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Modeling of axonal endoplasmic reticulum network by spastic paraplegia proteins

Axons contain an endoplasmic reticulum (ER) network that is largely smooth and tubular, thought to be continuous with ER throughout the neuron, and distinct in form and function from rough ER; the mechanisms that form this continuous network in axons are not well understood. Mutations affecting proteins of the reticulon or REEP families, which contain intramembrane hairpin domains that can model ER membranes, cause an axon degenerative disease, hereditary spastic paraplegia (HSP). Here, we show that these proteins are required for modeling the axonal ER network in Drosophila. Loss of reticulon or REEP proteins can lead to expansion of ER sheets, and to partial loss of ER from distal motor axons. Ultrastructural analysis reveals an extensive ER network in every axon of peripheral nerves, which is reduced in larvae that lack reticulon and REEP proteins, with defects including larger and fewer tubules, and occasional gaps in the ER network, consistent with loss of membrane curvature. Therefore HSP hairpin-containing proteins are required for shaping and continuity of the axonal ER network, suggesting an important role for ER modeling in axon maintenance and function.

Cell Biology

Loss of a doublecortin (DCX) domain containing protein causes structural defects in a tubulin-based organelle of Toxoplasma gondii and impairs host cell invasion.

The ~6000 species in phylum Apicomplexa are single-celled obligate intracellular parasites. Their defining characteristic is the \"apical complex\", membranous and cytoskeletal elements at the apical end of the cell that participate in host-cell invasion. The apical complex of Toxoplasma gondii and some other apicomplexans includes a cone-shaped assembly, the \"conoid\", which (in T. gondii) comprises 14 spirally arranged fibers that are non-tubular polymers of tubulin. The tubulin dimers used for the conoid fibers make canonical microtubules elsewhere in the same cell, suggesting that their special arrangement in the conoid fibers is dictated by non-tubulin proteins. One candidate for this role is TgDCX, which has a doublecortin (DCX) domain and a TPPP/P25-alpha domain, known modulators of tubulin polymer structure. Loss of TgDCX radically disrupts the structure of the conoid, severely impairs host cell invasion, and slows growth. The defects of TgDCX-null parasites are corrected by re-introduction of a TgDCX coding sequence.

Cell Biology

Separase Protease Activity is Required for Cytokinesis in addition to Chromosome Segregation

Chromosomal segregation and cytokinesis are tightly regulated processes required for successful cell division. The cysteine protease separase cleaves a subunit of the cohesin complex to allow chromosome segregation at anaphase onset. Separase also regulates meiotic cortical granule exocytosis and vesicle trafficking during cytokinesis, both of which involve RAB-11. Separase has non-proteolytic signaling functions in addition to its role in substrate cleavage, and its mechanism in exocytosis is unknown. We sought to determine whether separase regulates RAB-11 vesicle exocytosis through a proteolytic or non-proteolytic mechanism. To address this question, we generated a protease-dead separase, SEP-1PD::GFP, and unexpectedly found that it is dominant negative. Consistent with its role in cohesin cleavage, SEP-1PD::GFP causes chromosome segregation defects. Depletion of the substrate subunit of cohesin rescues this defect, suggesting that SEP-1PD::GFP impairs cohesin cleavage by a substrate trapping mechanism. We investigated whether SEP-1PD::GFP also impairs RAB-11 vesicle trafficking. SEP-1PD::GFP causes a low rate of cytokinesis failure that is synergistically exacerbated by depletion of the core exocytic t-SNARE protein SYX-4. Interestingly, SEP-1PD::GFP causes an accumulation of RAB-11 vesicles at the cleavage furrow site and delayed the exocytosis of cortical granules during anaphase I. Depletion of syx-4 further enhanced RAB-11::mCherry and SEP-1PD::GFP plasma membrane accumulation during cytokinesis. These findings suggest that the protease activity of separase is required for the exocytosis of RAB-11 vesicles during cortical granule exocytosis and mitotic cytokinesis.\n\nAuthor SummaryThe defining event of cell division is the equal distribution of the genetic material to daughter cells. Once sister chromatids align on the metaphase plate, the cell releases the brakes to enter anaphase by activating the protease separase. Separase cleaves the cohesin glue holding duplicated sister chromatids together allowing chromosome segregation. Subsequently, the cell must orchestrate a complex series of anaphase events to equally partition the chromatids and the rest of the cellular components into two distinct daughter cells during cytokinesis. Separase has multiple functions during anaphase to help regulate several key events, including promoting vesicle exocytosis required for cytokinesis. Previous studies have shown that separase can exert control over different events either through substrate cleavage, or by triggering signaling pathways. Here we analyze the cellular functions of separase that are impacted by protease inactive separase. Our results show that separase cleaves cohesin to promote chromosome segregation and also cleaves another independent substrate to promote exocytosis. These findings provide a foundation for understanding the molecular control of separase in exocytosis and indicate that separase has multiple independent substrates that it must cleave to execute various functions. This mechanism may enable the cell to coordinate multiple anaphase events with chromosome segregation.

