Acs is the cytoplasmic acetyl-coenzyme A synthetase (acetate--CoA ligase, AMP-forming; EC 6.2.1.1) of Escherichia coli, a member of the ATP-dependent AMP-binding (ANL) enzyme superfamily. It ligates acetate to coenzyme A at the expense of ATP in two half reactions through a covalently bound acetyl-adenylate intermediate, yielding acetyl-CoA, AMP and diphosphate. Acs is the high-affinity arm of acetate activation, scavenging acetate at low external concentrations where the low-affinity acetate kinase/phosphotransacetylase route cannot, and so allows the cell to use acetate as a carbon and energy source through the TCA cycle and the glyoxylate shunt. The same active site also activates propionate to propionyl-CoA, and acs is required for growth on propionate. Acs is itself a target of reversible lysine acetylation: the GNAT acetyltransferase Pat/PatZ acetylates its active-site Lys609 and inactivates it, and the sirtuin CobB deacetylates Lys609 and reactivates it. A separate body of work from one group reports that purified Acs can acetylate lysines of the chemotaxis response regulator CheY in vitro, and reverse that modification; the physiological significance of this is contested.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003987 acetyl-CoA synthetase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Acetate--CoA ligase (AMP-forming) activity is the defining, experimentally demonstrated activity of Acs, and the PAINT node places it in an ancient clade spanning bacteria, yeast, plants and animals. Reason: The IBD behind this row sits on a node whose descendants carry experimental acetyl-CoA synthetase annotations across kingdoms (ACS1/ACS2 in yeast, ACSS2 in human and mouse, AT5G36880 in Arabidopsis), and the target is squarely inside that clade. P27550 appearing in its own WITH/FROM is expected, not circular - the direct E. coli enzymology (PMID:7751300, PMID:21941) is one of the descendant evidences the curator used to place the node, so this row adds that the activity is inherited rather than lineage-specific. Core function. Supporting Evidence: file:ECOLI/acs/acs-uniprot.txt Reaction=acetate + ATP + CoA = acetyl-CoA + AMP + diphosphate; PMID:7751300 we conclude that this open reading frame encodes the acetate-activating enzyme, Acs |
| GO:0003987 acetyl-CoA synthetase activity | IDA PMID:7751300 Cloning, characterization, and functional expression of acs,... | ACCEPT | Summary: Purified E. coli Acs activates acetate in a CoA-dependent manner; this is the direct demonstration of acetate--CoA ligase activity and the core function of the protein. Reason: CACAO row (GOA carries this term/evidence/reference combination twice, once assigned by EcoCyc and once by CACAO; both are judged here). What the paper shows for acs: the cloned ORF was overexpressed, the 72-kDa product purified, and the purified protein assayed for acetate activation, which required coenzyme A; antiserum raised against the purified protein detected a 72-kDa band in wild type but not in the acs deletion, tying the activity to this gene. The CACAO term matches the assay exactly - right gene, right paper, right granularity (EC 6.2.1.1 is the enzyme's own reaction), and the evidence code IDA fits a purified-enzyme assay. This is the failure-pattern-free case: a correct and core CACAO annotation. Supporting Evidence: PMID:7751300 the E. coli enzyme activated acetate across a wide range of concentrations in a coenzyme A-dependent manner PMID:7751300 we conclude that this open reading frame encodes the acetate-activating enzyme, Acs PMID:21941 An inducible acetyl-CoA synthetase [acetate: CoA ligase (AMP-forming); EC 6.2.1.1] effects this uptake of acetate |
| GO:0003987 acetyl-CoA synthetase activity | IEA GO_REF:0000120 | ACCEPT | Summary: The electronic mapping is correct and converges on the experimentally established activity. Reason: The signature behind this row is the acetyl-CoA ligase family model (InterPro IPR011904, NCBIfam TIGR02188 Ac_CoA_lig_AcsA, HAMAP MF_01123), which the protein matches, and the mapped reaction is the one measured on the purified enzyme (PMID:7751300, PMID:21941). Although the evidence is electronic, the claim is the same as the IDA and IBA rows, so the action is the same. Supporting Evidence: file:ECOLI/acs/acs-uniprot.txt NCBIfam; TIGR02188; Ac_CoA_lig_AcsA; 1. PMID:7751300 the E. coli enzyme activated acetate