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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 1,099 records · Page 61Linked to original sources

bioRxiv2018

Systematic studies of all PIH proteins in zebrafish reveal their distinct roles in axonemal dynein assembly

Construction of motile cilia/flagella requires cytoplasmic preassembly of axonemal dyneins before transport into cilia. Axonemal dyneins have various subtypes, but the roles of each dynein subtype and their assembly processes remain elusive in vertebrates. The PIH protein family, consisting of four members, has been implicated in the assembly of different dynein subtypes, although evidence for this idea is sparse. Here, we established zebrafish mutants of all four PIH-protein genes: pih1d1, pih1d2, ktu, and twister, and analyzed the structures of axonemal dyneins in mutant spermatozoa by cryo-electron tomography. Mutations caused the loss of specific dynein subtypes, which was correlated with abnormal sperm motility. We also found organ-specific compositions of dynein subtypes, which could explain the severe motility defects of mutant Kupffers vesicle cilia. Our data demonstrate that all vertebrate PIH proteins are differently required for cilia/flagella motions and the assembly of axonemal dyneins, assigning specific dynein subtypes to each PIH protein.

cell biology↗

bioRxiv2018

PIP5k1 β controls bone homeostasis through modulating both osteoclast and osteoblast differentiation

PIP5K1{beta} is crucial to generation of phosphotidylinosotol (4, 5) P2. PIP5K1{beta} participates in numerous cellular activities, such as B cell and platelet activation, cell phagocytosis and endocytosis, cell apoptosis, and cytoskeletal organization. In the present work, we aimed to make insight into the function of PIP5K1{beta} in osteoclastogenesis and osteogenesis to provide promising strategies for osteoporosis prevention and treatment. We discovered that PIP5k1{beta} deletion in mice resulted in obvious bone loss and PIP5K1{beta} was highly expressed both during osteoclast and osteoblast differentiation, besides, PIP5K1{beta} deletion enhanced the proliferation and migration of BMMs to promote osteoclast differentiation. PIP5k1{beta}-/- osteoclast exhibited normal cytoskeleton architecture but stronger resorption activity. PIP5k1{beta} deficiency also promoted activation of MAPK and Akt signaling, enhanced TRAF6 and c-Fos expression, facilitated the expression and nuclear translocation of NFATC1 and upregulated Grb2 expression, thereby accelerating osteoclast differentiation and function. Finally, PIP5K1{beta} enhanced osteoblast differentiation by upregulating master genes expression through triggering smad1/5/8 signaling. Thereby, PIP5K1{beta} modulate bone homeostasis and remodeling.

cell biology↗

bioRxiv2018

Cumulative regulatory potential of clustered methyl-arginine protein modifications

Systematic analysis of human arginine methylation events bifurcates its signaling mechanism, functioning either in isolation akin to canonical PTM regulation or clustered within disordered protein sequence. Hundreds of proteins contain methyl-arginine clusters and are more prone to mutation and more tightly expression-regulated than dispersed methylation targets. Arginine clusters in the highly methylated RNA binding protein SYNCRIP were experimentally shown to function in concert providing a tunable protein interaction interface. Quantitative immuno-precipitation assays defined two distinct cumulative regulatory mechanisms operating across 18 proximal arginine-glycine motifs in SYNCRIP. Functional binding to the methyl-transferase PRMT1 was promoted by continual arginine stretches while interaction with the methyl-binding protein SMN1 was arginine content dependent irrespective of linear position within the unstructured region. This study highlights how highly repetitive di-amino acid motifs in otherwise low structural complexity regions can provide regulatory potential, and with SYNCRIP as an extreme example how PTMs leverage these disordered sequences to drive cellular functions.

cell biology↗

bioRxiv2018

Regulation of DVL2 ubiquitylation by USP9X biases participation in canonical or non-canonical WNT signalling

The WNT signaling network is comprised of multiple receptors that relay various input signals via distinct transduction pathways to execute multiple complex and context-specific output processes. Integrity of the WNT signaling network relies on proper specification between canonical and non-canonical pathways, which presents a regulatory challenge given that several signal transducing elements are shared between pathways. Here, we report that USP9X, a deubiquitylase, and WWP1, an E3 ubiquitin ligase, interact physically to regulate a ubiquitin switch on DVL2, a WNT signaling protein. Our findings indicate that USP9X-mediated deubiquitylation of DVL2 is required for canonical WNT activation, while DVL2 ubiquitylation promotes its localization to actin-rich projections and increased cellular motility. We propose that a WWP1-USP9X axis regulates a ubiquitin switch on DVL2 that specifies its participation in either canonical WNT or WNT-PCP pathways. These findings have important implications for therapeutic targeting of USP9X in human cancer.

