Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005737 cytoplasm	IEA GO_REF:0000120	ACCEPT	Summary: Citrate synthase is a soluble cytoplasmic enzyme; this localization is consistent with the enzyme class and with experimental detection of GltA in the soluble cell lysate fraction of P. putida KT2440. Reason: Bacterial citrate synthases are soluble cytosolic enzymes with no membrane anchor or signal peptide; the IEA assignment is correct and informative.
GO:0006099 tricarboxylic acid cycle	IEA GO_REF:0000120	ACCEPT	Summary: Citrate synthase catalyzes the entry/committed step of the TCA cycle (condensation of acetyl-CoA and oxaloacetate to citrate). This is the canonical biological process for the gene and is strongly supported by family membership and the UniPathway TCA assignment (UPA00223; isocitrate from oxaloacetate, step 1/2). Reason: Core biological process of the gene; directly supported by enzyme function and pathway assignment.
GO:0036440 citrate synthase activity	IEA GO_REF:0000120	ACCEPT	Summary: This is the precise molecular function of the gene product. The UniProt catalytic activity (RHEA:16845, EC 2.3.3.16; oxaloacetate + acetyl-CoA + H2O = citrate + CoA + H+), the conserved catalytic triad, and the citrate synthase family assignment all support citrate synthase activity as the core molecular function. Reason: Represents the core molecular function of gltA; well supported by sequence, family, and pathway evidence.
GO:0046912 acyltransferase activity, acyl groups converted into alkyl on transfer	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: This is a broad parent class of citrate synthase activity (citrate synthase transfers an acetyl group with conversion to a carboxymethyl group). While not incorrect, it is far less informative than GO:0036440 citrate synthase activity, which is already annotated and captures the precise reaction. Reason: Redundant, less-specific ancestor of the already-annotated specific function GO:0036440; provides no additional information about gltA function.

Core Functions

Citrate synthase catalyzing the committed first step of the TCA cycle, condensing acetyl-CoA and oxaloacetate to form citrate and CoA

Molecular Function:

citrate synthase activity

Directly Involved In:

tricarboxylic acid cycle

Cellular Locations:

cytoplasm

Supporting Evidence:

GO_REF:0000120
UniProt catalytic activity RHEA:16845 / EC 2.3.3.16 (oxaloacetate + acetyl-CoA + H2O = citrate + CoA + H+); citrate synthase family assignment.

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:12534463

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440

Deep Research

Falcon

(gltA-deep-research-falcon.md)

Research report: **gltA** (UniProt **Q88FA4**) in *Pseudomonas putida* KT2440 (PSEPK) Falcon Edison Scientific Literature 22 citations 2 artifacts 2026-06-11T17:32:55.520811

Edison artifact artifact-00 (text/markdown)

## Context ID: pqac-00000029 The requested information is found on page 8 of the document. 1. **Succinate titers (mM) vs pH for wild type vs gltA-KT**: This is (image/png)

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.

Research report: gltA (UniProt Q88FA4) in Pseudomonas putida KT2440 (PSEPK)

0) Target verification (mandatory disambiguation)

Verified identity

The UniProt accession Q88FA4 is annotated as citrate synthase (citrate synthase family) from Pseudomonas putida strain KT2440, with gene name gltA (ordered locus name PP_4194 per UniProt, provided by user). Within the retrieved KT2440-focused literature, gltA is explicitly treated as citrate synthase and is genetically perturbed (overexpression or deletion) in multiple studies, confirming that—here—gltA refers to citrate synthase, not glutamate synthase or other gltA usages in unrelated organisms. (mutyala2023citratesynthaseoverexpression pages 1-3, dong2024modificationofglucose pages 1-2, molina‐henares2010identificationofconditionally pages 3-4)

Notes on PP_4194 mapping

In the retrieved full texts, an explicit sentence mapping P. putida KT2440 gltA → PP_4194 was not captured by the evidence extraction, although PP_4194 appears as the P. putida locus identifier in the broader retrieved corpus (e.g., in KT2440 datasets) and is consistent with the user-provided UniProt context. Therefore, functional conclusions below are tied to “gltA/citrate synthase” in KT2440, and PP_4194 is used as the expected locus identifier with this caveat disclosed.

