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1.
Redox Biol ; 67: 102943, 2023 11.
Article in English | MEDLINE | ID: mdl-37883843

ABSTRACT

Accumulation of misfolded proteins or perturbation of calcium homeostasis leads to endoplasmic reticulum (ER) stress and is linked to the pathogenesis of neurodegenerative diseases. Hence, understanding the ability of neuronal cells to cope with chronic ER stress is of fundamental interest. Interestingly, several brain areas uphold functions that enable them to resist challenges associated with neurodegeneration. Here, we established novel clonal mouse hippocampal (HT22) cell lines that are resistant to prolonged (chronic) ER stress induced by thapsigargin (TgR) or tunicamycin (TmR) as in vitro models to study the adaption to ER stress. Morphologically, we observed a significant increase in vesicular und autophagosomal structures in both resistant lines and 'giant lysosomes', especially striking in TgR cells. While autophagic activity increased under ER stress, lysosomal function appeared slightly impaired; in both cell lines, we observed enhanced ER-phagy. However, proteomic analyses revealed that various protein clusters and signaling pathways were differentially regulated in TgR versus TmR cells in response to chronic ER stress. Additionally, bioenergetic analyses in both resistant cell lines showed a shift toward aerobic glycolysis ('Warburg effect') and a defective complex I of the oxidative phosphorylation (OXPHOS) machinery. Furthermore, ER stress-resistant cells differentially activated the unfolded protein response (UPR) comprising IRE1α and ATF6 pathways. These findings display the wide portfolio of adaptive responses of neuronal cells to chronic ER stress. ER stress-resistant neuronal cells could be the basis to uncover molecular modulators of adaptation, resistance, and neuroprotection as potential pharmacological targets for preventing neurodegeneration.


Subject(s)
Endoribonucleases , Protein Serine-Threonine Kinases , Mice , Animals , Protein Serine-Threonine Kinases/metabolism , Endoribonucleases/genetics , Proteomics , Endoplasmic Reticulum Stress , Unfolded Protein Response , Endoplasmic Reticulum/metabolism
2.
Autophagy ; 19(11): 2982-2996, 2023 11.
Article in English | MEDLINE | ID: mdl-37439113

ABSTRACT

The selective autophagic degradation of mitochondria via mitophagy is essential for preserving mitochondrial homeostasis and, thereby, disease maintenance and progression in acute myeloid leukemia (AML). Mitophagy is orchestrated by a variety of mitophagy receptors whose interplay is not well understood. Here, we established a pairwise multiplexed CRISPR screen targeting mitophagy receptors to elucidate redundancies and gain a deeper understanding of the functional interactome governing mitophagy in AML. We identified OPTN (optineurin) as sole non-redundant mitophagy receptor and characterized its unique role in AML. Knockdown and overexpression experiments demonstrated that OPTN expression is rate-limiting for AML cell proliferation. In a MN1-driven murine transplantation model, loss of OPTN prolonged overall median survival by 7 days (+21%). Mechanistically, we found broadly impaired mitochondrial respiration and function with increased mitochondrial ROS, that most likely caused the proliferation defect. Our results decipher the intertwined network of mitophagy receptors in AML for both ubiquitin-dependent and receptor-mediated mitophagy, identify OPTN as a non-redundant tool to study mitophagy in the context of leukemia and suggest OPTN inhibition as an attractive therapeutic strategy.Abbreviations: AML: acute myeloid leukemia; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats; CTRL: control; DFP: deferiprone; GI: genetic interaction; KD: knockdown; KO: knockout; ldMBM, lineage-depleted murine bone marrow; LFC: log2 fold change; LIR: LC3-interacting region; LSC: leukemic stem cell; MAGeCK: Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout; MDIVI-1: mitochondrial division inhibitor 1; MOI: multiplicity of infection; MOM: mitochondrial outer membrane; NAC: N-acetyl-L-cysteine; OA: oligomycin-antimycin A; OCR: oxygen consumption rate; OE: overexpression; OPTN: optineurin; PINK1: PTEN induced putative kinase 1; ROS: reactive oxygen species; SEM: standard error of the mean; TCGA: The Cancer Genome Atlas; TEM: transmission electron microscopy; UBD: ubiquitin-binding domain; WT: wild type.


