Open Biology
● The Royal Society
Preprints posted in the last 90 days, ranked by how well they match Open Biology's content profile, based on 106 papers previously published here. The average preprint has a 0.07% match score for this journal, so anything above that is already an above-average fit.
Thomas, M. S.; Galletta, B. J.; Ryniawec, J. M.; Amoiroglou, A.; Khan, C.; Fagerstrom, C. J.; Rogers, G. C.; Rusan, N. M.
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Centrosome dysfunction is linked to developmental disorders affecting brain and body size, including microcephaly and primordial dwarfism. However, the cellular mechanisms underlying these rare conditions remain poorly understood. In this study, we investigate a rare variant of the centrosome-associated protein Pericentrin, which was discovered in a single family with Majewski/microcephalic osteodysplastic primordial dwarfism type II (MOPD II). Unlike the majority of pathogenic PCNT variants that cause severe protein truncation, the p.Lys3154del variant ({Delta}K3154) involves a single amino acid deletion in the proteins only conserved functional domain, providing a unique opportunity to explore PCNT function in MOPD II. To model PCNT{Delta}K3154, we examined the effects of Drosophila Pericentrin-like protein (PLP) carrying an orthologous deletion (Plp{Delta}R). Our results show that plp{Delta}R animals exhibit smaller tissues that recapitulate MOPD II phenotypes. Behavioral assays revealed defects in climbing and mechanosensation, suggesting impaired sensory cilia function. We also found that Plp{Delta}R cells exhibit accelerated mitosis, increased apoptosis, and reduced pericentriolar material recruitment. In silico structural modeling, yeast two-hybrid, and co-immunoprecipitation experiments show that Plp{Delta}R produces a protein that disrupts PLP dimerization and PLP interaction with Asterless, another centrosome protein. Overall, modeling the human MOPD II patient variant PCNT{Delta}K3154 in Drosophila reveals how a single amino acid deletion affects biological processes from the molecular level to the organismal level. Our work offers new insights into the defective cellular mechanisms underlying MOPD II in patients with the PCNT{Delta}K3154 variant, potentially linking the etiology of the disease in these individuals to the loss of a single protein-protein interaction.
Roth-Carter, R.; Helms, E.; Saldivar, J. C.; Podrabsky, J.
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Hypoxia and anoxia are known to suppress cell proliferation due to an increase in replication stress and activation of DNA damage checkpoints. Embryos of the annual killifish Austrofundulus limnaeus show a strong tolerance to extended anoxic exposure, indicating an improved genomic stability under oxygen starvation. Here we investigate the cell cycle regulation of the anoxia tolerant killifish embryonic cell line PSU-AL-WS40NE during anoxic exposure. Live cell imaging confirms continued cell proliferation of WS40NE cells for the first 24 hours of anoxic exposure with minimal cell death. Fluorescent imaging shows that cells begin to accumulate in G1 after the first day in anoxia with a pronounced and rapid entry into the S phase upon reoxygenation. Pharmacological inhibition tests show that this response appears to be reliant more on ATR signaling then ATM, suggesting that increased {gamma}H2AX levels are driven by increased replication stress instead of DNA damage. This conclusion is further supported by an apparent lack of induction of a G2 checkpoint in these cells suggesting that DNA damage during anoxic replication is minimal. Maintaining cellular proliferation during initial exposure to anoxia and accumulating cells in the G1 phase for extended anoxic exposure is likely one way that embryos of the annual killifish are able to survive prolonged anoxia and provides insight into mechanisms that enable cells to proliferate under metabolic stress.
Parziale, J. V.; Attarde, S.; Khalid, F.; Sangana, P. D.; Holford, M.
