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

Rakpenthai, A., Apodiakou, A., Whitcomb, S. J., & Hoefgen, R. (2022). In silico analysis of cis-elements and identification of transcription factors putatively involved in the regulation of the OAS cluster genes SDI1 and SDI2. The Plant Journal, 110(5), 1286-1304. doi:10.1111/tpj.15735.

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Genre: Journal Article
Alternative Title : The Plant Journal

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Rakpenthai, A.1, Author              
Apodiakou, A.1, Author              
Whitcomb, S. J.1, Author              
Hoefgen, R.1, Author              
Affiliations:
1Amino Acid and Sulfur Metabolism, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753337              

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Free keywords: electrophoretic mobility shift assay, sulfur deficiency-induced (SDI), sulfur limitation1 (SLIM1), sulfur-responsive element (SURE), sulfur starvation, transcription factors, yeast-one-hybrid
 Abstract: SUMMARY A. 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 (TF) involved in regulating expression of the SDI genes. We performed in silico analysis of their promoter sequences cataloguing known cis-elements and identifying conserved sequence motifs. We screened by yeast one-hybrid (Y1H) 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 (EMSA): 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.

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Language(s): eng - English
 Dates: 2022-03-212022-06
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1111/tpj.15735
 Degree: -

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Title: The Plant Journal
  Other : Plant J.
Source Genre: Journal
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Publ. Info: Oxford : Blackwell Science
Pages: - Volume / Issue: 110 (5) Sequence Number: - Start / End Page: 1286 - 1304 Identifier: ISSN: 0960-7412
CoNE: https://pure.mpg.de/cone/journals/resource/954925579095_1