Subject(s)
Leukemia, Myeloid, Acute , Mitophagy , Animals , Mice , Autophagy , Mitophagy/genetics , Reactive Oxygen Species/metabolism , Ubiquitin-Protein Ligases/metabolism , Ubiquitins , Humans
3.
Autophagy ; 19(8): 2406-2407, 2023 08.
Article in English | MEDLINE | ID: mdl-36847417

ABSTRACT

Among the various signals governing autophagy, ubiquitination plays a critical role both by controlling the stability of upstream regulators or components of macroautophagy/autophagy pathways and by facilitating the recruitment of cargo to autophagy receptors. As such, modulators of ubiquitin signaling can influence autophagic substrate degradation. Recently, we identified a non-proteolytic ubiquitin signal at the Ragulator complex subunit LAMTOR1 that is reversed by the deubiquitinase USP32. Loss of USP32 promotes ubiquitination within the unstructured N-terminal region of LAMTOR1 and prevents its efficient interaction with the vacuolar-type H+-ATPase, a prerequisite for full activation of MTORC1 at lysosomes. Consequently, MTORC1 activity is decreased and autophagy is upregulated in USP32 knockout cells. This phenotype is conserved in Caenorhabditis elegans. Depletion of USP32 homolog CYK-3 in worms results in LET-363/MTOR inhibition and autophagy induction. Based on our data, we propose an additional control layer of the MTORC1 activation cascade at lysosomes via USP32-regulated LAMTOR1 ubiquitination.


Subject(s)
Autophagy , Vacuolar Proton-Translocating ATPases , Autophagy/physiology , TOR Serine-Threonine Kinases/metabolism , Vacuolar Proton-Translocating ATPases/metabolism , Mechanistic Target of Rapamycin Complex 1/metabolism , Lysosomes/metabolism , Ubiquitination , Ubiquitins/metabolism
4.
J Cell Sci ; 136(3)2023 02 01.
Article in English | MEDLINE | ID: mdl-36644903

ABSTRACT

Autophagy is a catabolic process during which cytosolic material is enwrapped in a newly formed double-membrane structure called the autophagosome, and subsequently targeted for degradation in the lytic compartment of the cell. The fusion of autophagosomes with the lytic compartment is a tightly regulated step and involves membrane-bound SNARE proteins. These play a crucial role as they promote lipid mixing and fusion of the opposing membranes. Among the SNARE proteins implicated in autophagy, the essential SNARE protein YKT6 is the only SNARE protein that is evolutionarily conserved from yeast to humans. Here, we show that alterations in YKT6 function, in both mammalian cells and nematodes, produce early and late autophagy defects that result in reduced survival. Moreover, mammalian autophagosomal YKT6 is phospho-regulated by the ULK1 kinase, preventing premature bundling with the lysosomal SNARE proteins and thereby inhibiting autophagosome-lysosome fusion. Together, our findings reveal that timely regulation of the YKT6 phosphorylation status is crucial throughout autophagy progression and cell survival.


Subject(s)
Autophagy , Saccharomyces cerevisiae Proteins , Animals , Humans , R-SNARE Proteins/metabolism , Phosphorylation , Autophagy/genetics , Autophagosomes/metabolism , SNARE Proteins/genetics , SNARE Proteins/metabolism , Membrane Fusion/physiology , Saccharomyces cerevisiae/metabolism , Lysosomes/metabolism , Mammals/metabolism , Autophagy-Related Protein-1 Homolog/genetics , Autophagy-Related Protein-1 Homolog/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism
5.
Autophagy ; 19(7): 2146-2147, 2023 07.
Article in English | MEDLINE | ID: mdl-36416088

ABSTRACT

Autophagosome isolation enables the thorough investigation of structural components and engulfed materials. Recently, we introduced a novel antibody-based FACS-mediated method for isolation of native macroautophagic/autophagic vesicles and confirmed the quality of the preparations. We performed phospholipidomic and proteomic analyses to characterize autophagic vesicle-associated phospholipids and protein cargoes under different autophagy conditions. Lipidomic analyses identified phosphoglycerides and sphingomyelins within autophagic vesicles and revealed that the lipid composition was unaffected by different rates of autophagosome formation. Proteomic analyses identified more than 4500 potential autophagy substrates and showed that in comparison to autophagic vesicles isolated under basal autophagy conditions, starvation only marginally affected the cargo profile. Proteasome inhibition, however, resulted in the enhanced degradation of ubiquitin-proteasome system components. Taken together, the novel isolation method enriched large quantities of autophagic vesicles and enabled detailed analyses of their lipid and cargo composition.


