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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 199 records · Page 11Linked to original sources

bioRxiv2017

Synergism between a simple sugar and a small intrinsically disordered protein mitigate the lethal stresses of severe water loss

Anhydrobiotes are rare microbes, plants and animals that tolerate severe water loss. Understanding the molecular basis for their desiccation tolerance may provide novel insights into stress biology and critical tools for engineering drought-tolerant crops. Using the anhydrobiote, budding yeast, we show that trehalose and Hsp12, a small intrinsically disordered protein (sIDP) of the hydrophilin family, synergize to mitigate completely the inviability caused by the lethal stresses of desiccation. We show that these two molecules help to stabilize the activity and prevent aggregation of model proteins both in vivo and in vitro. We also identify a novel role for Hsp12 as a membrane remodeler, a protective feature not shared by another yeast hydrophilin, suggesting that sIDPs have distinct biological functions.

cell biology↗

bioRxiv2017

A role for the Tgf-β/Bmp co-receptor Endoglin in the molecular oscillator that regulates the hair follicle cycle

The hair follicle is a biological oscillator that alternates growth, regression and rest phases driven by the sequential activation of the proliferation/differentiation programs of resident stem cell populations. The activation of hair follicle stem cell niches and subsequent entry into the growing phase is mainly regulated by Wnt/{beta}-catenin signalling, while regression and resting phases are mainly regulated by Tgf-{beta}/Bmp/Smad activity. A major question still unresolved is the nature of the molecular switch that dictates the coordinated transition between both signalling pathways. Here we have focused on the role of Endoglin (Eng), a key coreceptor for members of the Tgf-{beta}/Bmp family of growth factors.\n\nUsing an Eng haploinsufficient mouse model we report that Eng is required to maintain a correct follicle cycling pattern and for an adequate stimulation of hair follicle stem cell niches. We further report that {beta}-catenin binds to the Eng promoter depending on Bmp signalling. Moreover, we show that {beta}-catenin interacts with Smad4 in a Bmp/Eng dependent context and both proteins act synergistically to activate Eng promoter transcription. These observations point to the existence of a growth/rest switching mechanism in the hair follicle that is based on an Eng-dependent feedback crosstalk between Wnt/{beta}-catenin and Bmp/Smad signals.

cell biology↗

bioRxiv2017

Multimodal Sensorimotor System in Unicellular Zoospores of a Fungus

Complex sensory suites often underlie critical behaviors, including avoiding predators or locating prey, mates, and shelter. Multisensory systems that control motor behavior even appear in unicellular eukaryotes, such as Chlamydomonas, which are important laboratory models for sensory biology. However, we know of no unicellular opisthokont models that control motor behavior using a multimodal sensory suite. Therefore, existing single-celled models for multimodal sensorimotor integration are very distantly related to animals. Here, we describe a multisensory system that controls the motor function of unicellular, fungal zoospores. We find zoospores of Allomyces arbusculus exhibit both phototaxis and chemotaxis. While swimming, they move towards light and settle on cellulose membranes exuding combinations of amino acids. Furthermore, we report that closely related Allomyces species do not share this multisensory system. Instead, each possesses only one of the two modalities present in A. arbusculus. This diversity of sensory suites within Allomyces provides a rare example of a comparative framework that can be used to examine the evolution of sensory suites. The tractability of Allomyces and related fungi as laboratory organisms will allow detailed mechanistic investigations into how sensory systems may have functioned in early opisthokonts before multicellularity allowed for the evolution of specialized cell types.\n\nSummary StatementZoospores ability to detect light or chemical gradients varies within Allomyces. Here, we report a multimodal sensory system controlling behavior in a fungus, and previously unknown variation in zoospore sensory suites.

cell biology↗

bioRxiv2018

Identification of substrates for the conserved prolyl hydroxylase Ofd1 using quantitative proteomics in fission yeast

