1
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Wulff TF, Hahnke K, Lécrivain AL, Schmidt K, Ahmed-Begrich R, Finstermeier K, Charpentier E. Dynamics of diversified A-to-I editing in Streptococcus pyogenes is governed by changes in mRNA stability. Nucleic Acids Res 2024:gkae629. [PMID: 39087550 DOI: 10.1093/nar/gkae629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 07/01/2024] [Accepted: 07/23/2024] [Indexed: 08/02/2024] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing plays an important role in the post-transcriptional regulation of eukaryotic cell physiology. However, our understanding of the occurrence, function and regulation of A-to-I editing in bacteria remains limited. Bacterial mRNA editing is catalysed by the deaminase TadA, which was originally described to modify a single tRNA in Escherichia coli. Intriguingly, several bacterial species appear to perform A-to-I editing on more than one tRNA. Here, we provide evidence that in the human pathogen Streptococcus pyogenes, tRNA editing has expanded to an additional tRNA substrate. Using RNA sequencing, we identified more than 27 editing sites in the transcriptome of S. pyogenes SF370 and demonstrate that the adaptation of S. pyogenes TadA to a second tRNA substrate has also diversified the sequence context and recoding scope of mRNA editing. Based on the observation that editing is dynamically regulated in response to several infection-relevant stimuli, such as oxidative stress, we further investigated the underlying determinants of editing dynamics and identified mRNA stability as a key modulator of A-to-I editing. Overall, our findings reveal the presence and diversification of A-to-I editing in S. pyogenes and provide novel insights into the plasticity of the editome and its regulation in bacteria.
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Affiliation(s)
- Thomas F Wulff
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | - Karin Hahnke
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | | | - Katja Schmidt
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | | | | | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
- Institute for Biology, Humboldt University Berlin, 10115 Berlin, Germany
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2
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Schmitt MA, Tittle JM, Fisk JD. Codon decoding by orthogonal tRNAs interrogates the in vivo preferences of unmodified adenosine in the wobble position. Front Genet 2024; 15:1386299. [PMID: 38706795 PMCID: PMC11066159 DOI: 10.3389/fgene.2024.1386299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/30/2024] [Indexed: 05/07/2024] Open
Abstract
The in vivo codon decoding preferences of tRNAs with an authentic adenosine residue at position 34 of the anticodon, the wobble position, are largely unexplored because very few unmodified A34 tRNA genes exist across the three domains of life. The expanded wobble rules suggest that unmodified adenosine pairs most strongly with uracil, modestly with cytosine, and weakly with guanosine and adenosine. Inosine, a modified adenosine, on the other hand, pairs strongly with both uracil and cytosine and to a lesser extent adenosine. Orthogonal pair directed sense codon reassignment experiments offer a tool with which to interrogate the translational activity of A34 tRNAs because the introduced tRNA can be engineered with any anticodon. Our fluorescence-based screen utilizes the absolute requirement of tyrosine at position 66 of superfolder GFP for autocatalytic fluorophore formation. The introduced orthogonal tRNA competes with the endogenous translation machinery to incorporate tyrosine in response to a codon typically assigned another meaning in the genetic code. We evaluated the codon reassignment efficiencies of 15 of the 16 possible orthogonal tRNAs with A34 anticodons. We examined the Sanger sequencing chromatograms for cDNAs from each of the reverse transcribed tRNAs for evidence of inosine modification. Despite several A34 tRNAs decoding closely-related C-ending codons, partial inosine modification was detected for only three species. These experiments employ a single tRNA body with a single attached amino acid to interrogate the behavior of different anticodons in the background of in vivo E. coli translation and greatly expand the set of experimental measurements of the in vivo function of A34 tRNAs in translation. For the most part, unmodified A34 tRNAs largely pair with only U3 codons as the original wobble rules suggest. In instances with GC pairs in the first two codon positions, unmodified A34 tRNAs decode the C- and G-ending codons as well as the expected U-ending codon. These observations support the "two-out-of-three" and "strong and weak" codon hypotheses.