cell biology↗

bioRxiv2018

Visualizing multiple inter-organelle contact sites using the organelle-targeted split-GFP system

Functional integrity of eukaryotic organelles relies on direct physical contacts between distinct organelles. However, the entity of organelle-tethering factors is not well understood due to lack of means to analyze inter-organelle interactions in living cells. Here we evaluate the split-GFP system for visualizing organelle contact sites in vivo and show its advantages and disadvantages. We observed punctate GFP signals from the split-GFP fragments targeted to any pairs of organelles among the ER, mitochondria, peroxisomes, vacuole and lipid droplets in yeast cells, which suggests that these organelles form contact sites with multiple organelles simultaneously although it is difficult to rule out the possibilities that these organelle contacts sites are artificially formed by the irreversible associations of the split-GFP probes. Importantly, split-GFP signals in the overlapped regions of the ER and mitochondria were mainly co-localized with ERMES, an authentic ER-mitochondria tethering structure, suggesting that split-GFP assembly depends on the preexisting inter-organelle contact sites. We also confirmed that the split-GFP system can be applied to detection of the ER-mitochondria contact sites in HeLa cells. We thus propose that the split-GFP system is a potential tool to observe and analyze inter-organelle contact sites in living yeast and mammalian cells.

cell biology↗

bioRxiv2018

Asymmetrically Positioned Flagellar Control Units Regulate Human Sperm Rotation

The ability of sperm to fertilize an egg is controlled by ion channels, one of which is the pH-dependent calcium channel of sperm CatSper. For CatSper to be fully activated, the cytoplasmic pH must be alkaline, which is accomplished by either proton transporters, or a faster mechanism, such as the voltage-gated proton channel Hv1. To ensure effective regulation, these channels and regulatory proteins must be tightly compartmentalized. Here, we characterize human sperm nanodomains that are comprised of Hv1, CatSper and regulatory protein ABHD2. Super-resolution microscopy revealed that Hv1 forms asymmetrically positioned bilaterally distributed longitudinal lines that span the entire length of the sperm tail. Such a distribution provides a direct structural basis for the selective activation of CatSper, and subsequent flagellar rotation along the long axis that, together with hyperactivated motility, enhances sperm fertility. Indeed, Hv1 inhibition leads to a decrease in sperm rotation. Thus, sperm ion channels are organized in distinct regulatory nanodomains that control hyperactivated motility and rotation.

cell biology↗

bioRxiv2018

Systematic genetic mapping of necroptosis identifies SLC39A7 as modulator of death receptor trafficking

Regulation of cell and tissue homeostasis by programmed cell death is a fundamental process with wide physiological and pathological implications. The advent of scalable somatic cell genetic technologies creates the opportunity to functionally map these essential pathways, thereby identifying potential disease-relevant components. We investigated the genetic basis underlying necroptotic cell death by performing a complementary set of loss- and gain-of-function genetic screens. To this end, we established FADD-deficient haploid human KBM7 cells, which specifically and efficiently undergo necroptosis after a single treatment with either TNF or the SMAC mimetic compound birinapant. A series of unbiased gene-trap screens identified key signaling mediators, such as TNFR1, RIPK1, RIPK3, and MLKL. Among the novel components, we focused on the zinc transporter SLC39A7, whose knock-out led to necroptosis resistance by affecting TNF receptor trafficking and ER homeostasis. Orthogonal, solute carrier (SLC)-focused CRISPR/Cas9-based genetic screens revealed the exquisite specificity of SLC39A7, among ~ 400 SLC genes, for TNFR1- and FAS-but not TRAIL-R1-mediated responses. The newly established cellular model also allowed genome-wide gain-of-function screening for genes conferring resistance to necroptosis via the CRISPR/Cas9 synergistic activation mediator approach. Among these, we found cIAP1 and cIAP2, and characterized the role of TNIP1 (TNFAIP3-interacting protein 1), which prevented pathway activation in a ubiquitin-binding dependent manner. Altogether, the gain- and loss-of-function screens described here provide a global genetic chart of the molecular factors involved in necroptosis and death receptor signaling, prompting investigation of their individual contribution and potential role in pathological conditions.

