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Method Article
We describe a method for generating glmS-based conditional knockdown mutants in Plasmodium falciparum using CRISPR/Cas9 genome editing.
Malaria is a significant cause of morbidity and mortality worldwide. This disease, which primarily affects those living in tropical and subtropical regions, is caused by infection with Plasmodium parasites. The development of more effective drugs to combat malaria can be accelerated by improving our understanding of the biology of this complex parasite. Genetic manipulation of these parasites is key to understanding their biology; however, historically the genome of P. falciparum has been difficult to manipulate. Recently, CRISPR/Cas9 genome editing has been utilized in malaria parasites, allowing for easier protein tagging, generation of conditional protein knockdowns, and deletion of genes. CRISPR/Cas9 genome editing has proven to be a powerful tool for advancing the field of malaria research. Here, we describe a CRISPR/Cas9 method for generating glmS-based conditional knockdown mutants in P. falciparum. This method is highly adaptable to other types of genetic manipulations, including protein tagging and gene knockouts.
Malaria is a devastating disease caused by protozoan parasites of the genus Plasmodium. P. falciparum, the most deadly human malaria parasite, causes approximately 445,000 deaths per year, mostly in children under the age of five1. Plasmodium parasites have an intricate life cycle involving a mosquito vector and a vertebrate host. Humans first become infected when an infected mosquito takes a blood meal. Then, the parasite invades the liver where it grows, develops, and divides for approximately one week.After this process, the parasites are released into the bloodstream, where they undergo asexual replication in red blood cells (RBCs). Growth of the parasites within the RBCs are directly responsible for the clinical symptoms associated with malaria2.
Until recently, production of transgenic P. falciparum was a laborious process, involving several rounds of drug selection that took many months and had a high failure rate. This time-consuming procedure relieson the generation of random DNA breaks in the region of interest and the endogenous ability of the parasite to mend its genome though homologous repair3,4,5,6. Recently, Clustered Regularly Interspaced Palindromic Repeat/Cas9 (CRISPR/Cas9) genome editing has been successfully utilized in P. falciparum7,8. The introduction of this new technology in malaria research has been critical for advancing understanding of the biology of these deadly Plasmodium parasites. CRISPR/Cas9 allows for specific targeting of genes through guide RNAs (gRNAs) that are homologous to the gene of interest. The gRNA/Cas9 complex recognizes the gene through the gRNA, and Cas9 then introduces a double-strand break, forcing the initiation of repair mechanisms in the organism9,10. Because P. falciparum lacks the machinery to repair DNA breaks through non-homologous end joining, it utilizes homologous recombination mechanisms and integrates transfected homologous DNA templates to repair the Cas9/gRNA-induced double-strand break11,12.
Here, we present a protocol for the generation of conditional knockdown mutants in P. falciparum using CRISPR/Cas9 genome editing. The protocol demonstrates usage of the glmS ribozyme to conditionally knockdown protein levels of PfHsp70x (PF3D7_0831700), a chaperone exported by P. falciparum into host RBCs13,14. The glmS ribozyme is activated by treatment with glucosamine (which is converted to glucosamine-6-phosphate in cells) to cleave its associated mRNA, leading to a reduction in the protein14. This protocol can be easily adapted to utilize other conditional knockdown tools, such as destabilization domains or RNA aptamers4,5,15. Our protocol details the generation of a repair plasmid consisting of a hemagglutinin (HA) tag and glmS ribozyme coding sequence flanked by sequences that are homologous to the PfHsp70x open reading frame (ORF) and 3'-UTR. We also describe the generation of a second plasmid to drive expression of the gRNA. These two plasmids, along with a third that drives expression of Cas9, are transfected into RBCs and used to modify the genome of P. falciparum parasites. Finally, we describe a polymerase chain reaction (PCR)-based technique to verify integration of the tag and glmS ribozyme. This protocol is highly adaptable for the modification or complete knockout of any P. falciparum genes, enhancing our ability to generate new insights into the biology of the malaria parasite.
Continuous culture of P. falciparum requires the use of human RBCs, and we utilized commercially purchased units of blood that were stripped of all identifiers and anonymized. The Institutional Review Board and the Office of Biosafety at the University of Georgia reviewed our protocols and approved all protocols used in our lab.
1. Choosing a gRNA Sequence
2. Cloning the gRNA Sequence into pMK-U6
3. Designing Homology Regions of the Repair Template
4. Cloning Homology Regions into the Repair Plasmid
5. Precipitating DNA for Transfection
6. Isolating Human RBCs from Whole Blood in Preparation for Transfection
7. Transfecting RBCs with the CRISPR/Cas9 Plasmids (To Be Done Aseptically)
NOTE: P. falciparum cultures are maintained as described in other reports17. Maintain all the cultures at 37 °C under 3% O2, 3% CO2, and 94% N2 unless stated otherwise. Whenever blood is used in this protocol, it is referring to the pure red blood cells prepared in step 6. The blood used should not be older than 6 weeks, as there is typically a decrease in parasite proliferation in older blood. The following steps describe pre-loading RBCs with DNA and adding a parasite culture to the transfected cells. Other established transfection protocols are compatible with transfecting these constructs18,19.
