Proteomic profile of Toxoplasma gondii stress granules by high-resolution mass spectrometry.

Ribonucleoprotein granules are bio-condensates that form a diverse group of dynamic membrane-less organelles implicated in several cellular functions, including stress response and cellular survival. In Toxoplasma gondii, a type of bio-condensates referred to as stress granules (SGs) are formed prior to the parasites' egress from the host cell and are implicated in the survival and invasion competency of extracellular tachyzoites. We used paraformaldehyde to fix and cross-link SG proteins to allow purification by centrifugation and analysis by mass spectrometry. We profiled protein components of SGs at 10 and 30 min post-egress when parasite's invasion ability is significantly diminished. Thirty-three proteins were identified from 10 min SGs, and additional 43 proteins were identified from 30 min SGs. Notably, common SG components such as proteins with intrinsically disordered domains were not identified. Gene ontology analysis of both 10 and 30 min SGs shows that overall molecular functions of SGs' proteins are ATP-binding, GTP-binding, and GTPase activity. Discernable differences between 10 and 30 min SGs are in the proportions of translation and microtubule-related proteins. Ten-minute SGs have a higher proportion of microtubule-related proteins and a lower proportion of ribosome-related proteins, while a reverse correlation was identified for those of 30 min. It remains to be investigated whether this reverse correlation contributes to the ability of extracellular tachyzoites to reinvade host cells.

Formation of mRNP granules in Toxoplasma gondii during the lytic cycle.

Two poly(A) binding proteins (PABPs) of Toxoplasma gondii, were identified and characterized. They were named TgPABPC and TgPABPN as they were found to localize in the cytoplasm and nucleus respectively. TgPABPC, which colocalizes with mRNA granules, is therefore used as a cellular marker of mRNP granules. We detected that the formation of mRNP granules was independent of polymerized microtubules, and that the granules were distributed stochastically within the cytosol. Formation of mRNP granules was found to occur prior to parasite egress when a Ca2+ ionophore is used to induce egress. It was also found that maturation of mRNP granules could be described as a two-phase process. First, prior to host cell lysis, mRNP granules were formed rapidly within the cytosol. Second, the mRNP granule load was reduced within 10 min post egress. To investigate the link between translational state and mRNP granule formation, treatments with salubrinal, nutrient deprivation, and pH stress were used. While salubrinal induced granule formation in tachyzoites, nutrient starvation and pH stress showed no induction effect on mRNP granule formation. Interestingly, salubrinal treatment in bradyzoites did not induce RNP granule formation, thus suggesting that mRNP granule formation is not a ubiquitous response or directly related to translational repression. Instead, mRNP granule formation is likely a response to the rapid increase in non-translating RNA brought on by sudden changes in translational state.

Characterization of natural antisense transcripts arisen from the locus encoding Toxoplasma gondii ubiquitin-like protease.

Natural antisense transcripts (NATs) are non-protein coding RNAs that could play an important role in regulating the expression of their counterpart protein encoding sense transcript. Although NATs are widespread in most eukaryotic genomes, very little is known about their functions. This study focuses on gaining a better understanding of the function of NATs in Toxoplasma gondii, a pathogenic unicellular eukaryote. Previously, we characterized the gene encoding the first committed enzyme in sumoylation, named ubiquitin-like protease 1 (TgUlp1), and showed that the expression of TgUlp1 is vital to the life cycle of T. gondii. Interestingly, the locus of TgUlp1 also transcribes a NAT species. Using a dual luciferase assay, we identified the promoter of TgUlp1 NAT to be located within the 3'-region of its counterpart coding sequence. While TgUlp1 mRNA level was detected at a lower level throughout the life cycle of T. gondii, its NAT level was upregulated when the parasite converts from actively replicating tachyzoite form to slowly growing bradyzoite form. To investigate the effect of TgUlp1 NAT on the expression of its counterpart mRNA, we used a reporter system bearing TgUlp1 mRNA sequences and showed that the single-stranded TgUlp1 NAT and its in vitro RNase III processed products have the ability to lower the expression of the reporter system. Using a transgenic Dicer-knockout (TgDicer-KO) strain, we showed that TgDicer is required for the function of TgUlp1 NAT in vivo. The findings strongly suggest that the RNA interference pathway is necessary for the function of TgUlp1 NAT.

