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<article doi="10.1038/emboj.2009.405" abstract="Autophagy is primarily considered a non-selective degradation process induced by starvation. Nutrient-independent basal autophagy, in contrast, imposes intracellular QC by selective disposal of aberrant protein aggregates and damaged organelles, a process critical for suppressing neurodegenerative diseases. The molecular mechanism that distinguishes these two fundamental autophagic responses, however, remains mysterious. Here, we identify the ubiquitin-binding deacetylase, histone deacetylase-6 (HDAC6), as a central component of basal autophagy that targets protein aggregates and damaged mitochondria. Surprisingly, HDAC6 is not required for autophagy activation; rather, it controls the fusion of autophagosomes to lysosomes. HDAC6 promotes autophagy by recruiting a cortactin-dependent, actin-remodelling machinery, which in turn assembles an F-actin network that stimulates autophagosome-lysosome fusion and substrate degradation. Indeed, HDAC6 deficiency leads to autophagosome maturation failure, protein aggregate build-up, and neurodegeneration. Remarkably, HDAC6 and F-actin assembly are completely dispensable for starvation-induced autophagy, uncovering the fundamental difference of these autophagic modes. Our study identifies HDAC6 and the actin cytoskeleton as critical components that define QC autophagy and uncovers a novel regulation of autophagy at the level of autophagosome-lysosome fusion."><fig id="2492"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2492"/><sd-panel panel_id="7057"><sd-tag id="sdTag325" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO MEF cells are defective in aggregate clearance but not in autophagosome induction or targeting. (A) <sd-tag id="sdTag327" source="sdapi" category="assay" entity_type="" role="" text="Filter‐trap analysis" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Filter‐trap analysis</sd-tag> of <sd-tag id="sdTag328" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag>‐induced, <sd-tag id="sdTag329" source="sdapi" category="entity" entity_type="molecule" role="component" text="SDS" ext_ids="CHEBI:8984" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sodium dodecyl sulfate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">SDS</sd-tag>‐insoluble ubiquitinated aggregates generated in wild‐type (WT), <sd-tag id="sdTag335" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO, and KO <sd-tag id="sdTag331" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> reconstituted with different <sd-tag id="sdTag336" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> constructs as indicated. The signal intensity from the <sd-tag id="sdTag330" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P0CG50///P0CG49///Q6ZWU9///P62984" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="//////Rps27///Uba52" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag><sd-tag id="sdTag332" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> (bottom panel) was quantified and presented as the average of the means from three independent experiments along with the standard deviation (top). Note the significant accumulation of <sd-tag id="sdTag337" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P0CG50///P0CG49///Q6ZWU9///P62984" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="//////Rps27///Uba52" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive aggregates in <sd-tag id="sdTag338" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag339" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> and KO <sd-tag id="sdTag340" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> stably expressing <sd-tag id="sdTag341" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag>‐CD and ΔBUZ mutants. WT, <sd-tag id="sdTag342" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO, and <sd-tag id="sdTag343" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag344" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> stably expressing human <sd-tag id="sdTag345" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> (hHDAC6 WT), <sd-tag id="sdTag346" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> CD (catalytically inactive mutant), or <sd-tag id="sdTag347" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> ΔBUZ (<sd-tag id="sdTag348" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P0CG50///P0CG49///Q6ZWU9///P62984" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="//////Rps27///Uba52" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐binding‐deficient mutant) were analysed for the level of <sd-tag id="sdTag349" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> using an anti‐human <sd-tag id="sdTag350" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> antibody. Mouse endogenous <sd-tag id="sdTag351" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> (m<sd-tag id="sdTag334" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HDAC6" ext_ids="Q9Z2V5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">HDAC6</sd-tag>) and <sd-tag id="sdTag333" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag> levels were determined by each corresponding antibody.<graphic href="https://api.sourcedata.io/file.php?panel_id=7057"/></sd-panel><sd-panel panel_id="7058">(B) WT and <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were treated with <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> and subjected to <sd-tag id="sdTag35" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analysis for <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>, <sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag>, and <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HDAC6" ext_ids="Q9Z2V5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">HDAC6</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7058"/></sd-panel><sd-panel panel_id="7059">(C) Cells were treated with <sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> as described under Materials and methods and <sd-pretag id="sdPretag14389602041840" parent-tag-id="352">immunostained</sd-pretag> with antibodies to <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> (green) and <sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> (red). Arrows indicate <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive aggregates that colocalize with <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>‐positive <sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0044754" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autolysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag>. Scale bar, 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7059"/></sd-panel><sd-panel panel_id="7060">(D) WT and <sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG5</sd-tag> KO <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> are treated with 2.5 μM <sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> for 1 day and incubated with normal growth media for 18 h. <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> are <sd-tag id="sdTag352" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag> with anti‐<sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> (red) and anti‐<sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> antibody (green).