1
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Weiss JL, Decker JC, Bolano A, Krahn N. Tuning tRNAs for improved translation. Front Genet 2024; 15:1436860. [PMID: 38983271 PMCID: PMC11231383 DOI: 10.3389/fgene.2024.1436860] [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: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
Transfer RNAs have been extensively explored as the molecules that translate the genetic code into proteins. At this interface of genetics and biochemistry, tRNAs direct the efficiency of every major step of translation by interacting with a multitude of binding partners. However, due to the variability of tRNA sequences and the abundance of diverse post-transcriptional modifications, a guidebook linking tRNA sequences to specific translational outcomes has yet to be elucidated. Here, we review substantial efforts that have collectively uncovered tRNA engineering principles that can be used as a guide for the tuning of translation fidelity. These principles have allowed for the development of basic research, expansion of the genetic code with non-canonical amino acids, and tRNA therapeutics.
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Affiliation(s)
- Joshua L Weiss
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - J C Decker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Ariadna Bolano
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Natalie Krahn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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2
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Smart A, Lancaster L, Donohue JP, Niblett D, Noller H. Implication of nucleotides near the 3' end of 16S rRNA in guarding the translational reading frame. Nucleic Acids Res 2024; 52:5950-5958. [PMID: 38452198 PMCID: PMC11162774 DOI: 10.1093/nar/gkae143] [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: 10/11/2023] [Revised: 01/24/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024] Open
Abstract
Loss of the translational reading frame leads to misincorporation and premature termination, which can have lethal consequences. Based on structural evidence that A1503 of 16S rRNA intercalates between specific mRNA bases, we tested the possibility that it plays a role in maintenance of the reading frame by constructing ribosomes with an abasic nucleotide at position 1503. This was done by specific cleavage of 16S rRNA at position 1493 using the colicin E3 endonuclease and replacing the resulting 3'-terminal 49mer fragment with a synthetic oligonucleotide containing the abasic site using a novel splinted RNA ligation method. Ribosomes reconstituted from the abasic 1503 16S rRNA were highly active in protein synthesis but showed elevated levels of spontaneous frameshifting into the -1 reading frame. We then asked whether the residual frameshifting persisting in control ribosomes containing an intact A1503 is due to the absence of the N6-dimethyladenosine modifications at positions 1518 and 1519. Indeed, this frameshifting was rescued by site-specific methylation in vitro by the ksgA methylase. These findings thus implicate two different sites near the 3' end of 16S rRNA in maintenance of the translational reading frame, providing yet another example of a functional role for ribosomal RNA in protein synthesis.
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Affiliation(s)
- Alexandria Smart
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Laura Lancaster
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - John Paul Donohue
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Dustin Niblett
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Harry F Noller
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
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3
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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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4
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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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5
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Davey-Young J, Hasan F, Tennakoon R, Rozik P, Moore H, Hall P, Cozma E, Genereaux J, Hoffman KS, Chan PP, Lowe TM, Brandl CJ, O’Donoghue P. Mistranslating the genetic code with leucine in yeast and mammalian cells. RNA Biol 2024; 21:1-23. [PMID: 38629491 PMCID: PMC11028032 DOI: 10.1080/15476286.2024.2340297] [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: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
Translation fidelity relies on accurate aminoacylation of transfer RNAs (tRNAs) by aminoacyl-tRNA synthetases (AARSs). AARSs specific for alanine (Ala), leucine (Leu), serine, and pyrrolysine do not recognize the anticodon bases. Single nucleotide anticodon variants in their cognate tRNAs can lead to mistranslation. Human genomes include both rare and more common mistranslating tRNA variants. We investigated three rare human tRNALeu variants that mis-incorporate Leu at phenylalanine or tryptophan codons. Expression of each tRNALeu anticodon variant in neuroblastoma cells caused defects in fluorescent protein production without significantly increased cytotoxicity under normal conditions or in the context of proteasome inhibition. Using tRNA sequencing and mass spectrometry we confirmed that each tRNALeu variant was expressed and generated mistranslation with Leu. To probe the flexibility of the entire genetic code towards Leu mis-incorporation, we created 64 yeast strains to express all possible tRNALeu anticodon variants in a doxycycline-inducible system. While some variants showed mild or no growth defects, many anticodon variants, enriched with G/C at positions 35 and 36, including those replacing Leu for proline, arginine, alanine, or glycine, caused dramatic reductions in growth. Differential phenotypic defects were observed for tRNALeu mutants with synonymous anticodons and for different tRNALeu isoacceptors with the same anticodon. A comparison to tRNAAla anticodon variants demonstrates that Ala mis-incorporation is more tolerable than Leu at nearly every codon. The data show that the nature of the amino acid substitution, the tRNA gene, and the anticodon are each important factors that influence the ability of cells to tolerate mistranslating tRNAs.
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Affiliation(s)
- Josephine Davey-Young
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Farah Hasan
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Rasangi Tennakoon
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Peter Rozik
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Henry Moore
- Department of Biomolecular Engineering, Baskin School of Engineering & UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Peter Hall
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Ecaterina Cozma
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | | | - Patricia P. Chan
- Department of Biomolecular Engineering, Baskin School of Engineering & UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Todd M. Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering & UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Christopher J. Brandl
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Patrick O’Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
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6
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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: 4] [Impact Index Per Article: 4.0] [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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7
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Soma A, Kubota A, Tomoe D, Ikeuchi Y, Kawamura F, Arimoto H, Shiwa Y, Kanesaki Y, Nanamiya H, Yoshikawa H, Suzuki T, Sekine Y. yaaJ, the tRNA-Specific Adenosine Deaminase, Is Dispensable in Bacillus subtilis. Genes (Basel) 2023; 14:1515. [PMID: 37628567 PMCID: PMC10454642 DOI: 10.3390/genes14081515] [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: 06/12/2023] [Revised: 07/11/2023] [Accepted: 07/20/2023] [Indexed: 08/27/2023] Open
Abstract
Post-transcriptional modifications of tRNA are crucial for their core function. The inosine (I; 6-deaminated adenosine) at the first position in the anticodon of tRNAArg(ICG) modulates the decoding capability and is generally considered essential for reading CGU, CGC, and CGA codons in eubacteria. We report here that the Bacillus subtilis yaaJ gene encodes tRNA-specific adenosine deaminase and is non-essential for viability. A β-galactosidase reporter assay revealed that the translational activity of CGN codons was not impaired in the yaaJ-deletion mutant. Furthermore, tRNAArg(CCG) responsible for decoding the CGG codon was dispensable, even in the presence or absence of yaaJ. These results strongly suggest that tRNAArg with either the anticodon ICG or ACG has an intrinsic ability to recognize all four CGN codons, providing a fundamental concept of non-canonical wobbling mediated by adenosine and inosine nucleotides in the anticodon. This is the first example of the four-way wobbling by inosine nucleotide in bacterial cells. On the other hand, the absence of inosine modification induced +1 frameshifting, especially at the CGA codon. Additionally, the yaaJ deletion affected growth and competency. Therefore, the inosine modification is beneficial for translational fidelity and proper growth-phase control, and that is why yaaJ has been actually conserved in B. subtilis.
