TY - JOUR
T1 - Genome-wide transcriptome and antioxidant analyses on gamma-irradiated phases of Deinococcus radiodurans R1
AU - Luan, Hemi
AU - Meng, Nan
AU - Fu, Jin
AU - Chen, Xiaomin
AU - Xu, Xun
AU - Feng, Qiang
AU - Jiang, Hui
AU - Dai, Jun
AU - Yuan, Xune
AU - Lu, Yanping
AU - Roberts, Alexandra A.
AU - Luo, Xiao
AU - Chen, Maoshan
AU - Xu, Shengtao
AU - Li, Jun
AU - Hamilton, Chris J.
AU - Fang, Chengxiang
AU - Wang, Jun
N1 - This study was supported by the Open Research Program of Shenzhen Key Laboratory of Environmental Genomics of Microbes and Applications, Shenzhen Key Laboratory of Trans-omics Biotechnologies and National Natural Science Foundation of China (No. 31300003). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Publisher copyright:
© 2014 Luan et al.
PY - 2014/1/23
Y1 - 2014/1/23
N2 - Adaptation of D. radiodurans cells to extreme irradiation environments requires dynamic interactions between gene expression and metabolic regulatory networks, but studies typically address only a single layer of regulation during the recovery period after irradiation. Dynamic transcriptome analysis of D. radiodurans cells using strand-specific RNA sequencing (ssRNA-seq), combined with LC-MS based metabolite analysis, allowed an estimate of the immediate expression pattern of genes and antioxidants in response to irradiation. Transcriptome dynamics were examined in cells by ssRNA-seq covering its predicted genes. Of the 144 non-coding RNAs that were annotated, 49 of these were transfer RNAs and 95 were putative novel antisense RNAs. Genes differentially expressed during irradiation and recovery included those involved in DNA repair, degradation of damaged proteins and tricarboxylic acid (TCA) cycle metabolism. The knockout mutant crtB (phytoene synthase gene) was unable to produce carotenoids, and exhibited a decreased survival rate after irradiation, suggesting a role for these pigments in radiation resistance. Network components identified in this study, including repair and metabolic genes and antioxidants, provided new insights into the complex mechanism of radiation resistance in D. radiodurans.
AB - Adaptation of D. radiodurans cells to extreme irradiation environments requires dynamic interactions between gene expression and metabolic regulatory networks, but studies typically address only a single layer of regulation during the recovery period after irradiation. Dynamic transcriptome analysis of D. radiodurans cells using strand-specific RNA sequencing (ssRNA-seq), combined with LC-MS based metabolite analysis, allowed an estimate of the immediate expression pattern of genes and antioxidants in response to irradiation. Transcriptome dynamics were examined in cells by ssRNA-seq covering its predicted genes. Of the 144 non-coding RNAs that were annotated, 49 of these were transfer RNAs and 95 were putative novel antisense RNAs. Genes differentially expressed during irradiation and recovery included those involved in DNA repair, degradation of damaged proteins and tricarboxylic acid (TCA) cycle metabolism. The knockout mutant crtB (phytoene synthase gene) was unable to produce carotenoids, and exhibited a decreased survival rate after irradiation, suggesting a role for these pigments in radiation resistance. Network components identified in this study, including repair and metabolic genes and antioxidants, provided new insights into the complex mechanism of radiation resistance in D. radiodurans.
UR - https://www.scopus.com/pages/publications/84899894462
U2 - 10.1371/journal.pone.0085649
DO - 10.1371/journal.pone.0085649
M3 - Journal article
C2 - 24465634
AN - SCOPUS:84899894462
SN - 1932-6203
VL - 9
JO - PLoS ONE
JF - PLoS ONE
IS - 1
M1 - e85649
ER -
