cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30427415
title: Human clearance systems have a layered architecture across tissues and cell types that supports varied proteome compositions

description: Protein clearance is fundamental to proteome health. In eukaryotes, it is carried out by two highly conserved proteolytic systems, the ubiquitin-proteasome system (UPS) and the autophagy-lysosome pathway (ALP). Despite their pivotal role, the basal organization of the human protein clearance systems across tissues and cell types remains uncharacterized. Here, we interrogated this organization using diverse bulk and single cell omics datasets. Relative to other protein-coding genes, UPS and ALP genes were more widely expressed, encoded more housekeeping proteins, and were more essential for growth, in accordance with their fundamental roles. Yet, UPS and ALP subsystems had varied expression patterns, and each system showed a layered organization. The smaller layer included genes that were stably and widely expressed across tissues, had elevated expression levels, interacted with more proteins, and were more essential for growth, suggesting that they act as a core. The second larger layer included genes that were differentially expressed across tissues. Tissue-specific upregulation of those genes was associated with tissue-specific functions, phenotypes, and disease susceptibility, as demonstrated computationally and experimentally. Last, we compared protein clearance to other branches of the proteostasis network. Protein clearance and folding were closely coordinated across tissues and more plastic than protein synthesis. Taken together, we propose that the human proteostasis network is organized hierarchically and is tailored to varied proteome compositions. This organization could contribute to and illuminate tissue-selective phenotypes. <b>Abbreviations</b>: ALP: autophagy-lysosome pathway; CDA: chaperone-directed autophagy; DUBs: deubiquitinases; ESCRT: endosomal sorting complexes required for transport; KS: Kolmogorov-Smirnov; MW: Mann-Whitney; TE: tissue-enriched; TS: tissue-specific; UBL: ubiquitin-like protein; UPS: ubiquitin-proteasome system
DOI: 10.6084/m9.figshare.30427415.v1
title: Human clearance systems have a layered architecture across tissues and cell types that supports varied proteome compositions

description: Protein clearance is fundamental to proteome health. In eukaryotes, it is carried out by two highly conserved proteolytic systems, the ubiquitin-proteasome system (UPS) and the autophagy-lysosome pathway (ALP). Despite their pivotal role, the basal organization of the human protein clearance systems across tissues and cell types remains uncharacterized. Here, we interrogated this organization using diverse bulk and single cell omics datasets. Relative to other protein-coding genes, UPS and ALP genes were more widely expressed, encoded more housekeeping proteins, and were more essential for growth, in accordance with their fundamental roles. Yet, UPS and ALP subsystems had varied expression patterns, and each system showed a layered organization. The smaller layer included genes that were stably and widely expressed across tissues, had elevated expression levels, interacted with more proteins, and were more essential for growth, suggesting that they act as a core. The second larger layer included genes that were differentially expressed across tissues. Tissue-specific upregulation of those genes was associated with tissue-specific functions, phenotypes, and disease susceptibility, as demonstrated computationally and experimentally. Last, we compared protein clearance to other branches of the proteostasis network. Protein clearance and folding were closely coordinated across tissues and more plastic than protein synthesis. Taken together, we propose that the human proteostasis network is organized hierarchically and is tailored to varied proteome compositions. This organization could contribute to and illuminate tissue-selective phenotypes. <b>Abbreviations</b>: ALP: autophagy-lysosome pathway; CDA: chaperone-directed autophagy; DUBs: deubiquitinases; ESCRT: endosomal sorting complexes required for transport; KS: Kolmogorov-Smirnov; MW: Mann-Whitney; TE: tissue-enriched; TS: tissue-specific; UBL: ubiquitin-like protein; UPS: ubiquitin-proteasome system
DOI: 10.6084/m9.figshare.29999872
title: Autophagy dictates PHGDH-mediated serine metabolism in a timely manner to support oocyte development

