YjhQ is an uncharacterized protein in E. coli K12 that contains a GNAT (GCN5-related N-acetyltransferase) domain (Pfam PF00583, PROSITE GNAT domain PS51186). UniProt designates it as "Uncharacterized N-acetyltransferase YjhQ" with an incomplete EC number (EC 2.3.1.-), reflecting that while the structural fold strongly suggests N-acetyltransferase activity, the specific substrate has never been experimentally determined. Yamaguchi and Inouye (PMID:26553797) identified yjhQ as the antitoxin component of a novel toxin-antitoxin (TA) system yjhX-yjhQ (renamed topAI-yjhQ), where the toxin TopAI (YjhX) inhibits topoisomerase I. YjhQ co-expression neutralizes TopAI toxicity, and the two proteins physically interact in pull-down assays. However, whether the antitoxin function of YjhQ is related to its acetyltransferase fold or represents a separate binding/sequestration activity is unknown. De Crecy-Lagard et al. 2025 (PMID:40703034) highlighted yjhQ as a case where DeepECTF incorrectly predicted EC 2.3.1.189 (mycothiol synthase), a biologically impossible assignment because mycothiol biosynthesis is entirely absent from E. coli (an Actinobacteria-specific pathway, BioCyc PWY1G-0). This represents a Non-Paralog Incorrect (NPI) prediction error arising from ML models lacking organism/pathway context.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0016747
acyltransferase activity, transferring groups other than amino-acyl groups
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: IBA annotation for acyltransferase activity based on phylogenetic inference (PANTHER family including P0A944, P46854, P9WJM7, Q9I1K2, I6YG32). YjhQ contains a well-defined GNAT domain (Pfam PF00583, InterPro IPR000182, PROSITE PS51186) and belongs to the acetyltransferase family per UniProt. The structural evidence strongly supports general acyltransferase activity at the fold level. However, the specific substrate is completely unknown. Note that the IBA inference includes P9WJM7 from Mycobacterium tuberculosis; de Crecy-Lagard et al. 2025 (PMID:40703034) showed that the specific prediction of EC 2.3.1.189 (mycothiol synthase) by DeepECTF for yjhQ is biologically impossible since mycothiol biosynthesis (BioCyc PWY1G-0) is absent from E. coli. The IBA term GO:0016747 is appropriately general and does NOT make a substrate-specific claim, so it remains valid as a domain-level prediction.
Reason: The GNAT domain fold is unambiguous from sequence and structural analysis (InterPro IPR000182, Pfam PF00583, CDD cd04301 NAT_SF, Gene3D 3.40.630.30, SUPFAM SSF55729). The IBA annotation at GO:0016747 is appropriately broad and does not commit to a specific substrate. This is a reasonable annotation for an uncharacterized acetyltransferase. The phylogenetic inference is sound at this level of generality even though the family includes mycobacterial members with substrate specificities that are impossible in E. coli.
Supporting Evidence:
PMID:40703034
YjhQ/b4307 is predicted to be a mycothiol synthase (EC 2.3.1.189), but mycothiol is not a molecule synthesized by E. coli, and the remaining pathway genes are absent from the genome (BioCyc ID: PWY1G-0)
file:ECOLI/yjhQ/yjhQ-deep-research-falcon.md
Falcon deep research confirms no substrate-level enzymatic reaction has been validated for YjhQ. Additional context includes biofilm-associated upregulation (expression ratio 11.3), Thr11 phosphorylation linked to YeaG kinase, and inclusion in ASKA acetyltransferase screen without positive result.
|
|
GO:0016747
acyltransferase activity, transferring groups other than amino-acyl groups
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: IEA annotation based on InterPro2GO mapping from InterPro domain IPR000182 (GNAT domain). This is consistent with the IBA annotation and the UniProt classification of YjhQ as an uncharacterized N-acetyltransferase (EC 2.3.1.-). The InterPro domain match is clear and unambiguous.