cell biology↗

bioRxiv2018

Fast calcium transients in neuronal spines is driven by extreme statistics

Extreme statistics describe the distribution of rare events that can define the timescales of transduction within cellular microdomains. We combine biophysical modeling and analysis of live-cell calcium imaging to explain the fast calcium transient in spines. We show that in the presence of a spine apparatus (SA), which is an extension of the smooth endoplasmic reticulum (ER), calcium transients during synaptic inputs rely on rare and extreme calcium ion trajectories. Using numerical simulations, we predicted the asymmetrical distributions of Ryanodine receptors and SERCA pumps that we confirmed experimentally. When calcium ions are released in the spine head, the fastest ions arriving at the base determine the transient timescale through a calcium-induced calcium release mechanism. In general, the fastest particles arriving at a small target are likely to be a generic mechanism that determines the timescale of molecular transduction in cellular neuroscience.\n\nSignificance statementIntrigued by fast calcium transients of few milliseconds in dendritic spines, we investigated its underlying biophysical mechanism. We show here that it is generated by the diffusion of the fastest calcium ions when the spine contains a Spine Apparatus, an extension of the endoplasmic reticulum. This timescale is modulated by the initial number of released calcium ions and the asymmetric distribution of its associated calcium release associated Ryanodyne receptors, present only at the base of a spine. This novel mechanism of calcium signaling that we have unraveled here is driven by the fastest particles. To conclude, the rate of arrival of the fastest particles (ions) to a small target receptor defines the timescale of activation instead of the classical forward rate of chemical reactions introduced by von Smoluchowski in 1916. Applying this new rate theory to transduction should refine our understanding of the biophysical mechanisms underlying molecular signaling.

cell biology↗

bioRxiv2018

Optimizing bioreactor growth of the smallest eukaryote

Photosynthetic organisms are adept at circumventing nutrient deprivation. Microalgae in particular present novel adaptations to nutrient and light starvation since they can scavenge external and internal nutrient pools to redistribute energy resources for survival. In this report, a turbidostatic photobioreactor was used to characterize environmental conditions and nutrient requirements for cultures of the smallest free-living eukaryote Ostreococcus tauri. Optimized growth conditions were identified that enable 4-times faster phototrophic growth-rates while increasing total biomass 10-fold. By achieving phototrophic doubling times shorter than 6 hours, these results highlight the potential of this smallest eukaryote for future industrial bioproduct applications.

cell biology↗

bioRxiv2018

The anti-apoptosis ubiquitin E3 ligase XIAP promotes autophagosome-lysosome fusion during autophagy

The Inhibitor of Apoptosis Protein (IAP) family members are well-known endogenous regulators of apoptosis. Whether these proteins regulate other degradation pathways is unclear. Here, we discovered that the IAP member X-linked IAP (XIAP) is crucial for macroautophagy. Loss of XIAP in mouse and human cells inhibited starvation-induced degradation of LC3 proteins and an autophagy substrate p62. It also led to the accumulation of mature autophagosomes, suggesting that XIAP controls autophagic flux by mediating autolysosome formation. Xiap{triangleup}RING/{triangleup}RING cells phenocopy the autophagy defects of Xiap-/- cells, suggesting that the ubiquitinating activity mediated by the catalytic RING domain is critical for autophagic flux. We found that XIAP physically interacts with Syntaxin 17, a regulator of autophagosome-lysosome fusion. Syntaxin 17-positive mature autophagosomes positive accumulate in the cytoplasm of starved Xiap-/- cells, suggesting that XIAP might regulate its dissociation from autophagosomes after fusion. XIAP selectively interacts with GABARAP among LC3 family members via the LIR-Docking Site (LDS). Together, our data suggest that XIAP-mediated ubiquitination regulates key autophagy regulators to promote autophagosome-lysosome fusion.

cell biology↗

bioRxiv2018

Fission yeast NDR/LATS kinase Orb6 regulates exocytosis via phosphorylation of exocyst complex

NDR/LATS kinases regulate multiple aspects of cell polarity and morphogenesis from yeast to mammals, but few of their substrates are known. Fission yeast NDR/LATS kinase Orb6 has been proposed to control cell polarity via spatial regulation of Gef1, a guanine nucleotide exchange factor for the small GTPase Cdc42. Here we show that Orb6 plays a critical role as a positive regulator of exocytosis, independent of Gef1. Through Orb6 inhibition in vivo and quantitative global phosphoproteomics, we identify several proteins involved in membrane trafficking as Orb6 targets, and we confirm Sec3 and Sec5, conserved components of the exocyst complex, as substrates of Orb6 both in vivo and in vitro. Our results suggest that Orb6 kinase activity is crucial for exocyst localization to actively-growing cell tips and for exocyst activity during septum dissolution after cytokinesis. We further show that Orb6 phosphorylation of Sec3 serine-201 contributes to exocyst function in parallel with exocyst protein Exo70. We propose that Orb6 contributes to polarized growth by regulating membrane trafficking at multiple levels.

