TY - JOUR

T1 - Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA

AU - Gao, Shangyu

AU - Sun, Yu

AU - Chen, Xiaoguang

AU - Zhu, Changhua

AU - Liu, Xiaoye

AU - Wang, Wenlei

AU - Gan, Lijun

AU - Lu, Yanwu

AU - Schaarschmidt, Frank

AU - Herde, Marco

AU - Witte, Claus Peter

AU - Chen, Mingjia

N1 - Funding Information: The Fundamental Research Funds for the Central Universities [YDZX2023013]; the Deutsche Forschungsgemeinschaft (DFG) [CH2292/1-1 to M.C. and C.-P.W., WI3411/8-1 and INST 187/741-1 FUGG to C.-P. W., and HE-5949/4-1 to M.H.]; the International Centre for Genetic Engineering and Biotechnology [CRP/CHN20-04_EC]; the National Natural Science Foundation of China [31900907]; the Natural Science Foundation of Jiangsu Province, China [BK20190528]; and Nanjing Agricultural University [start-up fund for advanced talents to M.C.]. Funding for open access charge: Nanjing Agricultural University, China.

PY - 2023/8/11

Y1 - 2023/8/11

N2 - 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 (m5U) is an abundant RNA modification (m5U/U ∼1%) in Arabidopsis. We show that m5U is introduced mainly by tRNA-SPECIFIC METHYLTRANSFERASE 2A and 2B. Genetic disruption of 5mU degradation in the NSH1 mutant causes m5U to occur in mRNA and results in reduced seedling growth, which is aggravated by external 5mU supplementation, also leading to more m5U 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 m5U modification.

AB - 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 (m5U) is an abundant RNA modification (m5U/U ∼1%) in Arabidopsis. We show that m5U is introduced mainly by tRNA-SPECIFIC METHYLTRANSFERASE 2A and 2B. Genetic disruption of 5mU degradation in the NSH1 mutant causes m5U to occur in mRNA and results in reduced seedling growth, which is aggravated by external 5mU supplementation, also leading to more m5U 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 m5U modification.

UR - http://www.scopus.com/inward/record.url?scp=85167844494&partnerID=8YFLogxK

U2 - 10.1093/nar/gkad529

DO - 10.1093/nar/gkad529

M3 - Article

C2 - 37334828

AN - SCOPUS:85167844494

VL - 51

SP - 7451

EP - 7464

JO - Nucleic acids research

JF - Nucleic acids research

SN - 0301-5610

IS - 14

ER -