Luan Hemi, Meng Nan, Fu Jin, Chen Xiaomin, Xu Xun, Feng Qiang, Jiang Hui, Dai Jun, Yuan Xune, Lu Yanping, Roberts Alexandra A, Luo Xiao, Chen Maoshan, Xu Shengtao, Li Jun, Hamilton Chris J, Fang Chengxiang, Wang Jun
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China ; Department of Chemistry, Hong Kong Baptist University, Hong Kong, China.
Department of Science and Technology, BGI-Shenzhen, Shenzhen, China.
PLoS One. 2014 Jan 23;9(1):e85649. doi: 10.1371/journal.pone.0085649. eCollection 2014.
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.
耐辐射球菌细胞适应极端辐射环境需要基因表达与代谢调控网络之间的动态相互作用，但研究通常仅关注辐射后恢复期的单一调控层面。利用链特异性RNA测序（ssRNA-seq）对耐辐射球菌细胞进行动态转录组分析，并结合基于液相色谱-质谱联用的代谢物分析，能够估计基因和抗氧化剂对辐射的即时表达模式。通过覆盖其预测基因的ssRNA-seq研究细胞中的转录组动态。在注释的144个非编码RNA中，其中49个是转运RNA，95个是推定的新型反义RNA。辐射和恢复过程中差异表达的基因包括参与DNA修复、受损蛋白质降解和三羧酸（TCA）循环代谢的基因。敲除突变体crtB（八氢番茄红素合酶基因）无法产生类胡萝卜素，且辐射后存活率降低，表明这些色素在抗辐射中发挥作用。本研究中鉴定的网络成分，包括修复和代谢基因以及抗氧化剂，为耐辐射球菌抗辐射的复杂机制提供了新见解。
