Diversity of circular RNAs and RNA ligases in archaeal cells

Becker, Hubert F.; L'Hermitte-Stead, Caroline; Myllykallio, Hannu

doi:10.1016/j.biochi.2019.06.011

Cited by 6 publications

(5 citation statements)

References 58 publications

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“…In contrast, Haloferax volcanii , Nanoarchaeum equitans , Sulfolobus solfataricus , Sulfolobus acidocaldarius , and Pyrobaculum aerophilum , do not encode homolog of type-3 Rnl. Circular tRNA intron and rRNA intermediates are present in abundance, but only a modest number of circular C/D box RNAs were reported in H. volcanii , S. solfataricu , S. acidocaldarius , and N. equitans ( Danan et al, 2012 ; Randau, 2012 ; Becker et al, 2019 ). The large subunits of S. acidocaldarius and P. aerophilum rRNAs were shown to retain H98 evinced by a continuous read coverage at the 3′-end ( Birkedal et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

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

Liu

Takagi

Sugijanto

et al. 2022

Front. Mol. Biosci.

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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.

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Section: Discussionmentioning

confidence: 99%

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

Liu

Takagi

Sugijanto

et al. 2022

Front. Mol. Biosci.

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“…Because of its circRNA genome, HDV has been considered unique amongst all known animal viruses (Taylor, 2014). In archaea, circRNA biogenesis involves remnants rRNA, tRNA intron and Box C/D RNAs forming ribonucleoprotein with dimeric RNA ligase (Rnl3) (Becker et al, 2019). The function of circRNA and primordial RNA binding proteins (RBPs) set the stage for eukaryotic circRNA biogenesis involving spliceosome RNPs (more below).…”

Section: Historical Perspectivementioning

confidence: 99%

Circular RNAs Are Regulators of Diverse Animal Transcriptomes: One Health Perspective

Zucko

Boris‐Lawrie

2020

Front. Genet.

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Derived from linear (parental) precursor mRNA, circRNA are recycled exons and introns whose ends are ligated. By titrating microRNAs and RNA binding proteins, circRNA interconnect networks of competing endogenous RNAs. Without altering chromosomal DNA, circRNA regulates skeletal muscle development and proliferation, lactation, ovulation, brain development, and responses to infections and metabolic stress. This review integrates emerging knowledge of circRNA activity coming from genome-wide characterizations in many clades of animals. circRNA research addresses one of the main pillars of the One Health vision-to improve the health and productivity of food animals and generate translational knowledge in animal species.

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“…Whereas the Rnl2 family binds to and repairs nicked duplex RNA substrates, with T4 Rnl2 demonstrating that the C-terminal domain is essential for binding and adenylation of RNA substrates ( 11 ). Rnl3 ligases are found primarily in archaea and some thermophilic bacteria and differ from other RNA ligases in that they have homodimeric structures ( 6 , 12–17 ). Rnl4 is a new RNA ligase family found in several bacterial species, and is a complex of two proteins (Pnkp and Hen1) that repairs transfer RNAs that have been cleaved by ribotoxins ( 18 , 19 ).…”

Section: Introductionmentioning

confidence: 99%

“…As mentioned above they are unique in that they have a homodimeric structure and can catalyse ligation and circularisation of single-stranded RNA. A third homologous structure from the hyperthermophilic bacterium Aquifex aeolicus (PDB ID 3QWU) was also identified, with bioinformatic analyses indicating Rnl3 ligases are prevalent in bacterial and archaeal thermophiles or hyperthermophiles, which typically thrive in temperature ranges between 50°C and 95°C ( 6 ). In vitro , the Rnl3 ligases can adenylate both RNA and DNA substrates, with primarily intra-molecular ligation (also described as RNA circularisation) observed with RNA substrates and display varying activity optima, and efficient activity at temperatures ranging from 50°C to 85°C ( 14 , 16 , 17 ).…”

Section: Introductionmentioning

confidence: 99%

Characterisation and engineering of a thermophilic RNA ligase from Palaeococcus pacificus

Rousseau,

Oulavallickal,

Williamson

et al. 2024

Nucleic Acids Research

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RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in next-generation sequencing of microRNAs. Thermophilic RNA ligases belonging to the RNA ligase 3 family are gaining attention for their use in molecular biology, for example a thermophilic RNA ligase from Methanobacterium thermoautotrophicum is commercially available for the adenylation of nucleic acids. Here we extensively characterise a newly identified RNA ligase from the thermophilic archaeon Palaeococcus pacificus (PpaRnl). PpaRnl exhibited significant substrate adenylation activity but low ligation activity across a range of oligonucleotide substrates. Mutation of Lys92 in motif I to alanine, resulted in an enzyme that lacked adenylation activity, but demonstrated improved ligation activity with pre-adenylated substrates (ATP-independent ligation). Subsequent structural characterisation revealed that in this mutant enzyme Lys238 was found in two alternate positions for coordination of the phosphate tail of ATP. In contrast mutation of Lys238 in motif V to glycine via structure-guided engineering enhanced ATP-dependent ligation activity via an arginine residue compensating for the absence of Lys238. Ligation activity for both mutations was higher than the wild-type, with activity observed across a range of oligonucleotide substrates with varying sequence and secondary structure.

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Diversity of circular RNAs and RNA ligases in archaeal cells

Cited by 6 publications

References 58 publications

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

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

Circular RNAs Are Regulators of Diverse Animal Transcriptomes: One Health Perspective

Characterisation and engineering of a thermophilic RNA ligase from Palaeococcus pacificus

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