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Affiliation(s)
| | | | - John D. Fisk
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
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3
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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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4
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Torres AG, Rodríguez-Escribà M, Marcet-Houben M, Santos Vieira H, Camacho N, Catena H, Murillo Recio M, Rafels-Ybern À, Reina O, Torres F, Pardo-Saganta A, Gabaldón T, Novoa E, Ribas de Pouplana L. Human tRNAs with inosine 34 are essential to efficiently translate eukarya-specific low-complexity proteins. Nucleic Acids Res 2021; 49:7011-7034. [PMID: 34125917 PMCID: PMC8266599 DOI: 10.1093/nar/gkab461] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/07/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022] Open
Abstract
The modification of adenosine to inosine at the wobble position (I34) of tRNA anticodons is an abundant and essential feature of eukaryotic tRNAs. The expansion of inosine-containing tRNAs in eukaryotes followed the transformation of the homodimeric bacterial enzyme TadA, which generates I34 in tRNAArg and tRNALeu, into the heterodimeric eukaryotic enzyme ADAT, which modifies up to eight different tRNAs. The emergence of ADAT and its larger set of substrates, strongly influenced the tRNA composition and codon usage of eukaryotic genomes. However, the selective advantages that drove the expansion of I34-tRNAs remain unknown. Here we investigate the functional relevance of I34-tRNAs in human cells and show that a full complement of these tRNAs is necessary for the translation of low-complexity protein domains enriched in amino acids cognate for I34-tRNAs. The coding sequences for these domains require codons translated by I34-tRNAs, in detriment of synonymous codons that use other tRNAs. I34-tRNA-dependent low-complexity proteins are enriched in functional categories related to cell adhesion, and depletion in I34-tRNAs leads to cellular phenotypes consistent with these roles. We show that the distribution of these low-complexity proteins mirrors the distribution of I34-tRNAs in the phylogenetic tree.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Marta Rodríguez-Escribà
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Marina Marcet-Houben
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Catalonia 08034, Spain
| | | | - Noelia Camacho
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Helena Catena
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Marina Murillo Recio
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Àlbert Rafels-Ybern
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Francisco Miguel Torres
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Ana Pardo-Saganta
- Centre for Applied Medical Research (CIMA Universidad de Navarra), Pamplona 31008, Spain
| | - Toni Gabaldón
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Catalonia 08034, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia 08010, Spain
| | - Eva Maria Novoa
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
- University Pompeu Fabra, Barcelona, Catalonia 08003, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia 08010, Spain
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5
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Srinivasan S, Torres AG, Ribas de Pouplana L. Inosine in Biology and Disease. Genes (Basel) 2021; 12:600. [PMID: 33921764 PMCID: PMC8072771 DOI: 10.3390/genes12040600] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 02/06/2023] Open
Abstract
The nucleoside inosine plays an important role in purine biosynthesis, gene translation, and modulation of the fate of RNAs. The editing of adenosine to inosine is a widespread post-transcriptional modification in transfer RNAs (tRNAs) and messenger RNAs (mRNAs). At the wobble position of tRNA anticodons, inosine profoundly modifies codon recognition, while in mRNA, inosines can modify the sequence of the translated polypeptide or modulate the stability, localization, and splicing of transcripts. Inosine is also found in non-coding and exogenous RNAs, where it plays key structural and functional roles. In addition, molecular inosine is an important secondary metabolite in purine metabolism that also acts as a molecular messenger in cell signaling pathways. Here, we review the functional roles of inosine in biology and their connections to human health.
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Affiliation(s)
- Sundaramoorthy Srinivasan
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
- Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Catalonia, Spain
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6
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Ehrlich R, Davyt M, López I, Chalar C, Marín M. On the Track of the Missing tRNA Genes: A Source of Non-Canonical Functions? Front Mol Biosci 2021; 8:643701. [PMID: 33796548 PMCID: PMC8007984 DOI: 10.3389/fmolb.2021.643701] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Cellular tRNAs appear today as a diverse population of informative macromolecules with conserved general elements ensuring essential common functions and different and distinctive features securing specific interactions and activities. Their differential expression and the variety of post-transcriptional modifications they are subject to, lead to the existence of complex repertoires of tRNA populations adjusted to defined cellular states. Despite the tRNA-coding genes redundancy in prokaryote and eukaryote genomes, it is surprising to note the absence of genes coding specific translational-active isoacceptors throughout the phylogeny. Through the analysis of different releases of tRNA databases, this review aims to provide a general summary about those “missing tRNA genes.” This absence refers to both tRNAs that are not encoded in the genome, as well as others that show critical sequence variations that would prevent their activity as canonical translation adaptor molecules. Notably, while a group of genes are universally missing, others are absent in particular kingdoms. Functional information available allows to hypothesize that the exclusion of isodecoding molecules would be linked to: 1) reduce ambiguities of signals that define the specificity of the interactions in which the tRNAs are involved; 2) ensure the adaptation of the translational apparatus to the cellular state; 3) divert particular tRNA variants from ribosomal protein synthesis to other cellular functions. This leads to consider the “missing tRNA genes” as a source of putative non-canonical tRNA functions and to broaden the concept of adapter molecules in ribosomal-dependent protein synthesis.
