scholarly journals RNA-Seq-Based Comparative Transcriptome Analysis Highlights New Features of the Heat-Stress Response in the Extremophilic Bacterium Deinococcus radiodurans

2019 ◽  
Vol 20 (22) ◽  
pp. 5603 ◽  
Author(s):  
Dong Xue ◽  
Wenzheng Liu ◽  
Yun Chen ◽  
Yingying Liu ◽  
Jiahui Han ◽  
...  
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
Deinococcus Radiodurans ◽  
Regulatory System ◽  
Hypothetical Protein ◽  
Stress Factors ◽  
Heat Stress Response ◽  
Heat Response ◽  
Shock Proteins ◽  
In Cells

Deinococcus radiodurans is best known for its extraordinary resistance to diverse environmental stress factors, such as ionizing radiation, ultraviolet (UV) irradiation, desiccation, oxidation, and high temperatures. The heat response of this bacterium is considered to be due to a classical, stress-induced regulatory system that is characterized by extensive transcriptional reprogramming. In this study, we investigated the key functional genes involved in heat stress that were expressed and accumulated in cells (R48) following heat treatment at 48 °C for 2 h. Considering that protein degradation is a time-consuming bioprocess, we predicted that to maintain cellular homeostasis, the expression of the key functional proteins would be significantly decreased in cells (RH) that had partly recovered from heat stress relative to their expression in cells (R30) grown under control conditions. Comparative transcriptomics identified 15 genes that were significantly downregulated in RH relative to R30, seven of which had previously been characterized to be heat shock proteins. Among these genes, three hypothetical genes (dr_0127, dr_1083, and dr_1325) are highly likely to be involved in response to heat stress. Survival analysis of mutant strains lacking DR_0127 (a DNA-binding protein), DR_1325 (an endopeptidase-like protein), and DR_1083 (a hypothetical protein) showed a reduction in heat tolerance compared to the wild-type strain. These results suggest that DR_0127, DR_1083, and DR_1325 might play roles in the heat stress response. Overall, the results of this study provide deeper insights into the transcriptional regulation of the heat response in D. radiodurans.

scholarly journals Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across different sites

2020 ◽  
Author(s):  
Anish M.S. Shrestha ◽  
Crissa Ann I. Lilagan ◽  
Joyce Emlyn B. Guiao ◽  
Maria Rowena R. Romana-Eguia ◽  
Ma. Carmen Ablan Lagman
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
The Philippines ◽  
Differentially Expressed ◽  
Scylla Serrata ◽  
Rna Seq ◽  
Heat Stress Response ◽  
Site Analysis ◽  
Mangrove Crab ◽  
Heat Response

Abstract Background: The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are expected to threaten the mangrove crab habitat and the supply of mangrove crab seeds from the wild. It is therefore important to understand the genomic and molecular basis of how mangrove crab populations from sites with different climate profiles respond to heat stress. Towards this, we performed RNA-seq on the gill tissue of S. serrata individuals sampled from 3 sites (Cagayan, Bicol, and Bataan) in the Philippines, under normal and heat-stressed conditions. To compare the transcriptome expression profiles, we designed a 2-factor generalized linear model containing interaction terms, which allowed us to simultaneously analyze within-site response to heat-stress and across-site differences in the response.Results: We present the first ever transcriptome assembly of S. serrata obtained from a massive data set containing ~66 Gbases of cleaned RNA-seq reads. With lowly-expressed and short contigs excluded, the assembly contains roughly 17,000 genes with an N50 length of 2,366 bp. Based on sequence comparison to the fruitfly and shrimp proteomes, our assembly contains several thousands of almost full-length transcripts. Differential expression analysis found population-specific differences in heat-stress response. Within-site analysis of heat response showed 177, 755, and 221 differentially expressed (DE) genes in the Cagayan, Bataan, and Bicol group, respectively. Across-site analysis of difference in heat response showed that between Cagayan and Bataan, there were 389 differently differentially expressed (DDE) genes associated with 48 signalling and stress-response pathways; and between Cagayan and Bicol, there were 101 DDE genes affecting 8 pathways.Conclusion: In light of previous work on climate profiling and on population genetics of marine species in the Philippines, our findings suggest that the variation in thermal response among populations might be derived from acclimatory plasticity due to pre-exposure to extreme temperature variations or from population structure shaped by connectivity which leads to adaptive genetic differences among populations.

scholarly journals Transcriptional Basis for Differential Thermosensitivity of Seedlings of Various Tomato Genotypes

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 655
Author(s):  
Yangjie Hu ◽  
Sotirios Fragkostefanakis ◽  
Enrico Schleiff ◽  
Stefan Simm
Keyword(s):  
Transcription Factors ◽  
Heat Stress ◽  
Stress Response ◽  
Elevated Temperatures ◽  
Heat Stress Response ◽  
Atp Production ◽  
Different Temperatures ◽  
Related Plant ◽  
Shock Proteins ◽  
Tomato Genotypes

