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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2018

Rac1 Activated by DOCK1 in Combination with Rab31 Promotes the Development of Diabetic Retinopathy

BackgroundDiabetic retinopathy (DR) is one of the most common and severe microvascular complications of diabetes. Its a fundus lesion with specific changes, and its specific molecular mechanism is still unclear.\n\nMethodsAll target proteins and markers expression in the study was verified by qPCR and western bloting. The morphology and behavior of human retinal epithelial cells ARPE-19 were analyzed using immunofluorescent and apoptosis detection assays, respectively. And, Small GTPase activity was detected by the GST-pull assay.\n\nResultsWe found that DOCK1 showed high expression in high glucose-induced DR. Moreover, its high expression is positively correlated with Rab31 in tissues. DOCK1 promotes the activation of Rac1 and promotes apoptosis of retinal epithelial cells. Rab31 promotes the degradation of TJ proteins by promoting the transport of TJ proteins from the plasma membrane to the endosomes, thereby affecting the tight junctions of epithelial cells. Inhibition of Rac1 activity can effectively reduce cell apoptosis. Similarly, inhibition of Rab31 activity can significantly inhibit the degradation of TJ proteins.\n\nConclusionThis study based on the high glucose-induced DR cell model reveals the role of two mutually synergistic signaling pathways through the important cytological phenomena of apoptosis and damage of tight junctions. One is the degradation of TJ proteins caused by Rab31-mediated vesicle trafficking, and the other is the apoptosis of retinal epithelial cells mediated by DOCK1-Rac1.

cell biology↗

bioRxiv2018

The NuA4 acetyltransferase and non-canonical chromatin-associated MRN/ATM activity temporally define senescence-associated secretory programs

Senescent cells display senescence-associated (SA) phenotypic programs such as proliferation arrest (SAPA) and secretory phenotype (SASP), which mediate their impact on tissue homeostasis. Curiously, senescence-inducing persistent DNA double-strand breaks (pDSBs) cause an immediate DNA damage response (DDR) and SAPA, but SASP requires days to develop, suggesting it requires additional molecular events. Here, we show that pDSBs provoke delayed recruitment of MRN/ATM and KAT5/TRRAP (NuA4/Tip60) complexes to global chromatin. This coincided with activating histone marks on up-regulated SASP genes, whereas depletion of these complexes compromised the SASP. Conversely, histone deacetylase inhibition triggered accelerated MRN/ATM/Tip60-dependent SASP without pDSBs, interlacing acetylation and non-canonical DNA damage-independent, low-level DDR activity in SASP maturation. DDR/acetylation regulation of SA programs is preserved in human cancer cells, suggesting novel targets for modifying treatment-induced SA phenotypes. We propose that delayed chromatin recruitment of acetyltransferases cooperates with non-canonical DDR signaling to ensure SASP activation only in the context of senescence, and not in response to a transient DNA damage-induced proliferation arrest.\n\nHIGHLIGHTS (4 MAX, 85 CHARACTERS EACH)-Tip60 complex cooperate with non-canonical DDR activity to trigger paracrine signals\n\n-Low-level chromatin-associated ATM activity is required for the SASP\n\n-The intensity and temporal dynamics of the SASP can be manipulated\n\neTOC blurb (40 words)A temporal ballet between DNA damage response ATM/MRN and NuA4/Tip60 complexes control senescence-associated paracrine signals that are important during aging and cancer therapy, suggesting that DNA damage responses, acetylation, and chromatin remodeling can be exploited to manipulate senescence and benefit health.

cell biology↗

bioRxiv2018

Membrane insertion function for SUN-KASH complex revealed by high resolution analysis of yeast centrosomes

Bipolar spindle formation in yeast requires insertion of centrosomes (known as spindle pole bodies (SPBs)) into fenestrated regions of the nuclear envelope (NE). Using structured-illumination microscopy and bimolecular fluorescence complementation, we map protein distribution at SPB fenestra and interrogate protein-protein interactions with high spatial resolution. We find that the Sad1-UNC-84 (SUN) protein Mps3 forms a ring-like structure around the SPB, similar to toroids seen for components of the SPB insertion network (SPIN). Mps3 and the SPIN component Mps2 (a Klarsicht-ANC-1-Syne-1 domain (KASH)-like protein) form a novel non-canonical linker of nucleoskeleton and cytoskeleton (LINC) complex that is connected in both luminal and extraluminal domains. This hairpin-like LINC complex forms during SPB insertion, suggesting it functions in NE reorganization at the pore membrane. The LINC complex also controls the distribution of a soluble SPIN component Bbp1. Taken together our work shows that Mps3 is a fifth SPIN component and suggests both direct and indirect roles for the LINC complex in NE remodeling.

