Specific functions for Mediator complex subunits from different modules in the transcriptional response of Arabidopsis thaliana to abiotic stress

AbstractAdverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of Arabidopsis thaliana to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization.

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In silico analysis and expression profiling of S-domain receptor-like kinases (SD-RLKs) under different abiotic stresses in Arabidopsis thaliana

BMC Genomics ◽

10.1186/s12864-021-08133-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Raju Mondal ◽

Subhankar Biswas ◽

Akanksha Srivastava ◽

Suvajit Basu ◽

Maitri Trivedi ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Abiotic Stress ◽

Signaling Pathways ◽

Differential Expression ◽

Stress Responses ◽

Abiotic Stresses ◽

Expression Patterns ◽

Light Stress ◽

Regulatory Elements ◽

Qrt Pcr

Abstract Background S-domain receptor-like kinases (SD-RLKs) are an important and multi-gene subfamily of plant receptor-like/pelle kinases (RLKs), which are known to play a significant role in the development and immune responses of Arabidopsis thaliana. The conserved cysteine residues in the extracellular domain of SD-RLKs make them interesting candidates for sensing reactive oxygen species (ROS), assisting oxidative stress mitigation and associated signaling pathways during abiotic stresses. However, how closely SD-RLKs are interrelated to abiotic stress mitigation and signaling remains unknown in A. thaliana. Results This study was initiated by examining the chromosomal localization, phylogeny, sequence and differential expression analyses of 37 SD-RLK genes using publicly accessible microarray datasets under cold, osmotic stress, genotoxic stress, drought, salt, UV-B, heat and wounding. Out of 37 SD-RLKs, 12 genes displayed differential expression patterns in both the root and the shoot tissues. Promoter structure analysis suggested that these 12 SD-RLK genes harbour several potential cis-regulatory elements (CREs), which are involved in regulating multiple abiotic stress responses. Based on these observations, we investigated the expression patterns of 12 selected SD-RLKs under ozone, wounding, oxidative (methyl viologen), UV-B, cold, and light stress at different time points using semi-qRT-PCR. Of these 12 SD-SRKs, the genes At1g61360, At1g61460, At1g61380, and At4g27300 emerged as potential candidates that maintain their expression in most of the stress treatments till exposure for 12 h. Expression patterns of these four genes were further verified under similar stress treatments using qRT-PCR. The expression analysis indicated that the gene At1g61360, At1g61380, and At1g61460 were mostly up-regulated, whereas the expression of At4g27300 either up- or down-regulated in these conditions. Conclusions To summarize, the computational analysis and differential transcript accumulation of SD-RLKs under various abiotic stresses suggested their association with abiotic stress tolerance and related signaling in A. thaliana. We believe that a further detailed study will decipher the specific role of these representative SD-RLKs in abiotic stress mitigation vis-a-vis signaling pathways in A. thaliana.

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Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals

Genome Biology ◽

10.1186/s13059-020-02258-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Guiomar Martín ◽

Yamile Márquez ◽

Federica Mantica ◽

Paula Duque ◽

Manuel Irimia

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Alternative Splicing ◽

Stress Responses ◽

Target Genes ◽

Intron Retention ◽

Single Gene ◽

Exon Skipping ◽

Environmental Response ◽

Biotic Stresses

Abstract Background Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehensive study contrasting stress-response and tissue-specific AS patterns and directly comparing them with those of animal models is still missing. Results We generate a massive resource for Arabidopsis thaliana, PastDB, comprising AS and gene expression quantifications across tissues, development and environmental conditions, including abiotic and biotic stresses. Harmonized analysis of these datasets reveals that A. thaliana shows high levels of AS, similar to fruitflies, and that, compared to animals, disproportionately uses AS for stress responses. We identify core sets of genes regulated specifically by either AS or transcription upon stresses or among tissues, a regulatory specialization that is tightly mirrored by the genomic features of these genes. Unexpectedly, non-intron retention events, including exon skipping, are overrepresented across regulated AS sets in A. thaliana, being also largely involved in modulating gene expression through NMD and uORF inclusion. Conclusions Non-intron retention events have likely been functionally underrated in plants. AS constitutes a distinct regulatory layer controlling gene expression upon internal and external stimuli whose target genes and master regulators are hardwired at the genomic level to specifically undergo post-transcriptional regulation. Given the higher relevance of AS in the response to different stresses when compared to animals, this molecular hardwiring is likely required for a proper environmental response in A. thaliana.

