Stress-induced Changes In Expression Research Articles

Discovery of two new isoforms of the human DUT gene

In human cells two dUTPase isoforms have been described: one nuclear (DUT-N) and one mitochondrial (DUT-M), with cognate localization signals. In contrast, here we identified two additional isoforms; DUT-3 without any localization signal and DUT-4 with the same nuclear localization signal as DUT-N. Based on an RT-qPCR method for simultaneous isoform-specific quantification we analysed the relative expression patterns in 20 human cell lines of highly different origins. We found that the DUT-N isoform is expressed by far at the highest level, followed by the DUT-M and the DUT-3 isoform. A strong correlation between expression levels of DUT-M and DUT-3 suggests that these two isoforms may share the same promoter. We analysed the effect of serum starvation on the expression of dUTPase isoforms compared to non-treated cells and found that the mRNA levels of DUT-N decreased in A-549 and MDA-MB-231 cells, but not in HeLa cells. Surprisingly, upon serum starvation DUT-M and DUT-3 showed a significant increase in the expression, while the expression level of the DUT-4 isoform did not show any changes. Taken together our results indicate that the cellular dUTPase supply may also be provided in the cytoplasm and starvation stress induced expression changes are cell line dependent.

Genome-Wide Identification of B3 DNA-Binding Superfamily Members (ABI, HIS, ARF, RVL, REM) and Their Involvement in Stress Responses and Development in Camelina sativa

The B3 DNA-binding superfamily is a group of gene families that contain a B3 domain in their proteins. Members of this superfamily are involved in responses to stresses including salt, drought, and cold stress. The B3 DNA-binding superfamily has not been fully studied in Camelina sativa. A total of eighty-seven members of this superfamily were identified in C. sativa. The identified genes were placed into five groups based on a phylogenetic analysis. All the proteins were predicted to be nuclear. The RAV and ARF gene family had the most conserved motifs, with nine out of ten motifs being preserved, while the REM gene family was discovered to have the fewest, with just one conserved motif being present. The RAV and REM gene families showed the least protein–protein interactions. The CsARF5 and CsARF7 genes showed the highest potent interaction score with multiple auxin-responsive proteins. A qPCR analysis was carried out on six genes that showed stress-induced expression changes. CsREM17, CsREM5, and CsRAVL5 were discovered to be considerably increased in response to drought stress, while CsARF10, CsARF4, and CsREM34 were found to be downregulated to a large extent. The B3 DNA-binding superfamily regulates abscisic acid signaling, which in turn influences plant growth and stress resistance.

Analysis of the cerebellar molecular stress response led to first evidence of a role for FKBP51 in brain FKBP52 expression in mice and humans

As the cerebellar molecular stress response is understudied, we assessed protein expression levels of hypothalamic-pituitary-adrenal (HPA) axis regulators and neurostructural markers in the cerebellum of a male PTSD mouse model and of unstressed vs. stressed male FK506 binding protein 51 (Fkbp5) knockout (KO) vs. wildtype mice. We explored the translatability of our findings in the Fkbp5 KO model to the situation in humans by correlating mRNA levels of candidates with those of FKBP5 in two whole transcriptome datasets of post-mortem human cerebellum and in blood of unstressed and stressed humans. Fkbp5 deletion rescued the stress-induced loss in hippocampal, prefrontal cortical, and, possibly, also cerebellar FKBP52 expression and modulated post-stress cerebellar expression levels of the glucocorticoid receptor (GR) and possibly (trend) also of glial fibrillary acidic protein (GFAP). Accordingly, expression levels of genes encoding for these three genes correlated with those of FKBP5 in human post-mortem cerebellum, while other neurostructural markers were not related to Fkbp5 either in mouse or human cerebellum. Also, gene expression levels of the two immunophilins correlated inversely in the blood of unstressed and stressed humans. We found transient changes in FKBP52 and persistent changes in GR and GFAP in the cerebellum of PTSD-like mice. Altogether, upon elucidating the cerebellar stress response we found first evidence for a novel facet of HPA axis regulation, i.e., the ability of FKBP51 to modulate the expression of its antagonist FKBP52 in the mouse and, speculatively, also in the human brain and blood and, moreover, detected long-term single stress-induced changes in expression of cerebellar HPA axis regulators and neurostructural markers of which some might contribute to the role of the cerebellum in fear extinction.

