CRISPR and bacteria

A new technique from the University of Edinburgh could activate bacteria genes to trigger greater yields of different products, or enable closer study of bacteria

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Learning to see bacteria as something useful could be a bit of a cognitive leap for some people, and certainly, the antagonistic aspects of bacteria—such as infections or antibiotic-resistant strains—don't help. But just as the bacteria in your gut (your microbiome) are helpful and significantly impact many biological processes, bacteria can in fact be a boon. Bacteria have long played a role in drug development thanks to the discovery that they can be used to produce a variety of proteins and other components for medicine, including useful and hard-to-harvest products such as insulin or human growth hormone. As explained in an article on Science Learning Hub, “Many proteins, particularly medicines, are produced by expressing the genes that encode them in bacteria. To obtain the proteins in industrial amounts, bacteria are grown in large fermentation vessels. They are then harvested, and the protein of interest is purified away from bacterial components.”
But as with many processes in the industry, there is room for improvement, and a team from the University of Edinburgh recently outlined a method that could be more productive: a new technique they refer to as programmable gene activation. The researchers noted that their new approach makes it possible to target a wider variety of genes and encourage increased production, and in fact, the Edinburgh team said they saw levels of gene activation that were roughly 100 times higher than current techniques. Their work appeared in Nature Communications in a paper titled “Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria.”
The authors explain that “options for CRISPR activation (CRISPRa) remained limited in flexibility and activity because they relied on σ70 promoters. Here we report a eukaryote-like bacterial CRISPRa system based on σ54-dependent promoters, which supports long distance, and hence multi-input regulation with high dynamic ranges. Our CRISPRa device can activate σ54-dependent promoters with biotechnology relevance in non-model bacteria. It also supports orthogonal gene regulation on multiple levels. Combining our CRISPRa with dxCas9 further expands flexibility in DNA targeting, and boosts dynamic ranges into regimes that enable construction of cascaded CRISPRa circuits.”
“σ54-dependent promoters play important roles in a variety of high-value physiological functions in bacteria, such as nitrogen assimilation and fixation41,45, pathogenicity29,46, host colonization47, motility46,47, biofilm formation47, environmental bioremediation48, and stress responses,” they add.
“This new method has the potential to be a powerful tool for programing bacteria, with diverse applications for research and industry. It could help save a lot of time and money,” said Dr. Baojun Wang, a member of the School of Biological Sciences at the University of Edinburgh and corresponding author for the paper.
This new approach uses CRISPR as well as small guide molecules and proteins that can target genes and switch them on. The team developed their technique for E. coli and a soil bacterium, but they claim it will likely work in other species as well.
With this work, the authors report, “we construct a reusable scanning platform for readily optimizing metabolic pathways without library reconstructions.”
Beyond the increased production benefits, the team added that this could also enable more and deeper avenues of study into the resilience and infectious potential of various bacteria strains.
“[W]e set up an efficient profile scanning platform for metabolic pathways, in which the sgRNA library and thus its encoded transcriptional activation profiles do not need to be rebuilt and can be applied to different pathways. Those profiles, when applied to multi-gene expression, show good stability and durability. This CRISPRa device not only enriches the genetic regulation toolbox, but also supports real-life application scenarios by its high performance,” they noted in their paper.

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