Yang Haitao, Bai Xin, Muhammad Tayeb, Yang Tao, Jia Chunping, Wang Baike, Yu Qinghui, Wang Juan
Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Fruits and Vegetables, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
College of Life Science and Technology, Xinjiang University, Urumqi, China.
BMC Plant Biol. 2025 Jul 3;25(1):850. doi: 10.1186/s12870-025-06857-4.
The GHMP kinase gene family is a class of structurally similar protein kinases that have been named by combining the first letter of its four members, galactokinase (GALK), homoserine kinase (HSK), mevalonate kinase (MK) and phosphomevalonate kinase (PMK). It plays a pivotal role in regulating plant growth and development, as well as mediating various responses. However, the identification and functional analysis of GHMP family members in tomato have not been carried out yet.
This study presents a comprehensive analysis of the GHMP gene family in cultivated tomato and three wild tomato species. The analysis encompasses phylogenetic classification, gene structure, collinearity, physical and chemical features, cis-acting elements, tissue-specific expression, and hormonal and abiotic stress responses. A total of 56 GHMP genes were identified in the four tomato species. The phylogenetic analysis classified the GHMP members into 10 subfamilies, which is in agreement with the results of motif distribution and gene structure analysis. Members of the same subfamily tend to exhibit similar or identical motif types and order of distribution. The synteny analysis suggests that dispersed and single-copy replication may have played a role in the expansion of the GHMP gene family in tomatoes with pure selection. A diverse set of cis-acting elements was identified in the promoters of the GHMPs, includingelements related to growth and development, hormone and stress responses and transcription factor interaction binding sites, indicating a multifaceted role of the GHMPs in tomato. RNA-seq data analysis revealed that GHMP members exhibited differential expression in distinct tissues, signifying their involvement in tomato growth and development. In response to exogenous hormonal and abiotic treatments, FKGP, PMK1, ARA1, PMK2, GALAK2 and ISPE were upregulated by hormonal treatments, while ISPE, PMK1, ARA1, ARA2, and MK responded to abiotic stresses.
Overall, the findings of this study contribute to a deeper understanding of the GHMP gene family, which could serve as a foundation for future investigations of their biological function, particularly in response to hormonal and abiotic stress.
GHMP激酶基因家族是一类结构相似的蛋白激酶，由其四个成员（半乳糖激酶（GALK）、高丝氨酸激酶（HSK）、甲羟戊酸激酶（MK）和磷酸甲羟戊酸激酶（PMK））的首字母组合命名。它在调节植物生长发育以及介导各种反应中起关键作用。然而，番茄中GHMP家族成员的鉴定和功能分析尚未开展。
本研究对栽培番茄和三种野生番茄物种中的GHMP基因家族进行了全面分析。分析内容包括系统发育分类、基因结构、共线性、理化特性、顺式作用元件、组织特异性表达以及激素和非生物胁迫反应。在这四个番茄物种中总共鉴定出56个GHMP基因。系统发育分析将GHMP成员分为10个亚家族，这与基序分布和基因结构分析结果一致。同一亚家族的成员往往表现出相似或相同的基序类型和分布顺序。共线性分析表明，分散和单拷贝复制可能在纯合选择的番茄中GHMP基因家族的扩展中发挥了作用。在GHMP基因的启动子中鉴定出了多种顺式作用元件，包括与生长发育、激素和胁迫反应以及转录因子相互作用结合位点相关的元件，表明GHMP基因在番茄中具有多方面的作用。RNA测序数据分析表明，GHMP成员在不同组织中表现出差异表达，表明它们参与了番茄的生长发育。响应外源激素和非生物处理时，FKGP、PMK1、ARA1、PMK2、GALAK2和ISPE受激素处理上调，而ISPE、PMK1、ARA1、ARA2和MK对非生物胁迫有响应。
总体而言，本研究结果有助于更深入地了解GHMP基因家族，可为未来对其生物学功能的研究奠定基础，特别是在响应激素和非生物胁迫方面。
