Developing a base‐editing system to expand the carbon source utilization spectra of Shewanella oneidensis MR‐1 for enhanced pollutant degradation

Abstract

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.

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Identifiers

DOI

10.1002/bit.27368

Journal

Biotechnology and Bioengineering

Year

2020