HdeA is a small (89-residue mature form) periplasmic acid-stress chaperone in E. coli that protects periplasmic proteins from aggregation during transit through the mammalian stomach (pH 1-3). At neutral pH, HdeA exists as a well-folded, inactive homodimer stabilized by an intramolecular disulfide bond (Cys39-Cys87). Upon exposure to extremely acidic pH (below 3), the dimer dissociates and each monomer undergoes an order-to-disorder transition, exposing hydrophobic surfaces that bind acid-denatured substrate proteins non-specifically (PMID:15911614, PMID:30573682). HdeA functions as an ATP-independent holdase in the ATP-devoid periplasm, preventing irreversible aggregation of denatured proteins. Upon return to neutral pH, HdeA slowly releases substrates, keeping the concentration of aggregation-sensitive folding intermediates below the aggregation threshold, thereby facilitating their refolding (PMID:20080625). HdeA cooperates with its paralog HdeB and other periplasmic chaperones (DegP, SurA) during acid stress recovery (PMID:17085547, PMID:21892184). HdeA is essential for acid resistance in pathogenic enteric bacteria (PMID:10623550).
Definition: Binding to an unfolded or misfolded protein to prevent its aggregation without actively catalyzing refolding. The holdase maintains the client protein in a soluble, folding-competent state.
Justification: HdeA directly binds acid-denatured periplasmic clients and prevents their aggregation in situ. Obsolete GO:0051082 captures binding only, GO:0044183 describes assistance with folding, and carrier-specific GO:0140309 requires escort to an acceptor or location not demonstrated for HdeA.
Parent term: molecular_function
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0030288 outer membrane-bounded periplasmic space | IEA GO_REF:0000002 | ACCEPT | Summary: IEA annotation based on InterPro domain matches (IPR024972, IPR036831). HdeA is well-established as a periplasmic protein with a cleavable signal peptide (residues 1-21). UniProt attributes direct sequencing of residues 22-33 and the signal-peptide boundary to PMID:9298646; the cached abstract itself does not specify HdeA's compartment. This IEA is consistent with and subsumed by the IDA annotation to the same term from PMID:9298646. Reason: Correct localization. HdeA is a secreted periplasmic protein. UniProt records a signal peptide at residues 1-21 and attributes direct sequencing of the mature N terminus (residues 22-33) to PMID:9298646. This establishes signal-peptide cleavage but is not, by itself, direct compartment evidence from the abstract. The IEA is redundant with the IDA but not incorrect. Supporting Evidence: PMID:9298646 enriched for proteins based on subcellular location and found several proteins in unexpected subcellular locations file:ECOLI/HdeA/HdeA-uniprot.txt PROTEIN SEQUENCE OF 22-33. file:ECOLI/HdeA/HdeA-uniprot.txt SIGNAL 1..21 file:ECOLI/HdeA/HdeA-uniprot.txt ECO:0000269|PubMed:9298646, |
| GO:0042597 periplasmic space | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation from UniProt subcellular location mapping (UniProtKB-SubCell:SL-0200). GO:0042597 "periplasmic space" is a more general term than GO:0030288 "outer membrane-bounded periplasmic space". HdeA is localized to the periplasm as confirmed by multiple experimental studies. Reason: Correct but more general than GO:0030288. The periplasm annotation is well supported by UniProt annotation and experimental evidence. Although the more specific GO:0030288 is also annotated, this broader IEA is not wrong. UniProt function comment states "Periplasm" with evidence from HAMAP-Rule:MF_00946 and PMID:17085547. Supporting Evidence: PMID:17085547 We extracted HdeB from bacteria by the osmotic-shock procedure ...[confirming periplasmic localization of hdeAB operon products]... both proteins are required for optimal protection of the bacterial periplasm against acid stress |
