Cutting Down Barriers In Bacterial Genome Editing

Scientists are fighting drug-resistant microbes with a new CRISPR-Cas gene editing method that can be transferred between bacterial strains.

AsianScientist (Sep. 14, 2021) – By taking a page out of the microbial playbook, a Hong Kong-China team has harnessed the gene editing powers of a naturally abundant yet previously untapped CRISPR-Cas system. The novel technique was reported in Nucleic Acids Research.

Found in single-celled organisms called prokaryotes, CRISPR-Cas systems are molecular snipping tools for DNA strands, with Class 2 type II CRISPR-Cas9 technology famously bagging the Nobel Prize in Chemistry. As these Class 2 systems occur in only 10 percent of prokaryotes, however, they have limited use in altering bacterial genomes.

In contrast, Class 1 type I systems are much more prevalent, accounting for nearly half of all known CRISPR-Cas systems. Their natural abundance makes type I-based editing platforms promising for bacterial genomes, with studies highlighting clear advantages like minimizing off-target effects.

But a genetic component called a Cascade has proven to be a stumbling block for type I systems, and is unable to function when introduced into heterologous hosts or organisms that do not naturally carry such genes.

To overcome this barrier, scientists led by Professor Aixin Yan from the University of Hong Kong developed a genome editing platform based on the type I-F CRISPR-Cas system of a Pseudomonas aeruginosa bacterial strain.

With some strains now dangerously resistant to multiple drugs, P. aeruginosa are notorious for infecting various sites such as the blood and the lungs, causing pneumonia in the latter.

By studying clinical samples of a drug-resistant strain, the researchers found a highly active type type I-F CRISPR-Cas system, devising a new editing method that helped with identifying resistance-linked genes and possible anti-resistance strategies.

Taking this exciting technique a step further, they cloned a stretch of DNA—including the Cascade genes—and used a tiny delivery vehicle to integrate it into the genome of heterologous hosts. The hosts expressed type I-F CRISPR-Cas as if it were a naturally occurring part of their system, ensuring stability of the transferred Cascade and leading to an even more efficient type I-based editing method.

With its ability to interfere with host DNA, the transferrable type I-F system also worked in other Pseudomonas species, expanding the realm of possibility for genetic manipulation across different organisms. Besides using CRISPR-based editing to suppress disease-causing agents, the team eyes harnessing this novel method to enhance friendly gut microbes and improve human health.

“Our approach provides a framework for widespread exploitation of the diverse type I CRISPR–Cas systems for heterologous genome editing and establishment of genome editing tools in non-model species,” the authors wrote.

The article can be found at: Xu et al. (2021) A Transferrable and Integrative Type I-F Cascade for Heterologous Genome Editing and Transcription Modulation .


Source: The University of Hong Kong; Illustration: Ajun Chuah/Asian Scientist Magazine.
Disclaimer: This article does not necessarily reflect the views of AsianScientist or its staff.

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