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Affiliation(s)
- Ricardo Ehrlich
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay.,Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Marcos Davyt
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Ignacio López
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Cora Chalar
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Mónica Marín
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
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7
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de Crécy-Lagard V, Jaroch M. Functions of Bacterial tRNA Modifications: From Ubiquity to Diversity. Trends Microbiol 2020; 29:41-53. [PMID: 32718697 DOI: 10.1016/j.tim.2020.06.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 01/21/2023]
Abstract
Modified nucleotides in tRNA are critical components of the translation apparatus, but their importance in the process of translational regulation had until recently been greatly overlooked. Two breakthroughs have recently allowed a fuller understanding of the importance of tRNA modifications in bacterial physiology. One is the identification of the full set of tRNA modification genes in model organisms such as Escherichia coli K12. The second is the improvement of available analytical tools to monitor tRNA modification patterns. The role of tRNA modifications varies greatly with the specific modification within a given tRNA and with the organism studied. The absence of these modifications or reductions can lead to cell death or pleiotropic phenotypes or may have no apparent visible effect. By linking translation through their decoding functions to metabolism through their biosynthetic pathways, tRNA modifications are emerging as important components of the bacterial regulatory toolbox.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Marshall Jaroch
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA
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8
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Structure of a tRNA-specific deaminase with compromised deamination activity. Biochem J 2020; 477:1483-1497. [PMID: 32270856 DOI: 10.1042/bcj20190858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 11/17/2022]
Abstract
Nucleotide 34 in tRNA is extensively modified to ensure translational fidelity and efficacy in cells. The deamination of adenosine at this site catalyzed by the enzyme TadA gives rise to inosine (I), which serves as a typical example of the wobble hypothesis due to its diverse basepairing capability. However, recent studies have shown that tRNAArgACG in Mycoplasma capricolum contains unmodified adenosine, in order to decode the CGG codon. The structural basis behind the poorly performing enzyme M. capricolum TadA (McTadA) is largely unclear. Here we present the structures of the WT and a mutant form of McTadA determined at high resolutions. Through structural comparison between McTadA and other active TadA enzymes as well as modeling efforts, we found that McTadA presents multiple structural conflicts with RNA substrates and thus offered support to previous studies from a structural perspective. These clashes would potentially lead to reduced substrate binding affinity of McTadA, consistent with our in vitro deamination activity and binding assays. To rescue the deamination activity of McTadA, we carried out two rounds of protein engineering through structure-guided design. The unsuccessful attempts of the activity restoration could be attributed to the altered dimer interface and stereo hindrance from the non-catalytic subunit of McTadA, which could be the inevitable outcome of the natural evolution. Our study provides structural insight into an alternative decoding and evolutionary strategy by a compromised TadA enzyme at a molecular level.
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9
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Wang Y, Zhu FC, He LS, Danchin A. Unique tRNA gene profile suggests paucity of nucleotide modifications in anticodons of a deep-sea symbiotic Spiroplasma. Nucleic Acids Res 2019; 46:2197-2203. [PMID: 29390076 PMCID: PMC5861454 DOI: 10.1093/nar/gky045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/18/2018] [Indexed: 12/22/2022] Open
Abstract
The position 34 of a tRNA is always modified for efficient recognition of codons and accurate integration of amino acids by the translation machinery. Here, we report genomics features of a deep-sea gut symbiotic Spiroplasma, which suggests that the organism does not require tRNA(34) anticodon modifications. In the genome, there is a novel set of tRNA genes composed of 32 species for recognition of the 20 amino acids. Among the anticodons of the tRNAs, we witnessed the presence of both U34- and C34-containing tRNAs required to decode NNR (A/G) 2:2 codons as countermeasure of probable loss of anticodon modification genes. In the tRNA fragments detected in the gut transcriptome, mismatches expected to be caused by some tRNA modifications were not shown in their alignments with the corresponding genes. However, the probable paucity of modified anticodons did not fundamentally change the codon usage pattern of the Spiroplasma. The tRNA gene profile that probably resulted from the paucity of tRNA(34) modifications was not observed in other symbionts and deep-sea bacteria, indicating that this phenomenon was an evolutionary dead-end. This study provides insights on co-evolution of translation machine and tRNA genes and steric constraints of codon-anticodon interactions in deep-sea extreme environment.
