Yan Ningning, Yang Shuqing, Chao Haoyu, Zhang Wenbing, Zhang Jian, Chen Ming, Zhao Jun
College of Horticultrue and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China.
College of Agriculture, Tarim University, Alaer, China.
Front Plant Sci. 2024 Dec 2;15:1450936. doi: 10.3389/fpls.2024.1450936. eCollection 2024.
Protein kinases play a significant role in plant responses to biotic and abiotic stresses, as well as in growth and development. While the kinome has been extensively investigated in crops such as , soybean, common bean, and cotton, studies on protein kinases in sunflower remain limited. Our objective is to explore protein kinases in sunflower to bridge the research gap and enhance the understanding of their functions. We identified a total of 2,583 protein kinases from sunflower, which were classified into 22 families and 121 subfamilies. By comparing the subfamily members between sunflower and other species, we found that three subfamilies in sunflower-RLK-Pelle_CrRLK1L-1, RLK-Pelle_SD-2b, and RLK-Pelle_WAK-had undergone significant expansion. We then investigated the chromosomal distribution, molecular weight, isoelectric point, transmembrane domain, signal peptide, and structural and evolutionary diversity of the protein kinases. Through these studies, we have obtained a basic understanding of protein kinases in sunflower. To investigate the role of protein kinases in sunflower's response to biotic and abiotic stresses, we obtained 534 transcriptome datasets from various research groups, covering eight types of abiotic stress and two types of biotic stress. For the first time, we overcame the batch effects in the data and utilized a gene scoring system developed by our lab to perform a comprehensive analysis of multiple transcriptome datasets from different research groups. Ultimately, 73 key protein kinases were identified from numerous candidates, and functional annotation revealed that they are key members of signaling pathways such as ABA, MAPK, and SOS, actively participating in sunflower's response to biotic and abiotic stresses. In summary, through the exploration of protein kinases in sunflower, we have filled the gap in protein kinase research and provided a substantial amount of foundational data. By using the new scoring method to eliminate batch effects between transcriptome datasets, we achieved the first comprehensive analysis of large-scale transcriptome data. This method allows for a more thorough and detailed identification of key protein kinases that are widely regulated under various stress conditions, providing numerous candidate genes for sunflower stress resistance research.
蛋白激酶在植物对生物和非生物胁迫的响应以及生长发育过程中发挥着重要作用。虽然在诸如大豆、菜豆和棉花等作物中对激酶组进行了广泛研究，但对向日葵中蛋白激酶的研究仍然有限。我们的目标是探索向日葵中的蛋白激酶，以填补研究空白并增进对其功能的理解。我们从向日葵中总共鉴定出2583个蛋白激酶，它们被分为22个家族和121个亚家族。通过比较向日葵与其他物种的亚家族成员，我们发现向日葵中的三个亚家族——RLK-Pelle_CrRLK1L-1、RLK-Pelle_SD-2b和RLK-Pelle_WAK——经历了显著扩张。然后，我们研究了这些蛋白激酶的染色体分布、分子量、等电点、跨膜结构域、信号肽以及结构和进化多样性。通过这些研究，我们对向日葵中的蛋白激酶有了基本了解。为了研究蛋白激酶在向日葵对生物和非生物胁迫响应中的作用，我们从各个研究小组获得了534个转录组数据集，涵盖八种非生物胁迫和两种生物胁迫。我们首次克服了数据中的批次效应，并利用我们实验室开发的基因评分系统对来自不同研究小组的多个转录组数据集进行了全面分析。最终，从众多候选激酶中鉴定出73个关键蛋白激酶，功能注释表明它们是ABA、MAPK和SOS等信号通路的关键成员，积极参与向日葵对生物和非生物胁迫的响应。总之，通过对向日葵中蛋白激酶的探索，我们填补了蛋白激酶研究的空白，并提供了大量基础数据。通过使用新的评分方法消除转录组数据集之间的批次效应，我们实现了对大规模转录组数据的首次全面分析。这种方法能够更全面、详细地鉴定在各种胁迫条件下广泛调控的关键蛋白激酶，为向日葵抗逆性研究提供了众多候选基因。