Reason: Straightforward domain-based annotation. The GNAT domain (IPR000182) maps to acyltransferase activity, which is appropriate for the structural fold. Redundant with the IBA annotation but independently derived and valid.
|
|
GO:0005515
protein binding
|
IPI
PMID:26553797 An endogenous protein inhibitor, YjhX (TopAI), for topoisome... |
MODIFY |
Summary: IPI annotation for protein binding based on the interaction between YjhQ and TopAI (YjhX, UniProtKB:Q2EEU2) demonstrated by pull-down assay in PMID:26553797. Yamaguchi and Inouye showed that YjhQ is the antitoxin component of the topAI-yjhQ TA system, and that YjhQ physically interacts with TopAI to neutralize its toxicity. However, GO:0005515 (protein binding) is an uninformative term per GO curation guidelines. The actual function demonstrated is toxin sequestration: YjhQ binds TopAI and neutralizes its inhibition of topoisomerase I. GO:0097351 (toxin sequestering activity) would be a much more informative and specific annotation for this interaction.
Reason: Per GO curation best practices, GO:0005515 (protein binding) is discouraged as it provides no information about the nature or consequence of the binding. The experimental evidence in PMID:26553797 clearly demonstrates that YjhQ functions as an antitoxin that sequesters TopAI. GO:0097351 (toxin sequestering activity) precisely captures this molecular function. The pull-down assay and co-expression rescue experiments establish that YjhQ binding to TopAI neutralizes TopAI toxicity.
Proposed replacements:
toxin sequestering activity
Supporting Evidence:
PMID:26553797
we found a novel, previously unidentified TA system in Escherichia coli named yjhX-yjhQ. Induction of YjhX (85 amino acid residues) causes cell-growth arrest resulting in cell death, while YjhQ (181 residues) co-induction resumes cell growth
PMID:26553797
co-induction of YjhQ in the presence of 0.2% arabinose with TopAI in the presence of 0.1 mM IPTG neutralized the toxicity of TopAI indicating that the overproduction of TopAI is toxic to the cells, while YjhQ is the antitoxin for TopAI
|
|
GO:0097351
toxin sequestering activity
|
IPI
PMID:26553797 An endogenous protein inhibitor, YjhX (TopAI), for topoisome... |
NEW |
Summary: NEW annotation proposed to replace GO:0005515. YjhQ functions as the antitoxin in the topAI-yjhQ toxin-antitoxin system, binding and sequestering TopAI to neutralize its inhibition of topoisomerase I (PMID:26553797). This is demonstrated by pull-down assays showing physical interaction and co-expression experiments showing rescue from TopAI toxicity.
Reason: GO:0097351 (toxin sequestering activity) is the appropriate molecular function term for the antitoxin role of YjhQ. The evidence from PMID:26553797 shows that YjhQ physically binds TopAI in pull-down assays, co-expression of YjhQ neutralizes TopAI-mediated cell death, and this represents a bona fide TA system. This term accurately captures the molecular mechanism by which YjhQ functions as an antitoxin.
Supporting Evidence:
PMID:26553797
we found a novel, previously unidentified TA system in Escherichia coli named yjhX-yjhQ. Induction of YjhX (85 amino acid residues) causes cell-growth arrest resulting in cell death, while YjhQ (181 residues) co-induction resumes cell growth
|
Q: What is the specific enzymatic substrate of YjhQ N-acetyltransferase activity? Is the acetyltransferase activity required for antitoxin function, or does YjhQ neutralize TopAI purely through protein-protein binding/sequestration?
Q: Is the topAI-yjhQ TA system active under physiological conditions, or only when artificially overexpressed? What are the native expression conditions?
Experiment: Enzymatic assay with purified YjhQ against a panel of candidate acetyl-CoA acceptor substrates (amino sugars, amino acids, antibiotics, etc.) to identify the native substrate.
Type: biochemical assay
Experiment: Structure determination of YjhQ alone and in complex with TopAI to understand whether the GNAT active site is involved in the antitoxin mechanism.
Type: structural biology
Experiment: Mutagenesis of GNAT catalytic residues to determine whether acetyltransferase activity is required for antitoxin function or whether binding alone suffices.