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Affiliation(s)
- Akiko Soma
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Atsushi Kubota
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Daisuke Tomoe
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Yoshiho Ikeuchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Fujio Kawamura
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Hijiri Arimoto
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Yuh Shiwa
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Yu Kanesaki
- Shizuoka Instrumental Analysis Center, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Hideaki Nanamiya
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
- Fukushima Translational Research Foundation, Capital Front Bldg., 7-4, 1-35, Sakae-machi, Fukushima 960-8031, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yasuhiko Sekine
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
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8
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9
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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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10
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Li H, Zhu D, Wu J, Ma Y, Cai C, Chen Y, Qin M, Dai H. New substrates and determinants for tRNA recognition of RNA methyltransferase DNMT2/TRDMT1. RNA Biol 2021; 18:2531-2545. [PMID: 34110975 PMCID: PMC8632113 DOI: 10.1080/15476286.2021.1930756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/16/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023] Open
Abstract
Methylation is a common post-transcriptional modification of tRNAs, particularly in the anticodon loop region. The cytosine 38 (C38) in tRNAs, such as tRNAAsp-GUC, tRNAGly-GCC, tRNAVal-AAC, and tRNAGlu-CUC, can be methylated by human DNMT2/TRDMT1 and some homologs found in bacteria, plants, and animals. However, the substrate properties and recognition mechanism of DNMT2/TRDMT1 remain to be explored. Here, taking into consideration common features of the four known substrate tRNAs, we investigated methylation activities of DNMT2/TRDMT1 on the tRNAGly-GCC truncation and point mutants, and conformational changes of mutants. The results demonstrated that human DNMT2/TRDMT1 preferred substrate tRNAGly-GCC in vitro. L-shaped conformation of classical tRNA could be favourable for DNMT2/TRDMT1 activity. The complete sequence and structure of tRNA were dispensable for DNMT2/TRDMT1 activity, whereas T-arm was indispensable to this activity. G19, U20, and A21 in D-loop were identified as the important bases for DNMT2/TRDMT1 activity, while G53, C56, A58, and C61 in T-loop were found as the critical bases. The conserved CUXXCAC sequence in the anticodon loop was confirmed to be the most critical determinant, and it could stabilize C38-flipping to promote C38 methylation. Based on these tRNA properties, new substrates, tRNAVal-CAC and tRNAGln-CUG, were discovered in vitro. Moreover, a single nucleotide substitute, U32C, could convert non-substrate tRNAAla-AGC into a substrate for DNMT2/TRDMT1. Altogether, our findings imply that DNMT2/TRDMT1 relies on a delicate network involving both the primary sequence and tertiary structure of tRNA for substrate recognition.
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Affiliation(s)
- Huari Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Daiyun Zhu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jian Wu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yunfei Ma
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chao Cai
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yong Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Mian Qin
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hanchuan Dai
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
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11
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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: 44] [Impact Index Per Article: 14.7] [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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12
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Datta M, Pillai M, Modak MJ, Liiv A, Khaja FT, Hussain T, Remme J, Varshney U. A mutation in the ribosomal protein uS12 reveals novel functions of its universally conserved PNSA loop. Mol Microbiol 2021; 115:1292-1308. [PMID: 33368752 DOI: 10.1111/mmi.14675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 11/28/2022]
Abstract
The ribosomal protein uS12 is conserved across all domains of life. Recently, a heterozygous spontaneous mutation in human uS12 (corresponding to R49K mutation immediately downstream of the universally conserved 44 PNSA47 loop in Escherichia coli uS12) was identified for causing ribosomopathy, highlighting the importance of the PNSA loop. To investigate the effects of a similar mutation in the absence of any wild-type alleles, we mutated the rpsL gene (encoding uS12) in E. coli. Consistent with its pathology (in humans), we were unable to generate the R49K mutation in E. coli in the absence of a support plasmid. However, we were able to generate the L48K mutation in its immediate vicinity. The L48K mutation resulted in a cold sensitive phenotype and ribosome biogenesis defect in the strain. We show that the L48K mutation impacts the steps of initiation and elongation. Furthermore, the genetic interactions of the L48K mutation with RRF and Pth suggest a novel role of the PNSA loop in ribosome recycling. Our studies reveal new functions of the PNSA loop in uS12, which has so far been studied in the context of translation elongation.
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Affiliation(s)
- Madhurima Datta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Maalavika Pillai
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Mamata Jayant Modak
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Aivar Liiv
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Faisal Tarique Khaja
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Tanweer Hussain
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Jaanus Remme
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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13
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2,6-Diaminopurine as a highly potent corrector of UGA nonsense mutations. Nat Commun 2020; 11:1509. [PMID: 32198346 PMCID: PMC7083880 DOI: 10.1038/s41467-020-15140-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/21/2020] [Indexed: 12/21/2022] Open
Abstract
Nonsense mutations cause about 10% of genetic disease cases, and no treatments are available. Nonsense mutations can be corrected by molecules with nonsense mutation readthrough activity. An extract of the mushroom Lepista inversa has recently shown high-efficiency correction of UGA and UAA nonsense mutations. One active constituent of this extract is 2,6-diaminopurine (DAP). In Calu-6 cancer cells, in which TP53 gene has a UGA nonsense mutation, DAP treatment increases p53 level. It also decreases the growth of tumors arising from Calu-6 cells injected into immunodeficient nude mice. DAP acts by interfering with the activity of a tRNA-specific 2′-O-methyltransferase (FTSJ1) responsible for cytosine 34 modification in tRNATrp. Low-toxicity and high-efficiency UGA nonsense mutation correction make DAP a good candidate for the development of treatments for genetic diseases caused by nonsense mutations. Nonsense mutations can be corrected by several molecules that activate readthrough of premature termination codon. Here, the authors report that 2,6-diaminopurine efficiently corrects UGA nonsense mutations with no significant toxicity.
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14
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Structural Bases for the Fitness Cost of the Antibiotic-Resistance and Lethal Mutations at Position 1408 of 16S rRNA. Molecules 2019; 25:molecules25010159. [PMID: 31906077 PMCID: PMC6983231 DOI: 10.3390/molecules25010159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/29/2019] [Accepted: 12/29/2019] [Indexed: 02/04/2023] Open
Abstract
To understand a structural basis for the fitness cost of the A1408G antibiotic-resistance mutation in the ribosomal A-site RNA, we have determined crystal structures of its A1408C and A1408U lethal mutants, and made comparison with previously solved structures of the wild type and the antibiotic-resistant mutant. The A-site RNA containing an asymmetric internal loop functions as a molecular switch to discriminate a single cognate tRNA from several near-cognate tRNAs by its conformational ON/OFF switching. Overall structures of the “off” states of the A1408C/U lethal mutants are very similar to those of the wild type and the A1408G antibiotic-resistant mutant. However, significant differences are found in local base stacking interactions including the functionally important A1492 and A1493 residues. In the wild type and the A1408G antibiotic-resistant mutant “off” states, both adenines are exposed to the solvent region. On the other hand, one of the corresponding adenines of the lethal A1408C/U mutants stay deeply inside their A-site helices by forming a purine-pyrimidine AoC or A-U base pair and is sandwiched between the upper and lower bases. Therefore, the ON/OFF switching might unfavorably occur in the lethal mutants compared to the wild type and the A1408G antibiotic-resistant mutant. It is probable that bacteria manage to acquire antibiotic resistance without losing the function of the A-site molecular switch by mutating the position 1408 only from A to G, but not to pyrimidine base C or U.
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15
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Noutahi E, Calderon V, Blanchette M, El-Mabrouk N, Lang BF. Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes. Mol Biol Evol 2019; 36:766-783. [PMID: 30698742 PMCID: PMC6551751 DOI: 10.1093/molbev/msz016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Genetic code deviations involving stop codons have been previously reported in mitochondrial genomes of several green plants (Viridiplantae), most notably chlorophyte algae (Chlorophyta). However, as changes in codon recognition from one amino acid to another are more difficult to infer, such changes might have gone unnoticed in particular lineages with high evolutionary rates that are otherwise prone to codon reassignments. To gain further insight into the evolution of the mitochondrial genetic code in green plants, we have conducted an in-depth study across mtDNAs from 51 green plants (32 chlorophytes and 19 streptophytes). Besides confirming known stop-to-sense reassignments, our study documents the first cases of sense-to-sense codon reassignments in Chlorophyta mtDNAs. In several Sphaeropleales, we report the decoding of AGG codons (normally arginine) as alanine, by tRNA(CCU) of various origins that carry the recognition signature for alanine tRNA synthetase. In Chromochloris, we identify tRNA variants decoding AGG as methionine and the synonymous codon CGG as leucine. Finally, we find strong evidence supporting the decoding of AUA codons (normally isoleucine) as methionine in Pycnococcus. Our results rely on a recently developed conceptual framework (CoreTracker) that predicts codon reassignments based on the disparity between DNA sequence (codons) and the derived protein sequence. These predictions are then validated by an evaluation of tRNA phylogeny, to identify the evolution of new tRNAs via gene duplication and loss, and structural modifications that lead to the assignment of new tRNA identities and a change in the genetic code.
