Biology subjects

Pain, A.

Publications and source records attributed to Pain, A..

At least 19 recordsLinked to original sources

bioRxiv2026

AP2-L-Dependent Processes Promote PVM Maintenance and Plasmodium Liver-stage Development

Successful malaria infection requires transformation of Plasmodium sporozoites into replicative exo-erythrocytic forms (EEFs) within hepatocytes, a process requiring a functional parasitophorous vacuole membrane (PVM) and interactions with host cellular pathways. ApiAP2 transcription factors regulate developmental progression throughout the Plasmodium life cycle. AP2-L consists of an extended amino terminal region and two AP2 domains and is highly expressed in asexual stage trophozoites, sporozoites and early EEFs, but its role in these stages is poorly understood. We characterized the functional consequences of deleting the entire P. berghei ap2-l coding sequence on the erythrocytic cycle in vivo, sporozoite gene expression, liver-stage development, and hepatocyte-parasite interactions. AP2L-KO parasites maintained erythrocytic replication but sporozoite inoculation failed to establish blood-stage infection in mice. AP2-L loss decreased transcripts encoding proteins involved in sporozoite gliding motility, host-cell entry, and rhoptry secretion. Motif discovery upstream of a subset of these genes suggests possible direct targets of AP2-L. Infected HepG2 cells showed reduced EEF numbers and sizes, impaired parasite DNA replication, and abnormal parasite positioning relative to the host nucleus. PVMs of AP2L-KO parasites exhibited aberrant localization of proteins, absence of tubular vacuolar network extensions, and sensitivity to detergent. These abnormalities were accompanied by increased accumulation of the host's autophagy-associated protein around parasites, suggesting efficient host-mediated elimination. Additionally, AP2L-KO parasites displayed reduced association with the host microtubule-organizing center, Golgi compartments, and COPB2-positive vesicular structures, suggesting an impairment in uptake of nutrients. Together, these findings demonstrate that AP2-L directs both vacuolar biogenesis and host cytoskeletal/vesicular capture in liver-stage parasites.

microbiology↗

bioRxiv2026

A chromosome-scale Plasmodium cynomolgi Berok genome reveals a distinct subtelomeric architecture and a highly diverged primate malaria lineage

Plasmodium cynomolgi is the closest relative of P. vivax and the primary experimental model for relapsing malaria, hypnozoite biology, and blood-stage drug susceptibility. Yet existing reference genomes remain fragmented, leaving structurally complex, AT-rich regions largely unresolved. We generated a chromosome-scale genome assembly for the K4-A7 cloned line of P. cynomolgi Berok by combining Hi-C chromosome conformation capture, Oxford Nanopore long reads, PacBio, and Illumina sequencing. The assembly spans 14 chromosomes plus mitochondrial and apicoplast genomes, with only seven unplaced minor contigs, the fewest for any non-P. falciparum Plasmodium genome, and an N50 of 3.06 Mb. Critically, this hybrid strategy resolved approximately 8 Mb of extremely AT-rich (~20% GC) sequence onto chromosomes 4, 8, and 13, anchoring what were previously unplaced or absent contigs into a continuous chromosomal framework. These subtelomere-like expansions (SLEs) constitute ~26.5% of the chromosomal genome and are enriched for PIR/VIR, STP1, variable surface antigen, and methyltransferase pseudogene families. Despite low gene density, SLE-encoded genes are transcriptionally active and show stage-specific expression across the erythrocytic cycle. Integrated lifecycle transcriptomics across 7,006 genes revealed a ~54-hour erythrocytic cycle with a "just-in-time" transcriptional cascade closely resembling that of P. vivax. Phylogenomic analyses and pairwise amino acid comparisons across more than 2,600 single-copy orthologs show that Berok forms a deeply diverged P. cynomolgi lineage, suggesting a distinct subspecies. This assembly establishes a high-resolution genomic foundation for comparative malaria biology, drug discovery, and the study of subtelomeric architecture, host adaptation, and lineage boundaries in primate Plasmodium.