Prolyl hydroxylation functions in diverse cellular pathways, such as collagen biogenesis, oxygen sensing, and translation termination. Prolyl hydroxylation is catalyzed by 2-oxoglutarate (2-OG) oxygenases. The fission yeast 2-OG oxygenase Ofd1 dihydroxylates the 40S ribosomal protein Rps23 and regulates the hypoxic response by controlling activity and stability of the sterol regulatory element-binding protein Sre1. Multiple substrates have been found for 2-OG oxygenases, yet the only known substrate of Ofd1 and its homologs is Rps23. Here, we report the first fission yeast prolyl hydroxylome and demonstrate that hydroxylation is more prevalent than previously known. Using quantitative mass spectrometry, we identify Rpb10, a shared subunit in RNA polymerase I, II, and III, as a novel Ofd1 substrate. In addition, we discovered six Ofd1 binding partners and 16 additional Ofd1 candidate substrates. Although Ofd1 promotes Sre1 degradation, proteomic analysis revealed that Ofd1 does not broadly regulate protein degradation. Instead, the effect of Ofd1 on the proteome is through negative regulation of Sre1N. Finally, we show that the interaction between Ofd1 and the Sre1 bHLH region is conserved across Sre1 homologs suggesting that Ofd1-dependent regulation of SREBPs may be conserved in other fungi. Collectively, these studies provide a new dataset of post-translational modifications and expand the biological functions for a conserved prolyl hydroxylase.

cell biology↗

bioRxiv2018

Force-based three-dimensional model predicts mechanical drivers of cell sorting

Many biological processes, including tissue morphogenesis, are driven by mechanical sorting. However, the primary mechanical drivers of cell sorting remain controversial, in part because there remains a lack of appropriate threedimensional computational methods to probe the mechanical interactions that drive sorting. To address this important issue, we developed a three-dimensional, local force-based simulation method to enable such investigation into the sorting mechanisms of multicellular aggregates. Our method utilises the subcellular element method, in which cells are modeled as collections of locally-interacting force-bearing elements, accommodating cell growth and cell division. We define two different types of intracellular elements, assigning different attributes to boundary elements to model a cell cortex, which mediates the interfacial interaction between different cells. By tuning interfacial adhesion and tension in each cell cortex, we can control and predict the degree of sorting in cellular aggregates. The method is validated by comparing the interface areas of simulated cell doublets to experimental data and to previous theoretical work. We then define numerical measures of sorting and investigate the effects of mechanical parameters on the extent of sorting in multicellular aggregates. Using this method, we find that a minimum adhesion is required for differential interfacial tension to produce inside-out sorting of two cell types with different mechanical phenotypes. We predict the value of the minimum adhesion, which is in excellent agreement with observations in several developmental systems. We also predict the level of tension asymmetry needed for robust sorting. The generality and flexibility of the method make it applicable to tissue self-organization in a myriad of biological processes, such as tumorigenesis and embryogenesis.

biophysics↗

bioRxiv2017

Single-cell analysis of clonal dynamics in direct lineage reprogramming: a combinatorial indexing method for lineage tracing

Single-cell technologies are offering unprecedented insight into complex biology, revealing the behavior of rare cell populations that are typically masked in bulk population analyses. The application of these methodologies to cell fate reprogramming holds particular promise as the manipulation of cell identity is typically inefficient, generating heterogeneous cell populations. One current limitation of single-cell approaches is that lineage relationships are lost as a result of cell processing, restricting interpretations of the data collected. Here, we present a single-cell resolution lineage-tracing approach based on the combinatorial indexing of cells, CellTagging. Application of this method, in concert with high-throughput single-cell RNA-sequencing, reveals the transcriptional dynamics of direct reprogramming from fibroblasts to induced endoderm progenitors. These analyses demonstrate that while many cells initiate reprogramming, complete silencing of fibroblast identity and transition to a progenitor-like state represents a rare event. Clonal analyses uncover a remarkable degree of heterogeneity arising from individual cells. Overall, very few cells fully reprogram to generate expanded populations with a low degree of clonal diversity. Extended culture of these engineered cells reveals an instability of the reprogrammed state and reversion to a fibroblast-like phenotype. Together, these results demonstrate the utility of our lineage-tracing approach to reveal dynamics of lineage reprogramming, and will be of broad utility in many cell biological applications.

genomics↗

bioRxiv2017

Non-canonical circadian oscillations in Drosophila S2 cells drive gene-expression cycles coupled to metabolic oscillations

