DataSheet_1_The effects of ERN1 on gene expression during early rhizobial infection in Lotus japonicus.zip

Legumes develop root nodules in association with compatible rhizobia to overcome nitrogen deficiency. Rhizobia enter the host legume, mainly through infection threads, and induce nodule primordium formation in the root cortex. Multiple transcription factors have been identified to be involved in the regulation of the establishment of root nodule symbiosis, including ERF Required for Nodulation1 (ERN1). ERN1 is involved in a transcription network with CYCLOPS and NODULE INCEPTION (NIN). Mutation of ERN1 often results in misshapen root hair tips, deficient infection thread formation, and immature root nodules. ERN1 directly activates the expression of ENOD11 in Medicago truncatula to assist cell wall remodeling and Epr3 in Lotus japonicus to distinguish rhizobial exopolysaccharide signals. However, aside from these two genes, it remains unclear which genes are regulated by LjERN1 or what role LjERN1 plays during root nodule symbiosis. Thus, we conducted RNA sequencing to compare the gene expression profiles of wild-type L. japonicus and Ljern1-6 mutants. In total, 234 differentially expressed genes were identified as candidate LjERN1 target genes. These genes were found to be associated with cell wall remodeling, signal transduction, phytohormone metabolism, and transcription regulation, suggesting that LjERN1 is involved in multiple processes during the early stages of the establishment of root nodule symbiosis. Many of these candidate genes including RINRK1 showed decreased expression levels in Ljnin-2 mutants based on a search of a public database, suggesting that LjERN1 and LjNIN coordinately regulate gene expression. Our data extend the current understanding of the pleiotropic role of LjERN1 in root nodule symbiosis.

豆科植物在与根瘤菌的协同作用下，在根皮层中形成根瘤，以克服氮素缺乏。根瘤菌主要通过感染丝进入宿主豆科植物，并在根部皮质中诱导根瘤原基的形成。已鉴定出多个转录因子参与调控根瘤共生关系的建立，包括参与结瘤1（ERN1）。ERN1参与CYCLOPS和根瘤起始（NIN）的转录网络。ERN1的突变通常导致根毛顶端形态异常、感染丝形成不足和根瘤发育不成熟。ERN1直接激活Medicago truncatula中ENOD11的表达以协助细胞壁重塑，以及Lotus japonicus中Epr3的表达以区分根瘤菌的胞外多糖信号。然而，除了这两个基因之外，尚不清楚哪些基因受LjERN1调控，以及LjERN1在根瘤共生过程中发挥何种作用。因此，我们进行了RNA测序，以比较野生型L. japonicus和Ljern1-6突变体的基因表达谱。共鉴定出234个差异表达基因作为LjERN1靶基因的候选者。这些基因与细胞壁重塑、信号转导、植物激素代谢和转录调控相关，表明LjERN1在根瘤共生建立早期阶段涉及多个过程。许多候选基因，包括RINRK1，根据公共数据库的搜索结果显示，在Ljnin-2突变体中的表达水平降低，这表明LjERN1和LjNIN协调调控基因表达。我们的数据扩展了当前对LjERN1在根瘤共生中多效作用的理解。