Acquisition of Dual Ribozyme-Functions in Nonfunctional Short Hairpin RNAs through Kissing-Loop Interactions

Mutsuro‐Aoki, Hiromi; Tamura, Koji

doi:10.3390/life12101561

Cited by 2 publications

(3 citation statements)

References 57 publications

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“…However, similar to a Ferrari, it is very forgiving and is fine-tuned to achieve the maximum performance. From an evolutionary point of view, the present study, which considers the conditions under which this ribozyme is split and generates ligation activity, is of great significance, as was the case in our previous series of studies on the R3C ligase ribozyme [19,21,22,24].…”

Section: Discussionmentioning

confidence: 91%

“…Several ligation ribozymes have been isolated from a large pool of random sequences [16,17], including the R3C ligase [9], L1 ligase [10], DSL ligase [11], and class I ligase ribozymes [12][13][14][15]. The R3C and L1 ribozymes have already been minimized [18][19][20], and kissing-loop interaction-mediated conformational changes have been shown to acquire activity from small non-active RNAs in the R3C ribozyme [21][22][23][24].…”

Section: Introductionmentioning

confidence: 99%

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Molecular Anatomy of the Class I Ligase Ribozyme for Elucidation of the Activity-Generating Unit

Kasuga

Mutsuro‐Aoki

Ando

et al. 2023

Biology

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The class I ligase ribozyme consists of 121 nucleotides and shows a high catalytic rate comparable to that found in natural proteinaceous polymerases. In this study, we aimed to identify the smaller active unit of the class I ligase ribozyme comprising ~50 nucleotides, comparable to the estimated length of prebiotically synthesized RNA. Based on the three-dimensional structure of the class I ligase ribozyme, mutants were prepared and their ligation activities were analyzed. Sufficient ligation activity was maintained even when shortening to 94 nucleotides. However, because it would be difficult to approach the target of ~50 nucleotides by removing only the partial structure, the class I ligase ribozyme was then split into two molecules. The ligation activity was maintained even when splitting into two molecules of 55 and 39 nucleotides. Using a system with similar split ribozymes, we analyzed the ligation activity of mutants C30, C47, and A71, which have been previously identified as the positions that contribute to catalytic activity, and discussed the structural basis of the activity of these bases. Our findings suggest the rationale for the class I ligase ribozyme’s assembling from multiple fragments that would be achievable with prebiotic synthesis.

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Section: Discussionmentioning

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Molecular Anatomy of the Class I Ligase Ribozyme for Elucidation of the Activity-Generating Unit

Kasuga

Mutsuro‐Aoki

Ando

et al. 2023

Biology

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“…Using this interaction, two RNAs with complementary sequences in the loop regions of R3C ligase variants were prepared, and the mixed RNA system showed significantly increased ligation activity compared to that of the individually performed reactions. Multiple functions can be achieved via kissing loop interactions, suggesting their versatility in the evolution of RNA [27].…”

Section: Introductionmentioning

confidence: 99%

Development of Allosteric Ribozymes for ATP and l-Histidine Based on the R3C Ligase Ribozyme

Akatsu,

Mutsuro-Aoki,

Tamura

2024

Life

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During the evolution of the RNA, short RNAs are thought to have joined together to form long RNAs, enhancing their function as ribozymes. Previously, the artificial R3C ligase ribozyme (73 nucleotides) was successfully reduced to 46 nucleotides; however, its activity decreased significantly. Therefore, we aimed to develop allosteric ribozymes, whose activities could be regulated by effector compounds, based on the reduced R3C ligase ribozyme (R3C-A). Among the variants prepared by fusing an ATP-binding aptamer RNA with R3C-A, one mutant showed increased ligation activity in an ATP-dependent manner. Melting temperature measurements of the two RNA mutants suggested that the region around the aptamer site was stabilized by the addition of ATP. This resulted in a suitable conformation for the reaction at the ligation site. Another ribozyme was prepared by fusing R3C-A with a l-histidine-binding aptamer RNA, and the ligase activity increased with increasing l-histidine concentrations. Both ATP and l-histidine play prominent roles in current molecular biology and the interaction of RNAs and these molecules could be a key step in the evolution of the world of RNAs. Our results suggest promise in the development of general allosteric ribozymes that are independent of the type of effector molecule and provide important clues to the evolution of the RNA world.

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Acquisition of Dual Ribozyme-Functions in Nonfunctional Short Hairpin RNAs through Kissing-Loop Interactions

Cited by 2 publications

References 57 publications

Molecular Anatomy of the Class I Ligase Ribozyme for Elucidation of the Activity-Generating Unit

Molecular Anatomy of the Class I Ligase Ribozyme for Elucidation of the Activity-Generating Unit

Development of Allosteric Ribozymes for ATP and l-Histidine Based on the R3C Ligase Ribozyme

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