Biology subjects

Toth, A.

Publications and source records attributed to Toth, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Chromosome-level genome and caste transcriptomes for Africa's most widespread social wasp (Belonogaster juncea) reveal unexpected genomic diversity

Belonogaster is an African genus of primitively eusocial wasps. They are widespread and conspicuous across sub-Saharan Africa and yet are among the least studied groups of social wasps. Here, we present the first high-quality, chromosome-level genome assembly for a representative of this genus, Belonogaster juncea, complemented by an RNA-seq analysis of brain transcription among individuals representing reproductive and non-reproductive castes. The assembled genome spans 315.8 Mb with a scaffold N50 of 7.91 Mb. The annotation contained 15,159 protein-coding genes and 20,046 isoforms, with Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 98.0% for the genome and 97.8% for the annotation. Using this new assembly, we show that the B. juncea genome differs notably from other social wasp genomes: a single satellite repeat makes up a fifth of its chromosome-scale sequence, it has the highest putative chromosome number in a sequenced wasp genome to date, and it shows high levels of syntenic breaks. We find caste neuro-transcription differences between queens and workers, revealing 573 differentially expressed genes (341 worker biased, 232 queen biased), with significant overlap in caste-specific genes when compared to Polistes dominula and Liostenogaster flavolineata. This genomic resource provides a foundation for understanding the molecular mechanisms underlying primitive eusociality and social evolution in wasps, and opens up new research opportunities for a genus of little-studied insects from the Global South.

genomics↗

bioRxiv2026

Alveolar-Basal Intermediates Drive Pulmonary Fibrosis via Coordination of a Pro-Fibrotic Signaling Niche in Silicosis

Pulmonary fibrosis is a progressive, terminal disease with high morbidity. Existing therapeutics slow disease progression but do not reverse fibrotic lung remodeling, accentuating the importance of identifying cellular mechanisms that underlie lung fibrosis. Recent literature suggests that alveolar type 2 (AT2) progenitors undergo transition to stressed Krt8high cells following lung injury. Accumulation of stressed Krt8high cells is a hallmark of acute and chronic lung diseases, particularly pulmonary fibrosis. Whether Krt8high cells actively participate in the fibrotic process or are simply an epiphenomenon of lung injury remains unclear. We previously described a genetic model in which deletion of the lung transcription factor Nkx2-1 in the AT2 progenitor lineage induces AT2 progenitors to transition to the Krt8high cell state. Here, we use this tractable genetic model to directly test the pathogenic influence of Krt8high cells. We show that Nkx2-1-/- Krt8high cells accumulate in a Krt7high/Krt19high/Krt17neg alveolar-basal intermediate cell state (ABI). Following induction of fibrotic lung injury with inhaled silica, ABI enter a unique inflammatory state (iABI) that drives fibrotic remodeling via coordination of a fibrotic signaling niche containing inflammatory alveolar fibroblasts (iAF) and pulmonary osteoclast-like cells (POLC). Computational analysis predicts that iABI elaborate pro-inflammatory signals which increase matrix deposition by iAF and induce differentiation of interstitial macrophages to a profibrotic POLC variant. Niche mapping demonstrates that iABI, iAF, and POLCs interact within newly formed fibrotic niches in the lung alveolus in mice with pre-existing accumulation of ABI. These data provide direct evidence that ABI accumulation in fibrotic lung disease is pathogenic.

systems biology↗

bioRxiv2026

The chromatin remodeling complex PRC2 safeguards cell fate in alveolar epithelial type 2 cells