Subject(s)
Autophagy , Proteasome Endopeptidase Complex , Autophagy/physiology , Proteasome Endopeptidase Complex/metabolism , Proteomics , Autophagosomes/metabolism , Lipids
6.
Cell Rep ; 41(10): 111653, 2022 12 06.
Article in English | MEDLINE | ID: mdl-36476874

ABSTRACT

The endosomal-lysosomal system is a series of organelles in the endocytic pathway that executes trafficking and degradation of proteins and lipids and mediates the internalization of nutrients and growth factors to ensure cell survival, growth, and differentiation. Here, we reveal regulatory, non-proteolytic ubiquitin signals in this complex system that are controlled by the enigmatic deubiquitinase USP32. Knockout (KO) of USP32 in primary hTERT-RPE1 cells results among others in hyperubiquitination of the Ragulator complex subunit LAMTOR1. Accumulation of LAMTOR1 ubiquitination impairs its interaction with the vacuolar H+-ATPase, reduces Ragulator function, and ultimately limits mTORC1 recruitment. Consistently, in USP32 KO cells, less mTOR kinase localizes to lysosomes, mTORC1 activity is decreased, and autophagy is induced. Furthermore, we demonstrate that depletion of USP32 homolog CYK-3 in Caenorhabditis elegans results in mTOR inhibition and autophagy induction. In summary, we identify a control mechanism of the mTORC1 activation cascade at lysosomes via USP32-regulated LAMTOR1 ubiquitination.


Subject(s)
Autophagy , Mechanistic Target of Rapamycin Complex 1
7.
EMBO Rep ; 23(12): e53065, 2022 12 06.
Article in English | MEDLINE | ID: mdl-36215690

ABSTRACT

Autophagy is responsible for clearance of an extensive portfolio of cargoes, which are sequestered into vesicles, called autophagosomes, and are delivered to lysosomes for degradation. The pathway is highly dynamic and responsive to several stress conditions. However, the phospholipid composition and protein contents of human autophagosomes under changing autophagy rates are elusive so far. Here, we introduce an antibody-based FACS-mediated approach for the isolation of native autophagic vesicles and ensured the quality of the preparations. Employing quantitative lipidomics, we analyze phospholipids present within human autophagic vesicles purified upon basal autophagy, starvation, and proteasome inhibition. Importantly, besides phosphoglycerides, we identify sphingomyelin within autophagic vesicles and show that the phospholipid composition is unaffected by the different conditions. Employing quantitative proteomics, we obtain cargo profiles of autophagic vesicles isolated upon the different treatment paradigms. Interestingly, starvation shows only subtle effects, while proteasome inhibition results in the enhanced presence of ubiquitin-proteasome pathway factors within autophagic vesicles. Thus, here we present a powerful method for the isolation of native autophagic vesicles, which enabled profound phospholipid and cargo analyses.


Subject(s)
Proteasome Endopeptidase Complex , Proteomics , Humans , Autophagy , Phospholipids
8.
Protein Sci ; 31(7): e4360, 2022 07.
Article in English | MEDLINE | ID: mdl-35762717

ABSTRACT

Recent studies revealed that molecular events related with the physiology and pathology of αS might be regulated by specific sequence motifs in the primary sequence of αS. The importance of individual residues in these motifs remains an important open avenue of investigation. In this work, we have addressed the structural details related to the amyloid fibril assembly and lipid-binding features of αS through the design of site-directed mutants at position 39 of the protein and their study by in vitro and in vivo assays. We demonstrated that aromaticity at position 39 of αS primary sequence influences strongly the aggregation properties and the membrane-bound conformations of the protein, molecular features that might have important repercussions for the function and dysfunction of αS. Considering that aggregation and membrane damage is an important driver of cellular toxicity in amyloid diseases, future work is needed to link our findings with studies based on toxicity and neuronal cell death. BRIEF STATEMENT OUTLINING SIGNIFICANCE: Modulation by distinct sequential motifs and specific residues of αS on its physiological and pathological states is an active area of research. Here, we demonstrated that aromaticity at position 39 of αS modulates the membrane-bound conformations of the protein, whereas removal of aromatic functionality at position 39 reduces strongly the amyloid assembly in vitro and in vivo. Our study provides new evidence for the modulation of molecular events related with the physiology and pathology of αS.