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Affiliation(s)
- Emmanuel Noutahi
- Département d'Informatique et de Recherche opérationnelle (DIRO), Université de Montréal, CP 6128 succursale Centre-Ville, Montreal, QC, Canada
| | - Virginie Calderon
- Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada
| | - Mathieu Blanchette
- School of Computer Science, McGill University, McConnell Engineering Bldg., Montréal, QC H3A 0E9, Canada
- McGill Centre for Bioinformatics, McGill University, Montréal, QC, Canada
| | - Nadia El-Mabrouk
- Département d'Informatique et de Recherche opérationnelle (DIRO), Université de Montréal, CP 6128 succursale Centre-Ville, Montreal, QC, Canada
| | - Bernd Franz Lang
- Département de Biochimie, Centre Robert Cedergren, Université de Montréal, CP 6128 succursale Centre-Ville, Montreal, QC, Canada
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16
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Abstract
This review summarizes our current understanding of translation in prokaryotes, focusing on the mechanistic and structural aspects of each phase of translation: initiation, elongation, termination, and ribosome recycling. The assembly of the initiation complex provides multiple checkpoints for messenger RNA (mRNA) and start-site selection. Correct codon-anticodon interaction during the decoding phase of elongation results in major conformational changes of the small ribosomal subunit and shapes the reaction pathway of guanosine triphosphate (GTP) hydrolysis. The ribosome orchestrates proton transfer during peptide bond formation, but requires the help of elongation factor P (EF-P) when two or more consecutive Pro residues are to be incorporated. Understanding the choreography of transfer RNA (tRNA) and mRNA movements during translocation helps to place the available structures of translocation intermediates onto the time axis of the reaction pathway. The nascent protein begins to fold cotranslationally, in the constrained space of the polypeptide exit tunnel of the ribosome. When a stop codon is reached at the end of the coding sequence, the ribosome, assisted by termination factors, hydrolyzes the ester bond of the peptidyl-tRNA, thereby releasing the nascent protein. Following termination, the ribosome is dissociated into subunits and recycled into another round of initiation. At each step of translation, the ribosome undergoes dynamic fluctuations between different conformation states. The aim of this article is to show the link between ribosome structure, dynamics, and function.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen 37077, Germany
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17
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Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis. Nat Chem Biol 2018; 14:1010-1020. [PMID: 30150682 DOI: 10.1038/s41589-018-0119-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 07/09/2018] [Indexed: 11/08/2022]
Abstract
Modification of tRNA anticodons plays a critical role in ensuring accurate translation. N4-acetylcytidine (ac4C) is present at the anticodon first position (position 34) of bacterial elongator tRNAMet. Herein, we identified Bacillus subtilis ylbM (renamed tmcAL) as a novel gene responsible for ac4C34 formation. Unlike general acetyltransferases that use acetyl-CoA, TmcAL activates an acetate ion to form acetyladenylate and then catalyzes ac4C34 formation through a mechanism similar to tRNA aminoacylation. The crystal structure of TmcAL with an ATP analog reveals the molecular basis of ac4C34 formation. The ΔtmcAL strain displayed a cold-sensitive phenotype and a strong genetic interaction with tilS that encodes the enzyme responsible for synthesizing lysidine (L) at position 34 of tRNAIle to facilitate AUA decoding. Mistranslation of the AUA codon as Met in the ΔtmcAL strain upon tilS repression suggests that ac4C34 modification of tRNAMet and L34 modification of tRNAIle act cooperatively to prevent misdecoding of the AUA codon.
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18
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Rozov A, Wolff P, Grosjean H, Yusupov M, Yusupova G, Westhof E. Tautomeric G•U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria. Nucleic Acids Res 2018; 46:7425-7435. [PMID: 29931292 PMCID: PMC6101523 DOI: 10.1093/nar/gky547] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 05/27/2018] [Accepted: 06/06/2018] [Indexed: 11/14/2022] Open
Abstract
We report new crystallographic structures of Thermus thermophilus ribosomes complexed with long mRNAs and native Escherichia coli tRNAs. They complete the full set of combinations of Watson-Crick G•C and miscoding G•U pairs at the first two positions of the codon-anticodon duplex in ribosome functional complexes. Within the tight decoding center, miscoding G•U pairs occur, in all combinations, with a non-wobble geometry structurally indistinguishable from classical coding Watson-Crick pairs at the same first two positions. The contacts with the ribosomal grip surrounding the decoding center are all quasi-identical, except in the crowded environment of the amino group of a guanosine at the second position; in which case a G in the codons may be preferred. In vivo experimental data show that the translational errors due to miscoding by G•U pairs at the first two positions are the most frequently encountered ones, especially at the second position and with a G on the codon. Such preferred miscodings involve a switch from an A-U to a G•U pair in the tRNA/mRNA complex and very rarely from a G = C to a G•U pair. It is concluded that the frequencies of such occurrences are only weakly affected by the codon/anticodon structures but depend mainly on the stability and lifetime of the complex, the modifications present in the anticodon loop, especially those at positions 34 and 37, in addition to the relative concentration of cognate/near-cognate tRNA species present in the cellular tRNA pool.
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Affiliation(s)
- Alexey Rozov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964, CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Philippe Wolff
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, F-67084, Strasbourg, France
| | - Henri Grosjean
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, F-67084, Strasbourg, France
| | - Marat Yusupov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964, CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Gulnara Yusupova
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964, CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Eric Westhof
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, F-67084, Strasbourg, France
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19
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Uhlenbeck OC, Schrader JM. Evolutionary tuning impacts the design of bacterial tRNAs for the incorporation of unnatural amino acids by ribosomes. Curr Opin Chem Biol 2018; 46:138-145. [PMID: 30059836 DOI: 10.1016/j.cbpa.2018.07.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 04/27/2018] [Accepted: 07/13/2018] [Indexed: 01/23/2023]
Abstract
In order to function on the ribosome with uniform rate and adequate accuracy, each bacterial tRNA has evolved to have a characteristic sequence and set of modifications that compensate for the differing physical properties of its esterified amino acid and its codon-anticodon interaction. The sequence of the T-stem of each tRNA compensates for the differential effect of the esterified amino acid on the binding and release of EF-Tu during decoding. The sequence and modifications in the anticodon loop and core of tRNA impact the codon-anticodon strength and the ability of the tRNA to bend during codon recognition. These discoveries impact the design of tRNAs for the efficient and accurate incorporation of unnatural amino acids into proteins using bacterial translation systems.
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Affiliation(s)
- Olke C Uhlenbeck
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | - Jared M Schrader
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA.
