OprE (PP_0234) is an outer membrane porin of Pseudomonas putida KT2440 belonging to the OprD/Occ (Opr) family of substrate-selective porins (TC 1.B.25; Pfam OprD, PF03573). Like other members of this family, it forms a beta-barrel channel embedded in the Gram-negative outer membrane that allows the selective diffusion of small hydrophilic solutes across the outer membrane permeability barrier. The mature protein (residues 22-444, following cleavage of an N-terminal signal peptide) localizes to the outer membrane and is also recovered in outer membrane vesicles. In Pseudomonas, OprE-family porins are typically substrate-selective, semi-specialized nutrient-uptake channels whose expression responds to environmental conditions; the OprE ortholog is classically described as anaerobically induced, and in P. putida OprE abundance varies with nutrient (glucose) availability. The precise substrate specificity of P. putida KT2440 OprE has not been established by direct transport assays; substrate predictions (e.g. basic amino acids) derive from the P. aeruginosa OprD-family framework and remain hypotheses for this ortholog.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0015288
porin activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Correctly captures the core molecular function of OprE as an outer membrane porin (beta-barrel channel allowing diffusion of solutes across the outer membrane). This is well supported by family/domain membership (OprD/Opr family, Pfam OprD) and by experimental treatment of OprE as an outer membrane porin in KT2440.
Reason: Porin activity is the defining function of the OprD/Occ-family proteins and is consistent with the InterPro/PANTHER-based inference and with literature describing OprE as an outer membrane integral porin in P. putida KT2440.
|
|
GO:0016020
membrane
|
IEA
GO_REF:0000002 |
MODIFY |
Summary: OprE is a membrane protein, but the available evidence supports the more specific localization to the bacterial outer membrane rather than the generic membrane term. OprE is described as an outer membrane integral porin in KT2440 and is recovered in outer membrane vesicles.
Reason: The generic membrane term (GO:0016020) is correct but uninformatively broad for a Gram-negative outer membrane porin. The OprD/Occ family is an outer membrane beta-barrel family, and OprE is experimentally and proteomically associated with the outer membrane, justifying refinement to the outer membrane term.
Proposed replacements:
outer membrane
|
|
GO:0055085
transmembrane transport
|
IEA
GO_REF:0000108 |
ACCEPT |
Summary: Consistent with the porin function. As a porin, OprE mediates the diffusion of solutes across the outer membrane, so participation in transmembrane transport is appropriate. This term was logically inferred from the porin activity annotation (GO:0015288).
Reason: Transmembrane transport is the biological process directly entailed by porin (channel) activity and is well supported as the process counterpart to the molecular function annotation.
|
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 requested gene/protein identity is supported by primary literature in the correct organism/strain: Poblete-Castro et al. engineered P. putida KT2440 using OprE (PP_0234) and explicitly describe it as an outer membrane integral porin, confirming that oprE ↔ PP_0234 in KT2440 matches the UniProt accession context provided by the user (Q88R99) (pobletecastro2020engineeringtheosmotic pages 2-4).
Outer membrane porins are water-filled channels in the Gram-negative outer membrane that enable diffusion of small, typically hydrophilic molecules across the outer membrane permeability barrier (pobletecastro2020engineeringtheosmotic pages 1-2). In Pseudomonas, many porins are substrate-selective rather than broad “general diffusion” pores.
A well-cited framework for Pseudomonas aeruginosa describes the OprD family as outer membrane porins functioning as semi-specialized nutrient uptake channels, often positively regulated (induced) by their substrates; subfamilies preferentially transport amino acids/related molecules or various carboxylic acids (tamber2006roleofthe pages 9-9).
Important scope note: the OprD-family substrate assignments and specific uptake phenotypes are best-established in P. aeruginosa. For P. putida KT2440 OprE/PP_0234, direct KT2440 transport assays were not located in the retrieved full texts, so substrate specificity below is flagged as “inferred” where applicable.
