Thousands of different species, including snails, algae, and amoebas, are
known to produce programmable DNA-cutting enzymes known as Fanzors. These
species have been discovered in a recent study by researchers at MIT's
McGovern Institute for Brain Research. Similar to the bacterial enzymes that
drive the popular CRISPR gene-editing system, fanzors are RNA-guided enzymes
that may be designed to cut DNA at particular locations. Scientists now have
a large repertoire of programmable enzymes to choose from when creating
novel research or therapeutic tools thanks to the recently identified
variety of natural Fanzor enzymes, which was published on September 27 in
the journal Science Advances.
"RNA-guided biology is the key to creating very user-friendly programmed
technologies. Thus, the more information we can get, the better, says Omar
Abudayyeh, a McGovern Fellow who oversaw the study alongside Jonathan
Gootenberg.
An old bacterial defensive mechanism called CRISPR has demonstrated the
utility of RNA-guided enzymes when modified for laboratory usage. The method
scientists alter DNA has altered as a result of the CRISPR-based genome
editing techniques created by MIT professor and McGovern investigator Feng
Zhang, Abudayyeh, Gootenberg, and others. This has sped up research and made
it possible to generate several experimental gene treatments.
Since then, other RNA-guide enzymes have been found in various bacterial
species by researchers, several of which have characteristics that make them
useful in the laboratory. An exciting new area of RNA-guided biology has
been revealed by the discovery of Fanzors, whose capacity to cut DNA in an
RNA-guided fashion was reported by Zhang's lab earlier this year. The first
of these enzymes to be discovered in eukaryotic creatures—a broad category
of living species that includes plants, animals, and fungi—were fanzors.
These organisms are distinguished by their membrane-bound nuclei, which
house the genetic material of each cell. (Bacteria are members of the
prokaryotes, a group that does not have a nucleus.)
"People have been searching for interesting tools in prokaryotic systems
for a long time, and I think that that has been incredibly fruitful,"
Gootenberg adds. "Eukaryotic systems are really just a whole new kind of
playground to work in."
According to Abudayyeh and Gootenberg, there is a chance that enzymes that
have developed spontaneously in eukaryotic creatures will be more adapted to
operate effectively and safely in the cells of other eukaryotic organisms,
such as humans. Fanzor enzymes can be created to precisely cut certain DNA
sequences in human cells, as Zhang's group has demonstrated. Abudayyeh and
Gootenberg found in their latest research that some Fanzors can target human
cell DNA sequences even in the absence of optimization. "The fact that they
work quite efficiently in mammalian cells was really fantastic to see,"
Gootenberg explains.
Hundreds of Fanzors have been discovered among eukaryotic creatures prior
to the current investigation. As a result of Gootenberg and Abudayyeh's team
doing a thorough search of genetic databases under the direction of lab
member Justin Lim, the known variety of these enzymes has now increased
significantly.
The researchers identified five distinct families of enzymes among the more
than 3,600 Fanzors they discovered in eukaryotes and the viruses that infect
them. Through detailed compositional comparison, scientists discovered
indications of a protracted evolutionary past.
Fanzors most likely descended from TnpBs, RNA-guided bacterial enzymes that
cleave DNA. In fact, Zhang's group and Gootenberg and Abudayyeh's team were
initially drawn to Fanzors because of their genetic resemblance to these
bacterial enzymes.
Gootenberg and Abudayyeh's evolutionary linkages imply that these
Fanzor-ancestors most likely invaded eukaryotic cells more than once,
starting their evolution. Some could have been brought in by symbiotic
bacteria, while others were probably spread by viruses. Additionally, the
study implies that the enzymes acquired adaptations to adapt to their new
home in eukaryotes, including a signal that enables them to enter a cell
nucleus and access DNA.
Under the direction of graduate student Kaiyi Jiang in biological
engineering, the team conducted genetic and biochemical studies that
revealed that Fanzors had evolved a DNA-cutting active site that is
different from that of their bacterial ancestors. The ancestors of TnpB,
when targeted to a DNA sequence in a test tube, get active and cut other
sequences in the tube; Fanzors lack this promiscuous activity. This appears
to allow the enzyme to cut its target sequence more accurately. They
discovered that some Fanzors could cut these target sequences with an
efficiency of around 10–20% when they employed an RNA guide to instruct the
enzymes to cut particular locations in the human cell genome.
Abudayyeh and Gootenberg want to construct a range of advanced genome
editing tools from Fanzors with more study. Gootenberg states, "It's a new
platform, and they have many capabilities."
"Opening up the whole eukaryotic world to these types of RNA-guided systems
is going to give us a lot to work on," says Abudayyeh.
Provided by
Massachusetts Institute of Technology
