HdeB is a periplasmic acid-stress chaperone in E. coli that functions as an ATP-independent holdase to prevent aggregation of periplasmic proteins under acidic conditions. It is a paralog of HdeA, and both proteins are encoded by the hdeAB acid stress operon. HdeB exists as a homodimer at neutral pH and dissociates into active monomers at acidic pH (complete dissociation at pH 3). While HdeA is more effective at pH 2, HdeB is more effective than HdeA at pH 3, and both are required for optimal protection against acid stress in vivo (PMID:17085547). Subsequent mechanistic work (Dahl et al. 2015, PMID:25391835; Ding et al. 2015, PMID:26593705) places HdeB's optimal chaperone activity at mildly acidic pH (~4-5), where its activation is coupled to pH-tuned conformational dynamics of a dynamic dimer rather than to wholesale monomerization/unfolding, distinguishing it from HdeA. HdeB exposes hydrophobic surfaces at acidic pH, consistent with its chaperone function. The protein is induced by the EvgS/EvgA two-component system and negatively regulated by H-NS and TorS/TorR.
| 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: IEA annotation via InterPro mapping. HdeB does bind unfolded/aggregation-prone periplasmic proteins under acidic conditions. However, its function is better described as a holdase chaperone rather than simple binding.
Reason: HdeB functions as an ATP-independent holdase chaperone that prevents aggregation of periplasmic proteins at acidic pH (PMID:17085547). The term GO:0051082 "unfolded protein binding" describes only the binding aspect, not the chaperone activity. GO:0140309 "unfolded protein carrier activity" (a protein carrier activity that binds a protein in an unfolded state, prevents its aggregation, and escorts it to an acceptor or location) better captures the ATP-independent holdase chaperone function and is well supported by the falcon deep research, which independently characterizes HdeB as an "acid-activated, ATP-independent holdase chaperone" that binds unfolding periplasmic proteins and prevents their irreversible aggregation.
Proposed replacements:
unfolded protein carrier 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. This term is appropriate and well-supported by the known biology.
Reason: This term accurately captures HdeB's role in the acid stress response. The protein functions specifically as an acid-activated chaperone (PMID:17085547).
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: IDA annotation for unfolded protein binding based on direct experimental evidence. Kern et al. demonstrated that HdeB prevents aggregation of periplasmic proteins at acidic pH, consistent with binding unfolded proteins. However, the function is better described as holdase/chaperone activity rather than simple binding.
Reason: While HdeB does bind unfolded proteins, its function is more accurately described as a holdase chaperone. GO:0140309 "unfolded protein carrier activity" better captures the ATP-independent holdase chaperone function that prevents aggregation and escorts substrates. The experimental evidence from PMID:17085547 demonstrates chaperone-like prevention of aggregation, not just binding. The falcon deep research independently corroborates this holdase characterization, describing HdeB as an acid-activated, ATP-independent holdase chaperone.
Proposed replacements:
unfolded protein carrier 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.
|
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
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Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
The literature retrieved and used here consistently describes HdeB as a small periplasmic acid-stress chaperone in E. coli encoded with hdeA in the hdeA–hdeB operon, matching the UniProt description for P0AET2 (acid stress chaperone HdeB; precursor/periplasmic protein). (dahl2015hdebfunctionsas pages 1-2)
A key ambiguity check is strain specificity: in enterohemorrhagic E. coli O157:H7, hdeB can be effectively silenced by a start-codon mutation (ATG→ATA), so O157:H7 “hdeB” phenotypes may not generalize to K‑12. This reinforces that functional claims should be anchored to K‑12-compatible HdeB evidence. (carter2012evolutionarysilenceof pages 1-1)
Note on aliases (yhhD/yhiC): these synonyms were provided in the prompt (from UniProt) but were not explicitly recovered in the retrieved full-text excerpts, so this report does not cite primary literature for those synonym mappings.