Subject(s)
Amyloid , alpha-Synuclein , Amyloid/genetics , Amyloid/metabolism , Membranes/metabolism , Protein Binding , Protein Structure, Secondary , alpha-Synuclein/chemistry
9.
J Cell Biochem ; 123(8): 1306-1326, 2022 08.
Article in English | MEDLINE | ID: mdl-35616269

ABSTRACT

Mitochondria are dynamic eukaryotic organelles involved in a variety of essential cellular processes including the generation of adenosine triphosphate (ATP) and reactive oxygen species as well as in the control of apoptosis and autophagy. Impairments of mitochondrial functions lead to aging and disease. Previous work with the ascomycete Podospora anserina demonstrated that mitochondrial morphotype as well as mitochondrial ultrastructure change during aging. The latter goes along with an age-dependent reorganization of the inner mitochondrial membrane leading to a change from lamellar cristae to vesicular structures. Particularly from studies with yeast, it is known that besides the F1 Fo -ATP-synthase and the phospholipid cardiolipin also the "mitochondrial contact site and cristae organizing system" (MICOS) complex, existing of the Mic60- and Mic10-subcomplex, is essential for proper cristae formation. In the present study, we aimed to understand the mechanistic basis of age-related changes in the mitochondrial ultrastructure. We observed that MICOS subunits are coregulated at the posttranscriptional level. This regulation partially depends on the mitochondrial iAAA-protease PaIAP. Most surprisingly, we made the counterintuitive observation that, despite the loss of lamellar cristae and of mitochondrial impairments, the ablation of MICOS subunits (except for PaMIC12) leads to a pronounced lifespan extension. Moreover, simultaneous ablation of subunits of both MICOS subcomplexes synergistically increases lifespan, providing formal genetic evidence that both subcomplexes affect lifespan by different and at least partially independent pathways. At the molecular level, we found that ablation of Mic10-subcomplex components leads to a mitohormesis-induced lifespan extension, while lifespan extension of Mic60-subcomplex mutants seems to be controlled by pathways involved in the control of phospholipid homeostasis. Overall, our data demonstrate that both MICOS subcomplexes have different functions and play distinct roles in the aging process of P. anserina.


Subject(s)
Mitochondrial Membranes , Podospora , Adenosine Triphosphate/metabolism , Longevity , Mitochondrial Membranes/metabolism , Mitochondrial Proteins/genetics , Phospholipids/metabolism , Podospora/genetics , Podospora/metabolism , Saccharomyces cerevisiae/genetics
10.
J Mol Biol ; 432(4): 1216-1234, 2020 02 14.
Article in English | MEDLINE | ID: mdl-31874152

ABSTRACT

Autophagy is dependent on appropriate lipid supply for autophagosome formation. The regulation of lipid acquisition and the autophagy network response to lipid-limiting conditions are mostly elusive. Here, we show that the knockout of the RAB GTPase RAB18 interferes with lipid droplet catabolism, causing an impaired fatty acid release. The resulting reduced lipid-droplet-derived lipid availability influences autophagy and provokes adaptive modifications of the autophagy network. These adjustments include increased expression and phosphorylation of ATG2B as well as augmented formation of the ATG12-ATG5 conjugate. Moreover, ATG9A shows an enhanced phosphorylation at amino acid residues tyrosine 8 and serine 14, resulting in an increased ATG9A trafficking. Via pharmacological inhibition of Y8 phosphorylation, we demonstrate that this ATG9A modification is important to maintain basal autophagy under RAB18 knockout conditions. However, while the network adaptations are sufficient to maintain basal autophagic activity, they are incapable of ensuring autophagy induction upon starvation, which is characterized by an enhanced lipid demand. Thus, here, we define the molecular role of RAB18 in connecting lipid droplets and autophagy, emphasize the significance of lipid droplets as lipid sources for the degradative pathway, and uncover a remarkable autophagy network plasticity, including phosphorylation-dependent ATG9A activation, to compensate reduced lipid availability in order to rescue basal autophagic activity.


Subject(s)
Lipid Droplets/chemistry , rab GTP-Binding Proteins/metabolism , Autophagosomes/metabolism , Autophagy/physiology , CRISPR-Cas Systems/genetics , CRISPR-Cas Systems/physiology , HeLa Cells , Humans , Immunoblotting , Immunohistochemistry , Microscopy, Confocal , Microscopy, Electron, Transmission , Phosphorylation , Real-Time Polymerase Chain Reaction , rab GTP-Binding Proteins/genetics , rab3 GTP-Binding Proteins/genetics , rab3 GTP-Binding Proteins/metabolism
11.
Blood ; 133(2): 168-179, 2019 01 10.
Article in English | MEDLINE | ID: mdl-30498063

