Likai Wang, Eun Esther Ko,  Jaclyn Tran, and Hong Qiao

PNAS November 17, 2020 117 (46) 29178-29189

Significance

Ethylene is an important plant hormone that is essential for many physiological and developmental processes such as apical hook formation, shoot and root growth, root nodulation, flower senescence, abscission, and fruit ripening. Transcriptional activation in the ethylene response has been well studied. However, the transcriptional repression in the ethylene response remains unclear. Here, by combined approaches of data analysis, molecular biology, and genetics, we found that a transcriptional repressor TREE1 interacts with EIN3 to regulate transcriptional repression, leading to an inhibition of shoot growth in response to ethylene. Our work provides insight into how the transcriptional activator can be tuned to repress downstream gene expression in hormone signals.

Abstract

Ethylene is an important plant hormone that regulates plant growth, in which the master transcriptionactivator EIN3 (Ethylene Insensitive 3)-mediated transcriptional activation plays vital roles. However, the EIN3-mediated transcriptional repression in ethylene response is unknown. We report here that a Transcriptional Repressor of EIN3-dependent Ethylene-response 1 (TREE1) interacts with EIN3 to regulate transcriptional repression that leads to an inhibition of shoot growth in response to ethylene. Tissue-specific transcriptome analysis showed that most of the genes are down-regulated by ethylene in shoots, and a DNA binding motif was identified that is important for this transcriptional repression. TREE1 binds to the DNA motif to repress gene expression in an EIN3-dependent manner. Genetic validation demonstrated that repression of TREE1-targeted genes leads to an inhibition of shoot growth. Overall, this work establishes a mechanism by which transcriptional repressor TREE1 interacts with EIN3 to inhibit shoot growth via transcriptional repression in response to ethylene.

See https://www.pnas.org/content/117/46/29178

Figure 1: Shoots and roots have distinct transcriptional responses to ethylene. (A) Comparison of genes that significantly differentially expressed in shoots and in roots in response to ethylene (q value ≤0.05; |Log2 fold change| ≥ 1). (B) Bar graph to show the numbers of genes that are up- and down-regulated by ethylene in shoots, in roots, and shared between shoots and roots. (C–E) qRT-PCR assays to show selected genes that are regulated by ethylene in specific tissues. The Arabidopsis ACTIN2 gene expression serves as a reference for normalization. ** indicates P value <0.05 compared with the same sample treated with air. Error bars indicate the SD (n = 3). (F) DNA binding motifs identified from the promoters of ethylene-activated shoot-specific genes, ethylene-activated genes between shoots and roots, and ethylene-activated root-specific genes that surround EIN3 binding regions. The canonical EIN3 binding motif sequence is: (A/T)(T/C)G(A/C/T)A(T/C/G)(C/G)T(T/G) (21). Dashed boxes highlight the motifs with a similarity to the known EIN3 binding motif. (G) DNA binding motifs identified from the promoter regions that surrounding the EIN3 binding motif in the shoot-specific ethylene-repressed genes. E values are indicated. Motifs were found by the MEME-ChIP (meme-suite.org/tools/meme-chip) using 200-base pair sequences centered on the EIN3 binding summit in EIN3-bound ethylene up- or down-regulated genes in shoots and in roots. (H) Boxplot shows the distance between the motif we identified and the known EIN3 binding motif in the genes that contained both motifs.