S rRNA C1054, A1196 (E. coli 16S numbering), and R146 of yeast ribosomal protein Rps3. R146 can be methylated by the Sfm1 methyltransferase which is downregulated in stressed cells. Through molecular dynamics analysis, we show here that methylation of R146 compromises the integrity of CAR by reducing the cation-pi stacking of the R146 guanidinium group with A1196, leading to reduced CAR hydrogen-bonding with the +1 codon. We propose that ribosomes assembled under stressed conditions have unmethylated R146, resulting in elevated CAR/+1 codon interactions, which tunes translation levels in response to the altered cellular context.
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Affiliation(s)
- Kristen Scopino
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA; (K.S.); (C.D.); (C.N.)
| | - Carol Dalgarno
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA; (K.S.); (C.D.); (C.N.)
| | - Clara Nachmanoff
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA; (K.S.); (C.D.); (C.N.)
| | - Daniel Krizanc
- Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459, USA; (D.K.); (K.M.T.)
- College of Integrative Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Kelly M. Thayer
- Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459, USA; (D.K.); (K.M.T.)
- College of Integrative Sciences, Wesleyan University, Middletown, CT 06459, USA
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Michael P. Weir
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA; (K.S.); (C.D.); (C.N.)
- College of Integrative Sciences, Wesleyan University, Middletown, CT 06459, USA
- Correspondence:
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45
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Huh D, Passarelli MC, Gao J, Dusmatova SN, Goin C, Fish L, Pinzaru AM, Molina H, Ren Z, McMillan EA, Asgharian H, Goodarzi H, Tavazoie SF. A stress-induced tyrosine-tRNA depletion response mediates codon-based translational repression and growth suppression. EMBO J 2021; 40:e106696. [PMID: 33346941 PMCID: PMC7809793 DOI: 10.15252/embj.2020106696] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic transfer RNAs can become selectively fragmented upon various stresses, generating tRNA-derived small RNA fragments. Such fragmentation has been reported to impact a small fraction of the tRNA pool and thus presumed to not directly impact translation. We report that oxidative stress can rapidly generate tyrosine-tRNAGUA fragments in human cells-causing significant depletion of the precursor tRNA. Tyrosine-tRNAGUA depletion impaired translation of growth and metabolic genes enriched in cognate tyrosine codons. Depletion of tyrosine tRNAGUA or its translationally regulated targets USP3 and SCD repressed proliferation-revealing a dedicated tRNA-regulated growth-suppressive pathway for oxidative stress response. Tyrosine fragments are generated in a DIS3L2 exoribonuclease-dependent manner and inhibit hnRNPA1-mediated transcript destabilization. Moreover, tyrosine fragmentation is conserved in C. elegans. Thus, tRNA fragmentation can coordinately generate trans-acting small RNAs and functionally deplete a tRNA. Our findings reveal the existence of an underlying adaptive codon-based regulatory response inherent to the genetic code.
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Affiliation(s)
- Doowon Huh
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Maria C Passarelli
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Jenny Gao
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | | | - Clara Goin
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Lisa Fish
- Department of Biochemistry & BiophysicsUniversity of California, San FranciscoSan FranciscoCAUSA
| | | | - Henrik Molina
- Proteome Resource CenterThe Rockefeller UniversityNew YorkNYUSA
| | - Zhiji Ren
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | | | - Hosseinali Asgharian
- Department of Biochemistry & BiophysicsUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Hani Goodarzi
- Department of Biochemistry & BiophysicsUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
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46
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Abstract
Peptide-chain elongation during protein synthesis entails sequential aminoacyl-tRNA selection and translocation reactions that proceed rapidly (2-20 per second) and with a low error rate (around 10-3 to 10-5 at each step) over thousands of cycles1. The cadence and fidelity of ribosome transit through mRNA templates in discrete codon increments is a paradigm for movement in biological systems that must hold for diverse mRNA and tRNA substrates across domains of life. Here we use single-molecule fluorescence methods to guide the capture of structures of early translocation events on the bacterial ribosome. Our findings reveal that the bacterial GTPase elongation factor G specifically engages spontaneously achieved ribosome conformations while in an active, GTP-bound conformation to unlock and initiate peptidyl-tRNA translocation. These findings suggest that processes intrinsic to the pre-translocation ribosome complex can regulate the rate of protein synthesis, and that energy expenditure is used later in the translocation mechanism than previously proposed.
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47
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Molecular Insights into Determinants of Translational Readthrough and Implications for Nonsense Suppression Approaches. Int J Mol Sci 2020; 21:ijms21249449. [PMID: 33322589 PMCID: PMC7764779 DOI: 10.3390/ijms21249449] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/27/2020] [Accepted: 12/05/2020] [Indexed: 02/07/2023] Open
Abstract
The fidelity of protein synthesis, a process shaped by several mechanisms involving specialized ribosome regions and external factors, ensures the precise reading of sense and stop codons. However, premature termination codons (PTCs) arising from mutations may, at low frequency, be misrecognized and result in PTC suppression, named ribosome readthrough, with production of full-length proteins through the insertion of a subset of amino acids. Since some drugs have been identified as readthrough inducers, this fidelity drawback has been explored as a therapeutic approach in several models of human diseases caused by nonsense mutations. Here, we focus on the mechanisms driving translation in normal and aberrant conditions, the potential fates of mRNA in the presence of a PTC, as well as on the results obtained in the research of efficient readthrough-inducing compounds. In particular, we describe the molecular determinants shaping the outcome of readthrough, namely the nucleotide and protein context, with the latter being pivotal to produce functional full-length proteins. Through the interpretation of experimental and mechanistic findings, mainly obtained in lysosomal and coagulation disorders, we also propose a scenario of potential readthrough-favorable features to achieve relevant rescue profiles, representing the main issue for the potential translatability of readthrough as a therapeutic strategy.