<graphic href="https://api.sourcedata.io/file.php?panel_id=7060"/></sd-panel></fig><fig id="2493"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2493"/><sd-panel panel_id="7061">(A) Wild‐type and <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were transfected with pcDNA, pcDNA‐HDAC6WT, HDAC6CD, or <sd-tag id="sdTag353" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag>ΔBuz, along with <sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="66734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Map1lc3a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> as indicated. Yellow signals indicate non‐acidic <sd-tag id="sdTag354" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag> and red signals indicate acidic <sd-tag id="sdTag355" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagolysosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagolysosomes</sd-tag>. Scale bar, 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7061"/></sd-panel><sd-panel panel_id="7062">(B) The total number of yellow <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicles" ext_ids="GO:0031982" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vesicle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicles</sd-tag> was quantified from three independent experiments (>12 cells each) and presented as the percentage of total <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> dots (red plus yellow) along with the standard deviation.<graphic href="https://api.sourcedata.io/file.php?panel_id=7062"/></sd-panel><sd-panel panel_id="7063">(C)<sd-tag id="sdTag86" source="sdapi" category="assay" entity_type="" role="" text="In vitro fusion assays" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">In vitro fusion assays</sd-tag>. <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosomes</sd-tag> (APGs) and <sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (Lys) purified from wild type and <sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag>−/− <sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were subjected to heterotypic and homotypic in vitro fusion assays (representative fields are shown in Supplementary Figure S3). Values are means+s.e. of the percentages of fusion from three independent experiments (more than 10 images per each experiment).<graphic href="https://api.sourcedata.io/file.php?panel_id=7063"/></sd-panel><sd-panel panel_id="7064">(D) <sd-tag id="sdTag91" source="sdapi" category="assay" entity_type="" role="" text="EM" ext_ids="BAO_0000449" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">EM</sd-tag> images of wild‐type and <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> in normal growth conditions. Yellow arrows, <sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag>; red arrows, <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagolysosomes" ext_ids="GO:0005776///GO:0044754" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="autophagic vacuole///autolysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">autophagolysosomes</sd-tag>; green arrowheads, <sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="multilamellar bodies" ext_ids="GO:0005771" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="multivesicular body" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">multilamellar bodies</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7064"/></sd-panel><sd-panel panel_id="7065">(E) Quantification of <sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag> and <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagolysosomes" ext_ids="GO:0005776///GO:0044754" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="autophagic vacuole///autolysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">autophagolysosomes</sd-tag>. The error bar represents the standard error.<graphic href="https://api.sourcedata.io/file.php?panel_id=7065"/></sd-panel></fig><fig id="2494"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2494"/><sd-panel panel_id="7066">(A) <sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosome" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosome</sd-tag>-<sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosome" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosome</sd-tag> fusion is analysed in wild‐type and <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> with or without starvation (6 h) using <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="66734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Map1lc3a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> as described in Figure 2A.<graphic href="https://api.sourcedata.io/file.php?panel_id=7066"/></sd-panel><sd-panel panel_id="7067">(B) Wild‐type and <sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag117" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were cultured in <sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="undefined" role="component" text="Hank's solution" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Hank's solution</sd-tag> for 3 h followed by <sd-pretag id="sdPretag14389612905050" parent-tag-id="368">immunoblotting</sd-pretag> with an antibody for <sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>, <sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HDAC6" ext_ids="Q9Z2V5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">HDAC6</sd-tag>, and <sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="GAPDH" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAPDH</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7067"/></sd-panel><sd-panel panel_id="7068">(C) <sd-tag id="sdTag131" source="sdapi" category="assay" entity_type="" role="" text="Long‐lived protein degradation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Long‐lived protein degradation</sd-tag> in wild‐type and <sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEF cells" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEF cells</sd-tag>. The degradation of <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="[14C]‐valine" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">[14C]‐valine</sd-tag> labelled long‐lived <sd-tag id="sdTag324" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="protein" ext_ids="CHEBI:36080" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="protein" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">protein</sd-tag> was measured in the presence or absence of 3‐methyl adenine (<sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3MA</sd-tag>, inhibits the formation of <sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="subcellular" role="component" text="autophagic vacuoles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic vacuoles</sd-tag>). The average of percentage degradation from three independent experiments is presented. The error bar represents the standard deviation.