Cell Biology

Growth Factors do not regulate Golgi Complex-to-ER relocation of GalNAc-Ts in HeLa cells

Mucin-type O-glycosylation is initiated by the UDP-GalNAc polypeptide:N-acetylgalactosaminyltransferase (GalNAc-T) family of enzymes. Their activity results in the GalNAc 1-O-Thr/Ser structure, termed the Tn antigen, which is further decorated with additional sugars. In neoplastic cells, the Tn antigen is often overexpressed. Because O-glycosylation is controlled by the activity of GalNAc-Ts, their regulation is of great interest. Previous reports suggest that growth factors, EGF or PDGF, induce Golgi complex-to-endoplasmic reticulum (ER) relocation of both GalNAc-Ts and Tn antigen in HeLa cells, offering a mechanism for Tn antigen overexpression termed \"GALA\". However, we were unable to reproduce these findings. Upon treatment of HeLa cells with either EGF or PDGF we observed no change in the co-localization of endogenous GalNAc-T1, GalNAc-T2 or Tn antigen with the Golgi complex marker TGN46. There was also no enhancement of localization with the ER marker calnexin. We conclude that growth factors do not cause redistribution of GalNAc-Ts from the Golgi complex to the ER in HeLa cells.

Cell Biology

Hepatocyte nuclear factor 4-mediated lipotoxicity provokes mitochondrial damage in peroxisome-deficient pex19 mutants

Peroxisomes are important metabolic organelles involved in the catabolism of several lipid classes, e.g. very-long-chain fatty acids. Malfunction or absence of peroxisomes leads to accumulation of educts for peroxisomal {beta}-oxidation and mitochondrial damage, resulting in fatal perturbation of metabolism. The impact of peroxisome deficiency on mitochondria is not elucidated yet. Here we present a model of Hepatocyte nuclear factor 4 (Hnf4)-induced lipotoxicity and accumulation of non-esterified fatty acids (NEFA) as the cause for mitochondrial damage in consequence of peroxisome loss in a Peroxin19 (pex19) mutant. Hyperactive Hnf4 signaling leads to upregulation of lipase 3 and enzymes for mitochondrial {beta}-oxidation. This results in enhanced lipolysis, elevated concentrations of NEFA, maximal {beta}-oxidation and mitochondrial swelling. NEFA are ligands for Hnf4 and further enhance its activity. By genetic removal of Hnf4 in pex19 mutants, lipotoxicity and mitochondrial swelling are reduced and their survival is rescued.\n\nAuthor summaryPeroxisomes are cell organelles which play a major role in lipid metabolism. They interact with mitochondria, the organelles which are responsible for cellular energy production. Loss of peroxisomes, as it occurs in the rare, inheritable human disease class of Peroxisome Biogenesis Disorders, is lethal. Over the past couple of years, a number of studies showed that peroxisome loss leads to mitochondrial damage as a secondary consequence, but the underlying mechanism has not been understood yet. In our study, we use a mutant of the fruitfly Drosophila melanogaster as a model for Peroxisome Biogenesis Disorders and find that a protein called Hepatocyte nuclear factor 4 is hyperactive upon peroxisome loss, which provokes the mobilization of storage fat and, as a consequence, the accumulation of toxic free fatty acids. These enter the mitochondria, but cannot be used for energy gain. Free fatty acids are then trapped in the mitochondria and lead to their swelling and damage, which provides an explanation for mitochondrial defects in Peroxisomal Biogenesis Disorders. Genetic reduction of Hepatocyte nuclear factor 4 activity rescues the viability of the peroxisome mutant by reducing the accumulation of free fatty acids and the subsequent mitochondrial damage, which might provide a novel target for therapy development.