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20
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Decoding on the ribosome depends on the structure of the mRNA phosphodiester backbone. Proc Natl Acad Sci U S A 2018; 115:E6731-E6740. [PMID: 29967153 DOI: 10.1073/pnas.1721431115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
During translation, the ribosome plays an active role in ensuring that mRNA is decoded accurately and rapidly. Recently, biochemical studies have also implicated certain accessory factors in maintaining decoding accuracy. However, it is currently unclear whether the mRNA itself plays an active role in the process beyond its ability to base pair with the tRNA. Structural studies revealed that the mRNA kinks at the interface of the P and A sites. A magnesium ion appears to stabilize this structure through electrostatic interactions with the phosphodiester backbone of the mRNA. Here we examined the role of the kink structure on decoding using a well-defined in vitro translation system. Disruption of the kink structure through site-specific phosphorothioate modification resulted in an acute hyperaccurate phenotype. We measured rates of peptidyl transfer for near-cognate tRNAs that were severely diminished and in some instances were almost 100-fold slower than unmodified mRNAs. In contrast to peptidyl transfer, the modifications had little effect on GTP hydrolysis by elongation factor thermal unstable (EF-Tu), suggesting that only the proofreading phase of tRNA selection depends critically on the kink structure. Although the modifications appear to have no effect on typical cognate interactions, peptidyl transfer for a tRNA that uses atypical base pairing is compromised. These observations suggest that the kink structure is important for decoding in the absence of Watson-Crick or G-U wobble base pairing at the third position. Our findings provide evidence for a previously unappreciated role for the mRNA backbone in ensuring uniform decoding of the genetic code.
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21
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Serrão VHB, Silva IR, da Silva MTA, Scortecci JF, de Freitas Fernandes A, Thiemann OH. The unique tRNASec and its role in selenocysteine biosynthesis. Amino Acids 2018; 50:1145-1167. [DOI: 10.1007/s00726-018-2595-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/26/2018] [Indexed: 12/26/2022]
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22
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Makarova TM, Bogdanov AA. The Ribosome as an Allosterically Regulated Molecular Machine. BIOCHEMISTRY (MOSCOW) 2018. [PMID: 29523059 DOI: 10.1134/s0006297917130016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The ribosome as a complex molecular machine undergoes significant conformational rearrangements during the synthesis of polypeptide chains of proteins. In this review, information obtained using various experimental methods on the internal consistency of such rearrangements is discussed. It is demonstrated that allosteric regulation involves all the main stages of the operation of the ribosome and connects functional elements remote by tens and even hundreds of angstroms. Data obtained using Förster resonance energy transfer (FRET) show that translocation is controlled in general by internal mechanisms of the ribosome, and not by the position of the ligands. Chemical probing data revealed the relationship of such remote sites as the decoding, peptidyl transferase, and GTPase centers of the ribosome. Nevertheless, despite the large amount of experimental data accumulated to date, many details and mechanisms of these phenomena are still not understood. Analysis of these data demonstrates that the development of new approaches is necessary for deciphering the mechanisms of allosteric regulation of the operation of the ribosome.
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Affiliation(s)
- T M Makarova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
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23
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Yusupova G, Yusupov M. Crystal structure of eukaryotic ribosome and its complexes with inhibitors. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0184. [PMID: 28138070 DOI: 10.1098/rstb.2016.0184] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 01/26/2023] Open
Abstract
A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated. In this review, we discuss the crystal structure of the entire 80S ribosome from yeast, which reveals its eukaryotic-specific features, and application of X-ray crystallography of the 80S ribosome for investigation of the binding mode for distinct compounds known to inhibit or modulate the protein-translation function of the ribosome. We also refer to a challenging aspect of the structural study of ribosomes, from higher eukaryotes, where the structures of major distinctive features of higher eukaryote ribosome-the high-eukaryote-specific long ribosomal RNA segments (about 1MDa)-remain unresolved. Presently, the structures of the major part of these high-eukaryotic expansion ribosomal RNA segments still remain unresolved.This article is part of the themed issue 'Perspectives on the ribosome'.
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Affiliation(s)
- Gulnara Yusupova
- Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, CNRS/INSERM, University of Strasbourg, BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France
| | - Marat Yusupov
- Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, CNRS/INSERM, University of Strasbourg, BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France
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24
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Rodnina MV, Fischer N, Maracci C, Stark H. Ribosome dynamics during decoding. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0182. [PMID: 28138068 PMCID: PMC5311926 DOI: 10.1098/rstb.2016.0182] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 11/24/2022] Open
Abstract
Elongation factors Tu (EF-Tu) and SelB are translational GTPases that deliver aminoacyl-tRNAs (aa-tRNAs) to the ribosome. In each canonical round of translation elongation, aa-tRNAs, assisted by EF-Tu, decode mRNA codons and insert the respective amino acid into the growing peptide chain. Stop codons usually lead to translation termination; however, in special cases UGA codons are recoded to selenocysteine (Sec) with the help of SelB. Recruitment of EF-Tu and SelB together with their respective aa-tRNAs to the ribosome is a multistep process. In this review, we summarize recent progress in understanding the role of ribosome dynamics in aa-tRNA selection. We describe the path to correct codon recognition by canonical elongator aa-tRNA and Sec-tRNASec and discuss the local and global rearrangements of the ribosome in response to correct and incorrect aa-tRNAs. We present the mechanisms of GTPase activation and GTP hydrolysis of EF-Tu and SelB and summarize what is known about the accommodation of aa-tRNA on the ribosome after its release from the elongation factor. We show how ribosome dynamics ensures high selectivity for the cognate aa-tRNA and suggest that conformational fluctuations, induced fit and kinetic discrimination play major roles in maintaining the speed and fidelity of translation. This article is part of the themed issue ‘Perspectives on the ribosome’.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Niels Fischer
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
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25
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Yang H, Noel JK, Whitford PC. Anisotropic Fluctuations in the Ribosome Determine tRNA Kinetics. J Phys Chem B 2017; 121:10593-10601. [PMID: 28910101 DOI: 10.1021/acs.jpcb.7b06828] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ribosome is a large ribonucleoprotein complex that is responsible for the production of proteins in all organisms. Accommodation is the process by which an incoming aminoacyl-tRNA (aa-tRNA) molecule binds the ribosomal A site, and its kinetics has been implicated in the accuracy of tRNA selection. In addition to rearrangements in the aa-tRNA molecule, the L11 stalk can undergo large-scale anisotropic motions during translation. To explore the potential impact of this protruding region on the rate of aa-tRNA accommodation, we used molecular dynamics simulations with a simplified model to evaluate the free energy as a function of aa-tRNA position. Specifically, these calculations describe the transition between A/T and elbow-accommodated (EA) configurations (∼20 Å displacement). We find that the free-energy barrier associated with elbow accommodation is proportional to the degree of mobility exhibited by the L11 stalk. That is, when L11 is more rigid, the free-energy barrier height is decreased. This effect arises from the ability of L11 to confine, and thereby destabilize, the A/T ensemble. In addition, when elongation factor Tu (EF-Tu) is present, the A/T ensemble is further destabilized in an L11-dependent manner. These results provide a framework that suggests how next-generation experiments may precisely control the dynamics of the ribosome.
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Affiliation(s)
- Huan Yang
- Department of Physics, Northeastern University , Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Jeffrey K Noel
- Max Delbrück Center for Molecular Medicine , Berlin, Germany.,Fritz Haber Institute of the Max Planck Society , Berlin, Germany
| | - Paul C Whitford
- Department of Physics, Northeastern University , Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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26
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Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position. Molecules 2017; 22:molecules22091427. [PMID: 28850078 PMCID: PMC5753802 DOI: 10.3390/molecules22091427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 08/15/2017] [Accepted: 08/22/2017] [Indexed: 02/05/2023] Open
Abstract
Accurate translation of the genetic code depends on mRNA:tRNA codon:anticodon base pairing. Here we exploit an emissive, isosteric adenosine surrogate that allows direct measurement of the kinetics of codon:anticodon base formation during protein synthesis. Our results suggest that codon:anticodon base pairing is subject to tighter constraints at the middle position than at the 5′- and 3′-positions, and further suggest a sequential mechanism of formation of the three base pairs in the codon:anticodon helix.
