Genetic and Functional Analyses of Archaeal ATP-Dependent RNA Ligase in C/D Box sRNA Circularization and Ribosomal RNA Processing

Yancheng Liu; Yuko Takagi; Milyadi Sugijanto; Kieu Duong My Nguyen; Akira Hirata; Hiroyuki Hori; C Kiong Ho

doi:10.3389/fmolb.2022.811548

Genetic and Functional Analyses of Archaeal ATP-Dependent RNA Ligase in C/D Box sRNA Circularization and Ribosomal RNA Processing

Front Mol Biosci. 2022 Mar 25:9:811548. doi: 10.3389/fmolb.2022.811548. eCollection 2022.

Authors

Yancheng Liu¹, Yuko Takagi², Milyadi Sugijanto³, Kieu Duong My Nguyen¹, Akira Hirata⁴, Hiroyuki Hori⁵, C Kiong Ho^{1

3}

Affiliations

¹ Human Biology Program, University of Tsukuba, Tsukuba, Japan.
² Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
³ Doctoral Program in Medical Sciences, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.
⁴ Department of Natural Science, Graduate School of Technology, Industrial and Social Science, Tokushima University, Tokushima, Japan.
⁵ Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan.

Abstract

RNA ligases play important roles in repairing and circularizing RNAs post-transcriptionally. In this study, we generated an allelic knockout of ATP-dependent RNA ligase (Rnl) in the hyperthermophilic archaeon Thermococcus kodakarensis to identify its biological targets. A comparative analysis of circular RNA reveals that the Rnl-knockout strain represses circularization of C/D box sRNAs without affecting the circularization of tRNA and rRNA processing intermediates. Recombinant archaeal Rnl could circularize C/D box sRNAs with a mutation in the conserved C/D box sequence element but not when the terminal stem structures were disrupted, suggesting that proximity of the two ends could be critical for intramolecular ligation. Furthermore, T. kodakarensis accumulates aberrant RNA fragments derived from ribosomal RNA in the absence of Rnl. These results suggest that Rnl is responsible for C/D box sRNA circularization and may also play a role in ribosomal RNA processing.

Keywords: C/D box sRNAs; RNA ligase; circular RNA; rRNA processing; thermococcus kodakarensis KOD1.