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Khalifah BA, Alghamdi SA, Alhasan AH. Unleashing the potential of catalytic RNAs to combat mis-spliced transcripts. Front Bioeng Biotechnol 2023; 11:1244377. [PMID: 38047291 PMCID: PMC10690607 DOI: 10.3389/fbioe.2023.1244377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/23/2023] [Indexed: 12/05/2023] Open
Abstract
Human transcriptome can undergo RNA mis-splicing due to spliceopathies contributing to the increasing number of genetic diseases including muscular dystrophy (MD), Alzheimer disease (AD), Huntington disease (HD), myelodysplastic syndromes (MDS). Intron retention (IR) is a major inducer of spliceopathies where two or more introns remain in the final mature mRNA and account for many intronic expansion diseases. Potential removal of such introns for therapeutic purposes can be feasible when utilizing bioinformatics, catalytic RNAs, and nano-drug delivery systems. Overcoming delivery challenges of catalytic RNAs was discussed in this review as a future perspective highlighting the significance of utilizing synthetic biology in addition to high throughput deep sequencing and computational approaches for the treatment of mis-spliced transcripts.
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Affiliation(s)
- Bashayer A. Khalifah
- Institute for Bioengineering, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Ali H. Alhasan
- Institute for Bioengineering, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- College of Science and General Studies, Alfaisal University, Riyadh, Saudi Arabia
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Siddika MA, Yamada T, Aoyama R, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Catalytic RNA Oligomers Formed by Co-Oligomerization of a Pair of Bimolecular RNase P Ribozymes. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238298. [PMID: 36500390 PMCID: PMC9740620 DOI: 10.3390/molecules27238298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022]
Abstract
Naturally occurring ribozymes with a modular architecture are promising platforms for construction of RNA nanostructures because modular redesign enables their oligomerization. The resulting RNA nanostructures can exhibit the catalytic function of the parent ribozyme in an assembly dependent manner. In this study, we designed and constructed open-form oligomers of a bimolecular form of an RNase P ribozyme. The ribozyme oligomers were analyzed biochemically and by atomic force microscopy (AFM).
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Affiliation(s)
- Mst. Ayesha Siddika
- Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Takahiro Yamada
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Risako Aoyama
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Kumi Hidaka
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
- Organization for Research and Development of Innovative Science and Technology, Kansai University, Osaka 564-8680, Japan
| | - Shigeyoshi Matsumura
- Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Yoshiya Ikawa
- Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
- Correspondence:
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Hieronymus R, Müller S. Engineering of hairpin ribozyme variants for RNA recombination and splicing. Ann N Y Acad Sci 2019; 1447:135-143. [PMID: 30941784 DOI: 10.1111/nyas.14052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/13/2019] [Accepted: 02/20/2019] [Indexed: 11/28/2022]
Abstract
The hairpin ribozyme is a small, naturally occurring RNA that catalyzes the reversible cleavage of RNA substrates. Among the small endonucleolytic ribozymes, the hairpin ribozyme possesses the unique feature of the internal equilibrium between cleavage and ligation being shifted toward ligation. This allows control of the reaction outcome by structural design: fragments that are strongly bound to the ribozyme are preferentially ligated, whereas substrates that easily dissociate upon cleavage, such that they are not available for religation, are preferentially cleaved. We have made use of this characteristic feature in engineering a number of hairpin ribozyme variants by programmed conformational design that carry out cascades of cleavage and ligation reactions, and as a result mediate more complex RNA processing reactions. Here, we review our work on the engineering of hairpin ribozyme variants for RNA recombination and regular and back-splicing, and discuss the relevance of such activities in early life.
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Affiliation(s)
| | - Sabine Müller
- Institut für Biochemie, Universität Greifswald, Greifswald, Germany
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Lee CH, Han SR, Lee SW. Group I Intron-Based Therapeutics Through Trans-Splicing Reaction. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 159:79-100. [PMID: 30340790 DOI: 10.1016/bs.pmbts.2018.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In 1982, the Cech group discovered that an intron structure in an rRNA precursor of Tetrahymena thermophila is sufficient to complete splicing without assistance from proteins. This was the first moment that scientists recognized RNAs can have catalytic activities derived from their own unique three-dimensional structures and thus play more various roles in biological processes than thought before. Several additional catalytic RNAs, called ribozymes, were subsequently identified in nature followed by intense studies to reveal their mechanisms of action and to engineer them for use in fields such as molecular cell biology, therapeutics, imaging, etc. Naturally occurring RNA-targeting ribozymes can be broadly classified into two categories by their abilities: Self-cleavage and self-splicing. Since ribozymes use base-pairing to recognize cleavage sites, identification of the catalytic center of naturally occurring ribozymes enables to engineer from "self" to "trans" acting ones which has accelerated to design and use ribozyme as valuable tools in gene therapy fields. Especially, group I intron-based trans-splicing ribozyme has unique property to use as a gene therapeutic agent. It can destroy and simultaneously repair (and/or reprogram) target RNAs to yield the desired therapeutic RNAs, maintaining endogenous spatial and temporal gene regulation of target RNAs. There have been progressive improvements in trans-splicing ribozymes and successful applications of these elements in gene therapy and molecular imaging approaches for various pathogenic conditions. In this chapter, current status of trans-splicing ribozyme therapeutics, focusing on Tetrahymena group I intron-based ribozymes, and their future prospects will be discussed.
