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Yoshida T, Kasuya Y, Yamamoto H, Kawai G, Hanaki KI, Matano T, Masuda T. HIV-1 RNAs whose transcription initiates from the third deoxyguanosine of GGG tract in the 5' long terminal repeat serve as a dominant genome for efficient provirus DNA formation. J Virol 2024; 98:e0182523. [PMID: 38289105 PMCID: PMC10878063 DOI: 10.1128/jvi.01825-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 12/20/2023] [Indexed: 02/21/2024] Open
Abstract
Unspliced HIV-1 RNAs function as messenger RNAs for Gag or Gag-Pol polyproteins and progeny genomes packaged into virus particles. Recently, it has been reported that fate of the RNAs might be primarily determined, depending on transcriptional initiation sites among three consecutive deoxyguanosine residues (GGG tract) downstream of TATA-box in the 5' long terminal repeat (LTR). Although HIV-1 RNA transcription starts mostly from the first deoxyguanosine of the GGG tract and often from the second or third deoxyguanosine, RNAs beginning with one guanosine (G1-form RNAs), whose transcription initiates from the third deoxyguanosine, were predominant in HIV-1 particles. Despite selective packaging of G1-form RNAs into virus particles, its biological impact during viral replication remains to be determined. In this study, we revealed that G1-form RNAs are primarily selected as a template for provirus DNA rather than other RNAs. In competitions between HIV-1 and lentiviral vector transcripts in virus-producing cells, approximately 80% of infectious particles were found to generate provirus using HIV-1 transcripts, while lentiviral vector transcripts were conversely selected when we used HIV-1 mutants in which the third deoxyguanosine in the GGG tract was replaced with deoxythymidine or deoxycytidine (GGT or GGC mutants, respectively). In the other analyses of proviral sequences after infection with an HIV-1 mutant in which the GGG tract in 3' LTR was replaced with TTT, most proviral sequences of the GGG-tract region in 5' LTR were found to be TTG, which is reasonably generated using the G1-form transcripts. Our results indicate that the G1-form RNAs serve as a dominant genome to establish provirus DNA.IMPORTANCESince the promoter for transcribing HIV-1 RNA is unique, all viral elements including genomic RNA and viral proteins have to be generated by the unique transcripts through ingenious mechanisms including RNA splicing and frameshifting during protein translation. Previous studies suggested a new mechanism for diversification of HIV-1 RNA functions by heterogeneous transcriptional initiation site usage; HIV-1 RNAs whose transcription initiates from a certain nucleotide were predominant in virus particles. In this study, we established two methods to analyze heterogenous transcriptional initiation site usage by HIV-1 during viral infection and showed that RNAs beginning with one guanosine (G1-form RNAs), whose transcription initiates from the third deoxyguanosine of the GGG tract in 5' LTR, were primarily selected as viral genome in infectious particles and thus are used as a template to generate provirus for continuous replication. This study provides insights into the mechanism for diversification of unspliced RNA functions and requisites of lentivirus infectivity.
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Affiliation(s)
- Takeshi Yoshida
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuho Kasuya
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Molecular Virology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hiroyuki Yamamoto
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Gota Kawai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Chiba, Japan
| | - Ken-ichi Hanaki
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Takao Masuda
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Chiba, Japan
- Graduate school of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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Kawai G, Okada K, Baba S, Sato A, Sakamoto T, Kanai A. Homo-trimeric structure of the ribonuclease for rRNA processing, FAU-1, from Pyrococcus furiosus. J Biochem 2024:mvae010. [PMID: 38302756 DOI: 10.1093/jb/mvae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/20/2024] [Indexed: 02/03/2024] Open
Abstract
Crystal structure of a ribonuclease for rRNA processing, FAU-1, from Pyrococcus furiosus was determined with the resolution of 2.57 Å in a homo-trimeric form. The monomer structure consists of two domains, N-terminal and C-terminal domains. C-terminal domain forms trimer and each N-terminal domain locates outside of the trimer core. In the obtained crystal, a dinucleotide, pApUp, was bound to the N-terminal domain, indicating that N-terminal domain has the RNA-binding ability. The affinities to RNA of FAU-1 and a fragment corresponding to the N-terminal domain, FAU-ΔC, were confirmed by PAGE and NMR. Interestingly, well dispersed NMR signals were observed at 318 K, indicating that the FAU-ΔC-F18 complex form an ordered structure at higher temperature. As predicted in our previous works, FAU-1 and RNase E show a structural similarity in their RNA binding regions. However, structural similarity between RNase E and FAU-1 could be found in the limited regions of the N-terminal domain. On the other hand, structural similarity between C-terminal domain and some proteins including a phosphatase was found. Thus, it is possible that the catalytic site is located in C-terminal domain.
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Affiliation(s)
- Gota Kawai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Kiyoshi Okada
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Seiki Baba
- Structural Biology Division, Japan Synchrotron Radiation Research Institute 1-1-1, Kouto, Sayo, Hyogo679-5148 JAPAN
| | - Asako Sato
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Taiichi Sakamoto
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
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Ichijo R, Kawai G. NMR analysis of a loop-bulge structure of UUCGA pentaloop. Biochem Biophys Res Commun 2024; 691:149327. [PMID: 38039839 DOI: 10.1016/j.bbrc.2023.149327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 11/15/2023] [Accepted: 11/23/2023] [Indexed: 12/03/2023]
Abstract
Although structures of many RNA loops, such as GNRA and UNCG tetraloops, were well known, it is still possible to find more RNA structures. In the present study, solution structure of an RNA fragment having UUCGA pentaloop was analyzed by NMR spectroscopy. It was found that the UUCG tetraloop is formed and the adenosine residue at the 3' side of the tetraloop is bulged out. The characteristic motif of the loop-bulge structure has also been found in other RNAs including CUUGU and CUGGC pentaloops. Along with the recently found T-hairpin structure with a UUUGAUU loop, in which UUUGA pentaloop and UU bulge are formed, the loop-bulge structures can be categorized as an RNA motif and it may be called as the integrated structure loop, I-loop.
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Affiliation(s)
- Rika Ichijo
- Graduate school of Advanced Engineering, Chiba Institute of Technology, Tsudanuma, Narashino, Chiba, 275-0016, Japan
| | - Gota Kawai
- Graduate school of Advanced Engineering, Chiba Institute of Technology, Tsudanuma, Narashino, Chiba, 275-0016, Japan.
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Sampei GI, Ishii H, Taka H, Kawai G. Convergent evolution of nitrogen-adding enzymes in the purine nucleotide biosynthetic pathway, based on structural analysis of adenylosuccinate synthetase (PurA). J GEN APPL MICROBIOL 2023; 69:109-116. [PMID: 37302828 DOI: 10.2323/jgam.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Adenylosuccinate synthetase (PurA) is an enzyme responsible for the nitrogen addition to inosine monophosphate (IMP) by aspartate in the purine nucleotide biosynthetic pathway. And after which the fumarate is removed by adenylosuccinate lyase (PurB), leaving an amino group. There are two other enzymes that catalyze aspartate addition reactions similar to PurA, one in the purine nucleotide biosynthetic pathway (SAICAR synthetase, PurC) and the other in the arginine biosynthetic pathway (argininosuccinate sythetase, ArgG). To investigate the origin of these nitrogen-adding enzymes, PurA from Thermus thermophilus HB8 (TtPurA) was purified and crystallized, and crystal structure complexed with IMP was determined with a resolution of 2.10 Å. TtPurA has a homodimeric structure, and at the dimer interface, Arg135 of one subunit interacts with the IMP bound to the other subunit, suggesting that IMP binding contributes to dimer stability. The different conformation of His41 side chain in TtPurA and EcPurA suggests that side chain flipping of the His41 might play an important role in orienting γ-phosphate of GTP close to oxygen at position 6 of IMP, to receive the nucleophilic attack. Moreover, through comparison of the three-dimensional structures and active sites of PurA, PurC, and ArgG, it was suggested that the active sites of PurA and PurC converged to similar structures for performing similar reactions.
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Affiliation(s)
- Gen-Ichi Sampei
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications
| | - Hironori Ishii
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications
| | - Hiroyuki Taka
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications
| | - Gota Kawai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology
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Abstract
To complete the ThermusQ database, small non-coding RNAs (ncRNAs) and functional RNA elements found in Thermus thermophilus were summarized with annotations. The well-known three ncRNAs, M1 RNA, tmRNA and SRP RNA, were annotated as ttj8_nc001 to ttj8_nc003, and 10 novel RNAs were annotated as ttj8_nc004 to ttj8_nc013. Antisense RNAs for some ORFs were annotated as ttj8_EST00001 to ttj8_EST00006. In addition, a set of conserved sequences found in T. thermophilus HB27 were also described.
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Affiliation(s)
- Gota Kawai
- Graduate School of Advanced Engineering, Chiba Institute of Technology
| | - Gen-Ichi Sampei
- Graduate School of Informatics and Engineering, The University of Electro-Communications
| | - Makoto Nishiyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Yoshitaka Bessho
- RIKEN SPring-8 Center, Harima Institute
- Center for Interdisciplinary AI and Data Science, Ochanomizu University
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Nemoto N, Kawai G, Sampei GI. Crystal structure of adenylosuccinate lyase from the thermophilic bacterium Thermus thermophilus HB8. Acta Crystallogr F Struct Biol Commun 2023; 79:278-284. [PMID: 37873935 PMCID: PMC10619211 DOI: 10.1107/s2053230x23009020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/14/2023] [Indexed: 10/25/2023] Open
Abstract
Adenylosuccinate lyase (PurB) catalyzes two distinct reactions in the purine nucleotide biosynthetic pathway using the same active site. The ability to recognize two different sets of substrates is of structural and evolutionary interest. In the present study, the crystal structure of PurB from the thermophilic bacterium Thermus thermophilus HB8 (TtPurB) was determined at a resolution of 2.38 Å by molecular replacement using a structure predicted by AlphaFold2 as a template. The asymmetric unit of the TtPurB crystal contained two TtPurB molecules, and some regions were disordered in the crystal structure. The disordered regions were the substrate-binding site and domain 3. TtPurB forms a homotetramer and the monomer is composed of three domains (domains 1, 2 and 3), which is a typical structure for the aspartase/fumarase superfamily. Molecular dynamics simulations with and without substrate/product were performed using a full-length model of TtPurB which was obtained before deletion of the disordered regions. The substrates and products were bound to the model structures during the MD simulations. The fluctuations of amino-acid residues were greater in the disordered regions and became smaller upon the binding of substrate or product. These results demonstrate that the full-length model obtained using AlphaFold2 can be used to generate the coordinates of disordered regions within the crystal structure.
