Papers by Vladimir Lupashin
Traffic, Jun 21, 2023
Deficiency in the conserved oligomeric Golgi (COG) complex that orchestrates SNARE‐mediated tethe... more Deficiency in the conserved oligomeric Golgi (COG) complex that orchestrates SNARE‐mediated tethering/fusion of vesicles that recycle the Golgi's glycosylation machinery results in severe glycosylation defects. Although two major Golgi v‐SNAREs, GS28/GOSR1, and GS15/BET1L, are depleted in COG‐deficient cells, the complete knockout of GS28 and GS15 only modestly affects Golgi glycosylation, indicating the existence of an adaptation mechanism in Golgi SNARE. Indeed, quantitative mass‐spectrometry analysis of STX5‐interacting proteins revealed two novel Golgi SNARE complexes—STX5/SNAP29/VAMP7 and STX5/VTI1B/STX8/YKT6. These complexes are present in wild‐type cells, but their usage is significantly increased in both GS28‐ and COG‐deficient cells. Upon GS28 deletion, SNAP29 increased its Golgi residency in a STX5‐dependent manner. While STX5 depletion and Retro2‐induced diversion from the Golgi severely affect protein glycosylation, GS28/SNAP29 and GS28/VTI1B double knockouts alter glycosylation similarly to GS28 KO, indicating that a single STX5‐based SNARE complex is sufficient to support Golgi glycosylation. Importantly, co‐depletion of three Golgi SNARE complexes in GS28/SNAP29/VTI1B TKO cells resulted in severe glycosylation defects and a reduced capacity for glycosylation enzyme retention at the Golgi. This study demonstrates the remarkable plasticity in SXT5‐mediated membrane trafficking, uncovering a novel adaptive response to the failure of canonical intra‐Golgi vesicle tethering/fusion machinery.
bioRxiv (Cold Spring Harbor Laboratory), May 31, 2023
Survival of the apicomplexan parasite Toxoplasma gondii depends on the proper functioning of many... more Survival of the apicomplexan parasite Toxoplasma gondii depends on the proper functioning of many glycosylated proteins. Glycosylation is performed in the major membranous organelles ER and Golgi apparatus that constitute a significant portion of the intracellular secretory system. The secretory pathway is bidirectional: cargo is delivered to target organelles in the anterograde direction, while the retrograde flow maintains the membrane balance and proper localization of glycosylation machinery. Despite the vital role of the Golgi in parasite infectivity, little is known about its biogenesis in apicomplexan parasites. In this study we examined T. gondii Conserved Oligomeric Golgi (COG) complex and determined that, contrary to predictions, T. gondii expresses the entire eight-subunit complex and each complex subunit is essential for tachyzoite growth. Deprivation of the COG complex induces a pronounced effect on Golgi and ER membranes, which suggests the T. gondii COG complex has wider role in intracellular membrane trafficking. We demonstrated that besides its conservative role in protein glycosylation and retrograde intra-Golgi trafficking, the COG complex also interacted with anterograde and novel transport machinery. Furthermore, we identified coccidian-specific components of the Golgi transport system: TgUlp1 and TgGlp1. Protein structure and phylogenetic analyses revealed that TgUlp1 is an adaptation of the conservative Golgi tethering factor Uso1/p115, and together with Golgi-localized TgGlp1, TgUlp1 showed dominant interactions with the trafficking machinery that predicted to operate the endosome-to-Golgi recycling. Together, our study showed that T. gondii has expanded function of the conservative Golgi tethering COG complex and evolved additional regulators of the transport likely to serve parasite-specific secretory organelles.
