RMgmDB - Rodent Malaria genetically modified Parasites

Summary

RMgm-759

Malaria parasite	P. berghei
Genotype
Genetic modification not successful
Disrupted	Gene model (rodent): PBANKA_1134600; Gene model (P.falciparum): PF3D7_1358300; Gene product: rhomboid protease ROM7 (ROM7)
Phenotype	No phenotype has been described

Last modified: 16 March 2013, 12:11

*RMgm-759

Successful modification	The gene/parasite could not be changed/generated by the genetic modification.
The following genetic modifications were attempted	Gene disruption
Number of attempts to introduce the genetic modification	3
Reference (PubMed-PMID number)	Reference 1 (PMID number) : 23490234
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Parent parasite used to introduce the genetic modification
Rodent Malaria Parasite	P. berghei
Parent strain/line	P. berghei ANKA
Name parent line/clone	P. berghei ANKA cl15cy1
Other information parent line	Two attempts to disrupt rom7 were made in P. berghei ANKA 1037m1f1mocl1 (1037cl1; RMgm-32). This is a reference ANKA mutant line which expresses GFP-luciferase under control of a schizont-specific promoter. This reference line does not contain a drug-selectable marker (PubMed: PMID: 20019192). A third attempt to disrupt rom7 was made in P. berghei ANKA 676m1cl1 (RMgm-29). This is a reference ANKA mutant line which expresses GFP-luciferase under control of a constitutive promoter. This reference line does not contain a drug-selectable marker (PubMed: PMID: 16242190).
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Attempts to generate the mutant parasite were performed by
Name PI/Researcher	J. Lin, G.R. Mair, C.J. Janse, S.M. Khan
Name Group/Department	Leiden Malaria Research Group
Name Institute	Leiden University Medical Center (LUMC)
City	Leiden
Country	The Netherlands

Disrupted: Mutant parasite with a disrupted gene

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Details of the target gene

Gene Model of Rodent Parasite PBANKA_1134600

Gene Model P. falciparum ortholog PF3D7_1358300

Gene product rhomboid protease ROM7

Gene product: Alternative name ROM7

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Details of the genetic modification

