RMgmDB - Rodent Malaria genetically modified Parasites

Summary

RMgm-5099
Malaria parasiteP. yoelii
Genotype
MutatedGene model (rodent): PY17X_0716800; Gene model (P.falciparum): PF3D7_0414600; Gene product: acylated pleckstrin-homology domain-containing protein, putative (APH)
Details mutation: loxP sequences inserted in intron 1 and in the 3'UTR
Transgene
Transgene not Plasmodium: diCre (Cre59-FKBP and Cre60-FRB)
Promoter: Gene model: PY17X_1134800; Gene model (P.falciparum): PF3D7_1357000; Gene product: elongation factor 1-alpha (eef1a)
3'UTR: Gene model: Not available; Gene product: Not available
Replacement locus: Gene model: PY17X_0306600; Gene product: 6-cysteine protein (P230p; 230p)
Phenotype Asexual bloodstage;
Last modified: 4 November 2021, 14:58
  *RMgm-5099
Successful modificationThe parasite was generated by the genetic modification
The mutant contains the following genetic modification(s) Gene mutation, Introduction of a transgene
Reference (PubMed-PMID number) Reference 1 (PMID number) : 34628068
MR4 number
Parent parasite used to introduce the genetic modification
Rodent Malaria ParasiteP. yoelii
Parent strain/lineP. yoelii 17XL
Name parent line/clone RMgm-5083
Other information parent lineThe mutant contains a diCre expression cassette containing the two genes Cre59-FKBP and Cre60-FRB placed on either side of the bidirectional eef1a promoter. This expression cassette has been introduced in the neutral p230p locus of wild type P. yoelii. This mutant does not contain a drug-selectable marker (SM). The hdhfr-yfcu SM, used to introduce the diCre cassette, has been removed by negative selection.
The mutant parasite was generated by
Name PI/ResearcherChaiyawong N, Kaneko O
Name Group/DepartmentGraduate school of Biomedical Sciences
Name InstituteNagasaki University
CityNagasaki
CountryJapan
Name of the mutant parasite
RMgm numberRMgm-5099
Principal namePyAPH-iKO cl1, cl2
Alternative name
Standardized name
Is the mutant parasite cloned after genetic modificationYes
Phenotype
Asexual blood stageFrom the abstract: 'We found that APH deletion' (i.e. knockdown after RAP treatment) resulted in a reduction in parasite asexual growth and erythrocyte invasion, with some parasites retaining the ability to invade and grow without APH. APH deletion impaired the secretion of microneme proteins, MTRAP and AMA1, and upon contact with erythrocytes the secretion of MTRAP, but not AMA1, was observed.'
Gametocyte/GameteNot tested
Fertilization and ookineteNot tested
OocystNot tested
SporozoiteNot tested
Liver stageNot tested
Additional remarks phenotype

Mutant/mutation
In the mutant the Pyaph gene (acylated pleckstrin-homology domain-containing protein, putative) of P. yoelii with a mutated PKAc gene that has  loxP sequences inserted in intron1 and in the 3'UTR. The aph gene is C-terminally-tagged with cmyc

In addition, the mutant contains a diCre expression cassette containing the two genes Cre59-FKBP and Cre60-FRB placed on either side of the bidirectional eef1a promoter (see the parent line RMgm-5083 for details about this transgene expression cassette). 

Protein (function)

According to a model largely generated by characterization of T. gondii MIC2 (a homolog of Plasmodium TRAP proteins) and AMA1, diacylglycerol is produced during a signaling cascade involving phospholipase C. The diacylglycerol is further converted to phosphatidic acid (PA) by a diacylglycerol kinase on the inner leaflet of the plasma membrane, which is then recognized by acylated pleckstrin homology (pH) domain-containing protein (APH) on the cytosolic face of the microneme membrane. The binding of APH to PA facilitates juxtaposition of these two membranes, to release the contents of micronemes.

