RMgmDB - Rodent Malaria genetically modified Parasites

Summary

RMgm-1025
Malaria parasiteP. berghei
Genotype
MutatedGene model (rodent): PBANKA_0501300; Gene model (P.falciparum): PF3D7_1017000; Gene product: DNA polymerase delta catalytic subunit
Details mutation: Two amino acid residues (D311, E313), critical for proofreading in yeast, mutated to alanine
Phenotype Asexual bloodstage; Gametocyte/Gamete;
Last modified: 26 April 2014, 21:26
  *RMgm-1025
Successful modificationThe parasite was generated by the genetic modification
The mutant contains the following genetic modification(s) Gene mutation
Reference (PubMed-PMID number) Reference 1 (PMID number) : 24670267
MR4 number
Parent parasite used to introduce the genetic modification
Rodent Malaria ParasiteP. berghei
Parent strain/lineP. berghei ANKA
Name parent line/clone P. berghei ANKA 2.34
Other information parent lineP. berghei ANKA 2.34 is a cloned, gametocyte producer line of the ANKA strain (PubMed: PMID: 15137943).
The mutant parasite was generated by
Name PI/ResearcherHonma, A; Tanabe, K.
Name Group/DepartmentLaboratory of Malariology
Name InstituteResearch Institute for Microbial Diseases, Osaka University
CitySuita, Osaka
CountryJapan
Name of the mutant parasite
RMgm numberRMgm-1025
Principal namePbMut
Alternative name
Standardized name
Is the mutant parasite cloned after genetic modificationYes
Phenotype
Asexual blood stagePbMut and PbCtl parasites were maintained by weekly passage in ddY mice for 122 weeks. High-throughput genome sequencing analysis revealed that two PbMut lines had 175–178 mutations and a 86- to 90-fold higher mutation rate than that of a PbCtl line. PbMut, PbCtl, and their parent strain, PbWT, showed similar course of infection.
Gametocyte/GametePbMut lines lost gametocyte production during serial passage in mice
Fertilization and ookineteNot tested
OocystNot tested
SporozoiteNot tested
Liver stageNot tested
Additional remarks phenotype

Mutant/mutation
The mutant expresses a mutated form of DNA polymerase delta catalytic subunit; the two amino acid residues (D311, E313), known to be critical for the proofreading activity of S. cerevisiae DNA polymerase-δ, are mutated to alanine

Protein (function)
In eukaryotic organisms, the spontaneous mutation rate is very low, e.g. 3.3X10-10/basepair (bp)/cell division in yeast, 2.7 x 10-9/bp/generation in C. elegans, and 5.8 x 10-9/bp/generation in D. melanogaster. The mutation rate of in vitro P. falciparum culture was recently reported as 1.0–9.7 x 10-9/bp/generation.

DNA polymerases α, δ, and e are involved in nuclear genome DNA synthesis, of which polymerases δ and e possess a proofreading 3' to 5' exonuclease activity for lagging and leading DNA strand replication, respectively.

Disruption of the proofreading activity by site-directed mutagenesis significantly increased  mutation rate in yeast by as much as 10-fold to >100-fold, and the mutator effect is particularly strong in DNA polymerase δ.Furthermore, in microorganisms such as yeast and fungi, the mutator system has been employed to generate various mutated phenotypes including drug resistance

Phenotype
High-throughput genome sequencing analysis revealed that two PbMut lines had 175–178 mutations and a 86- to 90-fold higher mutation rate than that of a control parent line (PbCtl line).

Additional information
A control P. berghei line with wild-type (non-mutated) DNA polymerase δ (referred to as PbCtl) was generated.

PbMut and PbCtl parasites were maintained by weekly passage in ddY mice for 122 weeks. High-throughput genome sequencing analysis revealed that two PbMut lines had 175–178 mutations and a 86- to 90-fold higher mutation rate than that of a PbCtl line. PbMut, PbCtl, and their parent strain, PbWT, showed similar course of infection.

Other mutants


  Mutated: Mutant parasite with a mutated gene
Details of the target gene
Gene Model of Rodent Parasite PBANKA_0501300
Gene Model P. falciparum ortholog PF3D7_1017000
Gene productDNA polymerase delta catalytic subunit
Gene product: Alternative name
Details of the genetic modification
Short description of the mutationTwo amino acid residues (D311, E313), critical for proofreading in yeast, mutated to alanine
Inducable system usedNo
Short description of the conditional mutagenesisNot available
Additional remarks inducable system
Click to view information
Click to hide information
The two amino acid residues (D311, E313), known to be critical for the proofreading activity of S. cerevisiae DNA polymerase-δ, are mutated to alanine
Type of plasmid/constructPlasmid double cross-over
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 parasitetgdhfr
Promoter of the selectable markerpbdhfr
Selection (positive) procedureNo
Selection (negative) procedureNo
Additional remarks genetic modificationPrimer sequences: see below.

