Protein methylation has been proposed as an important post-translational modification, which occurs predominantly on lysine and arginine residues. Recent discoveries have revealed that protein methylation is also present on non-histones besides histones, and plays critical roles in regulating protein stability and function. However, proteome-wide identification of methylated proteins in plants remains unexplored. Here, we present the first global survey of monomethyl arginine, symmetric and asymmetric dimethyl arginine, and monomethyl, dimethyl, trimethyl lysine modifications in the proteomes of 10-day-old Arabidopsis seedlings through a combination of immunoaffinity purification and mass spectrometry analysis. In total, we identified 617 methylation sites which mapped to 412 proteins, with 263 proteins harboring 381 lysine methylation sites and 149 proteins harboring 236 arginine methylation sites. Among them, 607 methylation sites on 408 proteins were novel findings. Motif analysis revealed that glycine preferentially flanked methylated arginine residues, whereas aspartate and glutamate enriched around mono- and dimethylated lysine sites. Methylated proteins were involved in a variety of metabolic processes, showing significant enrichment in RNA-related metabolic pathways including spliceosome, RNA transport, and ribosome. Our data provide a global view of methylated non-histone proteins in Arabidopsis, laying foundations for elucidating the biological function of protein methylation in plants. SIGNIFICANCE: Protein methylation has emerged as a common and important modification both in eukaryotes and prokaryotes. The identification of methylated sites/peptides is fundamental for further functional analysis of protein methylation. This study was the first proteome-scale identification of lysine and arginine methylation in plants. We found that methylation occurred widely on non-histone proteins in Arabidopsis and was involved in diverse biological functions. The results provide foundations for the investigation of the protein methylome in Arabidopsis and provide powerful resources for the functional analysis of protein methylation in plants.

中文翻译：

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拟南芥中的蛋白质甲基化组分析揭示了RNA相关过程中的调控。

已经提出蛋白质甲基化是重要的翻译后修饰，其主要发生在赖氨酸和精氨酸残基上。最近的发现表明，除组蛋白外，蛋白质非组蛋白也存在蛋白质甲基化，并且在调节蛋白质的稳定性和功能中起着至关重要的作用。但是，尚未对蛋白质组范围内的植物甲基化蛋白质进行鉴定。在这里，我们结合免疫亲和纯化和质谱分析，对10天大拟南芥幼苗蛋白质组中的单甲基精氨酸，对称和不对称二甲基精氨酸以及单甲基，二甲基，三​​甲基赖氨酸修饰进行了首次全球调查。我们总共确定了617个甲基化位点，它们映射到412种蛋白质，其中263个蛋白具有381个赖氨酸甲基化位点，而149个蛋白具有236个精氨酸甲基化位点。其中，在408个蛋白质上的607个甲基化位点是新发现。基序分析表明，甘氨酸优先位于甲基化的精氨酸残基的侧翼，而天冬氨酸和谷氨酸在单和二甲基化的赖氨酸位点附近富集。甲基化蛋白参与各种代谢过程，显示出与RNA相关的代谢途径（包括剪接体，RNA转运和核糖体）的大量富集。我们的数据提供了拟南芥中甲基化非组蛋白的全球视野，为阐明植物中蛋白质甲基化的生物学功能奠定了基础。意义：蛋白质甲基化已成为真核生物和原核生物中常见且重要的修饰。甲基化位点/肽的鉴定是蛋白质甲基化进一步功能分析的基础。这项研究是首次蛋白质组规模鉴定植物中的赖氨酸和精氨酸甲基化。我们发现甲基化广泛发生在拟南芥中的非组蛋白上，并参与多种生物学功能。该结果为拟南芥中蛋白质甲基化组的研究奠定了基础，为植物中蛋白质甲基化的功能分析提供了有力的资源。我们发现甲基化广泛发生在拟南芥中的非组蛋白上，并参与多种生物学功能。该结果为拟南芥中蛋白质甲基化组的研究奠定了基础，为植物中蛋白质甲基化的功能分析提供了有力的资源。我们发现甲基化广泛发生在拟南芥中的非组蛋白上，并参与多种生物学功能。该结果为拟南芥中蛋白质甲基化组的研究奠定了基础，为植物中蛋白质甲基化的功能分析提供了有力的资源。