across a wide range of concentrations in a coenzyme A-dependent manner |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: Acs is a soluble cytoplasmic enzyme and acts there. Reason: The protein has no transmembrane segment, signal peptide or lipid anchor in the curated record, its substrates (acetate, ATP, CoA) are cytoplasmic pools, and it is recovered in the E. coli cytosolic proteome (PMID:18304323). For a bacterium GO:0005829 is as precise as the compartmentalisation allows, so no refinement is proposed. Consistent with the IDA row to the same term. Supporting Evidence: file:ECOLI/acs/acs-uniprot.txt /note="Acetyl-coenzyme A synthetase" PMID:18304323 we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100 |
| GO:0005829 cytosol | IDA PMID:18304323 Protein abundance profiling of the Escherichia coli cytosol. | ACCEPT | Summary: Acs was identified in a fractionated E. coli cytosolic proteome. Reason: The cited study prepared a cytosolic fraction of E. coli MC4100 and identified 1103 proteins from it by LC-MS/MS with abundance estimates. Acs is named only in the paper's supplementary abundance table and not in the cached body text, so this row is accepted on the EcoCyc curator's reading of that table together with the absence of any membrane, signal-peptide or periplasmic feature in the UniProt record, not on a quotation naming the protein. A whole-fraction proteomic identification cannot resolve anything finer than the cytosol in a bacterium. Supporting Evidence: PMID:18304323 we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100 |
| GO:0006085 acetyl-CoA biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: Acs performs the reaction that forms acetyl-CoA from acetate, so it executes a step of acetyl-CoA biosynthesis rather than merely enabling it. Reason: This is the process term that directly corresponds to the gene product's own reaction, the participation test is satisfied by the catalysis itself, and the node placement matches the conserved ligase clade. GO:0019427 (acetyl-CoA biosynthetic process from acetate) would be the exactly matching term but is obsolete (checked against OLS on 2026-10-29), so GO:0006085 is the most specific live term available and is kept as written. Supporting Evidence: file:ECOLI/acs/acs-uniprot.txt Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways |
| GO:0006085 acetyl-CoA biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Same claim as the IBA row, derived from the family signature; correct. Reason: The HAMAP/InterPro acetyl-CoA ligase model asserts exactly the reaction the enzyme performs, and that reaction is acetyl-CoA formation. Retained for consistency with the IBA row to the same term. Supporting Evidence: file:ECOLI/acs/acs-uniprot.txt In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA |
| GO:0006935 chemotaxis | IEA GO_REF:0000104 | MODIFY | Summary: Acs executes no step of chemotaxis - it neither senses a gradient nor moves the cell. Its only reported connection is covalent modification of the response regulator CheY, which is a regulatory input, so the regulation term is the correct level. Reason: Two problems with the term as written. (i) Relation and granularity: the curated experimental basis is that Acs acetylates CheY, altering CheY clockwise bias at the flagellar switch (PMID:1390767, PMID:15327942). Modifying a signalling component is regulation of the process, not participation in it - the cell's chemotaxis is performed by the receptor, CheA, CheY and the flagellar motor. Replacing GO:0006935 with GO:0050920 regulation of chemotaxis keeps the biological claim and corrects the relation; this is a lateral correction rather than a refinement, so the replacement is not a descendant. (ii) Over-propagation: this is a UniRule IEA, so the term is asserted for every bacterial AcsA from a lineage-specific and contested E. coli observation. The contest is real - Li et al. repeated the semi-solid-agar chemotaxis assay in two strain backgrounds and found the acs deletion behaved like wild type (PMID:20345663), against PMID:11359578. Kept at the regulation level rather than removed because UniProt curates the CheY-acetylation statement with experimental evidence, but deliberately excluded from core_functions. Proposed replacements: regulation of chemotaxis Supporting Evidence: file:ECOLI/acs/acs-uniprot.txt Acetylates CheY, the response regulator involved in flagellar movement and chemotaxis. PMID:11359578 The Deltaacs mutant exhibited much reduced sensitivity to chemotactic stimuli PMID:20345663 In contrast, the Ξacs mutant was indistinguishable from the W3110 parental strain |
