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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 739 records · Page 41Linked to original sources

bioRxiv2017

Dynamic changes in oligomeric complexes of UPR sensors induced by misfolded proteins in the ER

The endoplasmic reticulum (ER) localized unfolded protein response (UPR) sensors, IRE1, PERK, and ATF6, are activated upon accumulation of misfolded proteins caused by ER stress. It is debated whether these UPR sensors are activated either by the release of their negative regulator BiP chaperone or directly binding to misfolded proteins during ER stress. Here we simultaneously examined oligomerization and activation of all three endogenous UPR sensors. We found that UPR sensors existed as preformed oligomers even in unstressed cells, which shifted to large oligomers for PERK and small oligomers for ATF6, but little changed for IRE1 upon ER stress. Neither depletion nor overexpression of BiP had significant effects on oligomeric complexes of UPR sensors both in unstressed and stressed cells. Thus, our results find less evidence for the BiP-mediated activation of UPR sensors in mammalian cells and support that misfolded proteins bind and activate the preformed oligomers of UPR sensors.

cell biology↗

bioRxiv2017

Receptor-mediated Drp1 oligomerization on endoplasmic reticulum

Drpl is a dynamin GTPase important for mitochondrial and peroxisomal division. Drp1 oligomerization and mitochondrial recruitment are regulated by multiple factors, including interaction with mitochondrial receptors such as Mff, MiD49, MiD51 and Fis. In addition, both endoplasmic reticulum (ER) and actin filaments play positive roles in mitochondrial division, but mechanisms for their roles are poorly defined. Here, we find that a population of Drp1 oligomers is ER-associated in mammalian cells, and is distinct from mitochondrial or peroxisomal Drp1 populations. Sub-populations of Mff and Fis1, which are tail-anchored proteins, also localize to ER. Drp1 oligomers assemble on ER, from which they can transfer to mitochondria. Suppression of Mff or inhibition of actin polymerization through the formin INF2 significantly reduces all Drp1 oligomer populations (mitochondrial, peroxisomal, ER-bound) and mitochondrial division, while Mff targeting to ER has a stimulatory effect on division. Our results suggest that ER can function as a platform for Drp1 oligomerization, and that ER-associated Drp1 contributes to mitochondrial division.\n\nSummaryAssembly of the dynamin GTPase Drp1 into constriction-competent oligomers is a key event in mitochondrial division. Here, Ji et al show that Drp1 oligomerization can occur on endoplasmic reticulum through an ER-bound population of the tail-anchored protein Mff.\n\nAbbreviations used in this paper: Drp1, dynamin-related protein 1; Fis1, mitochondrial fission 1 protein; INF2, inverted formin 2; KD, siRNA-mediated knock down; KI, CRISPR-mediated knock in; KO, CRISPR-mediated knock out; LatA, Latrunculin A; MDV, mitochondrially-derived vesicle; Mff, mitochondrial fission factor; MiD49 and MiD51, mitochondrial dynamics protein of 49 and 51 kDa; OMM, outer mitochondrial membrane; TA, tail-anchored.

cell biology↗

bioRxiv2017

C. elegans DBL-1/BMP Regulates Lipid Accumulation via Interaction with Insulin Signaling

Metabolic homeostasis is coordinately controlled by diverse inputs, which must be understood to combat metabolic disorders. Here we introduce DBL-1, the C. elegans BMP2/4 homolog, as a significant regulator of lipid homeostasis. We used neutral lipid staining and a lipid droplet marker to demonstrate that both increases and decreases in DBL-1/BMP signaling result in reduced lipid stores and lipid droplet count. We find that lipid droplet size, however, correlates positively with the level of DBL 1/BMP signaling. Regulation of lipid accumulation in the intestine occurs through non-cell-autonomous signaling, since expression of SMA-3, a Smad signal transducer, in the epidermis (hypodermis) is sufficient to rescue the loss of lipid accumulation. Finally, genetic evidence indicates that DBL-1/BMP functions upstream of Insulin/IGF-1 Signaling (IIS) in lipid metabolism. We conclude that BMP signaling regulates lipid metabolism in C. elegans through inter-organ signaling to IIS, shedding light on a less well-studied regulatory mechanism for metabolic homeostasis.