cell biology↗

bioRxiv2018

Parental Allele-Specific Protein Synthesis Dynamics in Single Cells In Vivo

Allelic expression from each parent-of-origin is important as a backup and to ensure that enough protein products of a gene are produced. Thus far, it is not known how each cell throughout a tissue differs in parental allele expression at the level of protein synthesis. Here, we measure the expression of the Ribosomal protein L13a (Rpl13a) from both parental alleles simultaneously in single cells in the living animal. We use genome-edited Drosophila that have a quantitative reporter of protein synthesis inserted into the endogenous Rpl13a locus. We find that individual cells can have large (>10-fold) differences in protein expression between the two parental alleles. Cells can produce protein from only one allele oftentimes, and time-lapse imaging of protein production from each parental allele in each cell showed that the imbalance in expression from one parental allele over the other can invert over time. One sentence summaryParental allele-specific protein expression varies widely across cells and over time. HighlightsO_LIWe used genome editing to insert a quantifiable protein translation reporter into the endogenous Ribosomal protein L13a gene and thus track the protein expression of both parental alleles simultaneously in every single cell in the awake animal. C_LIO_LICells can have a large difference in protein expression for one parental allele over the other, and this can invert over time, and can occur in clusters of cells within a tissue. C_LIO_LIWe demonstrate the highly variable nature of heterozygous and homozygous definitions across single cells, and over time. C_LIO_LIOur study demonstrates a new paradigm that can be used to examine inherited epigenetic control of expression from a specific parent-of-origin allele across single clonal cells from a common progenitor in vivo. C_LI

cell biology↗

bioRxiv2018

A lysosomal dimmer switch regulates cellular quiescence depth

Numerous physiological and pathological phenomena are associated with the quiescent state of a cell. Cellular quiescence is a heterogeneous resting state; cells in deep than shallow quiescence require stronger growth stimulation to exit quiescence and reenter the cell cycle. Despite the importance of quiescent cells such as stem and progenitor cells to tissue homeostasis and repair, cellular mechanisms controlling the depth of cellular quiescence are poorly understood. Here we began by analyzing transcriptome changes as rat embryonic fibroblasts moved progressively deeper into quiescence under increasingly longer periods of serum starvation. We found that lysosomal gene expression was significantly upregulated in deep than shallow quiescence, which compensated for gradually reduced autophagy flux observed during quiescence deepening. Consistently, we show that inhibiting lysosomal function drove cells deeper into quiescence and eventually into a senescence-like irreversibly arrested state. By contrast, increasing lysosomal function progressively pushed cells into shallower quiescence. That is, lysosomal function modulates quiescence depth continuously like a dimmer switch. Mechanistically, we show that lysosomal function prevents quiescence deepening by reducing oxidative stress in the cell. Lastly, we show that a gene expression signature developed by comparing deep and shallow quiescent cells can correctly classify senescent and aging cells in a wide array of cell lines in vitro and tissues in vivo, suggesting that quiescence deepening, senescence, and aging may share common regulatory mechanisms.

cell biology↗

bioRxiv2018

Fascetto Interacting Protein (FIP) Regulates Fascetto (PRC1) to Ensure Proper Cytokinesis and Ploidy