Maintenance of the gas exchange surface throughout life and regeneration of the lung after injury requires tight regulation of epithelial cell fate and function. Alveolar epithelial type 2 (AT2) cells serve as the progenitors of the distal epithelium, differentiating into alveolar epithelial type 1 (AT1) cells or proliferating to maintain the quorum of AT2 cells. Here we describe the role of the chromatin regulator polycomb repressive complex 2 (PRC2) in the maintenance of AT2 cell fate in the adult alveolus. Cross-species single-cell transcriptomic analyses identified PRC2 activation in proliferative AT2 populations. PRC2 loss of function in human iPSC-derived AT2 (iAT2) cells and primary murine AT2 cells in vitro resulted in loss of AT2 cell state and emergence of programs reminiscent of alveolar-basal intermediate (ABI) cell states, while overexpression of the PRC2 enzymatic component EZH2 in human iAT2 cells augmented the AT2 cell program. Genetic loss of PRC2 function in the AT2 lineage in adult mice in vivo led to emphysematous remodeling of the lung and induced a time-dependent series of transitions of AT2 cells through an alveolar-basal intermediate (ABI) state into Krt5+ basal-like cells. Comparison of murine ABI cells to human disease-associated ABI cells demonstrates de-repression of canonical PRC2 targets during transition to ABI and basal-like states in human fibrosis, implicating PRC2 is a conserved regulator of AT2 cell fate. Together, these findings define PRC2 complex function during AT2 cell self-renewal as a critical guardrail for maintaining epithelial cell fate in the adult lung.

genetics↗

bioRxiv2026

ZCWPW1 organizes telomeric architecture to drive meiotic chromosome movements

Meiotic homolog pairing relies on programmed DNA recombination and large-scale chromosome movements, yet, how these genetic and mechanical events are coordinated remains unclear. ZCWPW1 is a histone reader that recognizes PRDM9-deposited chromatin marks. We identify an unexpected role for ZCWPW1 as a regulator of rapid prophase movements (RPMs). Using super-resolution imaging, we show that ZCWPW1 is strongly enriched at subtelomeric regions of mouse spermatocytes, where it stabilizes TRF1, LINC complex components, dynein, and meiosis-specific cohesin (STAG3). Loss of ZCWPW1 disrupts telomere architecture, weakens telomere-LINC- motor coupling, and abolishes chromosome movement, leading to defective synapsis and pairing, and persistence of DSBs. These defects are more severe than, and mechanistically independent of, those observed in Prdm9-/- spermatocytes. Together, our findings reveal that ZCWPW1 acts independently of PRDM9 as a chromatin-based intranuclear regulator of telomere architecture and telomere-led chromosome movements, thereby linking telomeric chromatin state to nuclear force transmission required for faithful meiotic progression. Significance StatementMeiotic pairing requires recombination and telomere-led chromosome movements, yet no chromatin factor has been shown to regulate both. We identify ZCWPW1 as the first chromatin-based regulator of rapid prophase movements. ZCWPW1 organizes telomeric chromatin and promotes cohesin and motor assembly at telomeres that for force transmission across the nuclear envelope. Loss of ZCWPW1 disrupts the telomere-nuclear envelope mechanical coupling, impairing motion and altering recombination. This function doesnt rely on PRDM9 despite their co-evolution and co-expression, challenging the prevailing view that ZCWPW1 only acts downstream of PRDM9 in DNA repair. Our findings show that chromatin readers can function as structural regulators of genome organization, revealing a conserved mechanism integrating chromosome structure, motion, and repair to ensure proper pairing and fertility.

cell biology↗

bioRxiv2026

Chromosome axis protein SYCP2 recruits HORMAD2 to enable meiotic synapsis quality control in mice

Faithful chromosome segregation during meiosis depends on accurate recombination and synapsis of homologous chromosomes. These processes are monitored in mammals by checkpoint mechanisms involving the meiotic HORMA-domain proteins HORMAD1 and HORMAD2, which bind unsynapsed chromosome axes and promote activation of the DNA damage-response kinase ATR independently of DNA double-strand breaks (DSBs). However, no mechanism for axis recruitment of HORMAD1 or HORMAD2 had been demonstrated, nor had its role in checkpoint function been tested. We establish that a putative HORMAD-interacting region--the closure motif (CM)--within the chromosome-axis component SYCP2 is selectively required for HORMAD2, but not HORMAD1, localization. Deletion of the SYCP2 CM disrupts SYCP2-HORMAD2 complexes and prevents HORMAD2 axis binding without affecting axis assembly or recombination. Consequently, ATR accumulation and signaling on unsynapsed axes are reduced, and the prophase checkpoint malfunctions in a sexually dimorphic manner--causing aberrant elimination of synapsis-proficient spermatocytes and persistence of asynaptic oocytes. The phenotypes of SYCP2-CM-deficient and HORMAD2-null mice are indistinguishable, establishing the requirement for HORMAD2 axis recruitment in synapsis surveillance. We propose that axial recruitment generates a HORMAD2 scaffold that drives clustering-mediated ATR network activation independently of DSBs, thereby linking chromosome-axis architecture to synapsis quality control in mammalian meiosis.