1) Key concepts and current understanding

1.1 Definition and primary biochemical function

Citrate synthase (EC 2.3.3.1) catalyzes the committed entry step into the tricarboxylic acid (TCA) cycle by condensing acetyl‑CoA and oxaloacetate (OAA) to form citrate (and CoA-SH). In Pseudomonas spp., biochemical characterization of GltA confirms the canonical substrate pair acetyl‑CoA + OAA for citrate synthase activity. (dolan2022systemswidedissectionof pages 8-12)

In P. putida KT2440 specifically, recent work frames acetate assimilation as being initiated by gltA (citrate synthase) converting acetyl‑CoA to citrate, i.e., channeling acetyl‑CoA into the TCA cycle. (mutyala2023citratesynthaseoverexpression pages 1-3)

1.2 Enzyme family/structure and regulatory features (best-available evidence)

Direct structure/kinetic characterization of KT2440 GltA was not retrieved in full text. However, a high-quality Pseudomonas aeruginosa study provides close-genus evidence that GltA:

is a ~429 aa enzyme assembling as a hexamer (“trimer of dimers”),
contains the canonical catalytic triad (His/His/Asp), and
carries residues implicated in NADH binding, consistent with potential NADH regulation (not experimentally proven for KT2440 in the retrieved text). (dolan2022systemswidedissectionof pages 8-12)

This same study reports no detectable 2‑methylcitrate synthase activity for GltA (i.e., it does not substitute for PrpC), which helps separate citrate synthase from paralogous methylcitrate synthases in related metabolism. (dolan2022systemswidedissectionof pages 8-12)

1.3 Pathway placement and cellular role

In KT2440, gltA is positioned at a key metabolic “gate” controlling whether carbon enters oxidative metabolism via TCA:

Acetate → acetyl‑CoA → citrate (via GltA) is highlighted as a key step in acetate utilization and in engineered succinate formation under microaerobic conditions. (mutyala2023citratesynthaseoverexpression pages 1-3)
Conversely, deleting gltA is used as a strategy to prevent acetyl‑CoA from entering the TCA cycle, thereby increasing availability of acetyl‑CoA for other biosynthetic objectives (e.g., malonyl‑CoA-dependent products). (favoino2024enhancedbiosynthesisof pages 2-4)

2) Subcellular localization (where the protein functions)

No paper in the retrieved set provides an explicit localization statement (e.g., “cytosolic enzyme”). However, in the KT2440 succinate engineering study, citrate synthase overexpression was evaluated by SDS-PAGE using “soluble fractions of the cell lysate”, consistent with GltA behaving as a soluble intracellular enzyme rather than a membrane protein. (mutyala2023citratesynthaseoverexpression pages 3-4)

3) Essentiality and fitness impact in P. putida KT2440

3.1 Evidence suggesting broad essentiality of expression

A genome-wide mutant-library screen / conditional essentiality analysis in KT2440 (minimal medium contexts) uses gltA (citrate synthase) as a high-expression reference and states that gltA expression is “essential under all growth conditions for this strict aerobe” (as written in the extracted text). (molina‐henares2010identificationofconditionally pages 3-4)

3.2 Evidence that ΔgltA can be viable under some engineered conditions

In a 2024 metabolic engineering study (in a P. putida chassis closely related to KT2440, using KT2440-derived promoters/parts), markerless ΔgltA mutants were constructed and exhibited similar growth and glucose consumption to the parent strain under batch cultivation on glucose (20 g/L), implying that gltA is not strictly essential under those specific conditions. (dong2024modificationofglucose pages 5-7)

3.3 Interpretation

The evidence supports a context-dependent essentiality/fitness role:

GltA is central to aerobic energy metabolism and anabolic precursor supply, and can be “essential” in some physiological definitions/conditions (e.g., strict aerobic growth in certain minimal contexts). (molina‐henares2010identificationofconditionally pages 3-4)
Yet engineered strains can tolerate gltA deletion under some cultivation regimes, likely via metabolic rerouting, medium composition, or strain background differences. (dong2024modificationofglucose pages 5-7)

Because the retrieved texts do not reconcile these findings experimentally in KT2440 side-by-side, essentiality should be treated as conditional rather than absolute.