Localization and protein class. In KT2440, OprE (PP_0234) is experimentally treated as an outer membrane porin and manipulated as such in strain engineering, consistent with a role as a membrane channel protein (pobletecastro2020engineeringtheosmotic pages 2-4).
Presence in outer membrane vesicles (OMVs). Proteomic characterization of KT2440 OMVs identified OprE among OMV-associated outer membrane proteins, supporting that OprE is part of the outer membrane protein repertoire that can be packaged into OMVs (choi2014proteomiccharacterizationof pages 1-2).
Regulation by nutrient status (“hunger response”). In KT2440, OprE abundance in outer membrane protein preparations was reported to be lower under glucose-limiting conditions, described as “hunger-repressed.” Specifically, an ~50 kDa OprE band was distinct at 0.4% or 0.8% glucose but barely detectable at 0.2% glucose (with protein identity supported by mass spectrometry) (putrins2011thecolrssystem pages 8-10).
Likely functional category. Based on OprD-family porin literature, OprE is discussed as part of a group of substrate-selective porins that contribute to nutrient uptake (tamber2006roleofthe pages 9-9).
Putative substrates (not validated for KT2440 PP_0234 in retrieved texts). Within the OprD-family nutrient-uptake framework, OprE has been described/predicted (in P. aeruginosa-focused work) to take up arginine or proline (tamber2006roleofthe pages 9-9). A thesis figure excerpted in our evidence set also lists compounds tested as substrates for an OprE ortholog context and includes growth testing of an oprE mutant on proline (but this evidence is P. aeruginosa-oriented and therefore should not be interpreted as KT2440 PP_0234 substrate proof) (tamber2010physiologicalcontributionof pages 83-87).
KT2440 OprE is an outer membrane integral porin (pobletecastro2020engineeringtheosmotic pages 2-4) and is detectable among proteins associated with outer membrane vesicles (choi2014proteomiccharacterizationof pages 1-2). These findings support a function at the cell-envelope interface (outer membrane) rather than cytosolic metabolism.
Two non-exclusive regulatory contexts emerge from KT2440 and broader Pseudomonas annotations:
A clear real-world biotechnology use case exists where KT2440 OprE is leveraged as a cell-envelope engineering part to facilitate rapid, high-yield recovery of intracellular polyhydroxyalkanoates (PHA).
In Poblete-Castro et al. (Frontiers in Bioengineering and Biotechnology; published March 2020; https://doi.org/10.3389/fbioe.2020.00161), KT2440 was engineered by:
* deleting mscL (an inner-membrane mechanosensitive “rescue valve”), and
* overproducing outer membrane porins OprF and OprE (PP_0234) from an inducible plasmid system,
then applying a hypertonic-to-hypotonic transition to trigger disruption (pobletecastro2020engineeringtheosmotic pages 2-4, pobletecastro2020engineeringtheosmotic pages 5-6).
This porin-based envelope engineering strategy is subsequently treated as an example platform for improving PHA recovery and reducing downstream processing burden in a 2023 PHA engineering review (Microbial Biotechnology; July 2023; https://doi.org/10.1111/1751-7915.14109) (acuna2023rationalengineeringof pages 15-17) and is also referenced in a 2024 review on bacterial programmed autolysis (Microbial Cell Factories; October 2024; https://doi.org/10.1186/s12934-024-02566-z) (acuna2023rationalengineeringof pages 15-17).
The strongest KT2440 quantitative evidence for OprE comes from the 2020 KT2440 engineering study (Poblete-Castro et al.):
Separately, Putrinš et al. (BMC Microbiology; July 2011; https://doi.org/10.1186/1471-2180-11-170) provide a semi-quantitative outer membrane proteomics observation: an OprE-associated ~50 kDa band is readily seen at 0.4–0.8% glucose but is barely detectable at 0.2% glucose (putrins2011thecolrssystem pages 8-10).