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Coleoid cephalopods, squids, cuttlefish, and octopuses, have emerged as powerful model organisms for studying neurobiology, development, and behavior, however, cellular tools for investigating their specialized tissues remain limited. In particular, their venom producing gland, the posterior salivary gland (PSG), has been extensively described anatomically and histologically, yet remains largely inaccessible to experimental investigation at the cellular level. Here, we report the first establishment of primary cell cultures derived from both the optical lobe and PSG tissues of Octopus bimaculoides. Building on recent advances in cephalopod brain cultures, we adapted and optimized dissociation and culture conditions to support short-term survival and attachment of cells in vitro. We show that passive cell release during tissue handling, rather than enzymatic treatment, yields viable cultures from both tissues, and poly-D-lysine markedly improves the adherence of PSG-derived cells. Morphological analyses and fluorescent staining confirm the presence and viability of distinct cell populations, while cell cycle analysis indicates that the majority of cells reside in G0/G1 phase. Notably, O. bimaculoides brain cultures exhibit features comparable to those previously described in squid, suggesting conserved aspects of coleoid cellular physiology. Together, our findings establish a foundational in vitro platform for studying octopus PSG and neural cell biology, providing a tractable system for probing venom biosynthesis, secretion, and neural regulation in coleoid cephalopods.
Bennett Ness, C.; Rizzi, M.; Love, H.; Balkic, N.; Marshall, G.; von Kriegsheim, A.; Osterweil, E. K.; Abbott, C. M.
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Heterozygous de novo missense mutations in the EEF1A2 gene encoding translation elongation factor eEF1A2 result in neurodevelopmental disorders, typically characterised by early onset epilepsy and intellectual disability (ID). The E122K mutation is the most commonly reported missense mutation and is amongst the more severe in terms of epilepsy and ID. Here we made use of a recently developed mouse model which recapitulates the E122K mutation to examine how mutations in EEF1A2 might disrupt neuronal gene expression. Primary neurons from mutant mice and transfected HEK293T cells were used to examine effects on global protein synthesis. In contrast to previous reports, we were unable to detect a change in global protein synthesis using either of two different assay systems. TRAP-seq and mass spectrometry were then employed to study the effects of the mutation on the translatome and proteome respectively. These analyses revealed perturbation of expression of a subset of genes, with a slight skew towards downregulation, particularly for longer transcripts. Further analysis indicated a down regulation of proteins involved in synaptic function in both the translatomic and proteomic datasets.
Lopez, M. d. R.; Gitman, I. F. B.; Prego, A. F.; Lavignolle-Heguy, R.; Zambrano-Siri, R. T.; Carena, S.; Arguello, R. J.; Vilchez-Larrea, S. C.; Alonso, G. D.; Ocampo, J.
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In trypanosmatids genes, transcribed by RNA polymerase II do not have canonical promoters and are organized into directional gene clusters that mature into monocistronic transcripts by a co-transcriptional process known as trans-splicing. Even though gene expression is regulated mainly post-transcriptionally, it is currently understood that chromatin and epigenetics are also involved in this regulation. In eukaryotes, specific signals are normally required for the occurrence of an appropriate transcription initiation. Among them, trimethylation of histone H3 in lysine 4 is the most conserved signal normally detected at transcription start sites of actively transcribed genes. Unlike many model organisms, trypanosomes do not have defined promoters. Instead, transcription initiates in a bidirectional manner from dispersed regions coincident with divergent strand switch regions located between directional gene clusters (DGCs). In T. cruzi, H3K4me3 was observed at the origins of transcription coincident with divergent strand switch regions (dSSRs) in epimastigotes, but it has not been mapped throughout the whole genome at base-pair resolution or in other life stages so far. Here, we set up the CUT&RUN technique for T. cruzi epimastigotes and trypomastigotes. Consistent with a predominant post-transcriptional regulation along the life cycle, we did not find significant differences between life stages. We corroborated that H3K4me3 is enriched at dSSR adjacent to actively expressed DGCs. Moreover, we noticed that this histone mark exhibits different patterns that correlate with the genomic span of the transcription initiation regions and with transcriptional activity. Furthermore, we unveiled that the most actively transcribed DGCs are associated with shorter dSSRs and are located within the core compartment of the genome displaying a more accessible chromatin.
Grossjohann, A.; Richter, V.; Reinhardt, F.; Hahmann, M.; Badelt, R.; Kinnigkeit, J.; Breitfeld, J.; Kovacs, P.; Stadler, P. F.; Coin, I.; Thum, A. S.