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27
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Nagao A, Ohara M, Miyauchi K, Yokobori SI, Yamagishi A, Watanabe K, Suzuki T. Hydroxylation of a conserved tRNA modification establishes non-universal genetic code in echinoderm mitochondria. Nat Struct Mol Biol 2017; 24:778-782. [PMID: 28783151 DOI: 10.1038/nsmb.3449] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/11/2017] [Indexed: 12/13/2022]
Abstract
The genetic code is not frozen but still evolving, which can result in the acquisition of 'dialectal' codons that deviate from the universal genetic code. RNA modifications in the anticodon region of tRNAs play a critical role in establishing such non-universal genetic codes. In echinoderm mitochondria, the AAA codon specifies asparagine instead of lysine. By analyzing mitochondrial (mt-) tRNALys isolated from the sea urchin (Mesocentrotus nudus), we discovered a novel modified nucleoside, hydroxy-N6-threonylcarbamoyladenosine (ht6A), 3' adjacent to the anticodon (position 37). Biochemical analysis revealed that ht6A37 has the ability to prevent mt-tRNALys from misreading AAA as lysine, thereby indicating that hydroxylation of N6-threonylcarbamoyladenosine (t6A) contributes to the establishment of the non-universal genetic code in echinoderm mitochondria.
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Affiliation(s)
- Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Mitsuhiro Ohara
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Shin-Ichi Yokobori
- Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Kimitsuna Watanabe
- Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
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28
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Ranjan N, Rodnina MV. Thio-Modification of tRNA at the Wobble Position as Regulator of the Kinetics of Decoding and Translocation on the Ribosome. J Am Chem Soc 2017; 139:5857-5864. [PMID: 28368583 DOI: 10.1021/jacs.7b00727] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Uridine 34 (U34) at the wobble position of the tRNA anticodon is post-transcriptionally modified, usually to mcm5s2, mcm5, or mnm5. The lack of the mcm5 or s2 modification at U34 of tRNALys, tRNAGlu, and tRNAGln causes ribosome pausing at the respective codons in yeast. The pauses occur during the elongation step, but the mechanism that triggers ribosome pausing is not known. Here, we show how the s2 modification in yeast tRNALys affects mRNA decoding and tRNA-mRNA translocation. Using real-time kinetic analysis we show that mcm5-modified tRNALys lacking the s2 group has a lower affinity of binding to the cognate codon and is more efficiently rejected than the fully modified tRNALys. The lack of the s2 modification also slows down the rearrangements in the ribosome-EF-Tu-GDP-Pi-Lys-tRNALys complex following GTP hydrolysis by EF-Tu. Finally, tRNA-mRNA translocation is slower with the s2-deficient tRNALys. These observations explain the observed ribosome pausing at AAA codons during translation and demonstrate how the s2 modification helps to ensure the optimal translation rates that maintain proteome homeostasis of the cell.
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Affiliation(s)
- Namit Ranjan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Goettingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Goettingen, Germany
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29
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Kollmar M, Mühlhausen S. Nuclear codon reassignments in the genomics era and mechanisms behind their evolution. Bioessays 2017; 39. [PMID: 28318058 DOI: 10.1002/bies.201600221] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The canonical genetic code ubiquitously translates nucleotide into peptide sequence with several alterations known in viruses, bacteria, mitochondria, plastids, and single-celled eukaryotes. A new hypothesis to explain genetic code changes, termed tRNA loss driven codon reassignment, has been proposed recently when the polyphyly of the yeast codon reassignment events has been uncovered. According to this hypothesis, the driving force for genetic code changes are tRNA or translation termination factor loss-of-function mutations or loss-of-gene events. The free codon can subsequently be captured by all tRNAs that have an appropriately mutated anticodon and are efficiently charged. Thus, codon capture most likely happens by near-cognate tRNAs and tRNAs whose anticodons are not part of the recognition sites of the respective aminoacyl-tRNA-synthetases. This hypothesis comprehensively explains the CTG codon translation as alanine in Pachysolen yeast together with the long known translation of the same codon as serine in Candida albicans and related species, and can also be applied to most other known reassignments.
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Affiliation(s)
- Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefanie Mühlhausen
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
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30
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Reynolds NM, Vargas-Rodriguez O, Söll D, Crnković A. The central role of tRNA in genetic code expansion. Biochim Biophys Acta Gen Subj 2017; 1861:3001-3008. [PMID: 28323071 DOI: 10.1016/j.bbagen.2017.03.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/14/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND The development of orthogonal translation systems (OTSs) for genetic code expansion (GCE) has allowed for the incorporation of a diverse array of non-canonical amino acids (ncAA) into proteins. Transfer RNA, the central molecule in the translation of the genetic message into proteins, plays a significant role in the efficiency of ncAA incorporation. SCOPE OF REVIEW Here we review the biochemical basis of OTSs for genetic code expansion. We focus on the role of tRNA and discuss strategies used to engineer tRNA for the improvement of ncAA incorporation into proteins. MAJOR CONCLUSIONS The engineering of orthogonal tRNAs for GCE has significantly improved the incorporation of ncAAs. However, there are numerous unintended consequences of orthogonal tRNA engineering that cannot be predicted ab initio. GENERAL SIGNIFICANCE Genetic code expansion has allowed for the incorporation of a great diversity of ncAAs and novel chemistries into proteins, making significant contributions to our understanding of biological molecules and interactions. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Noah M Reynolds
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
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31
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Schwartz MH, Pan T. Function and origin of mistranslation in distinct cellular contexts. Crit Rev Biochem Mol Biol 2017; 52:205-219. [PMID: 28075177 DOI: 10.1080/10409238.2016.1274284] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Mistranslation describes errors during protein synthesis that prevent the amino acid sequences specified in the genetic code from being reflected within proteins. For a long time, mistranslation has largely been considered an aberrant cellular process that cells actively avoid at all times. However, recent evidence has demonstrated that cells from all three domains of life not only tolerate certain levels and forms of mistranslation, but actively induce mistranslation under certain circumstances. To this end, dedicated biological mechanisms have recently been found to reduce translational fidelity, which indicates that mistranslation is not exclusively an erroneous process and can even benefit cells in particular cellular contexts. There currently exists a spectrum of mistranslational processes that differ not only in their origins, but also in their molecular and cellular effects. These findings suggest that the optimal degree of translational fidelity largely depends on a specific cellular context. This review aims to conceptualize the basis and functional consequence of the diverse types of mistranslation that have been described so far.
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Affiliation(s)
- Michael H Schwartz
- a Department of Biochemistry and Molecular Biology , University of Chicago, Chicago , IL , USA
| | - Tao Pan
- a Department of Biochemistry and Molecular Biology , University of Chicago, Chicago , IL , USA
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32
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Fischer N, Neumann P, Bock LV, Maracci C, Wang Z, Paleskava A, Konevega AL, Schröder GF, Grubmüller H, Ficner R, Rodnina MV, Stark H. The pathway to GTPase activation of elongation factor SelB on the ribosome. Nature 2016; 540:80-85. [PMID: 27842381 DOI: 10.1038/nature20560] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/24/2016] [Indexed: 01/29/2023]
Abstract
In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNASec) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNASec recodes a UGA stop codon next to a downstream mRNA stem-loop. Here we present the structures of six intermediates on the pathway of UGA recoding in Escherichia coli by single-particle cryo-electron microscopy. The structures explain the specificity of Sec-tRNASec binding by SelB and show large-scale rearrangements of Sec-tRNASec. Upon initial binding of SelB-Sec-tRNASec to the ribosome and codon reading, the 30S subunit adopts an open conformation with Sec-tRNASec covering the sarcin-ricin loop (SRL) on the 50S subunit. Subsequent codon recognition results in a local closure of the decoding site, which moves Sec-tRNASec away from the SRL and triggers a global closure of the 30S subunit shoulder domain. As a consequence, SelB docks on the SRL, activating the GTPase of SelB. These results reveal how codon recognition triggers GTPase activation in translational GTPases.