Type: site-directed mutagenesis
YjhQ DeepECTF prediction review. The DeepECTF prediction of mycothiol synthase (EC 2.3.1.189) is incorrect. Mycothiol is not synthesized by E. coli, and the remaining pathway enzymes are absent from the genome. YjhQ is actually an antitoxin component of the TopAI-YjhQ toxin-antitoxin system.
provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2026-03-22T18:13:53.328098'
end_time: '2026-03-22T18:22:48.074265'
duration_seconds: 534.75
template_file: templates/gene_research_go_focused.md
template_variables:
organism: ECOLI
gene_id: yjhQ
gene_symbol: yjhQ
uniprot_accession: P39368
protein_description: 'RecName: Full=Uncharacterized N-acetyltransferase YjhQ; EC=2.3.1.-;'
gene_info: Name=yjhQ; OrderedLocusNames=b4307, JW4269;
organism_full: Escherichia coli (strain K12).
protein_family: Belongs to the acetyltransferase family. .
protein_domains: Acyl_CoA_acyltransferase. (IPR016181); GNAT_dom. (IPR000182); Acetyltransf_1
(PF00583)
provider_config:
timeout: 600
max_retries: 3
parameters:
allowed_domains: []
temperature: 0.1
citation_count: 12
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'yjhQ' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene yjhQ (gene ID: yjhQ, UniProt: P39368) in ECOLI.
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.
Question: You are an expert researcher providing comprehensive, well-cited information.
Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies
Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'yjhQ' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene yjhQ (gene ID: yjhQ, UniProt: P39368) in ECOLI.
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 E. coli K-12 gene yjhQ (b4307; JW4269; UniProt P39368 per the user-supplied identity) encodes a small (~181 aa) protein that has historically been annotated as a hypothetical/uncharacterized ORF in experimental studies, despite being handled as a candidate acetyltransferase-family gene in systematic acetylation research. In the tool-accessible literature reviewed here, no substrate-level enzymatic reaction (EC assignment with validated substrate specificity) and no direct localization experiment were found for YjhQ. The strongest direct evidence available is: (i) biofilm-associated upregulation in a transcriptomics dataset (expression ratio 11.3) where it remains “hypothetical” (Herzberg 2006), and (ii) in vivo phosphorylation at Thr11 whose occupancy is reduced in a ΔyeaG ser/thr-kinase mutant during a glucose→malate shift, suggesting YjhQ participates in a kinase-regulated response to carbon-source transition (Sultan 2021). A recent preprint on ML annotation failures highlights YjhQ as an example where a supervised model predicted an implausible enzymatic function (mycothiol synthase) that conflicts with E. coli pathway context, reinforcing that current evidence does not justify a precise metabolic role (de Crécy-Lagard et al., bioRxiv posted Oct 15, 2024). (herzberg2006ydgg(tqsa)controls pages 8-9, sultan2021phosphoproteomestudyof pages 7-8, crecylagard2025limitationsofcurrent pages 7-9)
Gene symbol and organism match: The target is yjhQ from Escherichia coli K-12.
No evidence in the retrieved corpus indicated a different organism or an alternative gene/protein being conflated with E. coli K-12 yjhQ. (herzberg2006ydgg(tqsa)controls pages 8-9, christensen2018identificationofnovel pages 19-20)
For bacterial “unknowns” like YjhQ, functional annotation generally spans:
* Molecular function: specific biochemical activity (e.g., acetyltransferase with defined acceptor substrate).
* Biological process: role in pathways/phenotypes (e.g., adaptation to nutrient shifts, stress responses).
* Cellular component: localization (cytosol, membrane, periplasm).
The reviewed evidence supports biological-process association (expression in biofilm context; phosphorylation during metabolic shift) but does not establish a specific molecular function/substrate reaction. (herzberg2006ydgg(tqsa)controls pages 8-9, sultan2021phosphoproteomestudyof pages 7-8)
Phosphorylation of a protein at a specific site under defined physiology can indicate:
* participation in regulated pathways (e.g., carbon-source transitions),
* potential protein–protein interactions (kinase/substrate relationships),
* but does not by itself identify enzymatic function or substrates.
This distinction is explicit in Sultan et al., who caution that further evidence is required to declare YjhQ a direct substrate of YeaG, despite Thr11 occupancy changes. (sultan2021phosphoproteomestudyof pages 7-8)
Direct experimental function remains unvalidated in the retrieved literature.