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Octopamine is involved in a variety of different physiological and behavioral mecha-nisms in Drosophila melanogaster. Throughout the life cycle of the fruit fly, from the larva to the adult, octopaminergic neurons in both the central and the peripheral nerv-ous system target a multitude of neurons and even non-neuronal tissues, making it challenging to analyze individual mechanisms of octopamine function. One approach to deconstructing this complex system is to examine the postsynaptic components of signal transmission. In Drosophila, octopamine interacts with six distinct G-protein-coupled receptors. For some of these receptors, expression maps and functional im-plications have been described. In contrast, other receptors have been neglected, partly due to the lack of suitable genetic tools. Here, for the first time, we compiled a complete set of mutant lines of all known octopamine receptors, all generated using the same genetic tool, the recently established Trojan Exon system. It integrates the Gal4/UAS binary expression strategy while simultaneously impairing receptor func-tion. This enabled us to generate a comprehensive anatomical map of receptor ex-pression in the larva and, at the same time, analyze the function of individual octopa-mine receptors during larval development, chemosensory perception and locomotion. All octopamine receptors (Oamb, Oct2R, Oct{beta}1R, Oct{beta}2R, Oct{beta}3R, and Oct-TyrR) showed extensive signal in the central nervous system. The same was found for the peripheral nervous system, with the exception of Oct{beta}2R, which showed pronounced expression in the somatic muscles. We also observed a previously undescribed role of Oct{beta}1R, Oct{beta}3R, and Oct-TyrR in larval hatching and in the survival of larvae and pupae. Molecular evaluation of the Trojan Exon octopamine lines supports our analy-sis. In addition, we combined the experimental results with gene expression data from the different development stages of Drosophila melanogaster and from different tis-sues and cell populations throughout the body. Overall, we compiled, analyzed and validated a complete set of octopamine lines which, together with gene expression analysis, provides a basis for further functional studies on the larval octopaminergic system.
Nagula, I.; Kavalnyte, E.; Vitkute, K.; Dabkeviciene, D.; Neniskyte, U.; Alaburda, A.
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Early postnatal development is a critical period for hippocampal circuit maturation. While postnatal hippocampal development has been mostly studied in rats, less is known about the developmental trajectory of electrophysiological properties in mice, despite the wide use of these animal models for molecular and genetic studies of nervous system. In this study, we investigated the postnatal maturation of hippocampal CA1 pyramidal neurons in male and female wild-type mice. Whole-cell patch-clamp recordings were performed in acute hippocampal slices to assess passive and active membrane properties as well as spontaneous excitatory synaptic activity. We found that maturation of neuronal firing properties was associated with faster responses to stimulation, higher-amplitude and shorter-duration action potentials, and more precise control of neuronal firing. Simultaneously, synaptic activity changed across development, with decreased sEPSC inter-event intervals and stable event amplitudes, suggesting enhanced functional connectivity without major changes in synaptic strength. Sex-dependent differences in electrophysiological properties were observed primarily during the first postnatal week, indicating that sex influences the early trajectory of neuronal maturation. Together, our findings provide a comprehensive electrophysiological baseline for mouse hippocampal CA1 pyramidal neurons during postnatal development.
Guixeras-Fontana, A.; Gines, A.; Molina, M. D.; Cebria, F.
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BackgroundDuring embryonic development and regeneration, the growth of any organ must be tightly regulated in order to achieve their optimal final size and become fully functional. Freshwater planarians, with their remarkable plasticity and ability to regenerate any part of their body based upon the presence of adult pluripotent stem cells, provide an ideal model to study how the final organ size is regulated during this process. Also, the fact that planarians are constantly growing and degrowing depending on culture conditions, allows us to study how the size of the different organs is determined under homeostatic cell renewal. ResultsHere, we investigate the role of Smed-pctk-1, a cyclin dependent kinase that belongs to the PCTAIRE subfamily of CDKs, which remains largely understudied. Functional analyses show that Smed-pctk-1 silencing disrupts the normal size of the cephalic ganglia and results in an overgrowth of the eyes both in homeostatic and regenerating planarians. The increase in eye size correlates to an increase in the number of both progenitor and differentiated eye cell types. Phototaxis behavioral assays reveal that Smed-pctk-1 RNAi planarians exhibit a precocious sensitivity to light. ConclusionsOverall, our findings identify Smed-pctk-1 as a key regulator of eye and neural size in planarians, highlighting its contribution to the mechanisms that control organ growth during both regeneration and homeostasis.
