Endogenous CRISPR-Cas mediated in situ genome editing: State-of-the-art and the road ahead for engineering prokaryotes

Zhenlei Liu; Jiayu Liu; Zhihan Yang; Liying Zhu; Zhengming Zhu; He Huang; Ling Jiang

doi:10.1016/j.biotechadv.2023.108241

Endogenous CRISPR-Cas mediated in situ genome editing: State-of-the-art and the road ahead for engineering prokaryotes

Biotechnol Adv. 2023 Nov:68:108241. doi: 10.1016/j.biotechadv.2023.108241. Epub 2023 Aug 24.

Authors

Zhenlei Liu¹, Jiayu Liu², Zhihan Yang¹, Liying Zhu³, Zhengming Zhu⁴, He Huang⁵, Ling Jiang⁶

Affiliations

¹ College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China.
² College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China.
³ College of Chemical and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China.
⁴ College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China. Electronic address: zhuzm@njtech.edu.cn.
⁵ School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China. Electronic address: huangh@njnu.edu.cn.
⁶ College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China. Electronic address: jiangling@njtech.edu.cn.

PMID: 37633620
DOI: 10.1016/j.biotechadv.2023.108241

Abstract

The CRISPR-Cas systems have shown tremendous promise as heterologous tools for genome editing in various prokaryotes. However, the perturbation of DNA homeostasis and the inherent toxicity of Cas9/12a proteins could easily lead to cell death, which led to the development of endogenous CRISPR-Cas systems. Programming the widespread endogenous CRISPR-Cas systems for in situ genome editing represents a promising tool in prokaryotes, especially in genetically intractable species. Here, this review briefly summarizes the advances of endogenous CRISPR-Cas-mediated genome editing, covering aspects of establishing and optimizing the genetic tools. In particular, this review presents the application of different types of endogenous CRISPR-Cas tools for strain engineering, including genome editing and genetic regulation. Notably, this review also provides a detailed discussion of the transposon-associated CRISPR-Cas systems, and the programmable RNA-guided transposition using endogenous CRISPR-Cas systems to enable editing of microbial communities for understanding and control. Therefore, they will be a powerful tool for targeted genetic manipulation. Overall, this review will not only facilitate the development of standard genetic manipulation tools for non-model prokaryotes but will also enable more non-model prokaryotes to be genetically tractable.

Keywords: Endogenous CRISPR-Cas system; Genome editing; Transposon-associated CRISPR-Cas system.

Publication types

Review
Research Support, Non-U.S. Gov't

MeSH terms

CRISPR-Cas Systems / genetics
Gene Editing*
Microbiota*
RNA

Substances

RNA