cell biology↗

bioRxiv2025

Early cell autonomous and niche-mediated alveolar epithelial response to influenza infection in primary lung organoids

Influenza A virus (IAV) infection is a significant cause of morbidity and mortality for patients worldwide. Alveolar type 2 (AT2) cells are the preferential target of IAV as part of the pathogenesis of viral pneumonia and acute respiratory distress syndrome (ARDS). Early IAV infection of alveolar cells has been challenging to model both in vitro and in vivo. To address this challenge, we used a combination of murine and human primary alveolar organoids to define methods for robust IAV infection and evaluated cell-autonomous consequences of IAV using a temporal series of multiome paired single nuclei RNA/ATAC sequencing. Infected AT2 cells undergo conserved changes defined by early loss of surfactant secretion, decreased lipid biogenesis, a rapid burst of antiviral response, and late viral-mediated suppression. Surprisingly, uninfected AT2 cells undergo substantial transcriptional and epigenomic changes in IAV-treated cultures, leading to transition to damage-associated cell states within hours via a process driven by the inflammatory milieu of murine organoids. Together, these data provide new methods for high-fidelity modeling of IAV infection in alveolar cells and define a conserved AT2 cell response signature to IAV with implications for ARDS pathogenesis.

systems biology↗

bioRxiv2024

Membrane-Dependent Dynamics and Dual Translocation Mechanisms of ABCB4: Insights from Molecular Dynamics Simulations

ABCB4 is an ATP-binding cassette transporter expressed at the canalicular membrane of hepatocytes and responsible for translocating phosphatidylcholine into bile. Despite the recent cryo-EM structures of ABCB4, knowledge about the molecular mechanism of phosphatidylcholine transport remains fragmented. In this study, we used all-atom molecular dynamics simulations to investigate ABCB4 dynamics during its transport cycle, leveraging both symmetric and asymmetric membrane models. Our results demonstrate that membrane composition influences the local conformational dynamics of ABCB4, revealing distinct lipid-binding patterns across different conformers, particularly for cholesterol. We explored the two potential mechanisms for phosphatidylcholine translocation: the canonical ATP-driven alternating access model and the "credit-card swipe" model. Critical residues were identified for phosphatidylcholine binding and transport pathway modulation, supporting the canonical mechanism while also indicating a possible additional pathway. The conformer-specific roles of kinking in transmembrane helices (TMH4 and TMH10) were highlighted as key events in substrate translocation. Overall, ABCB4 may utilize a cooperative transport mechanism, integrating elements of both models to facilitate efficient phosphatidylcholine motion across the membrane. This study provides new insights into the relationship between membrane environment and ABCB4 function, contributing to our understanding of its role in bile physiology and susceptibility to genetic and xenobiotic influences.

biophysics↗

bioRxiv2024

Effect of pre-germination temperature conditions on germination characteristics of temperate grassland species