In Gram-negative enteric bacteria, the periplasm rapidly equilibrates with external pH because protons and small molecules diffuse through outer-membrane porins, exposing periplasmic proteins to strong acid during passage through environments such as the stomach. Consequently, periplasmic proteins are at high risk for acid-induced unfolding and aggregation, necessitating dedicated periplasmic protection systems. (hong2012chaperonedependentmechanismsfor pages 2-3)
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 (post-stress recovery), either directly or by enabling downstream periplasmic folding systems to act. (dahl2015hdebfunctionsas pages 8-9, dahl2015hdebfunctionsas pages 1-2)
HdeB and the homologous chaperone HdeA are functionally complementary across pH: 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. (dahl2015hdebfunctionsas pages 8-9, dahl2015hdebfunctionsas pages 1-2, hong2012chaperonedependentmechanismsfor pages 2-3)
A central finding across mechanistic studies is that HdeB is optimally active around pH 4–5. In vitro, HdeB shows negligible activity at pH 2, modest activity at pH 3, and optimal activity near pH ~4; correspondingly, overexpression phenotypes show that HdeB supports growth/survival at pH ~4, whereas HdeA supports survival at more extreme acidity (pH 2–3). (dahl2015hdebfunctionsas pages 1-2)
Mechanistically, HdeA is a classic example of “conditionally disordered” chaperones activated via acid-triggered dissociation and partial unfolding. In contrast, HdeB activation “precedes” acid-induced monomerization, indicating that activity at mild acidity is not simply caused by dimer breakup and global unfolding. Instead, HdeB appears to become chaperone-active via increased flexibility/local rearrangements at mildly acidic pH while remaining largely folded and dimeric. (dahl2015hdebfunctionsas pages 8-9)
NMR/biophysical data support a dynamic dimer model: HdeB remains dimeric at neutral pH (sedimentation ~1.5 S), is monomeric at very low pH (~1.2 S at pH 2), and shows altered sedimentation behavior at pH 4–5 (~1.9 S). Importantly, NMR indicates pH-dependent μs–ms conformational exchange focused at the dimer interface (including the α2–α3 loop), with reported exchange rates changing from ~2000 s−1 at neutral pH to ~1000 s−1 at pH 4.5/4.0. These observations are consistent with a mechanism where intrinsic dynamics (rather than wholesale unfolding) gates client interactions. (ding2015hdebchaperoneactivity pages 6-8)
The available excerpts support a general client concept—Hde proteins prevent aggregation of periplasmic proteins during acid stress—rather than a single specific substrate. Reviews and primary mechanistic work frame HdeB as protecting “periplasmic proteins” broadly under acid stress. (hong2012chaperonedependentmechanismsfor pages 2-3, dahl2015hdebfunctionsas pages 1-2)
HdeB sits within integrated acid-resistance networks that couple environmental sensing, transcriptional regulation, and protein-level protection.
A 2023 review of the EvgS/EvgA system summarizes a regulatory chain linking envelope signaling to periplasmic acid chaperones: GadE and PhoP can initiate hdeAB; upstream, PhoQ/PhoP can increase RpoS, and RpoS can initiate gadE, placing hdeAB under an RpoS→GadE axis. The same review connects EvgS/EvgA to PhoQ/PhoP via SafA, and highlights the EvgA–YdeO–GadE circuit as a core acid-resistance regulatory module. (zhang2023evgsevgatheunorthodox pages 7-10)
A 2024 narrative review in Microorganisms synthesizes known acid stress responses in E. coli and continues to present HdeA/HdeB as structurally related periplasmic chaperones in acid stress protection, consistent with the established mechanistic literature. (Li et al., 2024; URL: https://doi.org/10.3390/microorganisms12091774; publication month Aug 2024) (dahl2015hdebfunctionsas pages 1-2)
A 2024 PLOS Computational Biology paper introducing StressME explicitly treats HdeA/HdeB as periplasmic chaperones that enhance acid tolerance by preventing periplasmic protein aggregation and frames the model as useful for engineering and health applications. While not a mechanistic protein biophysics study, this work represents a recent trend: incorporating periplasmic chaperones into quantitative, genome-scale coupled metabolism–expression stress models to analyze stress trade-offs (e.g., cytoplasmic vs periplasmic chaperone allocation). (Zhao et al., 2024; URL: https://doi.org/10.1371/journal.pcbi.1011865; publication month Feb 2024) (zhao2024stressmeunifiedcomputing pages 1-2)
Evidence gap (2023–2024 primary HdeB biophysics): the tool search surfaced (but could not retrieve) a 2024 Biochemistry paper on HdeB’s chaperone-active state. Because it was not retrievable here, no claims from it are included.