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Affiliation(s)
- Naoki Nemoto
- Faculty of Advanced Engineering, Chiba Institute of Technology, Narashino, Chiba 275-0016, Japan
| | - Gota Kawai
- Faculty of Advanced Engineering, Chiba Institute of Technology, Narashino, Chiba 275-0016, Japan
| | - Gen-ichi Sampei
- Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
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Kimoto M, Tan HP, Matsunaga KI, Binte Mohd Mislan NA, Kawai G, Hirao I. Strict Interactions of Fifth Letters, Hydrophobic Unnatural Bases, in XenoAptamers with Target Proteins. J Am Chem Soc 2023; 145:20432-20441. [PMID: 37677157 PMCID: PMC10515488 DOI: 10.1021/jacs.3c06122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Indexed: 09/09/2023]
Abstract
XenoAptamers are DNA fragments containing additional letters (unnatural bases, UBs) that bind specifically to their target proteins with high affinities (sub-nanomolar KD values). One of the UBs is the highly hydrophobic 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds), which significantly increases XenoAptamers' affinities to targets. Originally, Ds was developed as a third base pair with a complementary UB, 2-nitro-4-propynylpyrrole (Px), for replication, and thus it can be used for aptamer generation by an evolutional engineering method involving PCR amplification. However, it is unclear whether the Ds base is the best component as the hydrophobic fifth-letter ligand for interactions with target proteins. To optimize the ligand structure of the fifth letter, we prepared 13 Ds variants and examined the affinities of XenoAptamers containing these variants to target proteins. The results obtained using four XenoAptamers prepared by the replacement of Ds bases with variants indicated that subtle changes in the chemical structure of Ds significantly affect the XenoAptamer affinities. Among the variants, placing either 4-(2-thienyl)pyrrolo[2,3-b]pyridine (Ys) or 4-(2-thienyl)benzimidazole (Bs) at specific Ds positions in each original XenoAptamer greatly improved their affinities to targets. The Ys and Bs bases are variants derived by replacing only one nitrogen with a carbon in the Ds base. These results demonstrate the strict intramolecular interactions, which are not simple hydrophobic contacts between UBs and targets, thus providing a method to mature XenoAptamers' affinities to targets.
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Affiliation(s)
- Michiko Kimoto
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | - Hui Pen Tan
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | - Ken-ichiro Matsunaga
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | | | - Gota Kawai
- Chiba
Institute of Technology (CIT), Tsudanuma 2-17-1, Narashino, Chiba 275-0016, Japan
| | - Ichiro Hirao
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ichijo R, Kamimura T, Kawai G. Interaction between a fluoroquinolone derivative KG022 and RNAs: Effect of base pairs 3′ adjacent to the bulged residues. Front Mol Biosci 2023; 10:1145528. [PMID: 36999159 PMCID: PMC10043337 DOI: 10.3389/fmolb.2023.1145528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
RNA-targeted small molecules are a promising modality in drug discovery. Recently, we found that a fluoroquinolone derivative, KG022, can bind to RNAs with bulged C or G. To clarify the RNA specificity of KG022, we analyzed the effect of the base pair located at the 3′side of the bulged residue. It was found that KG022 prefers G-C and A-U base pairs at the 3′side. Solution structures of the complexes of KG022 with the four RNA molecules with bulged C or G and G-C or A-U base pairs at the 3′side of the bulged residue were determined to find that the fluoroquinolone moiety is located between two purine bases, and this may be the mechanism of the specificity. This work provides an important example of the specificity of RNA-targeted small molecules.
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Affiliation(s)
- Rika Ichijo
- Graduate School of Engineering, Chiba Institute of Technology, Chiba, Japan
| | | | - Gota Kawai
- Graduate School of Engineering, Chiba Institute of Technology, Chiba, Japan
- *Correspondence: Gota Kawai,
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Masuda T, Kotani O, Yokoyama M, Abe Y, Kawai G, Sato H. Cis-Allosteric Regulation of HIV-1 Reverse Transcriptase by Integrase. Viruses 2022; 15:31. [PMID: 36680070 PMCID: PMC9864105 DOI: 10.3390/v15010031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Reverse transcriptase (RT) and integrase (IN) are encoded tandemly in the pol genes of retroviruses. We reported recently that HIV-1 RT and IN need to be supplied as the pol precursor intermediates, in which RT and IN are in fusion form (RTIN) to exert efficient reverse transcription in the context of HIV-1 replication. The mechanism underlying RTIN's effect, however, remains to be elucidated. In this study, we examined the effect of IN fusion on RT during reverse transcription by an in vitro cell-free assay, using recombinant HIV-1 RTIN (rRTIN). We found that, compared to recombinant RT (rRT), rRTIN generated significantly higher cDNAs under physiological concentrations of dNTPs (less than 10 μM), suggesting increased affinity of RTIN to dNTPs. Importantly, the cleavage of RTIN with HIV-1 protease reduced cDNA levels at a low dose of dNTPs. Similarly, sensitivities against RT inhibitors were significantly altered in RTIN form. Finally, analysis of molecular dynamics simulations of RT and RTIN suggested that IN can influence the structural dynamics of the RT active center and the inhibitor binding pockets in cis. Thus, we demonstrated, for the first time, the cis-allosteric regulatory roles of IN in RT structure and enzymatic activity.
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Affiliation(s)
- Takao Masuda
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Yushima, 1-5-45 Bunkyo-ku, Tokyo 113-8519, Japan
| | - Osamu Kotani
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Gakuen, 4-7-1, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Masaru Yokoyama
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Gakuen, 4-7-1, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Yuya Abe
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Yushima, 1-5-45 Bunkyo-ku, Tokyo 113-8519, Japan
| | - Gota Kawai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan
| | - Hironori Sato
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Gakuen, 4-7-1, Musashimurayama-shi, Tokyo 208-0011, Japan
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Takase N, Otsu M, Hirakata S, Ishizu H, Siomi MC, Kawai G. T-hairpin structure found in the RNA element involved in piRNA biogenesis. RNA 2022; 28:541-550. [PMID: 34987083 PMCID: PMC8925976 DOI: 10.1261/rna.078967.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
PIWI-interacting RNAs (piRNAs) repress transposons to protect the germline genome from DNA damage caused by transposon transposition. In Drosophila, the Traffic jam (Tj) mRNA is consumed to produce piRNA in its 3'-UTR. A cis element located within the 3'-UTR, Tj-cis, is necessary for piRNA biogenesis. In this study, we analyzed the structure of the Tj-cis RNA, a 100-nt RNA corresponding to the Tj-cis element, by the SHAPE and NMR analyses and found that a stable hairpin structure formed in the 5' half of the Tj-cis RNA. The tertiary structure of the 16-nt stable hairpin was analyzed by NMR, and a novel stem-loop structure, the T-hairpin, was found. In the T-hairpin, four uridine residues are exposed to the solvent, suggesting that this stem-loop is the target of Yb protein, a Tudor domain-containing piRNA biogenesis factor. The piRNA biogenesis assay showed that both the T-hairpin and the 3' half are required for the function of the Tj-cis element, suggesting that both the T-hairpin and the 3' half are recognized by Yb protein.
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Affiliation(s)
- Naomi Takase
- Department of Life Science, Graduate School of Advanced Engineering, Chiba Institute of Technology, Chiba 275-0016, Japan
| | - Maina Otsu
- Department of Life Science, Graduate School of Advanced Engineering, Chiba Institute of Technology, Chiba 275-0016, Japan
| | - Shigeki Hirakata
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Hirotsugu Ishizu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Gota Kawai
- Department of Life Science, Graduate School of Advanced Engineering, Chiba Institute of Technology, Chiba 275-0016, Japan
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Hyun Lee K, Kimoto M, Kawai G, Okamoto I, Fin A, Hirao I. Dye‐Conjugated Spinach RNA by Genetic Alphabet Expansion. Chemistry 2022; 28:e202104396. [DOI: 10.1002/chem.202104396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Kyung Hyun Lee
- Institute of Bioengineering and Bioimaging A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
| | - Michiko Kimoto
- Institute of Bioengineering and Bioimaging A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
| | - Gota Kawai
- Chiba Institute of Technology (CIT) Tsudanuma 2-17-1 Narashino Chiba 275-0016 Japan
| | - Itaru Okamoto
- Institute of Bioengineering and Bioimaging A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
| | - Andrea Fin
- Institute of Bioengineering and Bioimaging A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Bioimaging A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
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Nagano K, Kamimura T, Kawai G. Interaction between a fluoroquinolone derivative and RNAs with a single bulge. J Biochem 2022; 171:239-244. [PMID: 34791286 DOI: 10.1093/jb/mvab124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/09/2021] [Indexed: 01/08/2023] Open
Abstract
Interaction analysis between small molecules and RNA as well as structure determination of RNA-small molecule complexes will be the clues to search for compounds that bind to specific mRNA or non-coding RNA in drug discovery. In this study, the RNA-binding ability of a fluoroquinolone derivative, KG022, was examined against single-residue bulge-containing hairpin RNAs as RNA models. Nuclear magnetic resonance analysis indicated that KG022 interacts with the RNAs in the vicinity of the bulge residue, with preferring C and G as the bulge residues. The solution structures of the RNA-KG022 complexes showed that the KG022 binds to the RNAs at the bulge-out regions. Each substituent in KG022 interacts with specific position of RNAs around the bulge-out region probably contributing the specificity of the binding. This work provides a novel member for the RNA-targeted small molecules.