Porins as tunable permeability “control points.” The family-level OprD-porin literature emphasizes that substrate-selective porins can be induced by environmental substrates and that limiting outer-membrane channels can prevent entry of toxic compounds—framing porin expression as a trade-off between nutrient acquisition and permeability risk (tamber2006roleofthe pages 9-9).
Bioprocessing perspective (2023–2024). Recent reviews treat engineered autolysis/cell disruption as a key lever for improving microbial production economics by simplifying downstream processing. The 2023 Microbial Biotechnology review explicitly discusses porin overproduction (OprF/OprE) combined with mechanosensitive channel deletion (mscL) as an osmotic-imbalance approach for product recovery (acuna2023rationalengineeringof pages 15-17). The 2024 programmed autolysis review likewise highlights porin/outer-membrane manipulation among strategies to trigger controlled lysis, and cites the KT2440 porin-based system as an example implementation pathway (acuna2023rationalengineeringof pages 15-17).
The following table consolidates direct KT2440 evidence vs cross-species inference, with key metrics and source URLs/dates.
| Aspect | Finding for P. putida KT2440 oprE / OprE | Evidence type | Key quantitative details | Source (year; DOI/URL) |
|---|---|---|---|---|
| Identity verification | oprE = PP_0234 in Pseudomonas putida KT2440; described as an outer membrane integral porin. This matches the requested UniProt-linked gene/protein identity. | Direct experimental study in the correct organism | Constructs included KT-oprE, KT-oprFE, KTΔmscL-oprFE with cloned oprE (PP_0234) (pobletecastro2020engineeringtheosmotic pages 2-4) | Poblete-Castro et al., 2020; https://doi.org/10.3389/fbioe.2020.00161 |
| Subcellular localization | OprE is localized to the outer membrane; it is also detected among proteins in outer membrane vesicles (OMVs) from KT2440. | Direct for OM/OMV association | OMV proteomics identified OprE among major OMV protein components; no OprE-specific abundance values in excerpt (choi2014proteomiccharacterizationof pages 1-2) | Choi et al., 2014; https://doi.org/10.1021/pr500411d |
| Functional class | OprE is treated as a porin; broader Pseudomonas literature places OprE within the OprD-family / substrate-selective outer membrane porins. | Mixed: direct porin annotation in KT2440; family assignment inferred from homologous Pseudomonas literature | No KT2440 transport assay reported in retrieved evidence (tamber2006roleofthe pages 9-9, pobletecastro2020engineeringtheosmotic pages 2-4) | Tamber et al., 2006; https://doi.org/10.1128/JB.188.1.45-54.2006; Poblete-Castro et al., 2020; https://doi.org/10.3389/fbioe.2020.00161 |
| Regulation: anaerobiosis | OprE is reported as normally produced under anoxygenic/anaerobic conditions in other Pseudomonas strains; this is used as contextual functional annotation for KT2440 OprE. | Indirect/background inference, not a KT2440-specific induction experiment in retrieved evidence | No fold induction for KT2440 in retrieved evidence (pobletecastro2020engineeringtheosmotic pages 1-2, pobletecastro2020engineeringtheosmotic pages 2-4) | Poblete-Castro et al., 2020; https://doi.org/10.3389/fbioe.2020.00161 |
| Regulation: nutrient status | In KT2440, OprE is hunger-repressed: OprE abundance decreases under glucose limitation relative to richer glucose conditions. | Direct experimental proteomics in KT2440 | ~50 kDa OprE band in OM fractions was distinct at 0.4% or 0.8% glucose and barely detectable at 0.2% glucose; no fold-change provided (putrins2011thecolrssystem pages 8-10) | Putrinš et al., 2011; https://doi.org/10.1186/1471-2180-11-170 |
| Inferred substrate specificity | Specific substrate for P. putida PP_0234 is not directly demonstrated in retrieved KT2440 studies. From P. aeruginosa OprD-family literature, OprE is predicted to transport arginine or proline; additional tested compounds in ortholog work include sodium pantothenate, uracil, pyroglutamate, and p-aminobenzoic acid. | Inference from another species; should not be treated as proven for KT2440 PP_0234 | Growth/substrate testing was reported for the P. aeruginosa ortholog context, not directly for KT2440 PP_0234 (tamber2010physiologicalcontributionof pages 83-87, tamber2006roleofthe pages 9-9) | Tamber et al., 2006; https://doi.org/10.1128/JB.188.1.45-54.2006; Tamber, 2010 thesis; https://doi.org/10.14288/1.0093018 |