Cell Biology

Actin retrograde flow actively aligns and orients ligand-engaged integrins in focal adhesions.

Integrins are transmembrane receptors that, upon activation, bind extracellular matrix (ECM) or cell surface ligands and link them to the actin cytoskeleton to mediate cell adhesion and migration1,2. One model for the structural transitions mediating integrin activation termed \"the cytoskeletal force hypothesis\" posits that force transmitted from the cytoskeleton to ligand-bound integrins acts as an allosteric stabilizer of the extended-open, high-affinity state3. Since cytoskeletal forces in migrating cells are generated by centripetal \"retrograde flow\" of F-actin from the cell leading edge, where integrin-based adhesions are initiated4,5, this model predicts that F-actin flow should align and orient activated, ligand-bound integrins in integrin-based adhesions. Here, polarization-sensitive fluorescence microscopy of GFP-V{beta}3 integrin chimeras in migrating fibroblasts shows that integrins are aligned with respect to the axis of FAs and the direction of F-actin flow, and this alignment requires binding immobilized ligand and talin-mediated linkage to a flowing cytoskeleton. Polarization imaging and Rosetta modelling of chimeras engineered to orient GFP differentially with respect to the integrin headpiece suggest that ligand-bound V{beta}3 integrin may be markedly tilted by the force of F-actin flow. These results show that actin cytoskeletal forces actively sculpt an anisotropic molecular scaffold in FAs that may underlie the ability of cells to sense directional ECM and physical cues.

Cell Biology

Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration

Integrin {beta} heterodimer cell surface receptors mediate adhesive interactions that provide traction for cell migration. Here, we test whether the integrin head, known from crystal structures, adopts a specific orientation dictated by the direction of actin flow on the surface of migrating cells. We insert GFP into the rigid head of the full integrin, model with Rosetta the orientation of GFP and its transition dipole relative to the integrin, and measure orientation with fluorescence polarization microscopy. Dependent on coupling to the cytoskeleton, integrins orient in the same direction as retrograde actin flow with their cytoskeleton-binding {beta}-subunits tilted by applied force. The measurements demonstrate that intracellular forces can orient cell surface integrins and support a molecular model of integrin activation by cytoskeletal force. We have developed a method that places atomic, ~[A] structures of cell surface receptors in the context of functional, cellular length-scale, ~m measurements and shows that rotation and tilt of cell surface receptors relative to the membrane plane can be restrained by interactions with other cellular components.

Cell Biology

mTORC1 controls cytoplasmic crowding by regulating ribosome concentration

Summary (Abstract)Macromolecular crowding has a profound impact on reaction rates and the physical properties of the cell interior, but the mechanisms that regulate crowding are poorly understood. We developed Genetically Encoded Multimeric nanoparticles (GEMs) to dissect these mechanisms. GEMs are homomultimeric scaffolds fused to a fluorescent protein. GEMs self-assemble into bright, stable fluorescent particles of defined size and shape. By combining tracking of GEMs with genetic and pharmacological approaches, we discovered that the mTORC1 pathway can tune the effective diffusion coefficient of macromolecules [≥]15 nm in diameter more than 2-fold without any discernable effect on the motion of molecules [≥]5 nm. These mTORCI-dependent changes in crowding and rheology affect phase-separation both in vitro and in vivo. Together, these results establish a role for mTORCI in controlling both the biophysical properties of the cytoplasm and the phase-separation of biopolymers.

