A critical role of perinuclear filamentous actin in spatial repositioning and mutually exclusive expression of virulence genes in malaria parasites

Abstract

Many microbial pathogens, including the malaria parasite Plasmodium falciparum, vary surface protein expression to evade host immune responses. P. falciparium antigenic variation is linked to var gene family-encoded clonally variant surface protein expression. Mututally exclusive var gene expression is partially controlled by spatial positioning; silent genes are retained at distinct perinuclear sites and relocated to transcriptionally active locations for monoallelic expression. We show that var introns can control this process and that var intron addition relocalizes episomes from a random to a perinuclear position. This var intron-regulated nuclear tethering and repositioning is linked to an 18 bp nuclear protein-binding element that recruits an actin protein complex. Pharmacologically induced F-actin formation, which is restricted to the nuclear periphery, repositions intron-carrying episomes and var genes and disrupts mutually exclusive var gene expression. Thus, actin polymerization relocates var genes from a repressive to an active perinuclear compartment, which is crucial for P. falciparium phenotypic variation and pathogenesis.

Figure 1. Var Introns Target Episomes to the Nuclear Periphery

(A) Genomic organization, structure, and nuclear position of var genes. (Left panel) upsB or upsA corresponds to subtelomeric and upsC corresponds to chromosome internal var gene members. Each subtype var gene is labeled with a different color. Var introns contain up to four 18 bp repetitions in its region II (RII) domain. (Right panel) Schematic illustration of subnuclear localization of various subtype var genes on different chromosome sites. The area of the nuclear section was divided into three concentric zones with equal surfaces, and nuclear periphery corresponds to the zone 1. (B) pLN vector constructs with 3D7 upsC-type full-length intron (PFD1000c), the intron repeat region (RII-R4), the intron without the RII-R4 region, two distinct regions from var exon I and exon II, and the vector backbone control. The drug-selectable marker gene (bsd) and the region used as FISH probe are shown, respectively. (C) FISH signals of episomes (green) were localized into zones 1, 2, or 3 with equal surface (see A, right panel). The bar graph represents the position of FISH signals with respect to three concentric zones. DAPI (blue), nuclear DNA. n, number of nuclei analyzed from two independent ring stage samples. **p < 0.001 (χ² test). See also Figure S1 and Table S1.

Figure 2. Identification of a Nuclear Protein-Binding Element in var Introns

(A) EMSA screening strategy using biotin-labeled overlapping DNA fragments (bold sequences bound to nuclear proteins). The var intron (PF07_0048) containing a single repeat (RII-R1) was analyzed here. The sequences of the full-length intron and each probe are shown in Figure S1F and Table S4. (B) A single intron region (iNPE25 or iNPE18) binds to nuclear proteins. The two iNPE-binding complexes (CP1 and CP2) were labeled with asterisks, respectively. (C) Competition EMSA of biotin-labeled iNPE25 motif with various mutated nonlabeled iNPE18 sequences. Base pair exchanges in the mutated iNPE18 oligonucleotides are shown underlined. Competitor was used at a concentration of 100-fold excess of the labeled iNPE25 probe in each competition reaction. The decrease in intensity of CP1/CP2 bands was defined as strong (+++), medium (++), weak (+), and none (–), respectively, as shown in the table. Free probe, shifted bands CP1 and CP2, and running orientation of gel were labeled by arrows. See also Figure S2 and Table S2.

Figure 3. Actin Is a Component of the iNPE Protein Complex

(A) (Upper panel) Schematic procedure of affinity purification steps. Equal amount of preadsorbed nuclear extract were incubated with int-c1 or scrambled control DNA-coupled beads. Bound components were eluted in equal volume. (Lower panels) Equal volumes of the two eluted fractions were analyzed by EMSA with crude nuclear extract (N.E.) as positive control (left). Another aliquot was analyzed by 4%–12% SDS-PAGE/silver stain (middle) and western blot with rabbit antibody against Pfactin-I (right). A third aliquot was used for LC-MS/MS analysis. (B) Gel shift assay of recombinant AP2 domain (PF11_0091) with iNPE25, gbp130, iNPE25-mut2 (see Figure S2B), and scrambled probe, respectively. (C) Super gel shift assay with int-c1 probe and rabbit anti-Pfactin-I antibody (affinity purified IgG) and preimmune (PI) rabbit IgG as a negative control. The two shifted bands CP1/CP2 and anti-actin antibody-induced supershift band are indicated. (D) EMSA assay with int-c1 probe and nuclear extract depleted in actin (N.E. depleted) by incubation with 1 or 5 μg mouse anti-Pfactin-I antibody, respectively. The untreated crude nuclear extract (N.E.) was used as control. (E) Schematic representation of the HA-tagged Pfactin-I episomally transfected into 3D7 strain. A detailed description of the construction of this vector is provided in the Supplemental Experimental Procedures. (F) ChIP assay of HA-actin transfectant using monoclonal mouse anti-HA antibody. The enrichment folds of various gene loci were shown respectively. Regions used for PCR amplification are shown under the schematic gene structure. Data are represented as mean ± SEM of two independent experiments. See also Figure S3 and Table S3.

