MIT study finds more than 1m potential genome-editing tools in microbes

13 Sep 2021

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While investigating the ancestry of Cas proteins, researchers found a potential trove of programmable gene-editing proteins.

CRISPR gene editing is a field with many promises that has sometimes struggled to deliver. Now, a new study published in the journal Science has discovered programmable gene-editing proteins outside of CRISPR systems, which could result in more than 1m possible candidates for genome-editing tools.

Scientists at MIT’s McGovern Institute and the Broad Institute of MIT and Harvard found a new editing enzyme among a family of proteins called IscB. These proteins are thought to be the ancestors of Cas9, which is often the enzyme of choice used in CRISPR.

The discovery of how IscB operates lit the way for the researchers to find other proteins of interest.


CRISPR techniques work by using Cas proteins such as Cas9 alongside a guiding RNA. This is how it is possible to cut a DNA sequence. The use of RNA to guide Cas9 is critical, as it enables versatility in targeting which bits of the genome scientists intend to alter.

Zhang and his team were interested in new molecular systems that can be rationally programmed in a manner similar to Cas9. This is how they came to discover of a new class of programmable DNA modifying systems, which they called OMEGA (obligate mobile element guided activity).

IscBs were the first proteins in an OMEGA system that the team identified. The DNA responsible for encoding IscB proteins was often near the DNA that generates a type of RNA molecule, which they called omega-RNA. This omega-RNA guides the IscB proteins to cleave DNA at a specific site, much like Cas9 and its guide RNA.

The study then found two other classes of small proteins known as IsrBs and TnpBs that also use guiding proteins in a similar manner. The researchers think that TnpB could be an ancestor of Cas12, another common protein used in CRISPR. As these are some of the most abundant genes in bacteria, this means a huge number of candidates for future research.

Tools of the future

This research was important as programmable enzymes, especially those that use an RNA guide, can be adapted for different uses. This discovery of other RNA-targeted enzymes capable of cutting DNA could yield further tools for genome editing, the study’s authors said.

“These programmable proteins are very useful, beyond basic biological interest,” lead author Feng Zhang, a molecular biologist at MIT, told Nature.

“And this mechanism of RNA-guided DNA recognition is likely something that nature has created independently multiple times.”

The researchers explained that in nature, these genes could be performing a variety of functions, such as defence or the regulation of other genes’ expression. For lab purposes, however, it creates a myriad of possibilities.

“A lot of the things that we have been thinking about may already exist naturally in some capacity,” said Han Altae-Tran, graduate student and co-first author of the paper. “Natural versions of these types of systems might be a good starting point to adapt for that particular task.”

Sam Cox was a journalist at Silicon Republic covering sci-tech news