Although not a 2023–2024 paper, a concrete implementation example is regulatory engineering to shift stress regulon timing: engineering the DsrA/Hfq module to activate RpoS earlier improved acid tolerance, and this improvement coincided with activation of several acid-resistance-associated components including HdeB. This illustrates how hdeB can be mobilized as part of a broader engineered acid-tolerance program. (Lin et al., 2021; URL: https://doi.org/10.1128/aem.02923-20) (carter2012evolutionarysilenceof pages 1-1)
StressME represents an application layer where HdeA/HdeB are used as explicit model components for predicting acid-stress responses and trade-offs relevant to engineered strains and (more broadly) biotechnology and health contexts. (zhao2024stressmeunifiedcomputing pages 1-2)
A high-citation Trends in Microbiology review frames HdeA/HdeB as key periplasmic chaperones for acid resistance in enteric bacteria, emphasizing the periplasm’s exposure to environmental acid and the need for periplasm-specific aggregation prevention and recovery mechanisms. (Hong et al., 2012; URL: https://doi.org/10.1016/j.tim.2012.03.001; publication month Jul 2012) (hong2012chaperonedependentmechanismsfor pages 2-3)
Activation pH window and qualitative activity partitioning
- HdeB: negligible at pH 2, modest at pH 3, optimal at ~pH 4–5. (dahl2015hdebfunctionsas pages 1-2)
- HdeA vs HdeB complementarity: HdeA more efficient at stronger acidity; HdeB more efficient at milder acidity (e.g., pH ~3 in older synthesis; pH ~4–5 in detailed mechanistic studies). (dahl2015hdebfunctionsas pages 8-9, hong2012chaperonedependentmechanismsfor pages 2-3)
Biophysical parameters supporting mechanism
- Sedimentation coefficient shifts with pH and oligomeric state: ~1.5 S (pH 7), ~1.9 S (pH 4–5), ~1.2 S (pH 2). (ding2015hdebchaperoneactivity pages 6-8)
- pH-dependent conformational exchange rates: ~2000 s−1 at neutral pH vs ~1000 s−1 at pH 4.5/4.0 (reported). (ding2015hdebchaperoneactivity pages 6-8)
Genetic survival phenotypes (strain/lineage contextual statistics)
- In non-O157 contexts including K‑12-compatible lineages and EHEC O145, loss of both HdeA and HdeB can cause >100- to 1000-fold reductions in survival after acid challenge (example reported at pH 2.0). (carter2012evolutionarysilenceof pages 1-1)
- In E. coli O157:H7 specifically, hdeB deletion showed no effect on acid survival under tested conditions, consistent with a prevalent hdeB start-codon mutation that ablates HdeB protein expression in surveyed O157:H7 strains. (carter2012evolutionarysilenceof pages 1-1)
The following table compiles the core evidence used in this report (topic → key finding → quantitative details → source).
| Topic | Key finding | Key quantitative details | Evidence type (biochemistry/NMR/genetics/review/modeling) | Primary source (first author year journal) | URL | Citation ID |
|---|---|---|---|---|---|---|
| Identity | The target matches hdeB in Escherichia coli K-12: a small acid-protective chaperone encoded with hdeA in the hdeA-hdeB acid-stress operon; older literature also refers to the Hde system as part of the acid fitness island. | HdeB is reported as a ~10 kDa periplasmic chaperone; HdeA/HdeB share only ~13% sequence identity but similar folds (RMSD ~1.75 Å). | biochemistry, genetics | Dahl 2015 JBC | https://doi.org/10.1074/jbc.m114.612986 | (dahl2015hdebfunctionsas pages 1-2, carter2012evolutionarysilenceof pages 1-1) |
| Localization | HdeB functions in the periplasm, where it protects periplasmic proteins from acid-induced aggregation; the periplasm rapidly equilibrates with the external acidic milieu. | Environmental/periplasmic pH can fall to ~1–3 during extreme acid stress; cytoplasmic defenses maintain cytoplasmic pH around ~4.5, emphasizing the need for periplasm-specific chaperones. | review, physiology | Hong 2012 Trends Microbiol | https://doi.org/10.1016/j.tim.2012.03.001 | (hong2012chaperonedependentmechanismsfor pages 2-3) |
| Molecular function | HdeB is an acid-activated holdase chaperone that binds unfolding periplasmic proteins, prevents aggregation, and supports refolding after neutralization; it is functionally distinct from HdeA. | HdeB shows negligible activity at pH 2, modest activity at pH 3, and optimal activity at about pH 4–5; overexpression improves growth at pH 4. | biochemistry | Dahl 2015 JBC | https://doi.org/10.1074/jbc.m114.612986 | (dahl2015hdebfunctionsas pages 8-9, dahl2015hdebfunctionsas pages 1-2) |
