1
|
Morishita EC. Discovery of RNA-targeted small molecules through the merging of experimental and computational technologies. Expert Opin Drug Discov 2023; 18:207-226. [PMID: 36322542 DOI: 10.1080/17460441.2022.2134852] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The field of RNA-targeted small molecules is rapidly evolving, owing to the advances in experimental and computational technologies. With the identification of several bioactive small molecules that target RNA, including the FDA-approved risdiplam, the biopharmaceutical industry is gaining confidence in the field. This review, based on the literature obtained from PubMed, aims to disseminate information about the various technologies developed for targeting RNA with small molecules and propose areas for improvement to develop drugs more efficiently, particularly those linked to diseases with unmet medical needs. AREAS COVERED The technologies for the identification of RNA targets, screening of chemical libraries against RNA, assessing the bioactivity and target engagement of the hit compounds, structure determination, and hit-to-lead optimization are reviewed. Along with the description of the technologies, their strengths, limitations, and examples of how they can impact drug discovery are provided. EXPERT OPINION Many existing technologies employed for protein targets have been repurposed for use in the discovery of RNA-targeted small molecules. In addition, technologies tailored for RNA targets have been developed. Nevertheless, more improvements are necessary, such as artificial intelligence to dissect important RNA structures and RNA-small-molecule interactions and more powerful chemical probing and structure prediction techniques.
Collapse
|
2
|
Khaova EA, Tkachenko AG. The Influence of Polyamines on the Expression of Escherichia Coli Ribosome Hibernation Factor Raia. BIO WEB OF CONFERENCES 2023. [DOI: 10.1051/bioconf/20235702001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
RaiA is one of the main ribosome hibernation factors in Escherichia coli. Like other ribosome hibernation factors, this protein reversibly inhibits translation under stress conditions. According to published data, being induced by indole, RaiA is involved in bacterial persistence, which is considered to play important role in the recalcitrance of chronic infections to antibiotics. Previously, we showed that the raiA expression on the transcriptional level is stimulated by polyamines, in addition to indole. In this work, we investigated the influence of polyamines on the raiA expression on the translational level. We obtained the predicted secondary structures of raiA mRNA, the analysis of which showed the presence of the bulged-out region in the initiation site with a high probability. This may be a sign of gene involvement in the polyamine modulon. We constructed translational raiA::lacZ reporter fusion. Using this genetic construct, we studied the effects of polyamines on the raiA expression through an addition of putrescine, cadaverine or spermidine at concentrations of 1 mM and 2 mM. According to the results, the raiA expression is primarily stimulated by cadaverine at the stationary phase.
Collapse
|
3
|
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] [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.
Collapse
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
| |
Collapse
|
4
|
Kawai G, Aoki Y, Otsu M, Koike N, Sampei GI. RNomics of Thermus themophilus HB8 by DNA microarray and next-generation sequencing. J Biochem 2017; 162:423-430. [PMID: 29106607 DOI: 10.1093/jb/mvx046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 06/19/2017] [Indexed: 11/13/2022] Open
Abstract
By using the data obtained by the DNA microarray analysis for the intergenic regions applied to RNA samples extracted from Thermus thermophilus HB8, seven small non-coding RNAs, TtR-1 to TtR-7, were found to be expressed in the cells growing in rich and/or minimal media. By analysing the time course of the expression for the cell growth in combination with the sequence comparison to the known RNAs, two RNAs, TtR-1 and TtR-2, are suggested to be riboswitches. The existence of the seven RNAs and the exact sequence and length, ranging 77-284 nt, were confirmed by the next-generation sequencing. By the combination of these two high-throughput techniques, our understanding of RNAs in the cell will be increased significantly.
Collapse
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
| |
Collapse
|
5
|
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] [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.
Collapse
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
| |
Collapse
|
6
|
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] [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.
Collapse
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.
| |
Collapse
|
7
|
Abstract
The secondary structure of an RNA molecule represents the base-pairing interactions within the molecule and fundamentally determines its overall structure. In this chapter, we overview the main approaches and existing tools for predicting RNA secondary structures, as well as methods for identifying noncoding RNAs from genomic sequences or RNA sequencing data. We then focus on the identification of a well-known class of small noncoding RNAs, namely microRNAs, which play very important roles in many biological processes through regulating post-transcriptionally the expression of genes and which dysregulation has been shown to be involved in several human diseases.
Collapse
Affiliation(s)
- Fariza Tahi
- IBISC, UEVE/Genopole, 23 bv. de France, 91000, Evry, France.
- IPS2, University of Paris-Saclay, 91190, Gif-sur-Yvette, France.
| | - Van Du T Tran
- Vital-IT group, SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Anouar Boucheham
- IBISC, UEVE/Genopole, 23 bv. de France, 91000, Evry, France
- College of NTIC, Constantine University 2, Constantine, Algeria
| |
Collapse
|
8
|
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] [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.