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Affiliation(s)
- Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Fang-Chao Zhu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Antoine Danchin
- Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié-Salpêtrière, 47 boulevard de l'Hôpital, 75013 Paris, France.,School of Biomedical Sciences, Li Kashing Faculty of Medicine, University of Hong Kong, 21 Sassoon Road, SAR Hong Kong, China
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10
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Nilsson EM, Alexander RW. Bacterial wobble modifications of NNA-decoding tRNAs. IUBMB Life 2019; 71:1158-1166. [PMID: 31283100 DOI: 10.1002/iub.2120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 06/21/2019] [Indexed: 01/18/2023]
Abstract
Nucleotides of transfer RNAs (tRNAs) are highly modified, particularly at the anticodon. Bacterial tRNAs that read A-ending codons are especially notable. The U34 nucleotide canonically present in these tRNAs is modified by a wide range of complex chemical constituents. An additional two A-ending codons are not read by U34-containing tRNAs but are accommodated by either inosine or lysidine at the wobble position (I34 or L34). The structural basis for many N34 modifications in both tRNA aminoacylation and ribosome decoding has been elucidated, and evolutionary conservation of modifying enzymes is also becoming clearer. Here we present a brief review of the structure, function, and conservation of wobble modifications in tRNAs that translate A-ending codons. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1158-1166, 2019.
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Affiliation(s)
- Emil M Nilsson
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina
| | - Rebecca W Alexander
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina
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11
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Rafels-Ybern À, Torres AG, Camacho N, Herencia-Ropero A, Roura Frigolé H, Wulff TF, Raboteg M, Bordons A, Grau-Bove X, Ruiz-Trillo I, Ribas de Pouplana L. The Expansion of Inosine at the Wobble Position of tRNAs, and Its Role in the Evolution of Proteomes. Mol Biol Evol 2019; 36:650-662. [PMID: 30590541 DOI: 10.1093/molbev/msy245] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The modification of adenosine to inosine at the first position of transfer RNA (tRNA) anticodons (I34) is widespread among bacteria and eukaryotes. In bacteria, the modification is found in tRNAArg and is catalyzed by tRNA adenosine deaminase A, a homodimeric enzyme. In eukaryotes, I34 is introduced in up to eight different tRNAs by the heterodimeric adenosine deaminase acting on tRNA. This substrate expansion significantly influenced the evolution of eukaryotic genomes in terms of codon usage and tRNA gene composition. However, the selective advantages driving this process remain unclear. Here, we have studied the evolution of I34, tRNA adenosine deaminase A, adenosine deaminase acting on tRNA, and their relevant codons in a large set of bacterial and eukaryotic species. We show that a functional expansion of I34 to tRNAs other than tRNAArg also occurred within bacteria, in a process likely initiated by the emergence of unmodified A34-containing tRNAs. In eukaryotes, we report on a large variability in the use of I34 in protists, in contrast to a more uniform presence in fungi, plans, and animals. Our data support that the eukaryotic expansion of I34-tRNAs was driven by the improvement brought by these tRNAs to the synthesis of proteins highly enriched in certain amino acids.
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Affiliation(s)
- Àlbert Rafels-Ybern
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Andrea Herencia-Ropero
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Helena Roura Frigolé
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Thomas F Wulff
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Marina Raboteg
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Albert Bordons
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Xavier Grau-Bove
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiología i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiología i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain.,ICREA, Barcelona, Catalonia, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.,ICREA, Barcelona, Catalonia, Spain
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12
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Diwan GD, Agashe D. Wobbling Forth and Drifting Back: The Evolutionary History and Impact of Bacterial tRNA Modifications. Mol Biol Evol 2019; 35:2046-2059. [PMID: 29846694 PMCID: PMC6063277 DOI: 10.1093/molbev/msy110] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Along with tRNAs, enzymes that modify anticodon bases are a key aspect of translation across the tree of life. tRNA modifications extend wobble pairing, allowing specific (“target”) tRNAs to recognize multiple codons and cover for other (“nontarget”) tRNAs, often improving translation efficiency and accuracy. However, the detailed evolutionary history and impact of tRNA modifying enzymes has not been analyzed. Using ancestral reconstruction of five tRNA modifications across 1093 bacteria, we show that most modifications were ancestral to eubacteria, but were repeatedly lost in many lineages. Most modification losses coincided with evolutionary shifts in nontarget tRNAs, often driven by increased bias in genomic GC and associated codon use, or by genome reduction. In turn, the loss of tRNA modifications stabilized otherwise highly dynamic tRNA gene repertoires. Our work thus traces the complex history of bacterial tRNA modifications, providing the first clear evidence for their role in the evolution of bacterial translation.