description: The metabolic co-dependence of the oocyte and surrounding granulosa cells is crucial for oocyte developmental competence. Previous research has shown that serine-glycine and its key downstream metabolites are significantly involved in the process of oocyte maturation. However, the mechanism of serine metabolism and its influence on oocyte maturation remain unclear. In this study, we demonstrate that the serine metabolism enzyme PHGDH, which mediates <i>de novo</i> serine synthesis, is highly activated in granulosa cells and plays a crucial role in maintaining their metabolic and transcriptional homeostasis. By using our previously reported granulosa cell-oocyte co-culture system, we found that macroautophagy/autophagy regulates oocyte maturation by modulating PHGDH-mediated serine metabolism in a stage-specific manner, and this regulation is mediated by CALCOCO2/NDP52-dependent selective autophagy. Additional experiments indicated that S-adenosylmethionine (SAM) is a potential downstream product of serine metabolism, and that restoring SAM significantly rescues both granulosa cell homeostasis and oocyte quality. At the molecular level, we demonstrated that SAM regulates <i>Igf1</i> expression by altering the H3K4me3 modification level in its promoter region, highlighting a serine-SAM-H3K4me3<i>-Igf1</i> regulatory axis during oocyte maturation. Finally, we demonstrated that oocyte developmental capacity depends on <i>de novo</i> serine synthesis in granulosa cells during germinal vesicle breakdown (GVBD) stage rather than on the exogenous uptake of serine, and that disruption of serine synthesis significantly affects oocyte developmental capacity. Overall, our findings reveal how serine metabolism links granulosa cells and oocytes, provides new targets for predicting oocyte quality, and may help with strategies for early diagnosis or therapeutic intervention in improving reproductive outcomes. <b>Abbreviations</b> aa: amino acid; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; COCs: cumulus-oocyte complexes; CQ: chloroquine; DEG: differentially expressed gene; GV: germinal vesicle; GVBD: germinal vesicle breakdown; IGF1: insulin-like growth factor 1; MII: metaphase II stage of meiosis; OPTN: optineurin; Pb1: first polar body: PHGDH: 3-phosphoglycerate dehydrogenase; ROS: reactive oxygen species; SAM: s-adenosylmethionine; SQSTM1/p62: sequestosome 1; Ub: ubiquitin; WT: wild-type.
DOI: 10.6084/m9.figshare.29999872.v1
title: Autophagy dictates PHGDH-mediated serine metabolism in a timely manner to support oocyte development

description: The metabolic co-dependence of the oocyte and surrounding granulosa cells is crucial for oocyte developmental competence. Previous research has shown that serine-glycine and its key downstream metabolites are significantly involved in the process of oocyte maturation. However, the mechanism of serine metabolism and its influence on oocyte maturation remain unclear. In this study, we demonstrate that the serine metabolism enzyme PHGDH, which mediates <i>de novo</i> serine synthesis, is highly activated in granulosa cells and plays a crucial role in maintaining their metabolic and transcriptional homeostasis. By using our previously reported granulosa cell-oocyte co-culture system, we found that macroautophagy/autophagy regulates oocyte maturation by modulating PHGDH-mediated serine metabolism in a stage-specific manner, and this regulation is mediated by CALCOCO2/NDP52-dependent selective autophagy. Additional experiments indicated that S-adenosylmethionine (SAM) is a potential downstream product of serine metabolism, and that restoring SAM significantly rescues both granulosa cell homeostasis and oocyte quality. At the molecular level, we demonstrated that SAM regulates <i>Igf1</i> expression by altering the H3K4me3 modification level in its promoter region, highlighting a serine-SAM-H3K4me3<i>-Igf1</i> regulatory axis during oocyte maturation. Finally, we demonstrated that oocyte developmental capacity depends on <i>de novo</i> serine synthesis in granulosa cells during germinal vesicle breakdown (GVBD) stage rather than on the exogenous uptake of serine, and that disruption of serine synthesis significantly affects oocyte developmental capacity. Overall, our findings reveal how serine metabolism links granulosa cells and oocytes, provides new targets for predicting oocyte quality, and may help with strategies for early diagnosis or therapeutic intervention in improving reproductive outcomes. <b>Abbreviations</b> aa: amino acid; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; COCs: cumulus-oocyte complexes; CQ: chloroquine; DEG: differentially expressed gene; GV: germinal vesicle; GVBD: germinal vesicle breakdown; IGF1: insulin-like growth factor 1; MII: metaphase II stage of meiosis; OPTN: optineurin; Pb1: first polar body: PHGDH: 3-phosphoglycerate dehydrogenase; ROS: reactive oxygen species; SAM: s-adenosylmethionine; SQSTM1/p62: sequestosome 1; Ub: ubiquitin; WT: wild-type.
DOI: 10.5281/zenodo.18059282
title: Smartphone osmTracker for Android survey in Villa Bolasco

description: Tracks and waypoints of surveying path in Villa Bolasco and elements of interest (benches and trees)

