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<p>Systemic acquired resistance (SAR) and induced systemic resistance (ISR) are the defense strategies that protect plants from a broad range of pathogens. Due to the ever-evolving and dynamic microbial diversity, the SAR/ISR genes are gifted with a competent regulatory mechanism. Promoters are one of the niche regulating areas of gene expression, which harbour numerous <i>cis</i> regulatory elements. While there are many reports on whole genome profiling of these regulatory features, studies focussing on the defense genes alone are few. Deeper analyses of a subset of genome provides less diluted and sharper perspective. Hence, in silico profiles of putative binding sites of 31 transcription factor families (TFFs), 17 pathogenesis-related transcription factors (PRTFs), and microRNAs were compared in 162 <i>Arabidopsis thaliana</i> SAR/ISR gene promoters. This study revealed new insights into defense gene regulation. The AT-Hook motif, and putative binding sites for NAC and MYB TFFs and TGA1a PRTFs had the highest frequencies. Previous studies on involvement of AT-Hook motif and TGA1a in <i>A. thaliana</i> defense are few. Potential multi gene-targeting role of certain microRNAs, such as <i>MIR2934</i>, is suggested. The possibility of certain microRNAs previously known for post-transcription regulation, to be involved in transcription regulation is proposed. Though there are reports on plant transcriptomes under various biotic stresses, the reason for temporal expression pattern similarity of certain genes under multiple stresses is unclear. To understand this phenomenon, the regulatory profiles of defense genes under nine biotic stresses fetched from EFP browser were analysed. Similarly expressing gene pairs did not necessarily have the same regulatory features, indicating a stochastic correlation of temporal expression patterns and PRTFs/microRNAs putative binding sites/DNA and histone methylation sites. A vague similarity in the histone modification patterns was observed in their promoters. The findings highlighted in this study could be harnessed for molecular fine tuning of genomic pathways to mitigate broad range biotic stresses.</p>

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Revelations of Arabidopsis thaliana presumptive promoter regulatory profiles of defense genes, and their stochastic temporal expression correlations under biotic stresses

  • 期刊论文

  • 发表日期：

    2026年1月20日

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  • Riniya Najeeb,
  • K. Henna Parveen,
  • A. T. Meharban,
  • Gayathri Santhosh,
  • T. G. Ajith,
  • K. P. Mahitha,
  • R. Sripriya,
  • Jasmine M. Shah

摘要

Systemic acquired resistance (SAR) and induced systemic resistance (ISR) are the defense strategies that protect plants from a broad range of pathogens. Due to the ever-evolving and dynamic microbial diversity, the SAR/ISR genes are gifted with a competent regulatory mechanism. Promoters are one of the niche regulating areas of gene expression, which harbour numerous cis regulatory elements. While there are many reports on whole genome profiling of these regulatory features, studies focussing on the defense genes alone are few. Deeper analyses of a subset of genome provides less diluted and sharper perspective. Hence, in silico profiles of putative binding sites of 31 transcription factor families (TFFs), 17 pathogenesis-related transcription factors (PRTFs), and microRNAs were compared in 162 Arabidopsis thaliana SAR/ISR gene promoters. This study revealed new insights into defense gene regulation. The AT-Hook motif, and putative binding sites for NAC and MYB TFFs and TGA1a PRTFs had the highest frequencies. Previous studies on involvement of AT-Hook motif and TGA1a in A. thaliana defense are few. Potential multi gene-targeting role of certain microRNAs, such as MIR2934, is suggested. The possibility of certain microRNAs previously known for post-transcription regulation, to be involved in transcription regulation is proposed. Though there are reports on plant transcriptomes under various biotic stresses, the reason for temporal expression pattern similarity of certain genes under multiple stresses is unclear. To understand this phenomenon, the regulatory profiles of defense genes under nine biotic stresses fetched from EFP browser were analysed. Similarly expressing gene pairs did not necessarily have the same regulatory features, indicating a stochastic correlation of temporal expression patterns and PRTFs/microRNAs putative binding sites/DNA and histone methylation sites. A vague similarity in the histone modification patterns was observed in their promoters. The findings highlighted in this study could be harnessed for molecular fine tuning of genomic pathways to mitigate broad range biotic stresses.