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Role of anterograde motor Kif5b in clathrin-coated vesicle uncoating and clathrin-mediated endocytosis

Kif5b-driven anterograde transport and clathrin-mediated endocytosis (CME) are responsible for opposite intracellular trafficking, contributing to plasma membrane homeostasis. However, whether and how the two trafficking processes coordinate remain unclear. Here, we show that Kif5b directly interacts with clathrin heavy chain (CHC) at a region close to that for uncoating catalyst (Hsc70) and preferentially localizes on large clathrin-coated vesicles (CCVs). Uncoating in vitro is decreased for CCVs from the cortex of kif5b conditional knockout (mutant) mouse and facilitated by adding CHC-binding Kif5b fragments, while cell peripheral distribution of CHC or Hsc70 keeps unaffected by Kif5b depletion. Furthermore, cellular entry of vesicular stomatitis virus that internalized into large CCV is inhibited in cells by Kif5b depletion or introducing a dominant-negative Kif5b fragment. These findings showed a new role of Kif5b in CCV uncoating and CME, indicating Kif5b as a molecular knot connecting anterograde transport to CME.

cell biology

EXD2 and WRN exonucleases are required for interstrand crosslink repair in Drosophila

Interstrand crosslinks (ICLs) present a major threat to genome integrity, preventing both the correct transcription of active chromatin and complete replication of the genome. This is exploited in genotoxic chemotherapy where ICL induction is used to kill highly proliferative cancer cells. Repair of ICLs involves a complex interplay of numerous proteins, including those in the Fanconi anemia (FA) pathway, though alternative and parallel pathways have been postulated. Here, we investigate the role of the 3-5 exonuclease, EXD2, and the highly related WRN exonuclease (implicated in premature ageing human Werner syndrome), in repair of interstrand crosslinks in the fruit fly, Drosophila melanogaster. We find that flies mutant for EXD2 (DmEXD2) have elevated rates of genomic instability resulting from chromosome breakage and loss of the resulting acentric fragments, in contrast to WRN exonuclease (DmWRNexo) mutants where excess homologous recombination is the principal mechanism of genomic instability. Most notably, we demonstrate that proliferating larval neuroblasts mutant for either DmWRNexo or DmEXD2 are deficient in repair of DNA interstrand crosslinks caused by diepoxybutane or mitomycin C, strongly suggesting that each nuclease individually plays a role in repair of ICLs in flies. These findings have significant implications not only for understanding the complex process of ICL repair in humans, but also for enhancing cancer therapies that rely on ICL induction, with caveats for cancer therapy in Werner syndrome and Fanconi anemia patients.

cell biology

Murine SEC24D Can Substitute Functionally for SEC24C in vivo

The COPII component SEC24 mediates the recruitment of transmembrane cargoes or cargo adaptors into newly forming COPII vesicles on the ER membrane. Mammalian genomes encode four Sec24 paralogs (Sec24a-d), with two subfamilies based on sequence homology (SEC24A/B and C/D), though little is known about their comparative functions and cargo-specificities. Complete deficiency for Sec24d results in very early embryonic lethality in mice (before the 8 cell stage), with later embryonic lethality (E 7.5) observed in Sec24c null mice. To test the potential overlap in function between SEC24C/D, we employed dual recombinase mediated cassette exchange to generate a Sec24cc-d allele, in which the C-terminal 90% of SEC24C has been replaced by SEC24D coding sequence. In contrast to the embryonic lethality at E7.5 of SEC24C-deficiency, Sec24cc-d/c-d pups survive to term, though dying shortly after birth. Sec24cc-d/c-d pups are smaller in size, but exhibit no obvious developmental abnormality. These results suggest that tissue-specific and/or stage-specific expression of the Sec24c/d genes rather than differences in cargo function explain the early embryonic requirements for SEC24C and SEC24D.