Transcriptional reprograming after the exposure of plants to elevated temperatures is a hallmark of stress response which is required for the manifestation of thermotolerance. Central transcription factors regulate the stress survival and recovery mechanisms and many of the core responses controlled by these factors are well described. In turn, pathways and specific genes contributing to variations in the thermotolerance capacity even among closely related plant genotypes are not well defined. A seedling-based assay was developed to directly compare the growth and transcriptome response to heat stress in four tomato genotypes with contrasting thermotolerance. The conserved and the genotype-specific alterations of mRNA abundance in response to heat stress were monitored after exposure to three different temperatures. The transcripts of the majority of genes behave similarly in all genotypes, including the majority of heat stress transcription factors and heat shock proteins, but also genes involved in photosynthesis and mitochondrial ATP production. In turn, genes involved in hormone and RNA-based regulation, such as auxin- and ethylene-related genes, or transcription factors like HsfA6b, show a differential regulation that associates with the thermotolerance pattern. Our results provide an inventory of genes likely involved in core and genotype-dependent heat stress response mechanisms with putative role in thermotolerance in tomato seedlings.

scholarly journals A Novel Noncoding RNA dsr11 Involved in Heat Stress Tolerance in Deinococcus radiodurans

Biomolecules ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 22 ◽  
Author(s):  
Dong Xue ◽  
Yun Chen ◽  
Jiang Li ◽  
Jiahui Han ◽  
Zhengfu Zhou ◽  
...  
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
Environmental Stress ◽  
Noncoding Rna ◽  
Deinococcus Radiodurans ◽  
Pcr Analysis ◽  
Resistant Bacteria ◽  
Rna Seq ◽  
Environmental Stress Response ◽  
Heat Stress Response

Deinococcus radiodurans is an extremely resistant bacteria that has evolved masterful strategies to enable survival under various environmental stress conditions. Heat stress is a major environmental stress factor that can cause denaturation of proteins, membrane disruption, and oxidative stress. Previous studies have examined the mechanisms of the heat stress response by analyzing changes in protein levels; however, little is known about the role of small noncoding RNAs (ncRNAs), which are known to play important regulatory functions in bacteria during various environmental stress response. The ncRNA dsr11 of D. radiodurans was previously identified by RNA-seq and Northern blot. In this study, we showed that the transcription level of dsr11 was up-regulated 4.2-fold under heat stress by qRT-PCR analysis. Heat tolerance assay showed that deleting dsr11 significantly inhibited the viability under high temperature conditions. To assess the influence of dsr11 on the D. radiodurans transcriptome, 157 genes were found differentially expressed in the knock-out mutant by RNA-seq experiment. Combining RNA-seq and in silico analysis, we found that trmE (tRNA modification GTPase) and dr_0651 (arginase) were likely to be the direct targets of dsr11. Further microscale thermophoresis results demonstrated that dsr11 can directly bind to the mRNA of trmE and dr_0651. Our results indicated that dsr11 can enhance the tolerance to heat stress of D. radiodurans by binding to trmE and dr_0651 mRNA. Overall, these results extend our understanding of ncRNA regulation and provide new insights into the heat stress response in D. radiodurans.

scholarly journals Toward the discovery of biological functions associated with the mechanosensor Mtl1p of Saccharomyces cerevisiae via integrative multi-OMICs analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nelson Martínez-Matías ◽  
Nataliya Chorna ◽  
Sahily González-Crespo ◽  
Lilliam Villanueva ◽  
Ingrid Montes-Rodríguez ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Heat Stress ◽  
Stress Response ◽  
Yeast Cells ◽  
Metabolome Analysis ◽  
Signaling Mechanism ◽  
Heat Stress Response ◽  
Cell Wall Integrity Pathway ◽  
Enhanced Expression ◽  
Shock Proteins

AbstractFunctional analysis of the Mtl1 protein in Saccharomyces cerevisiae has revealed that this transmembrane sensor endows yeast cells with resistance to oxidative stress through a signaling mechanism called the cell wall integrity pathway (CWI). We observed upregulation of multiple heat shock proteins (HSPs), proteins associated with the formation of stress granules, and the phosphatase subunit of trehalose 6-phosphate synthase which suggests that mtl1Δ strains undergo intrinsic activation of a non-lethal heat stress response. Furthermore, quantitative global proteomic analysis conducted on TMT-labeled proteins combined with metabolome analysis revealed that mtl1Δ strains exhibit decreased levels of metabolites of carboxylic acid metabolism, decreased expression of anabolic enzymes and increased expression of catabolic enzymes involved in the metabolism of amino acids, with enhanced expression of mitochondrial respirasome proteins. These observations support the idea that Mtl1 protein controls the suppression of a non-lethal heat stress response under normal conditions while it plays an important role in metabolic regulatory mechanisms linked to TORC1 signaling that are required to maintain cellular homeostasis and optimal mitochondrial function.

Single Gene Consistently Associated with Heat Stress Response in Three Distinct Chicken Lines

2017 ◽  
Author(s):  
Xi Lan ◽  
John C. F. Hsieh ◽  
Carl J. Schmidt ◽  
Qing Zhu ◽  
Susan J. Lamont
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
Single Gene ◽  
Heat Stress Response

The Heat Stress Response and Diabetes: More Room for Mitochondrial Implication

2016 ◽  
Vol 22 (18) ◽  
pp. 2619-2639 ◽  
Author(s):  
Biljana Miova ◽  
Maja Dimitrovska ◽  
Suzana Dinevska-Kjovkarovska ◽  
Juan V. Esplugues ◽  
Nadezda Apostolova
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
Heat Stress Response
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