Important caution on incorrect computational assignments: de Crécy-Lagard et al. (bioRxiv preprint posted Oct 15, 2024; DOI minted July 2024) explicitly cite YjhQ/b4307 as being predicted by a supervised ML system to be mycothiol synthase (EC 2.3.1.189) and argue this is refutable because E. coli does not synthesize mycothiol and the rest of the pathway is absent. This is not evidence of YjhQ’s true activity; it is evidence that substrate-level predictions can be wrong without pathway context. (crecylagard2025limitationsofcurrent pages 7-9)
Conclusion: Based on tool-accessible primary literature, YjhQ’s primary enzymatic reaction and substrate specificity are currently unknown; any claim beyond acetyltransferase-family membership (from UniProt context) would be speculative without additional direct biochemical studies. (herzberg2006ydgg(tqsa)controls pages 8-9, christensen2018identificationofnovel pages 19-20, crecylagard2025limitationsofcurrent pages 7-9)
In a study focusing on AI-2 transport and biofilm formation, yjhQ (b4307) appears in a table of genes with altered expression, categorized under “Transport,” with an expression ratio of 11.3 and described as a hypothetical ORF (181 aa). This supports that yjhQ is biofilm-condition responsive in that dataset, though the paper’s mechanistic focus is on YdgG/TqsA rather than yjhQ itself. (herzberg2006ydgg(tqsa)controls pages 8-9, herzberg2006ydgg(tqsa)controls media 482a2066)
A SILAC-based proteome and phosphoproteome comparison of WT vs ΔyeaG during a glucose→malate shift reports that phosphorylation of YjhQ at Thr11 is significantly reduced in the ΔyeaG strain. The authors state that the “most logical explanation” is that YeaG directly phosphorylates YjhQ at this residue, while emphasizing alternative indirect mechanisms and the need for further validation. This associates YjhQ with YeaG-linked regulation during metabolic transition, but does not specify YjhQ’s downstream biochemical role. (sultan2021phosphoproteomestudyof pages 7-8)
No direct localization experiment for YjhQ (e.g., fractionation, fluorescence tagging, topology mapping) was found in the retrieved texts. The “Transport” grouping in Herzberg et al. reflects table categorization rather than a demonstrated membrane location, and the description remains “hypothetical protein.” (herzberg2006ydgg(tqsa)controls pages 8-9)
Direct 2023–2024 primary studies focused on YjhQ were not retrieved via the available tool searches. However, a highly relevant 2024 development affecting YjhQ annotation is methodological: systematic critique of ML-based enzyme function prediction for uncharacterized proteins.
Although YjhQ lacks a validated biochemical function, it appears in real-world functional genomics and systems biology workflows as a representative “unknown” gene:
de Crécy-Lagard et al. emphasize that supervised ML methods are fundamentally limited for “true unknowns” and can yield biologically inconsistent EC assignments; they highlight YjhQ/b4307 specifically as an example of a refutable prediction. This constitutes an expert methodological assessment relevant to how YjhQ should be annotated: avoid adopting specific enzymatic functions without orthogonal evidence and pathway plausibility. (crecylagard2025limitationsofcurrent pages 7-9)
Sultan et al. provide an expert interpretation framework for kinase knockout phosphoproteomes: decreased site occupancy in Δkinase can suggest a direct kinase–substrate relationship, but alternative indirect regulatory paths exist; accordingly, they explicitly require additional evidence before calling YjhQ a direct YeaG substrate. This is authoritative guidance on interpreting YjhQ Thr11 phosphorylation. (sultan2021phosphoproteomestudyof pages 7-8)
The following table consolidates the key direct observations about yjhQ from the retrieved sources.