cell biology↗

bioRxiv2018

A structural mechano-chemical model for dynamic instability of microtubule

Microtubules are a major component of the cytoskeleton and vital to numerous cellular processes. The central dogma of microtubules is that all their functions are driven by dynamic instability; understanding its key phenomena (i.e. catastrophe, rescue, pause, differential behaviors at the plus and minus ends) distilled from a myriad of experiments under a consistent and unified scheme, however, has been unattainable. Here, we present a novel statistical-physics-based model uniquely constructed from conformational states deduced from existing tubulin structures, with transitions between them controlled by steric constraints and mechanical energy of the microtubule lattice. This mechano-chemical model allows, for the first time, all the key phenomena of dynamic instability to be coherently reproduced by the corresponding kinetic simulations. Long-puzzling phenomena, such as aging, small GTP-cap size, fast catastrophe upon dilution and temperature-induced ribbon-to-tube transition of GMPCPP-tubulins, robustly emerge and thus can be understood with confidence.

cell biology↗

bioRxiv2018

FIT2 is a lipid phosphate phosphatase crucial for endoplasmic reticulum homeostasis

The endoplasmic reticulum (ER) protein Fat-Induced Transcript 2 (FIT2) has emerged as a key factor in lipid droplet (LD) formation, although its molecular function is unknown. Highlighting its importance, FIT2 orthologs are essential in worms and mice, and FIT2 deficiency causes a deafness/dystonia syndrome in humans. Here we show that FIT2 is a lipid phosphate phosphatase (LPP) enzyme that is required for maintaining the normal structure of the ER. Recombinant FIT2 exhibits LPP activity in vitro and loss of this activity in cells leads to ER membrane morphological changes and ER stress. Defects in LD formation in FIT2 depletion appear to be secondary to membrane lipid abnormalities, possibly due to alterations in phospholipids required for coating forming LDs. Our findings uncover an enzymatic role for FIT2 in ER lipid metabolism that is crucial for ER membrane homeostasis.

cell biology↗

bioRxiv2018

ImageJ Macro for Counting Stationary vs. Moving Items in Videos

In microfluidic devices, it is often necessary to determine whether cells or particles are stationary or moving. Here we outline the development of an ImageJ macro that can be used to analyze a video of moving, fluorescently labeled particles or cells, and determine which objects are stationary and which objects are moving at each point in time, providing information on the percentage of cells moving as well as their median radius.

cell biology↗

bioRxiv2018

A conserved Lkb1 signaling axis modulates TORC2 signaling in budding yeast

Nutrient availability, growth rate and cell size are closely linked. For example, in budding yeast, the rate of cell growth is proportional to nutrient availability, cell size is proportional to growth rate, and growth rate is proportional to cell size. Thus, cells grow slowly in poor nutrients and are nearly half the size of cells growing in rich nutrients. Moreover, large cells grow faster than small cells. A signaling network that surrounds Tor kinase complex 2 (TORC2) plays an important role in enforcing these proportional relationships. Cells that lack components of the TORC2 network fail to modulate their growth rate or size in response to changes in nutrient availability. Here, we show that budding yeast homologs of the Lkb1 tumor suppressor kinase are required for normal modulation of TORC2 signaling and in response to changes in carbon source. Lkb1 kinases activate Snf1/AMPK to initiate transcription of genes required for utilization of poor carbon sources. However, Lkb1 influences TORC2 signaling via a novel pathway that is independent of Snf1/AMPK. Of the three Lkb1 homologs in budding yeast, Elm1 plays the most important role in modulating TORC2. Elm1 activates a pair of related kinases called Gin4 and Hsl1. Previous work found that loss of Gin4 and Hsl1 causes cells to undergo unrestrained growth during a prolonged mitotic arrest, which suggests that play a role in linking cell cycle progression to cell growth. We found that Gin4 and Hsl1 also control the TORC2 network. In addition, Gin4 and Hsl1 are themselves influenced by signals from the TORC2 network, consistent with previous work showing that the TORC2 network constitutes a feedback loop. Together, the data suggest a model in which the TORC2 network sets growth rate in response to carbon source, while also relaying signals via Gin4 and Hsl1 that set the critical amount of growth required for cell cycle progression. This kind of close linkage between control of cell growth and size would suggest a simple mechanistic explanation for the proportional relationship between cell size and growth rate.