| GO:0071468 cellular response to acidic pH | IEA GO_REF:0000002 | ACCEPT | Summary: IEA annotation from InterPro domain matches. HdeA is a core component of the E. coli acid stress response, activated exclusively at pH below 3 (PMID:15911614). This is a parent term of GO:1990451 "cellular stress response to acidic pH" which is also annotated with experimental evidence. The IEA to this broader term is acceptable as consistent with the more specific experimental annotation. Reason: Correct and well-supported. HdeA is activated by acidic pH and functions specifically in the acid stress response. GO:0071468 is broader than GO:1990451 which is annotated with IMP evidence from PMID:10623550. The broader IEA is not wrong. Supporting Evidence: PMID:15911614 HdeA employs a novel strategy to modulate its chaperone activity: it possesses an ordered conformation that is unable to bind denatured substrate proteins under normal physiological conditions (i.e. at neutral pH) and transforms into a globally disordered conformation that is able to bind substrate proteins under stress conditions (i.e. at a pH below 3) |
| GO:1990451 cellular stress response to acidic pH | IEA GO_REF:0000104 | ACCEPT | Summary: IEA annotation transferred from manual annotations via shared sequence features (UniRule:UR000106130). GO:1990451 is a child of GO:0071468 "cellular response to acidic pH" and specifically captures the stress response aspect. HdeA is a key effector of the acid stress response, as demonstrated by genetic studies showing hdeA deletion mutants are sensitive to acid stress (PMID:10623550). Reason: Correct annotation. This IEA is consistent with the IMP annotation to the same term from PMID:10623550. HdeA is activated specifically under acid stress conditions (pH < 3) and is required for optimal acid stress protection. Supporting Evidence: PMID:10623550 HDEA, a periplasmic protein that supports acid resistance in pathogenic enteric bacteria |
| GO:0042802 identical protein binding | IPI PMID:20080625 Protein refolding by pH-triggered chaperone binding and rele... | MARK AS OVER ANNOTATED | Summary: IPI annotation from IntAct based on physical interaction data (HdeA self-interaction). HdeA forms a homodimer at neutral pH that dissociates into active monomers at acidic pH (PMID:10623550, PMID:20080625). The homodimerization is functionally important as the dimer-to-monomer transition is the activation mechanism. However, "identical protein binding" is an uninformative term. The more specific GO:0042803 "protein homodimerization activity" is already annotated with IDA evidence. Reason: GO:0042802 "identical protein binding" is too vague and does not convey meaningful information about HdeA function. The more specific and informative GO:0042803 "protein homodimerization activity" is already annotated (IDA, PMID:10623550). Per curation guidelines, vague binding terms like "protein binding" and "identical protein binding" should be avoided in favor of more informative MF terms. Supporting Evidence: PMID:10623550 HDEA is activated by a dimer-to-monomer transition at acidic pH |
| GO:0006457 protein folding | IDA PMID:10623550 HDEA, a periplasmic protein that supports acid resistance in... | MODIFY | Summary: IDA annotation for involvement in protein folding from EcoCyc, based on the demonstration that HdeA suppresses aggregation of acid-denatured proteins (PMID:10623550). However, HdeA is primarily a holdase that prevents aggregation rather than actively assisting protein folding. PMID:20080625 later showed that HdeA does facilitate refolding of acid-denatured proteins upon pH neutralization via slow substrate release, but this is a passive mechanism distinct from active foldase activity. Reason: The BP term "protein folding" is too general and uninformative about the demonstrated mechanism. PMID:20080625 showed that HdeA facilitates refolding upon pH neutralization through slow substrate release. GO:0042026 protein refolding is therefore the more specific term: HdeA's pH-triggered release cycle directly facilitates refolding while keeping aggregation-sensitive intermediates below their aggregation threshold. This is a process-level role, not a claim that HdeA catalyzes folding chemistry. Proposed replacements: protein refolding Supporting Evidence: PMID:20080625 HdeA stably binds substrates at low pH, thereby preventing their irreversible aggregation. pH neutralization subsequently triggers the slow release of substrate proteins from HdeA, keeping the concentration of aggregation-sensitive intermediates below the threshold where they begin to aggregate. This provides a straightforward and ATP-independent mechanism that allows HdeA to facilitate protein refolding. PMID:10623550 Functional studies demonstrate that HDEA is activated by a dimer-to-monomer transition at acidic pH, leading to suppression of aggregation by acid-denatured proteins |