cell biology

6mer Seed Toxicity Determines Strand Selection in miRNAs

Many siRNAs and shRNAs are toxic to cancer cells through a 6mer seed sequence (position 2-7 of the guide strand). A siRNA screen with all 4096 possible 6mer seed sequences in a neutral RNA backbone revealed a preference for guanine in positions 1-3 and a GC content of >80% of the 6mer seed in the most toxic siRNAs. These 6mer seed containing siRNAs exert their toxicity by targeting survival genes which contain GC-rich 3UTRs. The master tumor suppressor miRNA miR-34a was found to be toxic through such a G-rich 6mer seed suggesting that certain tumor suppressive miRNAs use a toxic 6mer seed to kill cancer cells. An analysis of all mature miRNAs suggests that most miRNAs evolved to avoid guanine at the 5' end of the 6mer seed sequence of the predominantly expressed arm. In contrast, for many tumor suppressive miRNAs the predominant arm contains a G-rich toxic 6mer seed, presumably to eliminate cancer cells.

cell biology

A novel microtubule nucleation pathway for meiotic spindle assembly in oocytes

The meiotic spindle in oocytes is assembled in the absence of centrosomes, the major microtubule nucleation sites in mitotic and male meiotic cells. A crucial, yet unresolved question in meiosis is how spindle microtubules are generated without centrosomes and only around chromosomes in the large volume of oocytes. Here we report a novel oocyte-specific microtubule nucleation pathway that is essential for assembling most spindle microtubules complementarily with the Augmin pathway, and sufficient for triggering microtubule assembly in oocytes. This pathway is mediated by the kinesin-6 Subito/MKlp2, which recruits the {gamma}-tubulin complex to the spindle equator to nucleate microtubules in Drosophila oocytes. Away from chromosomes, Subito interaction with the {gamma}-tubulin complex is suppressed by its N-terminal region to prevent ectopic microtubule assembly in oocytes. We further demonstrate that the Subito complex from ovaries can nucleate microtubules from pure tubulin dimers in vitro. Taken together, microtubule nucleation regulated by Subito drives spatially restricted spindle assembly in oocytes.

cell biology

Allosteric receptor modulation of FFA2R turns natural agonists into potent activators of the superoxide generating neutrophil NADPH-oxidase

Acetate, agonist for the free fatty acid receptor 2 (FFA2R/GPR43), triggers an increase in the cytosolic concentration of free Ca2+ in neutrophils without any assembly of the superoxide generating NADPH-oxidase. We show that the phenylacetamide compound 58 (Cmp58; (S)-2-(4-chlorophenyl)-3,3-dimethyl-N-(5-phenylthiazol-2-yl)butanamide, lacking a direct activating effect on neutrophils, acts as a positive allosteric FFA2R modulator that turns acetate into a potent activating agonist that triggers an assembly of the NADPH-oxidase. The NADPH-oxidase activity could be further increased in neutrophils treated with the pro-inflammatory cytokine TNF. Many neutrophil chemoattractant receptors are stored in secretory organelles but no FFA2R mobilization was induced in neutrophils treated with TNF. The receptor selectivity was demonstrated through the inhibition of the neutrophil response induced by the combined action of acetate and Cmp58 by the FFA2R antagonist CATPB. Allosteric modulators that positively co-operate with natural FFA2R agonists and prime neutrophils in their response to such agonists, may serve as good tools for further unraveling the physiological functions of the FFA2R and its involvement in various diseases. In this study, allosteric modulation of FFA2R is introduced as a novel receptor selective mechanism to prime neutrophils to produce increased amounts of reactive oxygen species.

cell biology

Establishment of signaling interactions with cellular resolution for every cell cycle of embryogenesis

Intercellular signaling interaction plays a key role in breaking fate symmetry during animal development. Identification of the signaling interaction at cellular resolution is technically challenging, especially in a developing embryo. Here we develop a platform that allows automated inference and validation of signaling interaction for every cell cycle of C. elegans embryogenesis. This is achieved by generation of a systems-level cell contact map that consists of 1,114 highly confident intercellular contacts by modeling analysis and is validated through cell membrane labeling coupled with cell lineage analysis. We apply the map to identify cell pairs between which a Notch signaling interaction takes place. By generating expression patterns for two ligands and two receptors of Notch signaling pathway with cellular resolution using automated expression profiling technique, we are able to refine existing and identify novel Notch interactions during C. elegans embryogenesis. Targeted cell ablation followed by cell lineage analysis demonstrates the roles of signaling interactions over cell division in breaking fate symmetry. We finally develop a website that allows online access to the cell-cell contact map for mapping of other signaling interaction in the community. The platform can be adapted to establish cellular interaction from any other signaling pathways.

