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Kumagai K, Kamba K, Suzuki T, Sekikawa Y, Yuki C, Hamada M, Nagata K, Takaori-Kondo A, Wan L, Katahira M, Nagata T, Sakamoto T. Selection and characterization of aptamers targeting the Vif-CBFβ-ELOB-ELOC-CUL5 complex. J Biochem 2024; 176:205-215. [PMID: 38740386 DOI: 10.1093/jb/mvae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/18/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024] Open
Abstract
The viral infectivity factor (Vif) of human immunodeficiency virus 1 forms a complex with host proteins, designated as Vif-CBFβ-ELOB-ELOC-CUL5 (VβBCC), initiating the ubiquitination and subsequent proteasomal degradation of the human antiviral protein APOBEC3G (A3G), thereby negating its antiviral function. Whilst recent cryo-electron microscopy (cryo-EM) studies have implicated RNA molecules in the Vif-A3G interaction that leads to A3G ubiquitination, our findings indicated that the VβBCC complex can also directly impede A3G-mediated DNA deamination, bypassing the proteasomal degradation pathway. Employing the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method, we have identified RNA aptamers with high affinity for the VβBCC complex. These aptamers not only bind to the VβBCC complex but also reinstate A3G's DNA deamination activity by inhibiting the complex's function. Moreover, we delineated the sequences and secondary structures of these aptamers, providing insights into the mechanistic aspects of A3G inhibition by the VβBCC complex. Analysis using selected aptamers will enhance our understanding of the inhibition of A3G by the VβBCC complex, offering potential avenues for therapeutic intervention.
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Affiliation(s)
- Kazuyuki Kumagai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Keisuke Kamba
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Takuya Suzuki
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Yuto Sekikawa
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Chisato Yuki
- Faculty of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku,Tokyo 169-8555, Japan
| | - Michiaki Hamada
- Faculty of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku,Tokyo 169-8555, Japan
| | - Kayoko Nagata
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawaracho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawaracho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Li Wan
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
- Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
- Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
- Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
- Integrated Research Center for Carbon Negative Science, Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Taiichi Sakamoto
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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Kumagai K, Okubo H, Amano R, Kozu T, Ochiai M, Horiuchi M, Sakamoto T. Selection of aptamers using β-1,3-glucan recognition protein-tagged proteins and curdlan beads. J Biochem 2023; 174:433-440. [PMID: 37500079 DOI: 10.1093/jb/mvad059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023] Open
Abstract
RNA aptamersare nucleic acids that are obtained using the systematic evolution of ligands by exponential enrichment (SELEX) method. When using conventional selection methods to immobilize target proteins on matrix beads using protein tags, sequences are obtained that bind not only to the target proteins but also to the protein tags and matrix beads. In this study, we performed SELEX using β-1,3-glucan recognition protein (GRP)-tags and curdlan beads to immobilize the acute myeloid leukaemia 1 (AML1) Runt domain (RD) and analysed the enrichment of aptamers using high-throughput sequencing. Comparison of aptamer enrichment using the GRP-tag and His-tag suggested that aptamers were enriched using the GRP-tag as well as using the His-tag. Furthermore, surface plasmon resonance analysis revealed that the aptamer did not bind to the GRP-tag and that the conjugation of the GRP-tag to RD weakened the interaction between the aptamer and RD. The GRP-tag could have acted as a competitor to reduce weakly bound RNAs. Therefore, the affinity system of the GRP-tagged proteins and curdlan beads is suitable for obtaining specific aptamers using SELEX.
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Key Words
- SELEX.Abbreviations:
AML1, acute myeloid leukaemia 1; βGRP, β-1,3-glucan recognition protein; GST, glutathione S-transferase; His-tag, poly histidine tag; HTS, high-throughput sequencing; MBP, maltose-binding protein; RD, Runt domain; RUNX1, RUNX family transcription factor 1; SELEX, systematic evolution of ligands by exponential enrichment; SPR, surface plasmon resonance
- aptamer
- curdlan
- βGRP
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Affiliation(s)
- Kazuyuki Kumagai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Hiroki Okubo
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Ryo Amano
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology, Saitama Cancer Center, 780 Komuro, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Masanori Ochiai
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Masataka Horiuchi
- Faculty of Pharmaceutical Science, Health Sciences University of Hokkaido, 1757 Kanazawa, Toubetsu, Ishikari, Hokkaido 061-0293, Japan
| | - Taiichi Sakamoto
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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Saito R, Otsu M, Kiyosawa H, Kawai G. Expression analysis of box C/D snoRNAs with SNPs between C57BL/6 and MSM/Ms strains in male mouse. PLoS One 2023; 18:e0288362. [PMID: 37428787 DOI: 10.1371/journal.pone.0288362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/24/2023] [Indexed: 07/12/2023] Open
Abstract
MSM/Ms mouse derived from the Japanese wild mouse has unique characteristics compared to the widely used C57BL/6 mouse. To examine the usefulness of the MSM/Ms mouse for the comparative genomic analysis, expression of small RNAs were analyzed by the large-scale sequence analysis for two strains of mouse, C57BL/6 and MSM/Ms. As a trial, expression of box C/D snoRNAs, which are the most abundant small RNAs in the cell, were analyzed. By the comparison of the read number for each fragment, 11 snoRNAs with single nucleotide polymorphisms (SNPs) were detected. One of the snoRNAs, SNORD53, shows the expression only for MSM/Ms and this snoRNA has a mutation in the box sequence in C57BL/6. Thus, it was demonstrated that the proposed experimental system using SNPs can give new insight for the gene expression regulation.