ABSTRACT

Autophagy maintains hematopoietic stem cell integrity and prevents malignant transformation. In addition to bulk degradation, selective autophagy serves as an intracellular quality control mechanism and requires autophagy receptors, such as p62 (SQSTM1), to specifically bridge the ubiquitinated cargos into autophagosomes. Here, we investigated the function of p62 in acute myeloid leukemia (AML) in vitro and in murine in vivo models of AML. Loss of p62 impaired expansion and colony-forming ability of leukemia cells and prolonged latency of leukemia development in mice. High p62 expression was associated with poor prognosis in human AML. Using quantitative mass spectrometry, we identified enrichment of mitochondrial proteins upon immunoprecipitation of p62. Loss of p62 significantly delayed removal of dysfunctional mitochondria, increased mitochondrial superoxide levels, and impaired mitochondrial respiration. Moreover, we demonstrated that the autophagy-dependent function of p62 is essential for cell growth and effective mitochondrial degradation by mitophagy. Our results highlight the prominent role of selective autophagy in leukemia progression, and specifically, the importance of mitophagy to maintain mitochondrial integrity.


Subject(s)
Autophagy , Leukemia, Experimental/pathology , Leukemia, Myeloid, Acute/pathology , Mitophagy , Sequestosome-1 Protein/metabolism , Sequestosome-1 Protein/physiology , Animals , Follow-Up Studies , Humans , Leukemia, Experimental/genetics , Leukemia, Experimental/metabolism , Leukemia, Myeloid, Acute/genetics , Leukemia, Myeloid, Acute/metabolism , Mice , Mice, Knockout , Prognosis , Survival Rate , Tumor Cells, Cultured
12.
EMBO J ; 37(2): 235-254, 2018 01 17.
Article in English | MEDLINE | ID: mdl-29158324

ABSTRACT

Retromer is an endosomal multi-protein complex that organizes the endocytic recycling of a vast range of integral membrane proteins. Here, we establish an additional retromer function in controlling the activity and localization of the late endosomal small GTPase RAB7. Surprisingly, we found that RAB7 not only decorates late endosomes or lysosomes, but is also present on the endoplasmic reticulum, trans-Golgi network, and mitochondrial membranes, a localization that is maintained by retromer and the retromer-associated RAB7-specific GAP TBC1D5. In the absence of either TBC1D5 or retromer, RAB7 activity state and localization are no longer controlled and hyperactivated RAB7 expands over the entire lysosomal domain. This lysosomal accumulation of hyperactivated RAB7 results in a striking loss of RAB7 mobility and overall depletion of the inactive RAB7 pool on endomembranes. Functionally, we establish that this control of RAB7 activity is not required for the recycling of retromer-dependent cargoes, but instead enables the correct sorting of the autophagy related transmembrane protein ATG9a and autophagosome formation around damaged mitochondria during Parkin-mediated mitophagy.


Subject(s)
Autophagosomes/metabolism , GTPase-Activating Proteins/metabolism , Mitochondria/metabolism , Mitophagy/physiology , rab GTP-Binding Proteins/metabolism , Autophagy-Related Proteins/metabolism , GTPase-Activating Proteins/genetics , HeLa Cells , Humans , Lysosomes/genetics , Lysosomes/metabolism , Membrane Proteins/metabolism , Mitochondria/genetics , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Vesicular Transport Proteins/metabolism , rab GTP-Binding Proteins/genetics , rab7 GTP-Binding Proteins
13.
Proc Natl Acad Sci U S A ; 114(23): E4621-E4630, 2017 06 06.
Article in English | MEDLINE | ID: mdl-28536193

ABSTRACT

Podocytes form the outer part of the glomerular filter, where they have to withstand enormous transcapillary filtration forces driving glomerular filtration. Detachment of podocytes from the glomerular basement membrane precedes most glomerular diseases. However, little is known about the regulation of podocyte adhesion in vivo. Thus, we systematically screened for podocyte-specific focal adhesome (FA) components, using genetic reporter models in combination with iTRAQ-based mass spectrometry. This approach led to the identification of FERM domain protein EPB41L5 as a highly enriched podocyte-specific FA component in vivo. Genetic deletion of Epb41l5 resulted in severe proteinuria, detachment of podocytes, and development of focal segmental glomerulosclerosis. Remarkably, by binding and recruiting the RhoGEF ARGHEF18 to the leading edge, EPB41L5 directly controls actomyosin contractility and subsequent maturation of focal adhesions, cell spreading, and migration. Furthermore, EPB41L5 controls matrix-dependent outside-in signaling by regulating the focal adhesome composition. Thus, by linking extracellular matrix sensing and signaling, focal adhesion maturation, and actomyosin activation EPB41L5 ensures the mechanical stability required for podocytes at the kidney filtration barrier. Finally, a diminution of EPB41L5-dependent signaling programs appears to be a common theme of podocyte disease, and therefore offers unexpected interventional therapeutic strategies to prevent podocyte loss and kidney disease progression.


