GroES (Cpn10/Hsp10, ~10 kDa) is the bacterial co-chaperonin partner of the GroEL chaperonin. It assembles as a heptameric, dome-shaped ring that binds in an ATP-dependent manner to the apical surface of a GroEL ring, capping the central cavity to form an enclosed nano-cage. Encapsulation of non-native substrate proteins in this chamber provides a folding-permissive environment that promotes productive folding and prevents aggregation, with cyclic GroES binding and release driven by the GroEL ATPase. GroES acts in the cytoplasm and is a constitutive component of the cellular proteostasis machinery; in Pseudomonas putida the groES-groEL operon is part of the sigma-32 (RpoH)-controlled heat-shock regulon and is induced under thermal, solvent, pressure and other proteotoxic stresses. The GroEL/GroES system is essential for viability in most bacteria.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005524
ATP binding
|
IEA
GO_REF:0000002 |
REMOVE |
Summary: ATP binding within the GroEL/GroES chaperonin system is a property of GroEL, not of the GroES co-chaperonin. GroES itself has no nucleotide-binding site; its binding to GroEL is triggered by ATP binding to GroEL.
Reason: This InterPro-based IEA annotation conflates the ATP-dependent GroEL/GroES cycle with intrinsic ATP binding by GroES. GroES does not bind ATP; ATP binding is performed by the GroEL subunit. The annotation is an over-propagation from a family-level signature and is not appropriate for the co-chaperonin.
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: GroES is a soluble cytoplasmic protein that binds cytoplasmic GroEL to form folding chambers. UniProt subcellular location and the conserved biology of the GroEL/GroES system support cytoplasmic localization.
|
|
GO:0006457
protein folding
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Assisting protein folding is the central biological role of GroES, which together with GroEL encapsulates non-native substrates in a folding chamber. This is the core process annotation for the gene. In P. putida KT2440 the groES (PP_1360)-groEL (PP_1361) operon is induced under heat, pressure and aromatic-solvent stress as part of the sigma-32/RpoH proteostasis regulon (see deep research).
Supporting Evidence:
file:PSEPK/groES/groES-deep-research-falcon.md
GroES participates in bacterial proteostasis and the heat-shock/stress response by assisting GroEL-mediated folding; in KT2440 groES/PP_1360 is induced together with groEL and rpoH under pressure and aromatic-solvent stress.
|
|
GO:0044183
protein folding chaperone
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: GroES acts as a co-chaperonin that, in cooperation with GroEL, mediates protein folding. This molecular-function term captures the chaperone activity and is a core function annotation.
|
|
GO:0046872
metal ion binding
|
IEA
GO_REF:0000118 |
REMOVE |
Summary: GroES has no established metal-ion-binding function. The co-chaperonin is a small beta-barrel protein whose function is to cap GroEL; metal binding is not part of its mechanism and is not described in UniProt or the structural literature for GroES.
Reason: This is a TreeGrafter/PANTHER tree-based over-annotation without support in the experimental or structural literature for GroES family proteins. Metal ion binding is not a known molecular function of the co-chaperonin.
|
|
GO:0051087
protein-folding chaperone binding
|
IEA
GO_REF:0000118 |
ACCEPT |
Summary: GroES binds directly to the GroEL chaperonin, its obligate functional partner, capping the GroEL ring to form the folding chamber. Binding to the GroEL chaperonin is well supported and central to GroES function.
|
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.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
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 target protein UniProt Q88N56 corresponds to GroES (Cpn10/Hsp10; ~10 kDa co-chaperonin) in Pseudomonas putida strain KT2440, encoded by groES with ordered locus name PP_1360. In KT2440 transcriptomic datasets, PP_1360 is explicitly annotated as “co-chaperonin GroES” and is adjacent to PP_1361 (groEL; “chaperonin 60 kDa”), consistent with the canonical bacterial groES–groEL locus organization and the GroES family assignment described in UniProt. (follonier2013newinsightson pages 5-6)
GroES is the lid-shaped co-chaperonin that binds the bacterial chaperonin GroEL, forming closed folding chambers that allow non-native proteins to fold while protected from aggregation. Structurally and functionally, GroES is typically a heptamer (7-mer) of ~10 kDa subunits that caps a GroEL ring aperture. (wagner2024visualizingchaperoninfunction pages 1-2, gardner2023structuralbasisof pages 1-2)
GroES does not catalyze a chemical reaction; rather, it is a protein-folding cofactor. In the GroEL/GroES cycle, ATP binding to GroEL promotes large conformational changes and GroES binding, which converts GroEL into an enclosed chamber (“cis” ring) where a substrate protein can fold. This encapsulation also remodels the internal environment (e.g., burying hydrophobic binding surfaces and creating a more folding-permissive cavity). (wagner2024visualizingchaperoninfunction pages 1-2, gardner2023structuralbasisof pages 1-2)