| Claim/Observation | Evidence type | Key details | Source (authors, journal) | Publication date | URL | Context citation ID |
|---|---|---|---|---|---|---|
| yjhQ maps to E. coli K-12 locus b4307 and was listed as a hypothetical protein in a biofilm-expression dataset | Transcriptomics | Table entry: yjhQ / b4307; grouped under Transport; annotated "ORF, hypothetical protein"; expression ratio 11.3; protein length 181 aa | Herzberg et al., Journal of Bacteriology | Jan 2006 | https://doi.org/10.1128/jb.188.2.587-598.2006 | (herzberg2006ydgg(tqsa)controls pages 8-9, herzberg2006ydgg(tqsa)controls media 482a2066) |
| YjhQ carries a phosphorylation site whose regulation is linked to YeaG during glucose-to-malate shift | Phosphoproteomics | Thr11 phosphorylation on YjhQ was significantly reduced in ΔyeaG versus wild type during the shift; authors say the most logical explanation is direct phosphorylation by YeaG, but further evidence is required before declaring YjhQ a direct substrate | Sultan et al., Frontiers in Microbiology | Apr 2021 | https://doi.org/10.3389/fmicb.2021.657562 | (sultan2021phosphoproteomestudyof pages 7-8) |
| yjhQ was included as an ASKA clone and expression construct in an E. coli acetyltransferase-screening workflow | Strain/plasmid resource | JW4269 = ASKA pCA24n-yjhQ listed in strain/plasmid resources; indicates yjhQ was among candidate genes available for overexpression/testing in the acetyltransferase study, but no direct functional result for YjhQ is shown in the retrieved excerpt | Christensen et al., mBio | Nov 2018 | https://doi.org/10.1128/mbio.01905-18 | (christensen2018identificationofnovel pages 19-19, christensen2018identificationofnovel pages 19-20) |
| A recent analysis explicitly rejects an ML-predicted annotation of YjhQ as mycothiol synthase in E. coli | Critique of ML prediction | DeepECTF predicted YjhQ/b4307 = mycothiol synthase (EC 2.3.1.189); authors argue this is biologically implausible because E. coli does not synthesize mycothiol and the rest of the pathway is absent | de Crécy-Lagard et al., bioRxiv | Oct 15 2024 posting / Jul 2025 record | https://doi.org/10.1101/2024.07.01.601547 | (crecylagard2025limitationsofcurrent pages 7-9) |
Table: This table compiles the direct evidence retrieved for E. coli K-12 yjhQ/P39368, including expression, phosphorylation, cloning-resource, and annotation-critique data. It is useful for separating experimentally observed facts from unvalidated or refuted functional predictions.
A cropped extract of Herzberg et al. (2006) Table 2 showing the yjhQ (b4307) row—expression ratio 11.3, “ORF, hypothetical protein,” length 181 aa—is available here: (herzberg2006ydgg(tqsa)controls media 482a2066)
References
(herzberg2006ydgg(tqsa)controls pages 8-9): Moshe Herzberg, Ian K. Kaye, Wolfgang Peti, and Thomas K. Wood. Ydgg (tqsa) controls biofilm formation in escherichia coli k-12 through autoinducer 2 transport. Journal of Bacteriology, 188:587-598, Jan 2006. URL: https://doi.org/10.1128/jb.188.2.587-598.2006, doi:10.1128/jb.188.2.587-598.2006. This article has 256 citations and is from a peer-reviewed journal.
(sultan2021phosphoproteomestudyof pages 7-8): Abida Sultan, Carsten Jers, Tariq A. Ganief, Lei Shi, Meriem Senissar, Julie Bonne Køhler, Boris Macek, and Ivan Mijakovic. Phosphoproteome study of escherichia coli devoid of ser/thr kinase yeag during the metabolic shift from glucose to malate. Frontiers in Microbiology, Apr 2021. URL: https://doi.org/10.3389/fmicb.2021.657562, doi:10.3389/fmicb.2021.657562. This article has 22 citations and is from a peer-reviewed journal.
(crecylagard2025limitationsofcurrent pages 7-9): Valérie de Crécy-Lagard, Raquel Dias, Nick Sexson, Iddo Friedberg, Yifeng Yuan, and Manal A. Swairjo. Limitations of current machine-learning models in predicting enzymatic functions for uncharacterized proteins. BioRxiv, Jul 2025. URL: https://doi.org/10.1101/2024.07.01.601547, doi:10.1101/2024.07.01.601547. This article has 8 citations.
(christensen2018identificationofnovel pages 19-20): David G. Christensen, Jesse G. Meyer, Jackson T. Baumgartner, Alexandria K. D’Souza, William C. Nelson, Samuel H. Payne, Misty L. Kuhn, Birgit Schilling, and Alan J. Wolfe. Identification of novel protein lysine acetyltransferases in escherichia coli. Nov 2018. URL: https://doi.org/10.1128/mbio.01905-18, doi:10.1128/mbio.01905-18. This article has 115 citations and is from a domain leading peer-reviewed journal.
(herzberg2006ydgg(tqsa)controls media 482a2066): Moshe Herzberg, Ian K. Kaye, Wolfgang Peti, and Thomas K. Wood. Ydgg (tqsa) controls biofilm formation in escherichia coli k-12 through autoinducer 2 transport. Journal of Bacteriology, 188:587-598, Jan 2006. URL: https://doi.org/10.1128/jb.188.2.587-598.2006, doi:10.1128/jb.188.2.587-598.2006. This article has 256 citations and is from a peer-reviewed journal.