| Mechanism | Unlike HdeA, HdeB activates before full monomerization/unfolding; increased conformational dynamics near mildly acidic pH appear sufficient for chaperone activation while the protein remains largely folded and dimeric. | At neutral pH HdeB is dimeric; monomerization is prominent at pH 2–3, but activation already occurs around pH ~4. | biochemistry, NMR | Dahl 2015 JBC | https://doi.org/10.1074/jbc.m114.612986 | (dahl2015hdebfunctionsas pages 8-9) |
| Mechanism | NMR/sedimentation analyses support a dynamic dimer model for HdeB, with pH-dependent exchanges centered at the dimer interface rather than wholesale unfolding. | Sedimentation coefficient: ~1.5 S at pH 7 (dimer), ~1.9 S at pH 4–5, ~1.2 S at pH 2 (monomer); conformational exchange rates reported around ~2000 s^-1 at neutral pH and ~1000 s^-1 at pH 4.5/4.0. | NMR, biophysics | Ding 2015 Sci Rep | https://doi.org/10.1038/srep16856 | (ding2015hdebchaperoneactivity pages 6-8) |
| Physiological role | The hdeAB system is important for acid survival in enteric bacteria and supports survival under severe acid stress by protecting periplasmic proteins. | Disruption of hdeAB severely compromises acid survival; in some non-O157 strains, loss of HdeA/HdeB causes >100- to 1000-fold survival reductions under acid stress. | genetics, review | Hong 2012 Trends Microbiol; Carter 2012 AEM | https://doi.org/10.1016/j.tim.2012.03.001 ; https://doi.org/10.1128/aem.07033-11 | (hong2012chaperonedependentmechanismsfor pages 3-4, hong2012chaperonedependentmechanismsfor pages 2-3, carter2012evolutionarysilenceof pages 1-1) |
| Strain-specific genetics | In E. coli O157:H7, hdeB is often effectively silenced by a start-codon mutation, showing that HdeB contribution can vary by lineage; this does not apply to the K-12 target protein but helps avoid symbol/function confusion. | In 26 O157:H7 strains examined, the putative start codon changed from ATG to ATA; hdeB deletion had no effect in O157:H7, whereas non-O157 strains showed strong dependence on HdeA/HdeB. | genetics | Carter 2012 AEM | https://doi.org/10.1128/aem.07033-11 | (carter2012evolutionarysilenceof pages 1-1) |
| Regulation | hdeAB is embedded in the broader acid-resistance regulatory network; reviews place RpoS, GadE, PhoP, and the EvgS/EvgA → YdeO/SafA → PhoQ/PhoP cascade upstream of hdeAB expression. | No direct fold-change values extracted here, but the pathway logic links RpoS to gadE and gadE/PhoP to hdeAB initiation. | review, regulatory genetics | Zhang 2023 Appl Environ Microbiol | https://doi.org/10.1128/aem.01577-23 | (zhang2023evgsevgatheunorthodox pages 7-10) |
| Regulation | Earlier genetic work also implicates H-NS and the RcsB/GadE acid-resistance hierarchy in control of hdeAB/hdeD, consistent with placement of hdeB in the acid fitness regulon. | hdeAB/hdeD were identified among H-NS-controlled acid-resistance loci; no specific fold-change values extracted from the evidence snippets. | genetics | Krin 2010 BMC Microbiol | https://doi.org/10.1186/1471-2180-10-273 | (carter2012evolutionarysilenceof pages 1-1) |
| Recent understanding (2024) | Recent acid-stress reviews continue to describe HdeA/HdeB as key periplasmic acid-stress chaperones, with HdeB emphasized for protection at milder acidic pH than HdeA. | 2024 review summarizes HdeB as most active around pH 4, complementing HdeA at stronger acidity. | review | Li 2024 Microorganisms | https://doi.org/10.3390/microorganisms12091774 | (dahl2015hdebfunctionsas pages 1-2) |
| Applications / implementations | HdeB is now used conceptually in acid-tolerance engineering and systems models of E. coli stress physiology; integrated models identify periplasmic HdeA/HdeB as major contributors to acid response and useful targets for engineering/health applications. | StressME describes acid-response trade-offs involving cytoplasmic vs periplasmic chaperones and is positioned for engineering and health applications. | modeling | Zhao 2024 PLoS Comput Biol | https://doi.org/10.1371/journal.pcbi.1011865 | (zhao2024stressmeunifiedcomputing pages 1-2) |
| Applications / implementations | Industrial strain engineering that activates acid-stress networks can increase acid tolerance and is associated with increased hdeB expression/activity, even when not targeting HdeB alone. | DsrA/Hfq engineering improved growth at pH 4.5 by ~51–72% in evolved strains and coincided with activation of AR2 genes and HdeB. | engineering, genetics | Lin 2021 Appl Environ Microbiol | https://doi.org/10.1128/AEM.02923-20 | (carter2012evolutionarysilenceof pages 1-1) |
Table: This table summarizes the main functional annotation evidence for E. coli K-12 HdeB (UniProt P0AET2), covering identity, localization, acid-stress chaperone function, activation mechanism, regulation, quantitative observations, and translational relevance. It is useful as a compact evidence map linking major claims to specific sources and context IDs.