8. Checking Parasites for Integration of the Repair Template
9. Cloning Parasites by Limiting Dilution
10. Knockdown of the Protein by Treating Parasites with Glucosamine and Confirmation via Western Blot Analysis
A schematic of the plasmids used in this method as well as an example of a shield mutation are shown in Figure 1. As an example of how to identify mutant parasites after transfection, results from PCRs for checking integration of the HA-glmS construct are shown in Figure 2. A representative image of a cloning plate is shown in Figure 3 to demonstrate the color change of the medium in the pre...
The implementation of CRISPR/Cas9 in P. falciparum has both increased the efficiency of and decreased the amount of time needed for modifying the parasite's genome, compared to previous methods of genetic manipulation. This comprehensive protocol outlines the steps necessary for generating conditional mutants using CRISPR/Cas9 in P. falciparum. While the method here is geared specifically for the generation of HA-glmS mutants, this strategy can be adapted for a variety of needs, including t...
The authors have nothing to disclose.
We thank Muthugapatti Kandasamy at the University of Georgia (UGA) Biomedical Microscopy Core for technical assistance and Jose-Juan Lopez-Rubio for sharing the pUF1-Cas9 and pL6 plasmids. This work was supported by ARCS Foundation awards to D.W.C. and to H.M.K., UGA startup funds to V.M., grants from the March of Dimes Foundation (Basil O'Connor Starter Scholar Research Award) to V.M., and US National Institutes of Health grants (R00AI099156 and R01AI130139) to V.M. and (T32AI060546) to H.M.K.
Name | Company | Catalog Number | Comments |
Gene Pulser Xcell Electroporator | Bio-Rad | 1652660 | |
Gene Pulser Xcell Electroporator | Bio-Rad | 165-2086 | We buy the ones that are individually wrapped |
Sodium Acetate | Sigma-Aldrich | S2889-250g | |
DSM1 | Gift from Akhil Vaidya lab | Ganesan et al. Mol. Biochem. Parasitol. 2011 177:29-34 | |
TPP Tissue Culture 6 Well Plates | MIDSCI | TP92006 | |
TPP 100 mm Tissue Culture Dishes (12 mL Plate) | MIDSCI | TP93100 | |
TPP Tissue Culture 96 Well Plates | MIDSCI | TP92096 | |
TPP Tissue Culture 24 Well Plates | MIDSCI | TP92024 | |
NEBuffer 2 | New England Biolabs | #B7002S | |
NEBuffer 2.1 | New England Biolabs | #B7202S | |
BtgZI | New England Biolabs | #R0703L | |
SacII | New England Biolabs | #R0157L | |
HindIII-HF | New England Biolabs | #R3104S | |
Afe1 | New England Biolabs | #R0652S | |
Nhe1-HF | New England Biolabs | #R3131L | |
T4 DNA Polymerase | New England Biolabs | #M0203S | |
500 mL Steritop bottle top filter unit | Millipore | SCGPU10RE | You can use any size that fits your needs |
EGTA | Sigma | E4378-100G | |
KCl | Sigma-Aldrich | P9333-500g | |
CaCl2 | Sigma-Aldrich | C7902-500g | |
MgCl2 | Sigma-Aldrich | M8266-100g | |
K2HPO4 | Fisher | P288-500 | |
HEPES | Sigma-Aldrich | H4034-500g | |
pMK-U6 | Generated by the Muralidharan Lab | n/a | |
pHA-glmS | Generated by the Muralidharan Lab | n/a | |
pUF1-Cas9 | Gift from the Jose-Juan Lopez-Rubio Lab | Ghorbal et al. Nature Biotech 2014 | |
Glucose | Sigma-Aldrich | G7021-1KG | |
Sodium bicarbonate | Sigma-Aldrich | S5761-500G | |
Sodium pyruvate | Sigma-Aldrich | P5280-100G | |
Hypoxanthine | Sigma-Aldrich | H9636-25g | |
Gentamicin Reagent | Gibco | 15710-064 | |
Thymidine | Sigma-Aldrich | T1895-1G | |
PL6-eGFP BSD | Generated by the Muralidharan Lab | ||
Puf1-cas9 eGFP gRNA | Generated by the Muralidharan Lab | ||
NucleoSpin Gel and PCR Clean-up | Macherey-Nagel | 740609.250 | |
Albumax I | Life Technologies | N/A | You will want to try a few batches to find out what the parasites will grow in best |
Human Red Blood Cells | Interstate Blood Bank, Inc | Email or call them directly for ordering | We typically use O+ blood |
3D7 parasite line | Available upon request | N/A | |
Lysogeny Broth (LB) | Fisher | BP1426-2 | You can make your own, it is not necessary to use exactly this |
Ampicilin | Fisher | BP1760-25 | We make a 1000X stock at 100mg/ml in water and store in the -20C |
Ampicilin | Clonetech | R050A | |
Anti-EF1alpha | Dr. Daniel Goldberg's Lab | Washington University in St. Louis | You can use your preferred loading control for western blots. This is just the one we use in our laboratory |
Rat Anti-HA Clone 3F10, monoclonal | Made by Roche, sold by Sigma | 11867423001 | You can use your preferred anti-HA antibody |
0.6 mL tubes | Fisher | AB0350 | |
Fisher HealthCare* PROTOCOL* Hema 3* Manual Staining System (Fixative+Solution I and II) | Fisher | 22-122-911 | You can also use giemsa stain |
Fisherfines Premium Frosted Microscope Slides - Size: 3 x 1 in. | Fisher | 12-544-3 |
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