Germination characteristics of target species used for grassland restoration are often unknown, despite such information would be essential for designing restoration interventions. Filling this knowledge gap and improving our understanding about germination responses of grassland species to varying cold and warm treatments could be especially important in the face of climate change. Here we studied the effect of three different durations of warm dry stratification and three different durations of cold wet stratification, and their combinations in a full factorial design (in total 15 different pre-germination treatments), on the germination capacity of 48 grassland species native to Central Europe. Stratification treatments modelled present and forecasted summer (1-3 months warm period) and winter (1-3 months cold period) temperature conditions, while the study of the combined effect of these treatments is especially important in spring-germinating species. As response variables, we calculated relative response indexes and germination uncertainties of each species separately and applied general linear models to study the effect of treatments on these variables. We found clear effect of warm- or cold stratification on relative response indexes only in four species: strong positive response to warm stratification was found in Silene conica, while strong positive response to cold stratification was found in Agrimonia eupatoria, Echium vulgare, and Plantago lanceolata. The responses to treatment combinations were contradictory or lacked clear trends in most of the species. Germination uncertainty in general was high for all species, supporting the fact that Central European grassland species often rely on bet hedging as risk spreading strategy, to avoid unfavourable conditions during seedling establishment.

plant biology↗

bioRxiv2024

Mitigation of chytrid infection on tadpoles with the antimicrobial metabolites of Xenorhabdus szentirmaii

Survival of amphibian assemblages is threatened by many factors. Among them, chytridiomycosis, the disease caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd) has great importance, also threatening the populations of the yellow-bellied toad (Bombina variegata), which has a scattered, isolated distribution in Hungary. Treatment with secondary metabolites of the entomopathogenic bacterium, Xenorhabdus szentirmaii is a promising method in the mitigation of chytridiomycosis, as recently demonstrated. To assess whether it may also be effective for lowering infection intensities in B. variegata tadpoles, we extracted cell-free culture media (CFCM) from liquid cultures of X. szentirmaii and tested their antifungal efficacy at a dilution of 0.1 % (v/v), while also measuring possible short-term malign effects on tadpoles experimentally infected with Bd or sham infection. According to our results, CFCM treatment alone did not compromise tadpoles survival probability, nor reduced the body mass and developmental speed of the individuals. At the same time, the treatment reduced the intensity and prevalence of Bd infection, but this effect was affected by the population of origin. The antimicrobial metabolites produced by X. szentirmaii may therefore be suitable for the safe mitigation of chytridiomycosis in B. variegata tadpoles, but further studies are needed, aiming to monitor and increase the efficacy of this method.

ecology↗

bioRxiv2024

Pathogen genomic surveillance as a scalable framework for precision phage therapy

Phage therapy is gaining increasing interest in the fight against critically resistant nosocomial pathogens. However, the narrow host range of bacteriophages hampers the development of broadly effective phage therapeutics and demands precision approaches. Here we combine large-scale phylogeographical analysis with high-throughput phage typing to guide the development of precision phage cocktails targeting carbapenem-resistant Acinetobacter baumannii, a top-priority pathogen. Our analysis reveals that a few strain types dominate infections in each world region, with their geographical distribution remaining stable within six years. As we demonstrate in Eastern Europe, this spatio-temporal distribution enables preemptive preparation of region-specific phage collections that target most local infections. Finally, we showcase the efficacy of a four-phage cocktail against the most prevalent strain type in both in vitro and in vivo animal infection models. Ultimately, genomic surveillance identifies patients benefiting from the same phages across geographical scales, thus providing a scalable framework for precision phage therapy. HighlightsO_LIA few carbapenem-resistant Acinetobacter baumannii types dominate infections worldwide C_LIO_LIPhylogeography reveals stable strain composition of individual countries over a six-year period C_LIO_LIThis spatio-temporal distribution allows preemptive preparation of region-specific phage collections C_LIO_LIA four-phage cocktail is efficacious against the most prevalent strain type in Europe. C_LI

microbiology↗

bioRxiv2024

Fundamental principles of chromosome organization for meiotic recombination

In meiotic cells, chromosomes are organized as chromatin loop arrays anchored to a protein axis. This organization is essential to regulate meiotic recombination, from DNA double-strand break (DSB) formation to their repair 1. In mammals, it is unknown how chromatin loops are organized along the genome and how proteins participating in DSB formation are tethered to the chromosome axes. Here, we identified three categories of axis-associated genomic sites: PRDM9 binding sites, where DSBs form 2, binding sites of the insulator protein CTCF, and H3K4me3-enriched sites. We demonstrated that PRDM9 promotes the recruitment of MEI4 and IHO1, two proteins essential for DSB formation 3,4. In turn, IHO1 anchors DSB sites to the axis components HORMAD1 and SYCP3. We discovered that IHO1, HORMAD1 and SYCP3 are associated at the DSB ends during DSB repair. Our results highlight how interactions of proteins with specific genomic elements shape the meiotic chromosome organization for recombination.