cell biology↗

bioRxiv2018

CD95 receptor activation by ligand-induced trimerization is independent of its partial pre-ligand assembly

CD95 (Fas, APO-1, TNFRSF6) is a widely expressed single-pass transmembrane protein that is implicated in cell death, inflammatory response, proliferation and cell migration. CD95 ligand (CD95L, FasL, TNFSF6), is a potent apoptotic inducer in the membrane form but not when cleaved into soluble CD95L (sCD95L). Here, we aimed at understanding the relation between ligand-receptor multimerization and receptor activation by correlating the kinetics of ligand binding, receptor oligomerization, FADD (FAS-Associated via Death Domain) recruitment and caspase-8 activation inside living cells. Using single molecule localization microscopy and Forster resonance energy transfer imaging we show that the majority of CD95 receptors on the plasma membrane are monomeric at rest. This was confirmed functionally as the wild-type receptor is not blocked by a receptor mutant that cannot bind ligand. Moreover, using time-resolved fluorescence imaging approaches we demonstrated that receptor multimerization follows instantaneously ligand binding, whereas FADD recruitment is delayed. This process can explain the typical delay time seen with caspase-8 activity reporters. Finally, the low activity of sCD95L, which was caused by inefficient FADD recruitment, was not explained by the low avidity for the receptor but by a receptor clustering mechanism that was different from the one induced by the strong apoptosis inducer IZ-sCD95L. Our results reveal that receptor activation is modulated by the capacity of its ligand to trimerize it.\n\nHighlightsO_LIAt a density of less than 10 receptors per {micro}m2 CD95 exists as monomer (58%) and dimer (42%)\nC_LIO_LIPre-formed dimers do not contribute to ligand-induced CD95 apoptotic signaling\nC_LIO_LIThe PLAD of CD95 attenuates overexpression-induced, ligand-independent cell death\nC_LIO_LIsoluble CD95L can rapidly multimerize CD95 after binding but it is still a poor inducer of apoptosis through inefficient FADD recruitment\nC_LIO_LIFADD recruitment kinetics but not ligand binding kinetics correlates with caspase-8 onset of activity\nC_LI

cell biology↗

bioRxiv2018

Native DNA electronics: the Nuclear Aggregates of Polyamines possible role

The genomic DNA is enveloped by nanotubes formed by the Nuclear Aggregates of Polyamines (NAPs) that induce DNA conformational changes, and provides protection and increased interactive abilities for the double strands. In a physiologic environment, the nanotube arrangement initiates with the spontaneous interaction among the terminal amino groups of polyamines and the phosphate ions, with the consequent formation of cyclic monomers that hook at DNA grooves. The polymer thus formed has the morphological features of an organic semiconductor and, therefore, can be considered able to conduce electric charges. Phosphate ions positioned on NAP external surface could regulate, as in a physical electric circuit, both protein linear and rotational (histones) motion, in accordance with the basilar principles of the electronics. A model of a carrier system for proteins motion along the polymer wrapping the DNA strands, based on the phosphate-phosphate complexation, is proposed.

cell biology↗

bioRxiv2018

The AP-1 complex is essential for fungal growth via its role in secretory vesicle polar sorting, endosomal recycling and cytoskeleton organization

The AP-1 complex is essential for membrane protein traffic via its role in the pinching-off and sorting of secretory vesicles from the trans-Golgi and/or endosomes. While its essentiality is undisputed in metazoa, its role in model simpler eukaryotes seems less clear. Here we dissect the role of AP-1 in the filamentous fungus Aspergillus nidulans and show that it is absolutely essential for growth due to its role in clathrin-dependent maintenance of polar traffic of specific membrane cargoes towards the apex of growing hyphae. We provide evidence that AP-1 is involved in both anterograde sorting of RabERab11-labeled secretory vesicles and RabA/BRab5- dependent endosome recycling. Additionally, AP-1 is shown to be critical for microtubule and septin organization, further rationalizing its essentiality in cells that face the challenge of cytoskeleton-dependent polarized cargo traffic. This work also opens a novel issue on how non-polar cargoes, such as transporters, are sorted to the eukaryotic plasma membrane.

cell biology↗