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Affiliation(s)
- Niels Fischer
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August University Göttingen, Justus-von Liebig Weg 11, 37077 Göttingen, Germany
| | - Lars V Bock
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Zhe Wang
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Alena Paleskava
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andrey L Konevega
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Gunnar F Schröder
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.,Physics Department, Heinrich-Heine Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August University Göttingen, Justus-von Liebig Weg 11, 37077 Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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33
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Noel JK, Whitford PC. How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome. Nat Commun 2016; 7:13314. [PMID: 27796304 PMCID: PMC5095583 DOI: 10.1038/ncomms13314] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 09/21/2016] [Indexed: 11/18/2022] Open
Abstract
It has long been recognized that the thermodynamics of mRNA–tRNA base pairing is insufficient to explain the high fidelity and efficiency of aminoacyl-tRNA (aa-tRNA) selection by the ribosome. To rationalize this apparent inconsistency, Hopfield proposed that the ribosome may improve accuracy by utilizing a multi-step kinetic proofreading mechanism. While biochemical, structural and single-molecule studies have provided a detailed characterization of aa-tRNA selection, there is a limited understanding of how the physical–chemical properties of the ribosome enable proofreading. To this end, we probe the role of EF-Tu during aa-tRNA accommodation (the proofreading step) through the use of energy landscape principles, molecular dynamics simulations and kinetic models. We find that the steric composition of EF-Tu can reduce the free-energy barrier associated with the first step of accommodation: elbow accommodation. We interpret this effect within an extended kinetic model of accommodation and show how EF-Tu can contribute to efficient and accurate proofreading.
The translation of mRNA by the ribosome is governed by a series of large-scale conformational transitions. Here the authors use MD simulations to demonstrate how the rate of dissociation of elongation factor Tu affects the dynamics of tRNA accommodation and proofreading.
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Affiliation(s)
- Jeffrey K Noel
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA.,Max Delbrück Center for Molecular Medicine, Kristallographie, Robert-Rössle-Strasse 10, Berlin 13125, Germany.,Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society, Berlin 14195, Germany
| | - Paul C Whitford
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, USA
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34
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Grosjean H, Westhof E. An integrated, structure- and energy-based view of the genetic code. Nucleic Acids Res 2016; 44:8020-40. [PMID: 27448410 PMCID: PMC5041475 DOI: 10.1093/nar/gkw608] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 06/11/2016] [Accepted: 06/17/2016] [Indexed: 12/25/2022] Open
Abstract
The principles of mRNA decoding are conserved among all extant life forms. We present an integrative view of all the interaction networks between mRNA, tRNA and rRNA: the intrinsic stability of codon-anticodon duplex, the conformation of the anticodon hairpin, the presence of modified nucleotides, the occurrence of non-Watson-Crick pairs in the codon-anticodon helix and the interactions with bases of rRNA at the A-site decoding site. We derive a more information-rich, alternative representation of the genetic code, that is circular with an unsymmetrical distribution of codons leading to a clear segregation between GC-rich 4-codon boxes and AU-rich 2:2-codon and 3:1-codon boxes. All tRNA sequence variations can be visualized, within an internal structural and energy framework, for each organism, and each anticodon of the sense codons. The multiplicity and complexity of nucleotide modifications at positions 34 and 37 of the anticodon loop segregate meaningfully, and correlate well with the necessity to stabilize AU-rich codon-anticodon pairs and to avoid miscoding in split codon boxes. The evolution and expansion of the genetic code is viewed as being originally based on GC content with progressive introduction of A/U together with tRNA modifications. The representation we present should help the engineering of the genetic code to include non-natural amino acids.
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Affiliation(s)
- Henri Grosjean
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084 Strasbourg, France
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35
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Rozov A, Demeshkina N, Westhof E, Yusupov M, Yusupova G. New Structural Insights into Translational Miscoding. Trends Biochem Sci 2016; 41:798-814. [PMID: 27372401 DOI: 10.1016/j.tibs.2016.06.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/23/2016] [Accepted: 06/02/2016] [Indexed: 01/16/2023]
Abstract
The fidelity of translation depends strongly on the selection of the correct aminoacyl-tRNA that is complementary to the mRNA codon present in the ribosomal decoding center. The ribosome occasionally makes mistakes by selecting the wrong substrate from the pool of aminoacyl-tRNAs. Here, we summarize recent structural advances that may help to clarify the origin of missense errors that occur during decoding. These developments suggest that discrimination between tRNAs is based primarily on steric complementarity and shape acceptance rather than on the number of hydrogen bonds between the molding of the decoding center and the codon-anticodon duplex. They strengthen the hypothesis that spatial mimicry, due either to base tautomerism or ionization, drives infidelity in ribosomal translation.
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Affiliation(s)
- Alexey Rozov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS, UMR7104/INSERM, U964/University of Strasbourg, Strasbourg, France
| | - Natalia Demeshkina
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS, UMR7104/INSERM, U964/University of Strasbourg, Strasbourg, France
| | - Eric Westhof
- Architecture and Reactivity of RNA, Institute of Molecular and Cellular Biology of the CNRS UPR9002/University of Strasbourg, Strasbourg, France
| | - Marat Yusupov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS, UMR7104/INSERM, U964/University of Strasbourg, Strasbourg, France
| | - Gulnara Yusupova
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS, UMR7104/INSERM, U964/University of Strasbourg, Strasbourg, France.
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36
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Xu Y, Vanommeslaeghe K, Aleksandrov A, MacKerell AD, Nilsson L. Additive CHARMM force field for naturally occurring modified ribonucleotides. J Comput Chem 2016; 37:896-912. [PMID: 26841080 PMCID: PMC4801715 DOI: 10.1002/jcc.24307] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 11/16/2015] [Accepted: 01/06/2016] [Indexed: 01/13/2023]
Abstract
More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all‐atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- You Xu
- Department of Biosciences and Nutrition, Karolinska Institutet, HUDDINGE, SE-141 83, Sweden
| | - Kenno Vanommeslaeghe
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland, 21201.,Department of Analytical Chemistry and Pharmaceutical Technology (FABI), Center for Pharmaceutical Research (CePhaR), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels, B-1090, Belgium
| | - Alexey Aleksandrov
- Department of Biology, Ecole Polytechnique, Laboratoire De Biochimie (CNRS UMR7654), Palaiseau, F-91128, France
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland, 21201
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, HUDDINGE, SE-141 83, Sweden
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37
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Rozov A, Demeshkina N, Khusainov I, Westhof E, Yusupov M, Yusupova G. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code. Nat Commun 2016; 7:10457. [PMID: 26791911 PMCID: PMC4736104 DOI: 10.1038/ncomms10457] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/13/2015] [Indexed: 02/07/2023] Open
Abstract
Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNA(Lys)(UUU) with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm(5)s(2)U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.
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Affiliation(s)
- Alexey Rozov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, BP 10142, Illkirch 67404, France
| | - Natalia Demeshkina
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, BP 10142, Illkirch 67404, France
| | - Iskander Khusainov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, BP 10142, Illkirch 67404, France.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Karl Marx 18, Kazan 420012, Russia
| | - Eric Westhof
- Architecture and Reactivity of RNA, Institute of Molecular and Cellular Biology of the CNRS, University of Strasbourg, UPR9002, 15 rue Rene Descartes, Strasbourg 67084, France
| | - Marat Yusupov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, BP 10142, Illkirch 67404, France
| | - Gulnara Yusupova
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, BP 10142, Illkirch 67404, France
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38
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Abstract
Structural centers of motion (pivot points) in the ribosome have recently been identified by measurement of conformational changes in rRNA resulting from EF-G GTP hydrolysis. This series of measurements is extended here to the ribosome's interactions with the cofactor EF-Tu. Four recent EF-Tu bound ribosome structures were compared to unbound structures. A total of 16 pivots were identified, of which 4 are unique to the EF-Tu interaction. Pivots in the GTPase associated center and the sarcin-ricin loop omitted previously, are found to be mobile in response to both EF-Tu and EF-G binding. Pivots in the intersubunit bridge rRNAs are found to be cofactor specific. Head swiveling motions in the small subunit are observed in the EF-Tu bound structures that were trapped post GTP hydrolysis. As in the case of pivots associated with EF-G, the additional pivots described here are associated with weak points in the rRNA structures such as non-canonical pairs and bulge loops. The combined set of pivots should be regarded as a minimal set. Only several states available to the ribosome have been presented in this work. Future, precise crystal structures in conjunction with experimental data will likely show additional functional pivoting elements in the rRNA.