cell biology↗

bioRxiv2017

Structured illumination to spatially map chromatin motions

We describe a simple optical method that creates structured illumination of a photoactivatable probe and apply this method to characterize chromatin motions in the nuclei of live cells. A laser beam coupled to a diffractive optical element at the back focal plane of an excitation objective generates an array of near diffraction-limited beamlets with FWHM of 340{+/-}30 nm, which simultaneously photoactivate a 7x7 matrix pattern of GFP-labeled histones, with spots 1.70 m apart. From the movements of the photoactivated spots, we map chromatin diffusion coefficients at multiple microdomains of the cell nucleus. The results show correlated motions of nearest chromatin microdomain neighbors, whereas chromatin movements are uncorrelated at the global scale of the nucleus. The method also reveals DNA damage-dependent decrease in chromatin diffusion. The DOE instrumentation can easily and cheaply be implemented on commercial inverted fluorescence microscopes to analyze adherent cell culture models. A protocol to measure chromatin motions in non-adherent human hematopoietic stem and progenitor cells is also described. We anticipate that the method will contribute to the identification of the mechanisms regulating chromatin mobility, which influences most genomic processes and may underlie the biogenesis of genomic translocations associated with hematologic malignancies.

cell biology↗

bioRxiv2017

Cyclin A2 localises in the cytoplasm at the S/G2 transition to activate Plk1

Cyclin A2 is a key regulator of the cell cycle, implicated both in DNA replication and mitotic entry. Cyclin A2 participates in feedback loops that activate mitotic kinases in G2-phase, but why active Cyclin A2-CDK2 during S phase does not trigger mitotic kinase activation remains unclear. Here we describe a change in localisation of Cyclin A2 from being only nuclear to both nuclear and cytoplasmic at the S/G2 border. We find that Cyclin A2-CDK2 can activate the mitotic kinase PLK1 through phosphorylation of Bora, and that only cytoplasmic Cyclin A2 interacts with Bora and PLK1. Expression of predominately cytoplasmic Cyclin A2 or phospho-mimicking PLK1 T210D can partially rescue a G2 arrest caused by Cyclin A2 depletion. Cytoplasmic presence of Cyclin A2 is restricted by p21, in particular after DNA damage. Cyclin A2 chromatin association during DNA replication and additional mechanisms contribute to Cyclin A2 localisation change in G2 phase. We find no evidence that such mechanisms involve G2 feedback loops and suggest that cytoplasmic appearance of Cyclin A2 at the S/G2 transition functions as a trigger for mitotic kinase activation. SynopsisMain mitotic kinases as PLK1 are activated at the S/G2 transition. A change in Cyclin A2 localisation at the S/G2 transition enables activation of PLK1. Main points-Cyclin A2 appears in the cytoplasm at the S/G2 transition -Association with replicating chromatin and p21 restricts Cyclin A2 to the nucleus -DNA damage ensures nuclear Cyclin A2 through p21 -Cytoplasmic Cyclin A2 initiates PLK1 activation Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/191437v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@7e7e82org.highwire.dtl.DTLVardef@a3c9aforg.highwire.dtl.DTLVardef@10e11edorg.highwire.dtl.DTLVardef@baf6bd_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2017

Nano-scale size holes in ER sheets provide an alternative to tubules for highly-curved membranes

The endoplasmic reticulum (ER) is composed of interconnected membrane sheets and tubules. Super-resolution microscopy recently revealed densely packed, rapidly moving ER tubules, highlighting the importance of revisiting classical views of ER structure with high spatial resolution in living cells. Using live-cell Stimulated Emission Depletion (STED) microscopy, we show highly dynamic, subdiffraction-sized holes in ER sheets. Holes coexist with uniform sheet regions and are distinct from tubular ER structures. The curvature-stabilizing reticulon protein Rtn4 localizes to these holes and the ER luminal tether Climp63 controls their diameter and mobility. Analytical modeling demonstrates that holes in ER sheets can serve as reservoirs for curvature-stabilizing proteins to support ER tubule extension and retraction, thus providing an explanation for how the ER locally alters its morphology on fast time-scales.\n\nOne Sentence SummaryDynamic nano-scale sized holes are prominent features of ER sheets that serve as reservoirs for curvature-stabilizing proteins to support ER tubule extension and retraction.

cell biology↗

bioRxiv2017

Spatial and temporal translocation of PKCα in single endothelial cell in response to focal mechanical stimulus

We observed the kinetics of protein kinase C (PKC) and the intracellular Ca2+ wave in endothelial cells (ECs) in response to microscopic mechanical stress to investigate the effect of mechanical stress on PKC translocation. The results show that a focal mechanical stimulus induced biphasic and directional PKC translocation; PKC initially translocated toward distinct spots near or at the membrane and then accumulated at the stimulus point. The low initial translocation occurred simultaneously in parallel with the increase in Ca2+. Initial translocation was inhibited in spite of Ca2+ increase when the diacylglycerol (DAG) binding domain of PKC was inhibited, suggesting that translocation requires intracellular Ca2+ increase and DAG. On the other hand, high secondary translocation was delayed, occurring after the Ca2+ wave; however, this secondary translocation occurred even when Ca2+ release from the endoplasmic reticulum was inhibited, while it did not occur when the mechanosensitive (MS) channel was inhibited. These results indicated that at least Ca2+ influx through MS channels is required. Our results support the implication of PKC in the Ca2+ signaling pathway in response to mechanical stress in ECs.\n\nSummary statementIn response to a focal mechanical stimulus, PKC in an endothelial cell was initially translocated toward distinct spots near or at the membrane and then accumulated at the stimulus point.

