Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA.
mBio. 2024 Oct 16;15(10):e0177324. doi: 10.1128/mbio.01773-24. Epub 2024 Aug 27.
Lysine and arginine methylation is an important regulator of enzyme activity and transcription in eukaryotes. However, little is known about this covalent modification in bacteria. In this work, we investigated the role of methylation in bacteria. By reanalyzing a large phyloproteomics data set from 48 bacterial strains representing six phyla, we found that almost a quarter of the bacterial proteome is methylated. Many of these methylated proteins are conserved across diverse bacterial lineages, including those involved in central carbon metabolism and translation. Among the proteins with the most conserved methylation sites is ribosomal protein L11 (bL11). bL11 methylation has been a mystery for five decades, as the deletion of its methyltransferase PrmA causes no cell growth defects. Comparative proteomics analysis combined with inorganic polyphosphate and guanosine tetra/pentaphosphate assays of the mutant in revealed that bL11 methylation is important for stringent response signaling. In the stationary phase, we found that the mutant has impaired guanosine tetra/pentaphosphate production. This leads to a reduction in inorganic polyphosphate levels, accumulation of RNA and ribosomal proteins, and an abnormal polysome profile. Overall, our investigation demonstrates that the evolutionarily conserved bL11 methylation is important for stringent response signaling and ribosomal activity regulation and turnover.
Protein methylation in bacteria was first identified over 60 years ago. Since then, its functional role has been identified for only a few proteins. To better understand the functional role of methylation in bacteria, we analyzed a large phyloproteomics data set encompassing 48 diverse bacteria. Our analysis revealed that ribosomal proteins are often methylated at conserved residues, suggesting that methylation of these sites may have a functional role in translation. Further analysis revealed that methylation of ribosomal protein L11 is important for stringent response signaling and ribosomal homeostasis.
赖氨酸和精氨酸甲基化是真核生物中酶活性和转录的重要调节因子。然而，人们对细菌中的这种共价修饰知之甚少。在这项工作中，我们研究了甲基化在细菌中的作用。通过重新分析来自代表六个门的 48 个细菌菌株的大型phyloproteomics 数据集，我们发现几乎四分之一的细菌蛋白质组被甲基化。这些被甲基化的蛋白质中有许多在不同的细菌谱系中是保守的，包括那些参与中心碳代谢和翻译的蛋白质。在具有最保守甲基化位点的蛋白质中，核糖体蛋白 L11（bL11）。bL11 甲基化已经是一个五十年的谜团，因为其甲基转移酶 PrmA 的缺失不会导致细胞生长缺陷。比较蛋白质组学分析结合无机多磷酸盐和鸟苷四/五磷酸盐测定表明，bL11 甲基化对严格响应信号很重要。在停滞期，我们发现 突变体的鸟苷四/五磷酸盐产量受损。这导致无机多磷酸盐水平降低，RNA 和核糖体蛋白积累，以及异常的多核糖体谱。总的来说，我们的研究表明，进化上保守的 bL11 甲基化对严格响应信号和核糖体活性调节和周转很重要。
细菌中的蛋白质甲基化早在 60 多年前就被首次发现。从那时起，只有少数几种蛋白质的功能作用得到了确定。为了更好地了解甲基化在细菌中的功能作用，我们分析了一个包含 48 种不同细菌的大型 phyloproteomics 数据集。我们的分析表明，核糖体蛋白经常在保守残基上被甲基化，这表明这些位点的甲基化可能在翻译中具有功能作用。进一步的分析表明，核糖体蛋白 L11 的甲基化对于严格响应信号和核糖体的稳态很重要。