Subject(s)
Actomyosin/metabolism , Cytoskeletal Proteins/metabolism , Focal Adhesions/metabolism , Membrane Proteins/metabolism , Podocytes/metabolism , Animals , Cytoskeletal Proteins/deficiency , Cytoskeletal Proteins/genetics , Female , Focal Adhesions/pathology , Gene Knockout Techniques , Glomerulosclerosis, Focal Segmental/etiology , Glomerulosclerosis, Focal Segmental/metabolism , Glomerulosclerosis, Focal Segmental/pathology , Humans , Membrane Proteins/antagonists & inhibitors , Membrane Proteins/deficiency , Membrane Proteins/genetics , Mice , Mice, Knockout , Nephrotic Syndrome/etiology , Nephrotic Syndrome/metabolism , Nephrotic Syndrome/pathology , Podocytes/pathology , Pregnancy , Proteomics , Rho Guanine Nucleotide Exchange Factors/metabolism , Signal Transduction
14.
Cell ; 167(3): 722-738.e23, 2016 Oct 20.
Article in English | MEDLINE | ID: mdl-27768893

ABSTRACT

A functional crosstalk between epigenetic regulators and metabolic control could provide a mechanism to adapt cellular responses to environmental cues. We report that the well-known nuclear MYST family acetyl transferase MOF and a subset of its non-specific lethal complex partners reside in mitochondria. MOF regulates oxidative phosphorylation by controlling expression of respiratory genes from both nuclear and mtDNA in aerobically respiring cells. MOF binds mtDNA, and this binding is dependent on KANSL3. The mitochondrial pool of MOF, but not a catalytically deficient mutant, rescues respiratory and mtDNA transcriptional defects triggered by the absence of MOF. Mof conditional knockout has catastrophic consequences for tissues with high-energy consumption, triggering hypertrophic cardiomyopathy and cardiac failure in murine hearts; cardiomyocytes show severe mitochondrial degeneration and deregulation of mitochondrial nutrient metabolism and oxidative phosphorylation pathways. Thus, MOF is a dual-transcriptional regulator of nuclear and mitochondrial genomes connecting epigenetics and metabolism.


Subject(s)
Energy Metabolism/genetics , Epigenesis, Genetic , Histone Acetyltransferases/metabolism , Mitochondria, Muscle/enzymology , Transcription Factors/metabolism , Transcription, Genetic , Animals , Cardiomyopathy, Hypertrophic/genetics , Cell Respiration/genetics , DNA, Mitochondrial/genetics , DNA, Mitochondrial/metabolism , HeLa Cells , Heart Failure/genetics , Histone Acetyltransferases/genetics , Humans , Intracellular Signaling Peptides and Proteins , Mice , Mice, Knockout , Mitochondria, Heart/enzymology , Mitochondria, Heart/genetics , Mitochondria, Muscle/genetics , Myocytes, Cardiac/metabolism , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Oxidative Phosphorylation , Transcription Factors/genetics
15.
Elife ; 4: e08201, 2015 Sep 03.
Article in English | MEDLINE | ID: mdl-26335201

ABSTRACT

During development, proliferation must be tightly controlled for organs to reach their appropriate size. While the Hippo signaling pathway plays a major role in organ growth control, how it senses and responds to increased cell density is still unclear. In this study, we use the zebrafish lateral line primordium (LLP), a group of migrating epithelial cells that form sensory organs, to understand how tissue growth is controlled during organ formation. Loss of the cell junction-associated Motin protein Amotl2a leads to overproliferation and bigger LLP, affecting the final pattern of sensory organs. Amotl2a function in the LLP is mediated together by the Hippo pathway effector Yap1 and the Wnt/ß-catenin effector Lef1. Our results implicate for the first time the Hippo pathway in size regulation in the LL system. We further provide evidence that the Hippo/Motin interaction is essential to limit tissue size during development.