| GO:0016208 AMP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: True - Acs is an ANL-superfamily adenylate-forming enzyme with a canonical AMP-binding module and an acetyl-adenylate intermediate - but it describes a part of the catalytic cycle rather than a function of its own. Reason: The protein matches the AMP-binding signature (PROSITE PS00455, Pfam PF00501) and UniProt annotates a series of ATP-binding residues; the adenylate intermediate is the mechanistic reason AMP is both a product and a ligand. The term is as precise as a ligand-binding term can be here, so it is not modified, but ligand binding internal to the ligase reaction is already covered by the accepted GO:0003987 activity and does not belong in core_functions. Supporting Evidence: file:ECOLI/acs/acs-uniprot.txt In the first half reaction, Acs combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. file:ECOLI/acs/acs-uniprot.txt PROSITE; PS00455; AMP_BINDING; 1. |
| GO:0018394 peptidyl-lysine acetylation | IDA PMID:15327942 Acetylation of the chemotaxis response regulator CheY by ace... | KEEP AS NON CORE | Summary: Purified Acs acetylates CheY, and the modified residues were mapped by mass spectrometry to specific lysines, so the term fits the assay; but it is a peripheral, in-vitro-defined activity and acetyl-donor supply is not separated from catalysis. Reason: CACAO row. What the paper shows for acs: Acs was overproduced and purified, then shown to acetylate CheY using either acetate (via acetyl-adenylate) or acetyl-CoA as the acetyl donor; anti-acetyl-lysine Western blotting, MALDI-TOF and ESI mass spectrometry, and tryptic peptide fingerprinting mapped the modification to CheY Lys91, 92, 109, 119, 122 and 126, and also showed Acs autoacetylation. The CACAO term matches that evidence at the right granularity - peptidyl-lysine acetylation is precisely what was measured, not a downstream phenotype - so this is not the phenotype-as-process pattern. Three reasons it is kept as non-core rather than accepted as core: (a) the assay is in vitro with purified components; (b) Acs manufactures acetyl-adenylate and acetyl-CoA, and acyl-donor concentration alone drives non-enzymatic lysine acetylation in E. coli (PMID:23830618), so an Acs-dependent rise in CheY acetylation does not by itself establish Acs as the catalyst; (c) the same lab showed CheY is acetylated in a Ξacs strain and autoacetylates from acetyl-CoA at a comparable rate (PMID:16630631), and the dedicated E. coli protein acetyltransferase is PatZ, with Acs as its substrate rather than its peer (PMID:15236963, PMID:40498448). Per the curator-deference rule this experimental row is not removed on the strength of an abstract. Supporting Evidence: PMID:15327942 it could use either acetate or AcCoA as an acetyl donor for CheY acetylation PMID:15327942 the acetylation sites of CheY are clustered at the C terminus of the protein, with lysine residues 91, 92, 109, 119, 122 and 126 being the main acetylation sites file:ECOLI/acs/acs-uniprot.txt Acetylates CheY, the response regulator involved in flagellar movement and chemotaxis. |
| GO:0033558 protein lysine deacetylase activity | IDA PMID:16630631 The chemotaxis response regulator CheY can catalyze its own ... | MODIFY | Summary: The paper does report that Acs removes acetyl groups from CheY, but that is the reverse of Acs's own acetyl-transfer reaction rather than hydrolysis, and GO:0033558 inherits a hydrolytic definition Acs cannot satisfy. The transferase term covers both directions of the one reversible reaction. Reason: CACAO row. What the paper shows for acs: CheY purified from a Ξacs mutant was still partially acetylated, and [14C]acetyl-CoA labelling in the absence of Acs demonstrated CheY autoacetylation; the sentence the annotation rests on is that autoacetylated CheY, like Acs-acetylated CheY, could be deacetylated by Acs. So the claim is in the abstract and is about the right protein - this is not a paper-not-about-the-gene case. The problem is chemistry, which only the term definition exposes: GO:0033558 is_a GO:0019213 deacetylase activity, defined as catalysis of the hydrolysis of an