The rapamycin-inducible Cre recombinase (DiCre) established for use in P. falciparum uses the rapamycin-binding FKBP12 and FRB proteins to dimerise the two enzyme halves. In the DiCre system, Cre is expressed in the form of two separate, enzymatically inactive polypeptides, each fused to a different rapamycin‐binding protein (either FKBP12 or FRB, the rapamycin‐binding domain of the FKBP12‐rapamycin‐associated protein mTOR). 
Rapamycin‐induced heterodimerization of the two components restores recombinase activity (rapamycin‐mediated dimerization of two distinct, enzymatically inactive polypeptides approximately corresponding to the individual domains of Cre (residues Thr19–Asn59, called Cre59, and Asn60‐343, called Cre60) each fused to a different rapamycin‐binding protein (FKBP12 and FRB respectively) results in the reconstitution of Cre recombinase activity). This site–specific recombinase recognizes short, 34 bp sequences called loxP sites and catalyzes the excision or inversion of the floxed (flanked by loxP) DNA segment.

Phenotype
From the abstract: 'We found that APH deletion' (i.e. knockdown after RAP treatment) resulted in a reduction in parasite asexual growth and erythrocyte invasion, with some parasites retaining the ability to invade and grow without APH. APH deletion impaired the secretion of microneme proteins, MTRAP and AMA1, and upon contact with erythrocytes the secretion of MTRAP, but not AMA1, was observed.'

Additional information
About rapamycin (RAP) treatment: ' RAP (Sigma-Aldrich) was dissolved with dimethyl sulfoxide (DMSO) at 4 mg/mL and stored at 􀀀 20 ◦C. RAP (4 mg/kg) or an equivalent volume of DMSO were intraperitoneally (i.p.) injected into mice infected with PyAPH-iKO parasites when the parasitemias reached 20–30%, and parasites were collected 24 h later. Schizonts were enriched by density gradients using Nycodenz (1.077 g/mL) and incubated in vitro at 15 ◦C for 3 h for maturation. Matured schizonts (107) were then intravenously (i.v.) injected to BALB/c mice and RAP (4 mg/kg) or DMSO were immediately administrated (i.p.). Blood was collected at 3, 12, 24, 36, 60, and 84 h after parasite inoculation and thin blood smears and gDNA were prepared. Blood smears were stained with Giemsa's solution and parasitemias were determined.' 