Cell division is critical for development, organ growth, and tissue repair. The later stages of cell division include the formation of the microtubule (MT)-rich central spindle in anaphase, which is required to properly define the cell equator, guide the assembly of the acto-myosin contractile ring, and ultimately ensure complete separation and isolation of the two daughter cells via abscission. Much is known about the molecular machinery that forms the central spindle, including proteins needed to generate the antiparallel overlapping interzonal MTs. One critical protein that has garnered great attention is Protein Regulator of Cytokinesis 1 (PRC1), or Fascetto (Feo) in Drosophila, which forms a homodimer to crosslink interzonal MTs, ensuring proper central spindle formation and cytokinesis. Here, we report on a new direct protein interactor and regulator of Feo we named Fascetto Interacting Protein (FIP). Loss of FIP results in a significant reduction in Feo localization, rapid disassembly of interzonal MTs, and several cytokinesis defects. Simultaneous reduction in Feo and FIP results in tumor-like, DNA-filled masses in the brain. In aggregate our data show that FIP functions upstream of, and acts directly on, Feo to ensure fully accurate cell division.

cell biology↗

bioRxiv2018

Stem cell receptor degradation by niche cells restricts signaling

Stem-cell niche signaling is short-range in nature, such that only stem cells but not their differentiating progeny experience self-renewing signals. At the apical tip of the Drosophila testes, 8 to 10 germline stem cells (GSCs) surround the hub, a cluster of somatic cells that function as the major component of the stem cell niche. We have shown that GSCs form microtubule-based nanotubes (MT-nanotubes), which project into the hub cells, serving as the platform for niche signal reception: the receptor Tkv expressed by GSCs localizes to the surface of MT-nanotubes, where it receives the hub-derived ligand Decapentaplegic (Dpp), ensuring the reception of the ligand specifically by stem cells but not by differentiating cells. Here we show that receptor (Tkv)-ligand (Dpp) interaction at the surface of MT-nanotubes serves a second purpose of dampening the niche signaling: we found that the receptor Tkv and the ligand Dpp are internalized into hub cells and are degraded in the hub cell lysosomes. Perturbation of hub lysosomal function or MT-nanotube formation leads to excess receptor retention within germ cells as well as excess Dpp that diffuses out of the hub, leading to ectopic activation of niche signal in differentiating germ cells. Our results demonstrate that MT-nanotubes plays dual roles in ensuring the short-range nature of the niche signaling by 1) providing exclusive interphase of the niche ligand-receptor interaction and 2) limiting the amount of available ligand-receptor via their degradation.

cell biology↗

bioRxiv2018

Cex1 is a new component of the COPI Golgi-to-vacuole intracellular trafficking machinery

During translational elongation, aminoacylated tRNA are supplied to the ribosome by RNA-interacting proteins. Cex1, a HEAT-containing protein, has been shown to participate to this tRNA channeling by interacting with aminoacylated tRNA during their export from the nucleus. Here, we show that Cex1 is a component of COPI (coatomer complex I) coated vesicles involved in the Golgi-to-vacuole trafficking pathway in Saccharomyces cerevisiae. Cex1 interacts with key components of the COPI coat Sec27, Sec28 and Sec33 proteins. Moreover, fluorescent microscopy indicates that Cex1 is not localized at the nuclear periphery as expected for an effector of nuclear tRNA channeling, but is observed on endosomal trans-Golgi network (TGN) positive structures. This localization relies on the vacuolar protein sorting receptor Vps10. Our data not only resolve the functional ambiguity regarding Cex1 homologues across species, but also point to the possibility to develop yeast-based models to study neurodegenerative disorders linked to the Human Cex1 homologue SCYL1.

cell biology↗

bioRxiv2018

Transient intracellular acidification regulates the core transcriptional heat shock response

Heat shock induces a conserved transcriptional program regulated by heat shock factor 1 (Hsf1) in eukaryotic cells. Activation of this heat-shock response is triggered by heat-induced misfolding of newly synthesized polypeptides, and so has been thought to depend on ongoing protein synthesis. Here, using the the budding yeast Saccharomyces cerevisiae, we report the discovery that Hsf1 can be robustly activated when protein synthesis is inhibited, so long as cells undergo cytosolic acidification. Heat shock has long been known to cause transient intracellular acidification which, for reasons which have remained unclear, is associated with increased stress resistance in eukaryotes. We demonstrate that acidification is required for heat shock response induction in translationally inhibited cells, and specifically affects Hsf1 activation. Physiological heat-triggered acidification also increases population fitness and promotes cell cycle reentry following heat shock. Our results uncover a previously unknown adaptive dimension of the well-studied eukaryotic heat shock response.