acetyl group from a substrate molecule, and its grandparent GO:0160215 deacylase activity writes the reaction with water as co-substrate (both checked against OLS on 2026-10-29). Acs has no hydrolase chemistry; it is an adenylate-forming ligase whose acetyl transfer onto CheY PMID:15327942 explicitly reports as reversible, i.e. the acetyl group is handed back to CoA or AMP rather than released as free acetate by hydrolysis. By GO convention a reversible transferase is annotated to the transferase term, so the row is modified to GO:0061733 protein-lysine-acetyltransferase activity - the molecular function that carries both directions of this reaction, and one GOA otherwise lacks for Acs despite the two acetylation process rows. The same in-vitro and donor-supply caveats as the GO:0018394 row apply, so the replacement is not proposed as a core function. Proposed replacements: protein-lysine-acetyltransferase activity Supporting Evidence: PMID:16630631 Like CheY acetylated by Acs, autoacetylated CheY could be deacetylated by Acs PMID:15327942 The Acs-catalyzed acetylation of CheY was reversible PMID:16630631 this protein is partially acetylated in spite of the absence of Acs, suggesting that CheY can be post-translationally acetylated in vivo by additional means |
| GO:0034421 post-translational protein acetylation | IDA PMID:15327942 Acetylation of the chemotaxis response regulator CheY by ace... | MODIFY | Summary: The same single experiment as the GO:0018394 row, annotated a second time on the timing axis instead of the residue axis. True, but uninformative beside the residue-specific term. Reason: CACAO row, and an instance of the parent-level-restatement shape: PMID:15327942 is cited twice from one body of work, once as peptidyl-lysine acetylation and once as post-translational protein acetylation. Both are correct - CheY was purified, then acetylated in vitro, so the modification is post-translational - but GO:0034421 drops the only thing the experiment pinned down, namely the identity of the acetylated residues (CheY Lys91, 92, 109, 119, 122 and 126 by mass spectrometry). The two terms are siblings under GO:0006473 protein acetylation rather than parent and child, so this is a lateral move to the informative axis rather than a refinement; GO:0018394 is the term the gene already carries from the same paper and is retained as non-core. Not removed, because the underlying observation is sound and is shared with the kept row. Proposed replacements: peptidyl-lysine acetylation Supporting Evidence: PMID:15327942 the acetylation sites of CheY are clustered at the C terminus of the protein, with lysine residues 91, 92, 109, 119, 122 and 126 being the main acetylation sites PMID:15327942 By Western blotting with specific anti-acetyl-lysine antibody we demonstrated that Acs undergoes autoacetylation |
| GO:0045733 acetate catabolic process | IMP PMID:7751300 Cloning, characterization, and functional expression of acs,... | ACCEPT | Summary: Acs catalyses the committed activation step of acetate utilisation, so it executes a step of acetate breakdown; the knockout growth phenotype is the in-vivo confirmation, not the whole argument. Reason: This row passes the participation test on the enzymology rather than on the phenotype: the entity that performs the acetate to acetyl-CoA conversion is Acs itself, and everything downstream (TCA cycle, glyoxylate shunt) consumes the product. The genetics add the physiological scope - a single acs deletion grows poorly below about 10 mM acetate while an acs ackA pta triple deletion cannot grow on acetate at all, which locates Acs as the high-affinity arm of acetate activation alongside the low-affinity AckA-Pta arm. This is therefore not the fabY-style pattern in which a metabolic knockout's downstream consequences become separate process terms; acetate catabolism is the pathway whose first step Acs catalyses. Core function. Supporting Evidence: PMID:7751300 those deleted for acs grew poorly on low concentrations PMID:7751300 those deleted for acs, ackA, and pta did not grow on acetate at any concentration tested file:ECOLI/acs/acs-uniprot.txt Enables the cell to use acetate during aerobic growth to generate energy via the TCA cycle, and biosynthetic compounds via the glyoxylate shunt. |