Other mutants


  Mutated: Mutant parasite with a mutated gene
Details of the target gene
Gene Model of Rodent Parasite PY17X_0716800
Gene Model P. falciparum ortholog PF3D7_0414600
Gene productacylated pleckstrin-homology domain-containing protein, putative
Gene product: Alternative nameAPH
Details of the genetic modification
Short description of the mutationloxP sequences inserted in intron 1 and in the 3'UTR
Inducable system usedNo
Short description of the conditional mutagenesisNot available
Additional remarks inducable system
Type of plasmid/constructCRISPR/Cas9 construct: integration through double strand break repair
PlasmoGEM (Sanger) construct/vector usedNo
Modified PlasmoGEM construct/vector usedNo
Plasmid/construct map
Plasmid/construct sequence
Restriction sites to linearize plasmid
Selectable marker used to select the mutant parasitehdhfr/yfcu
Promoter of the selectable markereef1a
Selection (positive) procedurepyrimethamine
Selection (negative) procedureNo
Additional remarks genetic modificationGeneration of plasmids:
To construct the pDC2-Cas9-PyU6-PyAPH-3’loxP-hDHFR/yFCU plasmid, the pDC2-cam-Cas9-PyU6-hDHFR plasmid was digested with BbsI and ligated with DNA fragment containing a gRNA1 component targeting the P. yoelii aph gene locus (PY17X_0716800). The aph gene locus was amplified from P. yoelii 17XL genomic DNA (gDNA) with primers P18 and P19 using an In-Fusion HD cloning kit (Takara Bio Inc., Shiga, Japan). Then, a DNA fragment containing a sequence encoding the 5′ homologous region (HR1) of the aph gene locus followed by Myc epitopes and a DNA fragment containing a loxP sequence and 3’ HR (HR2) of the aph gene locus were PCR-amplified from P. yoelii 17XL gDNA using primers P20 and P21 or P24 and P25, respectively, then ligated using the In-fusion method with the above plasmid digested with HpaI and AatII. The generated plasmid was digested with NotI and ligated using the In-Fusion method ith a DNA fragment containing an hDHFR/yFCU expression cassette amplified from the pDC2-Cas9-PyU6-PypPK1-Myc [24] plasmid with P22 and P23. Parasite gDNA was extracted using a QIAamp DNA blood mini kit (Qiagen, Hilden, Germany). To construct the pDC2-Cas9-PyU6-PyAPH-5’loxPi plasmid, pDC2-cam-Cas9-PyU6-hDHFR plasmid was digested with BbsI and ligated with a DNA fragment containing the gRNA2 component targeting the aph gene locus and amplified from P. yoelii 17XL gDNA with primers P26 and P27 using an In-Fusion HD cloning kit. Then, HR3 and HR4 were amplified from parasite gDNA with primers P28 and P29 or P30 and P31, respectively. LoxP-intron sequence (103 bp) and a NotI site were added to primers P30 and P31, respectively, for HR4 [25]. The gRNA2-inserted plasmid was digested with HpaI and AatII and the HR3 and HR4 fragments were inserted using the In-Fusion method. The resulting plasmid was digested with NotI and a DNA fragment containing hDHFR/ yFCU expression cassette amplified with P32 and P33 was then inserted as described. To construct the pDC2-Cas9-PyU6-PyMTRAP-Ty plasmid, the pDC2-cam-Cas9-PyU6-hDHFR plasmid was digested with BbsI and ligated with a DNA fragment containing the gRNA3 component targeting the mtrap gene locus. The mtrap gene locus was amplified from P. yoelii 17XL gDNA with primers P34 and P35 using an In-Fusion HD cloning kit. Then, the HR5 with a sequence coding for a Ty epitope and HR6 were amplified from parasite gDNA with primers P36 and P37 or P40 and P41, respectively. The gRNA3-inserted plasmid was digested with HpaI and AatII and these two DNA fragments were inserted using the In-Fusion method. A DNA fragment containing an hDHFR/yFCU expression cassette was amplified with P38 and P39 and ligated with the above NotI-digested plasmid. All primers used to generate plasmids are shown in the supplemental Table S1. The plasmids for transfection were prepared using a HiSpeed Plasmid Midi Kit (Qiagen, Hilden, Germany).

Generation of transgenic parasite lines:
Firstly, the 3′ side of the aph gene locus of a P. yoelii 17XL-based parasite cloned line expressing DiCre recombinase [23] was modified using the CRISPR/Cas9 genome editing method using the plasmid pDC2-Cas9-PyU6-PyAPH-3’loxP-hDHFR/yFCU to yield two APH-3’loxP pre-5FC parasite lines. To remove the hDHFR/yFCU expression cassette from the parasite genome, negative selection was done by oral administration of 5-fluorocytosine (5FC; Sigma-Aldrich, St. Louis, Missouri, USA) via drinking water (1 mg/mL) to yield 2 APH-3’loxP parasite lines [26]. After cloning, the 5′ side of the aph gene locus of two APH-3’loxP cloned parasite lines was further modified using a plasmid pDC2-Cas9-PyU6-PyAPH-5’loxPi, the hDHFR/yFCU expression cassette was removed as above, and then cloning was performed to yield PyAPH-iKO clones #1 and #2. PyAPH-iKO clone #1 was further modified to tag its PyMTRAP with a Ty epitope using the plasmid pDC2-Cas9-PyU6-PyMTRAP-
Ty.
Additional remarks selection procedure
Primer information: Primers used for amplification of the target sequences  Click to view information
Primer information: Primers used for amplification of the target sequences  Click to hide information
Sequence Primer 1
Additional information primer 1
Sequence Primer 2
Additional information primer 2
Sequence Primer 3
Additional information primer 3
Sequence Primer 4
Additional information primer 4
Sequence Primer 5
Additional information primer 5
Sequence Primer 6
Additional information primer 6