Krolak, P.; Ribeiro, O.; Gehl-Vaisanen, B.; Hiltunen, M.; Goldman, A.; Vidilaseris, K.
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Acidocalcisomes are evolutionarily conserved acidic organelles that are rich in cations and inorganic phosphate, primarily polyphosphates. In kinetoplastid parasites, acidocalcisomes and their polyphosphate content are essential for osmoregulation and environmental adaptation during host switching. In this organelle, polyphosphate is synthesised and transported to the lumen by the vacuolar transporter chaperone (VTC) complex. Interestingly, unlike yeast VTC, which has five components, only two have been observed in kinetoplastids: Vtc1, which contains only a transmembrane domain and Vtc4, which, in addition to a transmembrane domain, also consists of SPX and catalytic domains. In this study, we used proximity-dependent biotinylation (BioID) in Leishmania tarentolae to identify proteins located close to the VTC complex. The complex was found near several known acidocalcisomal proteins, including membrane-bound pyrophosphatase (mPPase), vacuolar-type H-ATPase (V-H+-ATPase), Ca{superscript 2}-transporting P-type ATPase (Ca2+-ATPase), zinc transporter (ZnT), and palmitoyl acyltransferase 2 (PAT2). Importantly, this approach revealed three novel VTC binding partners (VBPs) that colocalise and interact with the complex in acidocalcisomes, as confirmed by confocal microscopy, pulldown assays, and AlphaFold3 structural predictions. Together, our results expand the acidocalcisome interactome and suggest that the newly identified VBPs may contribute to the structural organisation and regulatory function of the VTC complex in phosphate homeostasis of kinetoplastid parasites. Author summaryProtozoan parasites such as Leishmania and Trypanosoma cause serious diseases affecting millions of people worldwide. To better understand how these parasites survive environmental changes during transmission between hosts, we studied a specialised organelle called the acidocalcisome, which stores polyphosphates and helps regulate stress responses. In this work, we used the non-pathogenic Leishmania tarentolae as a safe and cost-effective model that shares key cellular features with disease-causing species. Using a combination of CRISPR-Cas9 genome editing, proximity-based labelling (BioID), confocal microscopy, pulldown assays and AlphaFold3 structure prediction, we investigated the vacuolar transporter chaperone (VTC) complex, which synthesises and transports polyphosphate into the acidocalcisome lumen. Proximity proteomics identified several known proteins located near the VTC complex, and importantly, led us to discover three novel proteins that interact with it. These findings open new directions for exploring the organisation and regulation of the VTC complex in protozoan parasites. By revealing novel protein interactions, our study contributes to a deeper understanding of parasite biology and may help identify therapeutic targets for treating neglected tropical diseases.
Pillon, A.; Nadi, A.; Martin, J.; Hanna, M. A.; Fidalgo da Silva, E.; Porter, L.
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How cells balance growth (cell size) and division (cell number) requires a complex interplay between response to external signals including growth factors, nutrient availability and metabolic cues, along with regulation of the cell cycle. The protein Tuberin (gene TSC2) is a critical regulator of these decisions. In a complex with the protein Hamartin, Tuberin functions as a negative regulator of the Target of Rapamycin (mTOR) pathway, preventing excessive growth under unfavorable conditions. However, how this growth pathway connects to decisions to progress through the G2 phase of the cell cycle and permit cell division is still unclear. In this study, we show that post-translational modification of Tuberin by the Extracellular Signal-Regulated Kinase (ERK) pathway abrogates binding between Tuberin and the mitotic cyclin, Cyclin B1. This causes an increase in mitotic cells, due to an unregulated G2/M transition, increasing the proliferation rate. Our work shows a novel role of Tuberin in cell cycle regulation by growth and mitogenic factors independent of mTOR regulation.
Syeda, A. H.; Leek, V. A.; Maxwell, A.; Leake, M. C.