cell biology↗

bioRxiv2017

Streamlined histone-based fluorescence lifetime imaging microscopy reveals ATM regulation of chromatin compaction

Changes in chromatin compaction are crucial during genomic responses. Thus, methods that enable such measurements are instrumental for investigating genome function. Here, we address this challenge by developing, validating, and streamlining histone-based fluorescence lifetime imaging microscopy (FLIM) that robustly detects chromatin compaction states in fixed and live cells; in 2D and 3D. We present quality-controlled and detailed method that is simpler and faster than previous approches, and uses FLIMfit open-source software. We demonstrate the versatility of our method through its combination with immunofluorescence and its implementation in immortalised cells and primary neurons. Owing to these developments, we applied this method to elucidate the function of the DNA damage response kinase, ATM, in regulating chromatin organisation after genotoxic-stress. We unravelled a role for ATM in regulating chromatin compaction independently of DNA damage. Collectively, we present an adaptable chromatin FLIM method for examining chromatin structure in cells, and establish its broader utility.

cell biology↗

bioRxiv2017

Propagating actomyosin-generated force to intercellular junction

Actomyosin II contractility in epithelial cells plays an essential role in tension-dependent adhesion strengthening. One key unsettling question is how cellular contraction transmits force to nascent cell-cell adhesion when there is no stable attachment between the nascent adhesion complex and actin filament. Here, we showed that application of intercellular tension induces myosin 1c accumulation at the lateral membrane between epithelial cells. We hypothesized that the accumulation of myosin 1c at the cell-cell interface allows coupling of actomyosin contractility to the generation of intercellular tension, thus is essential for tension-induced junction maturation. We showed that myosin 1c KD compromises a-actinin-4 recruitment to cell-cell adhesion during normal junction maturation driven by endogenous actomyosin contractility. However, application of cyclic tension to intercellular junction from outside of the cells rescued tension-dependent a-actinin-4 accumulation, suggesting that myosin-1c KD did not compromise the tension response or disrupt the overall integrity of the junctional complex. Our study identifies myosin-1c as a novel tension-sensitive protein on the lateral membrane and underscores a non-junctional contribution to adhesion strengthening at the epithelial cell-cell adhesion interface.

cell biology↗

bioRxiv2017

Sensory neuropathy-causing mutations in ATL3 cause aberrant ER membrane tethering

The ER is a complex network of sheets and tubules that is continuously being remodeled. The relevance of this membrane dynamics is underscored by the fact that mutations in Atlastins (ATL), the ER fusion proteins in mammals, cause neurodegeneration. How defects in this process disrupt neuronal homeostasis is largely unknown. Here we show by EM volume reconstruction of transfected cells, neurons and patient fibroblasts that the HSAN-causing ATL3 mutants promote aberrant ER tethering hallmarked by bundles of laterally attached ER tubules. In vitro, these mutants cause excessive liposome tethering, recapitulating the results in cells. Moreover, ATL3 variants retain their dimerization-dependent GTPase activity, but are unable to promote membrane fusion, suggesting a defect on an intermediate step of the ATL3 functional cycle. Our data therefore show that the effects of ATL3 mutations on ER network organization stretch beyond a loss of fusion, shedding a new light on neuropathies caused by atlastin defects.

cell biology↗

bioRxiv2017

Actin enhances ER-mitochondrial calcium transfer and IMM constriction during mitochondrial division

Mitochondrial division requires division of both the inner and outer mitochondrial membranes (IMM and OMM, respectively). Interaction with endoplasmic reticulum (ER) promotes OMM division by recruitment of the dynamin Drp1, but effects on IMM division are not well characterized. We previously showed that actin polymerization through the ER-bound formin INF2 stimulates Drp1 recruitment in mammalian cells. Here, we show that INF2-mediated actin polymerization stimulates a second mitochondrial response independent of Drp1: a rise in mitochondrial matrix calcium through the mitochondrial calcium uniporter. ER stores supply the increased mitochondrial calcium, and the role of actin is to increase ER-mitochondria contact. Myosin IIA is also required for this mitochondrial calcium increase. Elevated mitochondrial calcium in turn activates IMM constriction in a Drp1-independent manner. IMM constriction requires electron transport chain activity. IMM division precedes OMM division. These results demonstrate that actin polymerization independently stimulates the dynamics of both membranes during mitochondrial division: IMM through increased matrix calcium, and OMM through Drp1 recruitment.