cell biology

Lipid perturbation-activated IRE-1 modulates autophagy and lipolysis during endoplasmic reticulum stress

Metabolic disorders such as obesity and nonalcoholic fatty liver disease (NAFLD) are emerging diseases that affect the global population. One facet of these disorders is attributed to the disturbance of membrane lipid composition. Perturbation of endoplasmic reticulum (ER) homeostasis through changes in membrane phospholipid composition results in activation of the unfolded protein response (UPR) and causes dramatic translational and transcriptional changes in the cell. To restore cellular homeostasis, the three highly conserved UPR transducers ATF6, IRE1, and PERK mediate cellular processes upon ER stress. The role of the UPR in proteotoxic stress caused by the accumulation of misfolded proteins is well understood but much less so under lipid perturbation-induced UPR (UPRLP). We found that genetically disrupted phosphatidylcholine synthesis in C. elegans causes, lipid perturbation, lipid droplet accumulation, and induced ER stress, all hallmarks of NAFLD. Transcriptional profiling of UPRLP animals shows a unique subset of genes modulated in an UPR-dependent manner that is unaffected by proteotoxic stress (UPRPT). Among these, we identified autophagy genes bec-1 and lgg-1 and the lipid droplet-associated lipase atgl-1 to be modulated by IRE-1. Considering the important role of lipid homeostasis and how its impairment contributes to the pathology of metabolic diseases, our data uncovers the indispensable role of a fully functional UPR program in regulating lipid homeostasis in the face of chronic ER stress and lipotoxicity.

cell biology

Complex Interplay between Serum and Fibroblasts in 3D Hepatocyte Co-culture

Previous studies have suggested that primary hepatocytes cultured in vitro undergo a rapid loss of function. On the other hand, in the clinic, drug induced liver injury typically manifests 5 days to 3 months after starting a medication. Thus, novel approaches that can maintain the function of primary human hepatocytes for longer durations of time may enable the development of improved in vitro assays for detecting hepatotoxicity. Previous studies have demonstrated that two-dimensional micro-patterning of hepatocytes with fibroblasts leads to improved maintenance of the hepatocyte phenotype relative to hepatocyte monocultures, in serum containing medium. Additionally, we, and others, have shown that three-dimensional culture of hepatocytes leads to enhanced function (in serum-free medium). In this study we wanted to (i) examine the effect of combining the above two approaches on hepatocyte function, and (ii) to further delineate the effect of serum on hepatocyte function. We developed a user-friendly and inexpensive approach for constructing layered spheroids. Similar to previous results in two-dimensional (2d) culture, we observed that 3d culture of hepatocytes alone (i.e. monoculture) in serum-containing medium led to an increase in the urea production rate, but near-complete loss of cytochrome activity in both lots of primary human hepatocytes (PHH) tested. In serum-free sandwich culture, cytochrome activity was maintained at the level observed in freshly thawed PHH for one lot, but almost completely lost in another lot. Spheroid culture of both lots of PHH in serum-free medium led to maintenance of CYP3A4 and CYP1A2 activity at the fresh thaw level, though CYP2B6 activity was reduced. In contrast to PHH monoculture, co-cultures of PHH with NIH 3T3 fibroblast cells benefitted from the presence of serum, and led to 3-5-fold increases in CYP activity relative to even serum-free spheroid monocultures. Layering of the fibroblasts did not result in improvements over mixed co-cultures. These results indicate the importance of appropriate serum-free monoculture control experiments in the evaluation of novel biomaterials and techniques for hepatocyte co-culture. Further, urea production and cytochrome production are decoupled; therefore, urea production is an insufficient readout when developing models for pharmaceutical applications.

cell biology

Microtubule end tethering of a processive Kinesin-8 motor Kif18b is required for spindle positioning

