HdeB is an ATP-independent periplasmic acid-stress chaperone in Escherichia coli that binds acid-unfolding client proteins and prevents their irreversible aggregation in situ, allowing refolding after pH neutralization. It is a paralog of HdeA encoded in the hdeAB operon, but is optimally active at mildly acidic pH (~4-5), where it remains a largely folded, dynamic homodimer; stronger acidification eventually promotes monomerization and unfolding. HdeA predominates at more extreme acidity, while both proteins contribute to survival across periplasmic acid stress. HdeB activation is coupled to pH-tuned conformational dynamics rather than requiring wholesale dimer dissociation. Expression is induced by the EvgS/EvgA two-component system and negatively regulated by H-NS and TorS/TorR.
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: HdeB directly prevents aggregation of acid-unfolding periplasmic clients and supports their subsequent refolding after neutralization. This is an in-situ holdase mechanism. Obsolete GO:0051082 describes binding only, GO:0044183 implies assistance with folding, and GO:0140309 requires escort to an acceptor or location that has not been demonstrated for HdeB.
Parent term: molecular_function
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009268 response to pH | IEA GO_REF:0000002 | ACCEPT | Summary: IEA annotation via InterPro mapping. HdeB is indeed involved in the cellular response to pH, specifically acidic pH. This is a broader parent of the more specific GO:0010447 (response to acidic pH), which is already annotated with experimental evidence. Reason: While this is a broader IEA term, it is not incorrect. HdeB is fundamentally a pH-responsive chaperone. The more specific term GO:0010447 is already annotated with IDA/IMP evidence, so this broader IEA is acceptable as a supporting annotation. |
| GO:0042597 periplasmic space | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation for periplasmic space localization. This is consistent with the experimentally determined localization (IDA for GO:0030288, outer membrane-bounded periplasmic space). This IEA is a broader parent term. Reason: Periplasmic localization is well established for HdeB. The more specific term GO:0030288 (outer membrane-bounded periplasmic space) is annotated with IDA. This broader IEA is acceptable. |
| GO:0051082 unfolded protein binding | IEA GO_REF:0000002 | MODIFY | Summary: The InterPro IEA captures genuine binding of acid-unfolding periplasmic clients, but GO:0051082 is obsolete and HdeB's mechanism is an in-situ holdase activity rather than passive binding or carrier-mediated escort. Reason: HdeB prevents aggregation of clients within the periplasm and supports refolding after neutralization, but no defined acceptor, destination, or escort step has been demonstrated. Carrier-specific GO:0140309 therefore does not fit. The project-defined general holdase chaperone activity NTR is the correct replacement. Proposed replacements: holdase chaperone activity Supporting Evidence: PMID:17085547 HdeB has a molecular mass of 10 kDa... HdeB is more efficient than HdeA in preventing periplasmic-protein aggregation [at pH 3]... we can conclude that Escherichia coli possesses two acid stress chaperones that prevent periplasmic-protein aggregation at acidic pH. file:ECOLI/HdeB/HdeB-deep-research-falcon.md **HdeB** is an **acid-activated, ATP-independent “holdase” chaperone** in the periplasm. Its primary function is to **bind unfolding periplasmic proteins under acidic conditions**, prevent their **irreversible aggregation**, and support **refolding during neutralization** |
| GO:1990451 cellular stress response to acidic pH | IEA GO_REF:0000104 | ACCEPT | Summary: IEA annotation from UniRule transfer. HdeB is specifically involved in the cellular stress response to acidic pH, protecting periplasmic proteins from acid-induced aggregation. It is the most specific of the three pH-response terms in this review, below GO:0010447 and GO:0009268. Reason: This term accurately captures HdeB's core acid-stress role. Its `involved_in` qualifier is also more direct than the two experimental GO:0010447 rows' inherited `acts_upstream_of_or_within` qualifier; those physical qualifier differences are preserved exactly from GOA. Supporting Evidence: PMID:17085547 the hdeA and hdeB mutants both display reduced viability upon acid stress file:ECOLI/HdeB/HdeB-deep-research-falcon.md HdeA is most effective at stronger acidity (classically below pH ~3), whereas HdeB is optimized for **milder acidic pH** and remains active when HdeA activity drops. |
