Annotation inferences using phylogenetic trees
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PAINT/IBA methodology propagates experimental annotations within a phylogenetic tree. Source of all 7 current IBA annotations on HSP104: cytoplasm (GO:0005737), ATP hydrolysis activity (GO:0016887), protein refolding (GO:0042026), protein unfolding (GO:0043335), cytosol (GO:0005829), protein-folding chaperone binding (GO:0051087), and cellular heat acclimation (GO:0070370). All are consistent with the well-established HSP100/Clp disaggregase family function.
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Electronic Gene Ontology annotations created by ARBA machine learning models
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ARBA machine-learning rule-mining methodology that propagates GO terms from UniProtKB feature evidence. Source of six IEA annotations on HSP104: cytosol (GO:0005829), protein folding (GO:0006457), cellular response to heat (GO:0034605), identical protein binding (GO:0042802), protein unfolding (GO:0043335), and intracellular organelle lumen (GO:0070013).
Combined Automated Annotation using Multiple IEA Methods
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Combined automated annotation pipeline that aggregates multiple electronic GO assignment methods. Source of the IEA "ATP binding" (GO:0005524) and "ATP hydrolysis activity" (GO:0016887) annotations on HSP104, which are redundant with experimental evidence for the ATP-dependent disaggregase activity.
HSP104 required for induced thermotolerance.
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HSP104 deletion mutants cannot acquire thermotolerance after mild heat pretreatment, establishing HSP104 as essential for induced thermotolerance.
"when given a mild pre-heat treatment, the mutant cells did not acquire tolerance to heat, as did wild-type cells."
Protein disaggregation mediated by heat-shock protein Hsp104.
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HSP104 mediates resolubilization of heat-inactivated protein from insoluble aggregates, establishing the disaggregation function.
"Hsp104 functions in a manner not previously described for other heat-shock proteins: it mediates the resolubilization of heat-inactivated luciferase from insoluble aggregates."
Hsp104, Hsp70, and Hsp40: a novel chaperone system that rescues previously aggregated proteins.
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HSP104 in concert with Hsp70 and Hsp40 can reactivate aggregated proteins via a protein remodeling activity requiring specific chaperone interactions.
"in concert with Hsp40 and Hsp70, Hsp104 can reactivate proteins that have been denatured and allowed to aggregate, substrates refractory to the action of other chaperones."
Evidence for the interplay between trehalose metabolism and Hsp104 in yeast.
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HSP104 disruption affects trehalose metabolism during heat shock, likely through indirect effects on enzyme integrity.
"The activities of trehalose-synthesizing and -hydrolyzing enzymes are low in the HSP104 disruption mutant during heat shock."
Direct evidence for the intracellular localization of Hsp104 in Saccharomyces cerevisiae by immunoelectron microscopy.
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ImmunoEM shows HSP104 in cytoplasm and nucleus, concentrating around protein aggregates during heat shock.
"At normal temperature (25 degrees C), a small amount of Hsp104 was located in the cytoplasm and nucleus."
Trehalose is required for conformational repair of heat-denatured proteins in the yeast endoplasmic reticulum but not for maintenance of membrane traffic functions after severe heat stress.
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Cytosolic HSP104 is required for conformational repair of heat-denatured proteins in the ER, suggesting indirect role in ER protein quality control.
"not only ER chaperones but also the cytosolic Hsp104 chaperone is required for conformational repair events in the ER lumen."
Analysis of the AAA sensor-2 motif in the C-terminal ATPase domain of Hsp104 with a site-specific fluorescent probe of nucleotide binding.
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Fluorescent probe (Y819W) directly measures ATP and ADP binding at NBD2; R826M sensor-2 mutation decreases nucleotide affinity and reveals interdomain communication.
"The fluorescence of this tryptophan changes in response to ATP and ADP binding, allowing the K(d) and Hill coefficient to be determined for each nucleotide."
Substrate binding to the molecular chaperone Hsp104 and its regulation by nucleotides.
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ATP-dependent substrate binding demonstrated; ATP at NBD1 is crucial for polypeptide interaction, and substrate binding triggers conformational change committing to ATP hydrolysis.