<graphic href="https://api.sourcedata.io/file.php?panel_id=7068"/></sd-panel></fig><fig id="2495"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2495"/><sd-panel panel_id="7069">(A) Wild‐type and <sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag137" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were treated with <sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> and <sd-tag id="sdTag358" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag> with antibodies to <sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Lamp‐1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Lamp‐1</sd-tag> (a <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="subcellular" role="component" text="lysosome" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosome</sd-tag> marker, red) and <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> (green) as indicated. <sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="protein" role="assayed" text="F‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">F‐actin</sd-tag> was detected by <sd-tag id="sdTag133" source="sdapi" category="assay" entity_type="" role="" text="phalloidin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">phalloidin</sd-tag> (blue). The arrows indicate <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive aggregates that are surrounded by <sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="protein" role="assayed" text="F‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">F‐actin</sd-tag> and <sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Lamp‐1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Lamp‐1</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7069"/></sd-panel><sd-panel panel_id="7070">(B, C) Wild‐type and <sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were transfected with <sd-tag id="sdTag146" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag147" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="66734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Map1lc3a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag>, followed by treatment with <sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LatA" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LatA</sd-tag> (100 nM) or <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nocodazole" ext_ids="CHEBI:34892" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nocodazole" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nocodazole</sd-tag> (250 nM) for 6 h and analysed as described in Figure 3A.<graphic href="https://api.sourcedata.io/file.php?panel_id=7070"/></sd-panel><sd-panel panel_id="7071">(D) <sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosomes</sd-tag> (APGs) and <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (Lys) isolated from fed <sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="organism" role="component" text="mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mouse</sd-tag> <sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="cell_type" role="component" text="hepatocytes" ext_ids="CL:0000182" norm_text="" ext_dbs="CL" in_caption="True" ext_names="hepatocyte" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">hepatocytes</sd-tag> were treated or not with <sd-tag id="sdTag162" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="latrunculin" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">latrunculin</sd-tag> (<sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LatA" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LatA</sd-tag>) as indicated, extensively washed to remove traces of the inhibitor, and then labelled with the antibody and subjected to <sd-tag id="sdTag163" source="sdapi" category="assay" entity_type="" role="" text="in vitro fusion assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">in vitro fusion assay</sd-tag> in the presence or absence of purified <sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="protein" role="intervention" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag>. The number of total fusion events/total number of <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicles" ext_ids="GO:0031982" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vesicle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicles</sd-tag> for each condition was as follows: 176/880; 233/1110; 84/930; and 180/950. The differences with untreated samples were significant at **P0.01.<graphic href="https://api.sourcedata.io/file.php?panel_id=7071"/></sd-panel><sd-panel panel_id="7072">(E) <sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosomes</sd-tag> (APGs) and <sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (Lys) isolated from fed or starved <sd-tag id="sdTag166" source="sdapi" category="entity" entity_type="organism" role="component" text="mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mouse</sd-tag> <sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="cell_type" role="component" text="hepatocytes" ext_ids="CL:0000182" norm_text="" ext_dbs="CL" in_caption="True" ext_names="hepatocyte" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">hepatocytes</sd-tag> were treated or not with <sd-tag id="sdTag168" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="latrunculin" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">latrunculin</sd-tag> (<sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LatA" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LatA</sd-tag>) as labelled and subjected to <sd-tag id="sdTag171" source="sdapi" category="assay" entity_type="" role="" text="in vitro fusion assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">in vitro fusion assay</sd-tag>. The differences with untreated samples were significant at *P0.05. The number of total fusion events/total number of <sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicles" ext_ids="GO:0031982" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vesicle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicles</sd-tag> for each condition was as follows: 169/1250; 87/972; 190/1120; and 175/1165.