molecular biology↗

bioRxiv2024

Genome-wide transcriptional silencing and mRNA stabilization allow the coordinated expression of the meiotic program in mice

The transcriptional dynamic of mammalian cells when these transit from the ubiquitous mitotic to a meiotic specific program is key to understand this switch central to sexual reproduction. By quantifying active RNA polymerase II and nascent transcripts using single cell dataset and ethynyl-uridine pool-down with sorted cells from synchronised testes, we detailed the transcriptional activity of murine male germ cells. When spermatogonia differentiate, transcription slows down, reaching minimal activity at meiotic entry and resumes during pachytene stage. This event, we termed EMLT (for early meiotic low transcription), is distinct from the silencing of sex chromosomes as it is independent of Setdb1 though it is accompanied by the same chromatin mark, H3K9me3. EMLT is delayed in Stra8KO but occurs in mutants altering meiotic chromosome structure or DSB formation or repair. By comparing transcript abundance and neotranscription we unveil a massive event of mRNA stabilization that parallels EMLT. Altogether our data indicate that meiosis is initiated with a nearly silent genome and we propose that the stabilization of transcripts at that time facilitates the meiotic entry by synchronising the expression of several meiotic sub-programs.

cell biology↗

bioRxiv2023

Seeding the meiotic DNA break machinery and initiating recombination on chromosome axes

Programmed DNA double-strand break (DSB) formation is a unique meiotic feature that initiates recombination-mediated linking of homologous chromosomes, thereby enabling chromosome number halving in meiosis. DSBs are generated on chromosome axes by heterooligomeric focal clusters of DSB-factors. Whereas DNA-driven protein condensation is thought to assemble the DSB-machinery, its targeting to chromosome axes is poorly understood. We discovered in mice that efficient biogenesis of DSB-machinery clusters requires seeding by axial IHO1 platforms, which are based on a DBF4-dependent kinase (DDK)-modulated interaction between IHO1 and the chromosomal axis component HORMAD1. IHO1-HORMAD1-mediated seeding of the DSB-machinery on axes ensures sufficiency of DSBs for efficient pairing of homologous chromosomes. Without IHO1-HORMAD1 interaction, residual DSBs depend on ANKRD31, which enhances both the seeding and the growth of DSB-machinery clusters. Thus, recombination initiation is ensured by complementary pathways that differentially support seeding and growth of DSB-machinery clusters, thereby synergistically enabling DSB-machinery condensation on chromosomal axes.

cell biology↗

bioRxiv2023

Hypoxia-inducible factor (HIF) activation promotes osteogenic transition of valve interstitial cells and accelerates heart valve calcification in chronic kidney disease (CKD)