4) Recent developments (prioritized 2023–2024)

4.1 2023: gltA overexpression increases succinate production from acetate (microaerobic)

Mutyala et al. (published July 2023) engineered P. putida KT2440 to overexpress gltA (IPTG-inducible plasmid), motivated by the view that citrate synthase is a bottleneck for acetate assimilation into the TCA cycle. (mutyala2023citratesynthaseoverexpression pages 3-4)

Key quantitative findings:

Under controlled pH, the gltA-overexpression strain (gltA-KT) produced 4.73 ± 0.63 mM succinate at pH 7.5, vs 0.99 ± 0.13 mM in WT (~4.7×). (mutyala2023citratesynthaseoverexpression pages 7-9, mutyala2023citratesynthaseoverexpression media 7beed0b4)
Resting (nitrogen-limited) cells produced 4.94 ± 0.04 mM succinate from 200 mM acetate. (mutyala2023citratesynthaseoverexpression pages 7-9)
Carbon recovery (acetate → products) was estimated at ~85.8%, with the carbon balance table indicating substantial carbon flow to biomass and CO2 relative to succinate (Table 3). (mutyala2023citratesynthaseoverexpression pages 7-9, mutyala2023citratesynthaseoverexpression media d07f77bb)

Mechanistic framing:

The authors explicitly state that acetate metabolism is initiated by gltA converting acetyl‑CoA to citrate, i.e., increasing entry flux into TCA to support downstream succinate accumulation under microaerobic conditions. (mutyala2023citratesynthaseoverexpression pages 1-3)

Real-world implementation angle: the study targets bioconversion of acetate (a common waste/byproduct stream) into succinate in a robust soil bacterium, under microaerobic process conditions. (mutyala2023citratesynthaseoverexpression pages 1-3)

4.2 2024: gltA deletion as a carbon-redirection strategy for PHA overproduction

Dong et al. (published Nov 2024) knocked out gltA (citrate synthase) to reduce competing TCA flux and redirect carbon to medium-chain-length PHA (mcl‑PHA) in P. putida. (dong2024modificationofglucose pages 1-2)

Key quantitative findings (batch glucose cultivation; 20 g/L glucose):

ΔgltA increased mcl‑PHA content to 32.6 wt% (vs 27.3 wt% in parent) and titer to 1.2 g/L (vs 1.0 g/L). (dong2024modificationofglucose pages 5-7)
Combinatorial knockouts amplified gains, with ΔhexR Δgcd ΔgltA reaching 49.1 wt% mcl‑PHA and 2.1 g/L titer. (dong2024modificationofglucose pages 5-7)

Real-world implementation angle: mcl-PHAs are biodegradable polymers with medical and industrial applications; the work explicitly uses pathway truncation/rewiring as a chassis-improvement strategy. (dong2024modificationofglucose pages 1-2, dong2024modificationofglucose pages 5-7)

4.3 2024: gltA perturbation in malonyl‑CoA engineering (qualitative in retrieved pages)

Favoino et al. (published Nov 2024) describe gltA deletion as a strategy to prevent acetyl‑CoA entry into the TCA cycle to increase precursor availability (acetyl‑CoA/malonyl‑CoA) for value-added products, including PHB via a non-canonical pathway. The retrieved pages provide qualitative outcomes (enhanced biopolymer accumulation; growth penalties) but do not give gltA-specific numeric titers in the captured excerpts. (favoino2024enhancedbiosynthesisof pages 2-4)

5) Applications and real-world implementations

5.1 Bioproduction from acetate (succinate)

Overexpressing citrate synthase (gltA) is used as a single-gene intervention to improve conversion of acetate carbon into succinate under microaerobic cultivation in KT2440, with measurable gains in succinate titers and clear dependence on induction (IPTG) and pH control. (mutyala2023citratesynthaseoverexpression pages 7-9, mutyala2023citratesynthaseoverexpression pages 9-10, mutyala2023citratesynthaseoverexpression media 7beed0b4)

5.2 Bioplastics and chassis optimization (PHAs)

Deleting citrate synthase is used to reduce TCA-cycle drain of acetyl‑CoA and increase polymer synthesis capacity; this is implemented in multi-gene strategies improving both PHA content (%CDW) and titer (g/L). (dong2024modificationofglucose pages 5-7)

6) Expert interpretation and analysis (from authoritative sources)

6.1 Why gltA is a high-leverage node

Across the engineering studies, gltA is treated as a flux-control point for acetyl‑CoA allocation:

For catabolic oxidation / energy: increasing gltA can raise acetyl‑CoA entry into TCA, supporting downstream succinate accumulation under oxygen limitation. (mutyala2023citratesynthaseoverexpression pages 1-3, mutyala2023citratesynthaseoverexpression pages 9-10)
For anabolic diversion: decreasing/removing gltA limits acetyl‑CoA oxidation and can favor acetyl‑CoA (and malonyl‑CoA) availability for product pathways (PHA/PHB). (favoino2024enhancedbiosynthesisof pages 2-4, dong2024modificationofglucose pages 5-7)

This “push/pull” around citrate synthase is consistent with its biochemical position as the TCA entry step.