cell biology↗

bioRxiv2018

The anaphase-promoting complex regulates the degradation of the inner nuclear membrane protein Mps3 in budding yeast

The nucleus is enclosed by the inner nuclear membrane (INM) and the outer nuclear membrane (ONM). While the ONM is continuous with the endoplasmic reticulum (ER), the INM is independent and separates the nucleoplasm from the ER lumen. To maintain INM homeostasis, proteins mislocalized to the INM are degraded by the ER-associated protein degradation (ERAD) pathway. However, the mechanism for turnover of resident INM proteins is less clear. Here we show that the anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase, regulates the degradation of Mps3, a conserved integral protein of the INM. Turnover of Mps3 requires the ubiquitin-conjugating enzymes Ubc7 and Ubc6, but not the three known ERAD ubiquitin ligases, Doa10, Hrd1, and the Asi1-Asi3 complex. Using a genetic approach, we have found that Cdh1, a coactivator of APC/C, modulates Mps3 stability. APC/C controls Mps3 degradation through Mps3s N-terminus, which resides in the nucleoplasm and possesses two putative APC/C-dependent destruction motifs. Accumulation of Mps3 at the INM impairs nuclear morphological changes and cell division. Our findings therefore reveal an unexpected mechanism of APC/C-mediated protein quality control at the INM that coordinates nuclear morphogenesis and cell-cycle progression.

cell biology↗

bioRxiv2018

TDP-43 is more toxic in respiring than in non-respiring cells, but respiration is not absolutely required for TDP-43 toxicity.

The trans-activating response DNA-binding protein 43 (TDP-43) is a transcriptional repressor and splicing factor. TDP-43 is normally mostly in the nucleus, although it shuttles to the cytoplasm. Mutations in TDP-43 are one cause of familial amyotrophic lateral sclerosis (ALS). In neurons of these patients, TDP-43 forms cytoplasmic aggregates. In addition, wild-type TDP-43 is also frequently found in neuronal cytoplasmic aggregates in patients with neurodegenerative diseases not caused by TDP-43 mutations. TDP-43 expressed in yeast causes toxicity and forms cytoplasmic aggregates. This disease model has been validated because genetic modifiers of TDP-43 toxicity in yeast have led to the discovery that conserved genes in humans are ALS genetic risk factors. While it is still unknown how TDP-43 is associated with toxicity, several studies find that TDP-43 alters mitochondrial function. We now report that TDP-43 is much more toxic when yeast is grown in non-fermentable media requiring respiration than when grown on fermentable carbon sources. However, we also establish that TDP-43 remains toxic in the absence of respiration. Thus, there is a TDP-43 toxicity target in yeast distinct from respiration and respiration is not required for this toxicity. Since we find that H2O2 increases the toxicity of TDP-43, the free oxygen radicals associated with respiration could likewise enhance the toxicity of TDP-43. In this case, the TDP-43 toxicity targets in the presence or absence of respiration could be identical, with the free radical oxygen species produced by respiration activating TDP-43 to become more toxic or making TDP-43 targets more vulnerable.\n\nHighlightsO_LITDP-43 toxicity and aggregation is enhanced when yeast are grown in media that requires respiration.\nC_LIO_LIRespiration is not the sole target of TDP-43 toxicity because TDP-43 still aggregates and is toxic in cells that are not respiring.\nC_LIO_LIHydrogen peroxide enhances TDP-43 toxicity in the absence of respiration suggesting that reactive oxygen species (ROS) produced by respiration may likewise enhance TDP-43 toxicity.\nC_LIO_LIROS could activate TDP-43 to become more toxic or make TDP-43 targets more vulnerable.\nC_LI\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC=\"FIGDIR/small/415893_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@85d24aorg.highwire.dtl.DTLVardef@1b103d3org.highwire.dtl.DTLVardef@72280dorg.highwire.dtl.DTLVardef@a3a82e_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2018

Tension on kinetochore substrates is insufficient to prevent Aurora-triggered detachment