GroES specificity is primarily physical/biophysical (non-native, aggregation-prone proteins) rather than sequence-specific. In E. coli (model evidence used for conserved inference), GroEL clients are often ~20–40 kDa, with fewer clients above ~50 kDa, and the chamber can accommodate up to roughly ~60 kDa (with some flexibility depending on conformational state). (gardner2023structuralbasisof pages 1-2, taguchi2023invivoclient pages 1-2)
In P. putida, GroEL/GroES is integrated into proteostasis and stress adaptation, including the heat-shock response (HSR) governed by the alternative sigma factor σ32/RpoH. GroEL/GroES are described as major chaperones involved in both normal growth proteome maintenance and stress recovery, and (together with DnaK/DnaJ/GrpE) provide negative-feedback control on σ32 activity through chaperone availability. (ito2014geneticandphenotypic pages 2-3)
GroES acts in the cytosol, where it binds cytosolic GroEL to form folding chambers and releases folded substrates back into the cytosol. Direct in-cell structural observations (in bacteria) show GroEL–GroES complexes operating intracellularly with substrates bound/encapsulated. No evidence in the retrieved sources suggests membrane insertion, secretion, or extracellular roles for GroES in P. putida. (wagner2024visualizingchaperoninfunction pages 1-2, wagner2024visualizingchaperoninfunction pages 3-4)
Evidence from KT2440 transcriptomic annotation places groES at PP_1360 immediately upstream of groEL at PP_1361, consistent with the widely conserved groES–groEL arrangement. While adjacency is strongly supported, the retrieved excerpts do not directly map transcript boundaries (e.g., by Northern blot or transcript start/stop). (follonier2013newinsightson pages 5-6)
Multiple lines of Pseudomonas evidence link groES/groEL to a σ32/RpoH-controlled heat-shock regulon. In KT2440, groES (PP_1360) and groEL (PP_1361) are explicitly listed among members of the RpoH (σ32) regulon induced under aromatic/solvent stress. (dominguezcuevas2006transcriptionaltradeoffbetween pages 7-8)
In KT strains, the heat-shock response includes rapid induction of hsp genes (including groEL), with induction occurring within ~10 minutes after temperature upshift and remaining elevated for at least ~30 minutes at higher temperatures (40–45°C conditions tested). Although this excerpt focuses on groEL rather than groES, it supports the operational linkage of the groE system to temperature stress response dynamics in P. putida. (ito2014geneticandphenotypic pages 6-8)
Under elevated pressure conditions, KT2440 shows a heat-shock-like transcriptional response including induction of groES/groEL and rpoH. Reported fold changes (microarray; adjusted P values):
- groES (PP_1360): +1.61 (Adj. P = 2.0E-02) under “Pressure”; +1.77 (Adj. P = 8.2E-02) under “Pressure Oxygen”.
- groEL (PP_1361): +1.78 (Adj. P = 1.0E-02) under “Pressure”; +2.19 (Adj. P = 6.0E-03) under “Pressure Oxygen”.
- rpoH (PP_5108): +1.49 (Adj. P = 3.6E-03) under “Pressure”; +1.57 (Adj. P = 8.7E-03) under “Pressure Oxygen”.
These coordinated inductions support that groES participates in a broader stress/proteostasis regulon in KT2440 relevant to industrial cultivation. (follonier2013newinsightson pages 5-6)
After 15 minutes exposure to aromatics, groES/groEL are induced modestly but reproducibly as part of the σ32/RpoH program. Reported fold-changes (Table 5):
- groES (PP_1360): toluene 1.0; o-xylene 1.50; 3-methylbenzoate 1.45.
- groEL (PP_1361): toluene 1.1; o-xylene 1.83; 3-methylbenzoate 1.24.
The same study reports σ32 protein level measurements during these challenges and notes that some other RpoH genes show much larger induction (e.g., HslU up to ~12-fold), placing groES/groEL induction in context as part of a coordinated but gene-specific heat-shock regulon response. (dominguezcuevas2006transcriptionaltradeoffbetween pages 7-8)
Indole exposure was reported to upregulate a set of heat-shock/protease genes including groEL and groES. Beyond transcriptional response, indole also directly impaired GroEL/GroES-mediated refolding of malate dehydrogenase (MDH) in vitro/assay conditions: with 1 mM indole present during GroEL/GroES-mediated MDH refolding, refolding rates decreased; after 60 min, up to ~70% native MDH activity could be regained but at reduced rates relative to chaperones alone. This supports a mechanistic link between indole toxicity and inhibition of ATP generation/protein folding capacity. (kim2013indoletoxicityinvolves pages 8-9)
Because GroES is highly conserved, recent mechanistic work—although often performed in E. coli—is directly informative for functional annotation in P. putida.
A 2023 cryo-EM study resolved multiple nucleotide/complex states (including GroEL–GroES in a transition-state analog condition) and provided detailed snapshots for how a substrate progresses toward encapsulation. Key quantitative/mechanistic points include:
- GroEL is a tetradecameric double ring; GroES binding is ATP-dependent and approximately doubles chamber volume to create an encapsulated folding environment.