Comparative transcriptome profiling of a resistant vs susceptible bread wheat (Triticum aestivum L.) cultivar in response to water deficit and cold stress.

Bread wheat (Triticum aestivum L.) is one of the most important agricultural plants wearing abiotic stresses, such as water deficit and cold, that cause its productivity reduction. Since resistance to abiotic factors is a multigenic trait, therefore modern genome-wide approaches can help to involve various genetic material in breeding. One technique is full transcriptome analysis that reveals groups of stress response genes serving marker-assisted selection markers. Comparing transcriptome profiles of the same genetic material under several stresses is essential and makes the whole picture. Here, we addressed this by studying the transcriptomic response to water deficit and cold stress for two evolutionarily distant bread wheat varieties: stress-resistant cv. Saratovskaya 29 (S29) and stress-sensitive cv. Yanetzkis Probat (YP). For the first time, transcriptomes for these cultivars grown under abiotic stress conditions were obtained using Illumina based MACE technology. We identified groups of genes involved in response to cold and water deficiency stresses, including responses to each stress factor and both factors simultaneously that may be candidates for resistance genes. We discovered a core group of genes that have a similar pattern of stress-induced expression changes. The particular expression pattern was revealed not only for the studied varieties but also for the published transcriptomic data on cv. Jing 411 and cv. Fielder. Comparative transcriptome profiling of cv. S29 and cv. YP in response to water deficit and cold stress confirmed the hypothesis that stress-induced expression change is unequal within a homeologous gene group. As a rule, at least one changed significantly while the others had a relatively lower expression. Also, we found several SNPs distributed throughout the genomes of cv. S29 and cv. YP and distinguished the studied varieties from each other and the reference cv. Chinese Spring. Our results provide new data for genomics-assisted breeding of stress-tolerant wheat cultivars.

Proteomic Analysis of the Protective Effect of Early Heat Exposure against Chronic Heat Stress in Broilers.

Simple SummaryHeat stress affects the livestock industry, especially in poultry. Screening for metabolic changes after early and chronic heat exposure in poultry would be beneficial in resolving the production issues. In this study, we identified differentially expressed proteins that affected early heat exposure during chronic heat stress. Chronic heat stress affected 277 proteins, of which 95 differed in expression by early heat exposure. Differentially expressed proteins were related to actin metabolism and also involved in carbohydrate and carbon metabolism. According to our results, early heat exposed liver of broilers activates the different physiological mechanisms for protection from later heat stress.The increasing trend of global warming has affected the livestock industry through the heat stress, especially in poultry. Therefore, a better understanding of the mechanisms of heat stress in poultry would be helpful for maintaining the poultry production. Three groups were designed to determine early heat stress effects during chronic heat stress: CC, raised at a comfortable temperature; CH, chronic heat exposure at 35 °C for 21–35 days continuously; and HH, early heat exposure at 40 °C for 24 h at 5 days old with 35 °C temperature for 21–35 days continuously. In this study, proteome analysis was carried out to identify differentially expressed proteins in the liver tissue of broilers under chronic and early heat exposure. There were eight differentially expressed proteins from early heat stress during chronic heat exposure, which were related to actin metabolism. According to KEGG (Kyoto encyclopedia of genes and genomes) analysis, the proteins involved in carbohydrate metabolism were expressed to promote the metabolism of carbohydrates under chronic heat stress. Early heat reduced the heat stress-induced expression changes of select proteins. Our study has shown that early heat exposure suggests that the liver of broilers has various physiological mechanisms for regulating homeostasis to aid heat resistance.