(christensen2018identificationofnovel pages 19-19): David G. Christensen, Jesse G. Meyer, Jackson T. Baumgartner, Alexandria K. D’Souza, William C. Nelson, Samuel H. Payne, Misty L. Kuhn, Birgit Schilling, and Alan J. Wolfe. Identification of novel protein lysine acetyltransferases in escherichia coli. Nov 2018. URL: https://doi.org/10.1128/mbio.01905-18, doi:10.1128/mbio.01905-18. This article has 115 citations and is from a domain leading peer-reviewed journal.
id: P39368
gene_symbol: yjhQ
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:83333
label: Escherichia coli (strain K12)
description: >-
YjhQ is an uncharacterized protein in E. coli K12 that contains a GNAT
(GCN5-related N-acetyltransferase) domain (Pfam PF00583, PROSITE GNAT domain
PS51186). UniProt designates it as "Uncharacterized N-acetyltransferase YjhQ"
with an incomplete EC number (EC 2.3.1.-), reflecting that while the structural
fold strongly suggests N-acetyltransferase activity, the specific substrate has
never been experimentally determined. Yamaguchi and Inouye (PMID:26553797)
identified yjhQ as the antitoxin component of a novel toxin-antitoxin (TA)
system yjhX-yjhQ (renamed topAI-yjhQ), where the toxin TopAI (YjhX) inhibits
topoisomerase I. YjhQ co-expression neutralizes TopAI toxicity, and the two
proteins physically interact in pull-down assays. However, whether the
antitoxin function of YjhQ is related to its acetyltransferase fold or
represents a separate binding/sequestration activity is unknown. De Crecy-Lagard
et al. 2025 (PMID:40703034) highlighted yjhQ as a case where DeepECTF
incorrectly predicted EC 2.3.1.189 (mycothiol synthase), a biologically
impossible assignment because mycothiol biosynthesis is entirely absent from
E. coli (an Actinobacteria-specific pathway, BioCyc PWY1G-0). This represents
a Non-Paralog Incorrect (NPI) prediction error arising from ML models lacking
organism/pathway context.
existing_annotations:
- term:
id: GO:0016747
label: acyltransferase activity, transferring groups other than amino-acyl groups
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
IBA annotation for acyltransferase activity based on phylogenetic inference
(PANTHER family including P0A944, P46854, P9WJM7, Q9I1K2, I6YG32). YjhQ
contains a well-defined GNAT domain (Pfam PF00583, InterPro IPR000182,
PROSITE PS51186) and belongs to the acetyltransferase family per UniProt.
The structural evidence strongly supports general acyltransferase activity
at the fold level. However, the specific substrate is completely unknown.
Note that the IBA inference includes P9WJM7 from Mycobacterium tuberculosis;
de Crecy-Lagard et al. 2025 (PMID:40703034) showed that the specific
prediction of EC 2.3.1.189 (mycothiol synthase) by DeepECTF for yjhQ is
biologically impossible since mycothiol biosynthesis (BioCyc PWY1G-0) is
absent from E. coli. The IBA term GO:0016747 is appropriately general and
does NOT make a substrate-specific claim, so it remains valid as a
domain-level prediction.
action: ACCEPT
reason: >-
The GNAT domain fold is unambiguous from sequence and structural analysis
(InterPro IPR000182, Pfam PF00583, CDD cd04301 NAT_SF, Gene3D
3.40.630.30, SUPFAM SSF55729). The IBA annotation at GO:0016747 is
appropriately broad and does not commit to a specific substrate. This is a
reasonable annotation for an uncharacterized acetyltransferase. The
phylogenetic inference is sound at this level of generality even though the
family includes mycobacterial members with substrate specificities that are
impossible in E. coli.
supported_by:
- reference_id: PMID:40703034
supporting_text: >-
YjhQ/b4307 is predicted to be a mycothiol synthase (EC 2.3.1.189),
but mycothiol is not a molecule synthesized by E. coli, and the
remaining pathway genes are absent from the genome (BioCyc ID: PWY1G-0)
- reference_id: file:ECOLI/yjhQ/yjhQ-deep-research-falcon.md
supporting_text: Falcon deep research confirms no substrate-level enzymatic
reaction has been validated for YjhQ. Additional context includes
biofilm-associated upregulation (expression ratio 11.3), Thr11
phosphorylation linked to YeaG kinase, and inclusion in ASKA
acetyltransferase screen without positive result.