"the affinity of Hsp104 toward polypeptides is regulated by nucleotides. In the presence of ATP or adenosine-5' -O-(3-thiotriphosphate), the chaperone formed complexes with RCMLa, whereas no binding was observed in the presence of ADP."
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
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High-throughput TAP-tag/MS study identifying HSP104 interactions with multiple yeast proteins.
"We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae."
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell.
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Systematic TAP-tag analysis of all 63 yeast chaperones, mapping HSP104 interaction network.
"Systematic analysis of physical TAP-tag based protein-protein interactions of all known 63 chaperones in Saccharomyces cerevisiae has been carried out."
CryoEM structure of Hsp104 and its mechanistic implication for protein disaggregation.
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CryoEM structure confirms hexameric ring architecture with M-domain on the exterior, where it can interact with aggregated proteins.
"Hsp104 is a ring-forming AAA+ machine that recognizes both aggregated proteins and prion-fibrils as substrates and, together with the Hsp70 system, remodels substrates in an ATP-dependent manner."
A chaperone cascade sorts proteins for posttranslational membrane insertion into the endoplasmic reticulum.
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HSP104 identified as part of the TRC complex for tail-anchored protein targeting to ER.
"we reveal the composition of a conserved multiprotein TMD recognition complex (TRC) and show that distinct TRC subunits recognize the two types of TMD signals."
Species-specific collaboration of heat shock proteins (Hsp) 70 and 100 in thermotolerance and protein disaggregation.
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Middle domain of HSP104 determines species-specific interaction with Hsp70, required for disaggregation and thermotolerance.
"the interaction between Hsp70/DnaK and helix 2 of the middle domain of Hsp104/ClpB determines the specificity required for protein disaggregation both in vivo and in vitro, as well as for cellular thermotolerance."
Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress.
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High-throughput microscopy confirms HSP104 cytoplasmic localization.
"Relocalization of proteins is a hallmark of the DNA damage response. We use high-throughput microscopic screening of the yeast GFP fusion collection"
Coordination of translational control and protein homeostasis during severe heat stress.
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HSP104 and Hsp70 are required for stress granule disassembly and restoration of translation during heat stress recovery.
"heat-SG disassembly and restoration of translation activity during heat stress recovery is intimately linked to disaggregation of damaged proteins present in the mixed assemblies and requires Hsp104 and Hsp70 activity."
Cmr1/WDR76 defines a nuclear genotoxic stress body linking genome integrity and protein quality control.
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HSP104 localizes at the intranuclear quality control compartment (INQ) at the nuclear periphery.
"Cmr1--together with Mrc1/Claspin, Pph3, the chaperonin containing TCP1 (CCT) and 25 other proteins--define a novel intranuclear quality control compartment (INQ) that sequesters misfolded, ubiquitylated and sumoylated proteins in response to genotoxic stress."
Substrate threading through the central pore of the Hsp104 chaperone as a common mechanism for protein disaggregation and prion propagation.
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Substrate threading through HSP104's central pore is the mechanism for both protein disaggregation and prion propagation.
"HAP variants that harbour a reduced threading activity were affected in both protein disaggregation and prion propagation, demonstrating that substrate threading represents the common mechanism for the processing of both substrate classes."
Falcon deep research report on HSP104 (Saccharomyces cerevisiae)
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Hsp104 is a hexameric AAA+ ATP-dependent disaggregase of the Hsp100/ClpB
family that does not perform proteolysis but instead remodels aggregated
proteins to enable their reactivation; together with partner chaperones it
rescues previously aggregated proteins rather than merely preventing
aggregation.
"Hsp104 is a member of the Hsp100/Clp family of oligomeric AAA+ ATPases that does not itself perform proteolysis but instead remodels aggregated proteins to enable their reactivation."
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Hsp104 expression is sufficient for acquired thermotolerance and promotes
resolubilization and reactivation of proteins that unfolded and aggregated
after heat shock.
"expression of Hsp104 is sufficient for thermotolerance, and Hsp104 promotes resolubilization and reactivation of proteins that have unfolded and aggregated after heat shock."
