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Malbert B, Labaurie V, Dorme C, Paget E. Group I Intron as a Potential Target for Antifungal Compounds: Development of a Trans-Splicing High-Throughput Screening Strategy. Molecules 2023; 28:molecules28114460. [PMID: 37298936 DOI: 10.3390/molecules28114460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
The search for safe and efficient new antifungal compounds for agriculture has led to more efforts in finding new modes of action. This involves the discovery of new molecular targets, including coding and non-coding RNA. Rarely found in plants and animals but present in fungi, group I introns are of interest as their complex tertiary structure may allow selective targeting using small molecules. In this work, we demonstrate that group I introns present in phytopathogenic fungi have a self-splicing activity in vitro that can be adapted in a high-throughput screening to find new antifungal compounds. Ten candidate introns from different filamentous fungi were tested and one group ID intron found in F. oxysporum showed high self-splicing efficiency in vitro. We designed the Fusarium intron to act as a trans-acting ribozyme and used a fluorescence-based reporter system to monitor its real time splicing activity. Together, these results are opening the way to study the druggability of such introns in crop pathogen and potentially discover small molecules selectively targeting group I introns in future high-throughput screenings.
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Affiliation(s)
- Bastien Malbert
- Early Discovery, Biochemistry Excellence, Centre de Recherche La Dargoire, Bayer SAS, 69009 Lyon, France
| | - Virginie Labaurie
- Early Discovery, Biochemistry Excellence, Centre de Recherche La Dargoire, Bayer SAS, 69009 Lyon, France
| | - Cécile Dorme
- Early Discovery, Biochemistry Excellence, Centre de Recherche La Dargoire, Bayer SAS, 69009 Lyon, France
| | - Eric Paget
- Early Discovery, Biochemistry Excellence, Centre de Recherche La Dargoire, Bayer SAS, 69009 Lyon, France
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Ueda T, Nishimura KI, Nishiyama Y, Tominaga Y, Miyazaki K, Furuta H, Matsumura S, Ikawa Y. Pairwise Engineering of Tandemly Aligned Self-Splicing Group I Introns for Analysis and Control of Their Alternative Splicing. Biomolecules 2023; 13:biom13040654. [PMID: 37189401 DOI: 10.3390/biom13040654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
Alternative splicing is an important mechanism in the process of eukaryotic nuclear mRNA precursors producing multiple protein products from a single gene. Although group I self-splicing introns usually perform regular splicing, limited examples of alternative splicing have also been reported. The exon-skipping type of splicing has been observed in genes containing two group I introns. To characterize splicing patterns (exon-skipping/exon-inclusion) of tandemly aligned group I introns, we constructed a reporter gene containing two Tetrahymena introns flanking a short exon. To control splicing patterns, we engineered the two introns in a pairwise manner to design pairs of introns that selectively perform either exon-skipping or exon-inclusion splicing. Through pairwise engineering and biochemical characterization, the structural elements important for the induction of exon-skipping splicing were elucidated.
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Affiliation(s)
- Tomoki Ueda
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Kei-ichiro Nishimura
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yuka Nishiyama
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Yuto Tominaga
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Katsushi Miyazaki
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
- Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
- Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
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Box-shaped ribozyme octamer formed by face-to-face dimerization of a pair of square-shaped ribozyme tetramers. J Biosci Bioeng 2022; 134:195-202. [PMID: 35810135 DOI: 10.1016/j.jbiosc.2022.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 11/21/2022]
Abstract
Naturally occurring ribozymes with defined three-dimensional (3D) structures serve as promising platforms for the design and construction of artificial RNA nanostructures. We constructed a hexameric ribozyme nanostructure by face-to-face dimerization of a pair of triangular ribozyme trimers, unit RNAs of which were derived from the Tetrahymena group I ribozyme. In this study, we have expanded the dimerization strategy to a square-shaped ribozyme tetramer by introducing four pillar units. The resulting box-shaped nanostructures, which contained eight ribozyme units, can be assembled from either four or two components of their unit RNAs.
