Malonylome analysis in developing rice (Oryza saliva) seeds suggesting that protein lysine malonylation is well-conserved and overlaps with acetylation and succinylation substantially
Malonylome analysis in developing rice (Oryza saliva) seeds suggesting that protein lysine malonylation is well-conserved and overlaps with acetylation and succinylation substantially
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DOI：
10.1016/j.jprot.2017.08.021
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发表时间：
2018-01-06
影响因子：
3.3
通讯作者：
Peng, Zhaohua
中科院分区：
文献类型：
--
作者：
Mujahid, Hana;Meng, Xiaoxi;Peng, Zhaohua
近年来，赖氨酸丙二酰化由于其潜在的调节作用而引起了广泛的兴趣。虽然已经在细菌、小鼠和人类中进行了研究，但这种修饰在植物中的参与和生物学功能在很大程度上仍然未知。我们研究了全球蛋白质组的赖氨酸丙二酰化水稻种子开发使用亲和富集LC-MS/MS分析。我们在247种蛋白质中鉴定了421个丙二酰化赖氨酸位点。功能分析表明，丙二酰化蛋白主要存在于代谢过程中，包括碳代谢，糖酵解/异生，TCA循环，以及光合作用。水稻种子发育过程中淀粉合成途径中的酶也存在丙二酰化。此外，我们发现了一个显着的重叠之间的丙二酰化，琥珀酰化和乙酰化的网站在水稻中确定。此外，在不同界的生物体中观察到同源蛋白质保守位点的丙二酰化，包括小鼠、人类和细菌。最后，当分析水稻丙二酸化位点时，发现了不同的基序，并观察到从细菌到人类和水稻的保守基序。我们的研究结果提供了一个初步的了解赖氨酸丙二酸在植物中。该研究对进一步了解植物蛋白质赖氨酸丙二酰化的生物学功能具有重要的参考价值。生物学意义：赖氨酸丙二酰化是一种新发现的具有调节细胞代谢和活动功能的酰化。然而，丙二酰化状态尚未在植物中报道。谷物的产量和品质与粮食安全、人类健康和经济价值密切相关，主要决定于谷物种子的发育过程。为了研究植物中丙二酰化水平及其在种子发育中可能的调控功能，我们对水稻种子发育过程中丙二酰化水平进行了综合分析。在247个蛋白质中共发现了421个丙二酰化赖氨酸位点，这些位点参与了多个重要的代谢过程，包括中心碳代谢、脂类代谢、光合作用和淀粉合成。我们发现，带电荷的氨基酸，赖氨酸和精氨酸，是优选的残基的位置两侧的修饰的赖氨酸。通过序列比对分析，在不同的生物体中观察到组蛋白和非组蛋白上高度保守的修饰位点。更有趣的是，在水稻中发现了大量由丙二酰化、乙酰化和琥珀酰化所共有的修饰位点。该研究提供了对植物丙二酰化的全面了解，这将为进一步研究赖氨酸丙二酰化的功能，特别是在谷物种子发育中的功能提供初步平台。
In recent years, lysine malonylation has garnered wide spread interest due to its potential regulatory roles. While studies have been performed in bacteria, mouse, and human, the involvement and the biological function of this modification in plant are still largely unknown. We examined the global proteome profile of lysine malonylation in developing rice seeds using affinity enrichment followed by LC-MS/MS analysis. We identified 421 malonylated lysine sites across 247 proteins. Functional analyses showed predominant presence of malonylated proteins in metabolic processes, including carbon metabolism, glycolysis/gluconeogenesis, TCA cycle, as well as photosynthesis. Malonylation was also detected on enzymes in starch biosynthesis pathway in developing rice seeds. In addition, we found a remarkable overlap among the malonylated, succinylated and acetylated sites identified in rice. Furthermore, malonylation at conserved sites of homologous proteins was observed across organisnis of different kingdoms, including mouse, human, and bacteria. Finally, distinct motifs were identified when the rice malonylation sites were analyzed and conserved motifs were observed from bacterium to human and rice. Our results provide an initial understanding of the lysine malonylome in plants. The study has critical reference value for future understanding of the biological function of protein lysine malonylation in plants. Biological significance: Lysine malonylation is a newly discovered acylation with functional potential in regulating cellular metabolisms and activities. However, the malonylation status has not been reported in plants. Grain yield and quality, mainly determined during cereal seed development, are closely related to food security, human health and economic value. To evaluate malonylation level in plants and the possible regulatory functions of malonylation in seed development, we conducted comprehensive analyses of malonylome in developing rice seeds. A total of 421 malonylated lysine sites from 247 proteins were identified, which involved in multiple critical metabolic processes, including central carbon metabolism, lipid metabolism, photosynthesis, and starch biosynthesis. We found that charged amino acids, lysine and arginine, were the preferred residues in positions flanking the modified lysines. Highly conserved modification sites on both histone and non-histone proteins were observed among different organisms through sequence alignment analysis. More interestingly, a large number of modification sites shared by malonylation, acetylation and succinylation were identified in rice. The study presents a comprehensive understanding of malonylome in plants, which will serve as an initial platform for further investigation of the functions of lysine malonylation, especially in cereal seeds development.