microbiology↗

bioRxiv2026

Insect olfaction-inspired biohybrid sensor array for selective airborne pheromone detection and early monitoring of invasive Rhynchophorus ferrugineus

The red palm weevil, Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae), is a globally invasive quarantine pest threatening palm cultivation across 49 countries and inflicting annual economic losses estimated at over USD 100 million. Weevil larvae burrow into palm trunks, causing progressive internal structural damage that rarely produces visible external symptoms until lethal injury has occurred, rendering early detection exceptionally challenging. In the absence of effective early-warning surveillance technologies, tens of thousands of infested palm trees have been removed across major palm-cultivation regions in the Middle East and Mediterranean basin. Rapid, sensitive detection of volatile organic compounds (VOCs) emitted by weevil colonies and infested palm trees therefore represents a critical unmet need for timely pest surveillance and intervention. Existing artificial gas sensors lack the chemical selectivity required to discriminate among structurally similar VOCs, and no validated field-deployable early-detection platform has been established to date. Here, we report a portable biohybrid sensor array that mimics insect olfaction by exploiting two classes of diagnostic chemical signatures: the male-released aggregation pheromone (4RS,5RS)-4-methylnonan-5-ol (ferrugineol) and ethyl ester volatile blends emitted by weevil-infested palm trees. The R. ferrugineus odorant receptor RferOR1 was stabilised in lipid nanodiscs and co-immobilised with two in vivo-synthesised odorant-binding proteins (RferOBP1768 and RferOBP23) on quartz crystal microbalance (QCM) transducers to construct the biohybrid sensing platform. The sensor array achieved selective detection of airborne ferrugineol at a limit of detection of approximately 60 parts per billion (ppb) under field conditions, distinguishing infested from healthy palms. OBP- and OR-functionalised sensors retained full functional activity for 12 and 7 months, respectively, under ambient storage, confirming operational robustness and shelf life suitable for long-term field deployment. This work translates the molecular architecture of the insect olfactory system into a practical, field-validated chemical sensor platform with direct applicability to early-stage R. ferrugineus infestation monitoring and sustainable integrated pest management. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/744605v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@596c4org.highwire.dtl.DTLVardef@ed5336org.highwire.dtl.DTLVardef@f2229borg.highwire.dtl.DTLVardef@bdf1ad_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Malaria parasites coordinate host cell remodeling through the AP2-HCR DNA-binding protein

Parasite-induced host cell remodeling is essential for Plasmodium falciparum survival during the intraerythrocytic developmental cycle (IDC), yet the transcriptional mechanisms coordinating this process remain poorly understood. Here, we characterize an essential ApiAP2 transcription factor, PfAP2-HCR (host cell remodeling), during both the asexual and sexual blood stages of P. falciparum. Conditional truncation of pfap2-hcr demonstrated that PfAP2-HCR is essential for ring stage development and parasite maturation. Loss of PfAP2-HCR disrupted the expression of host cell remodeling genes, resulting in the absence of Maurers clefts and collapse of the parasite protein export machinery. Integrated RNA-seq and ChIP-seq analyses revealed that PfAP2-HCR directly or indirectly regulates approximately 30% of exported proteins, including 27 essential exported factors, the parasitophorous vacuole membrane (PVM) resident protein EXP1, and the core PTEX component EXP2. We further show that PfAP2-HCR is also indispensable for gametocytogenesis, as conditional truncation results in either complete ablation or the formation of severely deformed gametocytes. Together, these findings establish PfAP2-HCR as a central transcriptional regulator that orchestrates the expression of host cell remodeling factors required to transform a terminally differentiated erythrocyte into a permissive environment for parasite survival, development, and transmission.

