scholarly journals Discovery of Drought-Responsive Transposable Element-Related Peach miRNAs

2017 ◽  
Author(s):  
Asli Kurden Pekmezci ◽  
Gökhan Karakülah ◽  
Turgay Unver
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Stress Response ◽  
Transposable Element ◽  
Small Rna ◽  
Computational Analysis ◽  
Drought Response ◽  
Specific Target ◽  
Specific Manner ◽  
Regulatory Rnas

AbstractMicroRNAs (miRNA) are small non-coding regulatory RNAs that suppress their specific target transcripts either by cleavage or inhibition of translation. Transposable element related miRNAs (TE-miRNA) have been subjected to various studies so far, and some of them were found to be involved in stress response in plants. Here, small RNA (sRNA) sequencing libraries generated from drought stress treated peach tissues were utilized to identify TE-miRNAs. Our computational analysis led to the identification of 63 TE-miRNAs, which were either locating nearby of any TE (TE-related), or overlapping with a TE (TE-derived). Furthermore, 13 out of 63 TE-miRNAs were designated as drought-responsive. Expression pattern of the identified drought-responsive TE-miRNAs are observed as tissue-specific manner, and their specific target transcripts are mostly related to transcription factors and growth-associated genes. Our findings suggest that miRNAs in relation with transposable elements might be key molecular players in the regulation of drought response.

scholarly journals Genome-wide characterization and expression analysis of citrus NUCLEAR FACTOR-Y (NF-Y) transcription factors identified a novel NF-YA gene involved in drought-stress response and tolerance

PLoS ONE ◽  
2018 ◽  
Vol 13 (6) ◽  
pp. e0199187 ◽  
Author(s):  
Suzam L. S. Pereira ◽  
Cristina P. S. Martins ◽  
Aurizangela O. Sousa ◽  
Luciana R. Camillo ◽  
Caroline P. Araújo ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Stress Response ◽  
Expression Analysis ◽  
Nuclear Factor ◽  
Nuclear Factor Y ◽  
Genome Wide

scholarly journals Analysis of Non-Structural Carbohydrates and Xylem Anatomy of Leaf Petioles Offers New Insights in the Drought Response of Two Grapevine Cultivars

2020 ◽  
Vol 21 (4) ◽  
pp. 1457 ◽  
Author(s):  
Rachele Falchi ◽  
Elisa Petrussa ◽  
Enrico Braidot ◽  
Paolo Sivilotti ◽  
Francesco Boscutti ◽  
...  
Keyword(s):  
Water Stress ◽  
Drought Stress ◽  
Stress Response ◽  
Stress Responses ◽  
Cabernet Sauvignon ◽  
Drought Response ◽  
Xylem Anatomy ◽  
Anatomical Analysis ◽  
Starch Mobilization ◽  
Xylem Conduits

In grapevine, the anatomy of xylem conduits and the non-structural carbohydrates (NSCs) content of the associated living parenchyma are expected to influence water transport under water limitation. In fact, both NSC and xylem features play a role in plant recovery from drought stress. We evaluated these traits in petioles of Cabernet Sauvignon (CS) and Syrah (SY) cultivars during water stress (WS) and recovery. In CS, the stress response was associated to NSC consumption, supporting the hypothesis that starch mobilization is related to an increased supply of maltose and sucrose, putatively involved in drought stress responses at the xylem level. In contrast, in SY, the WS-induced increase in the latter soluble NSCs was maintained even 2 days after re-watering, suggesting a different pattern of utilization of NSC resources. Interestingly, the anatomical analysis revealed that conduits are constitutively wider in SY in well-watered (WW) plants, and that water stress led to the production of narrower conduits only in this cultivar.

scholarly journals Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA

PLoS Genetics ◽  
2012 ◽  
Vol 8 (2) ◽  
pp. e1002474 ◽  
Author(s):  
Andrea D. McCue ◽  
Saivageethi Nuthikattu ◽  
Sarah H. Reeder ◽  
R. Keith Slotkin
Keyword(s):  
Gene Expression ◽  
Stress Response ◽  
Transposable Element ◽  
Epigenetic Regulation ◽  
Small Rna

scholarly journals The Maize WRKY Transcription Factor ZmWRKY40 Confers Drought Resistance in Transgenic Arabidopsis