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48
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Chavali SS, Cavender CE, Mathews DH, Wedekind JE. Arginine Forks Are a Widespread Motif to Recognize Phosphate Backbones and Guanine Nucleobases in the RNA Major Groove. J Am Chem Soc 2020; 142:19835-19839. [PMID: 33170672 DOI: 10.1021/jacs.0c09689] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA recognition by proteins is central to biology. Here we demonstrate the existence of a recurrent structural motif, the "arginine fork", that codifies arginine readout of cognate backbone and guanine nucleobase interactions in a variety of protein-RNA complexes derived from viruses, metabolic enzymes, and ribosomes. Nearly 30 years ago, a theoretical arginine fork model was posited to account for the specificity between the HIV-1 Tat protein and TAR RNA. This model predicted that a single arginine should form four complementary contacts with nearby phosphates, yielding a two-pronged backbone readout. Recent high-resolution structures of TAR-protein complexes have unveiled new details, including (i) arginine interactions with the phosphate backbone and the major-groove edge of guanine and (ii) simultaneous cation-π contacts between the guanidinium group and flanking nucleobases. These findings prompted us to search for arginine forks within experimental protein-RNA structures retrieved from the Protein Data Bank. The results revealed four distinct classes of arginine forks that we have defined using a rigorous but flexible nomenclature. Examples are presented in the context of ribosomal and nonribosomal interfaces with analysis of arginine dihedral angles and structural (suite) classification of RNA targets. When arginine fork chemical recognition principles were applied to existing structures with unusual arginine-guanine recognition, we found that the arginine fork geometry was more consistent with the experimental data, suggesting the utility of fork classifications to improve structural models. Software to analyze arginine-RNA interactions has been made available to the community.
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Affiliation(s)
- Sai Shashank Chavali
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Chapin E Cavender
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Joseph E Wedekind
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, 601 Elmwood Avenue, Rochester, New York 14642, United States
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49
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Hoffer ED, Hong S, Sunita S, Maehigashi T, Gonzalez RL, Whitford PC, Dunham CM. Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon-anticodon pairing. eLife 2020; 9:51898. [PMID: 33016876 PMCID: PMC7577736 DOI: 10.7554/elife.51898] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/02/2020] [Indexed: 01/10/2023] Open
Abstract
Modifications in the tRNA anticodon loop, adjacent to the three-nucleotide anticodon, influence translation fidelity by stabilizing the tRNA to allow for accurate reading of the mRNA genetic code. One example is the N1-methylguanosine modification at guanine nucleotide 37 (m1G37) located in the anticodon loop andimmediately adjacent to the anticodon nucleotides 34, 35, 36. The absence of m1G37 in tRNAPro causes +1 frameshifting on polynucleotide, slippery codons. Here, we report structures of the bacterial ribosome containing tRNAPro bound to either cognate or slippery codons to determine how the m1G37 modification prevents mRNA frameshifting. The structures reveal that certain codon–anticodon contexts and the lack of m1G37 destabilize interactions of tRNAPro with the P site of the ribosome, causing large conformational changes typically only seen during EF-G-mediated translocation of the mRNA-tRNA pairs. These studies provide molecular insights into how m1G37 stabilizes the interactions of tRNAPro with the ribosome in the context of a slippery mRNA codon.
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Affiliation(s)
- Eric D Hoffer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
| | - Samuel Hong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
| | - S Sunita
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
| | - Tatsuya Maehigashi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, United States
| | - Paul C Whitford
- Department of Physics, Northeastern University, Boston, United States
| | - Christine M Dunham
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
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50
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Watson ZL, Ward FR, Méheust R, Ad O, Schepartz A, Banfield JF, Cate JH. Structure of the bacterial ribosome at 2 Å resolution. eLife 2020; 9:60482. [PMID: 32924932 DOI: 10.1101/2020.06.26.174334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/11/2020] [Indexed: 05/24/2023] Open
Abstract
Using cryo-electron microscopy (cryo-EM), we determined the structure of the Escherichia coli 70S ribosome with a global resolution of 2.0 Å. The maps reveal unambiguous positioning of protein and RNA residues, their detailed chemical interactions, and chemical modifications. Notable features include the first examples of isopeptide and thioamide backbone substitutions in ribosomal proteins, the former likely conserved in all domains of life. The maps also reveal extensive solvation of the small (30S) ribosomal subunit, and interactions with A-site and P-site tRNAs, mRNA, and the antibiotic paromomycin. The maps and models of the bacterial ribosome presented here now allow a deeper phylogenetic analysis of ribosomal components including structural conservation to the level of solvation. The high quality of the maps should enable future structural analyses of the chemical basis for translation and aid the development of robust tools for cryo-EM structure modeling and refinement.
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Affiliation(s)
- Zoe L Watson
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Fred R Ward
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Raphaël Méheust
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
- Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Omer Ad
- Department of Chemistry, Yale University, New Haven, United States
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
- Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, United States
| | - Jamie Hd Cate
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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