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Open AccessArticle

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

1
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
2
Microbial Processes and Interactions (MiPI), TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
3
School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
4
Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
5
College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(22), 5603; https://doi.org/10.3390/ijms20225603 (registering DOI)
Received: 5 September 2019 / Revised: 31 October 2019 / Accepted: 7 November 2019 / Published: 9 November 2019
(This article belongs to the Section Molecular Microbiology)
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. View Full-Text
Keywords: Deinococcus radiodurans; recovery; RNA-Seq; heat stress; novel heat-related gene; cell wall damage Deinococcus radiodurans; recovery; RNA-Seq; heat stress; novel heat-related gene; cell wall damage
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Xue, D.; Liu, W.; Chen, Y.; Liu, Y.; Han, J.; Geng, X.; Li, J.; Jiang, S.; Zhou, Z.; Zhang, W.; Chen, M.; Lin, M.; Ongena, M.; Wang, J. RNA-Seq-Based Comparative Transcriptome Analysis Highlights New Features of the Heat-Stress Response in the Extremophilic Bacterium Deinococcus radiodurans. Int. J. Mol. Sci. 2019, 20, 5603.

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