The putative full-length P. berghei catalytic subunit of the DNA polymerase-δ (PbPolDel) gene (pbpoldel) (PBANKA_050130) was amplified using the primers PolORF-attB1-F/PolORF-attB2-R and cloned into the pDONRP1-P2R plasmid (Invitrogen) to generate the pORF plasmid. PbPolDel possessed the two amino acid residues (D311 and E313), which are known to be critical for the proofreading activity of S. cerevisiae DNA polymerase-δ. These amino acid residues were mutated to alanine with a site-directed mutagenesis kit (Agilent) using the pORF plasmid as a template and the primers Mut-F/Mut-R to generate the pORFmut plasmid. The 5′ noncoding region (−2036 to −1) of pbpoldel was amplified using the primers Pol5UTR-attB4-F/Pol5UTR-attB1-R and cloned into pDONRP4-P1R (Invitrogen) to generate the p5UTR plasmid. The 3′ noncoding region (−477 to −1) of the P. berghei dihydrofolate reductase-thymidylate synthase (PbDHFR) gene was amplified with the primers PbDHFRF-attB2-F/PbDHFRR-attB3-R and cloned into the pDONRP2-P3R plasmid (Invitrogen) to generate the pPbDHFR3UTR plasmid. The 3′ noncoding region of pbpoldel was amplified using the primers Pol3UTR-KpnI-F/Pol3UTR-EcoRV-R. The PCR product was digested with KpnI and EcoRV and cloned into the corresponding restriction site in the pL0007 plasmid (obtained from MR4) to generate pL0007::3UTR plasmid. Subsequently, a R4-R3 fragment was amplified from pDEST R4-R3 plasmid (Invitrogen) with the primers R4R3-HindIII-F/ R4R3-HindIII-R and cloned into the HindIII site of pL0007::3UTR to generate a destination plasmid (R4-R3::pL0007::3UTR). The three entry plasmids (p5UTR, pORFmut, and pPbDHFR3UTR) were then cloned into the R4-R3::pL0007::3UTR plasmid by Multisite Gateway (Invitrogen) to generate the final plasmid, PbPolDelMut. A control plasmid containing the non-mutated PbPolDel (PbPolDelCtl) was constructed in a similar way using the procedures described above.
The PbPolDelMut plasmid was digested with ApaI and EcoRV, and it was introduced electroporetically into P. berghei (ANKA strain clone 2.34, referred to as PbWT), where the endogenous pbpoldel was replaced with PbPolDelMut by double crossover homologous recombination.
PolORF-attB1-F GGGGACAAGTTTGTACAAAAAAGCAGGCTACAAAAAATGGAAAAAAATATATTCTCG
PolORF-attB2-R GGGGACCACTTTGTACAAGAAAGCTGGGTTTACCATTCAATTTTGAGGGATGTAACTTG
Mut-F CCCAAATTAAGAATCCTTTCCTTTGCTATTGCGTGTATAAAATTAGATGGAAAAGGT
Mut-R ACCTTTTCCATCTAATTTTATACACGCAATAGCAAAGGAAAGGATTCTTAATTTGGG
Pol5UTR-attB4-F GGGGACAACTTTGTATAGAAAAGTTGGGGCCCACAAAAAATGGAAAAAAATATATTCTCG
Pol5UTR-attB1-R GGGGACTGCTTTTTTGTACAAACTTGTTACCATTCAATTTTGAGGGATGTAACTTG
PbDHFRF-attB2-F GGGGACAGCTTTCTTGTACAAAGTGGCGGAAATACAGAAGCTAGCTTTG
PbDHFRR-attB3-R GGGGACAACTTTGTATAATAAAGTTGGAAATTGAAGGAAAAAACATCA
Pol3UTR-KpnI-F GGTACCAAAAAATAAAAATAACAAGAGGG
Pol3UTR-EcoRV-R GATATCGAGAAATTATAGGGCGTT
R4R3-HindIII-F AAGCTTAGCTATGACCATGATTACGCCAAGC
R4R3-HindIII-R AAGCTTCAGCTATGACCATGATTACGCCAAGC
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