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Hsp104 is a hexameric AAA+ ATPase with two nucleotide-binding domains
(NBD1 and NBD2); it extracts clients by ATP-driven unfolding and threading
through an axial channel, with the NBD2 pore-loop (conserved GYVG-loop,
Tyr-662) required for disaggregation.
"Hsp104 extracts clients by ATP-driven unfolding and threading through an axial channel; integrity of the NBD2 pore-loop region (including the conserved GYVG-loop containing Tyr-662) is required for refolding/disaggregation function."
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Hsp104 operates in a multichaperone disaggregation pathway with Hsp70 and
Hsp40; reactivation of aggregated luciferase requires ATP and depends on
SSA-encoded Hsp70 and the Hsp40 co-chaperone Ydj1.
"Hsp104-mediated reactivation of aggregated luciferase in yeast lysates requires ATP and depends on SSA-encoded Hsp70 activity and the Hsp40 co-chaperone Ydj1."
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Hsp110 nucleotide-exchange factors (Sse1/Sse2) coordinate Hsp70 cycling and
are essential for efficient Hsp104-dependent disaggregation in both cytosol
and nucleus.
"yeast Hsp110 nucleotide-exchange factors (Sse1/Sse2) coordinate Hsp70 cycling and are essential for efficient Hsp104-dependent disaggregation in both cytosol and nucleus"
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A defining yeast-specific role of Hsp104 is amyloid prion fibril
fragmentation, generating transmissible seeds (propagons) needed for
prion inheritance such as [PSI+].
"A defining yeast-specific role of Hsp104 is its centrality in amyloid prion fragmentation, which generates transmissible seeds"
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Hsp104 levels must be finely tuned: both deletion and overexpression can
cure [PSI+], and Hsp70 (Ssa1) antagonizes Hsp104 overexpression-mediated
curing.
"both Hsp104 deletion and Hsp104 overexpression can cure [PSI+]. Importantly, Hsp70 (Ssa1) antagonizes Hsp104 overexpression-mediated curing"
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Hsp104 is predominantly cytosolic under non-stress conditions but
relocalizes to stress-induced protein quality control foci associated with
stress granules, Q-bodies/CytoQ, and nuclear deposits (INQ/IPOD).
"Hsp104 is largely cytosolic under non-stress conditions but relocalizes to stress-induced foci associated with CytoQ/Q-bodies, stress granules, and nuclear quality-control deposits such as INQ/IPOD."
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Under glucose starvation, ATP depletion drives sequestration of proteins
into stress compartments (stress granules and Q-bodies), and Hsp104 ATPase
activity is a key ATP-consuming process governing the abundance and size of
these compartments.
"is identified as a key ATP-consuming process that determines the abundance and size of these compartments"
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Heat-induced stress granules (Pab1-GFP) resolve within ~2 h in wild-type
cells but recovery is dramatically slower in hsp104-delta cells, consistent
with an Hsp104-dependent clearance process.
"stress granule foci (Pab1-GFP) begin resolving within ~2 hours in wild-type cells, whereas recovery is dramatically slower in hsp104Δ cells"
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Nucleotide-state-specific middle-domain (MD):NBD contacts tune Hsp104
activity and Hsp70 collaboration, and the MD can help ensure that
processed substrates remain functional after Hsp104 action.
"the MD helps ensure that processed substrates remain functional after Hsp104 action"
Gene Ontology annotation through association of InterPro records with GO terms
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
Hsp104 and Potentiated Variants Can Operate as Distinct Nonprocessive Translocases.
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Wild-type HSP104 performs ATP-dependent partial translocation of soluble polypeptide substrates through its axial pore, supporting HSP104's ATP-dependent disaggregase mechanism but not transmembrane protein transport.
"We establish that Hsp104 and Hsp104 A503S can operate as nonprocessive translocases for soluble substrates"
Hsp104-Hsp70-Hsp110 chaperones disintegrate kinase aggregates formed upon stress in Saccharomyces cerevisiae.
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A 2025 Ste11 model-substrate study further supports the involvement of HSP104 with Hsp70 and Hsp110/Sse1 in mobilizing stress-induced yeast kinase aggregates.
"Ste11 aggregates disappear upon recovery from stress. This phenomenon is impaired in the absence of Hsp104 or Sse1"