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Affiliation(s)
- Gaurav D Diwan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.,SASTRA University, Thanjavur, India
| | - Deepa Agashe
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
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13
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Hori H, Kawamura T, Awai T, Ochi A, Yamagami R, Tomikawa C, Hirata A. Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA. Microorganisms 2018; 6:E110. [PMID: 30347855 PMCID: PMC6313347 DOI: 10.3390/microorganisms6040110] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/11/2022] Open
Abstract
To date, numerous modified nucleosides in tRNA as well as tRNA modification enzymes have been identified not only in thermophiles but also in mesophiles. Because most modified nucleosides in tRNA from thermophiles are common to those in tRNA from mesophiles, they are considered to work essentially in steps of protein synthesis at high temperatures. At high temperatures, the structure of unmodified tRNA will be disrupted. Therefore, thermophiles must possess strategies to stabilize tRNA structures. To this end, several thermophile-specific modified nucleosides in tRNA have been identified. Other factors such as RNA-binding proteins and polyamines contribute to the stability of tRNA at high temperatures. Thermus thermophilus, which is an extreme-thermophilic eubacterium, can adapt its protein synthesis system in response to temperature changes via the network of modified nucleosides in tRNA and tRNA modification enzymes. Notably, tRNA modification enzymes from thermophiles are very stable. Therefore, they have been utilized for biochemical and structural studies. In the future, thermostable tRNA modification enzymes may be useful as biotechnology tools and may be utilized for medical science.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takuya Kawamura
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takako Awai
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Anna Ochi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
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14
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Abstract
The pool of transfer RNA (tRNA) molecules in cells allows the ribosome to decode genetic information. This repertoire of molecular decoders is positioned in the crossroad of the genome, the transcriptome, and the proteome. Omics and systems biology now allow scientists to explore the entire repertoire of tRNAs of many organisms, revealing basic exciting biology. The tRNA gene set of hundreds of species is now characterized, in addition to the tRNA genes of organelles and viruses. Genes encoding tRNAs for certain anticodon types appear in dozens of copies in a genome, while others are universally absent from any genome. Transcriptome measurement of tRNAs is challenging, but in recent years new technologies have allowed researchers to determine the dynamic expression patterns of tRNAs. These advances reveal that availability of ready-to-translate tRNA molecules is highly controlled by several transcriptional and posttranscriptional regulatory processes. This regulation shapes the proteome according to the cellular state. The tRNA pool profoundly impacts many aspects of cellular and organismal life, including protein expression level, translation accuracy, adequacy of folding, and even mRNA stability. As a result, the shape of the tRNA pool affects organismal health and may participate in causing conditions such as cancer and neurological conditions.
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Affiliation(s)
- Roni Rak
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100 Israel;
| | - Orna Dahan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100 Israel;
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100 Israel;
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15
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Schmitt MA, Biddle W, Fisk JD. Mapping the Plasticity of the Escherichia coli Genetic Code with Orthogonal Pair-Directed Sense Codon Reassignment. Biochemistry 2018; 57:2762-2774. [PMID: 29668270 DOI: 10.1021/acs.biochem.8b00177] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The relative quantitative importance of the factors that determine the fidelity of translation is largely unknown, which makes predicting the extent to which the degeneracy of the genetic code can be broken challenging. Our strategy of using orthogonal tRNA/aminoacyl tRNA synthetase pairs to precisely direct the incorporation of a single amino acid in response to individual sense and nonsense codons provides a suite of related data with which to examine the plasticity of the code. Each directed sense codon reassignment measurement is an in vivo competition experiment between the introduced orthogonal translation machinery and the natural machinery in Escherichia coli. This report discusses 20 new, related genetic codes, in which a targeted E. coli wobble codon is reassigned to tyrosine utilizing the orthogonal tyrosine tRNA/aminoacyl tRNA synthetase pair from Methanocaldococcus jannaschii. One at a time, reassignment of each targeted sense codon to tyrosine is quantified in cells by measuring the fluorescence of GFP variants in which the essential tyrosine residue is encoded by a non-tyrosine codon. Significantly, every wobble codon analyzed may be partially reassigned with efficiencies ranging from 0.8 to 41%. The accumulation of the suite of data enables a qualitative dissection of the relative importance of the factors affecting the fidelity of translation. While some correlation was observed between sense codon reassignment and either competing endogenous tRNA abundance or changes in aminoacylation efficiency of the altered orthogonal system, no single factor appears to predominately drive translational fidelity. Evaluation of relative cellular fitness in each of the 20 quantitatively characterized proteome-wide tyrosine substitution systems suggests that at a systems level, E. coli is robust to missense mutations.