Inducable system used No

Additional remarks inducable system

Type of plasmid/construct used PCR construct

PlasmoGEM (Sanger) construct/vector used No

Modified PlasmoGEM construct/vector used No

Plasmid/construct map

Plasmid/construct sequence

GAACTCGTACTCCTTGGTGACGTCGCGATGCTTTGTATTTTCATTGGAGATATAGTATTT

TTTTAATACTTATTTTTTAAAAATATCAATTTTTGTTCAAACACAAATTTTAACAAATAT

ATATTTTCTTCATATTATAAATTTTATCACTAAATTTATTTATTTAACAAATCCAATTGT

TTCTTGTGAATTTTTTTAAAGGGGTAGCATTATAATTTTTTTATCTTTTAAAATGAAAAT

TTACAACTTGCTAATTTTAGCACACACATATTATATATACATGGATGTATATATATATAT

ATATATATATATATGCAATTTACATATGCTGATTATAAAAATATGTTTGTAGTAATGTAT

ATCTATCCATTTGTCAAAACGTCACAAAATATCATTTGAAACAGAAAAGGAGGCGTGATA

AGAAAAGTAATACACATAAATACATACCTTATTAGCATATATTTATTGTTCTATTCAAAA

ATAATTTTGTGCCATACATGAAGTATATTAATGATTTCCCAAAGAAAGAAATAGGATTAG

GTAGAACTACAATAAAATATGTTTTTATAAAAAGGAGACAATTATGAATGCGCATATAAT

AAAATATATTTAAAAAAAAGTAAAAAAATGAATTAAGAATAGATATACAAAATAATTAGT

TGCAAAATATTTATAAAAGTTTTAAGCATATATATCACACATGTACACATACATGATTTT

CGAAGAATATATGGATATTCATATTTACATGCATGTATTGATATTACATTAGTCCATGGA

ATAATATCAAAGAGACATCATGGAGGTCGACGATGCTTGTAGATGGCCCAGCTTAATTCT

TTTCGAGCTCTTTATGCTTAAGTTTACAATTTAATATTCATACTTTAAGTATTTTTTGTA

GTATCCTAGATATTGTGCTTTAAATGCTCACCCCTCAAAGCACCAGTAATATTTTCATCC

ACTGAAATACCATTAAATTTTCAAAAAAATACTATGCATATAATGTTATACATATAAACA

TAAAACGCCATGTAAATCAAAAAATATATAAAAATATGTATAAAAATAAATATGCACTAA

ATATAAGCTAATTATGCATAAAAATTAAAGTGCCCTTTATTAACTAGTCGTAATTATTTA

TATTTCTATGTTATAAAAAAATCCTCATATAATAATATAATTAATATATGTAATGTTTTT

TTTATTTTATAATTTTAATATAAAATAATATGTAAATTAATTCAAAAAATAAATATAATT

GTTGTGAAACAAAAAACGTAATTTTTTCATTTGCCTTCAAAATTTAAATTTATTTTAATA

TTTCCTAAAATATATATACTTTGTGTATAAATATATAAAAATATATATTTGCTTATAAAT

AAATAAAAAATTTTATAAAACATAGGGGGATCCATGGTTGGTTCGCTAAACTGCATCGTC

GCTGTGTCCCAGAACATGGGCATCGGCAAGAACGGGGACCTGCCCTGGCCACCGCTCAGG

AACGAATTTAGATATTTCCAGAGAATGACCACAACCTCTTCAGTAGAAGGTAAACAGAAT

CTGGTGATTATGGGTAAGAAGACCTGGTTCTCCATTCCTGAGAAGAATCGACCTTTAAAG

GGTAGAATTAATTTAGTTCTCAGCAGAGAACTCAAGGAACCTCCACAAGGAGCTCATTTT

CTTTCCAGAAGTCTAGATGATGCCTTAAAACTTACTGAACAACCAGAATTAGCAAATAAA

GTAGACATGGTCTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAATCACCCA

GGCCATCTTAAACTATTTGTGACAAGGATCATGCAAGACTTTGAAAGTGACACGTTTTTT

CCAGAAATTGATTTGGAGAAATATAAACTTCTGCCAGAATACCCAGGTGTTCTCTCTGAT

GTCCAGGAGGAGAAAGGCATTAAGTACAAATTTGAAGTATATGAGAAGAATGATGCTAGC

GGAGGAGGTGGATCTGGTGGAGGTGGAAGTGCTAGCGTGACAGGGGGAATGGCAAGCAAG

TGGGATCAGAAGGGTATGGACATTGCCTATGAGGAGGCGGCCTTAGGTTACAAAGAGGGT

GGTGTTCCTATTGGCGGATGTCTTATCAATAACAAAGACGGAAGTGTTCTCGGTCGTGGT

CACAACATGAGATTTCAAAAGGGATCCGCCACACTACATGGTGAGATCTCCACTTTGGAA

AACTGTGGGAGATTAGAGGGCAAAGTGTACAAAGATACCACTTTGTATACGACGCTGTCT

CCATGCGACATGTGTACAGGTGCCATCATCATGTATGGTATTCCACGCTGTGTTGTCGGT

GAGAACGTTAATTTCAAAAGTAAGGGCGAGAAATATTTACAAACTAGAGGTCACGAGGTT

GTTGTTGTTGACGATGAGAGGTGTAAAAAGATCATGAAACAATTTATCGATGAAAGACCT

CAGGATTGGTTTGAAGATATTGGTGAGGCTTCGGAACCATTTAAGAACGTCTACTTGCTA

CCTCAAACAAACCAATTGCTGGGTTTGTACACCATCATCAGAAATAAGAATACAACTAGA

CCTGATTTCATTTTCTACTCCGATAGAATCATCAGATTGTTGGTTGAAGAAGGTTTGAAC

CATCTACCTGTGCAAAAGCAAATTGTGGAAACTGACACCAACGAAAACTTCGAAGGTGTC

TCATTCATGGGTAAAATCTGTGGTGTTTCCATTGTCAGAGCTGGTGAATCGATGGAGCAA

GGATTAAGAGACTGTTGTAGGTCTGTGCGTATCGGTAAAATTTTAATTCAAAGGGACGAG

GAGACTGCTTTACCAAAGTTATTCTACGAAAAATTACCAGAGGATATATCTGAAAGGTAT

GTCTTCCTATTAGACCCAATGCTGGCCACCGGTGGTAGTGCTATCATGGCTACAGAAGTC

TTGATTAAGAGAGGTGTTAAGCCAGAGAGAATTTACTTCTTAAACCTAATCTGTAGTAAG

GAAGGGATTGAAAAATACCATGCCGCCTTCCCAGAGGTCAGAATTGTTACTGGTGCCCTC

GACAGAGGTCTAGATGAAAACAAGTATCTAGTTCCAGGGTTGGGTGACTTTGGTGACAGA

TACTACTGTGTTTAACTCGATCCCGTTTTTCTTACTTATATATTTATACCAATTGATTGT

ATTTATAACTGTAAAAATGTGTATGTTGTGTGCATATTTTTTTTTGTGCATGCACATGCA

TGTAAATAGCTAAAATTATGAACATTTTATTTTTTGTTCAGAAAAAAAAAACTTTACACA

CATAAAATGGCTAGTATGAATAGCCATATTTTATATAAATTAAATCCTATGAATTTATGA

CCATATTAAAAATTTAGATATTTATGGAACATAATATGTTTGAAACAATAAGACAAAATT

ATTATTATTATTATTATTTTTACTGTTATAATTATGTTGTCTCTTCAATGATTCATAAAT

