College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany.
Nucleic Acids Res. 2023 Aug 11;51(14):7451-7464. doi: 10.1093/nar/gkad529.
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.
5-甲基胞嘧啶是真核生物 RNA 和 DNA 中的一种常见修饰，影响 mRNA 稳定性和基因表达。在这里，我们表明游离的 5-甲基胞嘧啶（5mC）和 5-甲基-2'-脱氧胞嘧啶是由拟南芥核酸周转产生的，并阐明了这些胞嘧啶是如何降解的，这在真核生物中尚不清楚。首先，胞嘧啶脱氨酶产生 5-甲基尿嘧啶（5mU）和胸腺嘧啶，随后被核苷酸水解酶 1（NSH1）水解为胸腺嘧啶和核糖或脱氧核糖。有趣的是，从 RNA 周转产生的胸腺嘧啶比从 DNA 周转产生的多得多，而且大多数 5mU 是直接从 RNA 释放的，没有 5mC 中间产物，因为 5-甲基化尿嘧啶（m5U）是拟南芥中丰富的 RNA 修饰（m5U/U∼1%）。我们表明，m5U 主要是由 tRNA 特异性甲基转移酶 2A 和 2B 引入的。在 NSH1 突变体中破坏 5mU 的降解会导致 m5U 出现在 mRNA 中，并导致幼苗生长受阻，而外部 5mU 的补充会加剧这种情况，也会导致所有 RNA 物种中的 m5U 更多。鉴于植物、哺乳动物和其他真核生物嘧啶分解代谢之间的相似性，我们假设嘧啶降解过程中去除 5mU 是许多生物体中嘧啶降解的一个重要功能，在植物中，这一功能可以保护 RNA 免受随机的 m5U 修饰。