cell biology

Cotranslational assembly imposes evolutionary constraints on homomeric proteins

There is increasing evidence that some proteins fold during translation, i.e. cotranslationally, which implies that partial protein function, including interactions with other molecules, could potentially be unleashed early on during translation. Although little is known about cotranslational assembly mechanisms, for homomeric protein complexes, translation by the ribosome, folding and assembly, should be well-coordinated to avoid misassembly in the context of polysomes. We analysed 3D structures of homomers and identified a statistically significant trend conserved across evolution that supports this hypothesis: namely that homomeric contacts tend to be localized towards the C-terminus rather than N-terminus of homomeric polypeptide chains. To probe this in more detail, we expressed a GFP-based library of 611 homomeric E. coli genes, and analyzing their folding and assembly in vivo. Consistent with our hypothesis, interface residues tend to be located near the N-terminus in cotranslationally aggregating homomers. In order to dissect the mechanisms of folding and assembly under controlled conditions, we engineered a protein library with three variable components: (i) the position and type homomerization domain, (ii) the reporter domain and (iii) the linker length that connects the two. By analyzing the misassembly rates of these engineered constructs in vivo, in vitro and in silico, we confirmed our hypothesis that C-terminal homomerization is favorable to N-terminal homomerization. More generally, these results provide a set of spatiotemporal constraints within polypeptide chains that favor efficient assembly, with implications for protein evolution and design.

Cell Biology

Functionally redundant control of cardiac hypertrophic signaling by inositol 1,4,5-trisphosphate receptors

Calcium plays an integral role to many cellular processes including contraction, energy metabolism, gene expression, and cell death. The inositol 1,4,5-trisphosphate receptor (IP3R) is a calcium channel expressed in cardiac tissue. There are three IP3R isoforms encoded by separate genes. In the heart, the IP3R-2 isoform is reported to being most predominant with regards to expression levels and functional significance. The functional roles of IP3R-1 and IP3R-3 in the heart are essentially unexplored despite measureable expression levels. Here we show that all three IP3Rs isoforms are expressed in both neonatal and adult rat ventricular cardiomyocytes and in human heart tissue. All three IP3R proteins were expressed throughout the cardiomyocyte sarcoplasmic reticulum. Using isoform specific siRNA, we found that expression of all three IP3R isoforms are required for hypertrophic signaling downstream of endothelin-1 stimulation. Mechanistically, IP3Rs specifically contribute to activation of the hypertrophic program by mediating the positive inotropic effects of endothelin-1 leading to downstream activation of nuclear factor of activated T-cells. Our findings highlight previously unidentified functions for IP3R isoforms in the heart with significant implications for hypertrophic signaling in animal models and human disease.\n\nSignificanceHypertrophy is an adaptive response to cardiac stress which can lead to arrhythmias and cardiac failure. The peptide hormone endothelin-1(ET-1) is a potent activator of the hypertrophic program in cardiomyocytes. IP3R calcium channels are activated downstream of ET-1 during hypertrophy. We now show that all three IP3R proteins are essential for hypertrophic signaling downstream of ET-1. Activation of IP3Rs did not lead to nuclear-specific calcium transients but instead led to altered contractility ultimately, leading to NFAT activation and activation of the hypertrophic program. These effects were independent of alterations in IP3R protein expression levels both in vitro and in the human failing heart. Our results identify a new paradigm in IP3R signaling in the heart with relevance to human disease.

Cell Biology

IMiQC: a novel protein quality control compartment protecting mitochondrial functional integrity

Aggregation processes can cause severe perturbations of cellular homeostasis and are frequently associated with diseases. We performed a comprehensive analysis of mitochondrial quality and function in presence of misfolded, aggregation-prone polypeptides. Although we observed significant aggregate formation inside mitochondria, we observed only a minor impairment of mitochondrial function. We could show that detoxification of misfolded reporter polypeptides as well as endogenous proteins inside mitochondria takes place via their sequestration into the specific organellar deposit site Intra-Mitochondrial Protein Quality Control Compartment (IMiQC). Only minor amounts of co-aggregated proteins were associated with IMiQC and neither resolubilization nor degradation by the mitochondrial PQC system were observed. The single IMiQC aggregate deposit was not transferred to daughter cells during cell division. Detoxification of misfolded polypeptides via IMiQC formation was highly dependent on a functional mitochondrial fission machinery. We conclude that the formation of the aggregate deposit is an important mechanism to maintain full functionality of mitochondria under proteotoxic stress conditions.\n\nList of Abbreviations

Cell Biology

The FACT complex and cell cycle progression are essential to maintain asymmetric transcription factor partitioning during cell division