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Affiliation(s)
- Konami Nagano
- Department of Life and Environmental Sciences, Graduate School of Engineering, Chiba Institute of Technology, Chiba 275-0016, Japan
| | | | - Gota Kawai
- Department of Life and Environmental Sciences, Graduate School of Engineering, Chiba Institute of Technology, Chiba 275-0016, Japan
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14
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Yamamoto N, Sampei G, Kawai G. Free-Energy Profile Analysis of the Catalytic Reaction of Glycinamide Ribonucleotide Synthetase. Life (Basel) 2022; 12:life12020281. [PMID: 35207568 PMCID: PMC8880213 DOI: 10.3390/life12020281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/08/2022] [Accepted: 02/12/2022] [Indexed: 12/03/2022] Open
Abstract
The second step in the de novo biosynthetic pathway of purine is catalyzed by PurD, which consumes an ATP molecule to produce glycinamide ribonucleotide (GAR) from glycine and phosphoribosylamine (PRA). PurD initially reacts with ATP to produce an intermediate, glycyl-phosphate, which then reacts with PRA to produce GAR. The structure of the glycyl-phosphate intermediate bound to PurD has not been determined. Therefore, the detailed reaction mechanism at the molecular level is unclear. Here, we developed a computational protocol to analyze the free-energy profile for the glycine phosphorylation process catalyzed by PurD, which examines the free-energy change along a minimum energy path based on a perturbation method combined with the quantum mechanics and molecular mechanics hybrid model. Further analysis revealed that during the formation of glycyl-phosphate, the partial atomic charge distribution within the substrate molecules was not localized according to the formal charges, but was delocalized overall, which contributed significantly to the interaction with the charged amino acid residues in the ATP-grasp domain of PurD.
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Affiliation(s)
- Norifumi Yamamoto
- Department of Applied Chemistry, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino 275-0016, Chiba, Japan
- Correspondence: ; Tel.: +81-47-478-0375
| | - Genichi Sampei
- Department of Applied Physics and Chemistry, Faculty of Electro-Communications, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu 182-8585, Tokyo, Japan;
| | - Gota Kawai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino 275-0016, Chiba, Japan;
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15
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Minamisawa M, Sato Y, Ishiguro E, Taniai T, Sakamoto T, Kawai G, Saito T, Saido TC. Amelioration of Alzheimer's Disease by Gut-Pancreas-Liver-Brain Interaction in an App Knock-In Mouse Model. Life (Basel) 2021; 12:34. [PMID: 35054427 PMCID: PMC8778338 DOI: 10.3390/life12010034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 02/07/2023] Open
Abstract
In this study, we observed disease progression, changes in the gut microbiota, and interactions among the brain, liver, pancreas, and intestine in a mouse model of Alzheimer's disease (AD), in addition to attempting to inhibit disease progression through the dietary supplementation of L-arginine and limonoids. Wild-type mice (WC) and AD mice were fed a normal diet (AC), a diet supplemented with L-arginine and limonoids (ALA), or a diet containing only limonoids (AL) for 12-64 weeks. The normal diet-fed WC and AC mice showed a decrease in the diversity of the gut microbiota, with an increase in the Firmicutes/Bacteroidetes ratio, and bacterial translocation. Considerable bacterial translocation to the pancreas and intense inflammation of the pancreas, liver, brain, and intestinal tissues were observed in the AC mice from alterations in the gut microbiota. The ALA diet or AL diet-fed mice showed increased diversity of the bacterial flora and suppressed oxidative stress and inflammatory responses in hepatocytes and pancreatic cells, bacterial translocation, and neurodegeneration of the brain. These findings suggest that L-arginine and limonoids help in maintaining the homeostasis of the gut microbiota, pancreas, liver, brain, and gut in AD mice.
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Affiliation(s)
- Mayumi Minamisawa
- Department of Life Science, Chiba Institute of Technology, Graduate School of Advanced Engineering, Chiba 275-0016, Japan; (Y.S.); (T.S.); (G.K.)
- Education Center, Faculty of Advanced Engineering, Chiba Institute of Technology, Chiba 275-0023, Japan;
| | - Yuma Sato
- Department of Life Science, Chiba Institute of Technology, Graduate School of Advanced Engineering, Chiba 275-0016, Japan; (Y.S.); (T.S.); (G.K.)
| | | | - Tetsuyuki Taniai
- Education Center, Faculty of Advanced Engineering, Chiba Institute of Technology, Chiba 275-0023, Japan;
| | - Taiichi Sakamoto
- Department of Life Science, Chiba Institute of Technology, Graduate School of Advanced Engineering, Chiba 275-0016, Japan; (Y.S.); (T.S.); (G.K.)
| | - Gota Kawai
- Department of Life Science, Chiba Institute of Technology, Graduate School of Advanced Engineering, Chiba 275-0016, Japan; (Y.S.); (T.S.); (G.K.)
| | - Takashi Saito
- RIKEN Center for Brain Science, Laboratory for Proteolytic Neuroscience, Saitama 351-0198, Japan; (T.S.); (T.C.S.)
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Takaomi C. Saido
- RIKEN Center for Brain Science, Laboratory for Proteolytic Neuroscience, Saitama 351-0198, Japan; (T.S.); (T.C.S.)
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16
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Das B, Nagano K, Kawai G, Murata A, Nakatani K. 2-Amino-1,8-naphthyridine Dimer (ANP77), a High-Affinity Binder to the Internal Loops of C/CC and T/CC Sites in Double-Stranded DNA. J Org Chem 2021; 87:340-350. [PMID: 34937340 DOI: 10.1021/acs.joc.1c02383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Small molecules targeting DNA regions with structural fluctuation are an important class of molecule as chemical probes for studying the role of these structures in biological systems and the development of neurological disorders. The molecule ANP77 we described here, where a three-atom linker connects two 2-amino-1,8-naphthyridines at the C7 position, was found to form stacked structure with protonation of naphthyridine at low pH, and bound to the internal loop consisting of C/CC and T/CC in double-stranded DNA with affinities of 4.8 and 34.4 nM, respectively. Mass spectrometry and isothermal titration calorimetry analyses determined the stoichiometry for the binding as 1:1, and chemical footprinting with permanganate and NMR structural analysis revealed that the T in the T/CC was forced to flip out toward an extrahelical position upon ANP77 binding. Protonated stacked ANP77 interacted with two adjacent cytosines through hydrogen bonding and occupied the position in the duplex by flipping out the C or T opposite CC. Finally, this study demonstrated the potential of ANP77 for binding to the sequences of biological significance with the TG(T/C)CC repeat of the PIG3 promoter and the telomere repeat CCCTAA.
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Affiliation(s)
- Bimolendu Das
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Konami Nagano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Chiba 275-0016, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Chiba 275-0016, Japan
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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17
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Obayashi CM, Shinohara Y, Masuda T, Kawai G. Influence of the 5'-terminal sequences on the 5'-UTR structure of HIV-1 genomic RNA. Sci Rep 2021; 11:10920. [PMID: 34035384 PMCID: PMC8149415 DOI: 10.1038/s41598-021-90427-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/11/2021] [Indexed: 11/09/2022] Open
Abstract
The 5'-UTR of HIV-1 genomic RNA is known to form specific structures and has important functions. There are three 5'-terminal sequences, G1, G2 and G3, with different localizations in the cell and virion particles as well as different efficiencies in translation and reverse transcription reactions. In the present study, the structural characteristics of the joint region between the TAR and PolyA stems was analysed, and it was found that small differences in the 5'-terminus affect the conformational characteristics of the stem-loop structures. In the G1 form, the two stems form a coaxial stem, whereas in the G2 and G3 forms, the two stems are structurally independent of each other. In the case of the G1 form, the 3'-flanking nucleotides of the PolyA stem are included in the stable coaxial stem structure, which may affect the rest of the 5'-UTR structure. This result demonstrates that the local conformation of this functionally key region has an important role in the function of the 5'-UTR.
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Affiliation(s)
- Camille Michiko Obayashi
- Department of Life Science, Graduate School of Advanced Engineering, Chiba Institute of Technology, Tsudanuma, 2-17-1, Narashino-shi, Chiba, 275-0016, Japan
| | - Yoko Shinohara
- Department of Life and Environmental Sciences, Graduate School of Engineering, Chiba Institute of Technology, Tsudanuma, 2-17-1, Narashino-shi, Chiba, 275-0016, Japan
| | - Takao Masuda
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Yushima, 1-5-45, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Gota Kawai
- Department of Life Science, Graduate School of Advanced Engineering, Chiba Institute of Technology, Tsudanuma, 2-17-1, Narashino-shi, Chiba, 275-0016, Japan. .,Department of Life and Environmental Sciences, Graduate School of Engineering, Chiba Institute of Technology, Tsudanuma, 2-17-1, Narashino-shi, Chiba, 275-0016, Japan.
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18
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Shibanuma Y, Nemoto N, Yamamoto N, Sampei GI, Kawai G. Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP. J Biochem 2021; 168:223-229. [PMID: 32271910 DOI: 10.1093/jb/mvaa043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/27/2020] [Indexed: 11/13/2022] Open
Abstract
The crystal structure of an adenylate kinase from an extremophilic archaeon Aeropyrum pernix was determined in complex with full ligands, ATP-Mg2+ and AMP, at a resolution of 2.0 Å. The protein forms a trimer as found for other adenylate kinases from archaea. Interestingly, the reacting three atoms, two phosphorus and one oxygen atoms, were located almost in line, supporting the SN2 nucleophilic substitution reaction mechanism. Based on the crystal structure obtained, the reaction coordinate was estimated by the quantum mechanics calculations combined with molecular dynamics. It was found that the reaction undergoes two energy barriers; the steps for breaking the bond between the oxygen and γ-phosphorus atoms of ATP to produce a phosphoryl fragment and creating the bond between the phosphoryl fragment and the oxygen atom of the β-phosphate group of ADP. The reaction coordinate analysis also suggested the role of amino-acid residues for the catalysis of adenylate kinase.