microbiology↗

bioRxiv2026

Identification of two genomic cryptotypes of Plasmodium malariae in Africa

Plasmodium malariae is a neglected human malaria parasite that causes persistent, often asymptomatic infections and remains difficult to diagnose. Despite being generally associated with lower prevalence and severity than other malaria parasites, P. malariae represents a significant public health concern, particularly in Africa, but also as a zoonosis in South America with monkey-adapted Plasmodium brasilianum. Plasmodium malariae and P. brasilianum population genetic structure, evolutionary history, and adaptive potential remain poorly understood, largely due to the historical scarcity of whole-genome data. By screening 226 monkey samples from two Latin American countries, we identified 20 Plasmodium-positives across multiple primate species, highlighting the persistence of this parasite in sylvatic transmission cycles. We also investigated the evolutionary history and genetic diversity of P. malariae using whole-genome sequencing data. By combining 79 newly sequenced genomes with 248 publicly available genomes, we analyzed a filtered dataset comprising 179 P. malariae, two P. brasilianum, and two P. malariae-like genomes. Population structure analyses revealed the presence of two genetically distinct but recombining clusters across African P. malariae populations. These clusters occur across multiple African countries at varying frequencies, without clear geographic segregation. Genome-wide scans of genetic differentiation and selection further identified numerous cluster-specific signatures of adaptation, including loci putatively involved in interactions with human hosts and mosquito vectors. Our results provide the first evidence for fine-scale population substructure within African P. malariae and reveal ongoing adaptive processes that may contribute to its persistence and transmission. By uncovering previously unrecognized genetic diversity and selection patterns, this study highlights the importance of population genomic approaches for understanding the evolutionary dynamics of this neglected malaria parasite. Author summaryHuman malaria is most often associated with few well-studied parasites (Plasmodium falciparum and Plasmodium vivax), while other species have received far less attention. One such species is Plasmodium malariae, which often causes long-lasting infections with few or no symptoms. Because infections are difficult to detect, the true impact of this parasite is likely underestimated, particularly in Africa, where it is widespread. A closely related form, known as Plasmodium brasilianum, infects monkeys in South America with transmission between humans and wild animals. In our study, we analyzed the parasite genomes from infected people and monkeys to better understand the genetic diversity of these parasites, their population structure, and the molecular evidence of adaptation. We found evidence that P. brasilianum continues to circulate in several wild monkey species in South America. By analyzing nearly 300 genomes, we discovered that African P. malariae consists of two genetically distinct but recombining groups that coexist across the continent. These groups differ in specific regions of their genomes, including genes likely involved in interactions with human hosts and mosquito vectors. Our results reveal cryptic genetic diversity and structure with evidence of ongoing adaptation. These findings highlight the importance of including neglected parasites in malaria surveillance and control efforts.

genomics↗

bioRxiv2025

plasmoRUtils: A one-stop R Package for Plasmodium and other Apicomplexan parasite-related Bioinformatics analysis

Bioinformatics analysis of non-model organisms remains challenging due to the limited availability of specialized tools, as most R packages are optimized for well-annotated model species. This problem is exacerbated by genomic and proteomic data being scattered across multiple databases, each employing different identifiers based on varying reference annotations. Comprehensive databases have been developed to disseminate knowledge related to Apicomplexan genomics and proteomics, such as VEupathDB. Several specialised databases, particularly for the malaria parasite Plasmodium, have been developed such as ApicoTFDB, malaria.tools, MPMP, MIIP, Phenoplasm, PlasmoBase, alongside broader resources like HitPredict and TED. However, these platforms often suffer from manual query interfaces, outdated identifiers, and inefficient data retrieval methods, complicating their use for large-scale bioinformatic analyses. To address these limitations, we present plasmoRUtils, an R package designed to streamline database access and data harmonization for Apicomplexan research. plasmoRUtils enables the retrieval of data tables using single-line R functions and standardized Ensembl gene IDs as input. Thanks to the APIs available for some databases such as VEuPathDB, the package also provides functions to build CLI-based queries for VEuPathDBs component databases. Additional support includes performing overrepresentation analyses and estimating parasite transcriptomic age/stage using single-cell or bulk RNA-Seq references. By automating data retrieval and transformation within RStudio, plasmoRUtils eliminates the need for manual database queries, facilitating end-to-end workflow development without leaving the R environment. Available on GitHub https://github.com/Rohit-Satyam/plasmoRUtils, with comprehensive documentation, plasmoRUtils represents a critical step toward efficient and reproducible bioinformatics for Apicomplexan research.