Figure 4. Pfactin-I Concentrates at the Nuclear Periphery and Colocalizes with var Genes

(A) Western blot assay of total protein extract, nuclear and cytoplasmic fractions of asynchronous or synchronous parasites at different intraerythrocytic stages with rabbit (#2) antibodies against Pfactin-I. The amount of nuclear and cytoplasmic fractions of a given stage corresponded to equal parasite numbers. Ring stage fractions were monitored using anti-histone H3 and anti-PfHSP70 antibodies. N, nuclear extract; C, cytoplasmic extract. (B) (Upper panel) IFA visualization of subcellular actin in rings using an anti-Pfactin-I antibody (rabbit #2). (Second panel) Two-color IFA assay using anti-Pfactin-I (rabbit #2, green) and anti-nuclear pore (PF14_0706) antibody (rat, red). (Third panel) Combined FISH/IFA assay in rings showing partial colocalization of chromosome internal var genes (upsC-type) and actin. (Fourth panel) IFA analysis of HA-actin-transfected ring stage parasites using mouse anti-HA antibody (red) and anti-Pfactin-I antibody (rabbit #2, green). (C) Immunoelectron microscopy of 3D7 rings. Double labeling with mouse anti-Pfactin-I (20 nm gold grain, bold arrow) and rabbit anti-histone H3 (10 nm gold grain, slim arrow). N, nucleus; C, cytoplasm. See also Figure S4 and Table S4.

Figure 5. JAS Induces Spatial Repositioning of var ^int Episomes and var Loci

(A) Schematic illustration of the opposite effect of actin inhibitors (CD and JAS) on dynamic equilibrium between G-actin and F-actin. (Lower section) var gene transcription profile during the 48 hr blood stage cycle and the protocol of two distinct assays. (B) (Upper panel) IFA of nuclear actin after JAS treatment using an anti-Pfactin-I antibody (rabbit #2, green) and anti-nuclear pore antibody (rat, red). (Lower panel) IFA visualization of F-actin using fluorescence-labeled phalloidin (green). DMSO- or CD-treated parasites were used as control (see also Figure S5B). (C) (Upper panel) Schematic of the perinuclear organization of subtelomeric and chromosome central var genes. (Middle and lower panels) Two-color FISH analysis of 3D7, pLN-Var ^int, and pLN-Var ^{intΔ(RII-R4)} transfectants treated with DMSO, CD, or JAS, respectively (assay 1). The upsC type var exon II and episomal probe were labeled with Alexa 568 (red); the subtelomeric DNA TARE6 probe was labeled with Alexa 488 (green). FISH signals that colocalize with TARE6 are shown in the right panels. n, counted number of nuclei from two independent samples. Data are represented as mean ± SEM of two independent experiments. **p < 0.001 (χ² test). See also Figure S5.

Figure 6. JAS Treatment Interferes with Mutually Exclusive var Gene Transcription

(A) qRT-PCR analysis of the transcription level of individual var genes of 3D7 (G7 clone) after actin inhibitor treatment (Figure 5A, assay 1). The data are shown as relative copy numbers for all the three samples using the seryl-tRNA synthetase gene (PF07_0073) as endogenous control (upper panel) and the fold change of transcription level with respect to DMSO-treated sample (lower panel). Reference genes are the following: 1–6, transcriptionally silent in asexual blood stage; 7–12, transcriptionally active during asexual blood stage (see Tables S3 and S5). The dominantly expressed var gene before drug treatment (PFD0625c) in G7 clone is indicated with triangle. (B) qRT-PCR analysis of transcription levels of individual var genes of 3D7 (G7 clone) treated with actin inhibitors for 3 hr and cultivated for 20 cycles in the absence of drugs (Figure 5A, assay 2). The data are treated and represented as in (A). Data of assays 1 and 2 are represented as mean ± SEM of two independent experiments. See also Figure S6 and Table S5.