Circadian rhythms are cell-autonomous biological oscillations with a period of about 24 hours. Current models propose that transcriptional feedback loops are the principal mechanism for the generation of circadian oscillations. In these models, Drosophila S2 cells are generally regarded as non-rhythmic cells, as they do not express several canonical circadian components. Using an unbiased multi-omics approach, we made the surprising discovery that Drosophila S2 cells do in fact display widespread daily rhythms. Transcriptomics and proteomics analyses revealed that hundreds of genes and their products are rhythmically expressed in a 24-hour cycle. Metabolomics analyses extended these findings and illustrated that central carbon metabolism and amino acid metabolism are the main pathways regulated in a rhythmic fashion. We thus demonstrate that daily genome-wide oscillations, coupled to metabolic cycles, take place in eukaryotic cells without the contribution of known circadian regulators.

systems biology↗

bioRxiv2018

Interferometric scattering microscopy reveals microsecond nanoscopic protein motion on a live cell membrane

Much of the biological functions of a cell are dictated by the intricate motion of proteins within its membrane over a spatial range of nanometers to tens of micrometers and time intervals of microseconds to minutes. While this rich parameter space is not accessible to fluorescence microscopy, it can be within reach of interferometric scattering (iSCAT) particle tracking. Being sensitive even to single unlabeled proteins, however, iSCAT is easily accompanied by a large speckle-like background, which poses a substantial challenge for its application to cellular imaging. Here, we show that these difficulties can be overcome and demonstrate tracking of transmembrane epidermal growth factor receptors (EGFR) with nanometer precision in all three dimensions at up to microsecond speeds and tens of minutes duration. We provide unprecedented examples of nanoscale motion and confinement in ubiquitous processes such as diffusion in the plasma membrane, transport on filopodia, and endocytosis.

biophysics↗

bioRxiv2017

Ligand-regulated entry into the HRD ERAD pathway: The dark side of allostery

HMG-CoA reductase (HMGR) undergoes regulated degradation as part of feedback control of the sterol pathway. In yeast the stability of the Hmg2 isozyme of HMGR is controlled by the 20 carbon isoprenoid geranylgeranyl pyrophosphate (GGPP): increasing levels of GGPP causes more efficient degradation by the HRD pathway, allowing feedback regulation of HMGR. The HRD pathway is a conserved quality control pathway critical for the ER-associated degradation of misfolded ER proteins. We have explored the action of GGPP in HRD-dependent Hmg2 degradation. GGPP was highly potent as a regulatory molecule in vivo, and in vitro, GGPP altered Hmg2 folding at nanomolar concentrations. These effects of GGPP were absent in a variety of stabilized or non-regulated Hmg2 mutants. Consistent with its high potency, the effects of GGPP were highly specific; other closely related molecules were ineffective in altering Hmg2 structure. In fact, two close GGPP analogues, 2F-GGPP and GGSPP were completely inactive at all concentrations tested, and GGSPP was an antagonist of GGPPs effects in vivo and in vitro. The effects of GGPP on Hmg2 structure and degradation were reversed by chemical chaperones, indicating that GGPP caused selective Hmg2 misfolding. These data indicate that GGPP functions in a manner analogous to an allosteric ligand, causing Hmg2 misfolding through interaction with a reversible, specific binding site. Consistent with this, the Hmg2 protein forms mulitmers. We propose that this \"allosteric misfolding,\" or mallostery, may be a widely used tactic of biological regulation, with potential for development of small molecule pharmaceuticals that induce selective misfolding.

cell biology↗

bioRxiv2017

Regulation of mesenchymal stem cell function by TGFβ-1 on mast cell extracellular vesicles -- role of endosomal retention

Extracellular vesicles (EVs) convey biological messages between cells, either by surface-to-surface interaction, or by shuttling of bioactive molecules to a recipient cell cytoplasm. Here we show that EVs released by human primary mast cells or transformed human mast cells (HMC1), carry TGF{beta}-1 on their surface. EV-associated TGF{beta}-1 enhance the migratory activity of human mesenchymal stem cells (MSCs) compared to free TGF{beta}-1, as both knockdown of TGF{beta}, or a TGF{beta}-antibody, attenuate the effect. The MSCs respond by increasing matrix metalloproteinase-2 and -9 (MMP) activity. Further, EVs given to MSCs are retained in the endosomal compartments at a time of biological function, prolonging EV-associated TGF{beta}-1 signaling vs free TGF{beta}-1. When exposed to EVs, MSCs home more toward allergen-exposed lung in a mouse allergen model, resulting in attenuated allergic inflammation. Our results show that mast cell-EVs are decorated with TGFb-1, are retained in endosomes, which influences both MSC phenotype and function.