bioinformatics↗

bioRxiv2025

Dengue virus susceptibility in Aedes aegypti linked to natural cytochrome P450 variants

The mosquito Aedes aegypti is the primary vector for dengue virus (DENV), which infects millions of people annually. Variability in DENV susceptibility among wild Ae. aegypti populations is governed by genetic factors, but specific causal variants are unknown. Here, we identify a cytochrome P450-encoding gene (CYP4G15) whose variants drive differences in DENV susceptibility in a natural Ae. aegypti population. CYP4G15 is transiently upregulated in DENV-resistant midguts, while knockdown increases susceptibility, and transgenic overexpression enhances resistance. A naturally occurring 18-base-pair promoter deletion reduces CYP4G15 expression and confers higher DENV susceptibility. The unexpected role of a cytochrome P450 in DENV susceptibility challenges the long-standing focus on canonical immune pathways and opens new avenues for understanding antiviral defense and DENV transmission in mosquitoes.

microbiology↗

bioRxiv2025

Epigenetic landscape of the H3K27me3 mark in macrophages transformed by Theileria annulata

Theileria annulata and T. parva are obligate intracellular parasites that induce bovine leukocyte transformation leading to uncontrolled proliferation and heightened dissemination of infected leukocytes. Early passage T. annulata-transformed macrophages are virulent, but with long-term culture, they become attenuated for dissemination. Loss of dissemination is restored when TGF-{beta}2-mediated signaling is re-established in attenuated macrophages, suggesting that epigenetic changes might be occurring that contribute to the attenuated phenotype. We focused on one of the important repressive histone marks, tri-methylated lysine 27 of histone H3 (H3K27me3) catalysed by the Polycomb Repressive Complex 2 and found that the global level of H3K27me3 is increased in attenuated macrophages. ChIP-seq revealed the genomic distribution of H3K27me3 is heavily remodeled from virulent to attenuated macrophages, where many genes transition from a focal peak of H3K27me3 around the transcription start site to larger chromatin domains. This transition is not paralleled by large-scale transcriptional downregulation. RNA-seq analysis following PRC2 inhibitor treatment reveals that fewer genes are derepressed in attenuated macrophages than in virulent macrophages, suggesting that broader H3K27me3 profiles do not systematically translate into increased gene silencing activity. Our findings shed light on the mechanisms underlying the dysregulation of epigenetic modifications in Theileria-induced leukocyte transformation. Significance statementTropical theileriosis is a major constraint to livestock production worldwide. Infection with Theileria annulata induces the transformation of bovine leukocytes, which subsequently exhibit similarities to human leukemia. Long-term in vitro culture of transformed leukocytes attenuates their tumorigenic properties. The molecular changes underlying this process are currently unclear. We focused on H3K27me3, a key histone tail post-translational modification that regulates chromatin structure and gene expression, and compared its genomic landscapes in virulent, highly disseminating macrophages versus attenuated macrophages with reduced dissemination potential that are used as a live vaccine against tropical theileriosis. Western blot and ChIP-seq revealed higher global levels of H3K27me3 and a striking broadening of its genomic distribution in attenuated macrophages. To our surprise, this reconfiguration is not associated with major changes in gene expression and attenuated cells appear to be less responsive to PRC2 inhibition, suggesting that large-scale broadening of H3K27me3 does not systematically translate into increased PRC2-mediated silencing activity. Despite these changes, H3K27me3 maintains the silencing of key tumor suppressor genes in both virulent and attenuated macrophages. These findings shed light on the interplay between infection, the evolution of oncogenic potential and reconfiguration of the chromatin landscape following attenuation of virulence.

microbiology↗

bioRxiv2024

Plasmodium NEK1 coordinates MTOC organisation and kinetochore attachment during rapid mitosis in male gamete formation