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Functional Characterization of DEAD-Box RNA Helicases in Arabidopsis thaliana under Abiotic Stress Conditions

Plant and Cell Physiology ◽

10.1093/pcp/pcn125 ◽

2008 ◽

Vol 49 (10) ◽

pp. 1563-1571 ◽

Cited By ~ 57

Author(s):

Jin Sun Kim ◽

Kyung Ae Kim ◽

Tae Rin Oh ◽

Chul Min Park ◽

Hunseung Kang

Keyword(s):

Arabidopsis Thaliana ◽

Abiotic Stress ◽

Functional Characterization ◽

Stress Conditions ◽

Rna Helicases ◽

Dead Box

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Jute Responses and Tolerance to Abiotic Stress: Mechanisms and Approaches

Plants ◽

10.3390/plants10081595 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1595

Author(s):

Khussboo Rahman ◽

Naznin Ahmed ◽

Md. Rakib Hossain Raihan ◽

Farzana Nowroz ◽

Faria Jannat ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Responses ◽

Growth Yield ◽

Climatic Conditions ◽

Stress Factors ◽

Growth Physiology ◽

Abiotic Stress Factors ◽

Hot And Humid Climates ◽

Adverse Environmental Conditions ◽

Cold Metal

Jute (Corchorus spp.) belongs to the Malvaceae family, and there are two species of jute, C. capsularis and C. olitorious. It is the second-largest natural bast fiber in the world according to production, which has diverse uses not only as a fiber but also as multiple industrial materials. Because of climate change, plants experience various stressors such as salt, drought, heat, cold, metal/metalloid toxicity, and flooding. Although jute is particularly adapted to grow in hot and humid climates, it is grown under a wide variety of climatic conditions and is relatively tolerant to some environmental adversities. However, abiotic stress often restricts its growth, yield, and quality significantly. Abiotic stress negatively affects the metabolic activities, growth, physiology, and fiber yield of jute. One of the major consequences of abiotic stress on the jute plant is the generation of reactive oxygen species, which lead to oxidative stress that damages its cellular organelles and biomolecules. However, jute’s responses to abiotic stress mainly depend on the plant’s age and type and duration of stress. Therefore, understanding the abiotic stress responses and the tolerance mechanism would help plant biologists and agronomists in developing climate-smart jute varieties and suitable cultivation packages for adverse environmental conditions. In this review, we summarized the best possible recent literature on the plant abiotic stress factors and their influence on jute plants. We described the possible approaches for stress tolerance mechanisms based on the available literature.

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Functional characterization of wheat myo-inositol oxygenase promoter under different abiotic stress conditions in Arabidopsis thaliana

Biotechnology Letters ◽

10.1007/s10529-020-02967-1 ◽

2020 ◽

Vol 42 (10) ◽

pp. 2035-2047

Author(s):

Anshu Alok ◽

Jaspreet Kaur ◽

Siddharth Tiwari

Keyword(s):

Arabidopsis Thaliana ◽

Abiotic Stress ◽

Functional Characterization ◽

Stress Conditions

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Functional characterization of a chloroplast-targeted RNA-binding protein CRP1 in Arabidopsis thaliana under abiotic stress conditions

Journal of Plant Biology ◽

10.1007/s12374-014-0372-y ◽

2014 ◽

Vol 57 (6) ◽

pp. 349-356 ◽

Cited By ~ 9

Author(s):

Tao Xu ◽

Nguyen Dinh Sy ◽

Hwa Jung Lee ◽

Kyung Jin Kwak ◽

Lili Gu ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Abiotic Stress ◽

Rna Binding ◽

Binding Protein ◽

Functional Characterization ◽

Rna Binding Protein ◽

Stress Conditions

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Transcriptional Distribution in Various Organs and Transcriptional Response to Abiotic Stress for Trehalose Metabolism Genes in Arabidopsis Thaliana

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.108.251 ◽

2011 ◽

Vol 108 ◽

pp. 251-256

Author(s):

Yan Zhai Song ◽

Shuang Liu ◽

Mei Wen ◽

Wei Huang ◽

Xiang Li Song ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Abiotic Stress ◽

Stress Tolerance ◽

Metabolic Pathway ◽

Transcriptional Response ◽

Floral Organ ◽

Trace Level ◽

Early Stress ◽

Genes Expression ◽

Trehalose Metabolism

Trehalose (α-D-glucopyranosyl-1,1-α-D-glucopyranoside) is a non-reducing disaccharide. It is currently thought that just trace level of trehalose was detected in plants, and that trehalose metabolic pathway was significantly related to stress tolerance. In this study, we report that expression levels of three genes with regard to trehalose metabolic pathway were measured in Arabidopsis thaliana, including AtTPS1, AtTPPA and AtTRE1. As a result, transcriptional levels of these genes are the highest in floral organ, and the expression of AtTRE1 is much more than AtTPS1 and AtTPPA. Additionally, we present transcriptional response analyses in drought and heat stresses, which have shown the changes of these genes expression from tolerance in early stress to senescence in later stress.