<graphic href="https://api.sourcedata.io/file.php?panel_id=7072"/></sd-panel><sd-panel panel_id="7073">(F) <sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosomes</sd-tag> (APGs) and <sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (Lys) isolated from <sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="gene" role="component" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were treated or not with <sd-tag id="sdTag176" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="latrunculin" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">latrunculin</sd-tag> (<sd-tag id="sdTag177" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LatA" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LatA</sd-tag>) as indicated and subjected to <sd-tag id="sdTag178" source="sdapi" category="assay" entity_type="" role="" text="in vitro fusion assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">in vitro fusion assay</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7073"/></sd-panel></fig><fig id="2496"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2496"/><sd-panel panel_id="7074">(A) Biochemical characterization of autophagic compartments isolated from <sd-tag id="sdTag179" source="sdapi" category="entity" entity_type="gene" role="component" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO cells. Different subcellular fractions (75 μg protein) isolated from the wild type (WT) were subjected to <sd-tag id="sdTag184" source="sdapi" category="assay" entity_type="" role="" text="SDS–PAGE" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDS-PAGE</sd-tag> and <sd-pretag id="sdPretag14389612949370" parent-tag-id="368">immunoblotting</sd-pretag> for the indicated proteins. Hom, homogenate; APG, <sd-tag id="sdTag181" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag>; APL, <sd-tag id="sdTag182" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="autophagolysosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagolysosomes</sd-tag>; Lys, <sd-tag id="sdTag183" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7074"/></sd-panel><sd-panel panel_id="7075">(B) <sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosomes</sd-tag> (APGs) and <sd-tag id="sdTag194" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (Lys) isolated from fed cells were treated or not with <sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="latrunculin" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">latrunculin</sd-tag> (<sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LatA" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LatA</sd-tag>) as labelled and subjected to <sd-tag id="sdTag197" source="sdapi" category="assay" entity_type="" role="" text="in vitro fusion assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">in vitro fusion assay</sd-tag>. The differences with untreated samples were significant at **P0.01.<graphic href="https://api.sourcedata.io/file.php?panel_id=7075"/></sd-panel><sd-panel panel_id="7076">(C) WT and <sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG5</sd-tag> KO <sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were treated with <sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> and <sd-tag id="sdTag359" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag> with antibodies to <sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> (green) as indicated. <sd-tag id="sdTag205" source="sdapi" category="entity" entity_type="protein" role="assayed" text="F‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">F‐actin</sd-tag> was detected by <sd-tag id="sdTag203" source="sdapi" category="assay" entity_type="" role="" text="phalloidin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">phalloidin</sd-tag> (red). The arrows indicated <sd-tag id="sdTag204" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive protein aggregates.<graphic href="https://api.sourcedata.io/file.php?panel_id=7076"/></sd-panel></fig><fig id="2497"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2497"/><sd-panel panel_id="7077">(A) Wild‐type and <sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were treated with <sd-tag id="sdTag212" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> and <sd-tag id="sdTag360" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag> with antibodies against <sd-tag id="sdTag207" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cortactin" ext_ids="Q60598" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">cortactin</sd-tag> (red), <sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> (green), and <sd-tag id="sdTag214" source="sdapi" category="assay" entity_type="" role="" text="phalloidin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">phalloidin</sd-tag> for <sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="protein" role="assayed" text="F‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">F‐actin</sd-tag> (blue) as indicated. The arrows indicated <sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive aggregates that were colocalized with <sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="protein" role="assayed" text="F‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">F‐actin</sd-tag> and <sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cortactin" ext_ids="Q60598" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">cortactin</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7077"/></sd-panel><sd-panel panel_id="7078">(B) Wild‐type <sd-tag id="sdTag219" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were transfected with control or <sd-tag id="sdTag220" source="sdapi" category="entity" entity_type="gene" role="intervention" text="cortactin" ext_ids="13043" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">cortactin</sd-tag> siRNA, treated with <sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag>, and stained with antibodies for <sd-tag id="sdTag228" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Lap‐1" ext_ids="P97449" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Anpep" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Lap‐1</sd-tag> (red, to label <sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosome" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosome</sd-tag>), or <sd-tag id="sdTag223" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> (green) and <sd-tag id="sdTag224" source="sdapi" category="assay" entity_type="" role="" text="phalloidin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">phalloidin</sd-tag> for <sd-tag id="sdTag225" source="sdapi" category="entity" entity_type="protein" role="assayed" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag> (blue). Note that <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="protein" role="assayed" text="F‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">F‐actin</sd-tag> staining at protein aggregates was lost, but <sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> remained concentrated in <sd-tag id="sdTag227" source="sdapi" category="entity" entity_type="gene" role="intervention" text="cortactin" ext_ids="13043" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">cortactin</sd-tag> knockdown cells (arrow).