scholarly journals The Transcriptional Landscape and Hub Genes Associated with Physiological Responses to Drought Stress in Pinus tabuliformis

2021 ◽  
Vol 22 (17) ◽  
pp. 9604
Author(s):  
Tariq Pervaiz ◽  
Shuang-Wei Liu ◽  
Saleem Uddin ◽  
Muhammad Waqas Amjid ◽  
Shi-Hui Niu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Expression Pattern ◽  
Expression Patterns ◽  
Intercellular Co2 Concentration ◽  
Co2 Concentration ◽  
Gene Families ◽  
Hub Genes ◽  
Pinus Tabuliformis ◽  
Prolonged Drought

Drought stress has an extensive impact on regulating various physiological, metabolic, and molecular responses. In the present study, the Pinus tabuliformis transcriptome was studied to evaluate the drought-responsive genes using RNA- Sequencing approache. The results depicted that photosynthetic rate and H2O conductance started to decline under drought but recovered 24 h after re-watering; however, the intercellular CO2 concentration (Ci) increased with the onset of drought. We identified 84 drought-responsive transcription factors, 62 protein kinases, 17 transcriptional regulators, and 10 network hub genes. Additionally, we observed the expression patterns of several important gene families, including 2192 genes positively expressed in all 48 samples, and 40 genes were commonly co-expressed in all drought and recovery stages compared with the control samples. The drought-responsive transcriptome was conserved mainly between P. tabuliformis and A. thaliana, as 70% (6163) genes had a homologous in arabidopsis, out of which 52% homologous (3178 genes corresponding to 2086 genes in Arabidopsis) were also drought response genes in arabidopsis. The collaborative network exhibited 10 core hub genes integrating with ABA-dependent and independent pathways closely conserved with the ABA signaling pathway in the transcription factors module. PtNCED3 from the ABA family genes had shown significantly different expression patterns under control, mild, prolonged drought, and recovery stages. We found the expression pattern was considerably increased with the prolonged drought condition. PtNCED3 highly expressed in all drought-tested samples; more interestingly, expression pattern was higher under mild and prolonged drought. PtNCED3 is reported as one of the important regulating enzymes in ABA synthesis. The continuous accumulation of ABA in leaves increased resistance against drought was due to accumulation of PtNCED3 under drought stress in the pine needles.

scholarly journals Identification and Expression Analysis of the PIN and AUX/LAX Gene Families in Ramie (Boehmeria nivea L. Gaud)

Agronomy ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 435 ◽  
Author(s):  
Yaning Bao ◽  
Xing Huang ◽  
Muzammal Rehman ◽  
Yunhe Wang ◽  
Bo Wang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Auxin Transport ◽  
Expression Patterns ◽  
Gene Families ◽  
Ramie Fiber ◽  
Biological Functions ◽  
Qrt Pcr ◽  
Boehmeria Nivea ◽  
Auxin Distribution ◽  
Indole 3 Acetic Acid

Auxin regulates diverse aspects of growth and development. Furthermore, polar auxin transport, which is mediated by the PIN-FORMED (PIN) and AUXIN1/LIKE-AUX (AUX/LAX) proteins, plays a crucial role in auxin distribution. In this study, six PIN and four AUX/LAX genes were identified in ramie (Boehmeria nivea L.). We used qRT-PCR to characterize and analyze the two gene families, including phylogenetic relationships, intron/exon structures, cis-elements, subcellular localization, and the expression patterns in different tissues. The expression of these genes in response to indole-3-acetic acid (IAA) treatment and drought stress was also assessed; the results indicate that most of the BnAUX/LAX and BnPIN genes were regulated as a result of IAA treatment and drought stress. Our study provides insights into ramie auxin transporters and lays the foundation for further analysis of their biological functions in ramie fiber development and adaptation to environmental stresses.

scholarly journals In Silico Analysis of the Gene Expression Patterns between Aldosterone-Producing Adenoma and Nonfunctional Adrenocortical Adenoma

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Yongfa Dai ◽  
Jing Li ◽  
Hong Wen ◽  
Jie Liu ◽  
Jianling Li
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Primary Aldosteronism ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Gene Expression Patterns ◽  
Pathophysiological Mechanism ◽  
Adrenocortical Adenoma ◽  
Hub Genes ◽  
Aldosterone Producing Adenoma

Primary aldosteronism is the most common form of secondary hypertension, and aldosteronoma makes up a significant proportion of primary aldosteronism cases. Aldosteronoma is also called aldosterone-producing adenoma (APA). Although there have been many studies about APA, the pathogenesis of this disease is not yet fully understood. In this study, we aimed to find out the difference of gene expression patterns between APA and nonfunctional adrenocortical adenoma (NFAA) using a weighted gene coexpression network (WGCNA) and differentially expressed gene (DEG) analysis; only the genes that meet the corresponding standards of both methods were defined as real hub genes and then used for further analysis. Twenty-nine real hub genes were found out, most of which were enriched in the phospholipid metabolic process. WISP2, S100A10, SSTR5-AS1, SLC29A1, APOC1, and SLITRK4 are six real hub genes with the same gene expression pattern between the combined and validation datasets, three of which indirectly or directly participate in lipid metabolism including WISP2, S100A10, and APOC1. According to the gene expression pattern of DEGs, we speculated five candidate drugs with potential therapeutic value for APA, one of which is cycloheximide, an inhibitor for phospholipid biosynthesis. All the evidence suggests that phospholipid metabolism may be an important pathophysiological mechanism for APA. Our study provides a new perspective regarding the pathophysiological mechanism of APA and offers some small molecules that may possibly be effective drugs against APA.