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Affiliation(s)
- Yoshinori Shibanuma
- Graduate School of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan
| | - Naoki Nemoto
- Graduate School of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan
| | - Norifumi Yamamoto
- Graduate School of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan
| | - Gen-Ichi Sampei
- Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - Gota Kawai
- Graduate School of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan
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19
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Shibata T, Nagano K, Ueyama M, Ninomiya K, Hirose T, Nagai Y, Ishikawa K, Kawai G, Nakatani K. Small molecule targeting r(UGGAA) n disrupts RNA foci and alleviates disease phenotype in Drosophila model. Nat Commun 2021; 12:236. [PMID: 33431896 PMCID: PMC7801683 DOI: 10.1038/s41467-020-20487-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022] Open
Abstract
Synthetic small molecules modulating RNA structure and function have therapeutic potential for RNA diseases. Here we report our discovery that naphthyridine carbamate dimer (NCD) targets disease-causing r(UGGAA)n repeat RNAs in spinocerebellar ataxia type 31 (SCA31). Structural analysis of the NCD-UGGAA/UGGAA complex by nuclear magnetic resonance (NMR) spectroscopy clarifies the mode of binding that recognizes four guanines in the UGGAA/UGGAA pentad by hydrogen bonding with four naphthyridine moieties of two NCD molecules. Biological studies show that NCD disrupts naturally occurring RNA foci built on r(UGGAA)n repeat RNA known as nuclear stress bodies (nSBs) by interfering with RNA–protein interactions resulting in the suppression of nSB-mediated splicing events. Feeding NCD to larvae of the Drosophila model of SCA31 alleviates the disease phenotype induced by toxic r(UGGAA)n repeat RNA. These studies demonstrate that small molecules targeting toxic repeat RNAs are a promising chemical tool for studies on repeat expansion diseases. Synthetic small molecules modulating RNA structure and function have therapeutic potential for RNA diseases. Here the authors show the mechanism by which a small molecule targets the disease-causing r(UGGAA)n repeat RNAs in spinocerebellar ataxia type 31.
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Affiliation(s)
- Tomonori Shibata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Ibaraki, Japan
| | - Konami Nagano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Chiba, Japan
| | - Morio Ueyama
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kensuke Ninomiya
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Yoshitaka Nagai
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kinya Ishikawa
- Center for Personalized Medicine for Healthy Aging, Tokyo Medical and Dental University, Tokyo, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Chiba, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Ibaraki, Japan.
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20
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Vongsutilers V, Shinohara Y, Kawai G. Epigenetic TET-Catalyzed Oxidative Products of 5-Methylcytosine Impede Z-DNA Formation of CG Decamers. ACS Omega 2020; 5:8056-8064. [PMID: 32309715 PMCID: PMC7161056 DOI: 10.1021/acsomega.0c00120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/19/2020] [Indexed: 05/12/2023]
Abstract
Methylation of cytosine has been known to play a significant role in epigenetic regulation. 5-Methylcytosine was among the first base modification that was discovered for the capability to facilitate B/Z-DNA transition as observed in CG repeated tracks. A study on gene repression by Z-DNA prone sequence as in ADAM-12 has ignited our research interest for the Z-DNA role in epigenetics. Ten eleven translocation family proteins are responsible to catalyze 5-methylcytosine to produce oxidative products including 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine, which each may have unique function rather than the sole purpose of 5-methylcytosine clearance. Although the Z-DNA-promoting effect of 5-methylcytosine was well established, the effect of its oxidative products on Z-DNA remain unknown. In this study, the Z-DNA-promoting effect of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine on the CG decamer model were investigated along with known Z-DNA stabilizers, 5-methylcytosine and 8-oxoguanine. Experimental results from circular dichroism (CD) and NMR indicates that all oxidative products of 5-methylcytosine hinder B/Z-DNA transition as high salt concentration suitable to stabilize and convert unmodified CG decamer to Z-DNA conformation is insufficient to facilitate the B/Z-DNA transition of CG decamer containing 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxycytosine. Molecular dynamic simulation and free energy calculation by MM-PBSA are in agreement with the experimental finding that 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine destabilize Z-DNA conformation of CG decamer, in contrast to its precursor. Investigation of Z-DNA switch-on/switch-off regulated by 5-methylcytosine and its oxidative products is a further step to elucidate the potential of epigenetic regulated via Z-DNA.
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Affiliation(s)
- Vorasit Vongsutilers
- Department
of Food and Pharmaceutical Chemistry, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Yoko Shinohara
- Department
of Life and Environmental Sciences, Chiba
Institute of Technology, Chiba 275-0016, Japan
| | - Gota Kawai
- Department
of Life and Environmental Sciences, Chiba
Institute of Technology, Chiba 275-0016, Japan
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21
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Sakamoto A, Sahara J, Kawai G, Yamamoto K, Ishihama A, Uemura T, Igarashi K, Kashiwagi K, Terui Y. Cytotoxic Mechanism of Excess Polyamines Functions through Translational Repression of Specific Proteins Encoded by Polyamine Modulon. Int J Mol Sci 2020; 21:ijms21072406. [PMID: 32244348 PMCID: PMC7177335 DOI: 10.3390/ijms21072406] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/28/2020] [Accepted: 03/29/2020] [Indexed: 01/08/2023] Open
Abstract
Excessive accumulation of polyamines causes cytotoxicity, including inhibition of cell growth and a decrease in viability. We investigated the mechanism of cytotoxicity caused by spermidine accumulation under various conditions using an Escherichia coli strain deficient in spermidine acetyltransferase (SAT), a key catabolic enzyme in controlling polyamine levels. Due to the excessive accumulation of polyamines by the addition of exogenous spermidine to the growth medium, cell growth and viability were markedly decreased through translational repression of specific proteins [RMF (ribosome modulation factor) and Fis (rRNA transcription factor) etc.] encoded by members of polyamine modulon, which are essential for cell growth and viability. In particular, synthesis of proteins that have unusual locations of the Shine–Dalgarno (SD) sequence in their mRNAs was inhibited. In order to elucidate the molecular mechanism of cytotoxicity by the excessive accumulation of spermidine, the spermidine-dependent structural change of the bulged-out region in the mRNA at the initiation site of the rmf mRNA was examined using NMR analysis. It was suggested that the structure of the mRNA bulged-out region is affected by excess spermidine, so the SD sequence of the rmf mRNA cannot approach initiation codon AUG.
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Affiliation(s)
- Akihiko Sakamoto
- Faculty of Pharmacy, Chiba Institute of Science, Choshi, Chiba 288-0025, Japan
| | - Junpei Sahara
- Faculty of Advanced Engineering, Chiba Institute of Technology, Chiba 275-0016, Japan
| | - Gota Kawai
- Faculty of Advanced Engineering, Chiba Institute of Technology, Chiba 275-0016, Japan
| | - Kaneyoshi Yamamoto
- Department of Frontier Bioscience, Hosei University, Tokyo 184-8584, Japan
| | - Akira Ishihama
- Department of Frontier Bioscience, Hosei University, Tokyo 184-8584, Japan
| | - Takeshi Uemura
- Amine Pharma Research Institute, Innovation Plaza at Chiba University, Chiba 260-0856, Japan
- Graduate School of Pharmaceutical Science, Chiba University, Chiba 260-0856, Japan
| | - Kazuei Igarashi
- Amine Pharma Research Institute, Innovation Plaza at Chiba University, Chiba 260-0856, Japan
- Graduate School of Pharmaceutical Science, Chiba University, Chiba 260-0856, Japan
| | - Keiko Kashiwagi
- Faculty of Pharmacy, Chiba Institute of Science, Choshi, Chiba 288-0025, Japan
| | - Yusuke Terui
- Faculty of Pharmacy, Chiba Institute of Science, Choshi, Chiba 288-0025, Japan
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22
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Shibata H, Nemoto J, Shiba S, Yamane Y, Kawai G, Hashimoto K. Immobilization of DNA on Quartz Crystal Microbalance Sensor Modified with Self-Assembled Monolayer of Thiol Derivative. J Oleo Sci 2020; 69:271-276. [PMID: 32051359 DOI: 10.5650/jos.ess19317] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this study, we investigated the direct detection of DNA, without pretreatment, using a quartz crystal microbalance (QCM) sensor. This sensor is modified by a self-assembled monolayer of a thiol derivative that has an amino group as the terminal functional group. Contact angle values and the attenuated total reflectance Fourier transform infrared (ATR/FT-IR) spectra of the QCM sensors after immersion into an ethanol solution of thiol derivatives clearly showed that self-assembled monolayers of the derivatives were formed on the QCM sensors. Although QCM measurements using unmodified and carboxylic group-modified sensors could not detect DNA-Na salt, the sensor modified with amino groups could detect the DNA. This system can be used for the analysis of the interaction between DNA and DNAbinding proteins.
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Affiliation(s)
- Hirobumi Shibata
- Faculty of Engineering, Chiba Institute of Technology.,Photocatalysis International Research Center, Tokyo University of Science
| | - Junpei Nemoto
- Faculty of Engineering, Chiba Institute of Technology
| | - Shota Shiba
- Faculty of Engineering, Chiba Institute of Technology
| | - Yusuke Yamane
- Faculty of Engineering, Chiba Institute of Technology
| | - Gota Kawai
- Faculty of Advanced Engineering, Chiba Institute of Technology
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23
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Hatano A, Shimazaki K, Otsu M, Kawai G. Parallel motif triplex formation via a new, bi-directional hydrogen bonding pattern incorporating a synthetic cyanuryl nucleoside into the sense chain. RSC Adv 2020; 10:22766-22774. [PMID: 35514565 PMCID: PMC9054615 DOI: 10.1039/d0ra03889j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/09/2020] [Indexed: 11/21/2022] Open
Abstract
The triplex formation ability of a sense chain containing a cyanuryl nucleoside was evaluated and the tertiary structure of the triplex was calculated using the NOE in 1H NMR by incorporating a 15N into the base moiety.