Chromosome segregation requires kinetochores to attach to microtubules from opposite spindle poles. Proper attachments come under tension and are stabilized, but defective attachments lacking tension are released, giving another chance for correct attachments to form. This error correction process requires the Aurora B kinase, which phosphorylates kinetochores to destabilize microtubule attachments. However, the mechanism by which Aurora B can distinguish kinetochore tension remains unclear because it is difficult to detect kinase-triggered detachment and manipulate kinetochore tension in vivo. To address these challenges, we developed an optical trapping-based flow assay with soluble Aurora B and reconstituted kinetochore-microtubule attachments. Strikingly, we found that tension on these attachments suppressed their Aurora B-triggered release, suggesting that tension-dependent changes in the conformation of kinetochores can regulate Aurora B activity or its outcome. Our work uncovers the basis for a key mechano-regulatory event that ensures accurate segregation and may inform studies of other mechanically regulated enzymes.

cell biology↗

bioRxiv2018

Subcellular localization of microcystin in the liver and the gonad of medaka fish acutely exposed to microcystin-LR

Among the diverse toxic components produced by cyanobacteria, microcystins (MCs) are one of the most toxic and notorious cyanotoxin groups. Besides their potent hepatotoxicity, MCs have been revealed to induce potential reproductive toxicity in various animal studies. However, little is still known regarding the distribution of MCs in the reproductive organ, which could directly affect reproductive cells. In order to respond to this question, an acute study was conducted in adult medaka fish (model animal) gavaged with 10 {micro}g.g-1 body weight of pure MC-LR. The histological and immunohistochemical examinations reveal an intense distribution of MC-LR within hepatocytes along with a severe liver lesion in the toxin-treated female and male fish. Besides being accumulated in the hepatocytes, MC-LR was also found in the connective tissue of the ovary and the testis, as well as in oocytes and degenerative spermatocyte-like structures. Both liver and gonad play important roles in the reproductive process of oviparous vertebrates. This observation constitutes the first observation of the presence of MC-LR in the reproductive cell of a vertebrate model with in vivo study. Our results, which provide intracellular localization of MC-LR in the gonad, advance our understanding of the potential reproductive toxicity of MC-LR in fish.

cell biology↗

bioRxiv2018

Drug-induced increase in lysobisphosphatidic acid reduces the cholesterol overload in Niemann-Pick type C cells and mice

Most cells acquire cholesterol by endocytosis of circulating LDLs. After cholesteryl ester de-esterification in endosomes, free cholesterol is redistributed to intracellular membranes via unclear mechanisms. Our previous work suggested that the unconventional phospholipid lysobisphosphatidic acid (LBPA) may play a role in modulating the cholesterol flux through endosomes. In this study, we used the Prestwick library of FDA-approved compounds in a high content, image-based screen of the endosomal lipids, lysobisphosphatidic acid and LDL-derived cholesterol. We report that thioperamide maleate, an inverse agonist of the histamine H3 receptor HRH3, increases highly selectively the levels of lysobisphosphatidic acid, without affecting any endosomal protein or function that we tested. Our data also show that thioperamide significantly reduces the endosome cholesterol overload in fibroblasts from patients with the cholesterol storage disorder Niemann-Pick type C (NPC), as well as in liver of Npc1-/- mice. We conclude that LBPA controls endosomal cholesterol mobilization and export to cellular destinations, perhaps by fluidifying or buffering cholesterol in endosomal membranes, and that thioperamide has repurposing potential for the treatment of NPC.

cell biology↗

bioRxiv2018

Molecular organization of integrin-based adhesion complexes in mouse Embryonic Stem Cells