Subject(s)
Gene Expression Regulation, Developmental , Membrane Proteins/metabolism , Trans-Activators/metabolism , Transcription Factors/metabolism , Zebrafish Proteins/metabolism , Zebrafish/growth & development , Angiomotins , Animals , Cell Proliferation , Epithelial Cells/physiology , YAP-Signaling Proteins , Zebrafish/genetics
16.
Nat Mater ; 14(1): 125-32, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25362355

ABSTRACT

Nanoscale biological materials formed by the assembly of defined block-domain proteins control the formation of cellular compartments such as organelles. Here, we introduce an approach to intentionally 'program' the de novo synthesis and self-assembly of genetically encoded amphiphilic proteins to form cellular compartments, or organelles, in Escherichia coli. These proteins serve as building blocks for the formation of artificial compartments in vivo in a similar way to lipid-based organelles. We investigated the formation of these organelles using epifluorescence microscopy, total internal reflection fluorescence microscopy and transmission electron microscopy. The in vivo modification of these protein-based de novo organelles, by means of site-specific incorporation of unnatural amino acids, allows the introduction of artificial chemical functionalities. Co-localization of membrane proteins results in the formation of functionalized artificial organelles combining artificial and natural cellular function. Adding these protein structures to the cellular machinery may have consequences in nanobiotechnology, synthetic biology and materials science, including the constitution of artificial cells and bio-based metamaterials.


Subject(s)
Escherichia coli/metabolism , Green Fluorescent Proteins/metabolism , Membrane Proteins/metabolism , Organelles/metabolism , Escherichia coli/genetics , Escherichia coli/ultrastructure , Green Fluorescent Proteins/chemistry , Green Fluorescent Proteins/genetics , Membrane Proteins/chemistry , Membrane Proteins/genetics , Microscopy, Electron, Transmission , Organelles/chemistry , Organelles/genetics , Organelles/ultrastructure , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism
17.
J Proteome Res ; 13(9): 3940-56, 2014 Sep 05.
Article in English | MEDLINE | ID: mdl-25090448

ABSTRACT

The nuclear matrix (NM) is an operationally defined structure of the mammalian cell nucleus that resists stringent biochemical extraction procedures applied subsequent to nuclease-mediated chromatin digestion of intact nuclei. This comprises removal of soluble biomolecules and chromatin by means of either detergent (LIS: lithium diiodosalicylate) or high salt (AS: ammonium sulfate, sodium chloride) treatment. So far, progress toward defining bona fide NM proteins has been hindered by the problem of distinguishing them from copurifying abundant contaminants and extraction-method-intrinsic precipitation artifacts. Here, we present a highly improved NM purification strategy, adding a FACS sorting step for efficient isolation of morphologically homogeneous lamin B positive NM specimens. SILAC-based quantitative proteome profiling of LIS-, AS-, or NaCl-extracted matrices versus the nuclear proteome together with rigorous statistical filtering enables the compilation of a high-quality catalogue of NM proteins commonly enriched among the three different extraction methods. We refer to this set of 272 proteins as the NM central proteome. Quantitative NM retention profiles for 2381 proteins highlight elementary features of nuclear organization and correlate well with immunofluorescence staining patterns reported in the Human Protein Atlas, demonstrating that the NM central proteome is significantly enriched in proteins exhibiting a nuclear body as well as nuclear speckle-like morphology.


Subject(s)
Nuclear Matrix-Associated Proteins/analysis , Nuclear Matrix/chemistry , Proteome/analysis , Proteomics/methods , Cell Line , Cell Nucleus/chemistry , Cell Nucleus/metabolism , Flow Cytometry , Humans , Nuclear Matrix-Associated Proteins/chemistry , Proteome/chemistry
18.
Cell Rep ; 8(1): 10-9, 2014 Jul 10.
Article in English | MEDLINE | ID: mdl-24953654

ABSTRACT

mTOR kinase is a master growth regulator that can be stimulated by multiple signals, including amino acids and the lysosomal small GTPase Rheb. Recent studies have proposed an important role for the V-ATPase in the sensing of amino acids in the lysosomal lumen. Using the Drosophila wing as a model epithelium, we show here that the V-ATPase is required for Rheb-dependent epithelial growth. We further uncover a positive feedback loop for the control of apical protein uptake that depends on V-ATPase/mTOR signaling. This feedback loop includes Rheb-dependent transcriptional regulation of the multiligand receptor Megalin, which itself is required for Rheb-induced endocytosis. In addition, we provide evidence that long-term mTOR inhibition with rapamycin in mice causes reduction of Megalin levels and proteinuria in the proximal tubular epithelium of the kidney. Thus, our findings unravel a homeostatic mechanism that allows epithelial cells to promote protein uptake under normal conditions and to prevent uptake in lysosomal stress conditions.