Mitotic spindle positioning specifies the plane of cell division during anaphase. Spindle orientation and positioning is therefore critical to ensure symmetric division in mitosis and asymmetric division during development. The control of astral microtubule length plays an essential role in positioning the spindle. Here we show using gene knockout that the Kinesin-8 Kif18b controls microtubule length to center the mitotic spindle at metaphase. Using an integrated approach, we reveal that Kif18b is a highly processive plus end-directed motor that uses a C-terminal non-motor microtubule-binding region to accumulate at growing microtubule plus ends. This region is regulated by phosphorylation to spatially control Kif18b accumulation at plus ends and is essential for Kif18b-dependent spindle positioning and regulation of microtubule length. Finally, we demonstrate that Kif18b shortens microtubules by increasing the catastrophe rate of dynamic microtubules. Overall, our work reveals that Kif18b utilizes its motile properties to reach microtubule ends where it regulates astral microtubule length to ensure spindle centering.

cell biology

Substrate channeling in oxylipin biosynthesis through a protein complex in the plastid envelope of Arabidopsis thaliana

Oxygenated membrane fatty acid derivatives dubbed oxylipins play important roles in the plants defense against biotic and abiotic cues. Plants challenged by insect pests, for example, synthesize a blend of different defense compounds that, amongst others, comprise volatile aldehydes and jasmonic acid (JA). Because all oxylipins are derived from the same pathway, we asked how their synthesis might be regulated and focused on two closely related, atypical cytochrome P450 enzymes designated CYP74A and CYP74B, i.e., allene oxide synthase (AOS) and hydroperoxide lyase (HPL). Both enzymes compete for the same substrate but give rise to different products. While the final product of the AOS branch is JA, those of the HPL branch comprise volatile aldehydes and alcohols. AOS and HPL are plastid envelope enzymes in Arabidopsis thaliana but accumulate at different locations. Biochemical experiments identified AOS as constituent of complexes also containing lipoxygenase 2 (LOX2) and allene oxide cyclase (AOC), which catalyze consecutive steps in JA precursor biosynthesis, while excluding the concurrent HPL reaction. Based on published X-ray data, the structure of this complex could be modelled and amino acids involved in catalysis and subunit interactions identified. Genetic studies identified the microRNA 319 (miR319)-regulated clade of TCP (TEOSINTE BRANCHED/CYCLOIDEA/PCF) transcription factor genes and CORONATINE INSENSITIVE 1 (COI1) to control JA production through the AOS-LOX2-AOC2 complex. Together, our results define a molecular branch point in oxylipin biosynthesis that allows fine-tuning the plants defense machinery in response to biotic and abiotic stimuli.

cell biology

Symbiosis-related genes sustain the development of a downy mildew pathogen on Arabidopsis thaliana

AO_SCPLOWBSTRACTC_SCPLOWThe interfaces through which nutrients are transferred from plant cells to arbuscular mycorrhiza fungi and biotrophic hyphal pathogens are structurally similar. We report that in Arabidopsis thaliana, mutations in homologs of common symbiosis genes (CSGs) encoding homologs of the symbiosis receptor kinase SYMRK, the nucleoporins NUP133 and SEC13 or the cation channel POLLUX reduce the reproductive success of Hyaloperonospora arabidopsidis (Hpa). Analysis of the multiplication of extracellular bacterial pathogens, Hpa-induced cell death or callose accumulation, as well as Hpa-or flg22-induced defence marker gene expression, did not reveal any traces of constitutive or exacerbated defence responses. We discovered an age-dependent, possibly senescence-related transition of haustorial shape that occurred significantly earlier and at higher frequency in the CSG mutants. These findings point to a function of the homologs of common symbiosis genes in haustorial maintenance thus revealing an overlapping gene set for the intracellular accommodation of hyphal symbionts and pathogens.

cell biology

Retrograde Transport and ATG-4.2-Mediated Maturation Cooperate to Remove Autophagosomes from the Synapse

