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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 1,135 records · Page 63Linked to original sources

bioRxiv2018

A multi-scale model of the yeast chromosome-segregation system

In dividing cells, depolymerizing spindle microtubules move chromosomes by pulling at their kinetochores. While kinetochore subcomplexes have been studied extensively in vitro, little is known about their in vivo structure and interactions with microtubules or their response to spindle damage. Here we combine electron cryotomography of serial cryosections with genetic and pharmacological perturbation to study the yeast chromosome-segregation machinery at molecular resolution in vivo. Each kinetochore microtubule has one (rarely, two) Dam1C/DASH outer-kinetochore assemblies.\n\nDam1C/DASH only contacts the flat surface of the microtubule and does so with its flexible \"bridges\". In metaphase, 40% of the Dam1C/DASH assemblies are complete rings; the rest are partial rings. Ring completeness and binding position along the microtubule are sensitive to kinetochore attachment and tension, respectively. Our study supports a model in which each kinetochore must undergo cycles of conformational change to couple microtubule depolymerization to chromosome movement.

cell biology↗

bioRxiv2018

SORLA-driven endosomal trafficking regulates the oncogenic fitness of HER2

Human epidermal growth factor receptor 2 (HER2) is an oncogene targeted by several kinase inhibitors and therapeutic antibodies. Endosomal trafficking of many other receptor tyrosine kinases regulates their oncogenic signaling, but the prevailing view is that HER2 is retained on the cell surface. Here we reveal that in cancer cells Sortilin related receptor 1 (SORLA; SORL1) forms a complex with HER2 and regulates its subcellular distribution by promoting recycling of endosomal HER2 back to plasma membrane. Expression of SORLA in cancer cell lines and bladder cancers correlates with HER2 levels. Depletion of SORLA targets HER2 to late endosomal/lysosomal compartments, impairs HER2-driven signaling and in vivo tumor growth. SORLA silencing also disrupts normal lysosome function and sensitizes anti-HER2 therapy sensitive and resistant cancer cells to lysosome-targeting cationic amphiphilic drugs. These findings reveal potentially important SORLA-dependent endosomal trafficking-linked vulnerabilities in HER2-driven cancers.

cell biology↗

bioRxiv2018

WDFY2 restrains matrix metalloprotease secretion and cell invasion by retention of VAMP3 in endosomal tubules

The endosomal FYVE- and WD40-domain-containing protein WDFY2 has been assigned a function as tumour suppressor, but its functional mechanism has remained elusive. Here we have used confocal, widefield and super-resolution fluorescence microscopy to show that WDFY2 localizes to the base of retromer-containing endosomal tubules by a mechanism that involves recognition of a specific pool of phosphatidylinositol 3-phosphate (PtdIns3P) by the WDFY2 FYVE domain. Affinity purification and mass spectrometry identified the v-SNARE VAMP3 as an interaction partner of WDFY2, and cellular knockout of WDFY2 caused a strong redistribution of VAMP3 into small vesicles near the plasma membrane. This was accompanied by increased secretion of the matrix metalloprotease MT1-MMP, enhanced degradation of extracellular matrix, and increased cell invasion. WDFY2 is frequently lost in metastatic cancers, most predominantly in ovarian and prostate cancer. We propose that WDFY2 acts as a tumor suppressor by serving as a gatekeeper for VAMP3 recycling.

cell biology↗

bioRxiv2018

Controlling fluid flow to improve cell seeding uniformity

Standard methods for seeding monolayer cell cultures in a multiwell plate or dish do not uniformly distribute cells on the surface. With traditional methods, users find aggregation around the circumference, in the centre, or a combination of the two. This variation is introduced due to the macro scale flow of the cell seeding suspension, and movement of the dish before cells can settle and attach to the surface. Reproducibility between labs, users, and experiments is hampered by this variability in cell seeding. We present a simple method for uniform and user-independent cell seeding using an easily produced uniform cell seeder (UCS) device. This allows precise control of cell density in a reproducible manner. By containing the cell seeding suspension in a defined volume above the culture surface with the UCS, fluctuations in cell density are minimised. Seeding accuracy, as defined by the actual cell density versus the target seeding density is improved dramatically across users with various levels of expertise. We go on to demonstrate the impact of local variation in cell density on the lineage commitment of human embryonic stem cells (hESCs) towards pancreatic endoderm (PE). Variations in the differentiation profile of cells across a culture well closely mirror variations in cell density introduced by seeding method - with the UCS correcting variations in differentiation efficiency. The UCS device provides a simple and reproducible method for uniform seeding across multiple culture systems.