Sensory cutaneous papillae in the sea lamprey (Petromyzon marinus L.): II. Ontogeny and immunocytochemical characterization of solitary chemosensory cells.

Solitary chemosensory cells (SCCs) and their innervating fibers are located in the respiratory system of many vertebrates, including papillae on lamprey gill pores. In order to gain stronger insight for the role of these chemosensory cells, we examined immunocytochemical and innervation characteristics, as well as abundance at the different stages of the lamprey life cycle. The SCCs were distinguished from the surrounding epithelial cells by calretinin and phospholipase C140 immunoreactivity. Nerve fibers extended into the gill pore papillae, as far as the SCCs and serotonergic fibers extended from the underlying dermis into the papillar base. Gill pore papillae were absent and SCCs were sparse during the larval stage and in newly transformed lamprey. Few SCCs were located on small nub-like papillae during the parasitic juvenile stage, but SCCs were abundant on prominent papillae in migrating and in spawning adults. These findings show similarities between the SCCs in lampreys and other vertebrates and suggest that gill SCC function may be important during the feeding juvenile and the adult stages of the lamprey life cycle.

Toxoplasma ubiquitin-like protease 1, a key enzyme in sumoylation and desumoylation pathways, is under the control of non-coding RNAs.

Sumoylation and desumoylation are reversible pathways responsible for modification of protein structures and functions by the reversible covalent attachment of a small ubiquitin-like modifier (SUMO) peptide. These pathways are important for a wide range of cellular processes and require a steady supply of SUMO, which is generated by an enzymatic reaction catalysed by the ubiquitin-like protease (Ulp) family. Here we show by functional complementation analysis that the Ulp1 of Toxoplasma gondii (TgUlp1) can rescue a growth-deficient phenotype of a yeast-Ulp1 knockout. Recombinant TgUlp1 is an active enzyme capable of removing SUMO from a sumoylated substrate. Using a clonal transgenic strain of T. gondii expressing an epitope-tagged version of TgUlp1, we detected that the expression of TgUlp1 is modulated by Tg-miR-60, the most abundant species of micro RNA found in the T. gondii type 1 strain. The introduction of Tg-miR-60 inhibitor caused an increase in TgUlp1 expression and its enzymatic activity, as well as affecting the parasite's growth fitness. Moreover, we discovered a polyadenylated antisense RNA transcribed from the TgUlp1 locus, referred to as TgUlp1-NAT1 (TgUlp1-natural antisense transcript 1). Both Tg-miR-60 and TgUlp1-NAT1 confer a regulatory function by down-regulating the expression of TgUlp1 and affecting the sumoylation and desumoylation pathways in T. gondii.

Toxoplasma gondii infection induces the formation of host's nuclear granules containing poly(A)-binding proteins.

To study the mechanism by which human host cells respond to an infection of Toxoplasma gondii, we monitored the level of poly(A)-binding protein (PABP), an indicator of translation. Here, we report an observation of the relocalization of PABPs in human host cells upon T. gondii infection. Notably, the aggregates of PABPs formed upon infection are mainly found in the nucleus, which is a different response from that found after exposure to heat shock. Pyrimethamine treatment of the infected monolayers inhibits the multiplicity of the parasite and reverses the relocalization of PABP aggregates. This active interaction between the infected mammalian host cells and T. gondii appears to be different from that caused by viral infection.

Antisense technologies in the studying of Toxoplasma gondii.

This review covers a brief history of antisense RNAs and its applications, and summarizes the current stage of antisense technologies used in Toxoplasma gondii, a fascinating model organism with a unique characteristic blend of genetic regulatory systems normally found in plants or animals. Based on the current knowledge of regulatory RNAs and non-coding RNA (ncRNA), the antisense technologies are reviewed according to the classification of ncRNAs, which are roughly categorized into small, ranging from ~20-200 nucleotides in length, and long >200 nucleotides. Techniques utilizing small regulatory RNAs such as siRNA, miRNA, antagomirs, ribozymes and morpholino oligomers are discussed along with long non-coding RNA (lncRNA) including antisense and double stranded. These antisense technologies can be used in forward and reverse genetics studies. The future of technologies is limitless, particularly by combining these technologies with conventional methods, and should allow for ever greater understanding of gene regulation of the organism and related pathogenic microorganisms.