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Affiliation(s)
- Margaret A Schmitt
- Department of Chemical and Biological Engineering , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Wil Biddle
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - John D Fisk
- Department of Chemical and Biological Engineering , Colorado State University , Fort Collins , Colorado 80523 , United States.,Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States.,School of Biomedical Engineering , Colorado State University , Fort Collins , Colorado 80523 , United States
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16
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Rafels-Ybern À, Torres AG, Grau-Bove X, Ruiz-Trillo I, Ribas de Pouplana L. Codon adaptation to tRNAs with Inosine modification at position 34 is widespread among Eukaryotes and present in two Bacterial phyla. RNA Biol 2017; 15:500-507. [PMID: 28880718 DOI: 10.1080/15476286.2017.1358348] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The modification of adenosine to inosine at position 34 of tRNA anticodons has a profound impact upon codon-anticodon recognition. In bacteria, I34 is thought to exist only in tRNAArg, while in eukaryotes the modification is present in eight different tRNAs. In eukaryotes, the widespread use of I34 strongly influenced the evolution of genomes in terms of tRNA gene abundance and codon usage. In humans, codon usage indicates that I34 modified tRNAs are preferred for the translation of highly repetitive coding sequences, suggesting that I34 is an important modification for the synthesis of proteins of highly skewed amino acid composition. Here we extend the analysis of distribution of codons that are recognized by I34 containing tRNAs to all phyla known to use this modification. We find that the preference for codons recognized by such tRNAs in genes with highly biased codon compositions is universal among eukaryotes, and we report that, unexpectedly, some bacterial phyla show a similar preference. We demonstrate that the genomes of these bacterial species contain previously undescribed tRNA genes that are potential substrates for deamination at position 34.
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Affiliation(s)
- Àlbert Rafels-Ybern
- a Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac, Barcelona, Catalonia , Spain
| | - Adrian Gabriel Torres
- a Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac, Barcelona, Catalonia , Spain
| | - Xavier Grau-Bove
- b Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra) , Barcelona, Catalonia , Spain.,c Departament de Genètica, Microbiología i Estadística , Universitat de Barcelona , Catalonia , Spain
| | - Iñaki Ruiz-Trillo
- b Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra) , Barcelona, Catalonia , Spain.,c Departament de Genètica, Microbiología i Estadística , Universitat de Barcelona , Catalonia , Spain.,d ICREA , Pg. Lluís Companys 23, Barcelona , Catalonia , Spain
| | - Lluís Ribas de Pouplana
- a Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac, Barcelona, Catalonia , Spain.,d ICREA , Pg. Lluís Companys 23, Barcelona , Catalonia , Spain
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17
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Bar-Yaacov D, Mordret E, Towers R, Biniashvili T, Soyris C, Schwartz S, Dahan O, Pilpel Y. RNA editing in bacteria recodes multiple proteins and regulates an evolutionarily conserved toxin-antitoxin system. Genome Res 2017; 27:1696-1703. [PMID: 28864459 PMCID: PMC5630033 DOI: 10.1101/gr.222760.117] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 08/07/2017] [Indexed: 12/31/2022]
Abstract
Adenosine (A) to inosine (I) RNA editing is widespread in eukaryotes. In prokaryotes, however, A-to-I RNA editing was only reported to occur in tRNAs but not in protein-coding genes. By comparing DNA and RNA sequences of Escherichia coli, we show for the first time that A-to-I editing occurs also in prokaryotic mRNAs and has the potential to affect the translated proteins and cell physiology. We found 15 novel A-to-I editing events, of which 12 occurred within known protein-coding genes where they always recode a tyrosine (TAC) into a cysteine (TGC) codon. Furthermore, we identified the tRNA-specific adenosine deaminase (tadA) as the editing enzyme of all these editing sites, thus making it the first identified RNA editing enzyme that modifies both tRNAs and mRNAs. Interestingly, several of the editing targets are self-killing toxins that belong to evolutionarily conserved toxin-antitoxin pairs. We focused on hokB, a toxin that confers antibiotic tolerance by growth inhibition, as it demonstrated the highest level of such mRNA editing. We identified a correlated mutation pattern between the edited and a DNA hard-coded Cys residue positions in the toxin and demonstrated that RNA editing occurs in hokB in two additional bacterial species. Thus, not only the toxin is evolutionarily conserved but also the editing itself within the toxin is. Finally, we found that RNA editing in hokB increases as a function of cell density and enhances its toxicity. Our work thus demonstrates the occurrence, regulation, and functional consequences of RNA editing in bacteria.