cell biology↗

bioRxiv2017

Genetic Single Neuron Anatomy reveals fine granularity of cortical interneuron subtypes

Parsing diverse nerve cells into biological types is necessary for understanding neural circuit organization. Morphology is an intuitive criterion for neuronal classification and a proxy of connectivity, but morphological diversity and variability often preclude resolving the granularity of discrete cell groups from population continuum. Combining genetic labeling with high-resolution, large volume light microscopy, we established a platform of genetic single neuron anatomy that resolves, registers and quantifies complete neuron morphologies in the mouse brain. We discovered that cortical axo-axonic cells (AACs), a cardinal GABAergic interneuron type that controls pyramidal neuron (PyN) spiking at axon initial segment, consist of multiple subtypes distinguished by laminar position, dendritic and axonal arborization patterns. Whereas the laminar arrangements of AAC dendrites reflect differential recruitment by input streams, the laminar distribution and local geometry of AAC axons enable differential innervation of PyN ensembles. Therefore, interneuron types likely consist of fine-grained subtypes with distinct input-output connectivity patterns.

neuroscience↗

bioRxiv2018

Autoamplification and competition drive symmetry breaking: Initiation of centriole duplication by the PLK4-STIL network

Symmetry breaking, a central principle of physics, has been hailed as the driver of self-organization in biological systems in general and biogenesis of cellular organelles in particular, but the molecular mechanisms of symmetry breaking only begin to become understood. Centrioles, the structural cores of centrosomes and cilia, must duplicate every cell cycle to ensure their faithful inheritance through cellular divisions. Work in model organisms identified conserved proteins required for centriole duplication and found that altering their abundance affects centriole number. However, the biophysical principles that ensure that, under physiological conditions, only a single procentriole is produced on each mother centriole remain enigmatic. Here we propose a mechanistic biophysical model for the initiation of procentriole formation in mammalian cells. We posit that interactions between the master regulatory kinase PLK4 and its activator-substrate STIL form the basis of the procentriole initiation network. The model faithfully recapitulates the experimentally observed transition from PLK4 uniformly distributed around the mother centriole, the \"ring\", to a unique PLK4 focus, the \"spot\", that triggers the assembly of a new procentriole. This symmetry breaking requires a dual positive feedback based on autocatalytic activation of PLK4 and enhanced centriolar anchoring of PLK4-STIL complexes by phosphorylated STIL. We find that, contrary to previous proposals, in situ degradation of active PLK4 is insufficient to break symmetry. Instead, the model predicts that competition between transient PLK4 activity maxima for PLK4-STIL complexes explains both the instability of the PLK4 ring and formation of the unique PLK4 spot. In the model, strong competition at physiologically normal parameters robustly produces a single procentriole, while increasing overexpression of PLK4 and STIL weakens the competition and causes progressive addition of procentrioles in agreement with experimental observations.

cell biology↗

bioRxiv2017

Inter-homologue repair in fertilized human eggs?

Many human diseases have an underlying genetic component. The development and application of methods to prevent the inheritance of damaging mutations through the human germline could have significant health benefits, and currently include preimplantation genetic diagnosis and carrier screening. Ma et al. take this a step further by attempting to remove a disease mutation from the human germline through gene editing1. They assert the following advances: (i) the correction of a pathogenic gene mutation responsible for hypertrophic cardiomyopathy in human embryos using CRISPR-Cas9 and (ii) the avoidance of mosaicism in edited embryos. In the case of correction, the authors conclude that repair using the homologous chromosome was as or more frequent than mutagenic nonhomologous end-joining (NHEJ). Their conclusion is significant, if validated, because such a \"self-repair\" mechanism would allow gene correction without the introduction of a repair template. While the authors analyses relied on the failure to detect mutant alleles, here we suggest approaches to provide direct evidence for inter-homologue recombination and discuss other events consistent with the data. We also review the biological constraints on inter-homologue recombination in the early embryo.

