title: Deep sequencing analysis of the Kineococcus radiotolerans transcriptome in response to ionizing radiation.
abstract: Kineococcus radiotolerans is a gram-positive, radiation-resistant bacterium that was isolated from a radioactive environment. The synergy of several groups of genes is thought to contribute to the radio-resistance of this species of bacteria. Sequencing of the transcriptome, RNA sequencing (RNA-seq), using deep sequencing technology can reveal the genes that are differentially expressed in response to radiation in this bacterial strain. In this study, the transcriptomes of two samples (with and without irradiation treatment) were sequencing by deep sequencing technology. After the bioinformatics process, 143 genes were screened out by the differential expression (DE) analysis. In all 143 differentially expressed genes, 20 genes were annotated to be related to the radio-resistance based on the cluster analysis by the cluster of orthologous groups of proteins (COG) annotation which were validated by the quantitative RT-PCR. The pathway analysis revealed that these 20 validated genes were related to DNA damage repair, including recA, ruvA and ruvB, which were considered to be the key genes in DNA damage repair. This study provides the foundation to investigate the regulatory mechanism of these genes.
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, No.2 Road, Xiasha, Hangzhou, Zhejiang, PR China. Electronic address: rabbitlee.bio@gmail.com.
authors.forename: Lufeng
authors.initials: L
authors.lastname: Li
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, No.2 Road, Xiasha, Hangzhou, Zhejiang, PR China. Electronic address: chenzhouweiwenzhou@126.com.
authors.forename: Zhouwei
authors.initials: Z
authors.lastname: Chen
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, No.2 Road, Xiasha, Hangzhou, Zhejiang, PR China. Electronic address: bdd114@163.com.
authors.forename: Xianfeng
authors.initials: X
authors.lastname: Ding
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, No.2 Road, Xiasha, Hangzhou, Zhejiang, PR China. Electronic address: zjzj@live.com.
authors.forename: Zhan
authors.initials: Z
authors.lastname: Shan
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, No.2 Road, Xiasha, Hangzhou, Zhejiang, PR China. Electronic address: llliu@zstu.edu.cn.
authors.forename: Lili
authors.initials: L
authors.lastname: Liu
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, No.2 Road, Xiasha, Hangzhou, Zhejiang, PR China. Electronic address: jfguo@zstu.edu.cn.
authors.forename: Jiangfeng
authors.initials: J
authors.lastname: Guo
mesh_terms: D000192:Actinomycetales / Q000235:genetics* / Q000528:radiation effects*; D019295:Computational Biology; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D011839:Radiation, Ionizing; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D059467:Transcriptome
keywords: Differential gene expression; K. radiotolerans; RNA sequencing; Radiation-resistance; Transcriptome