6.2 Tradeoffs noted in the literature

The succinate study reports that gltA overexpression can incur growth penalties and acetate assimilation complexities (e.g., limited conversion of consumed acetate carbon to succinate, with substantial carbon ending in biomass/CO2), underscoring that single-enzyme overexpression may expose other bottlenecks (electron acceptor limitation, competing pathways, succinate reassimilation). (mutyala2023citratesynthaseoverexpression pages 9-10, mutyala2023citratesynthaseoverexpression media d07f77bb)

The malonyl‑CoA strategy study highlights reduced growth rate and longer lag phases in strains with deletions including gltA, indicating typical growth–production tradeoffs when restricting central energy metabolism. (favoino2024enhancedbiosynthesisof pages 2-4)

7) Key statistics and data (recent studies)

Succinate from acetate (KT2440; 2023):

4.73 ± 0.63 mM succinate (gltA overexpression, pH 7.5) vs 0.99 ± 0.13 mM (WT). (mutyala2023citratesynthaseoverexpression pages 7-9, mutyala2023citratesynthaseoverexpression media 7beed0b4)
Carbon recovery reported as ~85.8% with carbon distribution quantified among succinate, biomass, and CO2 (Table 3). (mutyala2023citratesynthaseoverexpression media d07f77bb)

mcl‑PHA from glucose (2024):

ΔgltA: 32.6 wt% and 1.2 g/L vs parent 27.3 wt% and 1.0 g/L. (dong2024modificationofglucose pages 5-7)
ΔhexR Δgcd ΔgltA: 49.1 wt% and 2.1 g/L. (dong2024modificationofglucose pages 5-7)

8) Summary of evidence for functional annotation (recommended Gene Ontology-style statements)

Molecular function: citrate synthase activity; catalyzes condensation of acetyl‑CoA and oxaloacetate to citrate. (dolan2022systemswidedissectionof pages 8-12, mutyala2023citratesynthaseoverexpression pages 1-3)
Biological process: tricarboxylic acid cycle; acetate assimilation into central metabolism; controls acetyl‑CoA entry into TCA and affects carbon partitioning between respiration and biosynthesis. (mutyala2023citratesynthaseoverexpression pages 1-3, mutyala2023citratesynthaseoverexpression pages 9-10, favoino2024enhancedbiosynthesisof pages 2-4)
Cellular component/localization: intracellular soluble fraction (inferred from soluble lysate fraction used for protein detection); no explicit cellular compartment assignment in retrieved text. (mutyala2023citratesynthaseoverexpression pages 3-4)

9) Evidence table (quick reference)

