Greco Brittany M, Zapata Gerardo, Dandage Rohan, Papkov Mikhail, Pereira Vanessa, Lefebvre François, Bourque Guillaume, Parts Leopold, Kuzmin Elena
Department of Biology, Concordia University, 7141 Sherbrooke St. W., Montreal, QC, H4B 1R6, Canada.
Centre for Applied Synthetic Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montreal, QC, H4B 1R6, Canada.
G3 (Bethesda). 2025 Jun 28. doi: 10.1093/g3journal/jkaf148.
Whole-genome duplication (WGD) events are common across various organisms; however, the retention and evolution of WGD paralogs is not fully understood. Quantitative measure of protein redistribution in response to the deletion of their WGD paralog provides insight into sources of gene retention. Here, we describe PARPAL (PARalog Protein Redistribution using Abundance and Localization in Yeast), a web database that houses results of high-content screening and deep learning neural network analysis of the redistribution of 164 proteins reflecting how their subcellular localization and protein abundance change in response to their paralog deletion in the budding yeast, Saccharomyces cerevisiae. We interrogated a total of 82 paralog pairs in two genetic backgrounds for a total of ∼3,500 micrographs of ∼460,000 cells. For example, Skn7-Hms2 exhibited dependent redistribution and Cue1-Cue4 showed compensatory redistribution response. PARPAL also links to other studies on trigenic interactions, protein-protein interactions and protein abundance. PARPAL is available at https://parpal.c3g-app.sd4h.ca and is a valuable resource for the yeast community interested in understanding the retention and evolution of paralogs and can help researchers to investigate protein dynamics of paralogs in other organisms.
全基因组复制（WGD）事件在各种生物体中都很常见；然而，WGD旁系同源基因的保留和进化尚未完全了解。对其WGD旁系同源基因缺失做出响应的蛋白质重新分布进行定量测量，有助于深入了解基因保留的来源。在这里，我们描述了PARPAL（利用酵母中的丰度和定位进行旁系同源蛋白重新分布），这是一个网络数据库，其中存储了对164种蛋白质重新分布进行高内涵筛选和深度学习神经网络分析的结果，这些结果反映了在酿酒酵母中，它们的亚细胞定位和蛋白质丰度如何响应其旁系同源基因缺失而发生变化。我们在两种遗传背景下总共研究了82对旁系同源基因，共获得了约460,000个细胞的约3,500张显微照片。例如，Skn7-Hms2表现出依赖性重新分布，而Cue1-Cue4表现出补偿性重新分布响应。PARPAL还链接到其他关于三基因相互作用、蛋白质-蛋白质相互作用和蛋白质丰度的研究。PARPAL可在https://parpal.c3g-app.sd4h.ca获取，对于有兴趣了解旁系同源基因的保留和进化的酵母群体来说，它是一个宝贵的资源，并且可以帮助研究人员研究其他生物体中旁系同源基因的蛋白质动态。