| GO:0044183 protein folding chaperone | EXP PMID:10623550 HDEA, a periplasmic protein that supports acid resistance in... | ACCEPT | Summary: EXP annotation from DisProt for protein folding chaperone activity based on PMID:10623550. The crystal structure study demonstrated that HdeA suppresses aggregation of acid-denatured proteins and suggested chaperone-like functions. GO:0044183 "protein folding chaperone" is defined as "binding to a protein or a protein-containing complex to assist the protein folding process." While HdeA does assist in the overall folding process (preventing aggregation and facilitating refolding upon pH return), it is mechanistically a holdase rather than a foldase. However, GO:0044183 is the best available MF term for chaperone function pending creation of a holdase-specific term. Reason: GO:0044183 is the best available MF term for HdeA's chaperone activity. HdeA binds denatured proteins and assists in the folding process by preventing aggregation and facilitating refolding upon pH neutralization. Although HdeA is mechanistically a holdase (ATP-independent, prevents aggregation in situ), the definition of GO:0044183 ("binding to a protein...to assist the protein folding process") is broad enough to encompass holdase activity. This annotation should be retained as the primary MF annotation pending creation of a holdase-specific GO term. Supporting Evidence: PMID:10623550 We suggest that HDEA may support chaperone-like functions during the extremely acidic conditions PMID:20080625 This provides a straightforward and ATP-independent mechanism that allows HdeA to facilitate protein refolding file:ECOLI/HdeA/HdeA-deep-research-falcon.md it is a small (~11 kDa) ATP-independent holdase that prevents acid-denatured **periplasmic proteins** from aggregating and assists refolding after pH neutralization. It is inactive as a folded dimer at neutral pH and active in acid as a partially unfolded monomer/disordered state. |
| GO:0044183 protein folding chaperone | IDA PMID:10623550 HDEA, a periplasmic protein that supports acid resistance in... | ACCEPT | Summary: IDA annotation from DisProt for the same term and reference as the EXP annotation above. This is a duplicate with a different evidence code (IDA vs EXP) from the same source (DisProt) and same reference (PMID:10623550). Both are acceptable as duplicates with different evidence codes are permitted. Reason: Same rationale as the EXP annotation above. GO:0044183 is the best available MF term for HdeA's chaperone function. The IDA evidence code is appropriate given the direct aggregation suppression assays reported in PMID:10623550. Supporting Evidence: PMID:10623550 HDEA is activated by a dimer-to-monomer transition at acidic pH, leading to suppression of aggregation by acid-denatured proteins |
| GO:0044183 protein folding chaperone | EXP PMID:30573682 Structural basis and mechanism of the unfolding-induced acti... | ACCEPT | Summary: EXP annotation from DisProt based on PMID:30573682. This study used advanced NMR methods to characterize HdeA's activated-state conformation under acidic conditions and identified client-binding sites. It provided structural evidence for the chaperone mechanism: two hydrophobic patches are exposed upon acid-induced unfolding and are essential for client interactions. Reason: PMID:30573682 provides direct structural evidence for HdeA's chaperone function at the atomic level, identifying the client-binding sites and the multistep activation mechanism. GO:0044183 remains the best available MF term. Supporting Evidence: PMID:30573682 the structure of activated HdeA becomes largely disordered and exposes two hydrophobic patches essential for client interactions file:ECOLI/HdeA/HdeA-deep-research-falcon.md it is **inactive when folded** and becomes **active when partially unfolded/disordered** under acid stress. |
