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

Abstract

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.

The SLIM1 transcription factor affects sugar signaling during sulfur deficiency in Arabidopsis

“…Next, we checked the transcriptional response to high glucose of the selected genes known to respond to sulfur deficiency in a SLIM1-dependent manner, namely SULFUR DEFICIENCY-INDUCED 1 ( SDI1 ) and RESPONSE TO LOW SULFUR 1 ( LSU1 ) ( Wawrzynska and Sirko, 2016 ; Rakpenthai et al , 2022 ). Both genes belong to so-called ‘OAS cluster’ genes as their expression follows O -acetylserine (OAS; cysteine backbone) diurnal fluctuations, but they are also on the list of genes that are regulated by SLIM1 ( Maruyama-Nakashita et al , 2006 ; Hubberten et al , 2012 ).…”

New insights into the regulation of plant metabolism by O-acetylserine: sulfate and beyond

“…As such, the co-expressed genes are presumably part of a complex regulatory network integrating diverse inputs, eventually regulating plant cell homeostasis. This is reflected by the fact that the promoters of OAS cluster genes analyzed so far contain diverse sets of cis -elements, and various TFs have been identified to affect their respective expression ( Rakpenthai et al , 2022 ).…”

“…Jasmonate application induces the expression of numerous genes involved in sulfur assimilation, methionine biosynthesis, SAM biosynthesis, and further sulfur-related processes ( Jost et al , 2005 ) and SDI1 ( Rakpenthai et al , 2022 ). Transcriptome analyses of plants under sulfur-deprived conditions revealed that genes of MeJa biosynthesis are induced within 24–48 h ( Hirai et al , 2003 ; Nikiforova et al , 2003 ; Jost et al , 2005 ).…”

“…Which signals are perceived and how TFs regulate these responses is still not finally resolved ( Kopriva, 2006 ). Some progress has been achieved and suggestions provided ( Maruyama-Nakashita et al , 2006 ; Zhang et al ., 2014 ; Bielecka et al , 2015 ; Aarabi et al , 2016 ; Huang et al , 2016 ; Watanabe and Hoefgen, 2017 , 2019 ; Forzani et al , 2018 ; Rakpenthai et al , 2022 ; Wawrzyńska et al , 2022 ). In addition to these analyses, available databases allow the identification of TFs possibly involved in the OAS-driven response.…”

“…EIL3/SLIM1 is involved in the sulfate deprivation signaling pathway and is a central transcriptional regulator of plant sulfate metabolism ( Maruyama-Nakashita et al , 2006 ; Wawrzyńska et al , 2010 , 2022 ; Kawashima et al , 2011 ; Wawrzyńska and Sirko, 2014 , 2016 ; Dietzen et al , 2020 ; Rakpenthai et al , 2022 ), by controlling many sulfate deprivation response genes. EIL3/SLIM1 binds to the UPE box, the TEBS element, and the SURE element, which are present in many sulfate- and OAS-responsive genes ( Maruyama-Nakashita et al , 2005 ; Wawrzyńska et al , 2010 ; Rakpenthai et al , 2022 ). In addition to binding properties as displayed in the Plant Regulomics database, transcriptional regulation of OAS cluster genes and OAS network genes could be shown using transcriptome data ( Maruyama-Nakashita et al , 2006 ; O’Malley et al , 2016 ; Dietzen et al , 2020 ) ( Table 2 ).…”