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Affiliation(s)
- Rumiko Saito
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Narashino, Chiba, Japan
| | - Maina Otsu
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Narashino, Chiba, Japan
| | - Hidenori Kiyosawa
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Narashino, Chiba, Japan
- Department of Environmental Medicine, Kochi Medical School, Kochi University, Oko-cho, Nankoku, Kochi, Japan
| | - Gota Kawai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Narashino, Chiba, Japan
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Identification of a short form of a Caenorhabditis elegans Y RNA homolog Cel7 RNA. Biochem Biophys Res Commun 2021; 557:104-109. [PMID: 33862452 DOI: 10.1016/j.bbrc.2021.03.143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 11/23/2022]
Abstract
Cel7 RNA is a member of the Caenorhabditis elegans stem-bulge RNAs (sbRNAs) that are classified into the Y RNA family based on their structural similarity. We identified a 15-nucleotide-shorter form of Cel7 RNA and designated it Cel7s RNA. Both Cel7 and Cel7s RNAs increased during the development of worms from L1 to adult. Cel7s RNA was notably more abundant in embryos than in L1 to L3 larvae. Cel7 RNA in embryo was less than those in L2 to adult. The ratio of cellular level of Cel7 RNA to that of Cel7s RNA was higher in L1 to L4, but reversed in embryos and adults. In rop-1 mutants, in which the gene for the C. elegans Ro60 homolog, ROP-1, was disrupted, Cel7s RNA decreased similar to CeY RNA, another C. elegans Y RNA homolog. Surprisingly, Cel7 RNA, existed stably in the absence of ROP-1, unlike Cel7s and CeY RNAs. Gel-shift assays demonstrated that Cel7 and Cel7s RNAs bound to ROP-1 in a similar manner, which was much weaker than CeY RNA. The 5'-terminal 15-nt of Cel7 RNA could be folded into a short stem-loop structure, probably contributing to the stability of Cel7 RNA in vivo and the distinct expression patterns of the 2 RNAs.
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Kawai G, Aoki Y, Otsu M, Koike N, Sampei GI. RNomics of Thermus themophilus HB8 by DNA microarray and next-generation sequencing. J Biochem 2017; 162:423-430. [PMID: 29106607 DOI: 10.1093/jb/mvx046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 06/19/2017] [Indexed: 11/13/2022] Open
Abstract
By using the data obtained by the DNA microarray analysis for the intergenic regions applied to RNA samples extracted from Thermus thermophilus HB8, seven small non-coding RNAs, TtR-1 to TtR-7, were found to be expressed in the cells growing in rich and/or minimal media. By analysing the time course of the expression for the cell growth in combination with the sequence comparison to the known RNAs, two RNAs, TtR-1 and TtR-2, are suggested to be riboswitches. The existence of the seven RNAs and the exact sequence and length, ranging 77-284 nt, were confirmed by the next-generation sequencing. By the combination of these two high-throughput techniques, our understanding of RNAs in the cell will be increased significantly.
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Affiliation(s)
- Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Yuri Aoki
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Maina Otsu
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Naomi Koike
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - Gen-Ichi Sampei
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
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Okui S, Ushida C, Kiyosawa H, Kawai G. Sequence and structure analysis of a mirror tRNA located upstream of the cytochrome oxidase I mRNA in mouse mitochondria. J Biochem 2015; 159:341-50. [PMID: 26519737 DOI: 10.1093/jb/mvv106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 09/23/2015] [Indexed: 11/12/2022] Open
Abstract
RNA fragments corresponding to the mirror tRNA that is located upstream of the cytochrome oxidase I (COXI) gene in the mouse mitochondrial genome were found in the sequences obtained from the mouse brain by the next generation sequencing. RNA fragments corresponding to the 5' terminal of COXI mRNA were also found and it was suggested that the precursor of the COXI mRNA is processed at three residues upstream of the first AUG codon. The mirror tRNA fragment has poly(A) in its 3' terminal and variable 5' terminal, suggesting that this RNA is produced during the 5' processing of COXI mRNA. Secondary structure prediction and NMR analysis indicated that the mirror tRNA is folded into a tRNA-like secondary structure, suggesting that the tRNA-like conformation of the 5' adjacent sequence of COXI mRNA is involved in the COXI mRNA maturation in the mouse mitochondria.
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Affiliation(s)
- Saya Okui
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Tsudanuna 2-17-1, Narashino, Chiba 275-0016, Japan
| | - Chisato Ushida
- Department of Biochemistry and Biotechnology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori 036-8560, Japan
| | - Hidenori Kiyosawa
- Department of Environmental Medicine, Kochi Medical School, Kochi University,Kochi 783-8505, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Tsudanuna 2-17-1, Narashino, Chiba 275-0016, Japan;
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