Aspect	Evidence/Findings (concise)	Organism/Strain	Quantitative data (if any)	Primary source (author year journal)	DOI/URL
Identity	gltA is explicitly identified as the gene encoding citrate synthase in Pseudomonas putida; in KT2440 studies it was the target for overexpression or deletion as a central-carbon enzyme (mutyala2023citratesynthaseoverexpression pages 1-3, mutyala2023citratesynthaseoverexpression pages 4-5, dong2024modificationofglucose pages 1-2)	P. putida KT2440; derived strains gltA-KT, QSRZ602/QSRZ603/QSRZ606/QSRZ607	—	Mutyala et al. 2023, ACS Omega; Dong et al. 2024, Current Issues in Molecular Biology	https://doi.org/10.1021/acsomega.3c02520 ; https://doi.org/10.3390/cimb46110761
Reaction	In pathway context, citrate synthase GltA initiates acetate metabolism by converting acetyl-CoA to citrate; related Pseudomonas biochemical work assayed GltA with acetyl-CoA + oxaloacetate and found no detectable 2-methylcitrate synthase activity (mutyala2023citratesynthaseoverexpression pages 1-3, dolan2022systemswidedissectionof pages 8-12)	P. putida KT2440; P. aeruginosa GltA (comparative evidence)	Substrates/products stated: acetyl-CoA → citrate in KT2440 pathway context; acetyl-CoA + OAA assayed in P. aeruginosa	Mutyala et al. 2023, ACS Omega; Dolan et al. 2022, mBio	https://doi.org/10.1021/acsomega.3c02520 ; https://doi.org/10.1128/mbio.02541-22
Pathway role	GltA sits at the entry of acetyl-CoA into the TCA cycle and is described as a bottleneck for acetate assimilation into the TCA cycle; deleting gltA is used to prevent acetyl-CoA from entering the TCA cycle and increase malonyl-CoA availability (mutyala2023citratesynthaseoverexpression pages 1-3, favoino2024enhancedbiosynthesisof pages 2-4)	P. putida KT2440 / SEM11-derived engineering strains	gltA overexpression alone gave 9.5% of maximum theoretical succinate yield from acetate (mutyala2023citratesynthaseoverexpression pages 1-3)	Mutyala et al. 2023, ACS Omega; Favoino et al. 2024, Microbial Biotechnology	https://doi.org/10.1021/acsomega.3c02520 ; https://doi.org/10.1111/1751-7915.70044
Localization	No explicit subcellular localization for KT2440 GltA was reported in the gathered evidence; available studies discuss it as a central metabolic enzyme without localization data (mutyala2023citratesynthaseoverexpression pages 1-3, mutyala2023citratesynthaseoverexpression pages 3-4, dong2024modificationofglucose pages 5-7)	P. putida KT2440	—	Mutyala et al. 2023, ACS Omega; Dong et al. 2024, Current Issues in Molecular Biology	https://doi.org/10.1021/acsomega.3c02520 ; https://doi.org/10.3390/cimb46110761
Essentiality	A KT2440 conditional-essentiality study used gltA as a highly expressed internal calibrator and stated that gltA expression is essential under all growth conditions for this strict aerobe; however, later engineering studies successfully constructed ΔgltA mutants that grew on glucose batch cultures, implying gltA is not absolutely essential under those tested conditions (expression-essentiality statement vs knockout viability under specific conditions) (molina‐henares2010identificationofconditionally pages 3-4, dong2024modificationofglucose pages 5-7)	P. putida KT2440; QSRZ602/QSRZ603 derivatives	gltA relative expression benchmark: 14,500 units (molina‐henares2010identificationofconditionally pages 3-4); ΔgltA single mutant had similar growth/glucose consumption to parent on 20 g/L glucose (dong2024modificationofglucose pages 5-7)	Molina-Henares et al. 2010, Environmental Microbiology; Dong et al. 2024, Current Issues in Molecular Biology	https://doi.org/10.1111/j.1462-2920.2010.02166.x ; https://doi.org/10.3390/cimb46110761
Engineering perturbation: overexpression for succinate	IPTG-inducible gltA overexpression (gltA-KT) increased succinate production from acetate under microaerobic conditions; pH control improved output further (mutyala2023citratesynthaseoverexpression pages 7-9, mutyala2023citratesynthaseoverexpression pages 9-10)	P. putida KT2440 gltA-KT	4.73 ± 0.63 mM succinate at pH 7.5 vs WT 0.99 ± 0.13 mM (~4.7×); 3.35 ± 0.27 mM at pH 8.0; 2.64 ± 0.11 mM from 100 mM acetate without pH control; ~50% higher succinate from acetate than glucose (4.73 ± 0.63 vs 2.3 ± 0.05 mM); resting cells 4.94 ± 0.04 mM; WT microaerobic baseline 1.24 ± 0.17 mM from 100 mM acetate (mutyala2023citratesynthaseoverexpression pages 7-9, mutyala2023citratesynthaseoverexpression pages 9-10, mutyala2023citratesynthaseoverexpression pages 4-5)	Mutyala et al. 2023, ACS Omega	https://doi.org/10.1021/acsomega.3c02520
Engineering perturbation: deletion for mcl-PHA	Deleting gltA redirected carbon from the TCA cycle to mcl-PHA synthesis; single and combinatorial mutants improved polymer accumulation (dong2024modificationofglucose pages 5-7)	P. putida QSRZ6 derivatives	ΔgltA (QSRZ602): 32.6 wt% mcl-PHA and 1.2 g/L vs parent 27.3 wt% and 1.0 g/L; ΔgcdΔgltA (QSRZ603): 37.6 wt%, 1.3 g/L; ΔhexRΔgltA (QSRZ606): 39.5 wt%, 1.4 g/L; ΔhexRΔgcdΔgltA (QSRZ607): 49.1 wt%, 2.1 g/L (dong2024modificationofglucose pages 5-7)	Dong et al. 2024, Current Issues in Molecular Biology	https://doi.org/10.3390/cimb46110761
Engineering perturbation: deletion/CRISPRi for malonyl-CoA/PHB	gltA deletion or repression was used as a design strategy to prevent acetyl-CoA entry into the TCA cycle and increase malonyl-CoA availability for PHB/PHA pathways; pages retrieved reported qualitative benefit but not a gltA-specific numeric titer (favoino2024enhancedbiosynthesisof pages 2-4)	P. putida SEM11-derived engineered strains	Qualitative: increased malonyl-CoA/biopolymer accumulation, but reduced μmax and longer lag phases; no gltA-specific numeric titer in retrieved pages (favoino2024enhancedbiosynthesisof pages 2-4)	Favoino et al. 2024, Microbial Biotechnology	https://doi.org/10.1111/1751-7915.70044
Comparative structural/biochemical evidence	In related Pseudomonas, GltA is a type II-like bacterial citrate synthase with canonical catalytic triad and likely NADH regulation; forms a hexameric trimer of dimers and lacks detectable 2-methylcitrate synthase activity (useful for family-level inference, not direct KT2440 proof) (dolan2022systemswidedissectionof pages 8-12)	P. aeruginosa GltA (comparative family evidence)	429 aa; hexameric trimer of dimers; catalytic triad His-265/His-306/Asp-363 (dolan2022systemswidedissectionof pages 8-12)	Dolan et al. 2022, mBio	https://doi.org/10.1128/mbio.02541-22
Broader physiological significance outside KT2440	In Pseudomonas fluorescens 2P24, gltA mutation reduced 2,4-DAPG biosynthesis and biocontrol capacity, supporting a broader role for citrate synthase-derived citrate in regulatory physiology across pseudomonads (comparative evidence) (yang2023citratesynthaseglta pages 6-8)	P. fluorescens 2P24	946 DEGs; disease index 84.9% in gltA mutant vs 45.7% WT; plant survival 15.1% vs 54.3% WT (yang2023citratesynthaseglta pages 6-8)	Yang et al. 2023, Journal of Agricultural and Food Chemistry	https://doi.org/10.1021/acs.jafc.3c03051