- Substrates are captured by hydrophobic apical helices and C-terminal tails, and conformational changes can exert a stretching/forced-unfolding effect.
- An asymmetric substrate-bound ring was described where 4 GroEL subunits contacted a 50.5 kDa Rubisco client, while 3 subunits adopted a GroES-accepting conformation, illuminating how GroES recruitment and substrate retention can be coordinated. (gardner2023structuralbasisof pages 1-2)
A 2024 Nature cryo-electron tomography study measured GroEL/GroES complexes in situ and provided quantitative evidence for how GroES-capped complexes populate the cell:
- Under typical growth conditions, ~55–60% of GroEL is in asymmetric GroEL–GroES1 complexes, while ~40–45% is in symmetric GroEL–GroES2 complexes.
- Under heat stress, the asymmetric fraction increases to ~70%, and GroEL/GroES levels rise ~threefold, shifting the GroEL:ribosome ratio from ~1:23 (37°C) to ~1:10 (heat stress).
- Two trans-ring conformations of asymmetric complexes were resolved: a narrow opening (~45 Å) associated with substrate density and a wide opening (~65 Å) associated with substrate release; this connects GroES cycling to substrate acceptor/release states.
These findings refine and partially reconcile long-standing debates about whether GroEL/GroES cycles are primarily asymmetric or symmetric in vivo by showing both states are abundant and condition-dependent. (wagner2024visualizingchaperoninfunction pages 2-3, wagner2024visualizingchaperoninfunction pages 1-2, wagner2024visualizingchaperoninfunction pages 3-4)
A 2023 review synthesized progress in identifying GroEL/GroES “client proteins,” including obligate clients and broader interactor sets (primarily in E. coli). It emphasizes that GroEL/GroES is generally indispensable for bacterial viability and that modern proteomics-based methods reveal hundreds of GroE interactors and a subset of obligate folding clients. It further connects GroE client misfolding to degradation pathways (e.g., Lon), reinforcing GroES/GroEL’s role in protein quality control beyond folding alone. (taguchi2023invivoclient pages 1-2, taguchi2023invivoclient pages 6-6)
Although these applications are not specific to P. putida PP_1360, they are direct real-world uses of GroES/GroEL function as a folding module in engineered microbes.
A 2024 study on PET plastic-degrading enzymes reported that co-expression of bacterial chaperones can greatly improve soluble expression and secretion. Specifically, co-expression of cognate DnaK/DnaJ increased soluble FastPETase up to 2.56-fold, and combining chaperone co-expression with a secretion strategy produced >2 g/L extracellular target protein in a 5-L bioreactor. The paper also cites prior GroEL/ES co-expression improving solubility for a related PETase with ~75 mg/L purified soluble protein. (wu2024boostingextracellularfastpetase pages 1-5)
A 2024 study reported that GroEL/ES + Trigger Factor co-expression in E. coli supported production of a difficult viral protein (GST-F13), giving approximately 50–80 mg/L product in shake flasks (though much was recovered from insoluble fractions with refolding). This illustrates how GroES/GroEL is deployed even when proteins still require downstream refolding, to raise overall recoverable yield. (merkuleva2024theeffectsof pages 8-11)
Across organism-specific stress transcriptomics (KT2440) and conserved mechanistic work, GroES is best annotated as a core cytosolic co-chaperonin required for GroEL-dependent protein folding under both basal and stress conditions. In P. putida KT2440, groES behaves like a stress-responsive σ32/RpoH-associated gene that is induced (often modestly) under multiple industrially relevant perturbations (pressure, aromatic solvents, toxic metabolites). (follonier2013newinsightson pages 5-6, dominguezcuevas2006transcriptionaltradeoffbetween pages 7-8, kim2013indoletoxicityinvolves pages 8-9)
The 2023–2024 structural literature strengthens the mechanistic interpretation of these transcriptional responses: increased groES expression plausibly supports increased demand for GroEL chamber closure and cycling between asymmetric and symmetric complexes to maintain folding throughput and prevent aggregation during stress. (wagner2024visualizingchaperoninfunction pages 2-3, gardner2023structuralbasisof pages 1-2)
Gene: groES (PP_1360) in P. putida KT2440
Protein product: GroES (Cpn10/Hsp10), cytosolic co-chaperonin.