- term:
id: GO:0016747
label: acyltransferase activity, transferring groups other than amino-acyl groups
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
IEA annotation based on InterPro2GO mapping from InterPro domain IPR000182
(GNAT domain). This is consistent with the IBA annotation and the UniProt
classification of YjhQ as an uncharacterized N-acetyltransferase (EC 2.3.1.-).
The InterPro domain match is clear and unambiguous.
action: ACCEPT
reason: >-
Straightforward domain-based annotation. The GNAT domain (IPR000182) maps
to acyltransferase activity, which is appropriate for the structural fold.
Redundant with the IBA annotation but independently derived and valid.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:26553797
review:
summary: >-
IPI annotation for protein binding based on the interaction between YjhQ
and TopAI (YjhX, UniProtKB:Q2EEU2) demonstrated by pull-down assay in
PMID:26553797. Yamaguchi and Inouye showed that YjhQ is the antitoxin
component of the topAI-yjhQ TA system, and that YjhQ physically interacts
with TopAI to neutralize its toxicity. However, GO:0005515 (protein
binding) is an uninformative term per GO curation guidelines. The actual
function demonstrated is toxin sequestration: YjhQ binds TopAI and
neutralizes its inhibition of topoisomerase I. GO:0097351 (toxin
sequestering activity) would be a much more informative and specific
annotation for this interaction.
action: MODIFY
reason: >-
Per GO curation best practices, GO:0005515 (protein binding) is
discouraged as it provides no information about the nature or consequence
of the binding. The experimental evidence in PMID:26553797 clearly
demonstrates that YjhQ functions as an antitoxin that sequesters TopAI.
GO:0097351 (toxin sequestering activity) precisely captures this molecular
function. The pull-down assay and co-expression rescue experiments
establish that YjhQ binding to TopAI neutralizes TopAI toxicity.
proposed_replacement_terms:
- id: GO:0097351
label: toxin sequestering activity
supported_by:
- reference_id: PMID:26553797
supporting_text: >-
we found a novel, previously unidentified TA system in Escherichia
coli named yjhX-yjhQ. Induction of YjhX (85 amino acid residues)
causes cell-growth arrest resulting in cell death, while YjhQ (181
residues) co-induction resumes cell growth
- reference_id: PMID:26553797
supporting_text: >-
co-induction of YjhQ in the presence of 0.2% arabinose with TopAI in
the presence of 0.1 mM IPTG neutralized the toxicity of TopAI
indicating that the overproduction of TopAI is toxic to the cells,
while YjhQ is the antitoxin for TopAI
- term:
id: GO:0097351
label: toxin sequestering activity
evidence_type: IPI
original_reference_id: PMID:26553797
review:
summary: >-
NEW annotation proposed to replace GO:0005515. YjhQ functions as the
antitoxin in the topAI-yjhQ toxin-antitoxin system, binding and
sequestering TopAI to neutralize its inhibition of topoisomerase I
(PMID:26553797). This is demonstrated by pull-down assays showing physical
interaction and co-expression experiments showing rescue from TopAI
toxicity.
action: NEW
reason: >-
GO:0097351 (toxin sequestering activity) is the appropriate molecular
function term for the antitoxin role of YjhQ. The evidence from
PMID:26553797 shows that YjhQ physically binds TopAI in pull-down assays,
co-expression of YjhQ neutralizes TopAI-mediated cell death, and this
represents a bona fide TA system. This term accurately captures the
molecular mechanism by which YjhQ functions as an antitoxin.
supported_by:
- reference_id: PMID:26553797
supporting_text: >-
we found a novel, previously unidentified TA system in Escherichia
coli named yjhX-yjhQ. Induction of YjhX (85 amino acid residues)
causes cell-growth arrest resulting in cell death, while YjhQ (181
residues) co-induction resumes cell growth
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: PMID:26553797
title: An endogenous protein inhibitor, YjhX (TopAI), for topoisomerase I from
Escherichia coli.
findings:
- statement: >-
YjhQ is the antitoxin component of the topAI-yjhQ toxin-antitoxin system.