| Role in engineered cell-envelope permeability | Overexpressed OprE, especially with OprF, was used to increase outer membrane permeability/hydrophobicity in KT2440 for downstream bioprocessing. | Direct experimental engineering study | Porin-bearing strains showed >3-fold increased membrane hydrophobicity; KT-oprFE showed 21% membrane disturbance; permeability changes supported by NPN uptake (pobletecastro2020engineeringtheosmotic pages 4-5) | Poblete-Castro et al., 2020; https://doi.org/10.3389/fbioe.2020.00161 |
| Growth and biomass effects of oprE engineering | Single porin overexpression (including OprE alone) did not impair growth rate, final biomass, or PHA yield under PHA-producing conditions; dual OprF/OprE expression had a modest biomass cost. | Direct experimental evidence in KT2440 | After 48 h, individual porin overexpression caused no impairment; dual OprF/OprE in KTΔmscL-oprFE caused about 10% biomass reduction but higher PHA content as % CDM (pobletecastro2020engineeringtheosmotic pages 1-2) | Poblete-Castro et al., 2020; https://doi.org/10.3389/fbioe.2020.00161 |
| Autolysis/cell disruption performance | Combining mscL deletion with OprF/OprE overexpression enabled efficient osmotic-shock-driven cell disruption for intracellular product recovery. | Direct experimental evidence in KT2440 | Hypertonic step followed by hypotonic shock gave >95% disruption within 3 h; reported values include 96.3% cell disruption/death and viability losses of 20%, 80%, 96% after 1, 2, 3 h respectively (pobletecastro2020engineeringtheosmotic pages 1-2, pobletecastro2020engineeringtheosmotic pages 2-4, pobletecastro2020engineeringtheosmotic pages 5-6, pobletecastro2020engineeringtheosmotic pages 4-5) | Poblete-Castro et al., 2020; https://doi.org/10.3389/fbioe.2020.00161 |
| Process conditions used in the key engineering study | OprE/OprF overexpression was induced during PHA production on decanoate; disruption relied on controlled osmotic transitions. | Direct experimental protocol | Growth on 20 mM decanoate; porin expression induced with 1 mM IPTG at 30 h for 18 h; hypertonic step included 10 g/L NaCl, then transfer to distilled water for hypotonic shock (pobletecastro2020engineeringtheosmotic pages 2-4, pobletecastro2020engineeringtheosmotic pages 9-10, pobletecastro2020engineeringtheosmotic pages 5-6) | Poblete-Castro et al., 2020; https://doi.org/10.3389/fbioe.2020.00161 |
| Product recovery relevance | OprE participates in a real-world biotechnology implementation for PHA recovery from KT2440 by reducing downstream disruption burden. | Direct applied bioprocess evidence | Reported PHA recovery values were 94.2%, ~94%, or 93.3% depending on excerpted section; monomer composition reportedly unchanged (pobletecastro2020engineeringtheosmotic pages 1-2, pobletecastro2020engineeringtheosmotic pages 9-10, pobletecastro2020engineeringtheosmotic pages 5-6) | Poblete-Castro et al., 2020; https://doi.org/10.3389/fbioe.2020.00161 |
| 2023–2024 perspective | Recent reviews cite the OprF/OprE + mscL strategy as an example of engineered autolysis / improved PHA recovery in Pseudomonas. | Review-level synthesis | 2023 review confirms concurrent OprF/OprE overproduction with mscL deletion as an osmotic-imbalance strategy; 2024 autolysis review discusses this KT2440 system as a programmable cell disruption example (acuna2023rationalengineeringof pages 15-17, pobletecastro2020engineeringtheosmotic pages 1-2) | Acuña & Poblete-Castro, 2023; https://doi.org/10.1111/1751-7915.14109; Dong et al., 2024; https://doi.org/10.1186/s12934-024-02566-z |
Table: This table summarizes verified evidence for Pseudomonas putida KT2440 OprE/oprE (PP_0234; UniProt Q88R99), separating direct KT2440 findings from cross-species inference. It highlights localization, regulation, inferred substrate specificity, and the strongest quantitative data from the 2020 engineered cell-disruption study.