Mitosis is an important process in the cell cycle required for cells to divide. Never in mitosis (NIMA)-like kinases (NEKs) are regulators of mitotic functions in diverse organisms. Plasmodium spp, the causative agent of malaria is a divergent unicellular haploid eukaryote with some unusual features in terms of its mitotic and nuclear division cycle that presumably facilitate proliferation in varied environments. For example, during the sexual stage of male gametogenesis that occurs within the mosquito host, an atypical rapid closed endomitosis is observed. Three rounds of genome replication from 1N to 8N and successive cycles of multiple spindle formation and chromosome segregation occur within eight minutes followed by karyokinesis to generate haploid gametes. Our previous Plasmodium berghei kinome screen identified four Nek genes, of which two, NEK2 and NEK4, are required for meiosis. NEK1 is likely to be essential for mitosis in asexual blood stage schizogony in the vertebrate host, but its function during male gametogenesis is unknown. Here, we study NEK1 location and function, using live cell imaging, ultrastructure expansion microscopy (U-ExM) and electron microscopy, together with conditional gene knockdown and proteomic approaches. We report spatiotemporal NEK1 location in real-time, coordinated with microtubule organising centre (MTOC) dynamics during the unusual mitoses at various stages of the Plasmodium spp. life cycle. Knockdown studies reveal NEK1 to be an essential component of the MTOC in male cell differentiation, associated with rapid mitosis, spindle formation and kinetochore attachment. These data suggest that Plasmodium berghei NEK1 kinase is an important component of MTOC organisation and essential regulator of chromosome segregation during male gamete formation.

cell biology↗

bioRxiv2024

Impact of Plasmodium falciparum patient-derived isolates on brain endothelium in vitro

A hallmark of cerebral malaria (CM) is sequestration of Plasmodium falciparum infected erythrocytes (IE) within the brain microvasculature. Binding of IE to endothelium reduces microvascular flow and combined with an inflammatory response perturbs endothelial barrier function, resulting in breakdown of the blood- brain barrier (BBB). Cytoadherence leads to activation of the endothelium and alters a range of cell processes affecting signalling pathways, receptor expression, coagulation, and disruption of BBB integrity. Here, we investigated whether CM derived parasites elicit differential effects on human brain microvascular endothelial cells (HBMECs), as compared to uncomplicated malaria (UM) derived parasites. Patient-derived IE from UM and CM clinical cases, as well as non-binding skeleton-binding protein 1 knockout parasites, were overlaid onto TNF-activated HBMECs. Gene expression analysis of endothelial responses was performed using probe-based assays of a panel of genes involved in inflammation, apoptosis, endothelial barrier function, and prostacyclin synthesis pathway. We observed a significant effect on endothelial transcriptional responses in the presence of IE, yet there was no significant correlation between HBMEC responses and type of clinical syndrome (UM or CM). Further, there was no correlation between HBMEC gene expression and both binding itself and level of IE binding to HBMEC, as we detected the same change in endothelial responses when employing both binding and non-binding parasites. Our results suggest that interaction of IE with endothelial cells in this co-culture model induce some endothelial responses that are independent of clinical origin and independent of the expression of the major variant antigen PfEMP1 on the IE surface.

cell biology↗

bioRxiv2023

Proteome profiling of nasopharynx reveals pathophysiological signature of COVID-19 disease severity

An aberrant innate immune system caused by the beta coronavirus SARS-CoV-2 is a characteristic manifestation of severe coronavirus disease 2019 (COVID-19). Here, we performed proteome profiling of nasopharyngeal (NP) swabs from 273 hospitalized patients with mild and severe COVID-19 symptoms, including non-survivors. We identified depletion in STAT1-mediated type I interferon response, retinol metabolism and NRF2 antioxidant system that are associated with disease severity in our patient demography. We found that the dysregulation of glucocorticoid signaling and renin-angiotensin-aldosterone system (RAAS) contribute to the pathophysiology of COVID-19 fatality. Hyperactivation of host innate immune system was observed in severe patients, marked by elevated proteins involved in neutrophil degranulation and platelet aggregation. Our study using high-throughput proteomics on the nasopharynx of COVID-19 patients provides additional evidence on the SARS-CoV-2-induced pathophysiological signatures of disease severity and fatality.