DTM from drone lidar flight
DOI: 10.6084/m9.figshare.30094736
title: Microautophagy: definition, classification, and the complexity of the underlying mechanisms

description: Recently, rapid progress in the field of microautophagy (MI-autophagy) revealed the existence of multiple subtypes that differ in both intracellular membrane dynamics and molecular mechanisms. As a result, a single umbrella term “microautophagy” has become too vague, even creating some confusion among researchers both within and outside the field. We herein describe different subtypes of MI-autophagic processes and propose a systematic approach for naming them more accurately. <b>Abbreviation:</b> ATG, autophagy related; e-MI, endosomal microautophagy; ER, endoplasmic reticulum; ESCRT, endosomal sorting complex required for transport; EV, extracellular vesicle; HSPA8/HSC70, heat shock protein family A (Hsp70) member 8; ILVs, intralumenal vesicles; l-MI, lysosomal microautophagy; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MCOLN1, mucolipin TRP cation channel 1; microautophagy, MI-autophagy; MVBs, multivesicular bodies; SQSTM1, sequestosome 1; v-MI, vacuolar microautophagy.
DOI: 10.6084/m9.figshare.30094736.v1
title: Microautophagy: definition, classification, and the complexity of the underlying mechanisms

description: Recently, rapid progress in the field of microautophagy (MI-autophagy) revealed the existence of multiple subtypes that differ in both intracellular membrane dynamics and molecular mechanisms. As a result, a single umbrella term “microautophagy” has become too vague, even creating some confusion among researchers both within and outside the field. We herein describe different subtypes of MI-autophagic processes and propose a systematic approach for naming them more accurately. <b>Abbreviation:</b> ATG, autophagy related; e-MI, endosomal microautophagy; ER, endoplasmic reticulum; ESCRT, endosomal sorting complex required for transport; EV, extracellular vesicle; HSPA8/HSC70, heat shock protein family A (Hsp70) member 8; ILVs, intralumenal vesicles; l-MI, lysosomal microautophagy; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MCOLN1, mucolipin TRP cation channel 1; microautophagy, MI-autophagy; MVBs, multivesicular bodies; SQSTM1, sequestosome 1; v-MI, vacuolar microautophagy.
DOI: 10.6084/m9.figshare.30485123
title: NRBF2 homodimerization by its coiled-coil domain strengthens association with the PtdIns3K complex mediated by the MIT domain to promote autophagy

description: The mammalian class III phosphatidylinositol-3-kinase complex (PtdIns3K) forms two biochemically and functionally distinct subcomplexes including the ATG14-containing complex I (PtdIns3K-C1) and the UVRAG-containing complex II (PtdIns3K-C2). Both subcomplexes adopt a V-shaped architecture with a BECN1-ATG14 or UVRAG adaptor arm and a PIK3R4/VPS15-PIK3C3/VPS34 catalytic arm. NRBF2 is a pro-autophagic modulator that specifically associates with PtdIns3K-C1 to enhance its kinase activity and promotes macroautophagy/autophagy. How NRBF2 exerts such a positive effect is not fully understood. Here we report that NRBF2 binds to PIK3R4/VPS15 with moderate affinity through a conserved site on its N-terminal MIT domain. The NRBF2-PIK3R4/VPS15 interaction is incompatible with the UVRAG-containing PtdIns3K-C2 because the C2 domain of UVRAG outcompetes NRBF2 for PIK3R4/VPS15 binding. Our crystal structure of the NRBF2 coiled-coil (CC) domain reveals a symmetric homodimer with multiple hydrophobic pairings at the CC interface, which is in distinct contrast to the asymmetric dimer observed in the yeast ortholog Atg38. Mutations in the CC domain that rendered NRBF2 monomeric led to weakened binding to PIK3R4/VPS15 and only partial rescue of autophagy deficiency in <i>nrbf2</i> knockout cells. In comparison, NRBF2 with its CC domain replaced by a dimeric Gcn4 module showed proautophagic activity comparable to wild type while NRBF2 carrying a tetrameric Gcn4 module showed further enhanced activity. We propose that the oligomeric state of NRBF2 mediated by its CC domain is critical for strengthening the moderate NRBF2-PIK3R4/VPS15 interaction mediated by its MIT domain to fully activate PtdIns3K-C1 and promote autophagy. <b>Abbreviations:</b> ATG: autophagy related; ATG14: autophagy related 14; BECN1: beclin 1; CC: coiled-coil; dCCD: delete CCD; dMIT: delete MIT; Gcn4: general control nonderepressible 4; ITC: isothermal titration calorimetry; IP: immunoprecipitation; KO: knockout; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MIM: MIT-interacting motif; MIT: microtubule interacting and trafficking; NMR: nuclear magnetic resonance; NRBF2: nuclear receptor binding factor 2; PtdIns3K: class III phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PIK3R4/VPS15: phosphoinositide-3-kinase regulatory subunit 4; SQSTM1/p62: sequestosome 1; UVRAG: UV radiation resistance associated; VPS: vacuolar protein sorting; WT: wild type.
DOI: 10.5281/zenodo.7445698
title: Smartphone osmTracker for Android survey in Villa Bolasco

description: Tracks and waypoints of surveying path in Villa Bolasco and elements of interest (benches and trees)

