Natural circularly permuted group II introns in bacteria produce RNA circles

Roth, Adam; Weinberg, Zasha; Vanderschuren, Koen; Murdock, Mitchell H.; Breaker, Ronald R.

doi:10.1016/j.isci.2021.103431

Cited by 13 publications

(8 citation statements)

References 61 publications

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“…Large noncoding RNAs (ncRNAs) are rare in bacteria ( 1 , 2 ), but those whose functions have been established are remarkable for their sophisticated structures and fundamental biological roles ( 3 ). Comparative sequence analysis approaches conducted using computer algorithms have enabled the discovery of additional classes of large ncRNA classes in bacteria ( 1 , 4 , 5 , 6 , 7 , 8 ). Unfortunately, these RNAs do not often exist in genetically tractable model organisms, which make their biochemical and biological functions more challenging to establish.…”

mentioning

confidence: 99%

Ornate, large, extremophilic (OLE) RNA forms a kink turn necessary for OapC protein recognition and RNA function

Lyon¹,

Harris²,

Odzer³

et al. 2022

Journal of Biological Chemistry

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confidence: 99%

Ornate, large, extremophilic (OLE) RNA forms a kink turn necessary for OapC protein recognition and RNA function

Lyon¹,

Harris²,

Odzer³

et al. 2022

Journal of Biological Chemistry

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“…Identification of critical sequences to DucS circularization. No circular RNA was reported before in bacteria except for self-spliced and circularized group I or II introns 13,30,31 . No classical group II intron structure was found in DucS sequence through conserved group II introns prediction (http://webapps2.ucalgary.ca/~groupii/index.html#).…”

Section: Resultsmentioning

confidence: 99%

A linear and circular dual-conformation noncoding RNA involves in oxidative stress tolerance of Bacillus altitudinis

et al. 2023

Preprint

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Functional circular RNAs have been extensively studied in eukaryotes and progressively discovered in archaea, but not been identified in bacteria except some byproducts of self-spliced introns, devoid of biological function. In this study, using an experimental and computational pipeline, we confirm that a regulatory noncoding RNA DucS exists in both linear and circular conformations in Bacillus altitudinis. The 3’ end sequences of linear RNA are critical to RNA circularization. DucS promotes the tolerance of host to H2O2 stress through its linear forms, partly due to upregulating the translation of a stress-responsive gene htrA, whereas its circular forms can promote the degradation of linear cognates. Through re-evaluating published RNA-seq data from 30 bacteria and experimental identification, we demonstrate that circular RNAs also exist in other bacteria, occurred unexpectedly in some well-known noncoding RNAs. Our results reveal firstly a functional circular RNA in bacteria, highlighting the universal existence of functional circular RNAs in all three domains of life.

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“…Besides comparisons centered on sequentially-ordered RNA molecules, comparisons have to take into account molecules that are related but don’t keep the same structure topology and exhibit sequence permutations: Several viral and bacterial RNAs have been identified to mimic tRNA structures, exhibiting both circularly and non-circularly permuted sequence matchings [10, 11]. Circular permutations have been observed in various natural non-coding RNAs [12, 13]. Recently, a natural non-circularly permuted variant of a non-coding RNA, specifically the hammerhead ribozyme, was reported [14].…”

Section: Introductionmentioning

confidence: 99%

ARTEMIS - a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment

Bohdan,

Bujnicki,

Baulin

2024

Preprint

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Non-coding RNAs play a major role in diverse processes in living cells with their sequence and spatial structure serving as the principal determinants of their function. Superposition of RNA 3D structures is the most accurate method for comparative analysis of RNA molecules and for inferring sequence alignments. Topology-independent superposition is particularly relevant, as evidenced by structurally similar RNAs with sequence permutations such as tRNA and Y RNA. To date, state-of-the-art methods for RNA 3D structure superposition rely on intricate heuristics, and the potential for topology-independent superposition has not been exhausted. Recently, we introduced the ARTEM method for unrestrained pairwise superposition of RNA 3D modules and now we developed it further to solve the global RNA 3D structure alignment problem. Our new tool ARTEMIS significantly outperforms state-of-the-art tools in both sequentially-ordered and topology-independent RNA 3D structure superposition. Using ARTEMIS we discovered a helical packing motif to be preserved within different backbone topology contexts across various non-coding RNAs, including multiple ribozymes and riboswitches. We anticipate that ARTEMIS will be essential for elucidating the landscape of RNA 3D folds and motifs featuring sequence permutations that thus far remained unexplored due to limitations in previous computational approaches.

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Natural circularly permuted group II introns in bacteria produce RNA circles

Cited by 13 publications

References 61 publications

Ornate, large, extremophilic (OLE) RNA forms a kink turn necessary for OapC protein recognition and RNA function

Ornate, large, extremophilic (OLE) RNA forms a kink turn necessary for OapC protein recognition and RNA function

A linear and circular dual-conformation noncoding RNA involves in oxidative stress tolerance of Bacillus altitudinis

ARTEMIS - a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment

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