immunology↗

bioRxiv2023

PfAP2-MRP DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages

Malaria pathogenicity results from the parasites ability to invade, multiply within and then egress from the host red blood cell (RBC). Infected RBCs are remodeled, expressing antigenic variant proteins (such as PfEMP1, coded by the var gene family) for immune evasion and survival. These processes require the concerted actions of many proteins, but the molecular regulation is poorly understood. We have characterized an essential Plasmodium specific Apicomplexan AP2 (ApiAP2) transcription factor in Plasmodium falciparum (PfAP2-MRP; Master Regulator of Pathogenesis) during the intraerythrocytic developmental cycle (IDC). An inducible gene knockout approach showed that PfAP2-MRP is essential for development during the trophozoite stage, and critical for var gene regulation, merozoite development and parasite egress. ChIP-seq experiments performed at 16 hour post invasion (h.p.i.) and 40 h.p.i. matching the two peaks of PfAP2-MRP expression, demonstrate binding of PfAP2-MRP to the promoters of genes controlling trophozoite development and host cell remodeling at 16 h.p.i. and antigenic variation and pathogenicity at 40 h.p.i. Using single-cell RNA-seq and fluorescence-activated cell sorting, we show de-repression of most var genes in{Delta} pfap2-mrp parasites that express multiple PfEMP1 proteins on the surface of infected RBCs. In addition, the{Delta} pfap2-mrp parasites overexpress several early gametocyte marker genes at both 16 and 40 h.p.i., indicating a regulatory role in the sexual stage conversion. Using the Chromosomes Conformation Capture experiment (Hi-C), we demonstrate that deletion of PfAP2-MRP results in significant reduction of both intra-chromosomal and inter-chromosomal interactions in heterochromatin clusters. We conclude that PfAP2-MRP is a vital upstream transcriptional regulator controlling essential processes in two distinct developmental stages during the IDC that include parasite growth, chromatin structure and var gene expression.

genomics↗

bioRxiv2023

Epithelial cells maintain memory of prior infection with Streptococcus pneumoniae through di-methylation of histone H3

Epithelial cells are the first point of contact for bacteria entering the respiratory tract. Streptococcus pneumoniae is an obligate human pathobiont of the nasal mucosa, carried asymptomatically but also the cause of severe pneumonia. The role of the epithelium in maintaining homeostatic interactions or mounting an inflammatory response to invasive S. pneumoniae is currently poorly understood. However, studies have shown that chromatin modifications, at the histone level, induced by bacterial pathogens interfere with the host transcriptional program and promote infection. In this study, we demonstrate that S. pneumoniae actively induces di-methylation of lysine 4 on histone H3 (H3K4me2), which persists for at least 9 days upon clearance of bacteria with antibiotics. We show that infection establishes a unique epigenetic program affecting the transcriptional response of epithelial cells, rendering them more permissive upon secondary infection. Our results establish H3K4me2 as a unique modification induced by infection, distinct from H3K4me3, which localizes to enhancer regions genome-wide. Therefore, this study reveals evidence that bacterial infection leaves a memory in epithelial cells after bacterial clearance, in an epigenomic mark, thereby altering cellular responses for subsequent infection.

cell biology↗

bioRxiv2023

Reverse chemical ecology approach for sustainable palm tree protection against invasive palm weevils

