Proteome-Wide Analyses Reveal the Diverse Functions of Lysine 2-Hydroxyisobutyrylation in Oryza sativa.,Rice

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Proteome-Wide Analyses Reveal the Diverse Functions of Lysine 2-Hydroxyisobutyrylation in Oryza sativa.
Rice ( IF 4.8 ) Pub Date : 2020-06-05 , DOI: 10.1186/s12284-020-00389-1
Chao Xue _{1,

2} , Zhongying Qiao ₃ , Xu Chen _{1,

2} , Penghui Cao ₃ , Kai Liu _{1,

2} , Shuai Liu _{1,

2} , Lu Ye _{1,

2} , Zhiyun Gong _{1,

2}

Affiliation

Background

Lysine 2-hydroxyisobutyrylation (Khib), a newly identified post-translational modification, is known to regulate transcriptional activity in animals. However, extensive studies of the lysine 2-hydroxyisobutyrylome in plants and animals have yet to be performed.

Results

In this study, using LC-MS/MS qualitative proteomics strategies, we identified 4163 Khib sites on 1596 modified proteins in rice (Oryza sativa) seedlings. Motif analysis revealed 10 conserved motifs flanking the Khib sites, and subcellular localization analysis revealed that 44% of the Khib proteins are localized in the chloroplast. Gene ontology function, KEGG pathway, and protein domain enrichment analyses revealed that Khib occurs on proteins involved in diverse biological processes and is especially enriched in carbon metabolism and photosynthesis. Among the modified proteins, 20 Khib sites were identified in histone H2A and H2B, while only one site was identified in histone H4. Protein-protein interaction (PPI) network analysis further demonstrated that Khib participates in diverse biological processes including ribosomal activity, biosynthesis of secondary metabolites, and metabolic pathways. In addition, a comparison of lysine 2-hydroxyisobutyrylation, acetylation, and crotonylation in the rice proteome showed that 45 proteins with only 26 common lysine sites are commonly modified by three PTMs. The crosstalk of modified sites and PPI among these PTMs may form a complex network with both similar and different regulatory mechanisms.

Conclusions

In summary, our study comprehensively profiles the lysine 2-hydroxyisobutyrylome in rice and provides a better understanding of its biological functions in plants.

中文翻译：

全蛋白质组分析揭示了稻中赖氨酸 2-羟基异丁酰化的多种功能。

背景

赖氨酸 2-羟基异丁酰化 (Khib) 是一种新发现的翻译后修饰，已知可调节动物的转录活性。然而，尚未对植物和动物中的赖氨酸 2-羟基异丁酰组进行广泛的研究。

结果

在这项研究中，我们利用 LC-MS/MS 定性蛋白质组学策略，在水稻 ( Oryza sativa ) 幼苗的 1596 个修饰蛋白上鉴定出了 4163 个 Khib 位点。基序分析揭示了 Khib 位点侧翼的 10 个保守基序，亚细胞定位分析揭示了 44% 的 Khib 蛋白位于叶绿体中。基因本体功能、KEGG 通路和蛋白质结构域富集分析表明，Khib 发生在参与多种生物过程的蛋白质上，尤其在碳代谢和光合作用中富集。在修饰的蛋白质中，在组蛋白 H2A 和 H2B 中鉴定出 20 个 Khib 位点，而在组蛋白 H4 中仅鉴定出 1 个位点。蛋白质-蛋白质相互作用（PPI）网络分析进一步证明Khib参与多种生物过程，包括核糖体活性、次级代谢产物的生物合成和代谢途径。此外，对水稻蛋白质组中赖氨酸2-羟基异丁酰化、乙酰化和巴豆酰化的比较表明，仅具有26个常见赖氨酸位点的45种蛋白质通常被三个PTM修饰。这些 PTM 之间修饰位点和 PPI 的串扰可能形成一个具有相似和不同调控机制的复杂网络。