| GO:0050218 propionate-CoA ligase activity | IDA PMID:15327942 Acetylation of the chemotaxis response regulator CheY by ace... | ACCEPT | Summary: E. coli Acs activates propionate as well as acetate, and acs is required for growth on propionate; this is a genuine second catalytic capability of the same active site. Reason: The EcoCyc IDA rests on the purified-enzyme characterization in PMID:15327942, whose full text is not in our cache (abstract-only) but which reports the enzyme to behave as a typical prokaryotic Acs, i.e. with the short-chain acyl-CoA ligase substrate range; per the curator-deference rule this is not second-guessed. It is independently corroborated by PMID:24835953, which both measures propionyl-CoA synthetase activity of Acs and shows that deleting acs blocks propionate utilization in vivo. Accepted as a core function in its own right, with acetate as the preferred and physiologically dominant substrate. Supporting Evidence: PMID:15327942 The enzyme exhibited characteristics typical of prokaryotic Acs enzymes PMID:24835953 reversible acetylation also modulates the propionyl-CoA synthetase activity of Acs PMID:24835953 deletion of acs in E. coli results in blockage of propionate utilization |
| GO:0050218 propionate-CoA ligase activity | IEA GO_REF:0000117 | ACCEPT | Summary: An ARBA rule prediction that happens to match independently demonstrated biology. Reason: An ARBA association rule is an unvetted prediction and is not itself evidence, so this row is judged on the same independent grounds as the IDA row to the same term - direct propionyl-CoA synthetase measurement on Acs, and the propionate growth requirement of acs (PMID:24835953). Actions are kept consistent across the two rows. Supporting Evidence: PMID:24835953 deletion of acs in E. coli results in blockage of propionate utilization |
| GO:0019543 propionate catabolic process | IMP PMID:24835953 Acs is essential for propionate utilization in Escherichia c... | NEW | Summary: Acs catalyses the committed activation of propionate to propionyl-CoA, the entry step of propionate catabolism, and an acs deletion cannot utilise propionate at all. Reason: GOA carries the molecular function (GO:0050218 propionate-CoA ligase activity) from two independent sources but no corresponding process term, which leaves the enzyme's role in propionate utilisation unstated. The participation test is satisfied on the chemistry rather than on the knockout: the entity that converts propionate to propionyl-CoA is Acs, and every downstream step of the 2-methylcitrate cycle consumes that product. The knockout result adds physiological scope - deleting acs blocks propionate utilisation entirely - and the authors also measured the propionyl-CoA synthetase activity of Acs directly and showed it is modulated by reversible acetylation. This mirrors the accepted GO:0045733 acetate catabolic process row exactly, one substrate over. Proposed conservatively and as a single term: no regulatory or downstream 2-methylcitrate-cycle terms are proposed, because Acs performs no step in those. Supporting Evidence: PMID:24835953 deletion of acs in E. coli results in blockage of propionate utilization PMID:24835953 reversible acetylation also modulates the propionyl-CoA synthetase activity of Acs PMID:24835953 our data implies that, for propionate utilization in E. coli, a primary amount of propionyl-CoA seems to be required, which is synthesized by Acs |
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Download this section (compressed HTML)Q: Is Acs genuinely a protein-lysine acetyltransferase, or does it increase CheY acetylation by supplying acetyl-adenylate and acetyl-CoA for non-enzymatic modification? If the latter, should the CheY-related GO annotations on Acs be retired altogether rather than re-levelled?
Suggested experts: Michael Eisenbach, Alan J. Wolfe
Q: Why do the two published chemotaxis phenotypes of an acs deletion disagree (PMID:11359578 versus PMID:20345663), and under which conditions can they be reconciled?
Suggested experts: Michael Eisenbach, Jiao-Yu Deng
Q: Should the UniRule that propagates GO:0006935 chemotaxis to bacterial AcsA orthologues be narrowed or withdrawn, given that the underlying observation is an E. coli-specific, contested regulatory effect rather than a step of chemotaxis performed by the enzyme?
Q: In vivo, how much propionyl-CoA is made by Acs versus PrpE, and does Lys609 acetylation regulate the two acyl substrates equivalently?
