Biology subjects

Elahi, R.

Publications and source records attributed to Elahi, R..

13 recordsLinked to original sources

bioRxiv2026

Reduced expression of an essential blood-stage Plasmodium phosphatidylserine synthase does not modulate parasite resistance to PfATP4 inhibitors

Plasmodium falciparum ATP4 mutations A211V and G223R allow parasites to survive the lethal effects of antimalarials PA21A092 (PA92) and cipargamin (CIP), respectively. An A211V mutant line (Dd2A211V) treated with PA92 showed enhanced levels of lipid production, which prompted the idea that components of the phospholipid biosynthesis pathway could be involved in the survival mechanism of PfATP4 mutant parasites. As phosphatidylserine synthase (PfPSS) is the only enzyme that produces phosopholipid phosphatidylserine (PS) in P. falciparum parasites, we hypothesized that PfPSS is both essential for parasite survival and that reduced PfPSS expression would cause resistant PfATP4 mutant parasites to become susceptible to PA92 or CIP. We created a CIP-resistant G223R mutant line (Dd2G223R) via CRISPR-Cas9 and integrated a conditional PfPSS knockdown construct into a Dd2A211V ({downarrow}PSS-Dd2A211V) and our Dd2G223R line ({downarrow}PSS-Dd2G223R). We treated these knockdown lines with PA92 or CIP to determine the half-maximal effective concentration (EC50) of each antimalarial with normal or reduced PfPSS levels. While we found that PfPSS is essential for parasite survival, we did not find any significant alterations to the EC50 values of PA92 or CIP based on the reduced levels of PfPSS in our mutant lines. Although PfPSS does not appear to be involved, other components of the phospholipid production pathway could still affect the resistance mechanism of PfATP4 mutations. Identification of novel targets to counteract the mechanism by which PfATP4 mutant parasites resist lethal drug effects is crucial for the successful application of antimalarials in endemic countries where resistance is on the rise.

microbiology↗

bioRxiv2025

Genetic analysis of pyrimidine biosynthetic enzymes in Plasmodium falciparum

The malaria parasite Plasmodium falciparum depends entirely on de novo pyrimidine synthesis, as it is unable to salvage these essential nucleotides. This reliance makes the pyrimidine biosynthesis pathway a compelling target for antimalarial drugs, with several inhibitors targeting its rate-limiting enzyme, dihydroorotate dehydrogenase (PfDHODH), already in clinical development. In this study, we investigated the roles of three other pathway enzymes - aspartate transcarbamoylase (PfATC), carbamoyl phosphate synthetase II (PfCPSII), and dihydroorotase (PfDHO). PfATC features a unique N-terminal extension predicted to serve as an apicoplast trafficking peptide. However, using antibodies against the native protein and an epitope-tagged version, we found no evidence of apicoplast localization. Knockdown of PfATC expression proved lethal and could not be rescued by an apicoplast metabolic bypass. Complementation assays further revealed that truncation of the N-terminal domain impaired parasite growth, suggesting that this region is important for PfATC function or stability in vivo. PfCPSII, which harbors large Plasmodium-specific insertions between its catalytic domains, was likewise found to be essential for parasite proliferation. To assess the role of PfDHO, we engineered parasites to salvage uracil via heterologous expression of a yeast enzyme. Deletion of PfDHO in this parasite line resulted in uracil auxotrophy, confirming the enzymes essential function in pyrimidine synthesis. Together, these findings reveal multiple vulnerable nodes within the pyrimidine biosynthesis pathway. AUTHOR SUMMARYNucleotides are central metabolites that serve as building blocks for DNA and RNA, act as key energy carriers, and function as cofactors or regulators in several metabolic pathways. To satisfy these diverse demands, most organisms rely on both nucleotide salvage and de novo synthesis. The malaria parasite Plasmodium falciparum acquires purine nucleotides from the host but lacks the capacity to salvage pyrimidines, making de novo pyrimidine synthesis essential. Several enzymes in this pathway differ from their human counterparts in sequence, domain architecture, and evolutionary origin, enhancing their potential as selective drug targets. Dihydroorotate dehydrogenase (PfDHODH), the fourth enzyme in the pathway, has already been validated as an antimalarial target. Here, we systematically examined upstream enzymes using molecular genetic approaches. Each proved essential for asexual blood-stage parasite survival, with the Plasmodium-specific N-terminal extension of aspartate carbamoyltransferase (PfATC) required for optimal growth. The introduction of a yeast uracil salvage enzyme rescued parasites depleted of these biosynthetic enzymes, demonstrating that their essential functions are confined to pyrimidine production and that their distinctive structural features do not support additional metabolic roles. In summary, these results delineate additional enzymatic steps in this important metabolic pathway that warrant continued investigation from both biological and translational angles.