References
(pobletecastro2020engineeringtheosmotic pages 2-4): Ignacio Poblete-Castro, Carla Aravena-Carrasco, Matias Orellana-Saez, Nicolás Pacheco, Alex Cabrera, and José Manuel Borrero-de Acuña. Engineering the osmotic state of pseudomonas putida kt2440 for efficient cell disruption and downstream processing of poly(3-hydroxyalkanoates). Frontiers in Bioengineering and Biotechnology, Mar 2020. URL: https://doi.org/10.3389/fbioe.2020.00161, doi:10.3389/fbioe.2020.00161. This article has 28 citations.
(pobletecastro2020engineeringtheosmotic pages 1-2): Ignacio Poblete-Castro, Carla Aravena-Carrasco, Matias Orellana-Saez, Nicolás Pacheco, Alex Cabrera, and José Manuel Borrero-de Acuña. Engineering the osmotic state of pseudomonas putida kt2440 for efficient cell disruption and downstream processing of poly(3-hydroxyalkanoates). Frontiers in Bioengineering and Biotechnology, Mar 2020. URL: https://doi.org/10.3389/fbioe.2020.00161, doi:10.3389/fbioe.2020.00161. This article has 28 citations.
(tamber2006roleofthe pages 9-9): Sandeep Tamber, Martina M. Ochs, and Robert E. W. Hancock. Role of the novel oprd family of porins in nutrient uptake in pseudomonas aeruginosa. Journal of Bacteriology, 188:45-54, Jan 2006. URL: https://doi.org/10.1128/jb.188.1.45-54.2006, doi:10.1128/jb.188.1.45-54.2006. This article has 224 citations and is from a peer-reviewed journal.
(choi2014proteomiccharacterizationof pages 1-2): Chi-Won Choi, Edmond Changkyun Park, Sung Ho Yun, Sang-Yeop Lee, Yeol Gyun Lee, Yeonhee Hong, Kyeong Ryang Park, Sang-Hyun Kim, Gun-Hwa Kim, and Seung Il Kim. Proteomic characterization of the outer membrane vesicle of pseudomonas putida kt2440. Journal of proteome research, 13 10:4298-309, Sep 2014. URL: https://doi.org/10.1021/pr500411d, doi:10.1021/pr500411d. This article has 97 citations and is from a peer-reviewed journal.
(putrins2011thecolrssystem pages 8-10): Marta Putrinš, Andres Ainelo, Heili Ilves, and Rita Hõrak. The colrs system is essential for the hunger response of glucose-growing pseudomonas putida. BMC Microbiology, 11:170-170, Jul 2011. URL: https://doi.org/10.1186/1471-2180-11-170, doi:10.1186/1471-2180-11-170. This article has 16 citations and is from a peer-reviewed journal.
(tamber2010physiologicalcontributionof pages 83-87): Sandeep Tamber. Physiological contribution of the pseudomonas aeruginosa oprd family of porins. ArXiv, Jan 2010. URL: https://doi.org/10.14288/1.0093018, doi:10.14288/1.0093018. This article has 0 citations.