scholarly journals Genome-wide sequence and expression analysis of the NAC transcription factor family in polyploid wheat

2017 ◽  
Author(s):  
Philippa Borrill ◽  
Sophie A. Harrington ◽  
Cristobal Uauy
Keyword(s):  
Transcription Factors ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Rna Seq ◽  
Phylogenetic Groups ◽  
Future Studies ◽  
Nac Transcription Factors ◽  
Wide Range ◽  
Nac Family

ARTICLE SUMMARYTranscription factors are vital in plants to regulate gene expression in response to environmental stimuli and to control developmental processes. In this study, we annotated and classified transcription factors in polyploid bread wheat into gene families and explored the NAC family in detail. We combined phylogenetic analysis and transcriptome analysis, using publicly available RNA-seq data, to characterize the NAC gene family and provide hypotheses for putative functions of many NAC transcription factors. This study lays the groundwork for future studies on transcription factors in wheat which may be of great agronomic relevance.ABSTRACTMany important genes in agriculture correspond to transcription factors which regulate a wide range of pathways from flowering to responses to disease and abiotic stresses. In this study, we identified 5,776 transcription factors in hexaploid wheat (Triticum aestivum) and classified them into gene families. We further investigated the NAC family exploring the phylogeny, C-terminal domain conservation and expression profiles across 308 RNA-seq samples. Phylogenetic trees of NAC domains indicated that wheat NACs divided into eight groups similar to rice (Oryza sativa) and barley (Hordeum vulgare). C-terminal domain motifs were frequently conserved between wheat, rice and barley within phylogenetic groups, however this conservation was not maintained across phylogenetic groups. We explored gene expression patterns across a wide range of developmental stages, tissues, and abiotic stresses. We found that more phylogenetically related NACs shared more similar expression patterns compared to more distant NACs. However, within each phylogenetic group there were clades with diverse expression profiles. We carried out a co-expression analysis on all wheat genes and identified 37 modules of co-expressed genes of which 23 contained NACs. Using GO term enrichment we obtained putative functions for NACs within co-expressed modules including responses to heat and abiotic stress and responses to water: these NACs may represent targets for breeding or biotechnological applications. This study provides a framework and data for hypothesis generation for future studies on NAC transcription factors in wheat.

scholarly journals Genome-wide analysis of AP2/ERF Transcription Factors in sugarcane Saccharum spontaneum L. Reveals Functional Divergence During Drought, Salt Stress and Plant Hormones Treatment

2020 ◽  
Author(s):  
Piting Li ◽  
Zhe Chai ◽  
Pingping Lin ◽  
Chaohua Huang ◽  
Guoqiang Huang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Salt Stress ◽  
Drought Stress ◽  
Stress Responses ◽  
Environmental Changes ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Structure Evolution ◽  
Saccharum Spontaneum ◽  
Erf Transcription Factors

Abstract Background: APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play important roles in plant growth, development, metabolism, as well as in biotic and abiotic stress responses. However, there are few studies concerning AP2/ERF genes in sugarcane, which is the most critical sugar and energy crop worldwide. Results: A total of 218 AP2/ERF genes were identified in the Saccharum spontaneum genome. Phylogenetic analysis showed that these genes could be divided into four groups, including 43 AP2s, 160 ERFs, and Dehydration-responsive element-binding (DREB) factors, 11 ABI3/VPs (RAV) and 4 Soloist genes. These genes were unevenly distributed on 32 chromosomes. Analysis of the structural of SsAP2/ERF genes showed that 91 SsAP2/ERFs lacked introns. Sugarcane and sorghum have a collinear relationship between 168 SsAP2/ERF genes and sorghum AP2/ERF genes that reflects their similarity. Multiple cis-regulatory elements (CREs) are present in the SsAP2/ERF promoter, and many are related to abiotic stresses, suggesting that SsAP2/ERF activity could contribute to the adaptation of sugarcane crops to environmental changes. The tissue-specific analysis showed spatiotemporal expression of SsAP2/ERF in the stems and leaves of sugarcane at different stages of development. In 10 sugarcane samples, 39 SsAP2/ERFs were not expressed at all, whereas 58 SsAP2/ERFs were expressed in all samples. Quantitative PCR experiments showed that SsERF52 expression was up-regulated under salt stress, but suppressed under drought stress. SsSoloist4 had the most considerable upregulation in response to treatment with the exogenous hormones ABA and GA. Within 3 hours of ABA or PEG6000 treatment, SsSoloist4 expression was up-regulated, indicating that this gene could play a role in ABA and GA-associated drought stress response mechanisms. Analysis of AP2/ERF gene expression patterns under different treatments indicated that SsAP2/ERF genes play an important role in drought and salt stress responses of S. spontaneum. Conclusions: In this study, a total of 218 members of the AP2 / ERF superfamily were identified in sugarcane, and their genetic structure, evolution characteristics, and expression patterns were studied and analyzed. The results of this study provide a foundation for future analyses to elucidate the importance of AP2/ERF transcription factors in the function and molecular breeding of sugarcane.

