Hello,
I’m totally ignorant about it… but I just came across this article and wanted to ask @ThomasTu and @john.tavis what do you think? could this be used in HBVDNA?
New algorithm finds lots of gene-editing
enzymes in environmental DNA**
CRISPR—Clustered Regularly Interspaced Short Palindromic
Repeats—is the microbial world’s answer to adaptive immunity.
Bacteria don’t generate antibodies when they are invaded by a
pathogen and then hold those antibodies in abeyance in case
they encounter that same pathogen again, the way we do.
Instead, they incorporate some of the pathogen’s DNA into their
own genome and link it to an enzyme that can use it to
recognize that pathogenic DNA sequence and cut it to pieces if
the pathogen ever turns up again.The enzyme that does the
cutting is called Cas, for CRISPR associated. Although the
CRISPR-Cas system evolved as a bacterial defense mechanism,
it has been harnessed and adapted by researchers as a
powerful tool for genetic manipulation in laboratory studies. It
also has demonstrated agricultural uses, and the first CRISPR-
based therapy was just approved in the UK to treat sickle-cell
disease and transfusion-dependent beta-thalassemia.
Now, researchers have developed a new way to search
genomes for CRISPR-Cas-like systems. And they’ve found thatwe may have a lot of additional tools to work with.Modifying
DNA
To date, six types of CRISPR-Cas systems have been identified in
various microbes. Although they differ in detail, they all have the
same appeal: They deliver proteins to a given sequence of
genetic material with a degree of specificity that has heretofore
been technically difficult, expensive, and time-consuming to
achieve. Any DNA sequence of interest can be programmed
into the system and targeted.
The native systems found in microbes usually bring a nuclease—
a DNA-cleaving enzyme—to the sequence, to chop up the
genetic material of a pathogen. This ability to cut any chosen
DNA sequence can be used for gene editing; in tandem with
other enzymes and/or DNA sequences, it can be used to insert
or delete additional short sequences, correcting mutant genes.
Some CRISPR-Cas systems cleave specific RNA molecules
instead of DNA. These can be used to eliminate pathogenic
RNA, like the genomes of some viruses, the way they are
eliminated in their native bacteria. This can also be used to
rescue defects in RNA processing.
But there are lots of additional ways to modify nucleic acids that
might be useful. And it’s an open question as to whether
enzymes that perform additional modifications have evolved.
So, some researchers decided to search for them.Researchers at MIT developed a new tool to detect variable
CRISPR arrays and applied it to 8.8 tera (1012)-base pairs of
prokaryotic genomic information. Many of the systems they
found are rare and only appeared in the dataset in the past 10
years, highlighting how important it is to continue adding
environmental samples that were previously hard to attain into
these data repositories.The new tool was required because
databases of protein and nucleic acid sequences are expanding
at a ridiculous rate, so the techniques for analyzing all of that
data need to keep up. Some algorithms that are used to analyze
them try to compare every sequence to every other one, which
is obviously untenable when dealing with billions of genes.
Others rely on clustering, but these find only genes that are
highly similar so they can’t really shed light on the evolutionary
relationships between distantly related proteins. But fast locality-
sensitive hashtag-based clustering (“flash clust”) works by
binning billions of proteins into fewer, larger clusters of
sequences that differ slightly to identify new, rare relatives.
The search using FLSHclust successfully pulled out 188 new
CRISPR-Cas systems.
Lots of CRISPyness
A few themes emerged from the work. One is that some of the
newly identified CRISPR systems use Cas enzymes with never-
before-seen domains, or appear to be fusions with knowngenes. The scientists further characterized some of these and
found one to be more specific than the CRISPR enzymes
currently in use, and another that cuts RNA that they propose is
structurally distinct enough to comprise an entirely new seventh
type of CRISPR-Cas system.
A corollary of this theme is the linkage of enzymes with different
functionalities, not just nucleases (enzymes that cut DNA and
RNA), with CRISPR arrays. Scientists have harnessed CRISPR’s
remarkable gene-targeting ability by linking it to other kinds of
enzymes and molecules, like fluorescent dyes. But evolution
obviously got there first.
As one example, FLSHclust identified something called a
transposase associated with two different types of CRISPR
systems. A transposase is an enzyme that helps a particular
stretch of DNA jump to another part of the genome. CRISPR
RNA-guided transposition has been seen before, but this is
another example of it. A whole host of proteins with varying
functions, like proteins with transmembrane domains and
signaling molecules, were found linked to CRISPR arrays,
highlighting the mix-n-match nature of the evolution of these
systems. They even found a protein expressed by a virus that
binds to CRISPR arrays and renders them inactive—essentially,
the virus inactivates the CRISPR system that evolved to protect
against viruses.Not only did the researchers find novel proteins
associated with CRISPR arrays, but they also found otherregularly interspaced repeat arrays that were not associated
with any cas enzymes—similar to CRISPR but not CRISPR. They’re
not sure what the functionality of these RNA guided systems
might be but speculate that they are involved in defense just like
CRISPR is.
The authors set out to find “a catalog of RNA-guided proteins
that expand our understanding of the biology and evolution of
these systems and provide a starting point for the development
of new biotechnologies." It seems they achieved their goal:
“The results of this work reveal unprecedented organizational
and functional flexibility and modularity of CRISPR systems,”
they write. They go on to conclude: “This represents only a small
fraction of the discovered systems, but it illuminates the
vastness and untapped potential of Earth’s biodiversity, and the
remaining candidates will serve as a resource for future
exploration.” New algorithm finds lots of gene-editing
enzymes in environmental DNA
CRISPR—Clustered Regularly Interspaced Short Palindromic
Repeats—is the microbial world’s answer to adaptive immunity.