Utilization of inherent miRNAs in functional analyses of Toxoplasma gondii genes.

MicroRNAs (miRNAs) are crucial genetic effectors partaking in numerous mechanisms of gene regulation in eukaryotic organisms. Recent discoveries of miRNA in Toxoplasma gondii, an intracellular obligate parasite of the phylum Apicomplexa, suggested possible roles of T. gondii miRNAs (Tg-miRNAs) in the post-transcriptional gene regulation and in the cell biology of the parasite. To gain a better understanding of the involvement of Tg-miRNAs in regulating the parasite gene expression, a dual luciferase reporter system was used in the examination and evaluation of the effects of endogenous Tg-miRNAs, their mimics and inhibitors. A Renilla luciferase (Rnluc) transcript was engineered to carry independent binding sites of two abundant species, namely Tg-miR-60a and Tg-miR-4a, so that the expression of Rnluc was silenced in a sequence specific manner by Tg-miR-60a and Tg-miR-4a. Notably, Tg-miR-60a, but not Tg-miR-4a, caused the levels of Rnluc transcripts to decrease. These findings strongly suggested that T. gondii employs the Tg-miRNA species-specific mode of silencing actions: transcript degradation by Tg-miR-60a, and translational suppression by Tg-miR-4a. Herein we developed a genetic system that exploits and directs the most abundant Tg-miR-60a for loss-of-function analyses in T. gondii. As a proof of principle, we showed that when the binding sites for Tg-miR-60a were introduced into the parasite transcripts via homologous recombination at the locus of (i) DEAD-box RNA helicase (TgHoDI), or (ii) lactate dehydrogenase isoform 1 (TgLDH1), the expression levels of the selected genes can be altered. It was thus proven that inherit Tg-miR-60a could be directed and used to assist in the loss-of-function analyses.

Sustained translational repression of lactate dehydrogenase 1 in Toxoplasma gondii bradyzoites is conferred by a small regulatory RNA hairpin.

In response to environmental stresses, Toxoplasma gondii induces a global translational repression which allows for the remodeling of its transcriptome. While some transcripts are preferentially translated, another subset is translationally repressed and maintained in bradyzoites. Although little is known of how transcripts are targeted for sustained translational repression, the targeting probably operates through an RNA-centric mechanism relying on the recognition of cis-acting elements. In this study, we sought to determine if the targeting of transcripts through recognizable cis-acting elements could be responsible for the transcript-specific sustained translational repression displayed by Toxoplasma bradyzoites. We examined the UTRs of a translationally repressed gene, lactate dehydrogenase 1, and found a 40 nucleotide regulatory element in its 5'UTR. This element specifically induces translational repression in otherwise constitutively expressed transcripts. Mutational studies revealed that the formation of a small 16 nucleotide regulatory RNA hairpin is essential for this activity. We suggest that this hairpin may act as the nucleation site for the binding of an as yet to be identified trans-acting factor that allows for the transcript to be targeted for translational repression removal from the active translational pool. To our knowledge, this is the first report characterizing a specific cis-acting element contributing to post-transcriptional gene regulation in Toxoplasma and suggests the presence of a pathway by which the parasites can recognize, identify and specifically target transcripts for sustained translational repression under stressful conditions.

The potential of quinoline derivatives for the treatment of Toxoplasma gondii infection.