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Modulation of GmFAD3 expression alters responses to abiotic stress in soybean

10.22541/au.160569953.30220980/v1 ◽

2020 ◽

Author(s):

Ajay Singh ◽

Mahesh Kumar ◽

Susheel Raina ◽

Milind Ratnaparkhe ◽

Jagadish Rane ◽

...

Keyword(s):

Heat Stress ◽

Abiotic Stress ◽

Fatty Acid ◽

Stress Tolerance ◽

Salinity Stress ◽

Stress Responses ◽

Fatty Acid Desaturase ◽

Stress Conditions ◽

Omega 3 ◽

Soybean Plants

FAD3 play important roles in modulating membrane fluidity in response to various abiotic stresses. However, a comprehensive analysis of FAD3 in drought, salinity and heat stress tolerance is lacking in soybean. The present study assessed the functional role of fatty acid desaturase 3 to abiotic stress responses in soybean. We used Bean Pod Mottle Virus -based vector to alter expression of Glycine max omega-3 fatty acid desaturase . Higher levels of recombinant BPMV-GmFAD3 transcripts were detected in overexpressing soybean plants. Overexpression of GmFAD3 in soybean resulted in increased levels of jasmonic acid and higher expression of GmWRKY54 as compared to mock-inoculated, vector-infected and FAD3-silenced soybean plants under drought and salinity stress conditions. FAD3 overexpressing plants showed higher levels of chlorophyll content, leaf SPAD value, relative water content, chlorophyll fluorescence, transpiration rate, carbon assimilation rate, proline content and also cooler canopy under drought and salinity stress conditions as compared to mock-inoculated, vector-infected and FAD3-silenced soybean plants. Results from current study revealed that GmFAD3 overexpressing soybean plants exhibited drought and salinity stress tolerance although tolerance to heat stress was reduced. On the other hand, soybean plants silenced for GmFAD3 exhibited tolerance to heat stress, but were vulnerable to drought and salinity stress

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Recognition of microbe/damage-associated molecular patterns by leucine-rich repeat pattern recognition receptor kinases confers salt tolerance in plants

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-07-21-0185-fi ◽

2021 ◽

Author(s):

Yusuke Saijo ◽

Eliza Loo ◽

Yuri Tajima ◽

Kohji Yamada ◽

Shota Kido ◽

...

Keyword(s):

Pattern Recognition ◽

Abiotic Stress ◽

Salt Tolerance ◽

Stress Responses ◽

Pathogenic Bacteria ◽

Target Genes ◽

Leucine Rich Repeat ◽

Cross Tolerance ◽

Molecular Patterns ◽

Damage Associated Molecular Patterns

In plants, a first layer of inducible immunity is conferred by pattern recognition receptors (PRRs) that bind microbe- and damage-associated molecular patterns (MAMPs/DAMPs, respectively) to activate pattern-triggered immunity (PTI). PTI is strengthened or followed by another potent form of immunity when intracellular receptors recognize pathogen effectors, termed effector-triggered immunity (ETI). Immunity signaling regulators have been reported to influence abiotic stress responses as well, yet the governing principles and mechanisms remain ambiguous. Here, we report that PRRs of a leucine-rich repeat ectodomain also confer salt tolerance in Arabidopsis thaliana, following recognition of cognate ligands, such as bacterial flagellin (flg22 epitope) and EF-Tu (elf18 epitope), and the endogenous Pep peptides. Pattern-triggered salt tolerance (PTST) requires authentic PTI signaling components, namely the PRR-associated kinases BAK1 and BIK1, and the NADPH oxidase RBOHD. Exposure to salt stress induces the release of Pep precursors, pointing to the involvement of the endogenous immunogenic peptides in developing plant tolerance to high salinity. Transcriptome profiling reveals an inventory of PTST target genes, which increase or acquire salt responsiveness following a pre-exposure to immunogenic patterns. In good accordance, plants challenged with non-pathogenic bacteria also acquired salt tolerance in a manner dependent on PRRs. Our findings provide insight into signaling plasticity underlying biotic-abiotic stress cross-tolerance in plants conferred by PRRs.

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