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Affiliation(s)
- Chang Ho Lee
- Department of Integrated Life Sciences, Dankook University, Yongin, Republic of Korea
| | | | - Seong-Wook Lee
- Department of Integrated Life Sciences, Dankook University, Yongin, Republic of Korea; Rznomics Inc., Gwangju, Republic of Korea.
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Lee CH, Han SR, Lee SW. Therapeutic applications of group I intron-based trans-splicing ribozymes. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1466. [PMID: 29383855 DOI: 10.1002/wrna.1466] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/10/2017] [Accepted: 12/14/2017] [Indexed: 12/21/2022]
Abstract
Since the breakthrough discovery of catalytic RNAs (ribozymes) in the early 1980s, valuable ribozyme-based gene therapies have been developed for incurable diseases ranging from genetic disorders to viral infections and cancers. Ribozymes can be engineered and used to downregulate or repair pathogenic genes via RNA cleavage mediated by trans-cleaving ribozymes or repair and reprograming mediated by trans-splicing ribozymes, respectively. Uniquely, trans-splicing ribozymes can edit target RNAs via simultaneous destruction and repair (and/or reprograming) to yield the desired therapeutic RNAs, thus selectively inducing therapeutic gene activity in cells expressing the target RNAs. In contrast to traditional gene therapy approaches, such as simple addition of therapeutic transgenes or inhibition of disease-causing genes, the selective repair and/or reprograming abilities of trans-splicing ribozymes in target RNA-expressing cells facilitates the maintenance of endogenous spatial and temporal gene regulation and reduction of disease-associated transcript expression. In molecular imaging technologies, trans-splicing ribozymes can be used to reprogram specific RNAs in living cells and organisms by the 3'-tagging of reporter RNAs. The past two decades have seen progressive improvements in trans-splicing ribozymes and the successful application of these elements in gene therapy and molecular imaging approaches for various pathogenic conditions, such as genetic, infectious, and malignant disease. This review provides an overview of the current status of trans-splicing ribozyme therapeutics, focusing on Tetrahymena group I intron-based ribozymes, and their future prospects. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Chang Ho Lee
- Department of Integrated Life Sciences, Dankook University, Yongin, Republic of Korea
| | - Seung Ryul Han
- Department of Integrated Life Sciences, Dankook University, Yongin, Republic of Korea
| | - Seong-Wook Lee
- Department of Integrated Life Sciences, Dankook University, Yongin, Republic of Korea
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Tanaka T, Hirata Y, Tominaga Y, Furuta H, Matsumura S, Ikawa Y. Heterodimerization of Group I Ribozymes Enabling Exon Recombination through Pairs of Cooperative trans-Splicing Reactions. Chembiochem 2017; 18:1659-1667. [PMID: 28556398 DOI: 10.1002/cbic.201700053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Indexed: 12/31/2022]
Abstract
Group I (GI) self-splicing ribozymes are attractive tools for biotechnology and synthetic biology. Several trans-splicing and related reactions based on GI ribozymes have been developed for the purpose of recombining their target mRNA sequences. By combining trans-splicing systems with rational modular engineering of GI ribozymes it was possible to achieve more complex editing of target RNA sequences. In this study we have developed a cooperative trans-splicing system through rational modular engineering with use of dimeric GI ribozymes derived from the Tetrahymena group I intron ribozyme. The resulting pairs of ribozymes exhibited catalytic activity depending on their selective dimerization. Rational modular redesign as performed in this study would facilitate the development of sophisticated regulation of double or multiple trans-splicing reactions in a cooperative manner.
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Affiliation(s)
- Takahiro Tanaka
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yusuke Hirata
- 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, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, 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
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan
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Design and Experimental Evolution of trans-Splicing Group I Intron Ribozymes. Molecules 2017; 22:molecules22010075. [PMID: 28045452 PMCID: PMC6155759 DOI: 10.3390/molecules22010075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/27/2016] [Accepted: 12/29/2016] [Indexed: 12/31/2022] Open
Abstract
Group I intron ribozymes occur naturally as cis-splicing ribozymes, in the form of introns that do not require the spliceosome for their removal. Instead, they catalyze two consecutive trans-phosphorylation reactions to remove themselves from a primary transcript, and join the two flanking exons. Designed, trans-splicing variants of these ribozymes replace the 3′-portion of a substrate with the ribozyme’s 3′-exon, replace the 5′-portion with the ribozyme’s 5′-exon, or insert/remove an internal sequence of the substrate. Two of these designs have been evolved experimentally in cells, leading to variants of group I intron ribozymes that splice more efficiently, recruit a cellular protein to modify the substrate’s gene expression, or elucidate evolutionary pathways of ribozymes in cells. Some of the artificial, trans-splicing ribozymes are promising as tools in therapy, and as model systems for RNA evolution in cells. This review provides an overview of the different types of trans-splicing group I intron ribozymes that have been generated, and the experimental evolution systems that have been used to improve them.
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