DTM from drone lidar flight
DOI: 10.6084/m9.figshare.29625865
title: Npl3 is required for efficient autophagosome-vacuole fusion

description: Macroautophagy/autophagy is a highly conserved catabolic membrane trafficking process through which various intracellular constituents, from proteins to organelles, are targeted for vacuolar/lysosomal degradation. Autophagy is tightly regulated both temporally and in magnitude at multiple levels to prevent either excessive or insufficient activity. To date, only a few RNA-binding proteins have been characterized as regulating the expression of genes essential for autophagy, and the contribution of post-transcriptional regulation in autophagy activity remains poorly understood. Here, through a genetic screen for autophagy-defective mutants, we identified Npl3, a nucleus-cytoplasm shuttling mRNA-binding protein, as essential for both bulk and selective types of autophagy. Deletion of <i>NPL3</i> does not affect autophagosome biogenesis, closure, or maturation; however, it severely impairs autophagosome-vacuole fusion and results in minimal autophagosome turnover. We further demonstrated that this regulation depends on the RNA-binding domain of Npl3 and its capability for nuclear re-import. Together, our results reveal a novel layer of post-transcriptional regulation of autophagy. <b>Abbreviations:</b> Atg,autophagy related; HOPS: homotypic fusion and protein sorting; prApe1: precursor aminopeptidase I; RBP, RNA-binding protein; RRM, RNA-recognition motif; SNARE: soluble NSF attachment protein receptor; PAS: phagophore asse
DOI: 10.6084/m9.figshare.29625865.v2
title: Npl3 is required for efficient autophagosome-vacuole fusion

description: Macroautophagy/autophagy is a highly conserved catabolic membrane trafficking process through which various intracellular constituents, from proteins to organelles, are targeted for vacuolar/lysosomal degradation. Autophagy is tightly regulated both temporally and in magnitude at multiple levels to prevent either excessive or insufficient activity. To date, only a few RNA-binding proteins have been characterized as regulating the expression of genes essential for autophagy, and the contribution of post-transcriptional regulation in autophagy activity remains poorly understood. Here, through a genetic screen for autophagy-defective mutants, we identified Npl3, a nucleus-cytoplasm shuttling mRNA-binding protein, as essential for both bulk and selective types of autophagy. Deletion of <i>NPL3</i> does not affect autophagosome biogenesis, closure, or maturation; however, it severely impairs autophagosome-vacuole fusion and results in minimal autophagosome turnover. We further demonstrated that this regulation depends on the RNA-binding domain of Npl3 and its capability for nuclear re-import. Together, our results reveal a novel layer of post-transcriptional regulation of autophagy. <b>Abbreviations:</b> Atg,autophagy related; HOPS: homotypic fusion and protein sorting; prApe1: precursor aminopeptidase I; RBP, RNA-binding protein; RRM, RNA-recognition motif; SNARE: soluble NSF attachment protein receptor; PAS: phagophore asse
DOI: 10.6084/m9.figshare.30485123.v2
title: NRBF2 homodimerization by its coiled-coil domain strengthens association with the PtdIns3K complex mediated by the MIT domain to promote autophagy

