A new engineered gene editing system, proven in bacteria and with promise for use in plants, animals and humans, addresses some of the limitations of current gene editing tools with the hope of improving their applications for research, for better crops or to treat diseases.
Gene editing includes several technologies co-opted from bacteria, such as CRISPR-Cas systems, that allow scientists to modify or even disable a specific part of an organism’s DNA or RNA.
A new study describes how scientists fused together components in bacteria that do not naturally occur together, thereby creating the potential for important design opportunities that the group is currently exploring. These components include RNA-guided enzymes believed to represent the evolutionary origins of CRISPR-Cas systems.
In a different, but related set of experiments, the team used their knowledge of an existing CRISPR-Cas system to address some of its shortcomings for greater efficiency and accuracy than the current method allows. The new system increases the accuracy of the payload’s placement, reducing the chance that it will be inserted in the wrong location, which can be an issue in CRISPR-Cas systems and can lead to complications in a host.
Previous gene editing methods enabled researchers to change a single base pair of DNA (called base editing) or even a few of them (called prime editing), while this new technique joins a group of new technologies that can introduce whole sections of DNA to correct a disorder without complications. That’simportant, because many diseases involve stretches of DNA, making it necessary to change large sections of DNA at once.
If base editing can edit one letter of genetic code, and prime editing can change the equivalent of a few words, the new technique, described in a study published Oct. 1 in Molecular Cell, can replace a whole sentence or paragraph.
“You can program it to put in a huge block of DNA in a new location, and that’s got the field very excited,” said Joe Peters, professor of microbiology at the College of Agriculture and Life Sciences (CALS) and the study’s senior author. “There’s a huge amount of competition and other strategies all focused onthis idea of delivering a big payload.”
The research team has applied for a patent for the tool, called an RNA-guided transposition system.
In the study, the research team borrowed elements found in bacteria for altering DNA to engineer a new non-CRISPR system in the lab. “So, we took these vastly different kinds of components and we fused them together,” Peters said. The first one, TldR, is an RNA-guided protein that locates exactly where in the genome a DNA payload should be inserted. The second protein, called TniQ, helps integrate the machinery that inserts the genetic payload in a single orientation and at the precise position in the genome.
The researchers are testing a broad array of a larger family of proteins, of which TldR proteins are a subgroup, to see if there are other candidates that could serve a similar purpose but that could work in human or plant cells. Access to this large family of related proteins creates a vast array of potential design possibilities.
Another advantage of the new tool is, it’s much smaller than CRISPR-Cas systems. The viruses that often deliver gene editing systems have limited room for carrying DNA cargo. “You want things that are smaller and with fewer components because it makes delivery easier for editing technology,” Peters said. Also, since editing systems are derived from bacteria, when applying them in plant or human cells they require additional specialized components to make them compatible. The smaller system allows for this kind of specialization, the researchers said.
Co-first authors include former graduate student Richard Schargel, Ph.D. ’26, and current graduate student Laura Chacon Machado, both in the Department of Microbiology (CALS). Co-authors include Alba Guarné, professor of biochemistry at McGill University, Montreal, Quebec.
The study was funded by the National Institutes of Health, the Canadian Institutes of Health Research and the National Science Foundation.
