Raghu Darshan Hebbal, Dcunha Leona, Ahmed Mukhtar, Fahma Amal, Mahin Althaf, Gopalakrishnan Athira Perunelly, John Levin, Subair Suhail, Shivamurthy Prathik Basthikoppa, Varghese Susmi, Ummar Samseera, Nisar Mahammad, Ramesh Poornima, Madar Inamul Hasan, Raju Rajesh
Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore, Karnataka 575018, India.
Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia.
Biochim Biophys Acta Proteins Proteom. 2025 Jun 2;1873(5):141080. doi: 10.1016/j.bbapap.2025.141080.
Protein kinase C Delta (PRKCD) is a serine/threonine kinase involved in transcription regulation, cytoskeleton organization, DNA damage response, DNA repair and carcinogenesis. Several PRKCD phosphopeptides are frequently detected to be differentially regulated through mass spectrometry-based phosphoproteomics analysis. Here, we utilize publicly available phosphoproteomics data to decipher phosphoregulatory networks associated with PRKCD. Among 315 phosphoproteomics datasets demonstrating the differential regulation of phosphopeptides of PRKCD, the phosphosites S304, Y313, S645, S299, S302, S664, Y334, Y374, T295 and T507 predominantly represent PRKCD hyperphosphorylation in over 83 % of cases. Further, through co-differential regulation analysis of the predominant sites and associated phosphosites on other proteins, we propose that the autophosphorylation sites S302 and S304 are critically associated with the kinase activity of PRKCD and play a crucial role in modulating its downstream signaling pathways. Compared to known activation sites of PRKCD including Y313, Y334 and Y374, the sites S302 and S304 coregulated the most with the experimentally validated and predicted substrates. Besides that, phosphosites Y313, Y334 and Y374 are associated with stress signaling and cancer progression. Current study focuses on critical kinase-activation associated with phosphosites in kinases. This study highlights the sites S302 and S304 as activation sites and as key players in various cellular processes including cell cycle regulation, motility, adhesion and migration. Our approach and the stringent criteria adopted sets a robust platform to analyze differentially regulated phosphoproteome data in diverse biological contexts to interpret the predominant phosphosites, their co-regulation and the overall biological relevance of such regulation in pathophysiological processes.
蛋白激酶Cδ（PRKCD）是一种丝氨酸/苏氨酸激酶，参与转录调控、细胞骨架组织、DNA损伤反应、DNA修复和致癌作用。通过基于质谱的磷酸化蛋白质组学分析，经常检测到几种PRKCD磷酸化肽段存在差异调节。在此，我们利用公开可用的磷酸化蛋白质组学数据来解读与PRKCD相关的磷酸化调控网络。在315个显示PRKCD磷酸化肽段差异调节的磷酸化蛋白质组数据集中，磷酸化位点S304、Y313、S645、S299、S302、S664、Y334、Y374、T295和T507在超过83%的情况下主要代表PRKCD的过度磷酸化。此外，通过对主要位点和其他蛋白质上相关磷酸化位点的共差异调节分析，我们提出自磷酸化位点S302和S304与PRKCD的激酶活性密切相关，并在调节其下游信号通路中起关键作用。与PRKCD已知的激活位点（包括Y313、Y334和Y374）相比，位点S302和S304与经过实验验证和预测的底物共调节程度最高。除此之外，磷酸化位点Y313、Y334和Y374与应激信号传导和癌症进展相关。当前研究聚焦于激酶中与磷酸化位点相关的关键激酶激活。本研究突出了位点S302和S304作为激活位点以及在包括细胞周期调控、运动、黏附和迁移等各种细胞过程中的关键作用。我们的方法和所采用的严格标准建立了一个强大的平台，用于分析不同生物学背景下差异调节的磷酸化蛋白质组数据，以解读主要的磷酸化位点、它们的共调节以及这种调节在病理生理过程中的整体生物学相关性。