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Molecular motors travelling along DNA introduce positive supercoils that present as barriers to replication leading to genome instability. To counter these, bacterial cells express DNA gyrase, a topoisomerase that introduces negative supercoils. While much is known about DNA gyrase from genetic and in vitro biochemical studies, the spatiotemporal dynamics of this enzyme remain a mystery. Only recently have we been able to observe the in vivo spatiotemporal dynamics down to single molecule level using advanced super-resolution microscopy techniques. We used Slimfield microscopy, a cutting-edge molecule microscopy technique to address the gap in our knowledge. We analysed a dual fluorescently labelled Escherichia coli strain expressing the replisome marker DnaN-mCherry along with mYPet-GyrB as the enzyme marker. We performed sequential Slimfield microscopy of the labelled proteins from the same strain and analysed in vivo GyrB dynamics in live E. coli cells in relation to the replisome. We find that the majority of replisomes are associated with GyrB. Inhibition of gyrase activity reduces the proportion of replisomes associated with GyrB. Interestingly, GyrB behaviour is distinct from that observed for GyrA in a previous study. Our results reveal the previously unknown dynamics of GyrB inside living bacterial cells highlighting the advantages of in vivo single molecule investigations. Our findings also demonstrate the importance of analysing all subunits of a functional enzyme complex to gain comprehensive understanding of its in vivo mechanisms. This study demonstrates the utility of single-molecule super-resolved microscopy as a valuable underpinning technology to understand in vivo behaviour of biomedically important molecules. Our insights will help impact discovery and development of novel antibiotics that interfere with gyrase function, thus contributing to tackling the growing problem of antimicrobial resistance.
Pang, Y.; Klussmann-Fricke, B.; Cedden, D.; Zhang, J.; Schinko, J. B.; Averof, M.; Riemensperger, T. D.; Bucher, G.
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The brain is one of the most complex animal organs but the development of the many different neuron types remains enigmatic. A set of brain-specific transcription factors is known to be involved in brain patterning but their specific contributions remain to be elucidated in most cases, including foxQ2II. This transcription factor is known to be conserved in anterior neuroectodermal patterning of most animals while it has been lost from vertebrates. However, the contribution of foxQ2II-positive neurons to the adult brain has remained enigmatic. Here, we use an enhancer trap, immunostainings and our newly established beetle brainbow system to categorize Tc-foxQ2II-positive neurons into nine clusters with different projection patterns. All clusters contain neurons with the fast activating neurotransmitters acetylcholine and glutamate while no Tc-foxQ2II positive neuron is GABA-ergic or serotonin-positive. Interestingly, we found that many dopaminergic neurons were Tc-foxQ2II positive and we homologize them with dopaminergic neurons of the PPL2c, PPM1 and PPL1 cluster described in the Drosophila brain. Our results show that Tc-foxQ2II marks subsets of fast-acting interneurons contributing to the higher order brain centers mushroom bodies and central complex. Taken together, our work expands the known functional range of foxQ2 genes from sensory and neurosecretory cell specification to interneurons involved in the function of higher order brain centers.
Haider, A.;Zieminska, A.;Dubra, G.;Gaalswyk, K.;Houston, L.;Phillips, M.;Guindon, S.;Llères, D.;Ghosh, K.;Fisher, D.;Krasinska, L.
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The Ki-67 protein is a widely used marker of mammalian cell proliferation that plays critical roles in heterochromatin organisation and mitotic perichromosomal layer formation. Thus, its apparent restriction to vertebrates is puzzling. However, sequences with limited homology to subdomains of Ki-67 are present in genomes from some non-vertebrate species. Here, using structural modelling, biophysical and functional analysis, we identify Ki-67-like proteins across diverse non-vertebrate eukaryotes, including tunicates, sponges, molluscs, insects and fungi. Despite extremely low sequence homology, the disordered domains of Ki-67 homologues have generally conserved biophysical and molecular properties. This is further reflected by comparison of cellular localisation, dynamics and effects on chromatin organisation of human, Ciona and Drosophila Ki-67 homologues. These results reinforce the emerging paradigm that functions may be encoded by general biophysical features in highly diverged intrinsically disordered domains. Our approach provides a blueprint for comparative biology of disordered proteins and a foundation for future studies exploring functions of Ki-67 homologues across eukaryotes.
van Tartwijk, F. W.; Marty, A.-P. M.; Rahmani, A.; Jia, Y.; Ward, E. N.; Hussain, I.; Peck, L. S.; Kaminski, C. F.; Clark, M. S.