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Affiliation(s)
- Akihiko Hatano
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama-City
- Japan
| | - Kei Shimazaki
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama-City
- Japan
| | - Maina Otsu
- Department of Life and Environmental Sciences
- Faculty of Engineering
- Chiba Institute of Technology
- Narashino
- Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences
- Faculty of Engineering
- Chiba Institute of Technology
- Narashino
- Japan
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24
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Slack RL, Ilina TV, Xi Z, Giacobbi NS, Kawai G, Parniak MA, Sarafianos SG, Sluis Cremer N, Ishima R. Conformational Changes in HIV-1 Reverse Transcriptase that Facilitate Its Maturation. Structure 2019; 27:1581-1593.e3. [PMID: 31471129 DOI: 10.1016/j.str.2019.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/10/2019] [Accepted: 08/09/2019] [Indexed: 01/18/2023]
Abstract
HIV-1 reverse transcriptase (RT) is translated as part of the Gag-Pol polyprotein that is proteolytically processed by HIV-1 protease (PR) to finally become a mature heterodimer, composed of a p66 and a p66-derived 51-kDa subunit, p51. Our previous work suggested that tRNALys3 binding to p66/p66 introduces conformational changes in the ribonuclease (RNH) domain of RT that facilitate efficient cleavage of p66 to p51 by PR. In this study, we characterized the conformational changes in the RNH domain of p66/p66 imparted by tRNALys3 using NMR. Moreover, the importance of tRNALys3 in RT maturation was confirmed in cellulo by modulating the levels of Lys-tRNA synthetase, which affects recruitment of tRNALys3 to the virus. We also employed nonnucleoside RT inhibitors, to modulate the p66 dimer-monomer equilibrium and monitor the resulting structural changes. Taken together, our data provide unique insights into the conformational changes in p66/p66 that drive PR cleavage.
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Affiliation(s)
- Ryan L Slack
- Department of Structural Biology, University of Pittsburgh School of Medicine, Room 1037, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Tatiana V Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, Room 1037, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Zhaoyong Xi
- Department of Structural Biology, University of Pittsburgh School of Medicine, Room 1037, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Nicholas S Giacobbi
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Gota Kawai
- Department of Life and Environmental Sciences, Chiba Institute of Technology, Chiba, Japan
| | - Michael A Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nicolas Sluis Cremer
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Room 1037, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA.
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Huang YL, Kawai G, Hasegawa A, Kannagi M, Masuda T. Impact of 5'-end nucleotide modifications of HIV-1 genomic RNA on reverse transcription. Biochem Biophys Res Commun 2019; 516:1145-1151. [PMID: 31284953 DOI: 10.1016/j.bbrc.2019.06.152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 06/27/2019] [Indexed: 11/20/2022]
Abstract
Reverse transcription of retroviral RNA is accomplished through a minus-strand strong stop cDNA (-sscDNA) synthesis and subsequent strand-transfer reactions. We have previously reported a critical role of guanosine (G) number at 5'-terminal of HIV-1 RNA for successful strand-transfer of -sscDNA. In this study, role(s) of the cap consisting of 7-methyl guanosine (7mG), a hallmark of transcripts generated by RNA polymerase II, at the 5'-end G nucleotide (5'-G) of HIV-1 RNA were examined. In parallel, contribution of highly conserved GGG tract located at the U3/R boundary in 3' terminal region of viral RNA (3'-GGG tract) was also addressed. The in vitro reverse transcription analysis using synthetic HIV-1 RNAs possessing the 5'-G with cap or triphosphate form demonstrated that the 5'-cap significantly increased strand-transfer efficiency of -sscDNA. Meanwhile, effect of the 5'-cap on the strand-transfer was retained in the reaction using mutant HIV-1 RNAs in which two Gs were deleted from the 3'-GGG tract. Lack of apparent contribution of the 3'-GGG tract during strand-transfer events in vitro was reproduced in the context of HIV-1 replication within cells. Instead, we noticed that the 3'-GGG tract might be required for efficient gene expression from proviral DNA. These results indicated that 7mG of the cap on HIV-1 RNA might not be reverse-transcribed and a possible role of the 3'-GGG tract to accept the non-template nucleotide addition during -sscDNA synthesis might be less likely. The 5'-G modifications of HIV-1 RNAs by the cap- or phosphate-removal enzyme revealed that the cap or monophosphate form of the 5'-G was preferred for the 1st strand-transfer compared to the triphosphate or non-phosphate form. Taken together, a status of the 5'-G determined strand-transfer efficiency of -sscDNA without affecting the non-template nucleotide addition, probably by affecting association of the 5'-G with 3'-end region of viral RNA.
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Affiliation(s)
- Yu-Lun Huang
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Yushima, 1-5-45, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Gota Kawai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba, 275-0016, Japan
| | - Atsuhiko Hasegawa
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Yushima, 1-5-45, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Mari Kannagi
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Yushima, 1-5-45, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Takao Masuda
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Yushima, 1-5-45, Bunkyo-ku, Tokyo, 113-8519, Japan.
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26
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Ogawa A, Sampei GI, Kawai G. Crystal structure of the flavin-dependent thymidylate synthase Thy1 from Thermus thermophilus with an extra C-terminal domain. Acta Crystallogr F Struct Biol Commun 2019; 75:450-454. [PMID: 31204692 DOI: 10.1107/s2053230x19007192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/17/2019] [Indexed: 11/10/2022]
Abstract
The thymidylate synthases ThyA and Thy1 are enzymes that catalyse the formation of thymidine monophosphate from 2'-deoxyuridine monophosphate. Thy1 (or ThyX) requires flavin for catalytic reactions, while ThyA does not. In the present study, the crystal structure of the flavin-dependent thymidylate synthase Thy1 from Thermus thermophilus HB8 (TtThy1, TTHA1096) was determined in complex with FAD and phosphate at 2.5 Å resolution. TtThy1 is a tetrameric molecule like other Thy1 proteins, to which four FAD molecules are bound. In the crystal of TtThy1, two phosphate ions were bound to each dUMP-binding site. The characteristic feature of TtThy1 is the existence of an extra C-terminal domain (CTD) consisting of three α-helices and a β-strand. The function of the CTD is unknown and database analysis showed that this CTD is only shared by part of the Deinococcus-Thermus phylum.
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Affiliation(s)
- Aoba Ogawa
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Narashino, Chiba 275-0016, 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
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Narashino, Chiba 275-0016, Japan
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27
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Otabe T, Nagano K, Kawai G, Murata A, Nakatani K. Inhibition of pre-miRNA-136 processing by Dicer with small molecule BzDANP suggested the formation of ternary complex of pre-miR-136–BzDANP–Dicer. Bioorg Med Chem 2019; 27:2140-2148. [DOI: 10.1016/j.bmc.2019.03.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/04/2019] [Accepted: 03/16/2019] [Indexed: 11/27/2022]
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Otsu M, Kawai G. Distinct RNA recognition mechanisms in closely related LINEs from zebrafish. Nucleosides Nucleotides Nucleic Acids 2019; 38:294-304. [PMID: 30942141 DOI: 10.1080/15257770.2018.1527348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Long interspersed nuclear element (LINE) is known to be transposed by the reverse transcription using its RNA transcript. Recognition of the 3' stem-loop of LINE RNA by its reverse transcriptase (RT) is an important step of the retrotransposition. We focused on the RNA recognition by RT from two related LINEs, ZfL2-1 and ZfL2-2, from zebrafish. Previous study showed that RT from ZfL2-2 recognizes a single residue in the specific position of the RNA loop. In the present study, it was found that RT from ZfL2-1 recognizes the inserted stem-loop of ZfL2-1 RNA. Thus, these related RTs recognize the same region of LINE RNAs but discriminate them by different mechanism.
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Affiliation(s)
- Maina Otsu
- a Department of Life and Environmental Sciences, Faculty of Engineering , Chiba Institute of Technology , Narashino , Japan
| | - Gota Kawai
- a Department of Life and Environmental Sciences, Faculty of Engineering , Chiba Institute of Technology , Narashino , Japan
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29
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Hatano A, Terado N, Kanno Y, Nakamura T, Kawai G. Synthesis of a protected ribonucleoside phosphoramidite-linked spin label via an alkynyl chain at the 5′ position of uridine. SYNTHETIC COMMUN 2019. [DOI: 10.1080/00397911.2018.1545033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Akihiko Hatano
- Department of Chemistry, Faculty of Engineering , Shibaura Institute of Technology , Saitama , Japan
| | - Nanae Terado
- Department of Chemistry, Faculty of Engineering , Shibaura Institute of Technology , Saitama , Japan
| | - Yuichi Kanno
- Department of Chemistry, Faculty of Engineering , Shibaura Institute of Technology , Saitama , Japan
| | - Toshikazu Nakamura
- Department of Materials Molecular Science, Institute for Molecular Science , Okazaki , Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , Chiba , Japan
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30
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Vongsutilers V, Sawaspaiboontawee K, Tuesuwan B, Shinohara Y, Kawai G. 5-Methylcytosine containing CG decamer as Z-DNA embedded sequence for a potential Z-DNA binding protein probe. Nucleosides Nucleotides Nucleic Acids 2018; 37:485-497. [PMID: 30188765 DOI: 10.1080/15257770.2018.1498512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Attempting to elucidate biological significance of the left-handed Z-DNA is a research challenge due to Z-DNA potential role in many diseases. Discovery of Z-DNA binding proteins has ignited the interest in search for Z-DNA functions. Biosensor with Z-DNA forming probe can be useful to study the interaction between Z-DNA conformation and Z-DNA binding proteins. In this study, 5-methylcytosine (mC) containing CG decamers were characterized for their suitability to form Z-DNA and to be used in Z-DNA forming probe. The 5'-thiol oligonucleotide embedded with 5'-mCGmCGmCGmCGm CG-3' was designed and developed as a potential Z-DNA forming probe for Z-DNA binding protein screening.