microbiology↗

bioRxiv2024

tRNA modifying enzymes MnmE and MnmG are essential for Plasmodium falciparum apicoplast maintenance

The circular genome of the Plasmodium falciparum apicoplast contains a complete minimal set of tRNAs, positioning the apicoplast as an ideal model for studying the fundamental factors required for protein translation. Modifications at tRNA wobble base positions, such as xm5s2U, are critical for accurate protein translation. These modifications are ubiquitously found in tRNAs decoding two-family box codons ending in A or G in prokaryotes and in eukaryotic organelles. Here, we investigated the xm5s2U biosynthetic pathway in the apicoplast organelle of P. falciparum. Through comparative genomics, we identified orthologs of enzymes involved in this process: SufS, MnmA, MnmE, and MnmG. While SufS and MnmA were previously shown to catalyze s2U modifications, we now show that MnmE and MnmG are apicoplast-localized and contain features required for xm5s2U biosynthetic activity. Notably, we found that P. falciparum lacks orthologs of MnmC, MnmL, and MnmM, suggesting that the parasites contain a minimal xm5s2U biosynthetic pathway similar to that found in bacteria with reduced genomes. Deletion of either MnmE or MnmG resulted in apicoplast disruption and parasite death, mimicking the phenotype observed in {Delta}mnmA and {Delta}sufS parasites. Our data strongly support the presence and essentiality of xm5s2U modifications in apicoplast tRNAs. This study advances our understanding of the minimal requirements for protein translation in the apicoplast organelle. ImportanceThe apicoplast of Plasmodium falciparum is an ideal model for studying minimal translation machinery since it contains the fewest number of tRNA isotypes required for protein translation. In such reduced systems, tRNA modifications, particularly at the wobble anticodon position, are critical for proper decoding of mRNA codons by tRNAs. In this study, we investigated the enzymes responsible for the wobble modification xm5s2U in the apicoplast. Our findings reveal that only four enzymes are required in the apicoplast to carry out this modification, similar to the situation found in bacteria with highly reduced genomes. Based on their phylogenetic conservation, these four enzymes have been included in all proposed minimal genome concepts to date and it appears that the apicoplast has retained the same core machinery. Our findings provide novel insight into apicoplast biology and into minimal requirements for protein translation.

microbiology↗

bioRxiv2024

Passing the quadrat: inferring biodiversity change over time and across investigators

