CRISPR-Mediated Base Editing: From Precise Point Mutation to Genome-Wide Engineering in Nonmodel Microbes

SIMPLE SUMMARY: Gene engineering techniques are essential for genetic characterizations and metabolic engineering. A stable and robust gene editing method can speed up the explorations of nonmodel microbes which show tremendous potential for a variety of applications. In recent years, base editors have achieved precise point mutation and multiplex gene editing in a wide range of microbes. Without causing double stranded breaks and requiring a donor DNA template, base editors are more available than CRISPR/Cas9 for those species with a low homologous recombination system. Here, we introduce the latest development and applications of base editors in nonmodel microbes. This versatile method is suitable for gene editing from precise point mutation to genome-wide engineering in nonmodel microbes and holds good promise for future development of nonmodel microbes. ABSTRACT: Nonmodel microbes with unique and diverse metabolisms have become rising stars in synthetic biology; however, the lack of efficient gene engineering techniques still hinders their development. Recently, the use of base editors has emerged as a versatile method for gene engineering in a wide range of organisms including nonmodel microbes. This method is a fusion of impaired CRISPR/Cas9 nuclease and base deaminase, enabling the precise point mutation at the target without inducing homologous recombination. This review updates the latest advancement of base editors in microbes, including the conclusion of all microbes that have been researched by base editors, the introduction of newly developed base editors, and their applications. We provide a list that comprehensively concludes specific applications of BEs in nonmodel microbes, which play important roles in industrial, agricultural, and clinical fields. We also present some microbes in which BEs have not been fully established, in the hope that they are explored further and so that other microbial species can achieve arbitrary base conversions. The current obstacles facing BEs and solutions are put forward. Lastly, the highly efficient BEs and other developed versions for genome-wide reprogramming of cells are discussed, showing great potential for future engineering of nonmodel microbes.