AimsValve calcification (VC) is a widespread complication in chronic kidney disease (CKD) patients on hemodialysis. VC is an active process with the involvement of in situ osteogenic transition of valve interstitial cells (VICs). VC is accompanied by the activation of hypoxia inducible factor (HIF) pathway, but the role of HIF activation in the calcification process remains undiscovered. Methods and resultUsing in vitro and in vivo approaches we addressed the role of HIF activation in osteogenic transition of VICs and CKD-associated VC. Elevation of osteogenic (Runx2, Sox9) and HIF activation markers (HIF-1 and HIF-2) and VC occurred in adenine-induced CKD mice. High phosphate (Pi) induced upregulation of osteogenic (Runx2, alkaline-phosphatase, Sox9, osteocalcin) and hypoxia markers (HIF-1, HIF-2, Glut-1), and calcification in VICs. Down-regulation of HIF-1 and HIF-2 inhibited, whereas further activation of HIF pathway by hypoxic exposure (1% O2) or hypoxia mimetics (desferrioxamine, CoCl2, Daprodustat (DPD)) promoted Pi-induced calcification of VICs. Pi augmented the formation of reactive oxygen species (ROS) and decreased viability of VICs, whose effects were further exacerbated by hypoxia. N-acetyl cysteine inhibited Pi-induced ROS production, cell death and calcification under both normoxic and hypoxic conditions. DPD treatment corrected anemia but promoted VC in the CKD mice model. ConclusionsHIF activation plays a fundamental role in Pi-induced osteogenic transition of VICs and CKD-induced VC. The cellular mechanism involves stabilization of HIF-1 and HIF-2, increased ROS production and cell death. Targeting the HIF pathways may thus be investigated as a therapeutic approach to attenuate VC. Translational perspectiveOne in four hemodialysis-dependent CKD patients on DPD treatment experience a major cardiovascular event during a 2.5-year follow-up period. This work provides a possible explanation for this phenomenon and should initiate further studies to address whether DPD-mediated acceleration of valve calcification triggers the unbeneficial effect of DPD.

pathology↗

bioRxiv2022

Computational and structural insights into the pre- and post-hydrolysis states of multidrug resistance associated protein 1 in lipid bilayer membranes

ATP-binding cassette C-family drug membrane transporters play an important role in local pharmacokinetics, i.e., drug concentration in cellular compartments. From the structural point of view, only the bovine ortholog of the multidrug-resistance associated protein 1 (bMRP1) has been resolved. We here used s-scaled molecular dynamics simulations to investigate the structure and dynamics of bMRP1 in pre- and post-hydrolysis functional states. The present work aims to examine the slight but likely relevant structural differences between pre- and post-hydrolysis states of outward-facing conformations as well as the interactions between MRP1 and the surrounding lipid bilayer. Global conformational dynamics show unfavourable extracellular opening associated with nucleotide binding domain dimerization indicating that the post-hydrolysis state adopts a close-cleft conformation rather than an outward-open conformation. Our present simulations also highlight persistent interactions with annular cholesterol molecules and the expected active role of lipid bilayer in the allosteric communication between distant domains of MRP1 transporter.

pharmacology and toxicology↗

bioRxiv2022

Alveolar epithelial progenitor cells drive lung regeneration via dynamic changes in chromatin topology modulated by lineage-specific Nkx2-1 activity

Lung epithelial regeneration after acute injury requires coordination of extensive cellular and molecular processes controlling proliferation and differentiation of specialized alveolar cells to pattern the morphologically complex alveolar gas exchange surface. During regeneration, specialized Wnt-responsive alveolar epithelial progenitor (AEP) cells, a subset of alveolar type 2 (AT2) cells, proliferate and transition to alveolar type 1 (AT1) cells, though the precise molecular and epigenetic determinants of these processes remain unclear. Here, we report a refined primary murine alveolar organoid assay which recapitulates critical aspects of in vivo regeneration, providing a tractable model to dissect these regenerative processes. Clonal expansion of single AEPs generate complex alveolar organoids with extensive structural maturation and organization. These organoids contain properly patterned AT1 and AT2 cells surrounding numerous alveolar-like cavities with minimal structural contribution from mesenchymal cells, implying extensive cell autonomous regenerative function encoded in adult AEPs. Leveraging a time series of paired scRNAseq and scATACseq, we identified the AEP state at single cell resolution and described two distinct AEP to AT1 intermediate states: a widely reported Krt8+ transitional state defined by cell stress markers and a second state defined by differential activation of signaling pathways mediating AT1 cell differentiation. Transcriptional regulatory network (TRN) analysis demonstrated that these AT1 transition states were driven by distinct regulatory networks controlled in part by differential activity of Nkx2-1. Genetic ablation of Nkx2-1 in AEP-derived organoids was sufficient to cause transition to a proliferative stressed Krt8+ state characterized by disorganized, uncontrolled growth. Finally, AEP-specific deletion of Nkx2-1 in adult mice led to rapid loss of AEP state, clonal expansion, and disorganization of alveolar structure, implying a continuous requirement for Nkx2-1 in maintenance and function of adult lung progenitors. Together, these data provide new insight into cellular hierarchies in lung regeneration and implicate dynamic epigenetic maintenance via lineage transcription factors as central to control of facultative progenitor activity in AEPs.

