Interactions among Plant Transcription Factors Regulating Expression of Stress-responsive Genes

Plants are simultaneously subjected to a variety of stress conditions in the field and are known to combat the hostile conditions by up/downregulating number of genes. There exists a significant level of cross-talk between different stress responses in plants. In this study, we predict the interacting pairs of transcription factors that regulate the multiple abiotic stress-responsive genes in the plant Arabidopsis thaliana. We identified the interacting pair(s) of transcription factors (TFs) based on the spatial proximity of their binding sites. We also examined the interactions between the predicted pairs of TFs using molecular docking. Subsequent to docking, the best interaction pose was selected using our scoring scheme DockScore, which ranks the docked solutions based on several interface parameters and aims to find optimal interactions between proteins. We analyzed the selected docked pose for the interface residues and their conservation.

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STIFDB—Arabidopsis Stress Responsive Transcription Factor DataBase

International Journal of Plant Genomics ◽

10.1155/2009/583429 ◽

2009 ◽

Vol 2009 ◽

pp. 1-8 ◽

Cited By ~ 44

Author(s):

K. Shameer ◽

S. Ambika ◽

Susan Mary Varghese ◽

N. Karaba ◽

M. Udayakumar ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Transcription Factor ◽

Transcription Factors ◽

Abiotic Stress ◽

Stress Responses ◽

Binding Sites ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Factor Binding ◽

Stress Responsive Genes

Elucidating the key players of molecular mechanism that mediate the complex stress-responses in plants system is an important step to develop improved variety of stress tolerant crops. Understanding the effects of different types of biotic and abiotic stress is a rapidly emerging domain in the area of plant research to develop better, stress tolerant plants. Information about the transcription factors, transcription factor binding sites, function annotation of proteins coded by genes expressed during abiotic stress (for example: drought, cold, salinity, excess light, abscisic acid, and oxidative stress) response will provide better understanding of this phenomenon. STIFDB is a database of abiotic stress responsive genes and their predicted abiotic transcription factor binding sites in Arabidopsis thaliana. We integrated 2269 genes upregulated in different stress related microarray experiments and surveyed their 1000 bp and 100 bp upstream regions and 5′UTR regions using the STIF algorithm and identified putative abiotic stress responsive transcription factor binding sites, which are compiled in the STIFDB database. STIFDB provides extensive information about various stress responsive genes and stress inducible transcription factors of Arabidopsis thaliana. STIFDB will be a useful resource for researchers to understand the abiotic stress regulome and transcriptome of this important model plant system.

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Evolutionarily conserved transcription factors drive the oxidative stress response in Drosophila

Journal of Experimental Biology ◽

10.1242/jeb.221622 ◽

2020 ◽

Vol 223 (14) ◽

pp. jeb221622

Author(s):

Sarah M. Ryan ◽

Kaitie Wildman ◽

Briseida Oceguera-Perez ◽

Scott Barbee ◽

Nathan T. Mortimer ◽

...

Keyword(s):

Oxidative Stress ◽

Transcription Factor ◽

Transcription Factors ◽

Stress Responses ◽

Binding Sites ◽

Regulatory Elements ◽

Genomic Locus ◽

Biologically Relevant ◽

Protein Levels ◽

Putative Transcription Factor

ABSTRACTAs organisms are constantly exposed to the damaging effects of oxidative stress through both environmental exposure and internal metabolic processes, they have evolved a variety of mechanisms to cope with this stress. One such mechanism is the highly conserved p38 MAPK (p38K) pathway, which is known to be post-translationally activated in response to oxidative stress, resulting in the activation of downstream antioxidant targets. However, little is known about the role of p38K transcriptional regulation in response to oxidative stress. Therefore, we analyzed the p38K gene family across the genus Drosophila to identify conserved regulatory elements. We found that oxidative stress exposure results in increased p38K protein levels in multiple Drosophila species and is associated with increased oxidative stress resistance. We also found that the p38Kb genomic locus includes conserved AP-1 and lola-PT transcription factor consensus binding sites. Accordingly, over-expression of these transcription factors in D. melanogaster is sufficient to induce transcription of p38Kb and enhances resistance to oxidative stress. We further found that the presence of a putative lola-PT binding site in the p38Kb locus of a given species is predictive of the species' survival in response to oxidative stress. Through our comparative genomics approach, we have identified biologically relevant putative transcription factor binding sites that regulate the expression of p38Kb and are associated with resistance to oxidative stress. These findings reveal a novel mode of regulation for p38K genes and suggest that transcription may play as important a role in p38K-mediated stress responses as post-translational modifications.