The polarized partitioning of proteins in cells underlies asymmetric cell division, which is an important driver of development and cellular diversity. Like most cells, the budding yeast Saccharomyces cerevisiae divides asymmetrically to give two distinct daughter cells. This asymmetry mimics that seen in metazoans and the key regulatory proteins are conserved from yeast to human. A well-known example of an asymmetric protein is the transcription factor Ace2, which localizes specifically to the daughter nucleus, where it drives a daughter-specific transcriptional network. We performed a reverse genetic screen to look for regulators of asymmetry based on the Ace2 localization phenotype. We screened a collection of essential genes in order to analyze the effect of core cellular processes in asymmetric cell division. This identified a large number of mutations that are known to affect progression through the cell cycle, suggesting that cell cycle delay is sufficient to disrupt Ace2 asymmetry. To test this model we blocked cells from progressing through mitosis and found that prolonged cell cycle arrest is sufficient to disrupt Ace2 asymmetry after release. We also demonstrate that members of the evolutionary conserved FACT chromatin-remodeling complex are required for both asymmetric and cell cycle-regulated localization of Ace2.

Cell Biology

Lipid metabolic perturbation is an early-onset phenotype in adult spin mutants: a Drosophila model for lysosomal storage disorders

Intracellular accumulation of lipids and swollen dysfunctional lysosomes are linked to several neurodegenerative diseases including lysosomal storage disorders (LSD). A detailed characterization of lipid metabolic changes in relation to the onset and progression of neurodegeneration is currently missing. In this study, we systematically analyzed lipid perturbations in spinster (spin) mutants, a Drosophila model of neurodegeneration associated with LSD. Our results highlight an imbalance in brain ceramide and sphingosine as a crucial phenotype in the early stages of neurodegeneration. This perturbation in ceramide metabolism precedes the accumulation of endomembranous structures, manifestation of altered behavior and buildup of lipofuscin (the ageing pigment). Manipulating levels of ceramidase, and, consequently further altering these lipids in spin mutants have allowed us to conclude that ceramide/sphingosine homeostasis is the driving force in disease progression and is integral to spin function in the adult nervous system. Furthermore, we have identified 29 novel and direct interaction partners of Spin. We specifically focused on the lipid carrier protein, Lipophorin (Lpp), and demonstrate its localization with Spin in the adult nervous system and in organs specialized for lipid metabolism including fat bodies and oenocytes. Our observations in spin mutants of altered Lpp immunostaining, and of increased levels of lipid metabolites produced by oenocytes, allude to a functional relevance of the Spin-Lpp interaction.\n\nOverall, these results detailing the kinetics of ceramide perturbations in the context of lipofuscin accumulation, as well as the proteomics experiment, represent a valuable resource to further unravel the mechanistic link between systemic changes in lipid metabolism and lysosomal storage disorders.\n\nSummary StatementElevations in specific brain lipids and connections to relevant metabolic genes are identified in a fly model for lysosomal storage disorders. This enables a better understanding of disease progression.

Cell Biology

N-Acyl Dopamines Induce Apoptosis in PC12 Cell Line via the O-1918-Sensitive non-CB1-non-CB2 Receptor

Dopamine amides of long chain fatty acids (NADA) are a family of endogenous mammalian lipids with an unknown function; they are anti-proliferative for many cancer cell lines. The aim of this study was to identify the NADA receptor responsible for cell death induction. Using PC12 cells treated with NADA in combination with various receptor blockers, or pre-treated with the known receptor agonists to down-regulate the proposed receptor, NADA were shown to induce apoptosis. This activity was blocked only by the non-CB1-non-CB2 receptor antagonist O-1918, and by the pre-treatment with the agonists of this receptor ethanolamides of palmitic and oleic acids.

