E. coli and other prokaryotes are often metabolically engineered to produce valuable substances
such as biofuels, pharmaceuticals, and biochemicals.
For example, engineering E. coli to produce1,3-propanediol
involved as many as 26 genetic modifications.
This illustrates the need for a rapid and cost-effective gene editing method for use
in bacteria!
One gene editing method that is gaining a lot of traction is the CRISPR Cas9 system.
Although the CRISPR system originated in bacteria, it is more commonly used to edit eukaryotic
genomes.
This is because most bacteria do not possess robust DNA repair systems,
and therefore CRISPR-induced
double-stranded DNA breaks are typically lethal to bacteria.
Some may see this as a barrier to bacterial genome editing, but others have found it to
be a benefit.
How?
CRISPR Cas9 can be used as form of negative selection to dramatically improve the efficiency
of another gene editing technique called recombineering.
Gene editing experiments can be designed so that when a bacterium is edited via recombineering
it will lose a PAM sequence at the insert site.
This will prevent Cas9 from cleaving the DNA of edited cells.
In this way, CRISPR Cas9 is used to eliminate unedited cells, creating a highly precise
and robust bacterial gene editing system.
In this video, we will demonstrate how to perform a CRISPR-assisted knockout of the
chloramphenicol resistance cassette in E. coli.
This case study will cover three phases: Phase 1, the design and cloning of Cas9 and
sgRNA for bacterial systems
Phase 2, the preparation of electrocompetent cells and transformation
Phase 3, screening and confirmation of gene knockout
In phase 1, three components are prepared
for CRISPR Gene Editing in E. coli.
1) A plasmid with the sgRNA
2) A plasmid carrying Cas9 and the Lambda red genes and
3) the repair template
First, sgRNAs are required to guide the Cas9
nuclease to the target locus.
An sgRNA was designed against a chloramphenicol acetyltransferase cassette
or CAT gene
which was previously introduced into the E. coli genome.
When intact, this gene gives resistance to the antibiotic chloramphenicol.
The sgRNA was cloned into the pTarget plasmid.
Second, a construct carrying the Lambda red genes is required.
The Lambda red genes encode phage-derived proteins that are crucial for enabling recombination
of DNA fragments.
The pCas9 plasmid carries inducible lambda red genes, as well as constitutively expressed
Cas9 and a Kanamycin resistance gene.
Finally, to facilitate recombination, a repair template is required.
This template contains left and right homology arms that are complementary to the target
DNA.
In this case study, the repair template carries three stop codons for early termination of
the CAT gene and a unique restriction site for screening purposes.
Most importantly, upon recombination, the repair template eliminates the PAM site, thereby
preventing Cas9 from targeting and cleaving edited cells.
In phase two, all the components are transformed into E. coli.
pCas9 is transformed first,
and grown at 30'C on kanamycin plates to select for Cas9-expressing bacterial cells.
The lambda red genes are induced to begin expression and the cells are made electrocompetent.
Electroporation is used to co-transform pTarget, which carries the sgRNA, and the repair template
into the cells.
Once all the components are present, the lambda red proteins enable the recombination of the
repair template DNA with the bacterial genome.
The repair template is inserted, causing the CAT gene and PAM sequence to be disrupted.
Without an intact PAM sequence, successfully edited DNA will not be targeted and cleaved
by Cas9.
However, unedited cells will be targeted by Cas9
and will die when their DNA is cleaved.
With this combination of recombineering and CRISPR, the number of background unedited
colonies can be greatly reduced in comparison to recombineering alone.
In phase three, cells are screened for CAT gene knockouts.
Transformants are replica picked onto kanamycin and chloramphenicol agar plates.
Cells that are able to grow on kanamycin plates but not on chloramphenicol plates indicate
E. coli cells that had the CAT gene successfully knocked out.
In this case, 36/45 transformants are successfully edited.
Successfully edited transformants are also verified by restriction enzyme digest using
the unique SpeI site introduced by the repair template.
The target locus is PCR amplified then digested using SpeI and NcoI to reveal a unique digest
profile.
Three bands are observed to indicate a positive clone
and two bands to indicate a negative clone.
Finally, PCR products from positive clones are subjected to Sanger sequencing to confirm
correct repair template insertion and knockout of the CAT gene.
In this example, the sequence alignment shows that colonies 1, 2, and 3 have the correct
knockout insertion sequence containing three stop codons and the SpeI restriction site.
Using CRISPR Cas9 coupled with lambda red recombineering technology, scientists have
been able to achieve editing efficiencies from 65% to close to 100%, making this method
an excellent strategy for efficient genome editing in E. coli.
At abm, we offer CRISPR Knockout and Knock-in Services in E. coli based on this game-changing
technology.
Our service includes:
1) Your E. coli strain of choice
2) sgRNA vector design and construction
3) Gene knockout or knock-in, at the locus of your choice
4) Clonal screening and selection
5) Validation of edits via diagnostic PCR and Sanger Sequencing
Simply send us your project and we can deliver your sequence verified clones in just 8 weeks!
For more information about this service or any other CRISPR gene editing product or service,
visit our website at www.abmgood.com.
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