Bacteria don’t generate antibodies when they are invaded by a
pathogen and then hold those antibodies in abeyance in case
they encounter that same pathogen again, the way we do.
Instead, they incorporate some of the pathogen’s DNA into their
own genome and link it to an enzyme that can use it to
recognize that pathogenic DNA sequence and cut it to pieces if
the pathogen ever turns up again.The enzyme that does the
cutting is called Cas, for CRISPR associated. Although the
CRISPR-Cas system evolved as a bacterial defense mechanism,
it has been harnessed and adapted by researchers as a
powerful tool for genetic manipulation in laboratory studies. It
also has demonstrated agricultural uses, and the first CRISPR-
based therapy was just approved in the UK to treat sickle-cell
disease and transfusion-dependent beta-thalassemia.
Now, researchers have developed a new way to search
genomes for CRISPR-Cas-like systems. And they’ve found thatwe may have a lot of additional tools to work with.Modifying
DNA
To date, six types of CRISPR-Cas systems have been identified in
various microbes. Although they differ in detail, they all have the
same appeal: They deliver proteins to a given sequence of
genetic material with a degree of specificity that has heretofore
been technically difficult, expensive, and time-consuming to
achieve. Any DNA sequence of interest can be programmed
into the system and targeted.
The native systems found in microbes usually bring a nuclease—
a DNA-cleaving enzyme—to the sequence, to chop up the
genetic material of a pathogen. This ability to cut any chosen
DNA sequence can be used for gene editing; in tandem with
other enzymes and/or DNA sequences, it can be used to insert
or delete additional short sequences, correcting mutant genes.
Some CRISPR-Cas systems cleave specific RNA molecules
instead of DNA. These can be used to eliminate pathogenic
RNA, like the genomes of some viruses, the way they are
eliminated in their native bacteria. This can also be used to
rescue defects in RNA processing.
But there are lots of additional ways to modify nucleic acids that
might be useful. And it’s an open question as to whether
enzymes that perform additional modifications have evolved.
So, some researchers decided to search for them.Researchers at MIT developed a new tool to detect variable
CRISPR arrays and applied it to 8.8 tera (1012)-base pairs of
prokaryotic genomic information. Many of the systems they
found are rare and only appeared in the dataset in the past 10
years, highlighting how important it is to continue adding
environmental samples that were previously hard to attain into
these data repositories.The new tool was required because
databases of protein and nucleic acid sequences are expanding
at a ridiculous rate, so the techniques for analyzing all of that
data need to keep up. Some algorithms that are used to analyze
them try to compare every sequence to every other one, which
is obviously untenable when dealing with billions of genes.
Others rely on clustering, but these find only genes that are
highly similar so they can’t really shed light on the evolutionary
relationships between distantly related proteins. But fast locality-
sensitive hashtag-based clustering (“flash clust”) works by
binning billions of proteins into fewer, larger clusters of
sequences that differ slightly to identify new, rare relatives.
The search using FLSHclust successfully pulled out 188 new
CRISPR-Cas systems.
Lots of CRISPyness
A few themes emerged from the work. One is that some of the
newly identified CRISPR systems use Cas enzymes with never-
before-seen domains, or appear to be fusions with knowngenes. The scientists further characterized some of these and
found one to be more specific than the CRISPR enzymes
currently in use, and another that cuts RNA that they propose is
structurally distinct enough to comprise an entirely new seventh
type of CRISPR-Cas system.
A corollary of this theme is the linkage of enzymes with different
functionalities, not just nucleases (enzymes that cut DNA and
RNA), with CRISPR arrays. Scientists have harnessed CRISPR’s
remarkable gene-targeting ability by linking it to other kinds of
enzymes and molecules, like fluorescent dyes. But evolution
obviously got there first.
As one example, FLSHclust identified something called a
transposase associated with two different types of CRISPR
systems. A transposase is an enzyme that helps a particular
stretch of DNA jump to another part of the genome. CRISPR
RNA-guided transposition has been seen before, but this is
another example of it. A whole host of proteins with varying
functions, like proteins with transmembrane domains and
signaling molecules, were found linked to CRISPR arrays,
highlighting the mix-n-match nature of the evolution of these
systems. They even found a protein expressed by a virus that
binds to CRISPR arrays and renders them inactive—essentially,
the virus inactivates the CRISPR system that evolved to protect
against viruses.Not only did the researchers find novel proteins
associated with CRISPR arrays, but they also found otherregularly interspaced repeat arrays that were not associated
with any cas enzymes—similar to CRISPR but not CRISPR. They’re
not sure what the functionality of these RNA guided systems
might be but speculate that they are involved in defense just like
CRISPR is.
The authors set out to find “a catalog of RNA-guided proteins
that expand our understanding of the biology and evolution of
these systems and provide a starting point for the development
of new biotechnologies." It seems they achieved their goal:
“The results of this work reveal unprecedented organizational
and functional flexibility and modularity of CRISPR systems,”
they write. They go on to conclude: “This represents only a small
fraction of the discovered systems, but it illuminates the
vastness and untapped potential of Earth’s biodiversity, and the
remaining candidates will serve as a resource for future
exploration.”