cell biology↗

bioRxiv2018

Precise detection of S phase onset reveals decoupled G1/S transition events

The eukaryotic cell division cycle is the process by which cells duplicate their genomes and proliferate. Transitions between sequential cell cycle phases are tightly orchestrated to ensure precise and efficient cell cycle progression. Interrogating molecular events at these transitions is important for understanding normal and pathological cell proliferation and mechanisms that ensure genome stability. A popular fluorescent reporter system known as \"FUCCI\" has been widely adopted for identifying cell cycle phases. Using time-lapse fluorescence microscopy, we quantitatively analyzed the dynamics of the FUCCI reporters relative to the transitions into and out of S phase. Although the original reporters reflect the E3 ubiquitin ligase activities for which they were designed, SCFSkp2 and APCCdh1, their dynamics are significantly and variably offset from actual S phase boundaries. To precisely mark these transitions, we generated and thoroughly validated a new reporter containing a PCNA-interacting protein degron whose oscillations are directly coupled to the process of DNA replication itself. We combined this reporter with the geminin-based APCCdh1 reporter to create \"PIP-FUCCI.\" PIP degron reporter dynamics closely correlate with S phase transitions irrespective of reporter expression levels. Using PIP-FUCCI, we made the unexpected observation that the apparent timing of APCCdh1 inactivation frequently varies relative to the onset of S phase. We demonstrate that APCCdh1 inactivation is not a strict pre-requisite for S phase entry, though delayed APCCdh1 inactivation correlates with longer S phase. Our results illustrate the benefits of precise delineation of cell cycle phase boundaries for uncovering the sequences of molecular events at critical cell cycle transitions.

cell biology↗

bioRxiv2018

Insights into centriole biogenesis and evolution revealed by cryoTomography of doublet and triplet centrioles.

Centrioles are cylindrical assemblies comprised of 9 singlet, doublet, or triplet microtubules, essential for the formation of motile and sensory cilia. While the structure of the cilium is being defined at increasing resolution, centriolar structure remains poorly understood. Here, we used electron cryo-tomography to determine the structure of mammalian (triplet) and Drosophila (doublet) centrioles at 25 [A] resolution. Mammalian centrioles have two distinct domains: a 200 nm proximal core region connected by A-C linkers, and a distal domain where the C-tubule is incomplete and a pair of novel linkages stabilize the assembly producing a geometry more closely resembling the ciliary axoneme. Drosophila centrioles more closely resemble the mammalian core, but with their doublets linked through A tubules. The commonality of core region length, and the abrupt transition in mammalian centrioles, suggests a conserved length-setting mechanism. The unexpected linker diversity suggests how unique centriolar architectures arise in different tissues and organisms.

cell biology↗

bioRxiv2018

Trypanosomes have divergent kinesin-2 proteins that function differentially in IFT, cell division, and motility

Trypanosoma brucei, the causative agent of African sleeping sickness, has a flagellum that is crucial for motility, pathogenicity, and viability. In most eukaryotes, the intraflagellar transport (IFT) machinery drives flagellum biogenesis, and anterograde IFT requires kinesin-2 motor proteins. In this study, we investigated the function of the two T. brucei kinesin-2 proteins, TbKin2a and TbKin2b, in bloodstream form trypanosomes. We found that compared to other kinesin-2 proteins, TbKin2a and TbKin2b show greater variation in neck, stalk, and tail domain sequences. Both kinesins contributed additively to flagellar lengthening. Surprisingly, silencing TbKin2a inhibited cell proliferation, cytokinesis and motility, whereas silencing TbKin2b did not. TbKin2a was localized on the flagellum and colocalized with IFT components near the basal body, consistent with it performing a role in IFT. TbKin2a was also detected on the flagellar attachment zone, a specialized structure in trypanosome cells that connects the flagellum to the cell body. Our results indicate that kinesin-2 proteins in trypanosomes play conserved roles in IFT and exhibit a specialized localization, emphasizing the evolutionary flexibility of motor protein function in an organism with a large complement of kinesins.

cell biology↗

bioRxiv2018

Controlled cycling and quiescence enables homology directed repair in engraftment-enriched adult hematopoietic stem and progenitor cells