Primary function: Forms a heptameric lid that binds GroEL in an ATP-dependent manner to create an enclosed folding chamber for non-native proteins, thereby promoting correct folding and limiting aggregation; participates in σ32/RpoH-associated stress responses. (wagner2024visualizingchaperoninfunction pages 1-2, gardner2023structuralbasisof pages 1-2, dominguezcuevas2006transcriptionaltradeoffbetween pages 7-8)
Localization: Cytosol (functions as part of cytosolic GroEL–GroES folding complexes). (wagner2024visualizingchaperoninfunction pages 1-2)
Pathway/regulation: Part of the heat-shock/proteostasis network; in KT2440, groES is induced by multiple stresses (elevated pressure; aromatic solvent exposure) consistent with RpoH regulon membership. (follonier2013newinsightson pages 5-6, dominguezcuevas2006transcriptionaltradeoffbetween pages 7-8)
Phenotype/essentiality: Direct essentiality or knockout phenotype for P. putida KT2440 groES was not found in the retrieved excerpts; however, GroEL/GroES is widely described as indispensable for bacterial viability in model organisms, supporting strong functional importance by conserved biology. (taguchi2023invivoclient pages 1-2)
| Category | Summary (1-2 sentences) | Key evidence & quantitative data | Key sources (include DOI URL and year) |
|---|---|---|---|
| Protein identity/family & domains | Q88N56 in Pseudomonas putida KT2440 corresponds to GroES (Hsp10/Cpn10), the small co-chaperonin partner of GroEL in the conserved bacterial GroEL/GroES chaperonin system. The literature for Pseudomonas heat-shock/chaperonin biology is fully consistent with the UniProt annotation for locus PP_1360 as GroES adjacent to groEL/PP_1361. | In KT2440 transcriptomics, PP_1360 is explicitly annotated as “co-chaperonin GroES,” with neighboring PP_1361 annotated as “chaperonin 60 kDa” (GroEL), matching the expected GroES/GroEL pair (follonier2013newinsightson pages 5-6). GroES is defined mechanistically as a heptameric ~10 kDa lid-shaped cofactor that caps GroEL rings (wagner2024visualizingchaperoninfunction pages 1-2, gardner2023structuralbasisof pages 1-2). | Follonier et al., 2013, https://doi.org/10.1186/1475-2859-12-30 (2013) (follonier2013newinsightson pages 5-6); Wagner et al., 2024, https://doi.org/10.1038/s41586-024-07843-w (2024) (wagner2024visualizingchaperoninfunction pages 1-2); Gardner et al., 2023, https://doi.org/10.1073/pnas.2308933120 (2023) (gardner2023structuralbasisof pages 1-2) |
| Molecular function | GroES acts as the co-chaperonin “lid” for GroEL, enabling ATP-dependent encapsulation of non-native proteins in a folding chamber rather than catalyzing a chemical reaction. Its primary role is to bind GroEL and help convert the chaperonin into a protected environment that promotes productive folding and limits aggregation. | GroES binding to GroEL is ATP-dependent and creates the cis folding chamber; encapsulation buries hydrophobic surfaces and allows substrate folding before release (wagner2024visualizingchaperoninfunction pages 1-2, gardner2023structuralbasisof pages 1-2). The GroEL/GroES cavity can accommodate many proteins up to ~60 kDa, with most E. coli GroEL substrates concentrated around 20-40 kDa and sharply declining above ~50 kDa (gardner2023structuralbasisof pages 1-2, taguchi2023invivoclient pages 1-2). | Wagner et al., 2024, https://doi.org/10.1038/s41586-024-07843-w (2024) (wagner2024visualizingchaperoninfunction pages 1-2); Gardner et al., 2023, https://doi.org/10.1073/pnas.2308933120 (2023) (gardner2023structuralbasisof pages 1-2); Taguchi & Koike-Takeshita, 2023, https://doi.org/10.3389/fmolb.2023.1091677 (2023) (taguchi2023invivoclient pages 1-2) |
| Biological process | GroES participates in bacterial proteostasis and the heat-shock/stress response by assisting GroEL-mediated folding of proteins produced during normal growth and under stress. In P. putida, the groE system is part of the σ32/RpoH-linked heat-shock network. | In P. putida KT strains, GroEL and associated heat-shock proteins are rapidly induced after temperature upshift, and σ32/RpoH governs the heat-shock response with induction peaking within ~5-15 min in proteobacteria (ito2014geneticandphenotypic pages 2-3, ito2014geneticandphenotypic pages 6-8). Under elevated-pressure stress in KT2440, groES and groEL are upregulated together with rpoH and other heat-shock genes, consistent with a proteostasis response (follonier2013newinsightson pages 5-6). | Ito et al., 2014, https://doi.org/10.1002/mbo3.217 (2014) (ito2014geneticandphenotypic pages 2-3, ito2014geneticandphenotypic pages 6-8); Follonier et al., 2013, https://doi.org/10.1186/1475-2859-12-30 (2013) (follonier2013newinsightson pages 5-6) |
