State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China.
Xinjiang Key Laboratory of Special Environmental Microbiology, Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China.
Curr Microbiol. 2022 Aug 16;79(10):292. doi: 10.1007/s00284-022-02984-5.
Genome sequencing was performed by the PacBio RS II platform and Illumina HiSeq 4000 platform to discover the metabolic profile of the Deinococcus wulumuqiensis R12, which was isolated from radiation-contaminated soils in Xinjiang Uygur Autonomous Region of northwest China. The genome of 3.5 Mbp comprises one circular chromosome and four circular plasmids with 3679 genes and a GC content of 66.97%. A total of 41 new transcriptional factors were identified using the DeepTFactor tool. Genomic analysis revealed the presence of genes for homologous recombination repair, which suggested high recombination efficiency in R12. Three Type I and one Type II RM systems, two CRISPR arrays, and one Cas-Type IC protein were found, allowing the development of endogenous CRISPR-Cas gene-editing tools. Additionally, we found that R12 has a broad spectrum of substrate utilization, which was validated by physiological experiments. Genes involved in the carotenoid biosynthesis pathway and the antioxidative system were also identified. Overall, the comprehensive description of the genome of R12 will facilitate the additional exploitation of this strain as a versatile cell factory for biotechnological applications.
对来自中国西北新疆维吾尔自治区辐射污染土壤的 Deinococcus wulumuqiensis R12 进行了基因组测序，分别使用 PacBio RS II 平台和 Illumina HiSeq 4000 平台来发现其代谢特征。该基因组大小为 3.5 Mbp，由一条环状染色体和四条环状质粒组成，包含 3679 个基因，GC 含量为 66.97%。使用 DeepTFactor 工具总共鉴定出 41 个新的转录因子。基因组分析表明存在同源重组修复基因，这表明 R12 具有较高的重组效率。发现了三个 Type I 和一个 Type II RM 系统、两个 CRISPR 数组和一个 Cas-Type IC 蛋白，这使得开发内源性 CRISPR-Cas 基因编辑工具成为可能。此外，我们发现 R12 具有广泛的底物利用谱，这通过生理实验得到了验证。还鉴定了参与类胡萝卜素生物合成途径和抗氧化系统的基因。总之，对 R12 基因组的全面描述将有助于进一步开发该菌株作为生物技术应用的多功能细胞工厂。