cell biology↗

bioRxiv2018

A High Avidity Biosensor Reveals PI(3,4)P2 is Predominantly a Class I PI3K Signaling Product

Class I PI 3-kinase (PI3K) signaling is central to animal growth and metabolism, and disruption of this pathway occurs frequently in cancer and diabetes. However, the specific spatial/temporal dynamics and signaling roles of its minor lipid messenger, phosphatidylinositol (3,4)-bisphosphate [PI(3,4)P2], are not well understood. This owes principally to a lack of tools to study this scarce lipid. Here, we developed a high sensitivity genetically encoded biosensor for PI(3,4)P2, demonstrating high selectivity and specificity of the sensor for the lipid. We show that despite clear evidence for class II PI3K in PI(3,4)P2-driven function, the overwhelming majority of the lipid accumulates through degradation of class I PI3K-produced PIP3. However, we show that PI(3,4)P2 is also subject to hydrolysis by the tumor suppressor lipid phosphatase PTEN. Collectively, our results show that PI(3,4)P2 is potentially an important driver of class I PI3K-driven signaling, and provides powerful new tools to begin to resolve the biological functions of this lipid downstream of class I and II PI3K.

cell biology↗

bioRxiv2017

Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins

Many intracellular membraneless bodies appear to form via reversible phase transitions of multivalent proteins. Two relevant types of phase transitions are sol-gel transitions (gelation) and phase separation plus gelation. Gelation refers to the formation of a system spanning molecular network. This can either be enabled by phase separation or it can occur independently. Despite relevance for the formation and selectivity of compositionally distinct protein and RNA assemblies, the determinants of gelation as opposed to phase separation plus gelation remain unclear. Here, we focus on linear multivalent proteins that consist of interaction domains that are connected by disordered linkers. Using results from computer simulations and theoretical analysis we show that the lengths and sequence-specific features of disordered linkers determine the coupling between phase separation and gelation. Thus, the precise nature of phase transitions for linear multivalent proteins should be biologically tunable through genetic encoding of or post-translational modifications to linker sequences.

cell biology↗

bioRxiv2017

Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories

Computational systems biology methods enable rational design of cell factories on a genomescale and thus accelerate the engineering of cells for the production of valuable chemicals and proteins. Unfortunately, for the majority of these methods implementations are either not published, rely on proprietary software, or do not provide documented interfaces, which has precluded their mainstream adoption in the field. In this work we present cameo, a platform-independent software that enables in silico design of cell factories and targets both experienced modelers as well as users new to the field. It is written in Python and implements state-of-the-art methods for enumerating and prioritizing knock-out, knock-in, over-expression, and down-regulation strategies and combinations thereof. Cameo is an open source software project and is freely available under the Apache License 2.0. A dedicated website including documentation, examples, and installation instructions can be found at http://cameo.bio. Users can also give cameo a try at http://try.cameo.bio.

bioengineering↗

bioRxiv2017

Correlative three-dimensional fluorescence and refractive index tomography: bridging the gap between molecular specificity and quantitative bioimaging

Optical diffraction tomography (ODT) provides label-free three-dimensional (3D) refractive index (RI) measurement of biological samples. However, due to the nature of the RI values of biological specimens, ODT has limited access to molecular specific information. Here, we present an optical setup combining ODT with three-channel 3D fluorescence microscopy, to enhance the molecular specificity of the 3D RI measurement. The 3D RI distribution and 3D deconvoluted fluorescence images of HeLa cells and NIH-3T3 cells are measured, and the cross-correlative analysis between RI and fluorescence of live cells are presented.

cell biology↗

bioRxiv2018

Software tools for automated transmission electron microscopy

In the recent years, electron microscopy in the life sciences has witnessed increasing demand for high-throughput data collection in both structural and cellular biology. We present a combination of software tools that enable automated acquisition guided by image analysis for a wide variety of Transmission Electron Microscopy applications. Using these tools, we demonstrate dose-reduction in single particle cryo-EM experiments, fully automated acquisition of every single cell in a plastic section and automated targeting of features on serial sections for 3D volume imaging even across multiple grids.

cell biology↗