bioRxiv (Cold Spring Harbor Laboratory), May 25, 2022
Conserved Oligomeric Golgi (COG) complex controls Golgi trafficking and glycosylation, but the pr... more Conserved Oligomeric Golgi (COG) complex controls Golgi trafficking and glycosylation, but the precise COG mechanism is unknown. The auxin-inducible acute degradation system was employed to investigate initial defects resulting from COG dysfunction. We found that acute COG inactivation caused a massive accumulation of COG-dependent (CCD) vesicles that carry the bulk of Golgi enzymes and resident proteins. v-SNAREs (GS15, GS28) and v-tethers (giantin, golgin84, and TMF1) were relocalized into CCD vesicles, while t-SNAREs (STX5, YKT6), t-tethers (GM130, p115), and most of Rab proteins remained Golgi-associated. Airyscan microscopy and velocity gradient analysis revealed that different Golgi residents are segregated into different populations of CCD vesicles. Acute COG depletion significantly affected three Golgi-based vesicular coats-COPI, AP1, and GGA, suggesting that COG uniquely orchestrates tethering of multiple types of intra-Golgi CCD vesicles produced by different coat machineries. This study provided the first detailed view of primary cellular defects associated with COG dysfunction in human cells. .
HAL (Le Centre pour la Communication Scientifique Directe), May 20, 2020
Double stranded RNA (dsRNA) is the hallmark of many viral infections. dsRNA is produced either by... more Double stranded RNA (dsRNA) is the hallmark of many viral infections. dsRNA is produced either by RNA viruses during replication or by DNA viruses upon convergent transcription. Synthetic dsRNA is also able to mimic viral-induced activation of innate immune response and cell death. In this study, we employed a genome-wide CRISPR-Cas9 loss of function screen based on cell survival in order to identify genes implicated in the host response to dsRNA. By challenging HCT116 human cells with either synthetic dsRNA or Sindbis virus (SINV), we identified the heparan sulfate (HS) pathway as a crucial factor for dsRNA entry and we validated SINV dependency on HS. Interestingly, we uncovered a novel role for COG4, a component of the Conserved Oligomeric Golgi (COG) complex, as a factor involved in cell survival to both dsRNA and SINV in human cells. We showed that COG4 knockout led to a decrease of extracellular HS, specifically affected dsRNA transfection efficiency and reduced viral production, explaining the increased cell survival of these mutants. Importance When facing a viral infection, the organism has to put in place a number of defense mechanisms in order to clear the pathogen from the cell. At the early phase of this preparation for fighting against the invader, the innate immune response is triggered by the sensing of danger signals. Among those molecular cues, double-stranded (dsRNA) is a very potent inducer of different reactions at the cellular level that can ultimately lead to cell death. Using a genome-wide screening approach, we set to identify genes involved in dsRNA entry, sensing and apoptosis induction in human cells. This allowed us to determine that the heparan sulfate pathway and the Conserved Oligomeric Golgi complex are key determinants allowing entry of both dsRNA and viral nucleic acid leading to cell death.
Frontiers in Genetics, Jun 8, 2023
Methods in molecular biology, 2023
the book was inadvertently published without incorporating the ns mentioned below. The chapters h... more the book was inadvertently published without incorporating the ns mentioned below. The chapters have now been corrected and. and blue lines in Fig. 2 seem to be missing in print pdf. he authors' name has been updated as "Fromme JC".
Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature, Dec 13, 2019
Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature, Apr 9, 2021
Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature, Aug 20, 2020
Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature, Aug 30, 2022
Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature, Apr 14, 2023
Biochimica Et Biophysica Acta: Molecular Basis Of Disease, Aug 1, 2023
Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature, Aug 20, 2020
Cell Structure and Function, 2018
The Golgi apparatus is a central station for protein trafficking in eukaryotic cells. A widely ac... more The Golgi apparatus is a central station for protein trafficking in eukaryotic cells. A widely accepted model of protein transport within the Golgi apparatus is cisternal maturation. Each cisterna has specific resident proteins, which are thought to be maintained by COPI-mediated transport. However, the mechanisms underlying specific sorting of these Golgi-resident proteins remain elusive. To obtain a clue to understand the selective sorting of vesicles between the Golgi cisterenae, we investigated the molecular arrangements of the conserved oligomeric Golgi (COG) subunits in yeast cells. Mutations in COG subunits cause defects in Golgi trafficking and glycosylation of proteins and are causative of Congenital Disorders of Glycosylation (CDG) in humans. Interactions among COG subunits in cytosolic and membrane fractions were investigated by coimmunoprecipitation. Cytosolic COG subunits existed as octamers, whereas membrane-associated COG subunits formed a variety of subcomplexes. Relocation of individual COG subunits to mitochondria resulted in recruitment of only a limited number of other COG subunits to mitochondria. These results indicate that COG proteins function in the forms of a variety of subcomplexes and suggest that the COG complex does not comprise stable tethering without other interactors.
Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease
GARP is an evolutionary conserved heterotetrameric protein complex that is thought to tether endo... more GARP is an evolutionary conserved heterotetrameric protein complex that is thought to tether endosome-derived vesicles and promotes their fusion in thetrans-Golgi network. We have previously discovered the GARP’s role in maintaining Golgi glycosylation machinery. To further investigate the importance of the GARP complex for Golgi physiology, we employed Airyscan superresolution and electron microscopy, as well as the unbiased quantitative proteomic analysis of Golgi in RPE1 cells. Bothcisandtrans-Golgi compartments were significantly enlarged in GARP deficient cells with pronounced alterations of TGN morphology. In GARP-KO cells, proteomic analysis revealed a depletion of a subset of Golgi resident proteins, including Ca2+binding proteins, glycosylation enzymes, and v-SNAREs. We validated proteomics studies and discovered that two Golgi-resident proteins SDF4 and ATP2C1, related to Golgi calcium homeostasis, as well as intra-Golgi v-SNAREs GOSR1 and BET1L, are significantly depleted...
Traffic, 2021
The Conserved Oligomeric Golgi (COG) complex is an eight subunit protein complex associated with ... more The Conserved Oligomeric Golgi (COG) complex is an eight subunit protein complex associated with Golgi membranes. Genetic defects affecting individual COG subunits cause congenital disorders of glycosylation (CDGs), due to mislocalization of Golgi proteins involved in glycosylation mechanisms. While the resulting defects in N‐and O‐glycosylation have been extensively studied, no corresponding study of proteoglycan (PG) synthesis has been undertaken. We here show that glycosaminoglycan (GAG) modification of PGs is significantly reduced, regardless which COG subunit that is missing in HEK293T cells. Least reduction was observed for cells lacking COG1 and COG8 subunits, that bridge the A and B lobes of the complex. Lack of these subunits did not reduce GAG chain lengths of secreted PGs, which was reduced in cells lacking any other subunit (COG2‐7). COG3 knock out (KO) cells had particularly reduced ability to polymerize GAG chains. For cell‐associated GAGs, the mutant cell lines, excep...
F1000 - Post-publication peer review of the biomedical literature, 2018
Journal of Cell Biology, May 13, 2002
he Sec34/35 complex was identified as one of the evolutionarily conserved protein complexes that ... more he Sec34/35 complex was identified as one of the evolutionarily conserved protein complexes that regulates a cis-Golgi step in intracellular vesicular transport. We have identified three new proteins that associate with Sec35p and Sec34p in yeast cytosol. Mutations in these Sec34/35 complex subunits result in defects in basic Golgi functions, including glycosylation of secretory T proteins, protein sorting, and retention of Golgi resident proteins. Furthermore, the Sec34/35 complex interacts genetically and physically with the Rab protein Ypt1p, intra-Golgi SNARE molecules, as well as with Golgi vesicle coat complex COPI. We propose that the Sec34/35 protein complex acts as a tether that connects cis-Golgi membranes and COPI-coated, retrogradely targeted intra-Golgi vesicles.
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Papers by Vladimir Lupashin