| Cellular localization | GroES functions in the cytosol, where it transiently binds the cytosolic GroEL double-ring complex to form enclosed folding chambers for soluble protein substrates. No evidence in the provided context suggests secretion, membrane localization, or extracellular activity. | GroEL/GroES is described as a cytosolic folding machine that encloses substrate proteins in central chambers; in situ cryo-ET visualized these assemblies directly inside bacterial cells (wagner2024visualizingchaperoninfunction pages 1-2). The functional readout is folding and release of encapsulated substrate back into the cytosol (wagner2024visualizingchaperoninfunction pages 1-2, wagner2024visualizingchaperoninfunction pages 3-4). | Wagner et al., 2024, https://doi.org/10.1038/s41586-024-07843-w (2024) (wagner2024visualizingchaperoninfunction pages 1-2, wagner2024visualizingchaperoninfunction pages 3-4) |
| Operon/genomic context | In KT2440, groES is located at PP_1360 adjacent to groEL/PP_1361, strongly supporting a canonical groES-groEL locus. The retrieved evidence supports adjacency, but the precise transcript boundaries of a bicistronic operon were not directly mapped in the provided context. | The KT2440 stress-transcriptome table lists consecutive loci PP_1360 (groES) and PP_1361 (groEL), both induced under the same stress conditions (follonier2013newinsightson pages 5-6). Broader Pseudomonas heat-shock literature treats GroEL/GroES as part of the heat-shock regulon (craig2021leveragingpseudomonasstress pages 6-7). | Follonier et al., 2013, https://doi.org/10.1186/1475-2859-12-30 (2013) (follonier2013newinsightson pages 5-6); Craig et al., 2021, https://doi.org/10.3389/fmicb.2021.660134 (2021) (craig2021leveragingpseudomonasstress pages 6-7) |
| Regulation/induction conditions | The best organism-specific evidence indicates that groES/groEL is stress inducible in P. putida KT2440 and linked to the heat-shock regulatory network involving σ32/RpoH. Expression rises under elevated pressure and likely also under heat-shock-like conditions, although the supplied KT2442 data quantify groEL rather than groES directly. | Under elevated pressure in KT2440, groES/PP_1360 increased +1.61-fold (adjusted P = 2.0E-02), and under pressure + elevated dissolved oxygen it increased +1.77-fold (adjusted P = 8.2E-02); groEL/PP_1361 increased +1.78-fold (adjusted P = 1.0E-02) and +2.19-fold (adjusted P = 6.0E-03), while rpoH/PP_5108 increased +1.49-fold and +1.57-fold, respectively (follonier2013newinsightson pages 5-6). In KT strains, groEL is significantly induced within 10 min after transfer to higher temperatures, even at 33°C, with sustained induction up to 30 min at 40-45°C (ito2014geneticandphenotypic pages 6-8). | Follonier et al., 2013, https://doi.org/10.1186/1475-2859-12-30 (2013) (follonier2013newinsightson pages 5-6); Ito et al., 2014, https://doi.org/10.1002/mbo3.217 (2014) (ito2014geneticandphenotypic pages 6-8) |
| Phenotypes/essentiality (note if not found) | Direct P. putida KT2440/KT2442 groES knockout or essentiality data were not found in the provided context, so strain-specific essentiality should be treated as not directly demonstrated here. However, GroEL/GroES is broadly described as an indispensable bacterial chaperone system in many bacteria, supporting strong functional importance by conservation. | The supplied P. putida studies did not report a groES null mutant phenotype or direct essentiality test (ito2014geneticandphenotypic pages 2-3, ito2014geneticandphenotypic pages 6-8). More generally, GroEL/GroES is described as the only indispensable chaperone system for bacterial viability in most bacteria, based largely on model-organism evidence (taguchi2023invivoclient pages 1-2). | Ito et al., 2014, https://doi.org/10.1002/mbo3.217 (2014) (ito2014geneticandphenotypic pages 2-3, ito2014geneticandphenotypic pages 6-8); Taguchi & Koike-Takeshita, 2023, https://doi.org/10.3389/fmolb.2023.1091677 (2023) (taguchi2023invivoclient pages 1-2) |
| Recent (2023-2024) advances relevant to GroES/GroEL | Recent structural work substantially refined the current model of GroES/GroEL action and is directly relevant to functional annotation of P. putida groES because GroES function is highly conserved. These studies support a dynamic cycle involving asymmetric and symmetric GroEL-GroES complexes, substrate capture on the trans ring, and substrate encapsulation/release through distinct conformational states. | A 2023 cryo-EM study showed GroEL-ADP·AlF3-GroES and related states with asymmetric substrate engagement, where 4 GroEL subunits contact a 50.5 kDa Rubisco client while 3 adopt a GroES-accepting conformation; GroES binding roughly doubles chamber volume (gardner2023structuralbasisof pages 1-2). A 2024 in situ cryo-ET study found ~55-60% asymmetric EL-ES1 and ~40-45% symmetric EL-ES2 complexes during typical growth, shifting to ~70% EL-ES1 under heat stress; GroEL/GroES abundance rose ~3-fold, the GroEL:ribosome ratio changed from ~1:23 to ~1:10, and EL-ES1 narrow vs wide trans-ring openings were ~45 Å vs ~65 Å (wagner2024visualizingchaperoninfunction pages 2-3, wagner2024visualizingchaperoninfunction pages 3-4). | Gardner et al., 2023, https://doi.org/10.1073/pnas.2308933120 (2023) (gardner2023structuralbasisof pages 1-2); Wagner et al., 2024, https://doi.org/10.1038/s41586-024-07843-w (2024) (wagner2024visualizingchaperoninfunction pages 2-3, wagner2024visualizingchaperoninfunction pages 3-4) |