Subject(s)
Endocytosis , Low Density Lipoprotein Receptor-Related Protein-2/metabolism , TOR Serine-Threonine Kinases/metabolism , Vacuolar Proton-Translocating ATPases/metabolism , Animals , Drosophila/metabolism , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Epithelium/growth & development , Epithelium/metabolism , Feedback, Physiological , Low Density Lipoprotein Receptor-Related Protein-2/genetics , Male , Mice , Mice, Inbred C57BL , Monomeric GTP-Binding Proteins/genetics , Monomeric GTP-Binding Proteins/metabolism , Neuropeptides/genetics , Neuropeptides/metabolism , Proteinuria/metabolism , Ras Homolog Enriched in Brain Protein , Signal Transduction , TOR Serine-Threonine Kinases/genetics , Vacuolar Proton-Translocating ATPases/genetics
19.
Neuron ; 82(1): 167-80, 2014 Apr 02.
Article in English | MEDLINE | ID: mdl-24698274

ABSTRACT

Peptide neuromodulators are released from a unique organelle: the dense-core vesicle. Dense-core vesicles are generated at the trans-Golgi and then sort cargo during maturation before being secreted. To identify proteins that act in this pathway, we performed a genetic screen in Caenorhabditis elegans for mutants defective in dense-core vesicle function. We identified two conserved Rab2-binding proteins: RUND-1, a RUN domain protein, and CCCP-1, a coiled-coil protein. RUND-1 and CCCP-1 colocalize with RAB-2 at the Golgi, and rab-2, rund-1, and cccp-1 mutants have similar defects in sorting soluble and transmembrane dense-core vesicle cargos. RUND-1 also interacts with the Rab2 GAP protein TBC-8 and the BAR domain protein RIC-19, a RAB-2 effector. In summary, a pathway of conserved proteins controls the maturation of dense-core vesicles at the trans-Golgi network.


Subject(s)
Caenorhabditis elegans Proteins/metabolism , Mutation/genetics , Secretory Vesicles/metabolism , rab2 GTP-Binding Protein/metabolism , Analysis of Variance , Animals , Animals, Genetically Modified , Caenorhabditis elegans , Caenorhabditis elegans Proteins/genetics , Chromosome Mapping , Cloning, Molecular , Endosomes/metabolism , Endosomes/ultrastructure , Golgi Apparatus/metabolism , Golgi Apparatus/ultrastructure , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Microscopy, Electron, Transmission , Molecular Sequence Data , Protein Transport , Secretory Vesicles/genetics , Secretory Vesicles/ultrastructure , rab2 GTP-Binding Protein/genetics
20.
Genetics ; 196(3): 745-65, 2014 Mar.
Article in English | MEDLINE | ID: mdl-24653209

ABSTRACT

Neurons release neuropeptides via the regulated exocytosis of dense core vesicles (DCVs) to evoke or modulate behaviors. We found that Caenorhabditis elegans motor neurons send most of their DCVs to axons, leaving very few in the cell somas. How neurons maintain this skewed distribution and the extent to which it can be altered to control DCV numbers in axons or to drive release from somas for different behavioral impacts is unknown. Using a forward genetic screen, we identified loss-of-function mutations in UNC-43 (CaM kinase II) that reduce axonal DCV levels by ∼90% and cell soma/dendrite DCV levels by ∼80%, leaving small synaptic vesicles largely unaffected. Blocking regulated secretion in unc-43 mutants restored near wild-type axonal levels of DCVs. Time-lapse video microscopy showed no role for CaM kinase II in the transport of DCVs from cell somas to axons. In vivo secretion assays revealed that much of the missing neuropeptide in unc-43 mutants is secreted via a regulated secretory pathway requiring UNC-31 (CAPS) and UNC-18 (nSec1). DCV cargo levels in unc-43 mutants are similarly low in cell somas and the axon initial segment, indicating that the secretion occurs prior to axonal transport. Genetic pathway analysis suggests that abnormal neuropeptide function contributes to the sluggish basal locomotion rate of unc-43 mutants. These results reveal a novel pathway controlling the location of DCV exocytosis and describe a major new function for CaM kinase II.


Subject(s)
Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans/enzymology , Calcium-Calmodulin-Dependent Protein Kinase Type 2/metabolism , Motor Neurons/metabolism , Neuropeptides/metabolism , Secretory Vesicles/metabolism , Animals , Axons/diagnostic imaging , Axons/metabolism , Caenorhabditis elegans/genetics , Caenorhabditis elegans Proteins/genetics , Calcium-Binding Proteins/metabolism , Calcium-Calmodulin-Dependent Protein Kinase Type 2/genetics , Codon, Nonsense , Dendrites/diagnostic imaging , Dendrites/metabolism , Exocytosis , Microscopy, Electron , Motor Neurons/ultrastructure , Phosphoproteins/metabolism , Protein Transport , Secretory Vesicles/ultrastructure , Ultrasonography , Vesicular Transport Proteins/metabolism
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