Collapse
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
| |
Collapse
|
9
|
Lisowiec J, Magner D, Kierzek E, Lenartowicz E, Kierzek R. Structural determinants for alternative splicing regulation of the MAPT pre-mRNA. RNA Biol 2015; 12:330-42. [PMID: 25826665 DOI: 10.1080/15476286.2015.1017214] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Alternative splicing at the MAPT gene exon 10 yields similar levels of the 3R and 4R tau protein isoforms. (1) The presence of mutations, particularly in exon 10 and intron 10-11, changes the quantity of tau isoforms. Domination each of the isoform yields tau protein aggregation and frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17). Here, we report for the first time the secondary structure of the 194/195 nucleotide region for the wild type (WT) and 10 mutants of the MAPT gene pre-mRNA determined using both chemical and microarray mapping. Thermodynamic analyses indicate that single nucleotide mutations in the splicing regulatory element (SRE) that form a hairpin affect its stability by up to 4 and 7 kcal/mol. Moreover, binding the regulatory hairpin of small molecule ligands (neomycin, kanamycin, tobramycin and mitoxantrone) enhance its stability depending on the nature of the ligands and the RNA mutations. Experiments using the cos-7 cell line indicate that the presence of ligands and modified antisense oligonucleotides affect the quantity of 3R and 4R isoforms. This finding correlates with the thermodynamic stability of the regulatory hairpin. An alternative splicing regulation mechanism for exon 10 is postulated based on our experimental data and on published data.
Collapse
Key Words
- AD, Alzheimer disease
- DMS, dimethyl sulfide
- ESE, exonic splicing enhancer
- ESS, exonic splicing silencer
- FTD, frontotemporal dementia
- FTDP-17, frontotemporal dementia and Parkinsonism linked to chromosome 17
- ISM, intronic splicing modulator
- ISS, intronic splicing silencer
- MAPT, microtubule-associated protein tau
- NMIA, N-methylisotoic anhydride
- NMR, nuclear magnetic resonance
- PPE, polypurine enhancer
- RNA structure
- RNA thermodynamics
- RT-PCR, reverse transcription polymerase chain reaction
- SHAPE, selective 2′-hydroxyl acylation analyzed by primer extension
- SMA, spinal muscular atrophy
- SRE, splicing regulatory element
- U1 snRNP, U1 small nuclear ribonucleoprotein
- WT, wild type
- alternative splicing regulation
- antisense oligonucleotides
- neurodegradation
- pre-mRNA, pre-messenger RNA
- small molecule binding
Collapse
Affiliation(s)
- Jolanta Lisowiec
- a Institute of Bioorganic Chemistry; Polish Academy of Sciences ; Noskowskiego, Poland
| | | | | | | | | |
Collapse
|
10
|
Okui S, Ushida C, Kiyosawa H, Kawai G. Sequence and structure analysis of a mirror tRNA located upstream of the cytochrome oxidase I mRNA in mouse mitochondria. J Biochem 2015; 159:341-50. [PMID: 26519737 DOI: 10.1093/jb/mvv106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 09/23/2015] [Indexed: 11/12/2022] Open
Abstract
RNA fragments corresponding to the mirror tRNA that is located upstream of the cytochrome oxidase I (COXI) gene in the mouse mitochondrial genome were found in the sequences obtained from the mouse brain by the next generation sequencing. RNA fragments corresponding to the 5' terminal of COXI mRNA were also found and it was suggested that the precursor of the COXI mRNA is processed at three residues upstream of the first AUG codon. The mirror tRNA fragment has poly(A) in its 3' terminal and variable 5' terminal, suggesting that this RNA is produced during the 5' processing of COXI mRNA. Secondary structure prediction and NMR analysis indicated that the mirror tRNA is folded into a tRNA-like secondary structure, suggesting that the tRNA-like conformation of the 5' adjacent sequence of COXI mRNA is involved in the COXI mRNA maturation in the mouse mitochondria.
Collapse
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;
| |
Collapse
|
11
|
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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/05/2015] [Accepted: 05/13/2015] [Indexed: 01/21/2023]
|
12
|
Puton T, Kozlowski LP, Rother KM, Bujnicki JM. CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction. Nucleic Acids Res 2013; 41:4307-23. [PMID: 23435231 PMCID: PMC3627593 DOI: 10.1093/nar/gkt101] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We present a continuous benchmarking approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA web server. As of 3 October 2012, the performance of 28 single-sequence and 13 comparative methods has been evaluated on RNA sequences/structures released weekly by the Protein Data Bank. We also provide a static benchmark generated on RNA 2D structures derived from the RNAstrand database. Benchmarks on both data sets offer insight into the relative performance of RNA secondary structure prediction methods on RNAs of different size and with respect to different types of structure. According to our tests, on the average, the most accurate predictions obtained by a comparative approach are generated by CentroidAlifold, MXScarna, RNAalifold and TurboFold. On the average, the most accurate predictions obtained by single-sequence analyses are generated by CentroidFold, ContextFold and IPknot. The best comparative methods typically outperform the best single-sequence methods if an alignment of homologous RNA sequences is available. This article presents the results of our benchmarks as of 3 October 2012, whereas the rankings presented online are continuously updated. We will gladly include new prediction methods and new measures of accuracy in the new editions of CompaRNA benchmarks.