(pobletecastro2020engineeringtheosmotic pages 5-6): Ignacio Poblete-Castro, Carla Aravena-Carrasco, Matias Orellana-Saez, Nicolás Pacheco, Alex Cabrera, and José Manuel Borrero-de Acuña. Engineering the osmotic state of pseudomonas putida kt2440 for efficient cell disruption and downstream processing of poly(3-hydroxyalkanoates). Frontiers in Bioengineering and Biotechnology, Mar 2020. URL: https://doi.org/10.3389/fbioe.2020.00161, doi:10.3389/fbioe.2020.00161. This article has 28 citations.
(acuna2023rationalengineeringof pages 15-17): José Manuel Borrero‐de Acuña and Ignacio Poblete‐Castro. Rational engineering of natural polyhydroxyalkanoates producing microorganisms for improved synthesis and recovery. Microbial Biotechnology, 16:262-285, Jul 2023. URL: https://doi.org/10.1111/1751-7915.14109, doi:10.1111/1751-7915.14109. This article has 39 citations and is from a peer-reviewed journal.
(pobletecastro2020engineeringtheosmotic pages 6-9): Ignacio Poblete-Castro, Carla Aravena-Carrasco, Matias Orellana-Saez, Nicolás Pacheco, Alex Cabrera, and José Manuel Borrero-de Acuña. Engineering the osmotic state of pseudomonas putida kt2440 for efficient cell disruption and downstream processing of poly(3-hydroxyalkanoates). Frontiers in Bioengineering and Biotechnology, Mar 2020. URL: https://doi.org/10.3389/fbioe.2020.00161, doi:10.3389/fbioe.2020.00161. This article has 28 citations.
(pobletecastro2020engineeringtheosmotic pages 4-5): Ignacio Poblete-Castro, Carla Aravena-Carrasco, Matias Orellana-Saez, Nicolás Pacheco, Alex Cabrera, and José Manuel Borrero-de Acuña. Engineering the osmotic state of pseudomonas putida kt2440 for efficient cell disruption and downstream processing of poly(3-hydroxyalkanoates). Frontiers in Bioengineering and Biotechnology, Mar 2020. URL: https://doi.org/10.3389/fbioe.2020.00161, doi:10.3389/fbioe.2020.00161. This article has 28 citations.
(pobletecastro2020engineeringtheosmotic pages 9-10): Ignacio Poblete-Castro, Carla Aravena-Carrasco, Matias Orellana-Saez, Nicolás Pacheco, Alex Cabrera, and José Manuel Borrero-de Acuña. Engineering the osmotic state of pseudomonas putida kt2440 for efficient cell disruption and downstream processing of poly(3-hydroxyalkanoates). Frontiers in Bioengineering and Biotechnology, Mar 2020. URL: https://doi.org/10.3389/fbioe.2020.00161, doi:10.3389/fbioe.2020.00161. This article has 28 citations.
id: Q88R99
gene_symbol: oprE
product_type: PROTEIN
status: DRAFT
taxon:
id: NCBITaxon:160488
label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
description: >-
OprE (PP_0234) is an outer membrane porin of Pseudomonas putida KT2440
belonging to the OprD/Occ (Opr) family of substrate-selective porins (TC
1.B.25; Pfam OprD, PF03573). Like other members of this family, it forms a
beta-barrel channel embedded in the Gram-negative outer membrane that allows
the selective diffusion of small hydrophilic solutes across the outer membrane
permeability barrier. The mature protein (residues 22-444, following cleavage
of an N-terminal signal peptide) localizes to the outer membrane and is also
recovered in outer membrane vesicles. In Pseudomonas, OprE-family porins are
typically substrate-selective, semi-specialized nutrient-uptake channels whose
expression responds to environmental conditions; the OprE ortholog is
classically described as anaerobically induced, and in P. putida OprE
abundance varies with nutrient (glucose) availability. The precise substrate
specificity of P. putida KT2440 OprE has not been established by direct
transport assays; substrate predictions (e.g. basic amino acids) derive from
the P. aeruginosa OprD-family framework and remain hypotheses for this
ortholog.
existing_annotations:
- term:
id: GO:0015288
label: porin activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: >-
Correctly captures the core molecular function of OprE as an outer
membrane porin (beta-barrel channel allowing diffusion of solutes across
the outer membrane). This is well supported by family/domain membership
(OprD/Opr family, Pfam OprD) and by experimental treatment of OprE as an
outer membrane porin in KT2440.
action: ACCEPT
reason: >-
Porin activity is the defining function of the OprD/Occ-family proteins
and is consistent with the InterPro/PANTHER-based inference and with
literature describing OprE as an outer membrane integral porin in P.
putida KT2440.
