Molecular evolution and diversification of the GRF transcription factor family

Abstract - Growth Regulating Factors (GRFs) comprise a transcription factor family with important functions in plant growth and development. They are characterized by the presence of QLQ and WRC domains, responsible for interaction with proteins and DNA, respectively. The QLQ domain is named due to the similarity to a protein interaction domain found in the SWI2/SNF2 chromatin remodeling complex. Despite the occurrence of the QLQ domain in both families, the divergence between them had not been further explored. Here, we show evidence for GRF origin and determined its diversification in angiosperm species. Phylogenetic analysis revealed 11 well-supported groups of GRFs in flowering plants. These groups were supported by gene structure, synteny, and protein domain composition. Synteny and phylogenetic analyses allowed us to propose different sets of probable orthologs in the groups. Besides, our results, together with functional data previously published, allowed us to suggest candidate genes for engineering agronomic traits. In addition, we propose that the QLQ domain of GRF genes evolved from the eukaryotic SNF2 QLQ domain, most likely by a duplication event in the common ancestor of the Charophytes and land plants. Altogether, our results are important for advancing the origin and evolution of the GRF family in Streptophyta.

摘要——生长调节因子（Growth Regulating Factors, GRFs）是一类在植物生长发育中发挥关键功能的转录因子家族。其标志性特征为携带QLQ结构域与WRC结构域，二者分别负责介导蛋白质互作与DNA结合。QLQ结构域因与SWI2/SNF2染色质重塑复合物中存在的蛋白质互作结构域序列相似而得名。尽管两类家族中均存在QLQ结构域，但二者间的分化尚未得到深入探究。本研究为GRFs的起源提供了实证依据，并明确了其在被子植物物种中的分化历程。系统发育分析显示，开花植物中存在11个得到高支持度的GRFs类群，该分类结果得到了基因结构、共线性特征与蛋白质结构域组成的共同验证。借助共线性与系统发育分析，我们为各类群提出了不同的潜在直系同源基因集合。此外，结合已发表的功能数据，本研究可为农艺性状遗传工程改造筛选出候选基因。我们还提出，GRF基因的QLQ结构域起源于真核生物SNF2的QLQ结构域，该演化过程大概率通过轮藻（Charophytes）与陆生植物的共同祖先发生的一次基因复制事件实现。综上，本研究结果对推动链型植物（Streptophyta）中GRF家族的起源与演化研究具有重要意义。