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Li Y, Wu S, Ye K. Landscape of RNA pseudouridylation in archaeon Sulfolobus islandicus. Nucleic Acids Res 2024; 52:4644-4658. [PMID: 38375885 PMCID: PMC11077068 DOI: 10.1093/nar/gkae096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Pseudouridine, one of the most abundant RNA modifications, is synthesized by stand-alone or RNA-guided pseudouridine synthases. Here, we comprehensively mapped pseudouridines in rRNAs, tRNAs and small RNAs in the archaeon Sulfolobus islandicus and identified Cbf5-associated H/ACA RNAs. Through genetic deletion and in vitro modification assays, we determined the responsible enzymes for these modifications. The pseudouridylation machinery in S. islandicus consists of the stand-alone enzymes aPus7 and aPus10, and six H/ACA RNA-guided enzymes that account for all identified pseudouridines. These H/ACA RNAs guide the modification of all eleven sites in rRNAs, two sites in tRNAs, and two sites in CRISPR RNAs. One H/ACA RNA shows exceptional versatility by targeting eight different sites. aPus7 and aPus10 are responsible for modifying positions 13, 54 and 55 in tRNAs. We identified four atypical H/ACA RNAs that lack the lower stem and the ACA motif and confirmed their function both in vivo and in vitro. Intriguingly, atypical H/ACA RNAs can be modified by Cbf5 in a guide-independent manner. Our data provide the first global view of pseudouridylation in archaea and reveal unexpected structures, substrates, and activities of archaeal H/ACA RNPs.
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MESH Headings
- Pseudouridine/metabolism
- Sulfolobus/genetics
- Sulfolobus/metabolism
- RNA, Transfer/metabolism
- RNA, Transfer/genetics
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Archaeal/chemistry
- RNA, Ribosomal/metabolism
- RNA, Ribosomal/genetics
- Archaeal Proteins/metabolism
- Archaeal Proteins/genetics
- RNA Processing, Post-Transcriptional
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Intramolecular Transferases/genetics
- Intramolecular Transferases/metabolism
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Affiliation(s)
- Yuqian Li
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songlin Wu
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keqiong Ye
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Jády BE, Ketele A, Moulis D, Kiss T. Guide RNA acrobatics: positioning consecutive uridines for pseudouridylation by H/ACA pseudouridylation loops with dual guide capacity. Genes Dev 2022; 36:70-83. [PMID: 34916304 PMCID: PMC8763049 DOI: 10.1101/gad.349072.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/16/2021] [Indexed: 11/25/2022]
Abstract
Site-specific pseudouridylation of human ribosomal and spliceosomal RNAs is directed by H/ACA guide RNAs composed of two hairpins carrying internal pseudouridylation guide loops. The distal "antisense" sequences of the pseudouridylation loop base-pair with the target RNA to position two unpaired target nucleotides 5'-UN-3', including the 5' substrate U, under the base of the distal stem topping the guide loop. Therefore, each pseudouridylation loop is expected to direct synthesis of a single pseudouridine (Ψ) in the target sequence. However, in this study, genetic depletion and restoration and RNA mutational analyses demonstrate that at least four human H/ACA RNAs (SNORA53, SNORA57, SCARNA8, and SCARNA1) carry pseudouridylation loops supporting efficient and specific synthesis of two consecutive pseudouridines (ΨΨ or ΨNΨ) in the 28S (Ψ3747/Ψ3749), 18S (Ψ1045/Ψ1046), and U2 (Ψ43/Ψ44 and Ψ89/Ψ91) RNAs, respectively. In order to position two substrate Us for pseudouridylation, the dual guide loops form alternative base-pairing interactions with their target RNAs. This remarkable structural flexibility of dual pseudouridylation loops provides an unexpected versatility for RNA-directed pseudouridylation without compromising its efficiency and accuracy. Besides supporting synthesis of at least 6% of human ribosomal and spliceosomal Ψs, evidence indicates that dual pseudouridylation loops also participate in pseudouridylation of yeast and archaeal rRNAs.
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Affiliation(s)
- Beáta E Jády
- Molecular, Cellular, and Developmental Biology Department (MCD) UMR 5077, Centre de Biologie Intégrative (CBI), University of Toulouse, Centre National de la Recherche Scientifique, 31062 Toulouse, France
| | - Amandine Ketele
- Molecular, Cellular, and Developmental Biology Department (MCD) UMR 5077, Centre de Biologie Intégrative (CBI), University of Toulouse, Centre National de la Recherche Scientifique, 31062 Toulouse, France
| | - Dylan Moulis
- Molecular, Cellular, and Developmental Biology Department (MCD) UMR 5077, Centre de Biologie Intégrative (CBI), University of Toulouse, Centre National de la Recherche Scientifique, 31062 Toulouse, France
| | - Tamás Kiss
- Molecular, Cellular, and Developmental Biology Department (MCD) UMR 5077, Centre de Biologie Intégrative (CBI), University of Toulouse, Centre National de la Recherche Scientifique, 31062 Toulouse, France
- Biological Research Centre, 6726 Szeged, Hungary
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Jiang X, Xing L, Chen Y, Qin R, Song S, Lu Y, Xie S, Wang L, Pu H, Gui X, Li T, Xu J, Li J, Jia S, Lu D. CircMEG3 inhibits telomerase activity by reducing Cbf5 in human liver cancer stem cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 23:310-323. [PMID: 33425489 PMCID: PMC7779543 DOI: 10.1016/j.omtn.2020.11.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022]
Abstract
Circular RNA (CircRNA) is a newly identified special class of non-coding RNA (ncRNA) that plays an important regulatory role in the progression of certain diseases. Herein, our results indicate that CircMEG3 is downregulated expression and negatively correlated with the expression of telomerase-related gene Cbf5 in human liver cancer. Moreover, CircMEG3 inhibits the growth of human liver cancer stem cells in vivo and in vitro. CircMEG3 inhibits the expression of m6A methyltransferase METTL3 dependent on HULC. Moreover, CircMEG3 inhibits the expression of Cbf5, a component of telomere synthetase H/ACA ribonucleoprotein (RNP; catalyst RNA pseudouracil modification) through METTL3 dependent on HULC. Thereby, CircMEG3 inhibits telomerase activity and shortens telomere lifespan dependent on HULC and Cbf5 in human liver cancer stem cell. Strikingly, increased Cbf5 abrogates the ability of CircMEG3 to inhibit malignant differentiation of human liver cancer stem cells. In summary, these observations provide important basic information for finding effective liver cancer therapeutic targets.
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Affiliation(s)
- Xiaoxue Jiang
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Libo Xing
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Yingjie Chen
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Rushi Qin
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Shuting Song
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Yanan Lu
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Sijie Xie
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Liyan Wang
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Hu Pu
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Xin Gui
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Tianming Li
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Jie Xu
- School of Medicine, Tongji University, Shanghai 200092, China
| | - Jiao Li
- School of Medicine, Tongji University, Shanghai 200092, China
| | - Song Jia
- School of Medicine, Tongji University, Shanghai 200092, China
| | - Dongdong Lu
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
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