Suggested experts: Jiao-Yu Deng, Jorge C. Escalante-Semerena
Experiment: Construct Acs variants that separate the two half reactions - one that forms acetyl-adenylate but cannot transfer the acetyl group to a thiol or amine acceptor, and one with the adenylation site disabled - and assay CheY acetylation by anti-acetyl-lysine Western blotting and quantitative mass spectrometry, with acetyl-adenylate and acetyl-CoA concentrations held constant by exogenous addition. If CheY acetylation tracks donor concentration rather than Acs catalytic competence, the acetyltransferase assignment should be withdrawn.
Hypothesis: Acs raises CheY lysine acetylation by producing reactive acetyl donors rather than by catalysing acetyl transfer onto CheY.
Type: structure-function mutagenesis with quantitative acetylation proteomics
Experiment: Test the acs-deletion strains of both laboratories (the AJW series and the W3110-derived strains) side by side in tethering, capillary and semi-solid-agar assays across a range of acetate and glucose concentrations, measuring CheY acetylation stoichiometry by mass spectrometry in each condition and including patZ and cobB deletions and cheY lysine-to-arginine substitutions as controls.
Hypothesis: The chemotaxis phenotype of an acs deletion depends on acetate availability and strain background rather than on CheY acetylation as such.
Type: comparative phenotyping with site-level PTM quantification
Experiment: Grow wild type, acs, prpE and double deletions and an acs K609R/K609Q pair on 13C-labelled propionate and quantify propionyl-CoA and 2-methylcitrate-cycle intermediates by LC-MS/MS, alongside in-vitro propionate- and acetate-activation kinetics on enzymatically acetylated and CobB-deacetylated Acs.
Hypothesis: Acs contributes a defined fraction of propionyl-CoA flux in vivo, regulated by Lys609 acetylation.
Type: 13C metabolic flux analysis with parallel enzyme kinetics
What is not known β curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: Whether Acs is a true protein-lysine acetyltransferase acting on CheY, or whether it raises CheY acetylation indirectly by supplying acetyl-adenylate and acetyl-CoA for non-enzymatic modification, has never been resolved. No reported experiment separates catalysis by Acs from acetyl-donor production by Acs.
BIOLOGY RESIDUAL_SUBGAP
What is known: It is firmly established that purified Acs increases CheY lysine acetylation in vitro using acetate or acetyl-CoA as donor, that the modified residues are CheY Lys91, 92, 109, 119, 122 and 126, that the reaction is reversible, and that CheY also autoacetylates from acetyl-CoA in the absence of Acs (PMID:15327942, PMID:16630631). It is equally established that acetyl-phosphate drives non-enzymatic lysine acetylation globally in E. coli (PMID:23830618) and that PatZ, not Acs, is the organism's dedicated protein acetyltransferase (PMID:15236963).
Significance: The answer decides whether GO should carry any protein-acetyltransferase molecular function for Acs at all, and whether the CheY and chemotaxis link is a regulatory mechanism or a metabolic side effect. It also bears on how the many Acs orthologues inheriting the UniRule chemotaxis annotation should be treated.
What would resolve it: An Acs variant that is catalytically dead for acetyl transfer onto protein but still produces acetyl-adenylate, or the converse, assayed for CheY acetylation alongside wild type with acetyl-donor concentrations clamped.
Provenance (the field's own admissions):
Gap: The conflict between the two reported chemotaxis phenotypes of an acs deletion is unexplained; it is not known whether the difference is strain background, assay format, or the acetate concentration at which Acs is the dominant acetate-activating route.
BIOLOGY RESIDUAL_SUBGAP
What is known: PMID:11359578 reports much reduced chemotactic sensitivity for the acs deletion in tethering, ring-forming, plug and capillary assays, while PMID:20345663 reports it indistinguishable from wild type on semi-solid agar in two independent strain backgrounds and attributes the chemotaxis effect to CobB instead.
What would resolve it: Side-by-side re-testing of the two laboratories' strains in both assay formats under defined acetate and glucose regimes, with CheY acetylation stoichiometry measured in each condition.
Provenance (the field's own admissions):
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