| GO:0010447 response to acidic pH | IDA PMID:17085547 Escherichia coli HdeB is an acid stress chaperone. | ACCEPT | Summary: IDA annotation based on direct experimental evidence from Kern et al. (2007). The study demonstrated that HdeB is an acid stress chaperone that prevents periplasmic protein aggregation at acidic pH, reporting HdeB as more efficient than HdeA at pH 3. Note that later mechanistic work (Dahl et al. 2015, PMID:25391835; Ding et al. 2015, PMID:26593705) refined this picture, showing HdeB's chaperone activity is in fact optimal at mildly acidic pH (~4-5) and does not require full monomerization at pH 3. The response-to-acidic-pH annotation remains correct regardless of the precise pH optimum. Reason: Well-supported by direct experimental evidence. HdeB's chaperone activity is specifically activated at acidic pH and is required for protection against acid stress (PMID:17085547). Supporting Evidence: PMID:17085547 HdeB is more efficient than HdeA in preventing periplasmic-protein aggregation [at pH 3]... HdeB, like HdeA, dissociates from dimers at neutral pH into monomers at acidic pHs, but its dissociation is complete at pH 3 |
| GO:0010447 response to acidic pH | IMP PMID:17085547 Escherichia coli HdeB is an acid stress chaperone. | ACCEPT | Summary: IMP annotation based on mutant phenotype evidence. hdeB mutants display increased sensitivity to acid stress (PMID:17085547). This complements the IDA annotation for the same term. Reason: The mutant phenotype clearly demonstrates HdeB's role in the acid stress response. hdeB deletion mutants show reduced viability at pH 2 and pH 3 (PMID:17085547). Supporting Evidence: PMID:17085547 the hdeA and hdeB mutants both display reduced viability upon acid stress, and only the HdeA/HdeB expression plasmid can restore their viability to close to the wild-type level |
| GO:0030288 outer membrane-bounded periplasmic space | IDA PMID:17085547 Escherichia coli HdeB is an acid stress chaperone. | ACCEPT | Summary: IDA annotation for localization to the outer membrane-bounded periplasmic space. HdeB was extracted from bacteria by the osmotic-shock procedure, confirming its periplasmic localization (PMID:17085547). UniProt also confirms periplasm localization with a signal peptide (residues 1-29). Reason: Directly supported by experimental evidence. HdeB has a signal peptide and was purified from the periplasm by osmotic shock (PMID:17085547). Supporting Evidence: PMID:17085547 We extracted HdeB from bacteria by the osmotic-shock procedure and purified it to homogeneity by ion-exchange chromatography and hydroxyapatite chromatography. |
| GO:0051082 unfolded protein binding | IDA PMID:17085547 Escherichia coli HdeB is an acid stress chaperone. | MODIFY | Summary: Kern et al. directly showed that HdeB prevents aggregation of acid-damaged periplasmic proteins. This supports genuine substrate binding in the context of acid-activated in-situ holdase activity, but the annotated GO term is now obsolete. Reason: The experimental biology is valid and must be retained, but GO:0140309 is not an evidence-matched replacement because HdeB holds clients in situ and no escort to an acceptor or location is established. The proposed general holdase chaperone activity NTR captures aggregation prevention without active refolding. Proposed replacements: holdase chaperone activity Supporting Evidence: PMID:17085547 At pH 3, however, HdeB is more efficient than HdeA in preventing periplasmic-protein aggregation. The solubilization of several model substrate proteins at acidic pH supports the hypothesis that, in vitro, HdeA plays a major role in protein solubilization at pH 2 and that both proteins are involved in protein solubilization at pH 3. |
| GO:0050821 protein stabilization | IDA PMID:17085547 Escherichia coli HdeB is an acid stress chaperone. | NEW | Summary: Direct aggregation-suppression assays show that HdeB maintains acid-damaged periplasmic proteins in a soluble state, which is protein stabilization rather than active refolding. Reason: GO:0050821 is defined around maintaining protein integrity and preventing degradation or aggregation. HdeB directly prevents periplasmic-protein aggregation at acidic pH, making this an evidence-matched BP companion to the proposed holdase MF without claiming that HdeB catalyzes refolding. Supporting Evidence: PMID:17085547 Thus, we can conclude that Escherichia coli possesses two acid stress chaperones that prevent periplasmic-protein aggregation at acidic pH. PMID:25391835 Once activated, HdeB binds various unfolding client proteins, prevents their aggregation, and supports their refolding upon subsequent neutralization. |
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Download this section (compressed HTML)Q: Which native periplasmic proteins are direct HdeB clients at pH 4-5, and what sequence or structural features determine their capture?
Q: Does HdeB release clients directly for spontaneous refolding after neutralization, or hand them to another periplasmic folding factor despite the absence of a demonstrated carrier pathway?
Experiment: Use a substrate-release-defective HdeB variant and quantitative periplasmic proteomics across pH 7 to 4 to identify physiological clients and distinguish direct binding from downstream acid-stress effects.
Type: client-trapping proteomics
Experiment: Monitor binding, aggregation suppression, release, and refolding of purified native periplasmic clients during acidification and neutralization, with and without candidate downstream folding factors, to test whether HdeB acts entirely in situ.
Type: chaperone kinetic assay
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