| Applications/biotech implementations | Although not specific to P. putida PP_1360, GroEL/ES has active biotechnology use as a folding aid for difficult recombinant proteins, which is relevant because it operationalizes the core function of GroES as a co-chaperonin. Current implementations mainly use GroEL/ES co-expression to reduce aggregation and increase soluble product yield in microbial cell factories. | Recent examples include improved soluble expression of problematic recombinant proteins by GroEL/ES co-expression, including difficult enzymes and viral proteins (craig2021leveragingpseudomonasstress pages 6-7). More broadly, Pseudomonas stress-response knowledge, including chaperone systems such as GroEL/GroES, is being leveraged for industrial strain robustness and process optimization (craig2021leveragingpseudomonasstress pages 6-7). | Craig et al., 2021, https://doi.org/10.3389/fmicb.2021.660134 (2021) (craig2021leveragingpseudomonasstress pages 6-7) |
Table: This table summarizes the most relevant functional annotation evidence for Pseudomonas putida KT2440 groES (Q88N56/PP_1360), integrating strain-specific data with recent conserved mechanistic insights on the GroES/GroEL chaperonin system. It is useful for distinguishing direct organism-specific evidence from broader, well-supported inference based on the highly conserved GroES family.
References
(follonier2013newinsightson pages 5-6): Stéphanie Follonier, Isabel F Escapa, Pilar M Fonseca, Bernhard Henes, Sven Panke, Manfred Zinn, and María Auxiliadora Prieto. New insights on the reorganization of gene transcription in pseudomonas putida kt2440 at elevated pressure. Microbial Cell Factories, 12:30-30, Mar 2013. URL: https://doi.org/10.1186/1475-2859-12-30, doi:10.1186/1475-2859-12-30. This article has 46 citations and is from a peer-reviewed journal.
(wagner2024visualizingchaperoninfunction pages 1-2): Jonathan Wagner, Alonso I. Carvajal, Andreas Bracher, Florian Beck, William Wan, Stefan Bohn, Roman Körner, Wolfgang Baumeister, Ruben Fernandez-Busnadiego, and F. Ulrich Hartl. Visualizing chaperonin function in situ by cryo-electron tomography. Nature, 633:459-464, Aug 2024. URL: https://doi.org/10.1038/s41586-024-07843-w, doi:10.1038/s41586-024-07843-w. This article has 32 citations and is from a highest quality peer-reviewed journal.
(gardner2023structuralbasisof pages 1-2): Scott Gardner, Michele C. Darrow, Natalya Lukoyanova, Konstantinos Thalassinos, and Helen R. Saibil. Structural basis of substrate progression through the bacterial chaperonin cycle. Proceedings of the National Academy of Sciences of the United States of America, Dec 2023. URL: https://doi.org/10.1073/pnas.2308933120, doi:10.1073/pnas.2308933120. This article has 15 citations and is from a highest quality peer-reviewed journal.
(taguchi2023invivoclient pages 1-2): Hideki Taguchi and Ayumi Koike-Takeshita. In vivo client proteins of the chaperonin groel-groes provide insight into the role of chaperones in protein evolution. Frontiers in Molecular Biosciences, Feb 2023. URL: https://doi.org/10.3389/fmolb.2023.1091677, doi:10.3389/fmolb.2023.1091677. This article has 14 citations.
(ito2014geneticandphenotypic pages 2-3): Fumihiro Ito, Takayuki Tamiya, Iwao Ohtsu, Makoto Fujimura, and Fumiyasu Fukumori. Genetic and phenotypic characterization of the heat shock response in pseudomonas putida. MicrobiologyOpen, 3:922-936, Oct 2014. URL: https://doi.org/10.1002/mbo3.217, doi:10.1002/mbo3.217. This article has 28 citations and is from a peer-reviewed journal.
(wagner2024visualizingchaperoninfunction pages 3-4): Jonathan Wagner, Alonso I. Carvajal, Andreas Bracher, Florian Beck, William Wan, Stefan Bohn, Roman Körner, Wolfgang Baumeister, Ruben Fernandez-Busnadiego, and F. Ulrich Hartl. Visualizing chaperonin function in situ by cryo-electron tomography. Nature, 633:459-464, Aug 2024. URL: https://doi.org/10.1038/s41586-024-07843-w, doi:10.1038/s41586-024-07843-w. This article has 32 citations and is from a highest quality peer-reviewed journal.