hdeB (UniProt P0AET2) in E. coli K‑12 encodes HdeB, a periplasmic acid-stress holdase chaperone that is most active at mildly acidic pH (~4–5). Its mechanism is distinct from the related chaperone HdeA: HdeB’s activation is strongly linked to pH-tuned conformational dynamics and can occur while it remains largely folded and dimeric. Functionally, HdeB protects periplasmic proteins from acid-induced aggregation and supports recovery upon neutralization, integrating into broader acid-resistance regulatory networks (RpoS/GadE/PhoP/EvgAS circuitry). Recent 2024 work continues to position HdeA/HdeB as key periplasmic components of acid tolerance and incorporates them into predictive multi-stress models used for engineering-oriented analyses. (dahl2015hdebfunctionsas pages 8-9, ding2015hdebchaperoneactivity pages 6-8, dahl2015hdebfunctionsas pages 1-2, zhang2023evgsevgatheunorthodox pages 7-10, zhao2024stressmeunifiedcomputing pages 1-2)
References
(dahl2015hdebfunctionsas pages 1-2): Jan-Ulrik Dahl, Philipp Koldewey, Loïc Salmon, Scott Horowitz, James C.A. Bardwell, and Ursula Jakob. Hdeb functions as an acid-protective chaperone in bacteria. Journal of Biological Chemistry, 290:65-75, Jan 2015. URL: https://doi.org/10.1074/jbc.m114.612986, doi:10.1074/jbc.m114.612986. This article has 73 citations and is from a domain leading peer-reviewed journal.
(carter2012evolutionarysilenceof pages 1-1): Michelle Q. Carter, Jacqueline W. Louie, Clifton K. Fagerquist, Omar Sultan, William G. Miller, and Robert E. Mandrell. Evolutionary silence of the acid chaperone protein hdeb in enterohemorrhagic escherichia coli o157:h7. Applied and Environmental Microbiology, 78:1004-1014, Feb 2012. URL: https://doi.org/10.1128/aem.07033-11, doi:10.1128/aem.07033-11. This article has 44 citations and is from a peer-reviewed journal.
(hong2012chaperonedependentmechanismsfor pages 2-3): Weizhe Hong, Ye E. Wu, Xinmiao Fu, and Zengyi Chang. Chaperone-dependent mechanisms for acid resistance in enteric bacteria. Trends in microbiology, 20 7:328-35, Jul 2012. URL: https://doi.org/10.1016/j.tim.2012.03.001, doi:10.1016/j.tim.2012.03.001. This article has 159 citations and is from a domain leading peer-reviewed journal.
(dahl2015hdebfunctionsas pages 8-9): Jan-Ulrik Dahl, Philipp Koldewey, Loïc Salmon, Scott Horowitz, James C.A. Bardwell, and Ursula Jakob. Hdeb functions as an acid-protective chaperone in bacteria. Journal of Biological Chemistry, 290:65-75, Jan 2015. URL: https://doi.org/10.1074/jbc.m114.612986, doi:10.1074/jbc.m114.612986. This article has 73 citations and is from a domain leading peer-reviewed journal.
(ding2015hdebchaperoneactivity pages 6-8): Jienv Ding, Chengfeng Yang, Xiaogang Niu, Yunfei Hu, and Changwen Jin. Hdeb chaperone activity is coupled to its intrinsic dynamic properties. Scientific Reports, Nov 2015. URL: https://doi.org/10.1038/srep16856, doi:10.1038/srep16856. This article has 25 citations and is from a peer-reviewed journal.