Hematopoietic stem cells (HSCs) are the source of all blood components, and genetic defects in these cells are causative of disorders ranging from severe combined immunodeficiency to sickle cell disease. However, genome editing of long-term repopulating HSCs to correct mutated alleles has been challenging. HSCs have the ability to either be quiescent or cycle, with the former linked to stemness and the latter involved in differentiation. Here we investigate the link between cell cycle status and genome editing outcomes at the causative codon for sickle cell disease in adult human CD34+ hematopoietic stem and progenitor cells (HSPCs). We show that quiescent HSPCs that are immunophenotypically enriched for engrafting stem cells predominantly repair Cas9-induced double strand breaks (DSBs) through an error-prone non-homologous end-joining (NHEJ) pathway and exhibit almost no homology directed repair (HDR). By contrast, non-quiescent cycling stem-enriched cells repair Cas9 DSBs through both error-prone NHEJ and fidelitous HDR. Pre-treating bulk CD34+ HSPCs with a combination of mTOR and GSK-3 inhibitors to induce quiescence results in complete loss of HDR in all cell subtypes. We used these compounds, which were initially developed to maintain HSCs in culture, to create a new strategy for editing adult human HSCs. CD34+ HSPCs are edited, allowed to briefly cycle to accumulate HDR alleles, and then placed back in quiescence to maintain stemness, resulting in 6-fold increase in HDR/NHEJ ratio in quiescent, stem-enriched cells. Our results reveal the fundamental tension between quiescence and editing in human HSPCs and suggests strategies to manipulate HSCs during therapeutic genome editing.

cell biology↗

bioRxiv2018

Concurrent processes set E. coli cell division

A cell can divide only upon completion of chromosome segregation, or its daughters would lose genetic material [1, 2]. In E. coli bacteria, the prevalent view is that cells divide a fixed amount of time after they start to copy the chromosomes [3, 4], and a known pathway prevents cells from dividing if the chromosomes interfere with the cytokinesis machinery [5]. However, whether completion of segregation is typically the bottleneck process for the decision to divide has never been stringently tested on single cells. We show how key trends in single-cell data lead to challenge the classic idea of replication-segregation limiting cell division. Instead, the data agree with a model where two concurrent processes (setting replication initiation and inter-division time) set cell division on competing time scales. During each cell cycle, division is set by the slowest process (an \" ...

cell biology↗

bioRxiv2018

The GalNAc-T Activation (GALA) Pathway: Drivers and Markers

The enzymes GALNTs add GalNAc sugar to Ser and Thr residues, forming the Tn glycan. GALNTs are activated by trafficking from Golgi to ER, a process driven by the Src kinase and negatively regulated by ERK8. This GALNTs activation (aka GALA) pathway induces high Tn levels and is a key driver of liver tumor growth. Recently, Tabak and colleagues have contested our previous data that EGF stimulation can induce GALNTs relocation. Here, we show that relocation induced by EGF is actually detectable in the images acquired by Tabak et al. Furthermore, we show that expression of EGFR enhances relocation and appears required to drive relocation induced by ERK8 depletion. We also propose that quantification of O-glycosylation of the ER resident protein PDIA4 provides an alternative measure of GALA. In sum, we demonstrate that non-reproducibility was due to experimental errors, that EGFR is indeed a driver of GALA and propose additional markers to facilitate the study of this pathway.

cell biology↗

bioRxiv2018

Actin filaments regulate microtubule growth at the centrosome.

The centrosome is the main microtubule-organizing centre. It also organizes a local network of actin filaments. However, the precise function of the actin network at the centrosome is not well understood. Here we show that increasing densities of actin filaments at the centrosome of lymphocytes were correlated with reduced amounts of microtubules. Furthermore, lymphocyte activation resulted in centrosomal-actin disassembly and an increase in microtubule number. To further investigate the direct crosstalk between actin and microtubules at the centrosome, we performed in vitro reconstitution assays based on (i) purified centrosomes and (ii) on the co-micropatterning of microtubule seeds and actin filaments. The two assays demonstrated that actin filaments perturb microtubule growth by steric hindrance. Finally, we showed that cell adhesion and spreading leads to lower densities of centrosomal actin thus resulting in higher microtubule growth. Hence we propose a novel mechanism by which the number of centrosomal microtubules is regulated by cell adhesion and actin-network architecture.

cell biology↗

bioRxiv2018

NDUFAB1 Protects Heart by Coordinating Mitochondrial Respiratory Complex and Supercomplex Assembly

