Snf2 Family Gene Distribution in Higher Plant Genomes Reveals DRD1 Expansion and Diversification in the Tomato Genome

As part of large protein complexes, Snf2 family ATPases are responsible for energy supply during chromatin remodeling, but the precise mechanism of action of many of these proteins is largely unknown. They influence many processes in plants, such as the response to environmental stress. This analysis is the first comprehensive study of Snf2 family ATPases in plants. We here present a comparative analysis of 1159 candidate plant Snf2 genes in 33 complete and annotated plant genomes, including two green algae. The number of Snf2 ATPases shows considerable variation across plant genomes (17-63 genes). The DRD1, Rad5/16 and Snf2 subfamily members occur most often. Detailed analysis of the plant-specific DRD1 subfamily in related plant genomes shows the occurrence of a complex series of evolutionary events. Notably tomato carries unexpected gene expansions of DRD1 gene members. Most of these genes are expressed in tomato, although at low levels and with distinct tissue or organ specificity. In contrast, the Snf2 subfamily genes tend to be expressed constitutively in tomato. The results underpin and extend the Snf2 subfamily classification, which could help to determine the various functional roles of Snf2 ATPases and to target environmental stress tolerance and yield in future breeding.

作为大型蛋白质复合物的组成部分，Snf2家族ATP酶（Snf2 family ATPases）负责染色质重塑（chromatin remodeling）过程中的能量供给，但目前对于这类蛋白质中多数成员的精确作用机制仍知之甚少。它们可调控植物的诸多生理过程，例如对环境胁迫的应答。本分析是首个针对植物中Snf2家族ATP酶的综合性研究。我们在此呈现了覆盖33个已完成注释的植物基因组（包含2种绿藻）中的1159个候选植物Snf2基因的比较分析结果。不同植物基因组中的Snf2家族ATP酶数量存在显著差异，范围为17至63个。其中DRD1、Rad5/16及Snf2亚家族成员的出现频率最高。对相关植物基因组中植物特异性DRD1亚家族的详细分析显示，该亚家族经历了一系列复杂的进化事件。值得注意的是，番茄中存在DRD1基因成员的意外扩张。这些基因多数在番茄中存在表达，尽管表达水平较低且呈现出独特的组织或器官特异性。与之相反，Snf2亚家族基因在番茄中倾向于组成型表达。本研究结果巩固并拓展了Snf2亚家族的分类体系，这将有助于明确Snf2家族ATP酶的各类功能角色，并为未来育种中靶向调控环境胁迫耐受性与作物产量提供指导。