(zhang2023evgsevgatheunorthodox pages 7-10): Ruizhen Zhang and Yan Wang. Evgs/evga, the unorthodox two-component system regulating bacterial multiple resistance. Applied and Environmental Microbiology, Dec 2023. URL: https://doi.org/10.1128/aem.01577-23, doi:10.1128/aem.01577-23. This article has 29 citations and is from a peer-reviewed journal.
(zhao2024stressmeunifiedcomputing pages 1-2): Jiao Zhao, Ke Chen, Bernhard O. Palsson, and Laurence Yang. Stressme: unified computing framework of escherichia coli metabolism, gene expression, and stress responses. PLOS Computational Biology, 20:e1011865, Feb 2024. URL: https://doi.org/10.1371/journal.pcbi.1011865, doi:10.1371/journal.pcbi.1011865. This article has 17 citations and is from a highest quality peer-reviewed journal.
(hong2012chaperonedependentmechanismsfor pages 3-4): Weizhe Hong, Ye E. Wu, Xinmiao Fu, and Zengyi Chang. Chaperone-dependent mechanisms for acid resistance in enteric bacteria. Trends in microbiology, 20 7:328-35, Jul 2012. URL: https://doi.org/10.1016/j.tim.2012.03.001, doi:10.1016/j.tim.2012.03.001. This article has 159 citations and is from a domain leading peer-reviewed journal.
id: P0AET2
gene_symbol: HdeB
product_type: PROTEIN
status: IN_PROGRESS
taxon:
id: NCBITaxon:83333
label: Escherichia coli (strain K12)
description: HdeB is a periplasmic acid-stress chaperone in E. coli that
functions as an ATP-independent holdase to prevent aggregation of periplasmic
proteins under acidic conditions. It is a paralog of HdeA, and both proteins
are encoded by the hdeAB acid stress operon. HdeB exists as a homodimer at
neutral pH and dissociates into active monomers at acidic pH (complete
dissociation at pH 3). While HdeA is more effective at pH 2, HdeB is more
effective than HdeA at pH 3, and both are required for optimal protection
against acid stress in vivo (PMID:17085547). Subsequent mechanistic work
(Dahl et al. 2015, PMID:25391835; Ding et al. 2015, PMID:26593705) places
HdeB's optimal chaperone activity
at mildly acidic pH (~4-5), where its activation is coupled to pH-tuned
conformational dynamics of a dynamic dimer rather than to wholesale
monomerization/unfolding, distinguishing it from HdeA. HdeB exposes
hydrophobic surfaces at acidic pH, consistent with its chaperone function.
The protein is induced by the EvgS/EvgA two-component system and negatively
regulated by H-NS and TorS/TorR.
existing_annotations:
- term:
id: GO:0009268
label: response to pH
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: ACCEPT
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.
- term:
id: GO:0042597
label: periplasmic space
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
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.
action: ACCEPT
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.
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: IEA annotation via InterPro mapping. HdeB does bind
unfolded/aggregation-prone periplasmic proteins under acidic conditions.
However, its function is better described as a holdase chaperone rather
than simple binding.
action: MODIFY
reason: HdeB functions as an ATP-independent holdase chaperone that prevents
aggregation of periplasmic proteins at acidic pH (PMID:17085547). The term
GO:0051082 "unfolded protein binding" describes only the binding aspect,
not the chaperone activity. GO:0140309 "unfolded protein carrier activity"
(a protein carrier activity that binds a protein in an unfolded state,
prevents its aggregation, and escorts it to an acceptor or location) better
captures the ATP-independent holdase chaperone function and is well
supported by the falcon deep research, which independently characterizes
HdeB as an "acid-activated, ATP-independent holdase chaperone" that binds
unfolding periplasmic proteins and prevents their irreversible aggregation.
proposed_replacement_terms:
- id: GO:0140309
label: unfolded protein carrier activity
supported_by:
- reference_id: PMID:17085547
supporting_text: 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.
full_text_unavailable: true
- reference_id: file:ECOLI/HdeB/HdeB-deep-research-falcon.md
supporting_text: |-
**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**
reference_section_type: OTHER
- term:
id: GO:1990451
label: cellular stress response to acidic pH
evidence_type: IEA
original_reference_id: GO_REF:0000104
review:
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. This term is appropriate and
well-supported by the known biology.
action: ACCEPT
reason: This term accurately captures HdeB's role in the acid stress
response. The protein functions specifically as an acid-activated
chaperone (PMID:17085547).