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In the Antarctic Southern Ocean, cold-blooded animals have evolved to live at stable temperatures of 0{+/-}2 {degrees}C. This extremely low temperature affects their biology at every scale, from protein folding to development. However, how animal (sub)cellular organisation and dynamics are adapted to near-0 {degrees}C temperatures has not been studied. We therefore established methods to culture and fluorescently label cells from the Antarctic plunderfish Harpagifer antarcticus and a temperate comparator species, the shanny Lipophrys pholis. By imaging these cultures live at physiological temperatures, we found that subcellular organisation is broadly conserved in H. antarcticus, featuring known membranous organelles and biomolecular condensates that remain dynamic, with mitochondria in H. antarcticus and L. pholis moving at similar speeds. However, we also identified differences in organelle properties between H. antarcticus and L. pholis, including lysosomal enlargement and mitochondrial morphology changes. These differences may be functionally linked to protein misfolding and slow embryonic development in Antarctic species.
Johnson, T.; Miotla-Zarebska, J.; Midha, S.; Vincent, T. L.; Wann, A. K.; Jule, A. M.; Randall, G.; Apolinova, K.; Sansom, S. N.
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How cells and their organelles are positioned in three-dimensional, organ level, anatomical context, is rarely investigated. Here we focus on cells, centrioles and primary cilia in the growing limb. Through the ciliums mechanobiological role in skeletal development, we explored the mechanobiology of morphogenesis. A transgenic mouse model (Centrin 2-GFP.ARL13B-mCherry), combined with an image analysis pipeline, can map cellular size, positions and orientations, centriole position and ciliary axoneme orientation, all with respect to the anatomy of the epiphysis or growth plate. The line was crossed with an ift88fl/flCreERT2 line to enable ciliary ift88 deletion. We used limb immobilization, to test for a role of mechanical forces associated with ambulatory loading, in the organization of these elements and transcriptomics to understand the role of forces in regulating growth plate morphogenic programs. The pipeline can accurately quantify expected patterns of cell orientation and size through zones of the growth plate. Analysis across thousands of cells, through regions and zones of multiple murine growth plates, reveals cilia prevalence is increased in the periphery, highest in the resting zone in the outer limb, harboring stem cells. Cilia length is greatest in the hypertrophic cells about to die or transdifferentiate, as part of the formation of bone from cartilage by endochondral ossification. The inducible and cartilage-specific, deletion of ciliary gene ift88, alters cell orientation and sizes and reduces ciliation in the areas where endochondral ossification is most disrupted, the periphery and expanded hypertrophic zones, linking changes in structure to function. Most strikingly, centriole position, including that of the basal body, from which the ciliary axoneme is extended, is not preferentially organised. In contrast, cilia axoneme orientation is preferentially organised. Axonemes are directed posterior or anterior, 45 degrees to the axis of the limb, irrespective of their position, which is defined by basal body position. Immobilization of the limb for 2 weeks markedly alters the transcriptomic profile of the growth plate, with changes to size and orientation of cells and alterations in matrix and cytoskeletal profiles. Within altered genes, primary cilia genes themselves are regulated, including those indicative of altered cilia signaling such as hedgehog signaling. However, despite the role of cilia in mechanobiology of the growing limb, and ciliary signature within changes to loading of the limb, cilia orientation is unaltered by the removal of ambulatory associated forces. Patterns of ciliation in control and IFT88cKO mice help reconcile the previously observed anisotropic effects of cilia perturbation, focusing study on stem cell-resting chondrocytes and hypertrophy, when considering the mechanobiological role of cilia in limb development. Endochondral ossification is apparently highly sensitive to ambulatory loading at transcriptomic level, including effects on ciliary genes and signaling. A highly organized orientation of these putative antennae is governed by centriole position-independent mechanisms and is independent to changes to ambulatory loading, indicating a cell intrinsic mechanism. The resilient position of axonemes in the limb, points to mechano-regulatory mechanisms for how cilia integrate biophysical signals. We propose that predominant ventral or dorsal orientation at 45 degrees to horizonal plane but never parallel to cranial-chordal or medial-lateral axis, ensures multiple signal integration and avoids single signal blindness.
Simonicova, L.; Conway, T. P.; Brakhage, A. A.; Krueger, T.; Moye-Rowley, W. S.
