scholarly journals Wheat Heat Shock Factor TaHsfA6f Increases ABA Levels and Enhances Tolerance to Multiple Abiotic Stresses in Transgenic Plants

2020 ◽  
Vol 21 (9) ◽  
pp. 3121 ◽  
Author(s):  
Huihui Bi ◽  
Yue Zhao ◽  
Huanhuan Li ◽  
Wenxuan Liu
Keyword(s):  
Heat Shock ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Abiotic Stress Tolerance ◽  
Gene Expression Profiles ◽  
Heat Shock Factors ◽  
Plant Tolerance ◽  
Sequencing Data ◽  
Aba Metabolism ◽  
Enhanced Sensitivity

Abiotic stresses are major constraints limiting crop growth and production. Heat shock factors (Hsfs) play significant roles in mediating plant resistance to various environmental stresses, including heat, drought and salinity. In this study, we explored the biological functions and underlying mechanisms of wheat TaHsfA6f in plant tolerance to various abiotic stresses. Gene expression profiles showed that TaHsfA6f has relatively high expression levels in wheat leaves at the reproductive stage. Transcript levels of TaHsfA6f were substantially up-regulated by heat, dehydration, salinity, low temperature, and multiple phytohormones, but was not induced by brassinosteroids (BR). Subcellular localization analyses revealed that TaHsfA6f is localized to the nucleus. Overexpression of the TaHsfA6f gene in Arabidopsis results in improved tolerance to heat, drought and salt stresses, enhanced sensitivity to exogenous abscisic acid (ABA), and increased accumulation of ABA. Furthermore, RNA-sequencing data demonstrated that TaHsfA6f functions through up-regulation of a number of genes involved in ABA metabolism and signaling, and other stress-associated genes. Collectively, these results provide evidence that TaHsfA6f participates in the regulation of multiple abiotic stresses, and that TaHsfA6f could serve as a valuable gene for genetic modification of crop abiotic stress tolerance.

scholarly journals New Insights into Evolution of Plant Heat Shock Factors (Hsfs) and Expression Analysis of Tea Genes in Response to Abiotic Stresses

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 311
Author(s):  
Ping Xu ◽  
Qinwei Guo ◽  
Xin Pang ◽  
Peng Zhang ◽  
Dejuan Kong ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Shock ◽  
Plant Species ◽  
Abiotic Stresses ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Heat Shock Factors ◽  
Camellia Species ◽  
Species Specific

Heat shock transcription factor (Hsf) is one of key regulators in plant abotic stress response. Although the Hsf gene family has been identified from several plant species, original and evolution relationship have been fragmented. In addition, tea, an important crop, genome sequences have been completed and function of the Hsf family genes in response to abiotic stresses was not illuminated. In this study, a total of 4208 Hsf proteins were identified within 163 plant species from green algae (Gonium pectorale) to angiosperm (monocots and dicots), which were distributed unevenly into each of plant species tested. The result indicated that Hsf originated during the early evolutionary history of chlorophytae algae and genome-wide genetic varies had occurred during the course of evolution in plant species. Phylogenetic classification of Hsf genes from the representative nine plant species into ten subfamilies, each of which contained members from different plant species, imply that gene duplication had occurred during the course of evolution. In addition, based on RNA-seq data, the member of the Hsfs showed different expression levels in the different organs and at the different developmental stages in tea. Expression patterns also showed clear differences among Camellia species, indicating that regulation of Hsf genes expression varied between organs in a species-specific manner. Furthermore, expression of most Hsfs in response to drought, cold and salt stresses, imply a possible positive regulatory role under abiotic stresses. Expression profiles of nineteen Hsf genes in response to heat stress were also analyzed by quantitative real-time RT-PCR. Several stress-responsive Hsf genes were highly regulated by heat stress treatment. In conclusion, these results lay a solid foundation for us to elucidate the evolutionary origin of plant Hsfs and Hsf functions in tea response to abiotic stresses in the future.

Diversity of Plant Heat Shock Factors: Regulation, Interactions and Functions

2020 ◽  
Author(s):  
Norbert Andrási ◽  
Aladar Pettkó-Szandtner ◽  
László Szabados
Keyword(s):  
Heat Shock ◽  
Protein Interactions ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Variable Structure ◽  
Gene Families ◽  
Transcript Level ◽  
Published Data ◽  
Heat Shock Factors ◽  
Transcription Control