Long-term ecological monitoring inevitably requires a passing of the quadrat from one investigator to another. Here we present the challenge and opportunity of inferring biodiversity change over time and across investigators using a rocky intertidal case study. The intertidal transect was surveyed initially by Willis Hewatt in 1931-1933, then resurveyed in detail by Rafe Sagarin, Sarah Gilman, and their mentors in 1993. In total, the transect has been resurveyed 17 times over the past three decades, with annual surveys nested within five distinct investigator eras. We addressed two goals with our dataset. First, we asked whether temporal change in several biodiversity metrics (species richness, Hill-Shannon and Hill-Simpson diversity, spatial beta diversity) was sensitive to investigator era. Second, we identified recent ecological winners and losers, relative to the historical baseline, and asked whether such designations can change over time (1993-2023). We show that investigators contributed to variable trends in species richness over time, and we hypothesize that sampling effort contributed to this effect. In contrast, we highlight declines in the biodiversity of common species (Hill-Shannon) and dominant species (Hill-Simpson) over time, in the absence of investigator effects. These declines were associated with the rise of a few numerically dominant species and a trend of increasing spatial similarity. Relative to the historical baseline, ecological winners included certain barnacles, anemones, and turban snails, while losers included mussels, urchins, limpets and a host of more cryptic taxa. However, we show that such designations can be complicated by non-linear population trajectories and discuss mechanisms related to climate change versus potential artifacts related to investigator effort. We finish with recommendations and emphasize the value of marine stations in providing a venue for sustained periodic ecological monitoring at small spatial scales, long duration, and fine taxonomic resolution.

ecology↗

bioRxiv2024

tRNA lysidinylation is essential for the minimal translation system found in the apicoplast of Plasmodium falciparum

For decades, researchers have sought to define minimal genomes to elucidate the fundamental principles of life and advance biotechnology. tRNAs, essential components of this machinery, decode mRNA codons into amino acids. The apicoplast of malaria parasites encodes 25 tRNA isotypes in its organellar genome - the lowest number found in known translation systems. Efficient translation in such minimal systems depends heavily on post-transcriptional tRNA modifications, especially at the wobble anticodon position. Lysidine modification at the wobble position (C34) of tRNACAU distinguishes between methionine (AUG) and isoleucine (AUA) codons, altering the amino acid delivered by this tRNA and ensuring accurate protein synthesis. Lysidine is formed by the enzyme tRNA isoleucine lysidine synthetase (TilS) and is nearly ubiquitous in bacteria and essential for cellular viability. We identified a TilS ortholog (PfTilS) located in the apicoplast of Plasmodium falciparum parasites. By complementing PfTilS with a bacterial ortholog, we demonstrated that the lysidinylation activity of PfTilS is critical for parasite survival and apicoplast maintenance, likely due to its impact on apicoplast protein translation. Our findings represent the first characterization of TilS in an endosymbiotic organelle, advancing eukaryotic organelle research and our understanding of minimal translational machinery. Due to the absence of lysidine modifications in humans, this research also exposes a potential vulnerability in malaria parasites that could be targeted by antimalarial strategies. SignificanceIn recent decades, synthetic biologists have sought the minimal cellular components required for life, focusing on simpler systems for easier modeling. The apicoplast organelle of malaria parasites, with only 25 tRNA isotypes, contains the smallest known complete tRNA set, even smaller than in synthetic organisms. This makes it an ideal model for studying minimal translational machinery, where tRNAs depend on post-transcriptional modifications for efficient protein translation. A key modification, lysidine, is crucial for decoding isoleucine and methionine. This study describes a tRNA-isoleucine lysidine synthetase (TilS) enzyme, essential for apicoplast protein translation. These findings have implications for understanding eukaryotic organelles and minimal translation machinery. Additionally, the absence of lysidine in humans suggests a potential target for antimalarial strategies.

microbiology↗

bioRxiv2023

Schizophrenia Risk Mapping and Functional Engineering of the 3D Genome in Three Neuronal Subtypes

Common variants associated with schizophrenia are concentrated in non-coding regulatory sequences, but their precise target genes are context-dependent and impacted by cell-type-specific three-dimensional spatial chromatin organization. Here, we map long-range chromosomal conformations in isogenic human dopaminergic, GABAergic, and glutamatergic neurons to track developmentally programmed shifts in the regulatory activity of schizophrenia risk loci. Massive repressive compartmentalization, concomitant with the emergence of hundreds of neuron-specific multi-valent chromatin architectural stripes, occurs during neuronal differentiation, with genes interconnected to genetic risk loci through these long-range chromatin structures differing in their biological roles from genes more proximal to sequences conferring heritable risk. Chemically induced CRISPR-guided chromosomal loop-engineering for the proximal risk gene SNAP91 and distal risk gene BHLHE22 profoundly alters synaptic development and functional activity. Our findings highlight the large-scale cell-type-specific reorganization of chromosomal conformations at schizophrenia risk loci during neurodevelopment and establish a causal link between risk-associated gene-regulatory loop structures and neuronal function.