2018 ◽  
Vol 19 (9) ◽  
pp. 2580 ◽  
Author(s):  
Chang-Tao Wang ◽  
Jing-Na Ru ◽  
Yong-Wei Liu ◽  
Jun-Feng Yang ◽  
Meng Li ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Drought Stress ◽  
Stress Response ◽  
Abiotic Stresses ◽  
Transgenic Arabidopsis ◽  
Regulatory Elements ◽  
Wrky Transcription Factor ◽  
Growth And Yield ◽  
Abiotic Stress Response

Abiotic stresses restrict the growth and yield of crops. Plants have developed a number of regulatory mechanisms to respond to these stresses. WRKY transcription factors (TFs) are plant-specific transcription factors that play essential roles in multiple plant processes, including abiotic stress response. At present, little information regarding drought-related WRKY genes in maize is available. In this study, we identified a WRKY transcription factor gene from maize, named ZmWRKY40. ZmWRKY40 is a member of WRKY group II, localized in the nucleus of mesophyll protoplasts. Several stress-related transcriptional regulatory elements existed in the promoter region of ZmWRKY40. ZmWRKY40 was induced by drought, high salinity, high temperature, and abscisic acid (ABA). ZmWRKY40 could rapidly respond to drought with peak levels (more than 10-fold) at 1 h after treatment. Overexpression of ZmWRKY40 improved drought tolerance in transgenic Arabidopsis by regulating stress-related genes, and the reactive oxygen species (ROS) content in transgenic lines was reduced by enhancing the activities of peroxide dismutase (POD) and catalase (CAT) under drought stress. According to the results, the present study may provide a candidate gene involved in the drought stress response and a theoretical basis to understand the mechanisms of ZmWRKY40 in response to abiotic stresses in maize.

scholarly journals The Cyclophilin ROC3 Regulates ABA-Induced Stomatal Closure and the Drought Stress Response of Arabidopsis thaliana

2021 ◽  
Vol 12 ◽  
Author(s):  
Huiping Liu ◽  
Jianlin Shen ◽  
Chao Yuan ◽  
Dongxue Lu ◽  
Biswa R. Acharya ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Drought Stress ◽  
Stress Response ◽  
Stomatal Closure ◽  
Anion Channel ◽  
Crop Productivity ◽  
Drought Response ◽  
Wild Type ◽  
Ros Homeostasis ◽  
Ros Accumulation

Drought causes a major constraint on plant growth, development, and crop productivity. Drought stress enhances the synthesis and mobilization of the phytohormone abscisic acid (ABA). Enhanced cellular levels of ABA promote the production of reactive oxygen species (ROS), which in turn induce anion channel activity in guard cells that consequently leads to stomatal closure. Although Cyclophilins (CYPs) are known to participate in the biotic stress response, their involvement in guard cell ABA signaling and the drought response remains to be established. The Arabidopsis thaliana gene ROC3 encodes a CYP. Arabidopsis roc3 T-DNA mutants showed a reduced level of ABA-activated S-type anion currents, and stomatal closure than wild type (WT). Also, roc3 mutants exhibited rapid loss of water in leaf than wild type. Two complementation lines of roc3 mutants showed similar stomatal response to ABA as observed for WT. Both complementation lines also showed similar water loss as WT by leaf detached assay. Biochemical assay suggested that ROC3 positively regulates ROS accumulation by inhibiting catalase activity. In response to ABA treatment or drought stress, roc3 mutant show down regulation of a number of stress responsive genes. All findings indicate that ROC3 positively regulates ABA-induced stomatal closure and the drought response by regulating ROS homeostasis and the expression of various stress-activated genes.

Integration of transcriptomic and metabolic data reveals hub transcription factors involved in drought stress response in sunflower (Helianthus annuus L.)