Transcriptome profiling of short-term response to chilling stress in tolerant and sensitive Oryza sativa ssp. Japonica seedlings.

Low temperature is a major factor limiting rice growth and yield, and seedling is one of the developmental stages at which sensitivity to chilling stress is higher. Tolerance to chilling is a complex quantitative trait, so one of the most effective approaches to identify genes and pathways involved is to compare the stress-induced expression changes between tolerant and sensitive genotypes. Phenotypic responses to chilling of 13 Japonica cultivars were evaluated, and Thaibonnet and Volano were selected as sensitive and tolerant genotypes, respectively. To thoroughly profile the short-term response of the two cultivars to chilling, RNA-Seq was performed on Thaibonnet and Volano seedlings after 0 (not stressed), 2, and 10h at 10°C. Differential expression analysis revealed that the ICE-DREB1/CBF pathway plays a primary role in chilling tolerance, mainly due to some important transcription factors involved (some of which had never been reported before). Moreover, the expression trends of some genes that were radically different between Thaibonnet and Volano (i.e., calcium-dependent protein kinases OsCDPK21 and OsCDPK23, cytochrome P450 monooxygenase CYP76M8, etc.) suggest their involvement in low temperature tolerance too. Density of differentially expressed genes along rice genome was determined and linked to the position of known QTLs: remarkable co-locations were reported, delivering an overview of genomic regions determinant for low temperature response at seedling stage. Our study contributes to a better understanding of the molecular mechanisms underlying rice response to chilling and provides a solid background for development of low temperature-tolerant germplasm.

Transcriptomic profiling and identification of candidate genes in two Phoebe bournei ecotypes with contrasting cold stress responses

We identified a set of ecotype-specific cold-responsive genes, providing candidate genes for enhancing cold resistance in Phoebe bournei (Hemsl.) Yang and other woody plants. Phoebe bournei (Hemsl.) Yang is an indigenous, endangered, precious timber and ornamental tree in China. Cold stress greatly affects the survival of Phoebe species. To elucidate the molecular mechanisms of cold response and identify candidate genes for improving cold resistance, we used RNA-Seq and qRT-PCR to compare the transcriptomic profiles of two ecotypes of P. bournei, cold-resistant Wuyuan (WY) and cold-sensitive Wuping (WP), under cold stress. A total of 3970 and 4433 genes were differentially expressed in WY and WP, respectively, with 2030 differentially expressed genes (DEGs) were specific to WY. Specifically, the categories “defense response”, “secondary metabolites”, and “ABC transporters” were enriched among WY-specific DEGs. Several transcription factor genes might involve in cold stress response, including RAP2-3, NAC2, NAC43, WRKY47, and WRKY51, were induced only in WY, and CBF3, ZAT10, MYB308, and WER exhibited greater cold stress-induced expression changes in WY compared with WP, which may partially explain the distinct transcriptomic changes induced by cold stress between the two ecotypes. Greater fold changes in the expression of starch metabolism-related genes such as BAM1/3 and lower fold changes in the expression of DPE2 were detected in WY, which was consistent with its greater abundance of total soluble sugars. The stronger transcriptional differentiation of related genes under cold stress in WY may explain its greater cold resistance compared with the WP ecotype, providing important genetic resources for improving cold-resistant characteristics in P. bournei. In addition, two interaction networks were constructed, resulting in identification of a series of hub genes, which facilitates functional dissection of the molecular mechanisms involved in the response to cold stress of P. bournei and extends our ability to improve cold resistance in this valued species.

Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress.