Abstract Plants Heat Shock Factors (HSFs) are encoded by large gene families with variable structure, expression and function. HSFs are components of complex signaling systems which control responses not only to high temperatures but also to a number of abiotic stresses such as cold, drought, hypoxic conditions, soil salinity, toxic minerals, strong irradiation and to pathogen threats. Here we provide an overview of the diverse world of plant HSFs through compilation and analysis of their functional versatility, diverse regulation and interactions. Bioinformatic data on gene expression profiles of Arabidopsis HSF genes were re-analysed to reveal their characteristic transcript patterns. While HSFs are regulated primarily at the transcript level, alternative splicing and posttranslational modifications such as phosphorylation and sumoylation provides further variability. Plant HSFs are involved in an intricate web of protein-protein interactions which adds considerable complexity to their biological function. A list of such interactions was compiled from public databases, published data and discussed to pinpoint their relevance in transcription control. Although most fundamental studies of plant HSFs have been conducted in the model plant, Arabidopsis, information on HSFs is accumulating in other plants such as tomato, rice, wheat and sunflower.. Understanding the function, interactions and regulation of HSFs will facilitate the design of novel strategies to use engineered proteins to improve tolerance and adaptation of crops to adverse environmental conditions.

scholarly journals LncGSEA: a versatile tool to infer lncRNA associated pathways from large-scale cancer transcriptome sequencing data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yanan Ren ◽  
Ting-You Wang ◽  
Leah C. Anderton ◽  
Qi Cao ◽  
Rendong Yang
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Clinical Samples ◽  
Sequencing Data ◽  
Multiple Cancer ◽  
Regulatory Pathways ◽  
Cancer Transcriptome ◽  
Versatile Tool

Abstract Background Long non-coding RNAs (lncRNAs) are a growing focus in cancer research. Deciphering pathways influenced by lncRNAs is important to understand their role in cancer. Although knock-down or overexpression of lncRNAs followed by gene expression profiling in cancer cell lines are established approaches to address this problem, these experimental data are not available for a majority of the annotated lncRNAs. Results As a surrogate, we present lncGSEA, a convenient tool to predict the lncRNA associated pathways through Gene Set Enrichment Analysis of gene expression profiles from large-scale cancer patient samples. We demonstrate that lncGSEA is able to recapitulate lncRNA associated pathways supported by literature and experimental validations in multiple cancer types. Conclusions LncGSEA allows researchers to infer lncRNA regulatory pathways directly from clinical samples in oncology. LncGSEA is written in R, and is freely accessible at https://github.com/ylab-hi/lncGSEA.

scholarly journals Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Fredrik Barrenas ◽  
Kevin Raehtz ◽  
Cuiling Xu ◽  
Lynn Law ◽  
Richard R. Green ◽  
...  
Keyword(s):  
Wound Healing ◽  
Expression Profiles ◽  
Healing Process ◽  
Gene Expression Profiles ◽  
Gene Signature ◽  
African Green Monkey ◽  
Wound Healing Process ◽  
Sequencing Data ◽  
Green Monkey ◽  
Conserved Gene

Abstract Natural hosts of simian immunodeficiency virus (SIV) avoid AIDS despite lifelong infection. Here, we examined how this outcome is achieved by comparing a natural SIV host, African green monkey (AGM) to an AIDS susceptible species, rhesus macaque (RM). To asses gene expression profiles from acutely SIV infected AGMs and RMs, we developed a systems biology approach termed Conserved Gene Signature Analysis (CGSA), which compared RNA sequencing data from rectal AGM and RM tissues to various other species. We found that AGMs rapidly activate, and then maintain, evolutionarily conserved regenerative wound healing mechanisms in mucosal tissue. The wound healing protein fibronectin shows distinct tissue distribution and abundance kinetics in AGMs. Furthermore, AGM monocytes exhibit an embryonic development and repair/regeneration signature featuring TGF-β and concomitant reduced expression of inflammatory genes compared to RMs. This regenerative wound healing process likely preserves mucosal integrity and prevents inflammatory insults that underlie immune exhaustion in RMs.

scholarly journals Heat Shock Proteins: Dynamic Biomolecules to Counter Plant Biotic and Abiotic Stresses

2019 ◽  
Vol 20 (21) ◽  
pp. 5321 ◽  
Author(s):  
ul Haq ◽  
Khan ◽  
Ali ◽  
Khattak ◽  
Gai ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Proteins ◽  
Stress Tolerance ◽  
Abiotic Stresses ◽  
Plant Immunity ◽  
Abiotic Stress Tolerance ◽  
Special Focus ◽  
Biotic And Abiotic Stress ◽  
Biotic And Abiotic Stresses ◽  
Shock Proteins

Due to the present scenario of climate change, plants have to evolve strategies to survive and perform under a plethora of biotic and abiotic stresses, which restrict plant productivity. Maintenance of plant protein functional conformation and preventing non-native proteins from aggregation, which leads to metabolic disruption, are of prime importance. Plant heat shock proteins (HSPs), as chaperones, play a pivotal role in conferring biotic and abiotic stress tolerance. Moreover, HSP also enhances membrane stability and detoxifies the reactive oxygen species (ROS) by positively regulating the antioxidant enzymes system. Additionally, it uses ROS as a signal to molecules to induce HSP production. HSP also enhances plant immunity by the accumulation and stability of pathogenesis-related (PR) proteins under various biotic stresses. Thus, to unravel the entire plant defense system, the role of HSPs are discussed with a special focus on plant response to biotic and abiotic stresses, which will be helpful in the development of stress tolerance in plant crops.