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Arabidopsis thaliana transcription factors MYB28 and MYB29 shape ammonium stress responses by regulating Fe homeostasis

New Phytologist ◽

10.1111/nph.16918 ◽

2020 ◽

Vol 229 (2) ◽

pp. 1021-1035

Author(s):

Inmaculada Coleto ◽

Iraide Bejarano ◽

Agustín Javier Marín‐Peña ◽

Joaquín Medina ◽

Cristina Rioja ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Transcription Factors ◽

Stress Responses ◽

Ammonium Stress ◽

Fe Homeostasis

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Novel miR390-Dependent Transacting siRNA Precursors in Plants Revealed by a PCR-Based Experimental Approach and Database Analysis

Journal of Biomedicine and Biotechnology ◽

10.1155/2009/952304 ◽

2009 ◽

Vol 2009 ◽

pp. 1-9 ◽

Cited By ~ 12

Author(s):

M. S. Krasnikova ◽

I. A. Milyutina ◽

V. K. Bobrova ◽

L. V. Ozerova ◽

A. V. Troitsky ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Transcription Factors ◽

Experimental Approach ◽

Single Copy ◽

Small Interfering Rnas ◽

Database Analysis ◽

Plant Genomes ◽

Target Sites ◽

Number Of Genes ◽

Conservation Pattern

TAS loci in plant genomes encode transacting small interfering RNAs (ta-siRNAs) that regulate expression of a number of genes. The function of TAS3 precursor inArabidopsis thalianais controlled by two miR390 target sites flanking two ta-siARF sequences targeting mRNAs of ARF transcription factors. Cleavage of the3′-miR390-site initiates ta-siRNAs biogenesis. Here we describe the new method for identification of plant ta-siRNA precursors based on PCR with oligodeoxyribonucleotide primers mimicking miR390. The method was found to be efficient for dicotiledonous plants, cycads, and mosses. Based on sequences of amplified loci and a database analysis, a novel type of miR390-dependent TAS sequences was identified in dicots. These TAS loci are characterized by a smaller distance between miR390 sites compared to TAS3, a single copy of ta-siARF, and a sequence conservation pattern pointing to the possibility that processing of novel TAS-like locus is initiated by cleavage of the5′-terminal miR390 target site.

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Transcription Factor ANAC074 Binds to NRS1, NRS2, or MybSt1 Element in Addition to the NACRS to Regulate Gene Expression

International Journal of Molecular Sciences ◽

10.3390/ijms19103271 ◽

2018 ◽

Vol 19 (10) ◽

pp. 3271

Author(s):

Lin He ◽

Jingyu Xu ◽

Yucheng Wang ◽

Kejun Yang

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Transcription Factor ◽

Transcription Factors ◽

Biological Processes ◽

Regulate Gene Expression ◽

Cis Element ◽

Stress Responsive Genes ◽

Regulate Gene ◽

Gus Assays

NAC (NAM, ATAF1/2, and CUC2) transcription factors play important roles in many biological processes, and mainly bind to the NACRS with core sequences “CACG” or “CATGTG” to regulate gene expression. However, whether NAC proteins can bind to other motifs without these core sequences remains unknown. In this study, we employed a Transcription Factor-Centered Yeast one Hybrid (TF-Centered Y1H) screen to study the motifs recognized by ANAC074. In addition to the NACRS core cis-element, we identified that ANAC074 could bind to MybSt1, NRS1, and NRS2. Y1H and GUS assays showed that ANAC074 could bind the promoters of ethylene responsive genes and stress responsive genes via the NRS1, NRS2, or MybSt1 element. ChIP study further confirmed that the bindings of ANAC074 to MybSt1, NRS1, and NRS2 actually occurred in Arabidopsis. Furthermore, ten NAC proteins from different NAC subfamilies in Arabidopsis thaliana were selected and confirmed to bind to the MybSt1, NRS1, and NRS2 motifs, indicating that they are recognized commonly by NACs. These findings will help us to further reveal the functions of NAC proteins.

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