title: High-throughput sequencing reveals circular substrates for an archaeal RNA ligase.
abstract: It is only recently that the abundant presence of circular RNAs (circRNAs) in all kingdoms of Life, including the hyperthermophilic archaeon Pyrococcus abyssi, has emerged. This led us to investigate the physiologic significance of a previously observed weak intramolecular ligation activity of Pab1020 RNA ligase. Here we demonstrate that this enzyme, despite sharing significant sequence similarity with DNA ligases, is indeed an RNA-specific polynucleotide ligase efficiently acting on physiologically significant substrates. Using a combination of RNA immunoprecipitation assays and RNA-seq, our genome-wide studies revealed 133 individual circRNA loci in P. abyssi. The large majority of these loci interacted with Pab1020 in cells and circularization of selected C/D Box and 5S rRNA transcripts was confirmed biochemically. Altogether these studies revealed that Pab1020 is required for RNA circularization. Our results further suggest the functional speciation of an ancestral NTase domain and/or DNA ligase toward RNA ligase activity and prompt for further characterization of the widespread functions of circular RNAs in prokaryotes. Detailed insight into the cellular substrates of Pab1020 may facilitate the development of new biotechnological applications e.g. in ligation of preadenylated adaptors to RNA molecules.
authors.affiliation: a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France.|b Sorbonne Universités, UPMC Univ Paris 06 , 4 Place Jussieu, Paris , France.
authors.forename: Hubert F
authors.initials: HF
authors.lastname: Becker
authors.affiliation: a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France.|c LIX, Ecole Polytechnique, CNRS, Université Paris-Saclay, INRIA , Palaiseau , France.
authors.forename: Alice
authors.initials: A
authors.lastname: Héliou
authors.affiliation: a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France.
authors.forename: Kamel
authors.initials: K
authors.lastname: Djaout
authors.affiliation: a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France.
authors.forename: Roxane
authors.initials: R
authors.lastname: Lestini
authors.affiliation: c LIX, Ecole Polytechnique, CNRS, Université Paris-Saclay, INRIA , Palaiseau , France.
authors.forename: Mireille
authors.initials: M
authors.lastname: Regnier
authors.affiliation: a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France.
authors.forename: Hannu
authors.initials: H
authors.lastname: Myllykallio
mesh_terms: D017398:Alternative Splicing; D019843:Archaeal Proteins / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology; D020745:Genome, Archaeal; D047468:Immunoprecipitation; D043903:Pyrococcus abyssi / Q000201:enzymology / Q000235:genetics*; D012313:RNA / Q000235:genetics* / Q000378:metabolism; D011130:RNA Ligase (ATP) / Q000235:genetics* / Q000378:metabolism; D020871:RNA Stability; D019642:RNA, Archaeal / Q000235:genetics* / Q000378:metabolism; D000079962:RNA, Circular; D012341:RNA, Ribosomal, 5S / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013379:Substrate Specificity
chemical_list: D019843:Archaeal Proteins; D019642:RNA, Archaeal; D000079962:RNA, Circular; D012341:RNA, Ribosomal, 5S; D012313:RNA; D011130:RNA Ligase (ATP)
keywords: Archaea; RNA ligase; RNA-Seq; circular RNA; computational biology