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Affiliation(s)
- Maxim Paci
- a Department of Biology and Biochemistry , University of Houston , Houston , TX , USA
| | - George E Fox
- a Department of Biology and Biochemistry , University of Houston , Houston , TX , USA
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39
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Henley RY, Ashcroft BA, Farrell I, Cooperman BS, Lindsay SM, Wanunu M. Electrophoretic Deformation of Individual Transfer RNA Molecules Reveals Their Identity. NANO LETTERS 2016; 16:138-44. [PMID: 26609994 PMCID: PMC4890568 DOI: 10.1021/acs.nanolett.5b03331] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
It has been hypothesized that the ribosome gains additional fidelity during protein translation by probing structural differences in tRNA species. We measure the translocation kinetics of different tRNA species through ∼3 nm diameter synthetic nanopores. Each tRNA species varies in the time scale with which it is deformed from equilibrium, as in the translocation step of protein translation. Using machine-learning algorithms, we can differentiate among five tRNA species, analyze the ratios of tRNA binary mixtures, and distinguish tRNA isoacceptors.
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Affiliation(s)
- Robert Y. Henley
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Brian Alan Ashcroft
- Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Ian Farrell
- Anima Cell Metrology, Inc., Bernardsville, New Jersey 07924, United States
| | - Barry S. Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Stuart M. Lindsay
- Department of Physics, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85281, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Corresponding Author. . Fax: (617) 373 2943
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40
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Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection. Proc Natl Acad Sci U S A 2015; 112:E6446-55. [PMID: 26554019 DOI: 10.1073/pnas.1512088112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dicistrovirus intergenic region internal ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core ribosomal E, P, and A sites to directly recruit the ribosome and initiate translation at a non-AUG codon. A subset of dicistrovirus IRESs directs translation in the 0 and +1 frames to produce the viral structural proteins and a +1 overlapping open reading frame called ORFx, respectively. Here we show that specific mutations of two unpaired adenosines located at the core of the three-helical junction of the honey bee dicistrovirus Israeli acute paralysis virus (IAPV) IRES PKI domain can uncouple 0 and +1 frame translation, suggesting that the structure adopts distinct conformations that contribute to 0 or +1 frame translation. Using a reconstituted translation system, we show that ribosomes assembled on mutant IRESs that direct exclusive 0 or +1 frame translation lack reading frame fidelity. Finally, a nuclear magnetic resonance/small-angle X-ray scattering hybrid approach reveals that the PKI domain of the IAPV IRES adopts an RNA structure that resembles a complete tRNA. The tRNA shape-mimicry enables the viral IRES to gain access to the ribosome tRNA-binding sites and form intermolecular contacts with the ribosome that are necessary for initiating IRES translation in a specific reading frame.
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41
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Abstract
Deciphering AUA codons is a difficult task for organisms, because AUA and AUG specify isoleucine (Ile) and methionine (Met), separately. Each of the other purine-ending sense co-don sets (NNR) specifies a single amino acid in the universal genetic code. In bacteria and archaea, the cytidine derivatives, 2-lysylcytidine (L or lysidine) and 2-agmatinylcytidine (agm(2)C or agmatidine), respectively, are found at the first letter of the anticodon of tRNA(Ile) responsible for AUA codons. These modifications prevent base pairing with G of the third letter of AUG codon, and enable tRNA(Ile) to decipher AUA codon specifically. In addition, these modifications confer a charging ability of tRNA(Ile) with Ile. Despite their similar chemical structures, L and agm(2)C are synthesized by distinctive mechanisms and catalyzed by different classes of enzymes, implying that the analogous decoding systems for AUA codons were established by convergent evolution after the phylogenic split between bacteria and archaea-eukaryotes lineages following divergence from the last universal common ancestor (LUCA).
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Affiliation(s)
- Tsutomu Suzuki
- a Department of Chemistry and Biotechnology; Graduate School of Engineering ; University of Tokyo ; Hongo , Bunkyo-ku , Tokyo , Japan
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42
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Liu LC, Grundy FJ, Henkin TM. Non-Conserved Residues in Clostridium acetobutylicum tRNA(Ala) Contribute to tRNA Tuning for Efficient Antitermination of the alaS T Box Riboswitch. Life (Basel) 2015; 5:1567-82. [PMID: 26426057 PMCID: PMC4695836 DOI: 10.3390/life5041567] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 09/16/2015] [Accepted: 09/18/2015] [Indexed: 11/16/2022] Open
Abstract
The T box riboswitch regulates expression of amino acid-related genes in Gram-positive bacteria by monitoring the aminoacylation status of a specific tRNA, the binding of which affects the folding of the riboswitch into mutually exclusive terminator or antiterminator structures. Two main pairing interactions between the tRNA and the leader RNA have been demonstrated to be necessary, but not sufficient, for efficient antitermination. In this study, we used the Clostridium acetobutylicum alaS gene, which encodes alanyl-tRNA synthetase, to investigate the specificity of the tRNA response. We show that the homologous C. acetobutylicum tRNAAla directs antitermination of the C. acetobutylicum alaS gene in vitro, but the heterologous Bacillus subtilis tRNAAla (with the same anticodon and acceptor end) does not. Base substitutions at positions that vary between these two tRNAs revealed synergistic and antagonistic effects. Variation occurs primarily at positions that are not conserved in tRNAAla species, which indicates that these non-conserved residues contribute to optimal antitermination of the homologous alaS gene. This study suggests that elements in tRNAAla may have coevolved with the homologous alaS T box leader RNA for efficient antitermination.
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Affiliation(s)
- Liang-Chun Liu
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Frank J Grundy
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Tina M Henkin
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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Čech P, Hoksza D, Svozil D. MultiSETTER: web server for multiple RNA structure comparison. BMC Bioinformatics 2015; 16:253. [PMID: 26264783 PMCID: PMC4531852 DOI: 10.1186/s12859-015-0696-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/05/2015] [Indexed: 12/03/2022] Open
Abstract
Background Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. Results In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. Conclusion To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.
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Affiliation(s)
- Petr Čech
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28, Prague, Czech Republic
| | - David Hoksza
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28, Prague, Czech Republic. .,Department of Software Engineering, Faculty of Mathematics and Physics, Charles University in Prague, Malostranské nám. 25, CZ-118 00, Prague, Czech Republic.
| | - Daniel Svozil
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28, Prague, Czech Republic.
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Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome. Proc Natl Acad Sci U S A 2015. [PMID: 26195797 DOI: 10.1073/pnas.1506823112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We used a cell-free system with pure Escherichia coli components to study initial codon selection of aminoacyl-tRNAs in ternary complex with elongation factor Tu and GTP on messenger RNA-programmed ribosomes. We took advantage of the universal rate-accuracy trade-off for all enzymatic selections to determine how the efficiency of initial codon readings decreased linearly toward zero as the accuracy of discrimination against near-cognate and wobble codon readings increased toward the maximal asymptote, the d value. We report data on the rate-accuracy variation for 7 cognate, 7 wobble, and 56 near-cognate codon readings comprising about 15% of the genetic code. Their d values varied about 400-fold in the 200-80,000 range depending on type of mismatch, mismatch position in the codon, and tRNA isoacceptor type. We identified error hot spots (d = 200) for U:G misreading in second and U:U or G:A misreading in third codon position by His-tRNA(His) and, as also seen in vivo, Glu-tRNA(Glu). We suggest that the proofreading mechanism has evolved to attenuate error hot spots in initial selection such as those found here.
