Researchers with the University of California, Berkeley, have discovered simple CRISPR systems, or gene-editing tools, in previously unexplored bacteria.
The advance in CRISPR, short for clustered regularly interspaced short palindromic repeats, using the Cas9 protein as the scissor, formulating what is known as CRISPR-Cas9, has revolutionized biology in recent years.
The new systems, similar to CRISPR-Cas9, are highly compact, befitting their presence in some of the smallest life forms on the planet. If these systems can be re-engineered like CRISPR-Cas9, their small size could make them easier to insert into cells to edit deoxyribonucleic acid (DNA), expanding the gene-editing toolbox available to researchers and physicians.
When targeted to a specific sequence of DNA, the Cas protein binds and severs double-stranded DNA. The new discovery nearly doubles the number of simple and compact CRISPR-Cas systems potentially useful as laboratory and biomedical tools.
Referring to the findings reported Thursday in the journal Nature, Jill Banfield, a UC Berkeley professor of earth and planetary sciences and of environmental science, policy and management, noted "these are particularly interesting because the key protein in these CRISPR systems is approximately the same as Cas9, but is not Cas9. It is part of a minimal system that has obvious potential for gene editing."
The team also found the first CRISPR-Cas9 system in some of the world's smallest microbes: a nano-scale member of the archaea.
"The important thing here is that we found some of these CRISPR systems in a major branch of the bacterial tree, opening the door to a whole new world of microbes that are not cultured in the lab, so we don't really know what they are and what their habits are," said Jennifer Doudna, a UC Berkeley professor of molecular and cell biology and of chemistry and a Howard Hughes Medical Institute investigator, and co-author of the study.
The new CRISPR systems were found by scanning metagenome databases Banfield and her team have acquired over the past 15 years, in search of gene sequences similar to the sequences that code for the Cas9 protein. The database contains thousands of microbial genomes, the majority uncultivable bacteria and archaea.
One of the new CRISPR proteins, dubbed CasY, was discovered in a massive group of recently recognized bacteria that live in geysers and in soil several feet underground. Another new one, CasX, was found in bacteria from known phyla living in groundwater and sediment. The two groups of nanoarchaea found to contain CRISPR-Cas9 were first described by Banfield from acid mine drainage.
To date, only three compact Cas proteins, called Class II systems, have been experimentally shown to cut DNA: Cas9, Cpf1 and C2c1. A fourth, C2c2, cuts RNA, while a putative system, C2c3, may cut DNA.
"People have found dozens of CRISPR-Cas systems in bacteria, but not Class II systems. That is the critical piece of this research," Banfield was quoted as saying in a news release from UC Berkeley. "These simple systems are as rare as hen's teeth. We searched a massive amount of data that included 155 million proteins and only found two: CasX and CasY."