The mechanical microenvironment serves as an important factor influencing stem cell differentiation. Mechanobiological responses depend strongly on actomyosin contractility and integrin-based cell-extracellular matrix (ECM) interactions mediated by adhesive structures such as focal adhesions (FAs). While the roles of FAs in mechanobiology have been intensively studied in many mesenchymal and migratory cell types, recently it has been recognized that certain pluripotent stem cells (PSCs) exhibited significantly attenuated FA-mediated mechanobiological responses. FAs in such PSCs are sparsely distributed and much less prominent in comparison to \"classical\" FAs of typical adherent cells. Despite these differences, insights into how FAs in PSCs are structurally organized to perform their functions are still elusive. Using mouse embryonic stem cells (mESCs) to study PSC-ECM interactions, here we surveyed the molecular composition and nanostructural organization of FAs. We found that despite being small in size, mESC FAs appeared to be compositionally mature, containing markers such as vinculin, zyxin, and -actinin, and dependent on myosin II contractility. Using super-resolution microscopy, we revealed that mESC FAs were organized into a conserved multilayer nanoscale architecture. However, the nanodomain organization was compressed in mESCs, with the force transduction layer spanning [~] 10 nm, significantly more compact than in FAs of other cell types. Furthermore, we found that the position and orientation of vinculin, a key mechanotransduction protein, were modulated in an ECM-dependent manner. Our analysis also revealed that while most core FA genes were expressed, the expression of LIM domain proteins was comparatively lower in PSCs. Altogether our results suggest that while core structural and mechanosensitive elements are operational in mESC FAs, their structural organization and regulatory aspects may diverge significantly from \"classical\" FAs, which may account for the attenuated mechanobiological responses of these cell types.

cell biology↗

bioRxiv2018

Improved immunofluorescence staining protocol for STED nanoscopy of Plasmodium-infected red blood cells

Immunofluorescence staining is the key technique for visualizing organization of endogenous cellular structures in single cells. Labeling and imaging of blood stage Plasmodium falciparum has always been challenging since it is a small intracellular parasite. The gold standard for parasite immunofluorescence is fixation in suspension with addition of minute amounts of glutaraldehyde to the paraformaldehyde-based solution. While this maintains red blood cell integrity, it has been postulated that antigenicity of the parasite proteins was, if at all, only slightly reduced. Here we show the deleterious effect that even these small quantities of glutaraldehyde can have on immunofluorescence staining quality and present an alternative cell seeding protocol that allows fixation with only paraformaldehyde. The highly improved signal intensity and staining efficiency enabled us to carry out RescueSTED nanoscopy on microtubules and nuclear pores and describe their organization in greater detail throughout the blood stage cycle.\n\nHighlights- Omitting glutaraldehyde from fixative improves immunofluorescence staining\n\n- STED nanoscopy is readily applicable to infected red blood cells\n\n- Intranuclear microtubules are nucleated from distinct sites

cell biology↗

bioRxiv2018

Membrane capacitance recordings resolve dynamics and complexity of receptor-mediated endocytosis in Wnt signalling

Receptor-mediated endocytosis is an essential process in signaling pathways for an activation of intracellular signaling cascades. One example is the Wnt signaling pathway, which seems to depend on endocytosis of the ligand-receptor complex for initiation of Wnt signal transduction. So far, the role of different endocytic pathways in Wnt signaling, the molecular players and the kinetics of this process are unclear. Here, we monitor endocytosis in Wnt3a and Wnt5a mediated signaling by membrane capacitance recordings of HEK293 cells. Our measurements revealed a fast and substantial increase in the number of endocytic vesicles. This endocytotic activity is specifically elicited by extracellular Wnt ligands; it starts immediately upon ligand binding and ceases over a period of ten minutes. By using specific inhibitors, we can dissect Wnt induced endocytosis into two independent pathways, where canonical Wnt3a is taken up mainly by clathrin-independent endocytosis and Wnt5a exclusively by clathrin-mediated endocytosis.

cell biology↗

bioRxiv2018

Intrinsically aggregation-prone proteins form amyloid-like aggregates and contribute to tissue aging in C. elegans

Reduced protein homeostasis and increased protein instability is a common feature of aging. Yet it remains unclear whether protein instability is a cause of aging. In neurodegenerative diseases and amyloidoses, specific proteins self-assemble into amyloid fibrils and accumulate as pathological solid aggregates in a variety of tissues. More recently, widespread protein aggregation has been described during normal aging, in the absence of disease processes. Until now, an extensive characterization of the nature of age-dependent protein aggregation and its consequences for aging has been lacking. Here, we show that age-dependent aggregates are rapidly formed by newly synthesized proteins and contain amyloid-like structures similar to disease-associated protein aggregates. Moreover, we demonstrate that age-dependent protein aggregation accelerates the functional decline of different tissues in C. elegans. Together, these finding reveal that the formation of amyloid aggregates is a generic problem of aging and likely to be an important target for strategies designed to maintain physiological functions in later stages of life.

cell biology↗