The impairment of mitochondrial bioenergetics, often coupled with exaggerated reactive oxygen species (ROS) production, is emerging as a common mechanism in diseases of organs with a high demand for energy, such as the heart. Building a more robust cellular powerhouse holds promise for protecting these organs in stressful conditions. Here, we demonstrate that NDUFAB1 (NADH:ubiquinone oxidoreductase subunit AB1), acts as a powerful cardio-protector by enhancing mitochondrial energy biogenesis. In particular, NDUFAB1 coordinates the assembly of respiratory complexes I, II, and III and supercomplexes, conferring greater capacity and efficiency of mitochondrial energy metabolism. Cardiac-specific deletion of Ndufab1 in mice caused progressive dilated cardiomyopathy associated with defective bioenergetics and elevated ROS levels, leading to heart failure and sudden death. In contrast, transgenic overexpression of Ndufab1 effectively enhanced mitochondrial bioenergetics and protected the heart against ischemia-reperfusion injury. Our findings identify NDUFAB1 as a central endogenous regulator of mitochondrial energy and ROS metabolism and thus provide a potential therapeutic target for the treatment of heart failure and other mitochondrial bioenergetics-centered diseases.

cell biology↗

bioRxiv2018

HIR-1 Mediates Response to Hypoxia-Induced Extracellular Matrix Remodeling

Inadequate tissue oxygen, or hypoxia, is a central concept in pathophysiology of ischemic disorders and cancer. Hypoxia promotes extracellular matrix (ECM) remodeling, cellular metabolic adaptation and metastasis. To determine how cells respond to hypoxia-induced ECM remodeling, we performed a large-scale forward genetic screen in C. elegans. We identified a previously uncharacterized receptor tyrosine kinase (RTK) named HIR-1 as a key mediator in a pathway that orchestrates transcriptional responses to hypoxia-induced ECM remodeling. Impaired ECM integrity caused by hypoxia or deficiency of the oxygen-dependent procollagen hydroxylases, heme peroxidases or cuticular collagens activates gene expression through inhibition of HIR-1. Genetic suppressor screens identified NHR-49 and MDT-15 as transcriptional regulators downstream of HIR-1. Cellular responses through HIR-1 maintain ECM homeostasis and promote animal adaptation to severe hypoxia. We propose that C. elegans HIR-1 defines an unprecedented type of RTK that mediates responses to hypoxia-induced ECM remodeling by mechanisms that are likely conserved in other organisms.\n\nONE-SENTENCE SUMMARYA regulatory pathway for ECM homeostasis underlies adaptation to hypoxia and re-oxygenation

cell biology↗

bioRxiv2018

Novel organelle anion channels formed by chromogranin B drive normal granule maturation in endocrine cells

All endocrine cells need an anion conductance for maturation of secretory granules. Identity of this family of anion channels has been elusive for forty years. We now show that a family of granule protein, CHGB, serves the long-sought conductance. CHGB interacts with membranes through two amphipathic helices, and forms a chloride channel with large conductance and high anion selectivity. Fast kinetics and high cooperativity suggest that CHGB tetramerizes to form a functional channel. Nonfunctional mutants separate CHGBs function in granule maturation from that in granule biogenesis. In neuroendocrine cells, CHGB channel and a H+-ATPase drives normal insulin maturation inside or dopamine loading into secretory granules. CHGBs tight membrane-association after exocytotic release of secretory granules separates its intracellular function from extracellular functions of its proteolytic peptides. CHGB-null mice show consistent impairment of granule acidification in pancreatic beta-cells. These findings together support that the phylogenetically conserved CHGB proteins constitute a new family of organelle chloride channels in the regulated secretory pathway among various endocrine cells.

cell biology↗

bioRxiv2018

Avidity-driven polarity establishment via multivalent lipid-GTPase module interactions

While Rho GTPases are indispensible regulators of cellular polarity, the mechanisms underlying their anisotropic activation at membranes have been elusive. Using the budding yeast Cdc42 GTPase module, which includes a Guanine nucleotide Exchange Factor (GEF) Cdc24 and the scaffold Bem1, we find that avidity generated via multivalent anionic lipid interactions is a critical mechanistic constituent of polarity establishment. We identify Cationic-enriched Lipid Interacting Clusters (CLICs) in Bem1 that drive the interaction of the scaffold-GEF complex with anionic lipids at the cell pole. This interaction increases lipid acyl chain ordering, thus contributing to membrane rigidity and feedback between Cdc42 and the membrane environment. Sequential mutation of the Bem1 CLIC motifs, PX domain and the PH domain of Cdc24 lead to a progressive loss of cellular polarity stemming from defective Cdc42 nanoclustering on the plasma membrane and perturbed signaling. Our work demonstrates the importance of avidity via multivalent anionic lipid interactions in the spatial control of GTPase activation.