Cell Biology

Translational control of gurken mRNA in Drosophila development

Localised mRNA translation is a widespread mechanism for targeting protein synthesis, important for cell fate, motility and pathogenesis. In Drosophila, the spatiotemporal control of gurken/TGF- mRNA translation is required for establishing the embryonic body axes. A number of recent studies have highlighted key aspects of the mechanism of gurken mRNA translational control at the dorsoanterior corner of the mid-stage oocyte. Orb/CPEB and Wispy/GLD-2 are required for polyadenylation of gurken mRNA, but mis-localised gurken mRNA in the oocyte is not fully polyadenylated1. At the dorsoanterior corner, Orb and gurken mRNA have been shown to be enriched at the edge of Processing bodies, where translation occurs2. Over-expression of Orb in the adjacent nurse cells, where gurken mRNA is transcribed, is sufficient to cause mis-expression of Gurken protein3. In orb mutant egg chambers, reducing the activity of CK2, a Serine/Threonine protein kinase, enhances polarity defects, consistent with a phenotype relating to a mutation of a factor involved in gurken translation4. Here we show that sites phosphorylated by CK2 overlap with active Orb and with Gurken protein expression. We also consolidate the current literature into a working model for gurken mRNA translational control and review the role of kinases, cell cycle factors and polyadenylation machinery highlighting a multitude of conserved factors and mechanisms in the Drosophila egg chamber.

Cell Biology

Diverse roles of guanine nucleotide exchange factors in regulating collective cell migration

Efficient collective migration depends on a balance between contractility and cytoskeletal rearrangements, adhesion, and mechanical cell-cell communication, all controlled by GTPases of the RHO family. By comprehensive screening of guanine nucleotide exchange factors (GEFs) in human bronchial epithelial cell monolayers, we identified GEFs that are required for collective migration at large, such as SOS1 and {beta}-PIX, and RHOA GEFs that are implicated in intercellular communication. Downregulation of the latter GEFs differentially enhanced front-to-back propagation of guidance cues through the monolayer, and was mirrored by downregulation of RHOA expression and myosin-II activity. Phenotype-based clustering of knock-down behaviors identified RHOA-ARHGEF18 and ARHGEF3-ARHGEF28-ARHGEF11 clusters, indicating that the latter may signal through other RHO-family GTPases. Indeed, knock-down of RHOC produced an intermediate between the two phenotypes. We conclude that for effective collective migration the RHOA-GEFs-[->]ARHOA/C[->] actomyosin pathways must be optimally tuned to compromise between generation of motility forces and restriction of intercellular communication.

Cell Biology

Excitable RhoA dynamics drive pulsed contractions in the early C. elegans embryo.

Pulsed actomyosin contractility underlies diverse modes of tissue morphogenesis, but the underlying mechanisms remain poorly understood. Here, we combine quantitative imaging with genetic perturbations to identify a core mechanism for pulsed contractility in early C. elegans embryos. We show that pulsed accumulation of actomyosin is governed by local control of assembly and disassembly downstream of RhoA. Pulsed activation and inactivation of RhoA precede, respectively, accumulation and disappearance of actomyosin, and persist in the nearly complete absence of Myosin II. We find that fast positive feedback on RhoA activation drives pulse initiation, while F-actin dependent accumulation of the RhoA GTPase activating proteins (GAPs) RGA-3/4 provides delayed negative feedback to terminate each pulse. An experimentally constrained mathematical model confirms that in principle these feedbacks are sufficient to generate locally excitable RhoA dynamics. We propose that excitable RhoA dynamics are a common driver for pulsed contractility that can be differently tuned or coupled to actomyosin dynamics to produce a diversity of morphogenetic outcomes.

Cell Biology

In vitro profiling of endocrine cell death using UCHL1 and GAD65 as soluble biomarkers

BACKGROUNDPancreatic islet grafts are cultured in vitro prior to transplantation and this is associated to a variable degree of beta cell loss. Optimization of culture conditions is currently hampered by the lack of a specific and sensitive in vitro indicator of beta cell death. METHODSWe developed a high-sensitivity duplex bead-based immunoassay for two protein-type biomarkers of beta cell destruction, GAD65 and UCHL1, and investigated its proficiency for in vitro toxicity profiling on rodent and human beta cells, as compared to a semi-automatic and manual image-based assessment of beta cell death, and in vivo after intraportal islet transplantation. RESULTSBoth GAD65 and UCHL1 were discharged by necrotic and apoptotic beta cells proportionate to the number of dead beta cells as counted by microscopic methods. In vitro, UCHL1 was superior to GAD65, in terms of biomarker stability providing more sensitive detection of low grade beta cell death. In vivo, however, GAD65 was consistently detected after islet transplantation while UCHL1 remained undetectable. CONCLUSIONThe use of soluble biomarkers represents a fast, selective and sensitive method for beta cell toxicity profiling in vitro. UCHL1 is superior to GAD65 in vitro but not in vivo.

Cell Biology