In silico analysis of cis‐elements and identification of transcription factors putatively involved in the regulation of the OAS cluster genes SDI1 and SDI2

• Published in: The Plant journal : for cell and molecular biology Vol. 110; no. 5; pp. 1286 - 1304
• Main Authors: Rakpenthai, Apidet, Apodiakou, Anastasia, Whitcomb, Sarah J., Hoefgen, Rainer
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01-06-2022
• Subjects: Binding; Conserved sequence; Deoxyribonucleic acid; DNA; Electrophoretic mobility; electrophoretic mobility shift assay; Functional analysis; Gene expression; Gene regulation; Genes; Homology; Leucine; Leucine zipper proteins; Metabolites; Nucleotide sequence; Sulfur; sulfur deficiency‐induced (SDI); sulfur limitation1 (SLIM1); sulfur starvation; sulfur‐responsive element (SURE); Transcription factors; Yeasts; yeast‐one‐hybrid; sulfur-responsive element (SURE); electrophoretic mobility shift assay; yeast-one-hybrid; sulfur limitation1 (SLIM1); sulfur starvation; transcription factors; sulfur deficiency-induced (SDI)
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.15735

SUMMARY
Arabidopsis thaliana sulfur deficiency‐induced 1 and sulfur deficiency‐induced 2 (SDI1 and SDI2) are involved in partitioning sulfur among metabolite pools during sulfur deficiency, and their transcript levels strongly increase in this condition. However, little is currently known about the cis‐ and trans‐factors that regulate SDI expression. We aimed at identifying DNA sequence elements (cis‐elements) and transcription factors (TFs) involved in regulating expression of the SDI genes. We performed in silico analysis of their promoter sequences cataloging known cis‐elements and identifying conserved sequence motifs. We screened by yeast‐one‐hybrid an arrayed library of Arabidopsis TFs for binding to the SDI1 and SDI2 promoters. In total, 14 candidate TFs were identified. Direct association between particular cis‐elements in the proximal SDI promoter regions and specific TFs was established via electrophoretic mobility shift assays: sulfur limitation 1 (SLIM1) was shown to bind SURE cis‐element(s), the basic domain/leucine zipper (bZIP) core cis‐element was shown to be important for HY5‐homolog (HYH) binding, and G‐box binding factor 1 (GBF1) was shown to bind the E box. Functional analysis of GBF1 and HYH using mutant and over‐expressing lines indicated that these TFs promote a higher transcript level of SDI1 in vivo. Additionally, we performed a meta‐analysis of expression changes of the 14 TF candidates in a variety of conditions that alter SDI expression. The presented results expand our understanding of sulfur pool regulation by SDI genes.
Significance Statement
Sulfur limitation1 (SLIM1), a key regulator of sulfur‐deficiency responses in Arabidopsis, can bind to SURE cis‐element(s) in the promoters of sulfur deficiency‐induced 1 and 2 (SDI1 and SDI2). G‐box binding factor 1 (GBF1) and HY5‐homolog (HYH) affects to SDI1 expression. Meta‐analysis highlights that SDI1 and SDI2 also respond strongly to conditions other than S‐deficiency, which may be linked to the variety of TFs identified here to bind SDI promoters.