genomics↗

bioRxiv2023

Transmissibility of clinically relevant atovaquone-resistant Plasmodium falciparum by anopheline mosquitoes

Rising numbers of malaria cases and deaths underscore the need for new interventions. Long-acting injectable medications, such as those now in use for HIV prophylaxis, offer the prospect of a malaria "chemical vaccine", combining the efficacy of a drug (like atovaquone) with the durability of a biological vaccine. Of concern, however, is the possible selection and transmission of drug-resistant parasites. We addressed this question by generating clinically relevant, highly atovaquone-resistant, Plasmodium falciparum mutants competent to infect mosquitoes. Isogenic paired strains, that differ only by a single Y268S mutation in cytochrome b, were evaluated in parallel in southeast Asian (Anopheles stephensi) or African (Anopheles gambiae) mosquitoes, and thence in humanized mice. Fitness costs of the mutation were evident along the lifecycle, in asexual parasite growth in vitro and in a progressive loss of parasites in the mosquito. In numerous independent experiments, microscopic exam of salivary glands from hundreds of mosquitoes failed to detect even one Y268S sporozoite, a defect not rescued by coinfection with wild type parasites. Furthermore, despite uniformly successful transmission of wild type parasites from An. stephensi to FRG NOD huHep mice bearing human hepatocytes and erythrocytes, multiple attempts with Y268S-fed mosquitoes failed: there was no evidence of parasites in mouse tissues by microscopy, in vitro culture, or PCR. These studies confirm a severe-to-lethal fitness cost of clinically relevant atovaquone-resistant P. falciparum in the mosquito, and they significantly lessen the likelihood of their transmission in the field. SignificanceNew tools are needed to protect individuals from malaria and to control malaria in the field. Atovaquone plus proguanil is a commonly used and well-tolerated medicine to prevent malaria. No drug resistance has been reported from its prophylactic use, but tablets must be taken daily. Giving atovaquone as a single injection may provide much longer-lasting protection, against both falciparum and vivax malaria, but there is concern this may create drug resistance. In this study we showed that clinically relevant atovaquone-resistant malaria parasites survive poorly, if at all, in mosquitoes, and that mosquitoes do not transmit drug-resistant parasites to humanized mice. These findings lessen the likelihood that an atovaquone "chemical vaccine" would lead to the spread of atovaquone resistance.

microbiology↗

bioRxiv2022

The Plasmodium falciparum apicoplast cysteine desulfurase provides sulfur for both iron sulfur cluster assembly and tRNA modification

Iron sulfur clusters (FeS) are ancient and ubiquitous protein cofactors that play fundamental roles in many aspects of cell biology. These cofactors cannot be scavenged or trafficked within a cell and thus must be synthesized in any subcellular compartment where they are required. We examined the FeS synthesis proteins found in the relict plastid organelle, called the apicoplast, of the human malaria parasite Plasmodium falciparum. Using a chemical bypass method, we deleted four of the FeS pathway proteins involved in sulfur acquisition and cluster assembly and demonstrated that they are all essential for parasite survival. However, the effect that these deletions had on the apicoplast organelle differed. Deletion of the cysteine desulfurase SufS led to disruption of the apicoplast organelle and loss of the organellar genome, whereas the other deletions did not affect organelle maintenance. Ultimately, we discovered that the requirement of SufS for organelle maintenance is not driven by its role in FeS biosynthesis, but rather, by its function in generating sulfur for use by MnmA, a tRNA modifying enzyme that we localized to the apicoplast. By complementing the activity of the parasite MnmA and SufS with a bacterial MnmA and its cognate cysteine desulfurase, we showed that the parasite SufS provides sulfur for both FeS biosynthesis and tRNA modification in the apicoplast. The dual role of parasite SufS is likely to be found in other plastid-containing organisms and highlights the central role of this enzyme in plastid biology.

