Developing a base-editing system to expand the carbon source utilization spectra of Shewanella oneidensis MR-1 for enhanced pollutant degradation.,Biotechnology and Bioengineering

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Developing a base-editing system to expand the carbon source utilization spectra of Shewanella oneidensis MR-1 for enhanced pollutant degradation.
Biotechnology and Bioengineering ( IF 3.5 ) Pub Date : 2020-05-01 , DOI: 10.1002/bit.27368
Lei Cheng ₁ , Di Min ₂ , Ru-Li He ₂ , Zhou-Hua Cheng ₁ , Dong-Feng Liu ₂ , Han-Qing Yu ₂

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Shewanella oneidensis MR‐1, a model strain of exoelectrogenic bacteria (EEB), plays a key role in environmental bioremediation and bioelectrochemical systems because of its unique respiration capacity. However, only a narrow range of substrates can be utilized by S. oneidensis MR‐1 as carbon sources, resulting in its limited applications. In this study, a rapid, highly efficient, and easily manipulated base‐editing system pCBEso was developed by fusing a Cas9 nickase (Cas9n (D10A)) with the cytidine deaminase rAPOBEC1 in S. oneidensis MR‐1. The C‐to‐T conversion of suitable C within the base‐editing window could be readily and efficiently achieved by the pCBEso system without requiring double‐strand break or repair templates. Moreover, double‐locus simultaneous editing was successfully accomplished with an efficiency of 87.5%. With this tool, the key genes involving in N‐acetylglucosamine (GlcNAc) or glucose metabolism in S. oneidensis MR‐1 were identified. Furthermore, an engineered strain with expanded carbon source utilization spectra was constructed and exhibited a higher degradation rate for multiple organic pollutants (i.e., azo dyes and organoarsenic compounds) than the wild‐type when glucose or GlcNAc was used as the sole carbon source. Such a base‐editing system could be readily applied to other EEB. This study not only enhances the substrate utilization and pollutant degradation capacities of S. oneidensis MR‐1 but also accelerates the robust construction of engineered strains for environmental bioremediation.

中文翻译：

开发碱基编辑系统以扩展 Shewanella oneidensis MR-1 的碳源利用光谱，以增强污染物降解。

Shewanella oneidensis MR-1 是一种外生电细菌（EEB）模型菌株，由于其独特的呼吸能力，在环境生物修复和生物电化学系统中起着关键作用。然而，S. oneidensis MR-1只能利用很窄范围的底物作为碳源，导致其应用受到限制。在这项研究中，通过将 Cas9 切口酶 (Cas9n (D10A)) 与S. oneidensis 中的胞苷脱氨酶 rAPOBEC1 融合，开发了一种快速、高效且易于操作的碱基编辑系统 pCBEsoMR-1。pCBEso 系统可以轻松有效地实现碱基编辑窗口内合适 C 的 C 到 T 转换，而无需双链断裂或修复模板。此外，双位点同时编辑成功完成，效率为 87.5%。使用此工具，在S. oneidensis 中涉及N-乙酰氨基葡萄糖 (GlcNAc) 或葡萄糖代谢的关键基因MR-1 被确定。此外，构建了具有扩展碳源利用光谱的工程菌株，当葡萄糖或 GlcNAc 用作唯一碳源时，其对多种有机污染物（即偶氮染料和有机砷化合物）的降解率高于野生型。这种基础编辑系统可以很容易地应用于其他 EEB。这项研究不仅提高了S. oneidensis MR-1的底物利用率和污染物降解能力，而且还加速了环境生物修复工程菌株的稳健构建。

更新日期：2020-05-01

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