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Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA

5-Methylated cytosine is a frequent modification in eukaryotic RNA and DNA influencing mRNA stability and gene expression. Here we show that free 5-methylcytidine (5mC) and 5-methyl-2′-deoxycytidine are generated from nucleic acid turnover in Arabidopsis thaliana, and elucidate how these cytidines a...

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Autores principales: Gao, Shangyu, Sun, Yu, Chen, Xiaoguang, Zhu, Changhua, Liu, Xiaoye, Wang, Wenlei, Gan, Lijun, Lu, Yanwu, Schaarschmidt, Frank, Herde, Marco, Witte, Claus-Peter, Chen, Mingjia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10415118/
https://www.ncbi.nlm.nih.gov/pubmed/37334828
http://dx.doi.org/10.1093/nar/gkad529
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author Gao, Shangyu
Sun, Yu
Chen, Xiaoguang
Zhu, Changhua
Liu, Xiaoye
Wang, Wenlei
Gan, Lijun
Lu, Yanwu
Schaarschmidt, Frank
Herde, Marco
Witte, Claus-Peter
Chen, Mingjia
author_facet Gao, Shangyu
Sun, Yu
Chen, Xiaoguang
Zhu, Changhua
Liu, Xiaoye
Wang, Wenlei
Gan, Lijun
Lu, Yanwu
Schaarschmidt, Frank
Herde, Marco
Witte, Claus-Peter
Chen, Mingjia
author_sort Gao, Shangyu
collection PubMed
description 5-Methylated cytosine is a frequent modification in eukaryotic RNA and DNA influencing mRNA stability and gene expression. Here we show that free 5-methylcytidine (5mC) and 5-methyl-2′-deoxycytidine are generated from nucleic acid turnover in Arabidopsis thaliana, and elucidate how these cytidines are degraded, which is unclear in eukaryotes. First CYTIDINE DEAMINASE produces 5-methyluridine (5mU) and thymidine which are subsequently hydrolyzed by NUCLEOSIDE HYDROLASE 1 (NSH1) to thymine and ribose or deoxyribose. Interestingly, far more thymine is generated from RNA than from DNA turnover, and most 5mU is directly released from RNA without a 5mC intermediate, since 5-methylated uridine (m(5)U) is an abundant RNA modification (m(5)U/U ∼1%) in Arabidopsis. We show that m(5)U is introduced mainly by tRNA-SPECIFIC METHYLTRANSFERASE 2A and 2B. Genetic disruption of 5mU degradation in the NSH1 mutant causes m(5)U to occur in mRNA and results in reduced seedling growth, which is aggravated by external 5mU supplementation, also leading to more m(5)U in all RNA species. Given the similarities between pyrimidine catabolism in plants, mammals and other eukaryotes, we hypothesize that the removal of 5mU is an important function of pyrimidine degradation in many organisms, which in plants serves to protect RNA from stochastic m(5)U modification.
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spelling pubmed-104151182023-08-12 Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA Gao, Shangyu Sun, Yu Chen, Xiaoguang Zhu, Changhua Liu, Xiaoye Wang, Wenlei Gan, Lijun Lu, Yanwu Schaarschmidt, Frank Herde, Marco Witte, Claus-Peter Chen, Mingjia Nucleic Acids Res Molecular Biology 5-Methylated cytosine is a frequent modification in eukaryotic RNA and DNA influencing mRNA stability and gene expression. Here we show that free 5-methylcytidine (5mC) and 5-methyl-2′-deoxycytidine are generated from nucleic acid turnover in Arabidopsis thaliana, and elucidate how these cytidines are degraded, which is unclear in eukaryotes. First CYTIDINE DEAMINASE produces 5-methyluridine (5mU) and thymidine which are subsequently hydrolyzed by NUCLEOSIDE HYDROLASE 1 (NSH1) to thymine and ribose or deoxyribose. Interestingly, far more thymine is generated from RNA than from DNA turnover, and most 5mU is directly released from RNA without a 5mC intermediate, since 5-methylated uridine (m(5)U) is an abundant RNA modification (m(5)U/U ∼1%) in Arabidopsis. We show that m(5)U is introduced mainly by tRNA-SPECIFIC METHYLTRANSFERASE 2A and 2B. Genetic disruption of 5mU degradation in the NSH1 mutant causes m(5)U to occur in mRNA and results in reduced seedling growth, which is aggravated by external 5mU supplementation, also leading to more m(5)U in all RNA species. Given the similarities between pyrimidine catabolism in plants, mammals and other eukaryotes, we hypothesize that the removal of 5mU is an important function of pyrimidine degradation in many organisms, which in plants serves to protect RNA from stochastic m(5)U modification. Oxford University Press 2023-06-19 /pmc/articles/PMC10415118/ /pubmed/37334828 http://dx.doi.org/10.1093/nar/gkad529 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. 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 (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Molecular Biology
Gao, Shangyu
Sun, Yu
Chen, Xiaoguang
Zhu, Changhua
Liu, Xiaoye
Wang, Wenlei
Gan, Lijun
Lu, Yanwu
Schaarschmidt, Frank
Herde, Marco
Witte, Claus-Peter
Chen, Mingjia
Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA
title Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA
title_full Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA
title_fullStr Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA
title_full_unstemmed Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA
title_short Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA
title_sort pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in rna
topic Molecular Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10415118/
https://www.ncbi.nlm.nih.gov/pubmed/37334828
http://dx.doi.org/10.1093/nar/gkad529
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