The reverse chemical ecology approach facilitates sustainable plant protection by identifying odorant receptors (ORs) tuned to odorants, especially the volatile molecules emitted from host plants that insects use for detection. A few studies have explored such an approach to develop sustainable pest management programs, especially in host-specialized insect species. We revealed the molecular mechanism of host plant detection of a destructive, invasive insect pest of palm trees (Arecaceae), the Asian palm weevil (Rhynchophorus ferrugineus), by deorphanizing an OR (RferOR2) tuned to several palm-emitted odors. We found that RferOR2 responded explicitly to several ecologically relevant palm-emitted odors and significantly to palm esters when transgenically expressed in Drosophila olfactory neurons. We mapped RferOR2 expression in the R. ferrugineus genome and found that odor specificity is likely to develop equally in both sexes. We inferred that the semiochemicals that attract palm weevils to a palm tree might aid in weevil control efforts by improving attraction, enticing many palm weevils to the traps. We demonstrate that including synthetic palm volatiles in pheromone-based mass trapping has a synergistic effect on pheromones, resulting in significantly increased weevil catches. We proved that insect OR deorphanization could aid in the identification of novel behaviorally active volatiles for inclusion in pest management. These results suggest that targeting RferOR2 may help design receptor antagonists that can interfere with weevil host-searching behavior in sustainable pest management applications. SignificanceAsian and South American palm weevils are tremendously important agricultural pests primarily adapted to palm trees and cause severe destruction, threatening sustainable palm cultivation worldwide. The host plant selection of these weevils is mainly attributed to functional specialization of odorant receptors that detect palm-derived volatiles. We unraveled the intricacies of weevil-palm tree communication by deorphanizing an odorant receptor tuned to natural palm-emitted odors. We used palm ester volatiles, which produced a significant response in the functional studies, and proved their synergistic effect on the pheromone coinciding with increased weevil catches in the field. We revealed that insect odorant receptor deorphanization could help identify novel behaviorally active volatiles (reverse chemical ecology) for sustainable palm protection.

ecology↗

bioRxiv2022

Evolution of lineage-specific trafficking proteins and a novel post-Golgi trafficking pathway in Apicomplexa

The Organelle Paralogy Hypothesis (OPH) posits a mechanism to explain the evolution of non-endosymbiotically derived organelles, predicting that lineage-specific pathways organelles should result when identity-encoding membrane trafficking components duplicate and co-evolve. Here we investigate the presence of such lineage-specific membrane-trafficking machinery paralogs in the globally important lineage of parasites, the Apicomplexa. Using a new phylogenetic workflow, we are able to identify 18 novel paralogs of known membrane-trafficking machinery, the emergence of several of which correlate with the presence of new endomembrane organelles in apicomplexans or their larger lineage. Gene coregulation analysis of a large set of membrane-trafficking proteins in Toxoplasma both corroborate known molecular cell biological interactions between characterized machinery and suggest involvement of many of these new components into established pathways for biogenesis of or trafficking to the microneme and rhoptry invasion organelles. Moreover, focused molecular parasitological analysis of the apicomplexan Arf-like small GTPases, and the ArlX3 protein specifically, revealed a novel post-Golgi trafficking pathways involved in delivery of proteins to micronemes and rhoptries, with knock down demonstrating reduced invasion capacity. The totality of our data has identified an unforeseen post-Golgi trafficking pathway in apicomplexans and is consistent with the OPH mechanism acting to produce novel endomembrane pathways or organelles at various evolutionary stages across the Alveolate lineage. Significance statementThe mechanism of non-endosymbiotic organelle evolution has been relatively poorly explored and yet is relevant to many eukaryotic compartments, including the endomembrane system. The Organelle Paralogy Hypothesis predicts novel lineage-specific paralogs evolutionarily concurrent with emergence of new endomembrane organelles or pathways. By investigating this phenomenon in the apicomplexan parasites and their relatives, we identify and profile over a dozen new trafficking factors, several correlating with emergence of lineage-specific organelles. Cell biological study of one such factor demonstrates the existence of a novel post-Golgi trafficking pathway for components to the invasion organelles in the parasite Toxoplasma gondii. This work reveals how non-endosymbiotic organelle evolution has shaped cellular novelty in this lineage, relevant both to global health and fundamental evolutionary biology.

microbiology↗

bioRxiv2022

Theileria annulata histone deacetylase 1 (TaHDAC1) initiates schizont to merozoite stage conversion