2017 ◽  
Vol 94 (4-5) ◽  
pp. 549-564 ◽  
Author(s):  
Sebastián Moschen ◽  
Julio A. Di Rienzo ◽  
Janet Higgins ◽  
Takayuki Tohge ◽  
Mutsumi Watanabe ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Stress Response ◽  
Helianthus Annuus ◽  
Helianthus Annuus L ◽  
Metabolic Data

scholarly journals Prediction and characterization of transcription factors involved in drought stress response

2020 ◽  
Author(s):  
Chirag Gupta ◽  
Venkategowda Ramegowda ◽  
Supratim Basu ◽  
Andy Pereira
Keyword(s):  
Machine Learning ◽  
Transcription Factors ◽  
Drought Stress ◽  
Stress Response ◽  
Drought Tolerance ◽  
Web Application ◽  
Protein Structures ◽  
Gene Families ◽  
Supervised Machine Learning ◽  
Specific Gene

AbstractTranscription factors (TFs) play a central role in regulating molecular level responses of plants to external stresses such as water limiting conditions, but identification of such TFs in the genome remains a challenge. Here, we describe a network-based supervised machine learning framework that accurately predicts and ranks all TFs in the genome according to their potential association with drought tolerance. We show that top ranked regulators fall mainly into two ‘age’ groups; genes that appeared first in land plants and genes that emerged later in the Oryza clade. TFs predicted to be high in the ranking belong to specific gene families, have relatively simple intron/exon and protein structures, and functionally converge to regulate primary and secondary metabolism pathways. Repeated trials of nested cross-validation tests showed that models trained only on regulatory network patterns, inferred from large transcriptome datasets, outperform models trained on heterogenous genomic features in the prediction of known drought response regulators. A new R/Shiny based web application, called the DroughtApp, provides a primer for generation of new testable hypotheses related to regulation of drought stress response. Furthermore, to test the system we experimentally validated predictions on the functional role of the rice transcription factor OsbHLH148, using RNA sequencing of knockout mutants in response to drought stress and protein-DNA interaction assays. Our study exemplifies the integration of domain knowledge for prioritization of regulatory genes in biological pathways of well-studied agricultural traits.One Sentence SummaryNetwork-based supervised machine learning accurately predicts transcription factors involved in drought tolerance.

scholarly journals Transcriptome analysis and transcription factors responsive to drought stress in Hibiscus cannabinus

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8470
Author(s):  
Xia An ◽  
Guanrong Jin ◽  
Xiahong Luo ◽  
Changli Chen ◽  
Wenlue Li ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Stress Response ◽  
Transcriptome Analysis ◽  
Control Group ◽  
Response Mechanism ◽  
Control Groups ◽  
Stress Group ◽  
Significant Enrichment ◽  
And Control

Kenaf is an annual bast fiber crop. Drought stress influences the growth of kenaf stems and causes a marked decrease in fiber yield and quality. Research on the drought resistance of kenaf is therefore important, but limited information is available on the response mechanism of kenaf to drought stress. In this study, a transcriptome analysis of genes associated with the drought stress response in kenaf was performed. About 264,244,210 bp high-quality reads were obtained after strict quality inspection and data cleaning. Compared with the control group, 4,281 genes were differentially expressed in plants treated with drought stress for 7 d (the drought stress group). Compared with the control group, 605 genes showed differential expression in plants subjected to drought stress for 6 d and then watered for 1 d (the rewatering group). Compared with the rewatering group, 5,004 genes were differentially expressed in the drought stress group. In the comparisons between the drought stress and control groups, and between the drought stress and rewatering groups, the pathway that showed the most highly significant enrichment was plant hormone signal transduction. In the comparison between the rewatering and control groups, the pathways that showed the most highly significant enrichment were starch and sucrose metabolism. Eight transcription factors belonging to the AP2/ERF, MYB, NAC, and WRKY families (two transcription factors per family) detected in the leaf transcriptome were associated with the drought stress response. The identified transcription factors provide a basis for further investigation of the response mechanism of kenaf to drought stress.

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