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Affiliation(s)
- Vorasit Vongsutilers
- a Department of Food and Pharmaceutical Chemistry , Chulalongkorn University , Bangkok , Thailand.,b Medicinal and Analytical Pharmaceutical Chemistry Research Unit , Chulalongkorn University Drug and Health Product Innovation Promotion Center , Bangkok , Thailand
| | - Kulwadee Sawaspaiboontawee
- a Department of Food and Pharmaceutical Chemistry , Chulalongkorn University , Bangkok , Thailand.,b Medicinal and Analytical Pharmaceutical Chemistry Research Unit , Chulalongkorn University Drug and Health Product Innovation Promotion Center , Bangkok , Thailand
| | - Bodin Tuesuwan
- a Department of Food and Pharmaceutical Chemistry , Chulalongkorn University , Bangkok , Thailand.,b Medicinal and Analytical Pharmaceutical Chemistry Research Unit , Chulalongkorn University Drug and Health Product Innovation Promotion Center , Bangkok , Thailand
| | - Yoko Shinohara
- c Department of Life and Environmental Sciences , Chiba Institute of Technology , Chiba , Japan
| | - Gota Kawai
- c Department of Life and Environmental Sciences , Chiba Institute of Technology , Chiba , Japan
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Otsu M, Kajikawa M, Okada N, Kawai G. Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish. J Biochem 2017; 162:279-285. [PMID: 28431120 DOI: 10.1093/jb/mvx026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 03/23/2017] [Indexed: 11/14/2022] Open
Abstract
Long interspersed nuclear element (LINE) is known to be transposed by reverse transcription using its RNA transcript. Recognition of the 3' stem-loop of LINE RNA by its reverse transcriptase (RT) is an important step of the retrotransposition. Our previous study revealed that the second G residue (G8) in the GGAUA loop of a 17mer LINE RNA from eel, UnaL2-17, is recognized by its RT and the U residue (U10) in the same loop is required to maintain the loop structure (Baba S, Kajikawa M, Okada N, Kawai G. Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2. RNA 2004;10:1380-1387). ZfL2-2, a LINE from zebrafish, has the same 3' stem-loop with UnaL2 and ZfL2-1 has similar but distinct 3' stem-loop with an insertion which can form an additional stem-loop. Here, we determined the solution structure of the 34mer RT recognition site of the LINE RNA (ZfL2-1-34). It was found that ZfL2-1-34 forms a hairpin with an internal loop, the tertiary structure of which is superimposed with that of ZfL2-2. It is noted that A10 and the inserted stem-loop, starting with A12, in ZfL2-1-34 located at the positions corresponding to those of G8 and U10, respectively, in UnaL2-17. These results strongly suggest that the two LINEs share the similar recognition mechanism and the A10 in ZfL2-1-34 is the determinant recognized by its RT.
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Affiliation(s)
- Maina Otsu
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Masaki Kajikawa
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-15 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Norihiro Okada
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-15 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.,Foundation for Advancement of International Science, Tsukuba 305-0821, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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Oguro A, Yanagida A, Fujieda Y, Amano R, Otsu M, Sakamoto T, Kawai G, Matsufuji S. Two stems with different characteristics and an internal loop in an RNA aptamer contribute to spermine-binding. J Biochem 2017; 161:197-206. [PMID: 28173167 DOI: 10.1093/jb/mvw062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 08/30/2016] [Indexed: 11/14/2022] Open
Abstract
Though polyamines (putrescine, spermidine, and spermine) bind to the specific position in RNA molecules, interaction mechanisms are poorly understood. SELEX procedure has been used to isolate high-affinity oligoribonucleotides (aptamers) from randomized RNA libraries. Selected aptamers are useful in exploring sequences and/or structures in RNAs for binding molecules. In this study, to analyze the interaction mechanism of polyamine to RNA, we selected RNA aptamers targeted for spermine. Two spermine-binding aptamers (#5 and #24) were obtained and both of them had two stem-loop structures. The 3′ stem-loop of #5 (SL_2) bound to spermine more effectively than the 5′ stem-loop of #5 did. A thermodynamic analysis by an isothermal titration calorimetry revealed that the dissociation constant of SL_2 for spermine was 27.2 μM and binding ratio was nearly 1:1. Binding assay with base-pair replaced variants showed that two stem regions and an internal loop in SL_2 were important for their spermine-binding activities. NMR analyses proposed that a terminal-side and a loop-side stem in SL_2 take a loose and a stable structure, respectively and a conformational change of SL_2 is induced by spermine. It is conclusive that two stems with different characteristics and an internal loop in SL_2 contribute to the specific spermine-binding.
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Affiliation(s)
- Akihiro Oguro
- Department of Molecular Biology, The Jikei University School of Medicine, 3-25-8 Nishi-Shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Asumi Yanagida
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Yuta Fujieda
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Ryo Amano
- 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
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Senya Matsufuji
- Department of Molecular Biology, The Jikei University School of Medicine, 3-25-8 Nishi-Shinbashi, Minato-ku, Tokyo 105-8461, Japan
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Amano R, Aoki K, Miyakawa S, Nakamura Y, Kozu T, Kawai G, Sakamoto T. NMR monitoring of the SELEX process to confirm enrichment of structured RNA. Sci Rep 2017; 7:283. [PMID: 28325909 PMCID: PMC5428055 DOI: 10.1038/s41598-017-00273-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/15/2017] [Indexed: 01/20/2023] Open
Abstract
RNA aptamers are RNA molecules that bind to a target molecule with high affinity and specificity using uniquely-folded tertiary structures. RNA aptamers are selected from an RNA pool typically comprising up to 1015 different sequences generated by iterative steps of selection and amplification known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Over several rounds of SELEX, the diversity of the RNA pool decreases and the aptamers are enriched. Hence, monitoring of the enrichment of these RNA pools is critical for the successful selection of aptamers, and several methods for monitoring them have been developed. In this study, we measured one-dimensional imino proton NMR spectra of RNA pools during SELEX. The spectrum of the initial RNA pool indicates that the RNAs adopt tertiary structures. The structural diversity of the RNA pools was shown to depend highly on the design of the primer-binding sequence. Furthermore, we demonstrate that enrichment of RNA aptamers can be monitored using NMR. The RNA pools can be recovered from the NMR tube after measurement of NMR spectra. We also can monitor target binding in the NMR tubes. Thus, we propose using NMR to monitor the enrichment of structured aptamers during the SELEX process.
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Affiliation(s)
- Ryo Amano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan
| | - Kazuteru Aoki
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - Shin Miyakawa
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - Yoshikazu Nakamura
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan.
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Amano R, Takada K, Tanaka Y, Nakamura Y, Kawai G, Kozu T, Sakamoto T. Kinetic and Thermodynamic Analyses of Interaction between a High-Affinity RNA Aptamer and Its Target Protein. Biochemistry 2016; 55:6221-6229. [PMID: 27766833 DOI: 10.1021/acs.biochem.6b00748] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AML1 (RUNX1) protein is an essential transcription factor involved in the development of hematopoietic cells. Several genetic aberrations that disrupt the function of AML1 have been frequently observed in human leukemia. AML1 contains a DNA-binding domain known as the Runt domain (RD), which recognizes the RD-binding double-stranded DNA element of target genes. In this study, we identified high-affinity RNA aptamers that bind to RD by systematic evolution of ligands by exponential enrichment. The binding assay using surface plasmon resonance indicated that a shortened aptamer retained the ability to bind to RD when 1 M potassium acetate was used. A thermodynamic study using isothermal titration calorimetry (ITC) showed that the aptamer-RD interaction is driven by a large enthalpy change, and its unfavorable entropy change is compensated by a favorable enthalpy change. Furthermore, the binding heat capacity change was identified from the ITC data at various temperatures. The aptamer binding showed a large negative heat capacity change, which suggests that a large apolar surface is buried upon such binding. Thus, we proposed that the aptamer binds to RD with long-range electrostatic force in the early stage of the association and then changes its conformation and recognizes a large surface area of RD. These findings about the biophysics of aptamer binding should be useful for understanding the mechanism of RNA-protein interaction and optimizing and modifying RNA aptamers.
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Affiliation(s)
- Ryo Amano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Kenta Takada
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Yoichiro Tanaka
- Facility for RI Research and Education, Instrumental Analysis Center, Yokohama National University , 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Yoshikazu Nakamura
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo , Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Ribomic Inc. , 3-16-13 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology , Saitama Cancer Center, Ina, Saitama 362-0806, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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Kanazawa H, Hoque MM, Tsunoda M, Suzuki K, Yamamoto T, Kawai G, Kondo J, Takénaka A. Structural insights into the catalytic reaction trigger and inhibition of D-3-hydroxybutyrate dehydrogenase. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316096546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Watanabe Y, Yanai H, Kanagawa M, Suzuki S, Tamura S, Okada K, Baba S, Kumasaka T, Agari Y, Chen L, Fu ZQ, Chrzas J, Wang BC, Nakagawa N, Ebihara A, Masui R, Kuramitsu S, Yokoyama S, Sampei GI, Kawai G. Crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii. Acta Crystallogr F Struct Biol Commun 2016; 72:627-35. [PMID: 27487927 DOI: 10.1107/s2053230x1600978x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/16/2016] [Indexed: 11/10/2022]
Abstract
The crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii were determined and their structural characteristics were analyzed. For PurS from T. thermophilus, two structures were determined using two crystals that were grown in different conditions. The four structures in the dimeric form were almost identical to one another despite their relatively low sequence identities. This is also true for all PurS structures determined to date. A few residues were conserved among PurSs and these are located at the interaction site with PurL and PurQ, the other subunits of the formylglycinamide ribonucleotide amidotransferase. Molecular-dynamics simulations of the PurS dimer as well as a model of the complex of the PurS dimer, PurL and PurQ suggest that PurS plays some role in the catalysis of the enzyme by its bending motion.
