Retention of PCEN-Containing Plasmids in Parasites after Mosquito Passage
(Left panel) The GFP expressions in salivary gland sporozoites containing pbCEN5, pbCEN5A/T, or the control pbGFPcon are shown (BF, bright field image of the same sporozoites). (Right panel) The percentages of GFP-positive sporozoites (right) for parasites transfected with the various PCEN-containing plasmids were determined by fluorescence microscopic analysis. The error bars represent standard error.

The L-PAC Was Maintained as a Linear Form in the Parasite throughout the Complete Life Cycle
Southern analysis to examine the L-PAC construct in transfected parasites after 20 days of multiplication in the blood in the absence of pyrimethamine, as well as in the re-emerging parasite in the blood after mosquito passage and multiplication in the liver. Genomic DNA was digested with HindIII (lanes 6 and 10), KpnI (lanes 7 and 11), or NheI (lanes 8 and 12) and hybridized with the gfp gene. In addition, undigested genomic DNA (lanes 5 and 9) was also resolved. Undigested L-PAC (lane 1) and HindIII (lane 2)-, KpnI (lane 3)-, and NheI (lane 4)-digested L-PAC were analyzed under the same conditions.

Transfection of Parasites with the Linear Plasmodium Artificial Chromosome Construct, Containing PCEN and Telomere Sequences
(A) Schematic representation of the L-PAC construct. The construct contains the Tgdhfr-ts selectable marker and the GFP reporter protein under the control of the eef1αa promoter. Restriction sites for PmeI (P), HindIII (H), NheI (N), and KpnI (K) are shown, which were used for the Southern analysis to determine the size of the DNA fragments digested with each enzyme.
(B) The course of parasitemia in mice infected with pbGFPcon (open circle), pbCEN5A/T (closed circle)-, L-PAC (open triangle)-, and C-PAC (closed triangle)-transfected parasites. All parasites (1 × 10⁸) were transfected with 5 μg DNA, and mice were treated with pyrimethamine 1 day after i.v. injection of parasites. The error bars represent standard error.

PCENs Are Highly A/T Rich and Consist of Core and Repetitive Regions
(A) The DNA AT content of centromeric regions of P. berghei chromosome 5 and P. yoelii chromosomes 5 and 13 was analyzed using Artemis 10. Arrows indicate the ultra-high A/T-rich regions termed PCENs (pbcen5, 1189 bp; pycen5, 1498 bp; and pycen13, 1412 bp).
(B) Dot matrix analysis of the three rodent malaria PCENs using the Dotlet program. In this analysis, only the PCEN regions identified in (A) were used. Panels depict the graphical results of the matrix analysis of the rodent PCENs aligned either against themselves or against the other rodent PCENs. The diagonal line within each analysis represents sequence identity, and parallel lines to the diagonal indicate repetitive regions within each PCEN. Boxes highlight repetitive regions used for further analysis. See also Figure S1A.
(C) Lengths and numbers of sequence motifs in the repetitive regions (boxes in B) identified in the dot matrix analyses were determined using the Tandem Repeats Finder program (see also Figure S2 and Table S1). Based on these analyses, the locations, lengths, and numbers of repetitive elements are schematically depicted for the three rodent PCENs analyzed. Each triangle represents a repetitive sequence motif/element. See also Figure S1B and Table S1.

Addition of PCEN to Plasmids Improves Their Segregation Efficiency during P. berghei Blood-Stage Multiplication
(A) Schematic representation of the various PCEN plasmids. The plasmid contains the Tgdhfr-ts selectable marker and the GFP reporter protein under the control of the eef1αa promoter. pbGFPcon is a control plasmid without a PCEN. The names of the resulting PCEN plasmids are indicated to the left of the schematic drawings of the cloned PCEN DNA fragments.
(B) GFP expression of Hoechst 33258-stained (all parasites) blood-stage P. berghei transfected with the various PCEN plasmids, 18–21 days after drug withdrawal.
(C) The percentage of GFP-positive parasites during asexual multiplication of blood-stage P. berghei that have been transfected with the various PCEN-containing plasmids (left panel). Observed percentage (right panel) of GFP-positive parasites determined by fluorescence microscopy (solid lines) compared to the predicted percentage of GFP-positive parasites (dashed lines), based on the calculated segregation efficiencies of the various plasmids (see also Figure S2). The error bars represent standard error.
(D) Southern analysis of the presence of plasmids in the parasites either after 7 days of multiplication in the presence of pyrimethamine (+) or after 18–21 days in the absence of pyrimethamine (−). Blots were hybridized to the P. berghei 5′UTR dhfr-ts probe, which recognizes the plasmid (black triangle) and the endogenous single dhfr-ts genome copy (white triangle, 4.9 kb). The sizes of signals from each plasmid are as follows: pbGFPcon, 9.0 kb; pbCEN5, 12.4 kb; pyCEN5, 13.1 kb; pfCEN3, 11.5 kb; and pbCEN5A/T, 10.4 kb.

Efficient Segregation and Maintenance of Circular and Linear DNA Constructs Containing Both pbcen5 and Telomere Sequences
(A) (Left panel) The percentages of GFP-positive parasites during blood-stage asexual multiplication of P. berghei transfected with the C-PAC (blue), L-PAC (green), or the control plasmid pbGFPcon (red) are shown. The observed percentages of GFP-positive parasites are determined by fluorescence microscopy (solid lines) compared to the predicted percentages of GFP-positive parasites (dashed lines), based on the calculated segregation efficiencies of the various constructs. The error bars represent standard error. (Right panel) The GFP expressions (C-PAC- and L-PAC-containing parasites) of Hoechst 33258-stained transfected parasites (all parasites) were observed by fluorescence microscopy after 18–20 days of asexual multiplication in the blood, without drug pressure.
(B) (Left panel) The GFP expressions in salivary gland sporozoite of parasites transfected with the C-PAC or the L-PAC are shown (BF, bright field image of the same sporozoites). (Right panel) GFP expression in the blood stages of parasites transfected with the C-PAC and L-PAC after first completing a passage through the mosquito and multiplication in the liver are shown.
(C) Percentage of GFP-positive, variously transfected (C-PAC, L-PAC, and pbGFPcon) salivary gland sporozoites after parasite development in the mosquito, as well as the percentage of GFP-positive blood stages after parasite passage through multiplications in the mosquito and in the liver. The error bars represent standard error.
(D) Southern analysis showing the presence of the DNA constructs in blood-stage parasites after either 7 days of multiplication in the presence of pyrimethamine (+) or 20 days in the absence of pyrimethamine (−). Southern analysis was performed on HindIII-digested C-PAC- or L-PAC-transfected parasite DNA with P. berghei 5′UTR dhfr-ts as a probe, which recognizes both the construct (black triangle) and the endogenous dhfr-ts genome copy (white triangle). Based on this result, the copy numbers are estimated and given in Table 1. Southern analysis of C-PAC-transfected parasite DNA digested with KpnI using the gfp gene as a probe identified the presence of a single fragment, indicating that the C-PAC is not integrated into the parasite genome.