A fungal metabolite, FR235222, specifically inhibits a histone deacetylase of the apicomplexan parasite Toxoplasma gondii and TgHDAC3 has emerged as a key factor regulating developmental stage transition in this species. Here, we exploited FR235222 to ask if changes in histone acetylation regulate developmental stage transition of Theileria annulata, another apicomplexan species. We found that FR235222 treatment of T. annulata-infected transformed leukocytes induced a proliferation arrest. The blockade in proliferation was due to drug-induced conversion of intracellular schizonts to merozoites that lack the ability to maintain host leukocyte cell division. Induction of merogony by FR235222 leads to an increase in expression of merozoite-marker (rhoptry) proteins. RNA-seq of FR235222-treated T. annulata-infected B cells identified deregulated expression of 468 parasite genes including a number encoding parasite ApiAP2 transcription factors. Thus, similar to T. gondii, FR235222 inhibits T. annulata HDAC (TaHDAC1) activity and places parasite histone acetylation as a major regulatory event of the transition from schizonts to merozoites.

cell biology↗

bioRxiv2022

Rare CNVs and phenome-wide profiling: a tale of brain-structural divergence and phenotypical convergence

Copy number variations (CNVs) are rare genomic deletions and duplications that can exert profound effects on brain and behavior. Previous reports of pleiotropy in CNVs imply that they converge on shared mechanisms at some level of pathway cascades, from genes to large-scale neural circuits to the phenome. However, studies to date have primarily examined single CNV loci in small clinical cohorts. It remains unknown how distinct CNVs escalate the risk for the same developmental and psychiatric disorders. Here, we quantitatively dissect the impact on brain organization and behavioral differentiation across eight key CNVs. In 534 clinical CNV carriers from multiple sites, we explored CNV-specific brain morphology patterns. We extensively annotated these CNV-associated patterns with deep phenotyping assays through the UK Biobank resource. Although the eight CNVs cause disparate brain changes, they are tied to similar phenotypic profiles across [~]1000 lifestyle indicators. Our population-level investigation established brain structural divergences and phenotypical convergences of CNVs, with direct relevance to major brain disorders.

genetics↗

bioRxiv2022

Mitochondrial genomes in Perkinsus decode conserved frameshifts in all genes

Mitochondrial genomes of apicomplexans, dino-flagellates and chrompodellids, that collectively make up the Myzozoa, are uncommonly reduced in coding capacity and display divergent gene configuration and expression mechanisms. They encode only three proteins -- COB, COX1, COX3 -- contain rRNAs fragmented to [~]100-200 base pair elements, and employ extensive recombination, RNA trans-splicing, and RNA-editing for genome maintenance and expression. The early-diverging Perkinsozoa is the final major myzozoan lineage whose mitochondrial genomes remain poorly characterized. Previous reports of Perkinsus cox1 and cob partial gene sequences have indicated independent acquisition of non-canonical features, namely the occurrence of multiple frameshifts in both genes. To determine ancestral myzozoan mitochondrial genome features, as well as any novel ones in Perkinsozoa, we sequenced and assembled four Perkinsus species mitochondrial genomes. These data show a simple ancestral genome with the common reduced coding capacity, but one already prone to rearrangement. Moreover, we identified 75 frameshifts across the four species that are present in all genes, that are highly conserved in gene location, and that occur as four distinct types. A decoding mechanism apparently employs unused codons at the frameshift sites that advance translation either +1 or +2 frames to the next used codon. The locations of the frameshifts are seemingly positioned to regulate protein folding of the nascent protein as it emerges from the ribosome. COX3 is distinct in containing only one frameshift and showing strong selection against residues that are otherwise frequently encoded at the frameshift positions in COX3 and COB. All genes also lack cysteine codons implying a further constraint on these genomes with reduction to only 19 different amino acids. Furthermore, mitochondrion-encoded rRNA fragment complements are incomplete in Perkinsus spp. but some are found in the nuclear DNA, suggesting these may be imported into the organelle as for tRNAs. Perkinsus demonstrates additional remarkable trajectories of organelle genome evolution including pervasive integration of frameshift translation into genome expression.

molecular biology↗