<graphic href="https://api.sourcedata.io/file.php?panel_id=7078"/></sd-panel><sd-panel panel_id="7079">(C) Wild‐type <sd-tag id="sdTag361" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were transfected with control or <sd-tag id="sdTag362" source="sdapi" category="entity" entity_type="gene" role="intervention" text="cortactin" ext_ids="13043" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">cortactin</sd-tag> siRNA, treated <sd-tag id="sdTag363" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> 2.5 μM for 18 h, and subjected to <sd-tag id="sdTag365" source="sdapi" category="assay" entity_type="" role="" text="filter‐trap assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">filter‐trap assay</sd-tag> using a <sd-tag id="sdTag366" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P0CG49///Q6ZWU9///P62984///P0CG50" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="///Rps27///Uba52///" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> antibody. The knockdown level of endogenous <sd-tag id="sdTag367" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cortactin" ext_ids="Q60598" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">cortactin</sd-tag> was confirmed by <sd-tag id="sdTag368" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> using an antibody against <sd-tag id="sdTag370" source="sdapi" category="entity" entity_type="gene" role="intervention" text="cortactin" ext_ids="13043" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">cortactin</sd-tag> and <sd-tag id="sdTag369" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="GAPDH" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAPDH</sd-tag> in the right panel.<graphic href="https://api.sourcedata.io/file.php?panel_id=7079"/></sd-panel><sd-panel panel_id="7080">(D) <sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS cells" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS cells</sd-tag> were transfected with control siRNA and <sd-tag id="sdTag242" source="sdapi" category="entity" entity_type="gene" role="intervention" text="cortactin" ext_ids="13043" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">cortactin</sd-tag> siRNA. <sd-tag id="sdTag243" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosome" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosome</sd-tag>-<sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosome" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosome</sd-tag> fusion was analysed with or without starvation (6 h) using the <sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag247" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag248" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="66734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Map1lc3a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> reporter as described in Figure 3A.<graphic href="https://api.sourcedata.io/file.php?panel_id=7080"/></sd-panel><sd-panel panel_id="7081">(E) The <sd-tag id="sdTag250" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag251" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag252" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="66734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Map1lc3a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> plasmid was cotransfected with wild type, 9KQ (acetylation‐mimic), or 9KR (deacetylation‐mimic) <sd-tag id="sdTag253" source="sdapi" category="entity" entity_type="gene" role="intervention" text="cortactin" ext_ids="13043" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">cortactin</sd-tag>‐expressing plasmids into wild‐type <sd-tag id="sdTag254" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag>. <sd-tag id="sdTag255" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosome" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosome</sd-tag>-<sd-tag id="sdTag256" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosome" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosome</sd-tag> fusion was analysed as described in Figure 3A.<graphic href="https://api.sourcedata.io/file.php?panel_id=7081"/></sd-panel></fig><fig id="2498"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2498"/><sd-panel panel_id="7082">(A) <sd-tag id="sdTag372" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag373" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> accumulate <sd-tag id="sdTag374" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52//////" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive protein aggregates in the <sd-tag id="sdTag375" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag>. The <sd-tag id="sdTag376" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="hippocampus" ext_ids="UBERON:0001954" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="Ammon's horn" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">hippocampus</sd-tag> and <sd-tag id="sdTag377" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="cerebral cortex" ext_ids="UBERON:0000956" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebral cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cerebral cortex</sd-tag> regions from 6‐month‐old wild‐type and <sd-tag id="sdTag382" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52//////" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> KO littermates were subjected to <sd-tag id="sdTag379" source="sdapi" category="assay" entity_type="" role="" text="immunostaining" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostaining</sd-tag> with a <sd-tag id="sdTag390" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52//////" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> antibody and counterstained