microbiology↗

bioRxiv2022

Screening the Pathogen Box Compounds for Activity Against Plasmodium falciparum Sporozoite Motility

As the malaria parasite becomes resistant to every drug that we develop, identification and development of novel drug candidates is essential. Many studies have screened compounds designed to target the clinically important blood stages. However, if we are to shrink the malaria map, new drugs that block transmission of the parasite are needed. Sporozoites are the infective stage of the malaria parasite, transmitted to the mammalian host as mosquitoes probe for blood. Sporozoite motility is critical to their ability to exit the inoculation site and establish infection and drug-like compounds targeting motility are effective in blocking infection in the rodent malaria model. In this study, we established a moderate throughput motility assay for sporozoites of the human malaria parasite Plasmodium falciparum, enabling us to screen the 400 drug-like compounds from the Pathogen box provided by Medicines for Malaria Venture for their activity. Compounds exhibiting inhibitory effects on P. falciparum sporozoite motility were further assessed against transmission-blocking activity and asexual stage growth. Five compounds had a significant inhibitory effect on P. falciparum sporozoite motility at 1 M concentration and four of these compounds also showed significant inhibition on transmission of P. falciparum gametocytes to the mosquito and of these four, three had previously been shown to have inhibitory activity on asexual blood stage parasites. Our findings provide new antimalarial drug candidates that have multi-stage activity.

microbiology↗

bioRxiv2021

Induction of Dopaminergic Neurons for Neuronal Subtype-Specific Modeling of Psychiatric Disease Risk

Dopaminergic neurons are critical to movement, mood, addiction, and stress. Current techniques for generating dopaminergic neurons from human induced pluripotent stem cells (hiPSCs) yield heterogenous cell populations with variable purity and inconsistent reproducibility between donors, hiPSC clones, and experiments. Here, we report the rapid (5 weeks) and efficient (~90%) induction of induced dopaminergic neurons (iDANs) through transient overexpression of lineage-promoting transcription factors combined with stringent selection across five donors. We observe maturation-dependent increase in dopamine synthesis, together with electrophysiological properties consistent with midbrain dopaminergic neuron identity, such as slow-rising after hyperpolarization potentials, an action potential duration of ~3ms, tonic sub-threshold oscillatory activity, and spontaneous burst firing at frequency of ~1.0-1.75 Hz. Transcriptome analysis reveals robust expression of genes involved in fetal midbrain dopaminergic neuron identity. Specifically expressed genes in iDANs, relative to their isogenic glutamatergic and GABAergic counterparts, were linked to the genetic risk architecture of a broad range of psychiatric traits, with iDANs showing particularly strong enrichment in loci conferring heritability for cannabis use disorder, schizophrenia, and bipolar disorder. Therefore, iDANs provide a critical tool for modeling midbrain dopaminergic neuron development and dysfunction in psychiatric disease.

neuroscience↗

bioRxiv2019

Internalization of erythrocyte acylpeptide hydrolase is required for asexual replication of Plasmodium falciparum