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Yu K, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. A hexameric ribozyme nanostructure formed by double-decker assembly of a pair of triangular ribozyme trimers. Chembiochem 2022; 23:e202100573. [PMID: 35088928 DOI: 10.1002/cbic.202100573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/29/2021] [Indexed: 11/12/2022]
Abstract
The modular architecture of naturally occurring ribozymes makes them a promising class of structural platforms to design and assemble three-dimensional (3D) RNA nanostructures, into which the catalytic ability of the platform ribozyme can be installed. We have constructed and analyzed RNA nanostructures with polygonal-shaped (closed) ribozyme oligomers by assembling unit RNAs derived from the Tetrahymena group I intron with a typical modular architecture. In this study, we dimerized ribozyme trimers with a triangular shape by introducing three pillar units. The resulting double-decker nanostructures containing six ribozyme units were characterized biochemically and their structures were observed by atomic force microscopy. The double-decker hexamers exhibited higher catalytic activity than the parent ribozyme trimers.
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Affiliation(s)
- Kai Yu
- University of Toyama: Toyama Daigaku, Department of Chemistry, JAPAN
| | - Kumi Hidaka
- Kyoto University: Kyoto Daigaku, Department of Chemistry, JAPAN
| | | | | | | | - Yoshiya Ikawa
- University of Toyama, Chemistry, Gofuku 3190, 930-8555, Toyama, JAPAN
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Dobirul Islam M, Motiar Rahman M, Matsumura S, Ikawa Y. Effects of chain length of polyethylene glycol molecular crowders on a mutant Tetrahymena group I ribozyme lacking large peripheral module. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:867-883. [PMID: 34402751 DOI: 10.1080/15257770.2021.1956531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
While current group I ribozymes use several distinct strategies to function under conditions of low Mg2+ concentration (≤ 3 mM), a deletion mutant of the Tetrahymena ribozyme (ΔP5 ribozyme) is virtually inactive with 3 mM Mg2+ due to removal of the large peripheral module, P5abc, supporting the active conformation of the core module. We investigated the molecular crowding effects of synthetic polyethylene glycols (PEGs) on the activity of the ΔP5 ribozyme. Among PEG molecules with different chain lengths, PEG600 improved the activity of the ΔP5 ribozyme most effectively in the presence of 3 mM Mg2+.
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Affiliation(s)
- Md Dobirul Islam
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan
| | - Md Motiar Rahman
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan
| | - Shigeyoshi Matsumura
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan.,Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Yoshiya Ikawa
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan.,Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
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An RNA Triangle with Six Ribozyme Units Can Promote a Trans-Splicing Reaction through Trimerization of Unit Ribozyme Dimers. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11062583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Ribozymes are catalytic RNAs that are attractive platforms for the construction of nanoscale objects with biological functions. We designed a dimeric form of the Tetrahymena group I ribozyme as a unit structure in which two ribozymes were connected in a tail-to-tail manner with a linker element. We introduced a kink-turn motif as a bent linker element of the ribozyme dimer to design a closed trimer with a triangular shape. The oligomeric states of the resulting ribozyme dimers (kUrds) were analyzed biochemically and observed directly by atomic force microscopy (AFM). Formation of kUrd oligomers also triggered trans-splicing reactions, which could be monitored with a reporter system to yield a fluorescent RNA aptamer as the trans-splicing product.
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Kiyooka R, Akagi J, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Catalytic RNA nano-objects formed by self-assembly of group I ribozyme dimers serving as unit structures. J Biosci Bioeng 2020; 130:253-259. [PMID: 32451246 DOI: 10.1016/j.jbiosc.2020.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/16/2020] [Accepted: 04/24/2020] [Indexed: 12/24/2022]
Abstract
Ribozymes with modular structures are attractive platforms for the construction of nanoscale RNA objects with biological functions. We designed group I ribozyme dimers as unit ribozyme dimers (Urds), which self-assembled to form their polymeric states and also oligomeric states with defined numbers of Urds. Assembly of Urds yielded catalytic ability of a pair of distinct ribozyme units to cleave two distinct substrates. The morphologies of the assembled ribozyme structures were observed directly by atomic force microscopy (AFM).
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Affiliation(s)
- Ryuji Kiyooka
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Junya Akagi
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan.
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Catalytic RNA, ribozyme, and its applications in synthetic biology. Biotechnol Adv 2019; 37:107452. [DOI: 10.1016/j.biotechadv.2019.107452] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/21/2022]
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