with <sd-tag id="sdTag380" source="sdapi" category="assay" entity_type="" role="" text="hematoxylin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">hematoxylin</sd-tag>. The red arrows indicate <sd-tag id="sdTag384" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P62984///P0CG49///P0CG50///Q6ZWU9" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Uba52/////////Rps27" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive neuritic aggregates and black arrows indicate cytoplasmic aggregates. These <sd-tag id="sdTag383" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52//////" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive structures were rarely observed in control littermates. Scale bar, 50 μm<graphic href="https://api.sourcedata.io/file.php?panel_id=7082"/></sd-panel><sd-panel panel_id="7083">(B) Apoptotic cell death in the <sd-tag id="sdTag275" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="cortex" ext_ids="UBERON:0000956" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebral cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cortex</sd-tag> and <sd-tag id="sdTag277" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="hippocampus" ext_ids="UBERON:0001954" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="Ammon's horn" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">hippocampus</sd-tag> region of <sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag279" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> as determined by <sd-tag id="sdTag276" source="sdapi" category="assay" entity_type="" role="" text="TUNEL" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TUNEL</sd-tag> staining. Apoptotic cells were only observed in <sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>. Scale bar, 100 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7083"/></sd-panel><sd-panel panel_id="7084">(C) <sd-tag id="sdTag290" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="32461" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HDAC6" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> depletion in the Drosophila <sd-tag id="sdTag284" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> leads to <sd-tag id="sdTag291" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P15357///P18101///P0CG69" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="RpS27A///RpL40///Ubi-p63E" ext_tax_ids="7227///7227///7227" ext_tax_names="Drosophila melanogaster///Drosophila melanogaster///Drosophila melanogaster" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive pathology. <sd-tag id="sdTag299" source="sdapi" category="assay" entity_type="" role="" text="Immunostaining" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunostaining</sd-tag> for <sd-tag id="sdTag292" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P15357///P18101///P0CG69" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="RpS27A///RpL40///Ubi-p63E" ext_tax_ids="7227///7227///7227" ext_tax_names="Drosophila melanogaster///Drosophila melanogaster///Drosophila melanogaster" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> (green) in frontal <sd-tag id="sdTag293" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> sections of 1‐day‐old (d1) and 30‐day‐old (d30) fly eyes. The eyes of <sd-tag id="sdTag294" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="32461" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HDAC6" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag>‐depleted flies (GMR:<sd-tag id="sdTag288" source="sdapi" category="entity" entity_type="gene" role="component" text="GAL4" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAL4</sd-tag>/UAS‐<sd-tag id="sdTag289" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="32461" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HDAC6" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag>RNAi) developed <sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P15357///P18101///P0CG69" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="RpS27A///RpL40///Ubi-p63E" ext_tax_ids="7227///7227///7227" ext_tax_names="Drosophila melanogaster///Drosophila melanogaster///Drosophila melanogaster" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐ positive cytoplasmic inclusions that become more prominent at day 30 (d30). Blue, <sd-tag id="sdTag386" source="sdapi" category="assay" entity_type="" role="" text="DAPI" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DAPI</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7084"/></sd-panel><sd-panel panel_id="7085">(D) Depletion of <sd-tag id="sdTag302" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="32461" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HDAC6" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> in the Drosophila <sd-tag id="sdTag303" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> leads to age‐dependent degeneration. <sd-tag id="sdTag300" source="sdapi" category="assay" entity_type="" role="" text="Light micrographs" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Light micrographs</sd-tag> (left) and corresponding <sd-tag id="sdTag301" source="sdapi" category="assay" entity_type="" role="" text="Richardson‐stained" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Richardson‐stained</sd-tag> frontal <sd-tag id="sdTag389" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> sections (right) of 1‐day‐old and 30‐day‐old fly eyes. The eyes of control flies (GMR:<sd-tag id="sdTag307" source="sdapi" category="entity" entity_type="gene" role="component" text="GAL4" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAL4</sd-tag>/+) and <sd-tag id="sdTag308" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="32461" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HDAC6" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag>‐depleted flies (GMR:<sd-tag id="sdTag309" source="sdapi" category="entity" entity_type="gene" role="component" text="GAL4" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAL4</sd-tag>/UAS‐HDAC6RNAi) show normal highly organized ommatidial array at day 1; 30‐day‐old control animals also show no defects, but 30‐day‐old <sd-tag id="sdTag312" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="32461" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HDAC6" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag>‐depleted flies show degeneration with disorganization of the ommatidial array and loss of normal <sd-tag id="sdTag313" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> architecture ( × 40 and × 80).<graphic href="https://api.sourcedata.io/file.php?panel_id=7085"/></sd-panel></fig></article>