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Complete Genome Sequencing Analysis of Deinococcus wulumuqiensis R12, an Extremely Radiation-Resistant Strain

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Abstract

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.

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Acknowledgements

The authors thank the Beijing Genomics Institute (BGI, Shenzhen, China) for help with genome sequencing.

Funding

This work was supported by The National Natural Science Foundation of China (31922070, 22008114), and The Natural Science Foundation of Jiangsu Province (BK20180038, BK20200684), and The Natural Science Foundation of the Jiangsu Higher Education Institutions of China (20KJB530017).

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Authors and Affiliations

  1. State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China

    Zijie Dai, Zhengming Zhu & Ling Jiang

  2. College of Chemical and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China

    Liying Zhu

  3. College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, China

    Zhengming Zhu & Ling Jiang

  4. Xinjiang Key Laboratory of Special Environmental Microbiology, Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China

    Zhidong Zhang

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  1. Zijie Dai
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  4. Zhengming Zhu
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  5. Ling Jiang
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Contributions

The study was designed by LJ and the paper was written by ZMZ, bioinformatics analysis was performed by ZJD, the experiments were performed by ZJD, and ZDZ, and manuscript was critically revised by LJ, ZMZ, LYZ, ZJD, and ZDZ. All authors read and approved the final manuscript.

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Correspondence to Zhengming Zhu or Ling Jiang.

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Dai, Z., Zhang, Z., Zhu, L. et al. Complete Genome Sequencing Analysis of Deinococcus wulumuqiensis R12, an Extremely Radiation-Resistant Strain. Curr Microbiol 79, 292 (2022). https://doi.org/10.1007/s00284-022-02984-5

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