Collapse
Affiliation(s)
- Tomasz Puton
- Bioinformatics Laboratory, Institute for Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland
| | | | | | | |
Collapse
|
13
|
Tanaka T, Mega R, Kim K, Shinkai A, Masui R, Kuramitsu S, Nakagawa N. A non-cold-inducible cold shock protein homolog mainly contributes to translational control under optimal growth conditions. FEBS J 2012; 279:1014-29. [PMID: 22251463 DOI: 10.1111/j.1742-4658.2012.08492.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cold shock proteins (Csps) include both cold-induced and non-cold-induced proteins, contrary to their name. Cold-induced Csps are well studied; they function in cold acclimation by controlling transcription and translation. Some Csps have been reported to contribute to other cellular processes. However, the functions of non-cold-induced Csps under optimal growth conditions remain unknown. To elucidate these functions, we used transcriptome and proteome analyses as comprehensive approaches and have compared the outputs of wild-type and non-cold-induced Csp-deletion mutant cells. As a model organism, we selected Thermus thermophilus HB8 because it has only two csp genes (ttcsp1 and ttcsp2); ttCsp1 is the only non-cold-induced Csp. Surprisingly, the amount of transcripts and proteins upon deletion of the ttcsp1 gene was quite different. DNA microarray analysis revealed that the deletion of ttcsp1 did not affect the amount of transcripts, although the ttcsp1 gene was constantly expressed in the wild-type cell. Nonetheless, proteomic analysis revealed that the expression levels of many proteins were significantly altered when ttcsp1 was deleted. These results suggest that ttCsp1 functions in translation independent of transcription. Furthermore, ttCsp1 is involved in both the stimulation and inhibition of translation of specific proteins. Here, we have determined the crystal structure of ttCsp1 at 1.65 Å. This is the first report to present the structure of a non-cold-inducible cold shock protein. We also report the nucleotide binding affinity of ttCsp1. Finally, we discuss the functions of non-cold-induced Csps and propose how they modulate the levels of specific proteins to suit the prevailing environmental conditions.
Collapse
Affiliation(s)
- Toshiko Tanaka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Japan
| | | | | | | | | | | | | |
Collapse
|
14
|
Very rapid induction of a cold shock protein by temperature downshift in Thermus thermophilus. Biochem Biophys Res Commun 2010; 399:336-40. [PMID: 20655297 DOI: 10.1016/j.bbrc.2010.07.065] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 07/19/2010] [Indexed: 11/20/2022]
Abstract
A rapid temperature downshift induces the expression of many proteins termed 'cold-induced' proteins. Although some of these proteins are known to participate in metabolism, transcription, translation and protein folding, processes that are affected by cold stress, it has not yet been identified which proteins sense the temperature downshift. Here we analyzed the mRNA expression profiles of genes induced immediately following a temperature downshift in Thermus thermophilus HB8. The cold shock protein gene ttcsp2 displayed the most rapid and drastic increase in mRNA. ttcsp2 mRNA was induced at 30s after temperature downshift, although ttCSP2 protein was first detected at 10 min. A temperature-dependent secondary structure was predicted to form in the 5'-untranslated region, including the Shine-Dalgarno sequence, of ttcsp2 mRNA. Stabilization of this secondary structure at 45 degrees C was assumed to prevent degradation of ttcsp2 mRNA and to slow translation. Thus, ttCSP2 is considered to act as a 'thermosensor' during temperature downshift through changes in its secondary structure.
Collapse
|
15
|
Nakamura S. A novel virtual spectrometry: Visualized regulatory motifs on ADM, rPol{beta} and CD83 mRNAs in human-friendly manners. J Biochem 2009; 146:251-61. [PMID: 19386779 DOI: 10.1093/jb/mvp064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Recently, riboswitches and other structures discovered on mRNAs have been reported as examples of functional RNA structures, motifs. Such motifs were shown to be present as single-form valid structures but they are obscured among other less-valid structures. Here, I present a novel, practical virtual spectrometry (the GenoPoemics Spectrometry) visualizing motifs on mRNA strands as spectra at-a-glance. Every motif along with validity of their existences could be observed on the spectra in human-friendly manners, and whole structures of mRNAs could be overviewed. Therefore, the spectra helped distinguish valid and less valid motifs. The spectrometry was applied to variety of mRNAs such as ADM, rPolbeta and CD83 to identify structures of high validity on them, previously reported functional motifs were successfully revealed. These findings indicate that the structures of mRNAs that may be folded into multiple forms can be further discussed quantitatively based on the visual spectra to discover functional RNA motifs.