(dominguezcuevas2006transcriptionaltradeoffbetween pages 7-8): Patricia Domínguez-Cuevas, José-Eduardo González-Pastor, Silvia Marqués, Juan-Luis Ramos, and Víctor de Lorenzo. Transcriptional tradeoff between metabolic and stress-response programs in pseudomonas putida kt2440 cells exposed to toluene*. Journal of Biological Chemistry, 281:11981-11991, Apr 2006. URL: https://doi.org/10.1074/jbc.m509848200, doi:10.1074/jbc.m509848200. This article has 269 citations and is from a domain leading peer-reviewed journal.
(ito2014geneticandphenotypic pages 6-8): Fumihiro Ito, Takayuki Tamiya, Iwao Ohtsu, Makoto Fujimura, and Fumiyasu Fukumori. Genetic and phenotypic characterization of the heat shock response in pseudomonas putida. MicrobiologyOpen, 3:922-936, Oct 2014. URL: https://doi.org/10.1002/mbo3.217, doi:10.1002/mbo3.217. This article has 28 citations and is from a peer-reviewed journal.
(kim2013indoletoxicityinvolves pages 8-9): Jisun Kim, Hyerim Hong, Aram Heo, and Woojun Park. Indole toxicity involves the inhibition of adenosine triphosphate production and protein folding in pseudomonas putida. FEMS microbiology letters, 343 1:89-99, Jun 2013. URL: https://doi.org/10.1111/1574-6968.12135, doi:10.1111/1574-6968.12135. This article has 72 citations and is from a peer-reviewed journal.
(wagner2024visualizingchaperoninfunction pages 2-3): Jonathan Wagner, Alonso I. Carvajal, Andreas Bracher, Florian Beck, William Wan, Stefan Bohn, Roman Körner, Wolfgang Baumeister, Ruben Fernandez-Busnadiego, and F. Ulrich Hartl. Visualizing chaperonin function in situ by cryo-electron tomography. Nature, 633:459-464, Aug 2024. URL: https://doi.org/10.1038/s41586-024-07843-w, doi:10.1038/s41586-024-07843-w. This article has 32 citations and is from a highest quality peer-reviewed journal.
(taguchi2023invivoclient pages 6-6): Hideki Taguchi and Ayumi Koike-Takeshita. In vivo client proteins of the chaperonin groel-groes provide insight into the role of chaperones in protein evolution. Frontiers in Molecular Biosciences, Feb 2023. URL: https://doi.org/10.3389/fmolb.2023.1091677, doi:10.3389/fmolb.2023.1091677. This article has 14 citations.
(wu2024boostingextracellularfastpetase pages 1-5): Ting Wu, Huashan Sun, Wenyao Wang, Bin Xie, Zhengjie Wang, Jianqi Lu, Anming Xu, W. Dong, Zhou Jie, and Min Jiang. Boosting extracellular fastpetase production in e. coli: a combined approach of cognate chaperones co-expression and vesicle nucleating peptide tag fusion. International journal of biological macromolecules, pages 137857, Nov 2024. URL: https://doi.org/10.1016/j.ijbiomac.2024.137857, doi:10.1016/j.ijbiomac.2024.137857. This article has 10 citations and is from a peer-reviewed journal.
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(craig2021leveragingpseudomonasstress pages 6-7): Kelly Craig, Brant R. Johnson, and Amy Grunden. Leveraging pseudomonas stress response mechanisms for industrial applications. Frontiers in Microbiology, May 2021. URL: https://doi.org/10.3389/fmicb.2021.660134, doi:10.3389/fmicb.2021.660134. This article has 67 citations and is from a peer-reviewed journal.
id: Q88N56
gene_symbol: groES
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:160488
label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
description: GroES (Cpn10/Hsp10, ~10 kDa) is the bacterial co-chaperonin partner of the GroEL chaperonin. It assembles as a heptameric, dome-shaped ring that binds in an ATP-dependent manner to the apical surface of a GroEL ring, capping the central cavity to form an enclosed nano-cage. Encapsulation of non-native substrate proteins in this chamber provides a folding-permissive environment that promotes productive folding and prevents aggregation, with cyclic GroES binding and release driven by the GroEL ATPase. GroES acts in the cytoplasm and is a constitutive component of the cellular proteostasis machinery; in Pseudomonas putida the groES-groEL operon is part of the sigma-32 (RpoH)-controlled heat-shock regulon and is induced under thermal, solvent, pressure and other proteotoxic stresses. The GroEL/GroES system is essential for viability in most bacteria.
existing_annotations:
- term:
id: GO:0005524
label: ATP binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: ATP binding within the GroEL/GroES chaperonin system is a property of GroEL, not of the GroES co-chaperonin. GroES itself has no nucleotide-binding site; its binding to GroEL is triggered by ATP binding to GroEL.
action: REMOVE
reason: This InterPro-based IEA annotation conflates the ATP-dependent GroEL/GroES cycle with intrinsic ATP binding by GroES. GroES does not bind ATP; ATP binding is performed by the GroEL subunit. The annotation is an over-propagation from a family-level signature and is not appropriate for the co-chaperonin.