cell biology↗

bioRxiv2017

NECAPs are negative regulators of the AP2 clathrin adaptor complex

Eukaryotic cells internalize transmembrane receptors via clathrin-mediated endocytosis, but it remains unclear how the machinery underpinning this process is regulated. We recently discovered that membrane-associated muniscin proteins such as FCHo and SGIP initiate endocytosis by converting the AP2 clathrin adaptor complex to an open, active conformation that is then phosphorylated (Hollopeter et al., 2014). Here we report that loss of ncap-1, the sole C. elegans gene encoding an adaptiN Ear-binding Coat-Associated Protein (NECAP), bypasses the requirement for FCHO-1. Biochemical analyses reveal AP2 accumulates in an open, phosphorylated state in ncap-1 mutant worms, suggesting NECAPs promote the closed, inactive conformation of AP2. Consistent with this model, NECAPs preferentially bind open and phosphorylated forms of AP2 in vitro and localize with constitutively open AP2 mutants in vivo. NECAPs do not associate with phosphorylation-defective AP2 mutants, implying that phosphorylation precedes NECAP recruitment. We propose NECAPs function late in endocytosis to inactivate AP2.

cell biology↗

bioRxiv2017

Architecture of mammalian centriole distal appendages accommodates distinct blade and matrix functional elements

Distal appendages (DAPs) are nanoscale, pinwheel-like structures protruding from the distal end of the centriole that mediate membrane docking during ciliogenesis, marking the cilia base around the ciliary gate. Here, we determined a superresolved multiplex of 16 centriole-distal-end components. Surprisingly, rather than pinwheels, intact DAPs exhibit a cone-shaped architecture with components filling the space between each pinwheel blade, a new structural element we termed the distal appendage matrix (DAM). Specifically, CEP83, CEP89, SCLT1, and CEP164 form the backbone of pinwheel blades, with CEP83 confined at the root and CEP164 extending to the tip near the membrane-docking site. By contrast, FBF1 marks the distal end of the DAM near the ciliary membrane. Strikingly, unlike CEP164 which is essential for ciliogenesis, FBF1 is required for ciliary gating of transmembrane proteins, revealing DAPs as an essential component of the ciliary gate. Our findings redefine both the structure and function of DAPs.

cell biology↗

bioRxiv2017

Resolving ESCRT-III spirals at the intercellular bridge of dividing cells using 3D STORM imaging

The ESCRT machinery mediates membrane fission in a verity of processes in cells. According to the proposed mechanism, ESCRT-III proteins drive membrane fission by assembling into helical filaments on membranes. Yet, ESCRT-III filaments have never been directly visualized in a cellular process that utilizes this machinery for its function. Here we used 3D STORM imaging of endogenous ESCRT-III component IST1, to describe the structural organization of ESCRT-III during mammalian cytokinetic abscission. Using this approach, ESCRT-III ring and spiral assemblies were resolved at the intercellular tube of cells undergoing abscission. Characterization of these structures indicates the ESCRT-III helical filament undergoes remodeling during abscission. This work provides the first evidence that ESCRT-III proteins assemble into helical filaments in physiological context, indicating that the ESCRT-III machine indeed derives its contractile activity through spiral assemblies. Moreover, it provides new structural information on ESCRT-III filaments, which raise new mechanistic scenarios for ESCRT driven membrane constriction.

cell biology↗

bioRxiv2017

Uncoordinated centrosome duplication cycle underlies the instability of non-diploid states in mammalian somatic cells

In animals, somatic cells are usually diploid and are unstable when haploid for unknown reasons. In this study, by comparing isogenic human cell lines with different ploidies, we found frequent centrosome loss specifically in the haploid state, which profoundly contributed to haploid instability through monopolar spindle formation and subsequent mitotic defects. We also found that efficiency of centriole licensing and duplication, but not that of DNA replication, changes proportionally to ploidy level, causing gradual loss or frequent overduplication of centrioles in haploid and tetraploid cells, respectively. Centriole licensing efficiency seemed to be modulated by astral microtubules, whose development scaled with ploidy level, and artificial enhancement of aster formation in haploid cells restored centriole licensing efficiency to diploid levels. Haploid-specific centrosome loss was also observed in parthenogenetic mouse embryos. We propose that incompatibility between the centrosome duplication and DNA replication cycles arising from different scaling properties of these bioprocesses upon ploidy changes, underlies the instability of non-diploid somatic cells in mammals.\n\nSummaryYaguchi et al. show that a delay or acceleration of centriole licensing compromises the control of centrosome number in haploid or tetraploid human cells, respectively, suggesting a cellular basis of the instability of non-diploid somatic cells in mammals.