- term:
id: GO:0016020
label: membrane
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: located_in
review:
summary: >-
OprE is a membrane protein, but the available evidence supports the more
specific localization to the bacterial outer membrane rather than the
generic membrane term. OprE is described as an outer membrane integral
porin in KT2440 and is recovered in outer membrane vesicles.
action: MODIFY
reason: >-
The generic membrane term (GO:0016020) is correct but uninformatively
broad for a Gram-negative outer membrane porin. The OprD/Occ family is an
outer membrane beta-barrel family, and OprE is experimentally and
proteomically associated with the outer membrane, justifying refinement to
the outer membrane term.
proposed_replacement_terms:
- id: GO:0019867
label: outer membrane
- term:
id: GO:0055085
label: transmembrane transport
evidence_type: IEA
original_reference_id: GO_REF:0000108
qualifier: involved_in
review:
summary: >-
Consistent with the porin function. As a porin, OprE mediates the
diffusion of solutes across the outer membrane, so participation in
transmembrane transport is appropriate. This term was logically inferred
from the porin activity annotation (GO:0015288).
action: ACCEPT
reason: >-
Transmembrane transport is the biological process directly entailed by
porin (channel) activity and is well supported as the process counterpart
to the molecular function annotation.
core_functions:
- description: >-
Outer membrane porin (beta-barrel channel) of the OprD/Occ family that
mediates selective diffusion of small hydrophilic solutes across the
Gram-negative outer membrane, contributing to transmembrane transport at the
cell envelope.
supported_by:
- reference_id: PMID:32211393
supporting_text: >-
The second channel taken into analysis was the outer membrane integral
porin OprE (PP_0234), which is normally produced under anoxygenic
conditions in other Pseudomonas strains
molecular_function:
id: GO:0015288
label: porin activity
directly_involved_in:
- id: GO:0055085
label: transmembrane transport
locations:
- id: GO:0019867
label: outer membrane
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings: []
- id: GO_REF:0000108
title: Automatic assignment of GO terms using logical inference, based on on inter-ontology links
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:32211393
title: Engineering the Osmotic State of Pseudomonas putida KT2440 for Efficient Cell Disruption and Downstream Processing of Poly(3-Hydroxyalkanoates)
findings:
- statement: >-
OprE (PP_0234) of P. putida KT2440 is an outer membrane integral porin; it
was cloned and overexpressed (alone and with OprF) to modulate outer
membrane permeability for cell disruption.
reference_section_type: RESULTS
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
PMID:32211393 confirmed against PubMed (Poblete-Castro et al., Front
Bioeng Biotechnol 2020; doi 10.3389/fbioe.2020.00161); establishes OprE as
a KT2440 outer membrane porin. Corrected via DOI lookup from the
previously incorrect PMID:32195237, which is an unrelated PHA
immobilized-enzyme-scaffold review (Wong et al.).
- id: PMID:16352820
title: Role of the novel OprD family of porins in nutrient uptake in Pseudomonas aeruginosa
findings:
- statement: >-
Defines the OprD-family of outer membrane porins as substrate-selective
nutrient-uptake channels in Pseudomonas; provides family-level functional
context for OprE (substrate predictions are P. aeruginosa-oriented).
reference_section_type: DISCUSSION
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Tamber et al. OprD-family porins; PubMed-verified (consistent with the VERIFIED use of this PMID in oprD).