| GO:0030288 outer membrane-bounded periplasmic space | IDA PMID:9298646 Comparing the predicted and observed properties of proteins ... | ACCEPT | Summary: IDA annotation from EcoCyc based on the Link et al. (1997) proteomics study, whose cached abstract identifies HdeA by 2-DE and Edman sequencing but does not explicitly assign HdeA to a compartment. UniProt attributes direct sequencing of residues 22-33 and the signal peptide at residues 1-21 to this PMID, independently anchoring cleavage of the precursor. Reason: The experimental localization annotation is consistent with HdeA's established periplasmic biology. The abstract-only cache describes subcellular-location enrichment but does not expose the HdeA-specific compartment result. UniProt attributes mature N-terminal sequencing (residues 22-33) and the signal peptide boundary (residues 1-21) to PMID:9298646, directly supporting precursor cleavage; subsequent work independently places HdeA in the periplasm (PMID:17085547). Supporting Evidence: PMID:9298646 We identified several highly abundant proteins, YjbJ, YjbP, YggX, HdeA, and AhpC, which would not have been predicted from the genomic sequence alone PMID:9298646 We enriched for proteins based on subcellular location file:ECOLI/HdeA/HdeA-uniprot.txt PROTEIN SEQUENCE OF 22-33. file:ECOLI/HdeA/HdeA-uniprot.txt SIGNAL 1..21 file:ECOLI/HdeA/HdeA-uniprot.txt ECO:0000269|PubMed:9298646, file:ECOLI/HdeA/HdeA-deep-research-falcon.md HdeA operates in the **periplasm**, where it interacts with periplasmic proteins that are prone to acid denaturation/aggregation when external pH drops. |
| GO:0042803 protein homodimerization activity | IDA PMID:10623550 HDEA, a periplasmic protein that supports acid resistance in... | ACCEPT | Summary: IDA annotation from EcoCyc. The crystal structure of HdeA at 2.0 A resolution (PMID:10623550) revealed that HdeA forms a homodimer at neutral pH. The dimer-to- monomer transition at acidic pH is the activation mechanism for chaperone function. The proteomics study (PMID:9298646) also noted HdeA exists as a "covalent homomultimer." The homodimerization is functionally significant as it represents the inactive storage form. Reason: Accurate and functionally important annotation. HdeA homodimerization is well characterized structurally (PMID:10623550, PMID:9731767) and is directly relevant to the activation mechanism (dimer-to-monomer transition at low pH). This is more informative than the broader GO:0042802 "identical protein binding." Supporting Evidence: PMID:10623550 HDEA is activated by a dimer-to-monomer transition at acidic pH PMID:9298646 Our data suggest that AhpC, CspC, and HdeA exist as covalent homomultimers file:ECOLI/HdeA/HdeA-deep-research-falcon.md HdeA undergoes **dimer-to-monomer transition** plus **partial unfolding/order-to-disorder conversion**, exposing hydrophobic client-binding patches. |
| GO:0051082 unfolded protein binding | IDA PMID:15911614 Periplasmic protein HdeA exhibits chaperone-like activity ex... | MODIFY | Summary: PMID:15911614 directly demonstrates binding of acid-denatured proteins after HdeA's low-pH order-to-disorder transition. The biology is an ATP-independent, in-situ holdase activity, but GO:0051082 is now obsolete. Reason: GO:0051082 is obsolete, but the experimental holdase biology remains valid. HdeA binds and protects acid-denatured clients within the periplasm and releases them after neutralization; no defined acceptor molecule, delivery destination, or escort step is demonstrated. Carrier-specific GO:0140309 therefore does not fit. The general holdase chaperone activity NTR is the correct replacement. Proposed replacements: holdase chaperone activity Supporting Evidence: PMID:15911614 HdeA employs a novel strategy to modulate its chaperone activity: it possesses an ordered conformation that is unable to bind denatured substrate proteins under normal physiological conditions (i.e. at neutral pH) and transforms into a globally disordered conformation that is able to bind substrate proteins under stress conditions (i.e. at a pH below 3) PMID:15911614 our data indicate that HdeA exposes hydrophobic surfaces that appear to be involved in the binding of denatured substrate proteins at extremely low pH values PMID:20080625 HdeA stably binds substrates at low pH, thereby preventing their irreversible aggregation. pH neutralization subsequently triggers the slow release of substrate proteins from HdeA file:ECOLI/HdeA/HdeA-deep-research-falcon.md HdeA prevents irreversible aggregation while pH is low, and clients can refold upon neutralization when HdeA releases them. |