BackgroundRice (Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions and is characterized by a low water-use efficiency and a high sensitivity to a water deficit, with yield reductions occurring at lower stress levels compared to most other crops. To identify genes and pathways involved in the tolerant response to dehydration, a powerful approach consists in the genome-wide analysis of stress-induced expression changes by comparing drought-tolerant and drought-sensitive genotypes.ResultsThe physiological response to osmotic stress of 17 japonica rice genotypes was evaluated. A clear differentiation of the most tolerant and the most sensitive phenotypes was evident, especially after 24 and 48 h of treatment. Two genotypes, which were characterized by a contrasting response (tolerance/sensitivity) to the imposed stress, were selected. A parallel transcriptomic analysis was performed on roots and leaves of these two genotypes at 3 and 24 h of stress treatment. RNA-Sequencing data showed that the tolerant genotype Eurosis and the sensitive genotype Loto mainly differed in the early response to osmotic stress in roots. In particular, the tolerant genotype was characterized by a prompt regulation of genes related to chromatin, cytoskeleton and transmembrane transporters. Moreover, a differential expression of transcription factor-encoding genes, genes involved in hormone-mediate signalling and genes involved in the biosynthesis of lignin was observed between the two genotypes.ConclusionsOur results provide a transcriptomic characterization of the osmotic stress response in rice and identify several genes that may be important players in the tolerant response.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0098-1) contains supplementary material, which is available to authorized users.

Glucocorticoids and Stress-Induced Changes in the Expression of PERIOD1 in the Rat Forebrain.

The secretion of glucocorticoids in mammals is under circadian control, but glucocorticoids themselves are also implicated in modulating circadian clock gene expression. We have shown that the expression of the circadian clock protein PER1 in the forebrain is modulated by stress, and that this effect is associated with changes in plasma corticosterone levels, suggesting a possible role for glucocorticoids in the mediation of stress-induced changes in the expression of PER1 in the brain. To study this, we assessed the effects of adrenalectomy and of pretreatment with the glucocorticoid receptor antagonist, mifepristone, on the expression of PER1 in select limbic and hypothalamic regions following acute exposure to a neurogenic stressor, restraint, or a systemic stressor, 2-Deoxy-D-glucose (2DG) in rats. Acute restraint suppressed PER1 expression in the oval nucleus of the bed nucleus of the stria terminalis (BNSTov) and the central nucleus of the amygdala (CEAl), whereas 2DG increased PER1 in both regions. Both stressors increased PER1 expression in the paraventricular (PVN) and dorsomedial (DMH) nuclei of the hypothalamus, and the piriform cortex (Pi). Adrenalectomy and pretreatment with mifepristone reversed the effects of both stressors on PER1 expression in the BNSTov and CEAl, and blocked their effects in the DMH. In contrast, both treatments enhanced the effects of restraint and 2DG on PER1 levels in the PVN. Stress-induced PER1 expression in the Pi was unaffected by either treatment. PER1 expression in the suprachiasmatic nucleus, the master circadian clock, was not altered by either exposure to stress or by the glucocorticoid manipulations. Together, the results demonstrate a key role for glucocorticoid signaling in stress-induced changes in PER1 expression in the brain.

Strain differences in stress-induced changes in central CRF1 receptor expression

The Wistar Kyoto (WKY) rat is genetically predisposed to increased sensitivity to psychological and physical stressors. Evidence points towards the importance of corticotropin-releasing factor (CRF), a peptide secreted by the paraventricular nucleus of the hypothalamus, in this strain's aberrant response to stress. CRF binds to CRF1 and 2 receptors (CRFR1 and CRFR2) which are expressed in both hypothalamic and extra-hypothalamic brain regions. Phosphorylation of the signal transduction molecule, extracellular signal regulated kinase (ERK)1/2 has been linked with stress and the actions of CRF. Western blotting techniques were employed to examine changes in protein expression of CRFR1 and phosphorylated ERK1/2 in hypothalamic and extra-hypothalamic brain regions of open field-stressed Sprague Dawley (SD) and WKY rats. Stress exposure resulted in increased hypothalamic ERK1/2 phosphorylation and subsequent increases in CRFR1 expression in SD but not WKY rats. In extra-hypothalamic brain regions, the stressor caused decreased or unchanged ERK 1/2 phosphorylation in both strains. A potentiated increase in CRFR1 expression was noted in the frontal cortex of WKY rats following the stressor and expression of CRFR1 was reduced in the hippocampus of WKY rats. These data demonstrate region-specific differences in stress-induced changes in expression of CRF receptors and intracellular signaling molecules in stress-sensitive WKY rats and stress-resilient SD rats.

