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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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Torres AG, Wulff TF, Rodríguez-Escribà M, Camacho N, Ribas de Pouplana L. Detection of Inosine on Transfer RNAs without a Reverse Transcription Reaction. Biochemistry 2018; 57:5641-5647. [PMID: 30199619 DOI: 10.1021/acs.biochem.8b00718] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Inosine at the "wobble" position (I34) is one of the few essential posttranscriptional modifications in tRNAs (tRNAs). It results from the deamination of adenosine and occurs in bacteria on tRNAArgACG and in eukarya on six or seven additional tRNA substrates. Because inosine is structurally a guanosine analogue, reverse transcriptases recognize it as a guanosine. Most methods used to examine the presence of inosine rely on this phenomenon and detect the modified base as a change in the DNA sequence that results from the reverse transcription reaction. These methods, however, cannot always be applied to tRNAs because reverse transcription can be compromised by the presence of other posttranscriptional modifications. Here we present SL-ID (splinted ligation-based inosine detection), a reverse transcription-free method for detecting inosine based on an I34-dependent specific cleavage of tRNAs by endonuclease V, followed by a splinted ligation and polyacrylamide gel electrophoresis analysis. We show that the method can detect I34 on different tRNA substrates and can be applied to total RNA derived from different species, cell types, and tissues. Here we apply the method to solve previous controversies regarding the modification status of mammalian tRNAArgACG.
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Affiliation(s)
- Adrian G Torres
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Thomas F Wulff
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Marta Rodríguez-Escribà
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain.,Catalan Institution for Research and Advanced Studies (ICREA) , P/Lluis Companys 23 , 08010 Barcelona , Catalonia , Spain
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Chimeric mitochondrial peptides from contiguous regular and swinger RNA. Comput Struct Biotechnol J 2016; 14:283-97. [PMID: 27453772 PMCID: PMC4942731 DOI: 10.1016/j.csbj.2016.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/19/2016] [Accepted: 06/23/2016] [Indexed: 12/20/2022] Open
Abstract
Previous mass spectrometry analyses described human mitochondrial peptides entirely translated from swinger RNAs, RNAs where polymerization systematically exchanged nucleotides. Exchanges follow one among 23 bijective transformation rules, nine symmetric exchanges (X ↔ Y, e.g. A ↔ C) and fourteen asymmetric exchanges (X → Y → Z → X, e.g. A → C → G → A), multiplying by 24 DNA's protein coding potential. Abrupt switches from regular to swinger polymerization produce chimeric RNAs. Here, human mitochondrial proteomic analyses assuming abrupt switches between regular and swinger transcriptions, detect chimeric peptides, encoded by part regular, part swinger RNA. Contiguous regular- and swinger-encoded residues within single peptides are stronger evidence for translation of swinger RNA than previously detected, entirely swinger-encoded peptides: regular parts are positive controls matched with contiguous swinger parts, increasing confidence in results. Chimeric peptides are 200 × rarer than swinger peptides (3/100,000 versus 6/1000). Among 186 peptides with > 8 residues for each regular and swinger parts, regular parts of eleven chimeric peptides correspond to six among the thirteen recognized, mitochondrial protein-coding genes. Chimeric peptides matching partly regular proteins are rarer and less expressed than chimeric peptides matching non-coding sequences, suggesting targeted degradation of misfolded proteins. Present results strengthen hypotheses that the short mitogenome encodes far more proteins than hitherto assumed. Entirely swinger-encoded proteins could exist. Chimeric peptides are translated from contiguous regular and swinger RNA They are 200x rarer than mitochondrial swinger peptides Chimeric peptides integrated in regular mitochondrial proteins are downregulated Contiguous regular parts are matched positive controls for swinger parts The last point validates results beyond other statistical tests for robustness
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