cell biology↗

bioRxiv2018

Identification of a secretion-enhancing cis regulatory targeting element (SECReTE) involved in mRNA localization and protein synthesis

Earlier dogma states that mRNAs encoding secreted and membrane protein (mSMPs) reach the ER in a translation-dependent manner through the signal recognition particle (SRP) pathway. In this pathway, the signal sequence of the translation product is recognized by SRP and the mRNA-ribosome-nascent-chain-SRP complex is recruited to the ER via the interaction with an endoplasmic reticulum (ER)-localized SRP receptor. This model suggests that the translation product dictates the delivery of mRNAs to the ER and that the mRNA is a passive passenger. However, new evidence challenges this model and implies the existence of both translation - and SRP-independent mRNA localization to the ER, raising the possibility that mRNAs have an active role in determining their localization to the ER.\n\nBesides serving as a template for protein translation, mRNAs carry information required for other regulatory processes such as mRNA processing, translation and transcription efficiency, degradation and localization. In yeast, mRNA localization governed by cis-acting sequence elements has been characterized for asymmetrically (e.g. bud) localized mRNAs that localize to, and are transported with, cortical ER. Now, we identify a cis motif in mSMPs that targets mRNAs mainly to the nuclear ER in yeast and increases both protein synthesis and secretion. Termed SECReTE, for secretion-enhancing cis regulatory targeting element, this motif was identified by computational analysis of genes encoding secretome proteins. SECReTE consists of [≥]10 repetitive triplets enriched with pyrimidines (i.e. Cs and Us) every third base (i.e. NNY, N - any nucleotide, Y - pyrimidine), and is found particularly in mRNAs coding for cell wall proteins. To study the physiological relevance of SECReTE, we introduced synonymous mutations that either elevate or decrease its overall score in genes coding for secreted proteins, without changing the protein sequence, and examined the physiological effects in yeast. An increase in the SECReTE score elevated the synthesis and secretion of endogenous proteins while, in contrast, a reduction led to less secretion and physiological defects. Importantly, the addition of SECReTE to the 3UTR of an exogenous protein (e.g. SS-GFP) led to its increased secretion from yeast. SECReTE is present all through evolution and, thus, constitutes a novel RNA targeting motif found in both prokaryotes and eukaryotes.

cell biology↗

bioRxiv2018

Induction of muscle stem cell quiescence by the secreted niche factor Oncostatin M

The balance between stem cell quiescence and proliferation in skeletal muscle is tightly controlled, but perturbed in a variety of disease states. Despite progress in identifying activators of stem cell proliferation, the niche factor(s) responsible for quiescence induction remain unclear. Here we report an in vivo imaging-based screen which identifies Oncostatin M (OSM), a member of the interleukin-6 family of cytokines, as a potent inducer of muscle stem cell (MuSC, satellite cell) quiescence. OSM is produced by muscle fibers, induces reversible MuSC cell cycle exit, and maintains stem cell regenerative capacity as judged by serial transplantation. Conditional OSM receptor deletion in satellite cells leads to stem cell depletion and impaired regeneration following injury. These results identify Oncostatin M as a secreted niche factor responsible for quiescence induction, and for the first time establish a direct connection between induction of quiescence, stemness, and transplantation potential in solid organ stem cells.

cell biology↗

bioRxiv2018

Circadian Clock Regulation of the Secretory Pathway

Collagen is the most abundant secreted protein in vertebrates that persists throughout life without renewal. The unchanging nature of collagen contrasts with observed continued collagen synthesis throughout adulthood and with conventional transcriptional and translational homeostatic mechanisms that replace damaged proteins with new copies. Here we show circadian clock regulation of procollagen transport from ER-to-Golgi and Golgi-to-plasma membrane by sequential rhythmic expression of SEC61, TANGO1, PDE4D and VPS33B. The result is nocturnal procollagen synthesis and daytime collagen fibril assembly in mice. Rhythmic collagen degradation by CTSK maintains collagen homeostasis. This circadian cycle of collagen synthesis, assembly and degradation affects only a pool of newly-synthesized collagen whilst maintaining the persistent collagen network. Disabling the circadian clock causes collagen accumulation and abnormal fibrils in vivo. In conclusion, our study has identified a circadian clock mechanism of protein homeostasis in which a sacrificial pool of collagen is synthesized and removed to maintain tissue function.

cell biology↗