Differential contributions to the transcriptome of duplicated genes in response to abiotic stresses in natural and synthetic polyploids

Polyploidy has occurred throughout plant evolution and can result in considerable changes to gene expression when it takes place and over evolutionary time. Little is known about the effects of abiotic stress conditions on duplicate gene expression patterns in polyploid plants. We examined the expression patterns of 60 duplicated genes in leaves, roots and cotyledons of allotetraploid Gossypium hirsutum in response to five abiotic stress treatments (heat, cold, drought, high salt and water submersion) using single-strand conformation polymorphism assays, and 20 genes in a synthetic allotetraploid. Over 70% of the genes showed stress-induced changes in the relative expression levels of the duplicates under one or more stress treatments with frequent variability among treatments. Twelve pairs showed opposite changes in expression levels in response to different abiotic stress treatments. Stress-induced expression changes occurred in the synthetic allopolyploid, but there was little correspondence in patterns between the natural and synthetic polyploids. Our results indicate that abiotic stress conditions can have considerable effects on duplicate gene expression in a polyploid, with the effects varying by gene, stress and organ type. Differential expression in response to environmental stresses may be a factor in the preservation of some duplicated genes in polyploids.

Stress-Induced Norepinephrine Release in the Hypothalamic Paraventricular Nucleus and Pituitary-Adrenocortical and Sympathoadrenal Activity: In Vivo Microdialysis Studies

The hypothalamic-pituitary-adrenocortical (HPA) axis and the autonomic nervous system are major effector systems that serve to maintain homeostasis during exposure to stressors. In the past decade, interest in neurochemical regulation and in pathways controlling activation of the HPA axis has focused on catecholamines, which are present in high concentrations in specific brain areas—specially in the hypothalamus. The work described in this review has concentrated on the application of in vivo microdialysis in rat brain regions such as the paraventricular nucleus (PVN) of the hypothalamus, the central nucleus of the amygdala (ACE) the bed nucleus of the stria terminalis (BNST), and the posterolateral hypothalamus in order to examine aspects of catecholaminergic function and relationships between altered catecholaminergic function and the HPA axis and sympathoadrenal system activation in stress. Exposure of animals to immobilization (IMMO) markedly and rapidly increases rates of synthesis, release, and metabolism of norepinephrine (NE) in all the brain areas mentioned above and supports previous suggestions that in the PVN NE stimulates release of corticotropin-releasing hormone (CRH). The role of NE in the ACE and the BNST and most other areas possessing noradrenergic innervation remains unclear. Studies involving lower brainstem hemisections show that noradrenergic terminals in the PVN are derived mainly from medullary catecholaminergic groups rather than from the locus ceruleus, which is the main source of NE in the brain. Moreover, the medullary catecholaminergic groups contribute substantially to IMMO-induced noradrenergic activation in the PVN. Data obtained from adrenalectomized rats, with or without glucocorticoid replacement, and from hypercortisolemic rats suggest that glucocorticoids feedback to inhibit CRH release in the PVN, via attenuation of noradrenergic activation. Results from rats exposed to different stressors have indicated substantial differences among stressors in eliciting PVN noradrenergic responses as well as of responses of the HPA, sympathoneural, and adrenomedullary systems. Finally, involvement of other areas that participate in the regulation of the HPA axis such as the ACE, the BNST, and the hippocampus and the importance of stress-induced changes in expression of immediate early genes such as c- fos are discussed.