scholarly journals The effects of a globin blocker on the resolution of 3’mRNA sequencing data in porcine blood

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Kyu-Sang Lim ◽  
Qian Dong ◽  
Pamela Moll ◽  
Jana Vitkovska ◽  
Gregor Wiktorin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Data Sets ◽  
Globin Genes ◽  
Sequencing Data ◽  
Globin Mrna ◽  
Data Set ◽  
Mrna Sequencing ◽  
Porcine Blood

Abstract Background Gene expression profiling in blood is a potential source of biomarkers to evaluate or predict phenotypic differences between pigs but is expensive and inefficient because of the high abundance of globin mRNA in porcine blood. These limitations can be overcome by the use of QuantSeq 3’mRNA sequencing (QuantSeq) combined with a method to deplete or block the processing of globin mRNA prior to or during library construction. Here, we validated the effectiveness of QuantSeq using a novel specific globin blocker (GB) that is included in the library preparation step of QuantSeq. Results In data set 1, four concentrations of the GB were applied to RNA samples from two pigs. The GB significantly reduced the proportion of globin reads compared to non-GB (NGB) samples (P = 0.005) and increased the number of detectable non-globin genes. The highest evaluated concentration (C1) of the GB resulted in the largest reduction of globin reads compared to the NGB (from 56.4 to 10.1%). The second highest concentration C2, which showed very similar globin depletion rates (12%) as C1 but a better correlation of the expression of non-globin genes between NGB and GB (r = 0.98), allowed the expression of an additional 1295 non-globin genes to be detected, although 40 genes that were detected in the NGB sample (at a low level) were not present in the GB library. Concentration C2 was applied in the rest of the study. In data set 2, the distribution of the percentage of globin reads for NGB (n = 184) and GB (n = 189) samples clearly showed the effects of the GB on reducing globin reads, in particular for HBB, similar to results from data set 1. Data set 3 (n = 84) revealed that the proportion of globin reads that remained in GB samples was significantly and positively correlated with the reticulocyte count in the original blood sample (P < 0.001). Conclusions The effect of the GB on reducing the proportion of globin reads in porcine blood QuantSeq was demonstrated in three data sets. In addition to increasing the efficiency of sequencing non-globin mRNA, the GB for QuantSeq has an advantage that it does not require an additional step prior to or during library creation. Therefore, the GB is a useful tool in the quantification of whole gene expression profiles in porcine blood.

Heat shock factors in carrot: genome-wide identification, classification, and expression profiles response to abiotic stress

2014 ◽  
Vol 42 (5) ◽  
pp. 893-905 ◽  
Author(s):  
Ying Huang ◽  
Meng-Yao Li ◽  
Feng Wang ◽  
Zhi-Sheng Xu ◽  
Wei Huang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Heat Shock ◽  
Expression Profiles ◽  
Heat Shock Factors ◽  
Genome Wide

scholarly journals A map of tumor–host interactions in glioma at single-cell resolution

GigaScience ◽  
2020 ◽  
Vol 9 (10) ◽  
Author(s):  
Francesca Pia Caruso ◽  
Luciano Garofano ◽  
Fulvio D'Angelo ◽  
Kai Yu ◽  
Fuchou Tang ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Cross Talk ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Sequencing Data ◽  
Host Interaction ◽  
Receptor Interactions ◽  
Single Cell Rna Sequencing

ABSTRACT Background Single-cell RNA sequencing is the reference technique for characterizing the heterogeneity of the tumor microenvironment. The composition of the various cell types making up the microenvironment can significantly affect the way in which the immune system activates cancer rejection mechanisms. Understanding the cross-talk signals between immune cells and cancer cells is of fundamental importance for the identification of immuno-oncology therapeutic targets. Results We present a novel method, single-cell Tumor–Host Interaction tool (scTHI), to identify significantly activated ligand–receptor interactions across clusters of cells from single-cell RNA sequencing data. We apply our approach to uncover the ligand–receptor interactions in glioma using 6 publicly available human glioma datasets encompassing 57,060 gene expression profiles from 71 patients. By leveraging this large-scale collection we show that unexpected cross-talk partners are highly conserved across different datasets in the majority of the tumor samples. This suggests that shared cross-talk mechanisms exist in glioma. Conclusions Our results provide a complete map of the active tumor–host interaction pairs in glioma that can be therapeutically exploited to reduce the immunosuppressive action of the microenvironment in brain tumor.

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