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Endonucleolytic processing plays a critical role in the maturation of ribosomal RNA in Methanococcus maripaludis

Ribosomal RNA (rRNA) processing and maturation are fundamentally important for ribosome biogenesis, but the mechanisms in archaea, the third form of life, remains largely elusive. This study aimed to investigate the rRNA maturation process in Methanococcus maripaludis, a representative archaeon lack...

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Autores principales: Qi, Lei, Liu, Huan, Gao, Jian, Deng, Kai, Wang, Xiaoyan, Dong, Xiuzhu, Li, Jie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Taylor & Francis 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10515664/
https://www.ncbi.nlm.nih.gov/pubmed/37731260
http://dx.doi.org/10.1080/15476286.2023.2258035
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author Qi, Lei
Liu, Huan
Gao, Jian
Deng, Kai
Wang, Xiaoyan
Dong, Xiuzhu
Li, Jie
author_facet Qi, Lei
Liu, Huan
Gao, Jian
Deng, Kai
Wang, Xiaoyan
Dong, Xiuzhu
Li, Jie
author_sort Qi, Lei
collection PubMed
description Ribosomal RNA (rRNA) processing and maturation are fundamentally important for ribosome biogenesis, but the mechanisms in archaea, the third form of life, remains largely elusive. This study aimed to investigate the rRNA maturation process in Methanococcus maripaludis, a representative archaeon lacking known 3′-5′ exonucleases. Through cleavage site identification and enzymatic assays, the splicing endonuclease EndA was determined to process the bulge-helix-bulge (BHB) motifs in 16S and 23S rRNA precursors. After splicing, the circular processing intermediates were formed and this was confirmed by quantitative RT-PCR and Northern blot. Ribonuclease assay revealed a specific cleavage at a 10-nt A/U-rich motif at the mature 5′ end of pre-16S rRNA, which linearized circular pre-16S rRNA intermediate. Further 3′-RACE and ribonuclease assays determined that the endonuclease Nob1 cleaved the 3′ extension of pre-16S rRNA, and so generated the mature 3′ end. Circularized RT-PCR (cRT-PCR) and 5′-RACE identified two cleavage sites near helix 1 at the 5′ end of 23S rRNA, indicating that an RNA structure-based endonucleolytic processing linearized the circular pre-23S rRNA intermediate. In the maturation of pre-5S rRNA, multiple endonucleolytic processing sites were determined at the 10-nt A/U-rich motif in the leader and trailer sequence. This study demonstrates that endonucleolytic processing, particularly at the 10-nt A/U-rich motifs play an essential role in the pre-rRNA maturation of M. maripaludis, indicating diverse pathways of rRNA maturation in archaeal species.
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spelling pubmed-105156642023-09-23 Endonucleolytic processing plays a critical role in the maturation of ribosomal RNA in Methanococcus maripaludis Qi, Lei Liu, Huan Gao, Jian Deng, Kai Wang, Xiaoyan Dong, Xiuzhu Li, Jie RNA Biol Research Paper Ribosomal RNA (rRNA) processing and maturation are fundamentally important for ribosome biogenesis, but the mechanisms in archaea, the third form of life, remains largely elusive. This study aimed to investigate the rRNA maturation process in Methanococcus maripaludis, a representative archaeon lacking known 3′-5′ exonucleases. Through cleavage site identification and enzymatic assays, the splicing endonuclease EndA was determined to process the bulge-helix-bulge (BHB) motifs in 16S and 23S rRNA precursors. After splicing, the circular processing intermediates were formed and this was confirmed by quantitative RT-PCR and Northern blot. Ribonuclease assay revealed a specific cleavage at a 10-nt A/U-rich motif at the mature 5′ end of pre-16S rRNA, which linearized circular pre-16S rRNA intermediate. Further 3′-RACE and ribonuclease assays determined that the endonuclease Nob1 cleaved the 3′ extension of pre-16S rRNA, and so generated the mature 3′ end. Circularized RT-PCR (cRT-PCR) and 5′-RACE identified two cleavage sites near helix 1 at the 5′ end of 23S rRNA, indicating that an RNA structure-based endonucleolytic processing linearized the circular pre-23S rRNA intermediate. In the maturation of pre-5S rRNA, multiple endonucleolytic processing sites were determined at the 10-nt A/U-rich motif in the leader and trailer sequence. This study demonstrates that endonucleolytic processing, particularly at the 10-nt A/U-rich motifs play an essential role in the pre-rRNA maturation of M. maripaludis, indicating diverse pathways of rRNA maturation in archaeal species. Taylor & Francis 2023-09-20 /pmc/articles/PMC10515664/ /pubmed/37731260 http://dx.doi.org/10.1080/15476286.2023.2258035 Text en © 2023 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.
spellingShingle Research Paper
Qi, Lei
Liu, Huan
Gao, Jian
Deng, Kai
Wang, Xiaoyan
Dong, Xiuzhu
Li, Jie
Endonucleolytic processing plays a critical role in the maturation of ribosomal RNA in Methanococcus maripaludis
title Endonucleolytic processing plays a critical role in the maturation of ribosomal RNA in Methanococcus maripaludis
title_full Endonucleolytic processing plays a critical role in the maturation of ribosomal RNA in Methanococcus maripaludis
title_fullStr Endonucleolytic processing plays a critical role in the maturation of ribosomal RNA in Methanococcus maripaludis
title_full_unstemmed Endonucleolytic processing plays a critical role in the maturation of ribosomal RNA in Methanococcus maripaludis
title_short Endonucleolytic processing plays a critical role in the maturation of ribosomal RNA in Methanococcus maripaludis
title_sort endonucleolytic processing plays a critical role in the maturation of ribosomal rna in methanococcus maripaludis
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10515664/
https://www.ncbi.nlm.nih.gov/pubmed/37731260
http://dx.doi.org/10.1080/15476286.2023.2258035
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