Wang Juncheng, Li Chengdao, Yao Lirong, Ma Zengke, Ren Panrong, Si Erjing, Li Baochun, Meng Yaxiong, Ma Xiaole, Yang Ke, Shang Xunwu, Wang Huajun
State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China.
Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China.
Front Plant Sci. 2022 Aug 18;13:917652. doi: 10.3389/fpls.2022.917652. eCollection 2022.
Phosphate (Pi) stress is an important environmental factor that limits plant growth and development. Of various posttranslational modifications (PTMs), protein phosphorylation and succinylation are the two most important PTMs that regulate multiple biological processes in response to Pi stress. However, these PTMs have been investigated individually but their interactions with proteins in response to Pi stress remain poorly understood. In this study, to elucidate the underlying mechanisms of protein phosphorylation and succinylation in response to Pi stress, we performed a global analysis of the barley root phosphorylome and succinylome in Pi starvation and recovery stages, respectively. A total of 3,634 and 884 unique phosphorylated and succinylated proteins, respectively, corresponding to 11,538 and 2,840 phospho- and succinyl-sites, were identified; of these, 275 proteins were found to be simultaneously phosphorylated and succinylated. Gene Set Enrichment Analysis was performed with a Kyoto Encyclopedia of Genes and Genomes pathway database revealing pathways that significantly enriched in the phosphorylome and succinylome. Such pathways, were dynamically regulated by Pi starvation and recovery treatments, and could be partitioned into distinct metabolic processes. In particular, phosphorylated proteins related to purine, the mitogen-activated protein kinase (MAPK) signaling pathway, pyrimidine, and ATP-binding cassette (ABC) transporters were upregulated in both Pi deprivation and recovery stages. Succinylated proteins, significantly upregulated by both Pi starvation and recovery, were enriched in nitrogen metabolism and phenylpropanoid biosynthesis. Meanwhile, succinylated proteins that were significantly downregulated by both Pi starvation and recovery were enriched in lysine degradation and tryptophan metabolism. This highlighted the importance of these metabolic pathways in regulating Pi homeostasis. Furthermore, protein-protein interaction network analyses showed that the response of central metabolic pathways to Pi starvation and recovery was significantly modulated by phosphorylation or succinylation, both individually and together. In addition, we discovered relevant proteins involved in MAPK signaling and phenylpropanoid biosynthetic pathways existing in interactions between phosphorylated and succinylated proteins in response to Pi recovery. The current study not only provides a comprehensive analysis of phosphorylated and succinylated proteins in plant responses to Pi starvation and recovery, but also reveals detailed interactions between phosphorylated and succinylated proteins in barley roots.
磷（Pi）胁迫是限制植物生长发育的重要环境因素。在各种翻译后修饰（PTM）中，蛋白质磷酸化和琥珀酰化是响应Pi胁迫调节多种生物学过程的两个最重要的PTM。然而，这些PTM已被单独研究，但它们在响应Pi胁迫时与蛋白质的相互作用仍知之甚少。在本研究中，为了阐明响应Pi胁迫时蛋白质磷酸化和琥珀酰化的潜在机制，我们分别对大麦根在Pi饥饿和恢复阶段的磷酸化蛋白质组和琥珀酰化蛋白质组进行了全局分析。共鉴定出3634个和884个独特的磷酸化和琥珀酰化蛋白质，分别对应11538个和2840个磷酸化位点和琥珀酰化位点；其中，发现275个蛋白质同时发生磷酸化和琥珀酰化。利用京都基因与基因组百科全书途径数据库进行基因集富集分析，揭示了在磷酸化蛋白质组和琥珀酰化蛋白质组中显著富集的途径。这些途径受Pi饥饿和恢复处理的动态调节，可分为不同的代谢过程。特别是，与嘌呤、丝裂原活化蛋白激酶（MAPK）信号通路、嘧啶和ATP结合盒（ABC）转运蛋白相关的磷酸化蛋白质在Pi缺乏和恢复阶段均上调。Pi饥饿和恢复均显著上调的琥珀酰化蛋白质富集于氮代谢和苯丙烷生物合成。同时，Pi饥饿和恢复均显著下调的琥珀酰化蛋白质富集于赖氨酸降解和色氨酸代谢。这突出了这些代谢途径在调节Pi稳态中的重要性。此外，蛋白质-蛋白质相互作用网络分析表明中枢代谢途径对Pi饥饿和恢复的响应分别或共同受到磷酸化或琥珀酰化的显著调节。此外，我们发现响应Pi恢复时，参与MAPK信号和苯丙烷生物合成途径的相关蛋白质存在于磷酸化和琥珀酰化蛋白质之间的相互作用中。本研究不仅对植物响应Pi饥饿和恢复时的磷酸化和琥珀酰化蛋白质进行了全面分析，还揭示了大麦根中磷酸化和琥珀酰化蛋白质之间的详细相互作用。