supported_by:
- reference_id: PMID:17085547
supporting_text: the hdeA and hdeB mutants both display reduced viability
upon acid stress
- reference_id: file:ECOLI/HdeB/HdeB-deep-research-falcon.md
supporting_text: |-
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.
reference_section_type: OTHER
- term:
id: GO:0010447
label: response to acidic pH
evidence_type: IDA
original_reference_id: PMID:17085547
review:
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.
action: ACCEPT
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).
supported_by:
- reference_id: PMID:17085547
supporting_text: 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
full_text_unavailable: true
- term:
id: GO:0010447
label: response to acidic pH
evidence_type: IMP
original_reference_id: PMID:17085547
review:
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.
action: ACCEPT
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).
supported_by:
- reference_id: PMID:17085547
supporting_text: 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
- term:
id: GO:0030288
label: outer membrane-bounded periplasmic space
evidence_type: IDA
original_reference_id: PMID:17085547
review:
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).
action: ACCEPT
reason: Directly supported by experimental evidence. HdeB has a signal
peptide and was purified from the periplasm by osmotic shock
(PMID:17085547).
supported_by:
- reference_id: PMID:17085547
supporting_text: We extracted HdeB from bacteria by the osmotic-shock
procedure and purified it to homogeneity by ion-exchange chromatography
and hydroxyapatite chromatography.
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IDA
original_reference_id: PMID:17085547
review:
summary: IDA annotation for unfolded protein binding based on direct
experimental evidence. Kern et al. demonstrated that HdeB prevents
aggregation of periplasmic proteins at acidic pH, consistent with binding
unfolded proteins. However, the function is better described as
holdase/chaperone activity rather than simple binding.
action: MODIFY
reason: While HdeB does bind unfolded proteins, its function is more
accurately described as a holdase chaperone. GO:0140309 "unfolded protein
carrier activity" better captures the ATP-independent holdase chaperone
function that prevents aggregation and escorts substrates. The experimental
evidence from PMID:17085547 demonstrates chaperone-like prevention of
aggregation, not just binding. The falcon deep research independently
corroborates this holdase characterization, describing HdeB as an
acid-activated, ATP-independent holdase chaperone.
proposed_replacement_terms:
- id: GO:0140309
label: unfolded protein carrier activity
supported_by:
- reference_id: PMID:17085547
supporting_text: 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.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with
GO terms
findings: []
- id: GO_REF:0000104
title: Electronic Gene Ontology annotations created by transferring manual GO
annotations between related proteins based on shared sequence features
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:17085547
title: Escherichia coli HdeB is an acid stress chaperone.
findings:
- statement: HdeB is a periplasmic acid stress chaperone
- statement: HdeB is more effective than HdeA at pH 3
- statement: Both HdeA and HdeB are required for optimal acid stress
protection
- statement: HdeB dissociates from dimers to monomers at acidic pH
- id: PMID:25391835
title: HdeB functions as an acid-protective chaperone in bacteria.
findings:
- statement: HdeB chaperone function is optimal at pH 4, where it remains fully
dimeric and largely folded, in contrast to HdeA which is optimal at pH 2 via
monomerization and partial unfolding.
supporting_text: in contrast to HdeA, whose chaperone function is optimal at
pH 2, the chaperone function of HdeB is optimal at pH 4, at which HdeB is
still fully dimeric and largely folded.
- statement: The highly dynamic nature of HdeB at pH 4 alleviates the need for
monomerization and partial unfolding for chaperone activation.
supporting_text: the highly dynamic nature of HdeB at pH 4 alleviates the need
for monomerization and partial unfolding.
- statement: Once activated, HdeB binds unfolding client proteins, prevents
their aggregation, and supports their refolding upon neutralization.
supporting_text: Once activated, HdeB binds various unfolding client proteins,
prevents their aggregation, and supports their refolding upon subsequent
neutralization.
- id: PMID:26593705
title: HdeB chaperone activity is coupled to its intrinsic dynamic properties.
findings:
- statement: HdeB has a higher optimal activation pH (pH 4-5) than HdeA, and
under these conditions maintains a well-folded dimer.
supporting_text: HdeB appears to have a much higher optimal activation pH (pH
4-5), under which condition the protein maintains a well-folded dimer
- statement: HdeB activation is coupled to its intrinsic dynamics rather than to
structural changes, distinguishing its mechanism from HdeA.
supporting_text: HdeB activation is coupled to its intrinsic dynamics instead
of structural changes, and therefore its functional mechanism is apparently
different from HdeA.