cell biology↗

bioRxiv2017

Characterization of the Novel Mitochondrial Genome Replication Factor MiRF172 in Trypanosoma brucei

The unicellular parasite Trypanosoma brucei harbors one individual mitochondrial organelle with a singular genome the kinetoplast DNA or kDNA. The kDNA largely consists of concatenated minicircles and a few maxicircles that are also interlocked into the kDNA disc. More than 30 proteins involved in kDNA replication have been described, however several mechanistic questions are only poorly understood. Here, we describe and characterize MiRF172, a novel mitochondrial genome replication factor, which is essential for proper cell growth and kDNA maintenance. Using super-resolution microscopy, we localize MiRF172 to the antipodal sites of the kDNA. We demonstrate that depletion of MiRF172 leads to continuous loss of mini- and maxicircles during the cell division cycle. Detailed analysis suggests that MiRF172 is likely involved in the reattachment of replicated minicircles to the kDNA disc. Furthermore, we provide evidence that the localization of the replication factor MiRF172 not only depends on the kDNA itself, but also on the mitochondrial genome segregation machinery suggesting a tight interaction between the two essential entities.\n\nSummary StatementMiRF172 is a novel protein involved in the reattachment of replicated minicircles in Trypanosoma brucei, which requires the mitochondrial segregation machinery for proper localization.

cell biology↗

bioRxiv2017

Structure of the fission yeast actomyosin ring during constriction

Cell division in many eukaryotes is driven by a ring containing actin and myosin. While much is known about the main proteins involved, the precise arrangement of actin filaments within the contractile machinery, and how force is transmitted to the membrane remains unclear. Here we use cryosectioning and cryo-focused ion beam milling to gain access to cryo-preserved actomyosin rings in Schizosaccharomyces pombe for direct three-dimensional imaging by electron cryotomography. Our results show that straight, overlapping actin filaments, running nearly parallel to each other and to the membrane, form a loose bundle of approximately 150 nm in diameter that \"saddles\" the inward-bending membrane at the leading edge of the division septum. The filaments do not make direct contact with the membrane. Our analysis of the actin filaments reveals the variability in filament number, nearest-neighbor distances between filaments within the bundle, their distance from the membrane and angular distribution with respect to the membrane.\n\nSignificance StatementMost eukaryotic cells divide using a contractile actomyosin ring, but its structure is unknown. Here we use new specimen preparation methods and electron cryotomography to image constricting rings directly in 3D, in a near-native state in the model organism Schizosaccharomyces pombe. Our images reveal the arrangement of individual actin filaments within the contracting actomyosin ring.

cell biology↗

bioRxiv2017

Human replication licensing factor Cdt1 directly links mitotic kinetochores to spindle microtubules

Robust kinetochore-microtubule (kMT) attachment is critical for accurate chromosome segregation. G2/M-specific depletion of human Cdt1 that localizes to kinetochores in an Ndc80 complex-dependent manner, leads to abnormal kMT attachments and mitotic arrest. This indicates an independent mitotic role for Cdt1 in addition to its prototypic function in DNA replication origin licensing. Here, we show that Cdt1 directly binds to microtubules (MTs). Endogenous or transiently expressed Cdt1 localizes to both mitotic spindle MTs and kinetochores. Deletion mapping of Cdt1 revealed that the regions comprising the middle and C-terminal winged-helix domains but lacking the N-terminal unstructured region was required for efficient MT-binding. Mitotic kinase Aurora B interacts with and phosphorylates Cdt1. Aurora B-phosphomimetic Cdt1 exhibited attenuated MT-binding and its cellular expression induced defective kMT attachments with a concomitant delay in mitotic progression. Thus we provide mechanistic insight into how Cdt1 affects overall kMT stability in an Aurora B kinase phosphorylation-dependent manner; which is envisioned to augment the MT-binding of the Ndc80 complex.\n\neTOC summary* Cdt1 binds to microtubules\n\n* The middle and the C-terminal winged-helix domains of Cdt1 are involved in MT-binding\n\n* Aurora B Kinase phosphorylates Cdt1 and influences its MT-binding\n\n* Aurora B-mediated Cdt1 phosphorylation is necessary for kMT stability and mitotic progression

cell biology↗