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45
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Joseph AP, Bhat P, Das S, Srinivasan N. Re-analysis of cryoEM data on HCV IRES bound to 40S subunit of human ribosome integrated with recent structural information suggests new contact regions between ribosomal proteins and HCV RNA. RNA Biol 2015; 11:891-905. [PMID: 25268799 DOI: 10.4161/rna.29545] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In this study, we combine available high resolution structural information on eukaryotic ribosomes with low resolution cryo-EM data on the Hepatitis C Viral RNA (IRES) human ribosome complex. Aided further by the prediction of RNA-protein interactions and restrained docking studies, we gain insights on their interaction at the residue level. We identified the components involved at the major and minor contact regions, and propose that there are energetically favorable local interactions between 40S ribosomal proteins and IRES domains. Domain II of the IRES interacts with ribosomal proteins S5 and S25 while the pseudoknot and the downstream domain IV region bind to ribosomal proteins S26, S28 and S5. We also provide support using UV cross-linking studies to validate our proposition of interaction between the S5 and IRES domains II and IV. We found that domain IIIe makes contact with the ribosomal protein S3a (S1e). Our model also suggests that the ribosomal protein S27 interacts with domain IIIc while S7 has a weak contact with a single base RNA bulge between junction IIIabc and IIId. The interacting residues are highly conserved among mammalian homologs while IRES RNA bases involved in contact do not show strict conservation. IRES RNA binding sites for S25 and S3a show the best conservation among related viral IRESs. The new contacts identified between ribosomal proteins and RNA are consistent with previous independent studies on RNA-binding properties of ribosomal proteins reported in literature, though information at the residue level is not available in previous studies.
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Affiliation(s)
- Agnel Praveen Joseph
- Molecular Biophysics Unit. Indian Institute of Science, Bangalore, India; Present address: Science and Technology Facilities Council, RAL, Harwell, Didcot, UK
| | - Prasanna Bhat
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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46
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Structural insights into the translational infidelity mechanism. Nat Commun 2015; 6:7251. [PMID: 26037619 PMCID: PMC4468848 DOI: 10.1038/ncomms8251] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/22/2015] [Indexed: 12/11/2022] Open
Abstract
The decoding of mRNA on the ribosome is the least accurate process during genetic information transfer. Here we propose a unified decoding mechanism based on 11 high-resolution X-ray structures of the 70S ribosome that explains the occurrence of missense errors during translation. We determined ribosome structures in rare states where incorrect tRNAs were incorporated into the peptidyl-tRNA-binding site. These structures show that in the codon-anticodon duplex, a G·U mismatch adopts the Watson-Crick geometry, indicating a shift in the tautomeric equilibrium or ionization of the nucleobase. Additional structures with mismatches in the 70S decoding centre show that the binding of any tRNA induces identical rearrangements in the centre, which favours either isosteric or close to the Watson-Crick geometry codon-anticodon pairs. Overall, the results suggest that a mismatch escapes discrimination by preserving the shape of a Watson-Crick pair and indicate that geometric selection via tautomerism or ionization dominates the translational infidelity mechanism.
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47
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Structural Insights into tRNA Dynamics on the Ribosome. Int J Mol Sci 2015; 16:9866-95. [PMID: 25941930 PMCID: PMC4463622 DOI: 10.3390/ijms16059866] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 11/17/2022] Open
Abstract
High-resolution structures at different stages, as well as biochemical, single molecule and computational approaches have highlighted the elasticity of tRNA molecules when bound to the ribosome. It is well acknowledged that the inherent structural flexibility of the tRNA lies at the heart of the protein synthesis process. Here, we review the recent advances and describe considerations that the conformational changes of the tRNA molecules offer about the mechanisms grounded in translation.
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48
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Structure of the E. coli ribosome–EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM. Nature 2015; 520:567-70. [DOI: 10.1038/nature14275] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/30/2015] [Indexed: 12/18/2022]
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Satpati P, Åqvist J. Why base tautomerization does not cause errors in mRNA decoding on the ribosome. Nucleic Acids Res 2014; 42:12876-84. [PMID: 25352546 PMCID: PMC4227757 DOI: 10.1093/nar/gku1044] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The structure of the genetic code implies strict Watson–Crick base pairing in the first two codon positions, while the third position is known to be degenerate, thus allowing wobble base pairing. Recent crystal structures of near-cognate tRNAs accommodated into the ribosomal A-site, however, show canonical geometry even with first and second position mismatches. This immediately raises the question of whether these structures correspond to tautomerization of the base pairs. Further, if unusual tautomers are indeed trapped why do they not cause errors in decoding? Here, we use molecular dynamics free energy calculations of ribosomal complexes with cognate and near-cognate tRNAs to analyze the structures and energetics of G-U mismatches in the first two codon positions. We find that the enol tautomer of G is almost isoenergetic with the corresponding ketone in the first position, while it is actually more stable in the second position. Tautomerization of U, on the other hand is highly penalized. The presence of the unusual enol form of G thus explains the crystallographic observations. However, the calculations also show that this tautomer does not cause high codon reading error frequencies, as the resulting tRNA binding free energies are significantly higher than for the cognate complex.
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Affiliation(s)
- Priyadarshi Satpati
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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Liu W, Kavaliauskas D, Schrader JM, Poruri K, Birkedal V, Goldman E, Jakubowski H, Mandecki W, Uhlenbeck OC, Knudsen CR, Goldman YE, Cooperman BS. Labeled EF-Tus for rapid kinetic studies of pretranslocation complex formation. ACS Chem Biol 2014; 9:2421-31. [PMID: 25126896 PMCID: PMC4201349 DOI: 10.1021/cb500409y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
![]()
The universally conserved translation
elongation factor EF-Tu delivers
aminoacyl(aa)-tRNA in the form of an aa-tRNA·EF-Tu·GTP ternary
complex (TC) to the ribosome where it binds to the cognate mRNA codon
within the ribosomal A-site, leading to formation of a pretranslocation
(PRE) complex. Here we describe preparation of QSY9 and Cy5 derivatives
of the variant E348C-EF-Tu that are functional in translation elongation.
Together with fluorophore derivatives of aa-tRNA and of ribosomal
protein L11, located within the GTPase associated center (GAC), these
labeled EF-Tus allow development of two new FRET assays that permit
the dynamics of distance changes between EF-Tu and both L11 (Tu-L11
assay) and aa-tRNA (Tu-tRNA assay) to be determined during the decoding
process. We use these assays to examine: (i) the relative rates of
EF-Tu movement away from the GAC and from aa-tRNA during decoding,
(ii) the effects of the misreading-inducing antibiotics streptomycin
and paromomycin on tRNA selection at the A-site, and (iii) how strengthening
the binding of aa-tRNA to EF-Tu affects the rate of EF-Tu movement
away from L11 on the ribosome. These FRET assays have the potential
to be adapted for high throughput screening of ribosomal antibiotics.
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Affiliation(s)
| | | | - Jared M. Schrader
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Kiran Poruri
- Department
of Microbiology and Molecular Genetics, Rutgers University−New Jersey Medical School, Newark, New Jersey 07101, United States
| | | | - Emanuel Goldman
- Department
of Microbiology and Molecular Genetics, Rutgers University−New Jersey Medical School, Newark, New Jersey 07101, United States
| | - Hieronim Jakubowski
- Department
of Microbiology and Molecular Genetics, Rutgers University−New Jersey Medical School, Newark, New Jersey 07101, United States
| | - Wlodek Mandecki
- Department
of Microbiology and Molecular Genetics, Rutgers University−New Jersey Medical School, Newark, New Jersey 07101, United States
| | - Olke C. Uhlenbeck
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
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