Here we reported our investigation, as part of our drug repositioning effort, on anti-Toxoplasma properties of newly synthesized quinoline compounds. A collection of 4-aminoquinoline and 4-piperazinylquinoline analogs have recently been synthesized for use in cancer chemotherapy. Some analogs were able to outperform chloroquine, a quinoline derivative drug which is commonly used in the treatment of malaria and other parasitic infections. Herein 58 compounds containing one or two quinoline rings were examined for their effectiveness as potential anti-Toxoplasma compounds. Of these 58 compounds, 32 were efficient at inhibiting Toxoplasma growth (IC50<100 µM). Five compounds with single and simple quinoline rings exhibited similar cLogP values of ∼2 and IC50 values between 5 and 6 µM, with one exception of 8-hydroxyquinoline whose IC50 value was 213 nM. The addition of one hydroxyl group at position 8 caused a 40-fold increase in the inhibitory effect of quinoline. A significant improvement in anti-Toxoplasma effect among quinoline derivatives was detected in B11, B12, B23, and B24, whose structures carry two quinoline rings, and their resultant cLogP values are ⩾7. Among these compounds, B23 was the most effective compound with IC50 value of 425±35 nM, and TI value of 4.9. It was also noted that compounds with at least one quinoline ring, displaying anti-Toxoplasma effects were capable of causing the disappearance of the apicoplast, a plastid-like organelle. When treated with quinoline, 8-hydroxyquinoline or B23, 40-45% of the parasites lost their apicoplasts. Our findings recapitulate the properties of quinoline derivatives in diminishing apicoplast. This could aid further investigations of anti-parasitic treatments specific to Apicomplexan. More importantly, B12 and B23 which harbor superior anti-cancer properties than chloroquine, have effective anti-Toxoplasma activity. These compounds therefore have significant potential for future development of chemotherapeutic agents for patients suffering from breast cancers and parasitic infection.

Characterization of a homolog of DEAD-box RNA helicases in Toxoplasma gondii as a marker of cytoplasmic mRNP stress granules.

Toxoplasma gondii is an obligate intracellular protozoan which infects one-third of the human population. Due to its high infection prevalence, Toxoplasma offers an ideal system for the study of host-parasite interaction. Similar to other eukaryotes, Toxoplasma maintains levels and localization of cytoplasmic mRNAs throughout its life cycle as part of a gene regulation network to meet all cellular and biochemical requirements. More recently, it was reported that the presence of cytoplasmic mRNA granules could contribute to the parasite pathogenesis and viability. Here we identified a novel Toxoplasma DEAD-box RNA helicase, referred to as Toxoplasma gondiiHomolog of DOZI (TgHoDI), because of its high homology (81%) to Plasmodium DOZI. TgHoDI is the functional ortholog of yeast DHH1, and its function was authenticated by complementation studies in Δdhh1 yeast strain. We demonstrated that TgHoDI is a marker of cytoplasmic RNA stress granules, which assemble when the parasites experience cellular stresses and translational arrest.

Endoplasmic reticulum stress-mediated inhibition of NSMase2 elevates plasma membrane cholesterol and attenuates NO production in endothelial cells.

Chronic exposure of blood vessels to cardiovascular risk factors such as free fatty acids, LDL-cholesterol, homocysteine and hyperglycemia can give rise to endothelial dysfunction, partially due to decreased synthesis and bioavailability of nitric oxide (NO). Many of these same risk factors have been shown to induce endoplasmic reticulum (ER) stress in endothelial cells. The objective of this study was to examine the mechanisms responsible for endothelial dysfunction mediated by ER stress. ER stress elevated both intracellular and plasma membrane (PM) cholesterols in BAEC by ~3-fold, indicated by epifluorescence and cholesterol oxidase methods. Increases in cholesterol levels inversely correlated with neutral sphingomyelinase 2 (NSMase2) activity, endothelial nitric oxide synthase (eNOS) phospho-activation and NO-production. To confirm that ER stress-induced effects on PM cholesterol were a direct consequence of decreased NSMase2 activity, enzyme expression was either enhanced or knocked down in BAEC. NSMase2 over-expression did not significantly affect cholesterol levels or NO-production, but increased eNOS phosphorylation by ~1.7-fold. Molecular knock down of NSMase2 decreased eNOS phosphorylation and NO-production by 50% and 40%, respectively while increasing PM cholesterol by 1.7-fold and intracellular cholesterol by 2.7-fold. Furthermore, over-expression of NSMase2 in ER-stressed BAEC lowered cholesterol levels to within control levels as well as nearly doubled the NO production, restoring it to ~74% and 68% of controls using tunicamycin and palmitate, respectively. This study establishes NSMase2 as a pivotal enzyme in the onset of endothelial ER stress-mediated vascular dysfunction as its inactivation leads to the attenuation of NO production and the elevation of cellular cholesterol.