  Transgene: Mutant parasite expressing a transgene
Type and details of transgene
Is the transgene Plasmodium derived Transgene: not Plasmodium
Transgene namediCre (Cre59-FKBP and Cre60-FRB)
Details of the genetic modification
Inducable system usedNo
Additional remarks inducable system
Type of plasmid/constructCRISPR/Cas9 construct: integration through double strand break repair
PlasmoGEM (Sanger) construct/vector usedNo
Modified PlasmoGEM construct/vector usedNo
Plasmid/construct map
Plasmid/construct sequence
Restriction sites to linearize plasmid
Selectable marker used to select the mutant parasitehdhfr/yfcu
Promoter of the selectable markereef1a
Selection (positive) procedurepyrimethamine
Selection (negative) procedure5-fluorocytosine (5-FC)
Additional remarks genetic modificationThe plasmid pBS_DC_hsp86/Bip5’ was a kind gift from M. Blackman. The promoter to drive FRB-Cre60 and FKBP-Cre59 was replaced with the P. yoelii elongation factor 1 alpha (ef-1α) bi-directional promoter (pBS-DC-Pyef-1α). The DiCre expression cassette was PCR-amplified from pBS-DC-Pyef-1α using oligonucleotide primers DiCre.F and DiCre.R, and ligated into the pDC2-cam-Cas9-PyU6-hDHFR plasmid using an In-Fusion HD cloning kit (Takara Bio Inc., Shiga, Japan), yielding pDC2-Cas9-DC-Pyef-1α. A guide RNA (gRNA) sequence to introduce a double strand break in the p230p locus (PY17X_0306600) was designed using EupaGDT and ligated using T4 ligase (New England Biolabs, Ipswich, MA, USA). The 5’- and 3’- homologous regions (HRs) were PCR-amplified from parasite gDNA with oligonucleotide primers Pyp230p 5HR.F, Pyp230p-5HR.R, Pyp230p-3HR.F, and Pyp230p-3HR.R; and inserted into pDC2-Cas9-DC-Pyef-1α, yielding pDC2-Cas9-p230p-DC-Pyef-1α

To generate DiCre-expressing P. yoelii, a DNA fragment containing a DiCre expression cassette and a hDHFR-yFCU expression cassette was integrated into the Pyp230p gene locus, which is dispensable in all development stages. After validating the insertion of this DNA fragment into the target genome locus by genotype PCR, parasites were treated with 5-FC to remove the hDHFR-yFCU expression cassette, then cloned by limiting dilution
Additional remarks selection procedure
Other details transgene
Promoter
Gene Model of Parasite PY17X_1134800
Gene Model P. falciparum ortholog PF3D7_1357000
Gene productelongation factor 1-alpha
Gene product: Alternative nameeef1a
Primer information details of the primers used for amplification of the promoter sequence  Click to view information
Primer information details of the primers used for amplification of the promoter sequence  Click to hide information
Sequence Primer 1
Additional information primer 1
Sequence Primer 2
Additional information primer 2
3'-UTR
Gene Model of Parasite Not available
Gene productNot available
Gene product: Alternative name
Primer information details of the primers used for amplification the 3'-UTR sequences  Click to view information
Primer information details of the primers used for amplification the 3'-UTR sequences  Click to hide information
Sequence Primer 1
Additional information primer 1
Sequence Primer 2
Additional information primer 2
Insertion/Replacement locus
Replacement / InsertionReplacement locus
Gene Model of Parasite PY17X_0306600
Gene product6-cysteine protein
Gene product: Alternative nameP230p; 230p
Primer information details of the primers used for amplification of the target sequences  Click to view information
Primer information details of the primers used for amplification of the target sequences  Click to hide information
Sequence Primer 1
Additional information primer 1
Sequence Primer 2
Additional information primer 2
Sequence Primer 3
Additional information primer 3
Sequence Primer 4
Additional information primer 4