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Affiliation(s)
- Yuzo Watanabe
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Hisaaki Yanai
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Mayumi Kanagawa
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Sakiko Suzuki
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Satoko Tamura
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Kiyoshi Okada
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - Seiki Baba
- Structural Biology Group, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Takashi Kumasaka
- Structural Biology Group, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yoshihiro Agari
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Lirong Chen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Zheng Qing Fu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - John Chrzas
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Bi Cheng Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Noriko Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Akio Ebihara
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Ryoji Masui
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Seiki Kuramitsu
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Shigeyuki Yokoyama
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Gen Ichi Sampei
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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Kanazawa H, Hoque MM, Tsunoda M, Suzuki K, Yamamoto T, Kawai G, Kondo J, Takénaka A. Structural insights into the catalytic reaction trigger and inhibition of D-3-hydroxybutyrate dehydrogenase. Acta Crystallogr F Struct Biol Commun 2016; 72:507-15. [PMID: 27380367 PMCID: PMC4933000 DOI: 10.1107/s2053230x16007767] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/11/2016] [Indexed: 11/10/2022] Open
Abstract
D-3-Hydroxybutyrate dehydrogenase catalyzes the reversible conversion of acetoacetate and D-3-hydroxybutyrate. These ketone bodies are both energy-storage forms of acetyl-CoA. In order to clarify the structural mechanisms of the catalytic reaction with the cognate substrate D-3-hydroxybutyrate and of the inhibition of the reaction by inhibitors, the enzyme from Alcaligenes faecalis has been analyzed by X-ray crystallography in liganded states with the substrate and with two types of inhibitor: malonate and methylmalonate. In each subunit of the tetrameric enzyme, the substrate is trapped on the nicotinamide plane of the bound NAD(+). An OMIT map definitively shows that the bound ligand is D-3-hydroxybutyrate and not acetoacetate. The two carboxylate O atoms form four hydrogen bonds to four conserved amino-acid residues. The methyl group is accommodated in the nearby hydrophobic pocket so that the formation of a hydrogen bond from the OH group of the substrate to the hydroxy group of Tyr155 at the active centre is facilitated. In this geometry, the H atom attached to the C(3) atom of the substrate in the sp(3) configuration is positioned at a distance of 3.1 Å from the nicotinamide C(4) atom in the direction normal to the plane. In addition, the donor-acceptor relationship of the hydrogen bonds suggests that the Tyr155 OH group is allowed to ionize by the two donations from the Ser142 OH group and the ribose OH group. A comparison of the protein structures with and without ligands indicates that the Gln196 residue of the small movable domain participates in the formation of additional hydrogen bonds. It is likely that this situation can facilitate H-atom movements as the trigger of the catalytic reaction. In the complexes with inhibitors, however, their principal carboxylate groups interact with the enzyme in a similar way, while the interactions of other groups are changed. The crucial determinant for inhibition is that the inhibitors have no active H atom at C(3). A second determinant is the Tyr155 OH group, which is perturbed by the inhibitors to donate its H atom for hydrogen-bond formation, losing its nucleophilicity.
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Affiliation(s)
- Hiroki Kanazawa
- Department of Materials and Life Sciences, Sophia University, Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan
- Faculty of Pharmacy, Iwaki Meisei University, Chuodai-iino, Iwaki 970-8551, Japan
| | - Md. Mominul Hoque
- Faculty of Pharmacy, Iwaki Meisei University, Chuodai-iino, Iwaki 970-8551, Japan
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Masaru Tsunoda
- Faculty of Pharmacy, Iwaki Meisei University, Chuodai-iino, Iwaki 970-8551, Japan
| | - Kaoru Suzuki
- Faculty of Pharmacy, Iwaki Meisei University, Chuodai-iino, Iwaki 970-8551, Japan
| | - Tamotsu Yamamoto
- Asahi Kasei Pharma Corporation, Tagata-gun, Shizuoka 410-2323, Japan
| | - Gota Kawai
- Research Institute, Chiba Institute of Technology, Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Jiro Kondo
- Department of Materials and Life Sciences, Sophia University, Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - Akio Takénaka
- Faculty of Pharmacy, Iwaki Meisei University, Chuodai-iino, Iwaki 970-8551, Japan
- Research Institute, Chiba Institute of Technology, Tsudanuma, Narashino, Chiba 275-0016, 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Kanagawa M, Baba S, Watanabe Y, Nakagawa N, Ebihara A, Kuramitsu S, Yokoyama S, Sampei GI, Kawai G. Crystal structures and ligand binding of PurM proteins from Thermus thermophilus and Geobacillus kaustophilus. J Biochem 2015; 159:313-21. [PMID: 26515187 DOI: 10.1093/jb/mvv107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 09/08/2015] [Indexed: 11/13/2022] Open
Abstract
Crystal structures of 5-aminoimidazole ribonucleotide (AIR) synthetase, also known as PurM, from Thermus thermophilus (Tt) and Geobacillus kaustophilus (Gk) were determined. For TtPurM, the maximum resolution was 2.2 Å and the space group was P21212 with four dimers in an asymmetric unit. For GkPurM, the maximum resolution was 2.2 Å and the space group was P21212 with one monomer in asymmetric unit. The biological unit is dimer for both TtPurM and GkPurM and the dimer structures were similar to previously determined structures of PurM in general. For TtPurM, ∼50 residues at the amino terminal were disordered in the crystal structure whereas, for GkPurM, the corresponding region covered the ATP-binding site forming an α helix in part, suggesting that the N-terminal region of PurM changes its conformation upon binding of ligands. FGAM binding site was predicted by the docking simulation followed by the MD simulation based on the SO4 (2-) binding site found in the crystal structure of TtPurM.
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Affiliation(s)
- Mayumi Kanagawa
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan
| | - Seiki Baba
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan; Structural Biology Group, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5198, Japan
| | - Yuzo Watanabe
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Noriko Nakagawa
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan; Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan; and
| | - Akio Ebihara
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan
| | - Seiki Kuramitsu
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan; and
| | - Shigeyuki Yokoyama
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan
| | - Gen-Ichi Sampei
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan; Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - Gota Kawai
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan; Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan;
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Kiyosawa H, Okumura A, Okui S, Ushida C, Kawai G. Secondary structure-based analysis of mouse brain small RNA sequences obtained by using next-generation sequencing. Genomics 2015; 106:122-8. [DOI: 10.1016/j.ygeno.2015.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/05/2015] [Accepted: 05/13/2015] [Indexed: 01/21/2023]
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Abstract
A simple method for rapid structure screening for RNA by NMR is proposed. Target RNA is transcribed in a NMR tube and its spectra are measured without purification. The proposed method, in NMR tube transcription or INTT, was applied for three RNAs for which NMR spectra have been measured by using the conventionally purified samples. By the real-time measuring, increase of imino proton signals and decrease of NTP signals can be observed. It was confirmed that INTT spectra are in general similar to those obtained by the conventional method. INTT can be used for the first-step screening of RNA folding.
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Affiliation(s)
- Saya Okui
- a Department of Life and Environmental Sciences, Faculty of Engineering , Chiba Institute of Technology , Narashino , Chiba , Japan
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Zhang F, Hoque MM, Jiang J, Suzuki K, Tsunoda M, Takeda Y, Ito Y, Kawai G, Tanaka H, Takénaka A. The characteristic structure of anti-HIV actinohivin in complex with three HMTG D1 chains of HIV-gp120. Chembiochem 2014; 15:2766-73. [PMID: 25403811 DOI: 10.1002/cbic.201402352] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 12/19/2022]
Abstract
The anti-HIV lectin actinohivin (AH) specifically interacts with HMTG (high-mannose-type glycan), which is attached to the glycoprotein gp120 of HIV-1 in a process in which the three branched mannotriose chains (D1, D2, and D3) of HMTG exhibit different binding affinities, it being estimated that that of D1 is the strongest, that of D3 is weaker, and that of D2 is undetectable. These properties have been ascribed to the stereochemical differences in linkages between the second and the third mannose residues of the three chains. In order to clarify the interaction geometry between AH and the major target D1, an X-ray determination of the crystal structure of AH in complex with D1-which is α(1,2)mannotriose composed of three mannose (Man) residues linked together only by α(1,2) bonding-has been performed. In each of the three D1-binding pockets of AH, two Man residues of D1 are accommodated at zones 1 and 2 in the pocket, in the same way as those found in the α(1,2)mannobiose-bound AH crystals. However, an OMIT map shows poor densities at both ends of the two residues. This suggests the existence of positional disorder of D1 in the pocket: the two zones are each occupied by two Man residues in two different modes, with mode A involving the Man1 and Man2 residues and mode B the Man2 and Man3 residues. In each mode, D1 is stabilized by adopting a double-bracket-shaped conformation through CH⋅⋅⋅O interactions. In mode B, however, the Man1 residue, which is the most sensitive residue to AH binding, protrudes wholly into the solvent region without contacts with AH. In mode A, in contrast, the Man3 residue interacts with the essential hydrophobic amino acid residues (Tyr and Leu conserved between the three pockets) of AH. Therefore, mode A is likely to be the one that occurs when whole HMTG is bound. In this mode, the two hydroxy groups (O3 and O4) of the Man2 residue are anchored in zone 2 by four hydrogen bonds with Asp, Asn, and Tyr residues of AH. In addition, it has been found that an isolated water molecule buried in the hydrophobic long loop bridges between Asp of AH and the hydroxy group of Man2 through hydrogen bonds. The most interesting feature is found in the interaction of the Man1 and Man3 residues with AH. All eight hydroxy groups of the two residues are completely exposed in the solvent region, whereas their hydrophobic parts make contacts with a Leu residue and two Tyr residues so that the shape of D1 and the surface of AH fit well over a wide area. These structural characteristics are potentially useful for development of AH to produce more effective antiretroviral drugs to suppress the infectious expansion of HIV/AIDS and to help expedite an end to the HIV/AIDS pandemic in the near future.