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.

An HD-Zip transcription factor, VvHDZ4, in grapes (Vitis vinifera L.) confers enhanced drought tolerance in transgenic tomato

2021 ◽  
pp. 1-13
Author(s):  
Guirong Li ◽  
Ran Quan ◽  
Shanshan Cheng ◽  
Xiaojin Hou ◽  
Huiling Hu
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Vitis Vinifera ◽  
Environmental Stress ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Membrane Damage ◽  
Vitis Vinifera L ◽  
Stress Indicator

BACKGROUND: HD-Zip genes encode several large and highly conserved protein families of transcription factors that play important roles in plant development and responses to environmental stress. To date, information about the involvement of HD-Zip in grape to drought response is limited. OBJECTIVE: The production of grapes is limited by a range of biotic and abiotic stresses, which cause significant losses in yield every year as well as a reduction in fruit quality. Identification and analysis of stress related genes in grapes are very important for cultivating more robust varieties with environmental stress resistance METHODS: We isolated a homeodomain-leucine zipper gene (HD-Zip), VvHDZ4, from grape, Vitis vinifera L. “Yatomi Rose”, and characterized VvHDZ4 based on analyses of its expression patterns, subcellular localization, transcription activity, and overexpression. RESULTS: We found that VvHDZ4 was highly expressed in roots and leaves, localized to nucleus, and activated the expression of reporter genes in yeast. The overexpression (OE) of VvHDZ4 led to enhanced drought stress tolerance in Solanum lycopersicum L. “Ailsa Craig” (tomato). The drought-tolerant phenotypes of the OE lines exhibited decreases in electrolyte leakage and rate of water loss, higher photosynthetic production and net photosynthesis rate, and showed up-regulation of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX), all of which are key antioxidant enzymes known to be activated during drought stress. Moreover, we observed the up-regulation of four additional drought stress indicator genes, SIDREB2A, SIAREB, SIRD29 and SIERD10, in the OE lines. VvHDZ4 improved drought tolerance in tomato, and the modes of action possibly consist of reducing membrane damage, increasing photosynthetic productivity, and modulating the expression of stress defense genes. CONCLUSIONS: This work increases our understanding of the important roles HD-Zip transcription factors in the responses of plants to the environment, especially abiotic stress.

scholarly journals New insights on key genes involved in drought stress response of barley: gene networks reconstruction, hub, and promoter analysis

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Seyedeh Mehri Javadi ◽  
Zahra-Sadat Shobbar ◽  
Asa Ebrahimi ◽  
Maryam Shahbazi
Keyword(s):  
Drought Stress ◽  
Stress Response ◽  
Promoter Analysis ◽  
Gene Networks ◽  
Expression Patterns ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Drought Tolerant ◽  
Key Genes

Abstract Background Barley (Hordeum vulgare L.) is one of the most important cereals worldwide. Although this crop is drought-tolerant, water deficiency negatively affects its growth and production. To detect key genes involved in drought tolerance in barley, a reconstruction of the related gene network and discovery of the hub genes would help. Here, drought-responsive genes in barley were collected through analysis of the available microarray datasets (− 5 ≥ Fold change ≥ 5, adjusted p value ≤ 0.05). Protein-protein interaction (PPI) networks were reconstructed. Results The hub genes were identified by Cytoscape software using three Cyto-hubba algorithms (Degree, Closeness, and MNC), leading to the identification of 17 and 16 non-redundant genes at vegetative and reproductive stages, respectively. These genes consist of some transcription factors such as HvVp1, HvERF4, HvFUS3, HvCBF6, DRF1.3, HvNAC6, HvCO5, and HvWRKY42, which belong to AP2, NAC, Zinc-finger, and WRKY families. In addition, the expression pattern of four hub genes was compared between the two studied cultivars, i.e., “Yousef” (drought-tolerant) and “Morocco” (susceptible). The results of real-time PCR revealed that the expression patterns corresponded well with those determined by the microarray. Also, promoter analysis revealed that some TF families, including AP2, NAC, Trihelix, MYB, and one modular (composed of two HD-ZIP TFs), had a binding site in 85% of promoters of the drought-responsive genes and of the hub genes in barley. Conclusions The identified hub genes, especially those from AP2 and NAC families, might be among key TFs that regulate drought-stress response in barley and are suggested as promising candidate genes for further functional analysis.

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