Genome-wide transcriptome and antioxidant analyses on gamma-irradiated phases of deinococcus radiodurans R1.
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.
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China ; Department of Chemistry, Hong Kong Baptist University, Hong Kong, China.
Hemi
H
Luan
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China.
Nan
N
Meng
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China.
Jin
J
Fu
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China.
Xiaomin
X
Chen
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China.
Xun
X
Xu
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China.
Qiang
Q
Feng
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China.
Hui
H
Jiang
College of Life Sciences, Wuhan University, Wuhan, China ; Key Laboratory of Fermentation Engineering, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, China.
Jun
J
Dai
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China.
Xune
X
Yuan
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China.
Yanping
Y
Lu
School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
Alexandra A
AA
Roberts
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China.
Xiao
X
Luo
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China.
Maoshan
M
Chen
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China.
Shengtao
S
Xu
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China.
Jun
J
Li
School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
Chris J
CJ
Hamilton
College of Life Sciences, Wuhan University, Wuhan, China.
Chengxiang
C
Fang
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China ; Department of Biology, University of Copenhagen, Copenhagen, Denmark ; King Abdulaziz University, Jeddah, Saudi Arabia.
Jun
J
Wang
D000975:Antioxidants / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D004260:DNA Repair; D034301:Deinococcus / Q000235:genetics / Q000378:metabolism* / Q000528:radiation effects; D015964:Gene Expression Regulation, Bacterial / Q000528:radiation effects*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D055432:Metabolomics; D025341:Principal Component Analysis; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism; D011836:Radiation Tolerance; D017423:Sequence Analysis, RNA; D059467:Transcriptome
D000975:Antioxidants; D001426:Bacterial Proteins; D012329:RNA, Bacterial