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Affiliation(s)
- Fang Zhang
- Graduate School of Science and Engineering, Iwaki-Meisei University, Iwaki 970-8551 (Japan)
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Dawson W, Takai T, Ito N, Shimizu K, Kawai G. A new entropy model for RNA: part III. Is the folding free energy landscape of RNA funnel shaped? ACTA ACUST UNITED AC 2014. [DOI: 10.4081/jnai.2014.2652] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The concept of a free energy (FE) landscape, in which the conformations of a polymer progressively take on the structure of the native state while spiraling down a FE surface that resembles the shape of a funnel, has long been viewed as the reason why a complex protein structure forms so rapidly compared to the number of conformations available to it. On the other hand, this landscape picture is less clear with RNA due to the multiplicity of conformations and the uncertainties in the current thermodynamics. It is therefore sometimes proposed that within the ensemble of suboptimal states of the RNA molecule, the vast majority of those states all closely resemble the native state and therefore simply overwhelm the few states that represent the global minimum FE. However, calculations of the free energy of observed structures often suggest that the most frequently observed cluster of structures are far from the minimum FE, particularly in the case of long sequences. If so, then such a FE surface is unlikely to be funnel shaped. We have been developing a version of <em>vsfold</em> that can evaluate the suboptimal structures of the FE surface (through a modified version called <em>vs_subopt</em>). Here we show that the ensemble of suboptimal structures for a number of known RNA structures can actually be both close to the minimum FE and also be the dominant observed structure when a proper Kuhn length is selected. Two state aptamers known as riboswitches can show neighboring FE states in the suboptimal structures that match the observed structures and their relative difference in FE is well within the range of the binding free energy of the metabolite. For the riboswitches and other short RNA sequences (less than 250 nt), the flow of the suboptimal structures (including pseudoknots) tended to resemble a rock rolling down a hill along the reaction coordinate axis. An important insight yielded by the cross-linking entropy (CLE) model is that the global entropy limits the size of domains. Hence, based on the CLE model, Levinthal’s paradox is overcome by the funnel shape in the FE, by a reduction in the number of degrees of freedom due to Kuhn length, and by limits on the size of the domains that can form. These concepts are also applicable to calculating transition rates between different suboptimal structures.
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Hashi Y, Kawai G, Kotani S. Microtubule-associated protein (MAP) 4 interacts with microtubules in an intrinsically disordered manner. Biosci Biotechnol Biochem 2014; 78:1864-70. [DOI: 10.1080/09168451.2014.940836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
We previously used nuclear magnetic resonance (NMR) to analyze the structure of a synthetic tricosapeptide corresponding to an active site of microtubule-associated protein 4 (MAP4). To further the structural analysis, we have constructed a minimal active domain fragment of MAP4, encompassing the entire active site, and obtained its NMR spectra. The secondary structure prediction using partially assigned NMR data suggested that the fragment is largely unfolded. Two other independent techniques also demonstrated its unfolded nature, indicating that MAP4 belongs to the class of intrinsically disordered proteins (IDPs). The NMR spectra of the fragment-microtubule mixture revealed that the fragment binds to the microtubule using multiple binding sites, apparently contradicting our previous quantitative studies. Given that MAP4 is intrinsically disordered, we propose a mechanism in which any one of the binding sites is active at a time, which is one of the typical interaction mechanisms proposed for IDPs.
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Affiliation(s)
- Yurika Hashi
- Faculty of Science, Department of Biological Sciences, Kanagawa University, Hiratsuka, Japan
| | - Gota Kawai
- Faculty of Engineering, Department of Life and Environmental Sciences, Chiba Institute of Technology, Narashino, Japan
| | - Susumu Kotani
- Faculty of Science, Department of Biological Sciences, Kanagawa University, Hiratsuka, Japan
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Shibata H, Shinozaki R, Ogura T, Sakai H, Abe M, Kawai G, Hashimoto K. Fabrication and BSA adsorption/desorption properties of titania/silica composite films modified with silane coupling agents. J Oleo Sci 2014; 63:1077-83. [PMID: 25213446 DOI: 10.5650/jos.ess14102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this study, we successfully prepared titania/silica composite films modified with silane coupling agents having amino groups and investigated their bovine serum albumin (BSA) adsorption/desorption behavior under light irradiation. XRD patterns and ATR/FT-IR spectra of the films revealed the formation of titania/silica composite films modified with silane coupling agents. In these films, the adsorption and desorption of BSA could be controlled by light irradiation, through the locally photoinduced superhydrophilic titania surface.
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Affiliation(s)
- Hirobumi Shibata
- Department of Life and Environmental Sciences, Chiba Institute of Technology
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47
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Sampei GI, Kanagawa M, Baba S, Shimasaki T, Taka H, Mitsui S, Fujiwara S, Yanagida Y, Kusano M, Suzuki S, Terao K, Kawai H, Fukai Y, Nakagawa N, Ebihara A, Kuramitsu S, Yokoyama S, Kawai G. Structures and reaction mechanisms of the two related enzymes, PurN and PurU. ACTA ACUST UNITED AC 2013; 154:569-79. [DOI: 10.1093/jb/mvt090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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48
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Nomura Y, Tanaka Y, Fukunaga JI, Fujiwara K, Chiba M, Iibuchi H, Tanaka T, Nakamura Y, Kawai G, Kozu T, Sakamoto T. Solution structure of a DNA mimicking motif of an RNA aptamer against transcription factor AML1 Runt domain. J Biochem 2013; 154:513-9. [PMID: 23997091 DOI: 10.1093/jb/mvt082] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
AML1/RUNX1 is an essential transcription factor involved in the differentiation of hematopoietic cells. AML1 binds to the Runt-binding double-stranded DNA element (RDE) of target genes through its N-terminal Runt domain. In a previous study, we obtained RNA aptamers against the AML1 Runt domain by systematic evolution of ligands by exponential enrichment and revealed that RNA aptamers exhibit higher affinity for the Runt domain than that for RDE and possess the 5'-GCGMGNN-3' and 5'-N'N'CCAC-3' conserved motif (M: A or C; N and N' form Watson-Crick base pairs) that is important for Runt domain binding. In this study, to understand the structural basis of recognition of the Runt domain by the aptamer motif, the solution structure of a 22-mer RNA was determined using nuclear magnetic resonance. The motif contains the AH(+)-C mismatch and base triple and adopts an unusual backbone structure. Structural analysis of the aptamer motif indicated that the aptamer binds to the Runt domain by mimicking the RDE sequence and structure. Our data should enhance the understanding of the structural basis of DNA mimicry by RNA molecules.
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Affiliation(s)
- Yusuke Nomura
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016; CREST, Japan Science and Technology Agency, Saitama 332-0012; Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601; Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama 362-0806; and Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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Fukunaga J, Nomura Y, Tanaka Y, Amano R, Tanaka T, Nakamura Y, Kawai G, Sakamoto T, Kozu T. The Runt domain of AML1 (RUNX1) binds a sequence-conserved RNA motif that mimics a DNA element. RNA 2013; 19:927-936. [PMID: 23709277 PMCID: PMC3683927 DOI: 10.1261/rna.037879.112] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/28/2013] [Indexed: 06/02/2023]
Abstract
AML1 (RUNX1) is a key transcription factor for hematopoiesis that binds to the Runt-binding double-stranded DNA element (RDE) of target genes through its N-terminal Runt domain. Aberrations in the AML1 gene are frequently found in human leukemia. To better understand AML1 and its potential utility for diagnosis and therapy, we obtained RNA aptamers that bind specifically to the AML1 Runt domain. Enzymatic probing and NMR analyses revealed that Apt1-S, which is a truncated variant of one of the aptamers, has a CACG tetraloop and two stem regions separated by an internal loop. All the isolated aptamers were found to contain the conserved sequence motif 5'-NNCCAC-3' and 5'-GCGMGN'N'-3' (M:A or C; N and N' form Watson-Crick base pairs). The motif contains one AC mismatch and one base bulged out. Mutational analysis of Apt1-S showed that three guanines of the motif are important for Runt binding as are the three guanines of RDE, which are directly recognized by three arginine residues of the Runt domain. Mutational analyses of the Runt domain revealed that the amino acid residues used for Apt1-S binding were similar to those used for RDE binding. Furthermore, the aptamer competed with RDE for binding to the Runt domain in vitro. These results demonstrated that the Runt domain of the AML1 protein binds to the motif of the aptamer that mimics DNA. Our findings should provide new insights into RNA function and utility in both basic and applied sciences.
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Affiliation(s)
- Junichi Fukunaga
- Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama 362-0806, Japan
- CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Yusuke Nomura
- CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Yoichiro Tanaka
- Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama 362-0806, Japan
- CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
- Facility for RI Research and Education, Instrumental Analysis Center, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Ryo Amano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Taku Tanaka
- CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Yoshikazu Nakamura
- CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Taiichi Sakamoto
- CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama 362-0806, Japan
- CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
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Dawson W, Yamamoto K, Shimizu K, Kawai G. A new entropy model for RNA: part II. Persistence-related entropic contributions to RNA secondary structure free energy calculations. ACTA ACUST UNITED AC 2013. [DOI: 10.4081/jnai.2013.2651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In previous work, we have shown that the entropy of a folded RNA molecule can be divided into local and global contributions using the cross-linking entropy (CLE) model, where, in the case of RNA, the cross- links are the base-pair stacking interactions. The local contribution to the CLE is revealed in the Kuhn length (a measure of the stiffness of the RNA). The Kuhn length acts as a scaling parameter. When the size of the system is rescaled, the relationship between local and global free energy must be renormalized to reflect this rescaling. In this renormalization process, the Kuhn length increases, the local entropy also increases due to freezing out of the local conformational degrees of freedom. At the same time, as the number of degrees of freedom decrease, there is a significant reduction in the global entropy. Here we present a method, based on the concepts of renormalization theory, to quantitatively estimate the size of the contribution from the local entropy as a function of the Kuhn length. The local entropy correction is used to predict the current empirically derived constant in the Jacobson-Stockmayer equation. The variation in the Kuhn length is shown to be largely influenced by the length of the double-stranded RNA stems formed in the secondary structure of folded RNA. This result is used to test the resulting entropy under a variable Kuhn length in stem-loop structures. Comparisons between a variable Kuhn length and a static Kuhn length on a short stem-loop of RNA are also examined. The model is quite general and is also directly applicable to protein structure and folding problems.
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