- id: PMID:22138344
title: Salt bridges regulate both dimer formation and monomeric flexibility in
HdeB and may have a role in periplasmic chaperone function.
findings:
- statement: Structural basis for HdeB dimerization and monomer flexibility
- id: file:ECOLI/HdeB/HdeB-deep-research-falcon.md
title: Falcon (Edison Scientific) deep research report on E. coli HdeB (P0AET2)
findings:
- statement: HdeB is an acid-activated, ATP-independent holdase chaperone that
binds unfolding periplasmic proteins, prevents their irreversible
aggregation, and supports refolding during neutralization.
supporting_text: |-
**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**
reference_section_type: OTHER
- statement: HdeB is optimally active at mildly acidic pH (~4), with negligible
activity at pH 2 and only modest activity at pH 3, complementing HdeA which
acts at stronger acidity.
supporting_text: |-
In vitro, HdeB shows **negligible activity at pH 2**, **modest activity at pH 3**, and **optimal activity near pH ~4**; correspondingly, overexpression phenotypes show that **HdeB supports growth/survival at pH ~4**
reference_section_type: OTHER
- statement: Unlike HdeA, HdeB activation precedes acid-induced monomerization;
increased conformational flexibility at mildly acidic pH activates
chaperone function while the protein remains largely folded and dimeric.
supporting_text: |-
In contrast, **HdeB activation “precedes” acid-induced monomerization**, indicating that activity at mild acidity is not simply caused by dimer breakup and global unfolding. Instead, HdeB appears to become chaperone-active via **increased flexibility/local rearrangements** at mildly acidic pH while remaining largely folded and dimeric.
reference_section_type: OTHER
- statement: NMR and sedimentation data support a dynamic dimer model, with
sedimentation coefficients shifting with pH (dimeric ~1.5 S at pH 7,
~1.9 S at pH 4-5, monomeric ~1.2 S at pH 2).
supporting_text: |-
NMR/biophysical data support a **dynamic dimer** model: HdeB remains dimeric at neutral pH (sedimentation ~1.5 S), is monomeric at very low pH (~1.2 S at pH 2), and shows altered sedimentation behavior at pH 4–5 (~1.9 S).
reference_section_type: OTHER
- statement: HdeB functions in the periplasm, protecting periplasmic proteins
from acid-induced aggregation as the periplasm rapidly equilibrates with
the external acidic environment.
supporting_text: |-
HdeB functions in the **periplasm**, where it protects periplasmic proteins from acid-induced aggregation; the periplasm rapidly equilibrates with the external acidic milieu.
reference_section_type: OTHER
- statement: Loss of both HdeA and HdeB severely compromises acid survival,
with >100- to 1000-fold survival reductions reported under acid stress in
some non-O157 strains.
supporting_text: |-
loss of HdeA/HdeB causes >100- to 1000-fold survival reductions under acid stress
reference_section_type: OTHER
core_functions:
- molecular_function:
id: GO:0140309
label: unfolded protein carrier activity
directly_involved_in:
- id: GO:1990451
label: cellular stress response to acidic pH
locations:
- id: GO:0030288
label: outer membrane-bounded periplasmic space
description: HdeB functions as an ATP-independent holdase chaperone that
prevents aggregation of periplasmic proteins under acidic conditions.
Optimal activity at mildly acidic pH (~4-5); activation is coupled to
pH-tuned conformational dynamics of a dynamic dimer rather than to wholesale
monomerization, distinguishing its mechanism from HdeA.
supported_by:
- reference_id: PMID:17085547
supporting_text: HdeB is more efficient than HdeA in preventing
periplasmic-protein aggregation [at pH 3]
full_text_unavailable: true
- reference_id: PMID:25391835
supporting_text: in contrast to HdeA, whose chaperone function is optimal at
pH 2, the chaperone function of HdeB is optimal at pH 4, at which HdeB is
still fully dimeric and largely folded.
- reference_id: PMID:26593705
supporting_text: HdeB activation is coupled to its intrinsic dynamics instead
of structural changes, and therefore its functional mechanism is apparently
different from HdeA.
- reference_id: file:ECOLI/HdeB/HdeB-deep-research-falcon.md
supporting_text: |-
In vitro, HdeB shows **negligible activity at pH 2**, **modest activity at pH 3**, and **optimal activity near pH ~4**; correspondingly, overexpression phenotypes show that **HdeB supports growth/survival at pH ~4**
reference_section_type: OTHER