Autophagy is spatially compartmentalized in neurons, with autophagosome biogenesis occurring in the axon and degradation in the cell body. The mechanisms that coordinate autophagosome formation, trafficking and degradation across the polarized structure of the neuron are not well understood. Here we use genetic screens and in vivo imaging in single neurons of C. elegans to demonstrate that specific steps of autophagy are differentially required in distinct subcellular compartments of the neuron. We demonstrate that completion of autophagosome biogenesis and closure at the synapse are necessary for dynein-mediated retrograde transport. We uncover a role for UNC-16/JIP3/Sunday Driver in facilitating autophagosome retrograde transport. Through forward genetic screens we then determine that autophagosome maturation and degradation in the cell body depend on removal of LGG-1/Atg8/GABARAP from autophagosomes by the protease ATG-4.2. Our studies reveal that regulation of distinct ATG4 proteases contributes to the coordination of autophagy across subcellular regions of the neuron.\n\nHIGHLIGHTS and eTOC BlurbO_LIAutophagosome closure, but not maturation, occurs locally at presynaptic sites\nC_LIO_LIRetrograde transport of autophagosomes requires the motor adaptor UNC-16/JIP3\nC_LIO_LIThe autophagy protease ATG-4.2, but not the related ATG-4.1, is required for autophagosome maturation and degradation\nC_LIO_LIDefects in retrograde transport and maturation genetically interact and enhance accumulation of autophagosomes in presynaptic regions\nC_LI

cell biology

Mitotic progression, arrest, exit or death is determined by centromere integrity and independent of de novo transcription

Recent studies have challenged the prevailing dogma that transcription is repressed during mitosis. Transcription was also proposed to sustain the spindle assembly checkpoint (SAC) for several hours in response to unattached kinetochores. Here we used live-cell imaging of human cells in culture, combined with RNA-seq and qPCR, to investigate the requirement for de novo transcription during mitosis. Under conditions of persistently unattached kinetochores, transcription inhibition with actinomycin D, or treatment with other DNA-intercalating drugs, delocalized the chromosomal passenger complex (CPC) protein Aurora B from centromeres, compromising SAC robustness and cell fate. However, we were unable to detect significant changes in transcript levels. Moreover, inhibition of transcription independently of DNA intercalation had no effect on SAC response, mitotic progression, exit or death. Mechanistically, we show that DNA intercalating agents reduce the interaction of the CPC with nucleosomes. Thus, the capacity of human cells to progress, sustain, exit or die in mitosis relies on centromere integrity, rather than de novo transcription.

cell biology

Comparable affinity of RabGDIα for GTP- and GDP-bound forms of Rab7 supports a four-state transition model for Rab7 subcellular localization

Endolysosomal system is linked to almost all aspects of cell life and diseases, and Rab7 occupies a critical node in this crucial pathway. However, there have been conflicting views about the exact role of Rab7 in membrane trafficking, since some studies have reported that Rab7 regulates the trafficking from early to late endosomes, while others highlighted its role in late endosomes to lysosomes progression. In the present study, we have revisited this issue from a new viewpoint. In COS-7 cells, a GDP-bound Rab7 mutant, T22N, was located to vesicular membranes as well as in cytoplasm. Similarly, the GTPase-deficient Q67L mutant of Rab7 resided in cytoplasm as well as on membranes. Additionally, we found that RabGDI interacted with both GTP- and GDP-bound forms of Rab7 in vitro. These results have prompted us to propose a four-state transition model for Rab7. This four-state model matches with our recent findings that Rab7 was initially recruited to macropinosomes in a GDP-bound inactive form and subsequently became activated during endocytic maturation in EGF-stimulated COS-7 cells.

cell biology

Stabilising and destabilising kinesin complexes queue at plus tips to ensure microtubule catastrophe at cell ends

In fission yeast, the length of interphase microtubule (iMT) arrays are adapted to cell length so as to maintain cell polarity and to help centre the nucleus and cell division ring. Here we show that length regulation of iMTs is dictated by spatially-regulated competition between MT-stabilising Tea2/Tip1/Mal3 (Kinesin-7) and MT-destabilising Klp5/Klp6/Mcp1 (Kinesin-8) complexes at iMT plus tips. During MT growth, the Tea2/Tip1/Mal3 complex remains bound to the plus tips of iMT bundles and restricts access to the plus tips by Klp5/Klp6/Mcp1, which accumulates behind it. At cell ends, Klp5/Klp6/Mcp1 invades the space occupied by the Tea2/Tip1/Tea1 kinesin complex triggering its displacement from iMT plus tips and MT catastrophe. These data show that in vivo, whilst the \"antenna model\" for iMT length- and age-dependent catastrophase accumulation has validity, length control is an emergent property reflecting spatially-regulated competition between multiple complexes at the MT plus tip.

cell biology

Expression of fatty acid transport protein in retinal pigment cells promotes lipid droplet expansion and photoreceptor homeostasis