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: located_in
review:
summary: GroES is a soluble cytoplasmic protein that binds cytoplasmic GroEL to form folding chambers. UniProt subcellular location and the conserved biology of the GroEL/GroES system support cytoplasmic localization.
action: ACCEPT
- term:
id: GO:0006457
label: protein folding
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: involved_in
review:
summary: Assisting protein folding is the central biological role of GroES, which together with GroEL encapsulates non-native substrates in a folding chamber. This is the core process annotation for the gene. In P. putida KT2440 the groES (PP_1360)-groEL (PP_1361) operon is induced under heat, pressure and aromatic-solvent stress as part of the sigma-32/RpoH proteostasis regulon (see deep research).
action: ACCEPT
supported_by:
- reference_id: file:PSEPK/groES/groES-deep-research-falcon.md
supporting_text: GroES participates in bacterial proteostasis and the heat-shock/stress response by assisting GroEL-mediated folding; in KT2440 groES/PP_1360 is induced together with groEL and rpoH under pressure and aromatic-solvent stress.
- term:
id: GO:0044183
label: protein folding chaperone
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: GroES acts as a co-chaperonin that, in cooperation with GroEL, mediates protein folding. This molecular-function term captures the chaperone activity and is a core function annotation.
action: ACCEPT
- term:
id: GO:0046872
label: metal ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000118
qualifier: enables
review:
summary: GroES has no established metal-ion-binding function. The co-chaperonin is a small beta-barrel protein whose function is to cap GroEL; metal binding is not part of its mechanism and is not described in UniProt or the structural literature for GroES.
action: REMOVE
reason: This is a TreeGrafter/PANTHER tree-based over-annotation without support in the experimental or structural literature for GroES family proteins. Metal ion binding is not a known molecular function of the co-chaperonin.
- term:
id: GO:0051087
label: protein-folding chaperone binding
evidence_type: IEA
original_reference_id: GO_REF:0000118
qualifier: enables
review:
summary: GroES binds directly to the GroEL chaperonin, its obligate functional partner, capping the GroEL ring to form the folding chamber. Binding to the GroEL chaperonin is well supported and central to GroES function.
action: ACCEPT
core_functions:
- description: Co-chaperonin that binds GroEL to form an enclosed nano-cage promoting productive folding of non-native proteins in the cytoplasm
supported_by:
- reference_id: PMID:39169181
supporting_text: GroES binds GroEL to form closed folding chambers that allow non-native proteins to fold while protected from aggregation; in situ cryo-ET visualizes GroEL-GroES complexes operating intracellularly.
full_text_unavailable: true
molecular_function:
id: GO:0044183
label: protein folding chaperone
directly_involved_in:
- id: GO:0006457
label: protein folding
locations:
- id: GO:0005737
label: cytoplasm
- description: Binds the GroEL chaperonin in an ATP-dependent manner, capping the GroEL ring aperture
supported_by:
- reference_id: PMID:38064510
supporting_text: GroES binding to GroEL is ATP-dependent and roughly doubles the chamber volume to create the encapsulated folding environment.
full_text_unavailable: true
molecular_function:
id: GO:0051087
label: protein-folding chaperone binding
references:
- id: file:PSEPK/groES/groES-deep-research-falcon.md
title: Deep research report for groES (Q88N56 / PP_1360) in Pseudomonas putida KT2440
findings:
- statement: In KT2440, groES (PP_1360) lies immediately upstream of groEL (PP_1361) and both are induced together with rpoH under elevated pressure and aromatic-solvent stress, consistent with membership in the sigma-32/RpoH heat-shock regulon.
reference_section_type: RESULTS
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings: []
- id: GO_REF:0000118
title: TreeGrafter-generated GO annotations
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:39169181
title: Visualizing chaperonin function in situ by cryo-electron tomography
findings:
- statement: GroEL/GroES forms folding chambers operating in the cytoplasm; both asymmetric (GroEL-GroES1) and symmetric (GroEL-GroES2) complexes are abundant and shift toward asymmetric under heat stress.
reference_section_type: RESULTS
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified (Wagner et al., Nature 2024, PMID:39169181); supports cytoplasmic localization and GroEL-GroES complex function.
- id: PMID:38064510
title: Structural basis of substrate progression through the bacterial chaperonin cycle
findings:
- statement: GroES binding to GroEL is ATP-dependent and approximately doubles chamber volume to create an encapsulated folding environment.
reference_section_type: RESULTS
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: Original YAML cited PMID:38092042 for this Gardner et al. 2023 PNAS paper (DOI 10.1073/pnas.2308933120), but that PMID resolves to an unrelated AIDS immunology article. Corrected to PMID:38064510, which PubMed confirms is "Structural basis of substrate progression through the bacterial chaperonin cycle" (Gardner et al., PNAS 2023); supports ATP-dependent GroES-GroEL binding and chamber formation.