Evidence for behavioral preference toward environmental concentrations of urban-use herbicides in a model adult fish.

Fish live in waters of contaminant flux. In three urban, fish-bearing waterways of British Columbia, Canada, we found the active ingredients of WeedEx, KillEx, and Roundup herbicide formulations (2,4-D, dicamba, glyphosate, and mecoprop) at low to high ng/L concentrations (0.26 to 309 ng/L) in routine conditions, i.e., no rain for at least one week. Following rain, these concentrations increased by an average of eightfold, suggesting runoff as a major route of herbicide introduction in these waterways. To determine whether fish might be able to limit point-source exposures through sensory-driven behaviors, we introduced pulses of representative herbicide mixtures to individual adult zebrafish (a model species) in flow-through tanks. Fish did the opposite of limit exposure; they chose to spend more time in pulses of herbicide mixtures representative of those that may occur with rain events. This attraction response was not altered by a previous 4-d exposure to lower concentrations of the mixtures, suggesting fish will not learn from previous exposures. However, previous exposures did alter an attraction response to an amino acid prevalent in food (L-alanine). The present study demonstrates that fish living within urban waterways may elect to place themselves in herbicide-contaminated environments and that these exposures may alter their behavioral responses to cues necessary for survival.

Toxoplasma gondii: inhibitory activity and encystation effect of securinine and pyrrolidine derivatives on Toxoplasma growth.

Securinine, an alkaloid originally isolated from Securinega suffruticosa, exhibits a wide range of biological activities, including anti-malarial activity. Along with securinine, 10 pyrrolidine derivatives, generated via the retrosynthesis of (-)-securinine, were selected and tested for their inhibitory activity against Toxoplasma gondii growth in vitro. Anti-Toxoplasma activity correlated to hydrophobicity of the tested compounds. Three pyrrolidine derivatives along with securinine inhibit Toxoplasma proliferation at the micromolar range. These compounds act on parasite proliferation in different capacities, either by slowing the growth rate or inhibiting invasion of host cells. Securinine induces bradyzoite differentiation at comparable levels to treatment with alkali media in vitro.

Silencing of tachyzoite enolase 2 alters nuclear targeting of bradyzoite enolase 1 in Toxoplasma gondii.

In Toxoplasma gondii, an intracellular parasite of the phylum Apicomplexa, two isoforms of enolase (ENO1 and ENO2) are expressed in stage-specific manner. ENO2 is expressed only in rapidly growing tachyzoites, while ENO1 is in slowly growing bradyzoites. Interestingly, the localization of ENO1 and ENO2 in the nuclear compartment has suggested possible roles of the proteins in gene regulation and/or cell cycle. To understand the physiological role of ENO2 in T. gondii, the expression of ENO2 was silenced using a homologous gene silencing procedure. The introduction or expression of ENO2 dsRNA successfully silenced the expression of ENO2 at the levels of transcripts and proteins. While there was no change in the growth rate of both tachyzoites and bradyzoites, a subtle phenotypic change was observed in the localization of the ENO1 gene product in the bradyzoite stage.

Toxoplasma gondii: over-expression of lactate dehydrogenase enhances differentiation under alkaline conditions.