developmental biology↗

bioRxiv2022

Substrate binding and lipid-mediated allostery in the human organic anion transporter 1 at the atomic-scale

The Organic Anion Transporter 1 is a membrane transporter known for its central role in drug elimination by the kidney. hOAT1 is an antiporter translocating substrate in exchange for -ketoglutarate. The understanding of hOAT1 structure and function remains limited due to the absence of resolved structure of hOAT1. Benefiting from conserved structural and functional patterns shared with other Major Facilitator Superfamily transporters, the present study intended to investigate fragments of hOAT1 transport function and modulation of its activity in order to make a step forward the understanding of its transport cycle. s-long molecular dynamics simulation of hOAT1 were carried out suggesting two plausible binding sites for a typical substrate, adefovir, in line with experimental observations. The well-known B-like motif binding site was observed in line with previous studies. However, we here propose a new inner binding cavity which is expected to be involved in substrate translocation event. Binding modes of hOAT1 co-substrate -ketoglutarate were also investigated suggesting that it may binds to highly conserved intracellular motifs. We here hypothesize that -ketoglutarate may disrupt the pseudo-symmetrical intracellular charge-relay system which in turn may participate to the destabilisation of OF conformation. Investigations regarding allosteric communications along hOAT1 also suggest that substrate binding event might modulate the dynamics of intracellular charge relay system, assisted by surrounding lipids as active partners. We here proposed a structural rationalisation of transport impairments observed for two single nucleotide polymorphisms, p.Arg50His and p.Arg454Gln suggesting that the present model may be used to transport dysfunctions arising from hOAT1 mutations. HighlightsO_LIAdefovir has at least two binding pockets on hOAT1 in the outward-facing conformation. C_LIO_LIThe highly conserved B-motif within MFS is strongly involved in substrate binding. C_LIO_LI-Ketoglutarate binds to the intracellular domain of hOAT1 and destabilizes its OF conformation. C_LIO_LIThe lipid membrane bilayer plays an active role in the allosteric communication between intracellular and extracellular domains of hOAT1. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/500056v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@18d092corg.highwire.dtl.DTLVardef@5538e9org.highwire.dtl.DTLVardef@10b62cforg.highwire.dtl.DTLVardef@84421e_HPS_FORMAT_FIGEXP M_FIG The present work (from left): (i) reveals binding modes of adefovir (top) and -ketoglutarate (bottom) to hOAT1; (ii) maps Single Nucleotide Polymorphisms on outward-facing (top) and inward-facing (bottom) conformation of hOAT1; (iii) asses the allosteric effect of lipidic environment and presence of substrates. C_FIG

pharmacology and toxicology↗

bioRxiv2022

On the interplay between lipids and asymmetric dynamics of an NBS degenerate ABC transporter

Multidrug resistance-associated proteins are ABC C-family exporters. They are crucial in pharmacology as they transport various substrates across membranes. However, the role of the degenerate nucleotide-binding site (NBS) remains unclear likewise the interplay with the surrounding lipid environment. Here, we propose a dynamic and structural overview of MRP1 from ca. 110 {micro}s molecular dynamics simulations. ATP binding to NBS1 is likely maintained along several transport cycles. Asymmetric NBD behaviour is ensured by lower signal transduction from NBD1 to the rest of the protein owing to the absence of ball-and-socket conformation between NBD1 and coupling helices. Even though surrounding lipids play an active role in the allosteric communication between the substrate-binding pocket and NBDs, our results suggest that lipid composition has a limited impact, mostly by affecting transport kinetics. We believe that our work can be extended to other degenerate NBS ABC proteins and provide hints for deciphering mechanistic differences among ABC transporters.

biophysics↗