Collapse
Affiliation(s)
- Shingo Nakamura
- Takeda Pharmaceutical Company Limited, Wadai, Tsukuba, Ibaraki, Japan.
| |
Collapse
|
16
|
Childs L, Nikoloski Z, May P, Walther D. Identification and classification of ncRNA molecules using graph properties. Nucleic Acids Res 2009; 37:e66. [PMID: 19339518 PMCID: PMC2685108 DOI: 10.1093/nar/gkp206] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The study of non-coding RNA genes has received increased attention in recent years fuelled by accumulating evidence that larger portions of genomes than previously acknowledged are transcribed into RNA molecules of mostly unknown function, as well as the discovery of novel non-coding RNA types and functional RNA elements. Here, we demonstrate that specific properties of graphs that represent the predicted RNA secondary structure reflect functional information. We introduce a computational algorithm and an associated web-based tool (GraPPLE) for classifying non-coding RNA molecules as functional and, furthermore, into Rfam families based on their graph properties. Unlike sequence-similarity-based methods and covariance models, GraPPLE is demonstrated to be more robust with regard to increasing sequence divergence, and when combined with existing methods, leads to a significant improvement of prediction accuracy. Furthermore, graph properties identified as most informative are shown to provide an understanding as to what particular structural features render RNA molecules functional. Thus, GraPPLE may offer a valuable computational filtering tool to identify potentially interesting RNA molecules among large candidate datasets.
Collapse
Affiliation(s)
- Liam Childs
- Max-Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, Golm, Germany.
| | | | | | | |
Collapse
|
17
|
Fujii K, Ozawa M, Iwatsuki-Horimoto K, Horimoto T, Kawaoka Y. Incorporation of influenza A virus genome segments does not absolutely require wild-type sequences. J Gen Virol 2009; 90:1734-1740. [PMID: 19297607 DOI: 10.1099/vir.0.010355-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The efficient incorporation of influenza virus genome segments into virions is mediated by cis-acting regions at both ends of the viral RNAs. It was shown previously that nt 16-26 at the 3' end of the non-structural (NS) viral RNA of influenza A virus are important for efficient virion incorporation and that nt 27-56 also contribute to this process. To understand further the signalling requirements for genome packaging, this study performed linker-scanning mutagenesis in the latter region and found that nt 27-35 made an appreciable contribution to the efficient incorporation of the NS segment. An NS vRNA library was then generated composed of an RNA population with randomized nucleotides at positions 16-35 such that the virus could select the sequences it required for virion incorporation. The sequences selected differed from the wild-type sequence and no conserved nucleotides were selected. The ability of non-wild-type sequences to function in this manner indicates that the incorporation of influenza A virus genome segments does not absolutely require specific sequences.
Collapse
Affiliation(s)
- Ken Fujii
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan.,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Makoto Ozawa
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan.,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Kiyoko Iwatsuki-Horimoto
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan.,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Taisuke Horimoto
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan.,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yoshihiro Kawaoka
- ERATO Infection-Induced Host Responses Project, Japan Science and Technology Agency, Saitama 332-0012, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan.,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
18
|
Dawson WK, Fujiwara K, Kawai G. Prediction of RNA pseudoknots using heuristic modeling with mapping and sequential folding. PLoS One 2007; 2:e905. [PMID: 17878940 PMCID: PMC1975678 DOI: 10.1371/journal.pone.0000905] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Accepted: 08/08/2007] [Indexed: 12/01/2022] Open
Abstract
Predicting RNA secondary structure is often the first step to determining the structure of RNA. Prediction approaches have historically avoided searching for pseudoknots because of the extreme combinatorial and time complexity of the problem. Yet neglecting pseudoknots limits the utility of such approaches. Here, an algorithm utilizing structure mapping and thermodynamics is introduced for RNA pseudoknot prediction that finds the minimum free energy and identifies information about the flexibility of the RNA. The heuristic approach takes advantage of the 5′ to 3′ folding direction of many biological RNA molecules and is consistent with the hierarchical folding hypothesis and the contact order model. Mapping methods are used to build and analyze the folded structure for pseudoknots and to add important 3D structural considerations. The program can predict some well known pseudoknot structures correctly. The results of this study suggest that many functional RNA sequences are optimized for proper folding. They also suggest directions we can proceed in the future to achieve even better results.
Collapse
Affiliation(s)
- Wayne K Dawson
- Department of Life and Environmental Sciences, Chiba Institute of Technology, Narashino-shi, Chiba, Japan.
| | | | | |
Collapse
|