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Affiliation(s)
- Dan Bar-Yaacov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Ernest Mordret
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Ruth Towers
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Tammy Biniashvili
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Clara Soyris
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Orna Dahan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100 Israel
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18
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Grosjean H, Breton M, Sirand-Pugnet P, Tardy F, Thiaucourt F, Citti C, Barré A, Yoshizawa S, Fourmy D, de Crécy-Lagard V, Blanchard A. Predicting the minimal translation apparatus: lessons from the reductive evolution of mollicutes. PLoS Genet 2014; 10:e1004363. [PMID: 24809820 PMCID: PMC4014445 DOI: 10.1371/journal.pgen.1004363] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 03/24/2014] [Indexed: 11/18/2022] Open
Abstract
Mollicutes is a class of parasitic bacteria that have evolved from a common Firmicutes ancestor mostly by massive genome reduction. With genomes under 1 Mbp in size, most Mollicutes species retain the capacity to replicate and grow autonomously. The major goal of this work was to identify the minimal set of proteins that can sustain ribosome biogenesis and translation of the genetic code in these bacteria. Using the experimentally validated genes from the model bacteria Escherichia coli and Bacillus subtilis as input, genes encoding proteins of the core translation machinery were predicted in 39 distinct Mollicutes species, 33 of which are culturable. The set of 260 input genes encodes proteins involved in ribosome biogenesis, tRNA maturation and aminoacylation, as well as proteins cofactors required for mRNA translation and RNA decay. A core set of 104 of these proteins is found in all species analyzed. Genes encoding proteins involved in post-translational modifications of ribosomal proteins and translation cofactors, post-transcriptional modifications of t+rRNA, in ribosome assembly and RNA degradation are the most frequently lost. As expected, genes coding for aminoacyl-tRNA synthetases, ribosomal proteins and initiation, elongation and termination factors are the most persistent (i.e. conserved in a majority of genomes). Enzymes introducing nucleotides modifications in the anticodon loop of tRNA, in helix 44 of 16S rRNA and in helices 69 and 80 of 23S rRNA, all essential for decoding and facilitating peptidyl transfer, are maintained in all species. Reconstruction of genome evolution in Mollicutes revealed that, beside many gene losses, occasional gains by horizontal gene transfer also occurred. This analysis not only showed that slightly different solutions for preserving a functional, albeit minimal, protein synthetizing machinery have emerged in these successive rounds of reductive evolution but also has broad implications in guiding the reconstruction of a minimal cell by synthetic biology approaches.
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Affiliation(s)
- Henri Grosjean
- Centre de Génétique Moléculaire, UPR 3404, CNRS, Université Paris-Sud, FRC 3115, Gif-sur-Yvette, France
| | - Marc Breton
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
| | - Pascal Sirand-Pugnet
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
| | - Florence Tardy
- Anses, Laboratoire de Lyon, UMR Mycoplasmoses des Ruminants, Lyon, France
- Université de Lyon, VetAgro Sup, UMR Mycoplasmoses des Ruminants, Marcy L'Etoile, France
| | - François Thiaucourt
- Centre International de Recherche en Agronomie pour le Développement, UMR CMAEE, Montpellier, France
| | - Christine Citti
- INRA, UMR1225, Ecole Nationale Vétérinaire de Toulouse, Toulouse, France
- Université de Toulouse, INP-ENVT, UMR1225, Ecole Nationale Vétérinaire de Toulouse, Toulouse, France
| | - Aurélien Barré
- Univ. Bordeaux, Centre de bioinformatique et de génomique fonctionnelle, CBiB, Bordeaux, France
| | - Satoko Yoshizawa
- Centre de Génétique Moléculaire, UPR 3404, CNRS, Université Paris-Sud, FRC 3115, Gif-sur-Yvette, France
| | - Dominique Fourmy
- Centre de Génétique Moléculaire, UPR 3404, CNRS, Université Paris-Sud, FRC 3115, Gif-sur-Yvette, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University Florida, Gainesville, Florida, United States of America
| | - Alain Blanchard
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- * E-mail:
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19
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Godinic-Mikulcic V, Jaric J, Greber BJ, Franke V, Hodnik V, Anderluh G, Ban N, Weygand-Durasevic I. Archaeal aminoacyl-tRNA synthetases interact with the ribosome to recycle tRNAs. Nucleic Acids Res 2014; 42:5191-201. [PMID: 24569352 PMCID: PMC4005694 DOI: 10.1093/nar/gku164] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRS) are essential enzymes catalyzing the formation of aminoacyl-tRNAs, the immediate precursors for encoded peptides in ribosomal protein synthesis. Previous studies have suggested a link between tRNA aminoacylation and high-molecular-weight cellular complexes such as the cytoskeleton or ribosomes. However, the structural basis of these interactions and potential mechanistic implications are not well understood. To biochemically characterize these interactions we have used a system of two interacting archaeal aaRSs: an atypical methanogenic-type seryl-tRNA synthetase and an archaeal ArgRS. More specifically, we have shown by thermophoresis and surface plasmon resonance that these two aaRSs bind to the large ribosomal subunit with micromolar affinities. We have identified the L7/L12 stalk and the proteins located near the stalk base as the main sites for aaRS binding. Finally, we have performed a bioinformatics analysis of synonymous codons in the Methanothermobacter thermautotrophicus genome that supports a mechanism in which the deacylated tRNAs may be recharged by aaRSs bound to the ribosome and reused at the next occurrence of a codon encoding the same amino acid. These results suggest a mechanism of tRNA recycling in which aaRSs associate with the L7/L12 stalk region to recapture the tRNAs released from the preceding ribosome in polysomes.