Increasing evidence suggests that dysregulation of lipid metabolism is associated with neurodegeneration in retinal diseases such as age-related macular degeneration and in brain disorders such as Alzheimers and Parkinsons diseases. Lipid storage organelles (lipid droplets, LDs), accumulate in many cell types in response to stress, and it is now clear that LDs function not only as lipid stores but also as dynamic regulators of the stress response. However, whether these LD functions are always protective or can also be deleterious to the cell is unknown. Here, we investigated the consequences of LD accumulation on retinal cell homeostasis in transgenic flies and mice overexpressing fatty acid transport protein (FATP) in retinal pigment cells (RPCs). In wild-type Drosophila, overexpression of dFatp specifically in RPCs resulted in an expansion of LD size in both RPCs and in neighboring photoreceptors but was non-toxic. Similarly, in mice, LD accumulation induced by RPC-specific expression of human FATP1 was non-toxic and promoted mitochondrial energy metabolism in both RPCs and photoreceptor cells. In contrast, RPC-specific dFatp knockdown reduced neurodegeneration in Aats-metFB Drosophila mutants, which carry a defective respiratory chain, indicating that abnormal LD accumulation can be toxic under pathological conditions. Collectively, these findings indicate that FATP-mediated LD formation in RPCs induces a non-autonomous increase of LDs in photoreceptors that promotes homeostasis under physiological conditions but can be deleterious under pathological conditions.\n\nAuthor SummaryLipids are major cell constituents and are present in the membranes, as free lipids in the cytoplasm, or stored in vesicles called lipid droplets (LDs). Under conditions of stress, lipids stored in LDs can be released to serve as substrates for energy metabolism by mitochondria. However, lipid storage is deregulated in many degenerative disorders such as age-related macular degeneration and Alzheimers disease. Thus, it is unclear whether accumulation of LDs is protective or can also be toxic. To address this question, we examined the consequences of enforced LD accumulation on the health of retinal cells in flies and mice. Like humans, fly and mouse retinas contain retinal pigment cells (RPC) that support the functions of neighboring photoreceptor cells. We found that overexpression of the fatty acid transport protein (FATP) in RPCs induced accumulation of LDs in both transgenic flies and mice. Moreover, LD accumulation in RPCs had a beneficial effect on juxtaposed photoreceptors under normal physiological conditions, but was toxic under pathological stress conditions. We propose that lipid storage is a mechanism of cellular communication that is essential to maintain photoreceptor health.

cell biology

Thrombospondins 1 and 2 affect lysyl oxidase protein and collagen matrix maturation in cortical bone of growing male and female mice via non-redundant pathways

Thrombospondin-2-deficiency is associated with impaired matrix maturation in osteoblasts and cortical bone of growing mice. Here we addressed the possibility that lysyl oxidase (LOX) contributes to this phenotype. After overnight serum starvation, pro-LOX levels were elevated compared to wild-type in marrow-derived osteoblasts from male and female TSP2-/- mice. The liberated LOX pro-peptide (LOPP) was faintly visible in serum-starved cultures. When serum was maintained, pro-LOX content was not affected by TSP2 status, but relative LOPP levels were elevated in cultures from female TSP2-/- mice. Two isoforms of pro-LOX at 75 kDa and 50 kDa were detected in detergent soluble protein extracts of diaphyseal tissue from growing mice. In female mice, TSP2 status did not affect detergent soluble pro-LOX content or the relative contribution of each band to the total signal. Instead, levels of the 50 kDa band were reduced in female TSP1-/- samples. In male diaphyseal tissue, total pro-LOX content and the contribution each isoform made to the total signal was not affected by TSP1 or TSP2 status. We did not detect 32 kDa mature LOX in detergent soluble preparations of cells or whole bone tissue. Detergent insoluble hydroxyproline content was reduced in diaphyseal tissue obtained from female TSP1-/- and TSP2-/- mice. In male diaphyseal cortical samples, TSP2 but not TSP1 deficiency was associated with reduced insoluble hydroxyproline content. Our data suggest that the trimeric thrombospondins contribute to bone matrix quality via non-redundant mechanisms that are dependent on the unique tissue milieu of the male and female skeleton.

cell biology