The human malaria parasite Plasmodium falciparum causes disease as it replicates within the hosts erythrocytes. We have found that an erythrocyte serine hydrolase, acylpeptide hydrolase (APEH), accumulates within developing asexual parasites. Internalization of APEH was associated with a proteolytic event that reduced the size of the catalytic polypeptide from 80 to 55 kDa, which suggests that the enzyme resides in the food vacuole. A triazole urea APEH inhibitor, termed AA74-1, was employed to characterize the role of parasite-internalized APEH. In vitro, AA74-1 was a potent and highly selective inhibitor of both host erythrocyte and parasite-internalized APEH. When added to cultures of parasite-infected erythrocytes, AA74-1 was a relatively poor inhibitor of replication over one asexual replication cycle; however, its potency increased dramatically after a second cycle. This enhancement of potency was not abrogated by the addition of exogenous isopentenyl pyrophosphate, which distinguishes it from the well-characterized "delayed death" phenomenon that is observed with inhibitors that target the parasite apicoplast. Analysis of inhibition by AA74-1 in vivo revealed that a concentration of 100 nM was sufficient to quantitatively inhibit erythrocyte APEH. In contrast, the parasite-internalized APEH pool was inefficiently inhibited at concentrations up to 100-fold higher. Together, these findings provide evidence for an essential catalytic role for parasite-internalized APEH and suggest a model for AA74-1 growth inhibition whereby depletion of parasite APEH activity requires the internalization of inactive host cell APEH over two replication cycles. IMPORTANCENearly half a million deaths were attributed to malaria in 2017. Protozoan parasites of the genus Plasmodium cause disease in humans while replicating asexually within the hosts erythrocytes, with P. falciparum responsible for most of the mortality. Understanding how Plasmodium spp. has adapted to its unique host erythrocyte environment is important for developing malaria control strategies. Here, we demonstrate that P. falciparum co-opts a host erythrocyte serine hydrolase termed acylpeptide hydrolase. By showing that the parasite requires acylpeptide hydrolase activity for replication, we expand our knowledge of host cell factors that contribute to robust parasite growth.

microbiology↗

bioRxiv2018

The geography of the Anthropocene differs between the land and the sea

O_LIClimate change and other anthropogenic drivers of biodiversity change are unequally distributed across the world. The geographic patterns of different drivers, and the spatial overlap among these drivers, have important implications for the direction and pace of biodiversity change, yet are not well documented. Moreover, it is unknown if the geographic patterns of drivers differ between the terrestrial and marine realm, as expected due to marked differences in how humans interact with the land and ocean. C_LIO_LIWe compiled global gridded datasets on climate change, land-use, resource exploitation, pollution, species invasions, and human population density. We used multivariate statistics to examine the spatial relationships among the datasets and to characterize the typical combinations of drivers experienced by different parts of the world. C_LIO_LIWe found stronger positive correlations among drivers in the terrestrial than in the marine realm, leading to areas of high intensities of multiple drivers on land. Climate change tended to be negatively correlated with other drivers in the terrestrial realm (e.g., in the tundra and boreal forest with high climate change but low human use and pollution) whereas the opposite was true in the marine realm (e.g., in the Indo-Pacific with high climate change and high fishing). C_LIO_LIWe show that different regions of the world can be defined by anthropogenic threat complexes (ATCs), distinguished by different sets of drivers with varying intensities. The ATCs can be used to test hypothesis about the pattern of biodiversity change, especially the joint effects of multiple drivers. More generally, our global analysis highlights the broad conservation priorities needed to mitigate the effects of anthropogenic change on biodiversity responses, with different priorities emerging on land and in the ocean, and in different parts of the world. C_LI

ecology↗

bioRxiv2017

Human activities influence the direction and magnitude of local biodiversity change over time

In recent decades, environmental drivers of community change have been associated with changes in biodiversity from local to global scales. Here we evaluate the role of anthropogenic drivers in marine ecosystems as drivers of change in local species richness with a meta-analysis of a novel dataset of temporal change in species richness. We paired biodiversity data from 144 sites with large-scale drivers derived from geospatial databases: human cumulative impact scores, sea surface temperature change, nutrient loading, and invasion potential. Three specific drivers (nutrient inputs, rate of linear temperature change, and non-native species invasion potential) explained patterns in local marine species richness change. We show that these drivers have opposing effects on biodiversity trends. In some cases, variability in drivers can create contrasting directions of change yielding observations of no net change when localities are pooled in an attempt to find a global average. Further, long-term studies reveal different effects of drivers that are not observed in short-term studies. These findings begin to explain high variability observed in species diversity trends at local scales. Formally attributing local species diversity change to human drivers is essential to understanding global patterns of local species diversity change and their consequences.

ecology↗