description: The mammalian class III phosphatidylinositol-3-kinase complex (PtdIns3K) forms two biochemically and functionally distinct subcomplexes including the ATG14-containing complex I (PtdIns3K-C1) and the UVRAG-containing complex II (PtdIns3K-C2). Both subcomplexes adopt a V-shaped architecture with a BECN1-ATG14 or UVRAG adaptor arm and a PIK3R4/VPS15-PIK3C3/VPS34 catalytic arm. NRBF2 is a pro-autophagic modulator that specifically associates with PtdIns3K-C1 to enhance its kinase activity and promotes macroautophagy/autophagy. How NRBF2 exerts such a positive effect is not fully understood. Here we report that NRBF2 binds to PIK3R4/VPS15 with moderate affinity through a conserved site on its N-terminal MIT domain. The NRBF2-PIK3R4/VPS15 interaction is incompatible with the UVRAG-containing PtdIns3K-C2 because the C2 domain of UVRAG outcompetes NRBF2 for PIK3R4/VPS15 binding. Our crystal structure of the NRBF2 coiled-coil (CC) domain reveals a symmetric homodimer with multiple hydrophobic pairings at the CC interface, which is in distinct contrast to the asymmetric dimer observed in the yeast ortholog Atg38. Mutations in the CC domain that rendered NRBF2 monomeric led to weakened binding to PIK3R4/VPS15 and only partial rescue of autophagy deficiency in <i>nrbf2</i> knockout cells. In comparison, NRBF2 with its CC domain replaced by a dimeric Gcn4 module showed proautophagic activity comparable to wild type while NRBF2 carrying a tetrameric Gcn4 module showed further enhanced activity. We propose that the oligomeric state of NRBF2 mediated by its CC domain is critical for strengthening the moderate NRBF2-PIK3R4/VPS15 interaction mediated by its MIT domain to fully activate PtdIns3K-C1 and promote autophagy. <b>Abbreviations:</b> ATG: autophagy related; ATG14: autophagy related 14; BECN1: beclin 1; CC: coiled-coil; dCCD: delete CCD; dMIT: delete MIT; Gcn4: general control nonderepressible 4; ITC: isothermal titration calorimetry; IP: immunoprecipitation; KO: knockout; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MIM: MIT-interacting motif; MIT: microtubule interacting and trafficking; NMR: nuclear magnetic resonance; NRBF2: nuclear receptor binding factor 2; PtdIns3K: class III phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PIK3R4/VPS15: phosphoinositide-3-kinase regulatory subunit 4; SQSTM1/p62: sequestosome 1; UVRAG: UV radiation resistance associated; VPS: vacuolar protein sorting; WT: wild type.
DOI: 10.6084/m9.figshare.29625865.v1
title: Npl3 is required for efficient autophagosome-vacuole fusion

description: Macroautophagy/autophagy is a highly conserved catabolic membrane trafficking process through which various intracellular constituents, from proteins to organelles, are targeted for vacuolar/lysosomal degradation. Autophagy is tightly regulated both temporally and in magnitude at multiple levels to prevent either excessive or insufficient activity. To date, only a few RNA-binding proteins have been characterized as regulating the expression of genes essential for autophagy, and the contribution of post-transcriptional regulation in autophagy activity remains poorly understood. Here, through a genetic screen for autophagy-defective mutants, we identified Npl3, a nucleus-cytoplasm shuttling mRNA-binding protein, as essential for both bulk and selective types of autophagy. Deletion of <i>NPL3</i> does not affect autophagosome biogenesis, closure, or maturation; however, it severely impairs autophagosome-vacuole fusion and results in minimal autophagosome turnover. We further demonstrated that this regulation depends on the RNA-binding domain of Npl3 and its capability for nuclear re-import. Together, our results reveal a novel layer of post-transcriptional regulation of autophagy.
DOI: 10.6084/m9.figshare.30485123.v1
title: NRBF2 homodimerization by its coiled-coil domain strengthens association with the PtdIns3K complex mediated by the mit domain to promote autophagy

description: The mammalian class III phosphatidylinositol-3-kinase complex (PtdIns3K) forms two biochemically and functionally distinct subcomplexes including the ATG14-containing complex I (PtdIns3K-C1) and the UVRAG-containing complex II (PtdIns3K-C2). Both subcomplexes adopt a V-shaped architecture with a BECN1-ATG14 or UVRAG adaptor arm and a PIK3R4/VPS15-PIK3C3/VPS34 catalytic arm. NRBF2 is a pro-autophagic modulator that specifically associates with PtdIns3K-C1 to enhance its kinase activity and promotes macroautophagy/autophagy. How NRBF2 exerts such a positive effect is not fully understood. Here we report that NRBF2 binds to PIK3R4/VPS15 with moderate affinity through a conserved site on its N-terminal MIT domain. The NRBF2-PIK3R4/VPS15 interaction is incompatible with the UVRAG-containing PtdIns3K-C2 because the C2 domain of UVRAG outcompetes NRBF2 for PIK3R4/VPS15 binding. Our crystal structure of the NRBF2 coiled-coil (CC) domain reveals a symmetric homodimer with multiple hydrophobic pairings at the CC interface, which is in distinct contrast to the asymmetric dimer observed in the yeast ortholog Atg38. Mutations in the CC domain that rendered NRBF2 monomeric led to weakened binding to PIK3R4/VPS15 and only partial rescue of autophagy deficiency in <i>nrbf2</i> knockout cells. In comparison, NRBF2 with its CC domain replaced by a dimeric Gcn4 module showed proautophagic activity comparable to wild type while NRBF2 carrying a tetrameric Gcn4 module showed further enhanced activity. We propose that the oligomeric state of NRBF2 mediated by its CC domain is critical for strengthening the moderate NRBF2-PIK3R4/VPS15 interaction mediated by its MIT domain to fully activate PtdIns3K-C1 and promote autophagy.