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The biological conservation between fungi and mammals due to a common ancestor has made development of selective antifungal drugs a difficult challenge. Further complicating this situation is the selection of antifungal drug-resistant organisms during drug treatment. The pathogenic yeast Nakaseomyces glabratus (called here Candida glabrata) presents an especially challenging organism due to its tendency to frequently lose susceptibility to the major antifungal drug class the azoles. Additionally, C. glabrata develops resistance to echinocandin drugs, a second, more recently described antifungal agent at 10 times the rate of other organisms. Previous work has established that the sterol responsive transcriptional regulator Upc2A is a key determinant of azole susceptibility in C. glabrata and plays a role in echinocandin resistance. We used a biochemical approach to identify proteins that co-purified with Upc2A and identified the Ypk2 AGC kinase as an interacting protein. Strains lacking YPK2 exhibited increased susceptibility to fluconazole and the echinocandin caspofungin. A ypk2{Delta} strain failed to normally induce transcription of several ERG genes but exhibited normal induction of the CDR1 ATP-binding cassette transporter gene. Isogenic ypk2{Delta} strains were also highly susceptible to the three major classes of antifungal drugs, indicating that this kinase behaves as a multidrug susceptibility factor. RNA-seq analyses indicated that the transcriptional response to exposure is different for each drug and each response is differentially altered upon loss of Ypk2. Our data indicate that Ypk2 plays an important role in coordinating gene expression that impacts susceptibility to all major antifungal drug classes.
Geerlings, C.; Darmasaputra, G.; Jordan Ortiz, C.; Chuva de Sousa Lopes, S. M.; Clevers, H. M.; Galli, M.
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Polyploid cells, which contain more than two copies of the genome, are widely present across plants and animals, where they are often found in tissues with high biosynthetic and metabolic demands, such as the mammalian liver and placenta. While somatic polyploidy is frequently associated with increased cell growth and biosynthetic capacity, unscheduled polyploidization in cell types that are not normally programmed to become polyploid is often linked to reduced cellular fitness and genome instability. To understand whether these divergent outcomes stem from distinct immediate cellular responses to increased ploidy, we systematically compared the early consequences of polyploidization across naturally occurring and experimentally induced systems. Specifically, we examined physiological polyploid cells in the Caenorhabditis elegans intestine and human hepatocyte organoids, alongside unscheduled polyploid human retinal pigment epithelial (RPE1) cells generated through cytokinesis failure. Using quantitative imaging, flow cytometry, and FUCCI based cell-cycle reporters we measured cell size and protein translation dynamics during G1 in diploid and polyploid cells. Across all systems, we observed a strikingly conserved relationship between ploidy, cell size, and biosynthetic capacity: both cell size and protein translation showed similar scaling patterns after polyploidization, regardless of whether polyploidization occurred as part of normal development or by inducing cytokinesis failure. These findings indicate that the immediate cellular response to increased ploidy is broadly similar across contexts. However, in contrast to unscheduled polyploid RPE1 cells, polyploid human hepatocytes extend their G1 phase, leading to a higher accumulation of proteins before cell-cycle progression. Together, our findings suggest that polyploidization elicits similar growth responses across contexts, and that cell-type specific cell-cycle adaptations may determine whether polyploidy becomes advantageous or deleterious.
Zehra, M.; Sinha, D.; Sharma, A. K.; Gaddam, A.; Chacko, J. A.; Chen, Q.
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Although calmodulin is best known as an intracellular calcium sensor, it also possesses calcium-independent functions in unicellular organisms. This is exemplified by the budding yeast S. cerevisiae calmodulin, which binds its essential targets, the pericentrin-like protein Spc110 and type I and V myosins, without needing calcium. Whether such calcium-independent cellular functions are conserved in other yeasts and vertebrates nevertheless remains an open question. Here, we examined the calcium-independent functions of the fission yeast S. pombe calmodulin Cam1 by measuring its intracellular distribution. Using quantitative fluorescence microscopy, we assessed the intracellular localization of two cam1 mutants, where binding of Ca2+ had been compromised by mutations in their EF hands, compared to the wild type protein. Both Cam1-2V and -3V reduced their localization by 90% to the yeast microtubule-organizing center spindle pole bodies (SPB). In contrast, these two mutants did not affect the myosin-dependent localization to the equatorial division plane and to the cell tips. Replacing the endogenous cam1 with cam1-2V decreased the SPB localization of pericentrin Pcp1 by 69%, without changing the localization of either type V or I myosins. Over-expression of Pcp1 rescued the mitotic defects of cam1-2V cells at the restrictive temperature. Surprisingly, the cytokinesis of this cam1 mutant was largely normal. We concluded that fission yeast calmodulin Cam1 depends on Ca2+to be a component of SPBs, suggesting that calcium plays a critical role in the assembly of SPBs.