Toxoplasma gondii, an intracellular parasite, has two distinctive growth stages, namely rapidly growing tachyzoites and slowly growing bradyzoites. Here we report a unique physiological function of the last committed glycolytic enzyme of T. gondii, lactate dehydrogenase (TgLDH), which is present in two isoforms and expressed in a stage-specific manner. TgLDH1 is present in tachyzoites while TgLDH2 is found in bradyzoites. Using clonal transgenic parasites over-expressing either TgLDH1 or TgLDH2, we showed that the enzymatic activity, growth, and virulence of tachyzoites were unaffected by the presence of the recombinant protein. Interestingly, under alkaline conditions the presence of the recombinant TgLDH proteins increased the differentiation, as detected by the formation of cyst structures in vitro, while green fluorescent protein did not. The differentiation enhancement of the recombinant TgLDH1 and TgLDH2 strongly suggests that TgLDH1 and TgLDH2 have an important physiological function, in addition to being glycolytic enzymes and differentiation markers

Plasma membrane cholesterol content affects nitric oxide diffusion dynamics and signaling.

Nitric oxide (NO) signaling is inextricably linked to both its physical and chemical properties. Due to its preferentially hydrophobic solubility, NO molecules tend to partition from the aqueous milieu into biological membranes. We hypothesized that plasma membrane ordering provided by cholesterol further couples the physics of NO diffusion with cellular signaling. Fluorescence lifetime quenching studies with pyrene liposome preparations showed that the presence of cholesterol decreased apparent diffusion coefficients of NO approximately 20-40%, depending on the phospholipid composition. Electrochemical measurements indicated that the diffusion rate of NO across artificial bilayer membranes were inversely related to cholesterol content. Sterol transport-defective Niemann-Pick type C1 (NPC1) fibroblasts exhibited increased plasma membrane cholesterol content but decreased activation of both intracellular soluble guanylyl cyclase and vasodilator-stimulated phosphoprotein (VASP) phosphorylation at Ser(239) induced by exogenous NO exposure relative to their normal human fibroblast (NHF) counterparts. Augmentation of plasma membrane cholesterol in NHF diminished production of both cGMP and VASP phosphorylation elicited by NO to NPC1-comparable levels. Conversely, decreasing membrane cholesterol in NPC1 resulted in the augmentation in both cGMP and VASP phosphorylation to a level similar to those observed in NHF. Increasing plasma membrane cholesterol contents in NHF, platelets, erythrocytes and tumor cells also resulted in an increased level of extracellular diaminofluorescein nitrosation following NO exposure. These findings suggest that the impact of cholesterol on membrane fluidity and microdomain structure contributes to the spatial heterogeneity of NO diffusion and signaling.

Density functional theory investigation on the mechanism of the hepatitis delta virus ribozyme.

Density functional theory methods have been used to investigate the hepatitis delta virus (HDV) ribozyme and its catalyzed phosphodiester cleavage. In particular, the effects of the environment's polarity and/or specific hydrogen-bond interactions on the proton affinity of the active site cytosine's N3 ring center have been considered. In addition, the basicities of possible hydrated Mg2+ ion species were also examined. The mechanism previously proposed for the HDV ribozyme in which the active site cytosine (C75) is protonated and thus acts as an acid while the Mg2+ species acts as the complementary base was then investigated. The possible role of tautomerization of C75 is also discussed.

Single argonaute protein from Toxoplasma gondii is involved in the double-stranded RNA induced gene silencing.

Here, we report the characterization of the argonaute protein from Toxoplasma gondii. This is the first report on the function of an argonaute protein with structural features overlapping between argonaute proteins of archaeal bacteria and eukaryotes. The full-length cDNA clone has an open reading frame of 1575 bp, which encodes a 524 amino acid protein with a calculated molecular weight of 58.5 kDa and an estimated isoelectric point of 9.4. This argonaute protein, called TgAgo, exhibits unique features: (i) TgAgo is smaller than reported argonaute proteins derived from higher eukaryotic organisms (i.e. Arabidopsis, human and nematodes) but has a similar size to those from archaeal bacteria (i.e. Pyrococcus furiosus and Archaeoglobus fulgidus); (ii) TgAgo contains a conserved PIWI domain and non-conserved PAZ domain; (iii) TgAgo is mainly localized in the cytoplasm; and (iv) despite its small size, TgAgo participates in the double-stranded RNA induced gene silencing. Using a transgenic parasite line, in which TgAgo expression is lowered, we showed that the expression of TgAgo is required for the double-stranded RNA induced gene silencing, RNA interference mechanism.