| GO:1990451 cellular stress response to acidic pH | IMP PMID:10623550 HDEA, a periplasmic protein that supports acid resistance in... | ACCEPT | Summary: IMP annotation from EcoCyc. PMID:10623550 demonstrated that HdeA supports acid resistance in pathogenic enteric bacteria. The crystal structure study combined functional analysis showing that HdeA is activated at acidic pH and suppresses aggregation of acid-denatured proteins. This is the core biological process for HdeA. Reason: Core biological process annotation. HdeA is a central effector of the cellular stress response to acidic pH. The IMP evidence is appropriate as the study demonstrated the acid-resistance phenotype supported by HdeA. GO:1990451 is a child of GO:0071468 "cellular response to acidic pH" and specifically captures the stress response aspect, which is the relevant context for HdeA function. Supporting Evidence: PMID:10623550 HDEA, a periplasmic protein that supports acid resistance in pathogenic enteric bacteria PMID:10623550 HDEA is activated by a dimer-to-monomer transition at acidic pH, leading to suppression of aggregation by acid-denatured proteins file:ECOLI/HdeA/HdeA-deep-research-falcon.md loss of hdeA decreases survival/viability |
| GO:0030288 outer membrane-bounded periplasmic space | RCA PMID:8455549 Function of the Escherichia coli nucleoid protein, H-NS: mol... | ACCEPT | Summary: RCA annotation from EcoCyc based on PMID:8455549 (Yoshida et al., 1993), which originally identified the hdeA gene (then called 10K-S or yhiB) as part of an operon whose expression is enhanced in an hns deletion mutant. The study cloned and sequenced the gene but did not directly demonstrate periplasmic localization experimentally. However, the signal peptide is evident from the sequence. This is consistent with but weaker than the IDA annotation from PMID:9298646. Reason: The RCA evidence is appropriate for sequence-based prediction of periplasmic localization from the identified signal peptide. This annotation is redundant with the IDA from PMID:9298646 but not incorrect. The original identification paper correctly predicted periplasmic localization. Supporting Evidence: PMID:8455549 The genes coding for the other two proteins, 10K-L and 10K-S, are located at 77.5 min on the genetic map. Their nucleotide sequences were determined |
| GO:0050821 protein stabilization | IDA PMID:10623550 HDEA, a periplasmic protein that supports acid resistance in... | NEW | Summary: HdeA directly suppresses aggregation of acid-denatured proteins and maintains clients in a recoverable state during low-pH stress. Reason: GO:0050821 captures maintaining protein integrity and preventing aggregation. This is directly demonstrated for HdeA and complements the holdase NTR without asserting active catalysis of folding. Supporting Evidence: PMID:10623550 Functional studies demonstrate that HDEA is activated by a dimer-to-monomer transition at acidic pH, leading to suppression of aggregation by acid-denatured proteins. PMID:20080625 HdeA stably binds substrates at low pH, thereby preventing their irreversible aggregation. |
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Download this section (compressed HTML)Q: Which structural or kinetic features determine whether an acid-denatured periplasmic client is captured by HdeA, HdeB, or both?
Q: How do DegP and SurA participate after HdeA releases clients during neutralization, and does any physical handoff occur despite the absence of an established carrier endpoint?
Experiment: Measure HdeA-client binding, release, aggregation, and refolding during controlled acidification and neutralization to distinguish spontaneous client refolding from downstream assistance by DegP or SurA.
Type: client-release kinetics
Experiment: Compare wild-type HdeA with substrate-binding and release-defective variants using periplasmic crosslinking proteomics across acid stress and recovery to define direct clients and temporal chaperone cooperation.
Type: in vivo client-trapping proteomics
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