Kjaerner-Semb, E.; Fraser, T. W. K.; Vogelsang, P.; Skaftnesmo, K.; Ayllon, F.; Edvardsen, R. B.; Braathen, S.; Norberg, B.; Fjelldal, P. G.; Andersson, E.; Schulz, R. W.; Wargelius, A.
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The age at which Atlantic salmon reaches sexual maturity shows a strong hereditary component associated with the vgll3a locus. The role of Vgll3 in maturation has remained unknown in vertebrates until recently, when it has been linked to pleiotropic roles in killifish, both delaying male maturation and affecting lifespan by protecting against cancer. As Atlantic salmon has two vgll3 paralogs, where only vgll3a has been associated with sexual maturation, it may provide a suitable model for studying the maturation-specific function of vgll3, as the other paralog may buffer for pleiotropic roles of vgll3. To address this, we used CRISPR/Cas9 to generate fish highly mutated in the vgll3a gene. We monitored their maturation and crossed highly mutated crispants to generate two year-classes of complete loss-of-function. All groups were reared under environmental conditions triggering early maturation in one-year-old males. We found a clear difference in the proportion of sexually maturing or mature fish between the different genotypes: in all experiments significantly fewer vgll3a-/- males entered puberty and reached final maturation compared to vgll3a+/- and vgll3a+/+ males. Furthermore, loss of vgll3a resulted in lower frequencies of maturation also in females. We conclude that Vgll3a stimulates maturation and that its complete removal significantly reduced maturation rates in both sexes in Atlantic salmon. Our findings also identify vgll3a as the causative gene in the locus associated with age at sexual maturity. Together, our findings support a new role for Vgll3 in initiating puberty in vertebrates and identifying salmon as a promising model for functional studies regarding the timing of sexual maturation.
Hapugaswatta, H.; Parrales, A.; Park, H.; Kim, H.; Iwakuma, T.; Azuma, M.
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Ewing sarcoma is a pediatric cancer that develops in skeletal elements. The majority of Ewing sarcoma patients carry the aberrant EWSR1-FLI1 fusion gene. Despite trisomy 8 being an additional common aberration associated with a poor prognosis for patients, its induction mechanism remains unknown. When the EWSR1-FLI1 gene is formed, the cell loses one wildtype EWSR1 allele. To elucidate the induction mechanism of trisomy 8, we generated a cell line that allows for the conditional induction of EWSR1-FLI1 expression and EWSR1 knockdown (derived from a single EWSR1 allele. Specifically, the conditional cell line was generated by integrating the Tet-on EWSR1-FLI1 construct into the AAVS locus and adding a miniAID tag at the 5 end of the EWSR1 locus using auxin-degron system. A combination of the EWSR1-FLI1 expression and degradation of one allele-derived EWSR1 induced a high incidence of trisomy 8 within eight days, enhancing colony formation. Mechanistically, trisomy 8 is induced by the haploinsufficiency of EWSR1, and the remaining EWSR1 proteins are likely inhibited by interaction with EWSR1-FLI1. Our data showed that the knockout of EWSR1 alone was sufficient to increase the incidence of trisomy 8. Expression of wild-type EWSR1 in EWSR1 knockout cells rescued the high incidence of trisomy 8. In contrast, the EWSR1:R565A mutant, which lacks the ability to interact with Aurora B kinase, failed to rescue this phenotype. We propose that the combination of EWSR1-FLI1 expression and loss of EWSR1 contributes to the induction of trisomy 8 through the compromised EWSR1-Aurora B pathway. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/726567v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@999891org.highwire.dtl.DTLVardef@1ef6748org.highwire.dtl.DTLVardef@65e475org.highwire.dtl.DTLVardef@179da40_HPS_FORMAT_FIGEXP M_FIG C_FIG