TopAI (YjhX) inhibits topoisomerase I, causing cell death. YjhQ
co-expression neutralizes TopAI toxicity. YjhQ physically interacts with
TopAI in pull-down assays.
supporting_text: >-
we found a novel, previously unidentified TA system in Escherichia coli
named yjhX-yjhQ. Induction of YjhX (85 amino acid residues) causes
cell-growth arrest resulting in cell death, while YjhQ (181 residues)
co-induction resumes cell growth
- id: DOI:10.1128/jb.188.2.587-598.2006
title: YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through
autoinducer 2 transport.
findings:
- statement: yjhQ (b4307) shows biofilm-associated upregulation with an expression
ratio of 11.3 in transcriptomics data. Listed as a hypothetical ORF of 181 aa.
supporting_text: yjhQ/b4307 listed in table of genes with altered expression,
categorized under Transport, with expression ratio 11.3
- id: DOI:10.3389/fmicb.2021.657562
title: Phosphoproteome study of Escherichia coli devoid of Ser/Thr kinase YeaG
during the metabolic shift from glucose to malate.
findings:
- statement: YjhQ is phosphorylated at Thr11 in vivo, and phosphorylation occupancy
is significantly reduced in a delta-yeaG kinase mutant during glucose-to-malate
shift. Suggests YjhQ participates in a kinase-regulated response to carbon-source
transition.
supporting_text: phosphorylation of YjhQ at Thr11 is significantly reduced
in delta-yeaG versus wild type during glucose to malate shift
- id: DOI:10.1128/mbio.01905-18
title: Identification of novel protein lysine acetyltransferases in Escherichia
coli.
findings:
- statement: yjhQ is present in the ASKA overexpression library (JW4269, pCA24n-yjhQ)
and was included as a candidate in a systematic E. coli lysine acetyltransferase
discovery screen, though no positive functional result was reported for YjhQ.
supporting_text: JW4269 is listed as ASKA pCA24n-yjhQ in strain/plasmid
resources for the acetyltransferase study
- id: PMID:40703034
title: Limitations of current machine learning models in predicting enzymatic functions
for uncharacterized proteins.
findings:
- statement: >-
DeepECTF predicted EC 2.3.1.189 (mycothiol synthase) for YjhQ, which is
biologically impossible because mycothiol biosynthesis is entirely absent
from E. coli. This represents a Non-Paralog Incorrect (NPI) prediction
error category.
supporting_text: >-
YjhQ/b4307 is predicted to be a mycothiol synthase (EC 2.3.1.189), but
mycothiol is not a molecule synthesized by E. coli, and the remaining
pathway genes are absent from the genome (BioCyc ID: PWY1G-0)
core_functions:
- description: >-
Predicted N-acetyltransferase activity (EC 2.3.1.-) based on GNAT domain
(Pfam PF00583). Specific substrate unknown.
molecular_function:
id: GO:0016747
label: acyltransferase activity, transferring groups other than amino-acyl groups
- description: >-
Antitoxin function: sequesters TopAI (YjhX) toxin to neutralize its
inhibition of topoisomerase I in the topAI-yjhQ TA system (PMID:26553797).
Whether this antitoxin function is mechanistically related to the
acetyltransferase fold is unknown.
molecular_function:
id: GO:0097351
label: toxin sequestering activity
supported_by:
- reference_id: PMID:26553797
supporting_text: >-
we found a novel, previously unidentified TA system in Escherichia
coli named yjhX-yjhQ. Induction of YjhX (85 amino acid residues)
causes cell-growth arrest resulting in cell death, while YjhQ (181
residues) co-induction resumes cell growth
suggested_questions:
- question: >-
What is the specific enzymatic substrate of YjhQ N-acetyltransferase activity?
Is the acetyltransferase activity required for antitoxin function, or does
YjhQ neutralize TopAI purely through protein-protein binding/sequestration?
- question: >-
Is the topAI-yjhQ TA system active under physiological conditions, or only
when artificially overexpressed? What are the native expression conditions?
suggested_experiments:
- description: >-
Enzymatic assay with purified YjhQ against a panel of candidate acetyl-CoA
acceptor substrates (amino sugars, amino acids, antibiotics, etc.) to identify
the native substrate.
experiment_type: biochemical assay
- description: >-
Structure determination of YjhQ alone and in complex with TopAI to understand
whether the GNAT active site is involved in the antitoxin mechanism.
experiment_type: structural biology
- description: >-
Mutagenesis of GNAT catalytic residues to determine whether acetyltransferase
activity is required for antitoxin function or whether binding alone suffices.
experiment_type: site-directed mutagenesis