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Affiliation(s)
- Vlatka Godinic-Mikulcic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, HR-10000 Zagreb, Croatia, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland, Department of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102A, HR-10000 Zagreb, Croatia, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia and Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
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20
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Krishnakumar R, Ling J. Experimental challenges of sense codon reassignment: an innovative approach to genetic code expansion. FEBS Lett 2013; 588:383-8. [PMID: 24333334 DOI: 10.1016/j.febslet.2013.11.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 11/19/2013] [Accepted: 11/27/2013] [Indexed: 10/25/2022]
Abstract
The addition of new and versatile chemical and biological properties to proteins pursued through incorporation of non-canonical amino acids is at present primarily achieved by stop codon suppression. However, it is critical to find new "blank" codons to increase the variety and efficiency of such insertions, thereby taking 'sense codon recoding' to center stage in the field of genetic code expansion. Current thought optimistically suggests the use of the pyrrolysine system coupled with re-synthesis of genomic information towards achieving sense codon reassignment. Upon review of the serious experimental challenges reported in recent studies, we propose that success in this area will depend on the re-synthesis of genomes, but also on 'rewiring' the mechanism of protein synthesis and of its quality control.
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Affiliation(s)
- Radha Krishnakumar
- Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD 20850, USA.
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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21
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Köhrer C, Mandal D, Gaston KW, Grosjean H, Limbach PA, Rajbhandary UL. Life without tRNAIle-lysidine synthetase: translation of the isoleucine codon AUA in Bacillus subtilis lacking the canonical tRNA2Ile. Nucleic Acids Res 2013; 42:1904-15. [PMID: 24194599 PMCID: PMC3919564 DOI: 10.1093/nar/gkt1009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Translation of the isoleucine codon AUA in most prokaryotes requires a modified C (lysidine or agmatidine) at the wobble position of tRNA2Ile to base pair specifically with the A of the AUA codon but not with the G of AUG. Recently, a Bacillus subtilis strain was isolated in which the essential gene encoding tRNAIle-lysidine synthetase was deleted for the first time. In such a strain, C34 at the wobble position of tRNA2Ile is expected to remain unmodified and cells depend on a mutant suppressor tRNA derived from tRNA1Ile, in which G34 has been changed to U34. An important question, therefore, is how U34 base pairs with A without also base pairing with G. Here, we show (i) that unlike U34 at the wobble position of all B. subtilis tRNAs of known sequence, U34 in the mutant tRNA is not modified, and (ii) that the mutant tRNA binds strongly to the AUA codon on B. subtilis ribosomes but only weakly to AUG. These in vitro data explain why the suppressor strain displays only a low level of misreading AUG codons in vivo and, as shown here, grows at a rate comparable to that of the wild-type strain.
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Affiliation(s)
- Caroline Köhrer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH 45221, USA and Centre de Génétique Moléculaire, CNRS, Gif-sur-Yvette, F-91198, France
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22
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Krishnakumar R, Prat L, Aerni HR, Ling J, Merryman C, Glass JI, Rinehart J, Söll D. Transfer RNA misidentification scrambles sense codon recoding. Chembiochem 2013; 14:1967-72. [PMID: 24000185 DOI: 10.1002/cbic.201300444] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Indexed: 12/22/2022]
Abstract
Sense codon recoding is the basis for genetic code expansion with more than two different noncanonical amino acids. It requires an unused (or rarely used) codon, and an orthogonal tRNA synthetase:tRNA pair with the complementary anticodon. The Mycoplasma capricolum genome contains just six CGG arginine codons, without a dedicated tRNA(Arg). We wanted to reassign this codon to pyrrolysine by providing M. capricolum with pyrrolysyl-tRNA synthetase, a synthetic tRNA with a CCG anticodon (tRNA(Pyl)(CCG)), and the genes for pyrrolysine biosynthesis. Here we show that tRNA(Pyl)(CCG) is efficiently recognized by the endogenous arginyl-tRNA synthetase, presumably at the anticodon. Mass spectrometry revealed that in the presence of tRNA(Pyl)(CCG), CGG codons are translated as arginine. This result is not unexpected as most tRNA synthetases use the anticodon as a recognition element. The data suggest that tRNA misidentification by endogenous aminoacyl-tRNA synthetases needs to be overcome for sense codon recoding.
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Affiliation(s)
- Radha Krishnakumar
- Synthetic Biology and Bioenergy, J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850 (USA)
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