AGTTGGACTTGATTTTTAAAATGTTTATAATATGATTAGCATAGTTAAATAAAAAAAGTT

GAAAAATTAAAAAAAAACATATAAACACAAATGATGTTTTTTCCTTCAACCTTCAATTTC

GGATCCACTAGATGTCGTCCACATTAATTTTGTTTGATAATAATTAAGCTTTTTATTTTA

TTAGCACATTATTTATTACATACTATTTTTTTTTCGCAATTTCCATGAATGCTAATGGAA

ATTTCATTTTCAGTGTAAATTATGTTGTTTACGCGTTTGCATTTAGTTTTTTTTTCCATT

TTTTCGTTTTTGTATTTTTTTTTCAGCCTCACTATTAATAGTTTTTCAATTATCTATTTT

GCTTCAATCCTCTTTGTTTTTCCCCCGTTTTAATTAAATATTATTTTGAAAAGTATTCAG

ATTTATACTAACATTTATATTAATACAATCGTAAATGTCTTAGTAAAAAATTTAATATTT

TTATGATTGTTTTGAAAAGAAGATGTTAGACAAGCTTTTAAAAACAATGCAGAAAATTAC

CACATGCTTTGCACCATTTATTTTTTAAAATTTTTATCGAAAAAAAAAAATGAAGTAAAT

TAAAATAATGTAATGGAGATTTTTGAAATCATAAATGCATGAAGGTAAAGCAAGGAATTA

TCTATGAGAAAATACTCATGGACAAAAACATTAAAAAAAATATCATTAATATCCTTAAGT

ATATAGAATTACACACATACTATGTATATAGTGTGTATATACCCTAAAGTAGTATTGTAT

ATGCTATTATAATATGTATATTTATAAAGGCATACGGCAAAGTGAATTTTCCATAATCAC

CCTACCTTATGTAATGCTTCGGAATCGCGAGCTGAGTGTCAATGACCAACCT

Restriction sites to linearize plasmid NruI

Partial or complete disruption of the gene Complete

Additional remarks partial/complete disruption

Selectable marker used to select the mutant parasite hdhfr/yfcu

Promoter of the selectable marker eef1a

Selection (positive) procedure pyrimethamine

Selection (negative) procedure 5-fluorocytosine (5-FC)

Additional remarks genetic modification The unsuccessful attempts to disrupt the rom7 gene suggest that ROM7 is essential for asexual blood stage development (exp. 2120, 2121, 2141).

Rhomboid proteins are intra-membrane proteases that play a role in multiple processes. They belong to a family of serine proteases that cleave cell-surface proteins within their transmembrane domains. The Plasmodium genome encodes a total of 8 rhomboid proteases (ROM1, 3, 4, 6, 7, 8, 9 and 10).

Attempts to disrupt the gene were made using a linear construct that was generated using a 2-step, anchor tagging PCR method (for primer details see below).

The 5’- and 3’ targeting regions of the gene were PCR amplified from genomic DNA using primer pairs 1&2 and 3&4 respectively. Primers 2 and 3 have 5’- extensions homologues to the hdhfr::yfcu selectable marker cassette (CATCTACAAGCATCGTCGACCTC in primer 2 and CCTTCAATTTCGGATCCACTAG in primer 3). This selectable marker cassette was excised by digestion with XhoI and NotI from a plasmid (pL0048) that contains the P. berghei eef1a-hdfhr::yfcu-3’dhfr/ts (i.e. promoter-drug selectable marker-3’ terminator sequence) selection cassette. Primers 1 and 4 have 5’-terminal extensions with an anchor-tag suitable for the second PCR reaction. In the second PCR reaction, the amplified 5’- and 3’- targeting sequences were annealed to either side of the selectable marker cassette, and the joint fragment was amplified by the external anchor-tag primers 5/6, resulting in the PCR-based targeting construct

Before transfection, the PCR-based construct was digested with NruI (in primers 1 and 4) to remove the ‘anchor-tag’ and with DpnI that digests any residual pL0048 plasmid.

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	GAACTCGTACTCCTTGGTGACGTCGCGATGCTTTGTATTTTCATTGGAG
Additional information primer 1	7063 (NruI); 5’- rom7 targeting region F
Sequence Primer 2	CATCTACAAGCATCGTCGACCTCATGATGTCTCTTTGATATTATTC
Additional information primer 2	7064; 5’- rom7 targeting region R
Sequence Primer 3	CCTTCAATTTCGGATCCACTAGATGTCGTCCACATTAATTTTG
Additional information primer 3	7065; 3’- rom7 targeting region F
Sequence Primer 4	AGGTTGGTCATTGACACTCAGCTCGCGATTCCGAAGCATTACATAAGG
Additional information primer 4	7066 (NruI); 3’- rom7 targeting region R
Sequence Primer 5	GAACTCGTACTCCTTGGTGACG
Additional information primer 5	4661; anchor-tag primer, F
Sequence Primer 6	AGGTTGGTCATTGACACTCAGC
Additional information primer 6	4662: anchor-tag primer, R

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