Table: This table summarizes core functional annotation facts for Pseudomonas putida KT2440 gltA/Q88FA4 using only the gathered evidence. It highlights identity, catalytic role, pathway placement, unresolved localization, nuanced essentiality evidence, and quantitative outcomes from recent metabolic engineering studies.

References (URLs / publication dates)

Mutyala S. et al. Citrate Synthase Overexpression of Pseudomonas putida Increases Succinate Production from Acetate in Microaerobic Cultivation. ACS Omega (Published July 2023). https://doi.org/10.1021/acsomega.3c02520 (mutyala2023citratesynthaseoverexpression pages 1-3)
Dong Y. et al. Modification of Glucose Metabolic Pathway to Enhance Polyhydroxyalkanoate Synthesis in Pseudomonas putida. Current Issues in Molecular Biology (Published Nov 2024). https://doi.org/10.3390/cimb46110761 (dong2024modificationofglucose pages 1-2)
Favoino G. et al. Enhanced biosynthesis of poly(3-hydroxybutyrate) in engineered strains of Pseudomonas putida via increased malonyl-CoA availability. Microbial Biotechnology (Published Nov 2024). https://doi.org/10.1111/1751-7915.70044 (favoino2024enhancedbiosynthesisof pages 2-4)
Molina-Henares M.A. et al. Identification of conditionally essential genes for growth of Pseudomonas putida KT2440 on minimal medium… Environmental Microbiology (Published June 2010). https://doi.org/10.1111/j.1462-2920.2010.02166.x (molina‐henares2010identificationofconditionally pages 3-4)
Dolan S.K. et al. Systems-wide dissection of organic acid assimilation in Pseudomonas aeruginosa… mBio (Published Dec 2022). https://doi.org/10.1128/mbio.02541-22 (dolan2022systemswidedissectionof pages 8-12)

References

(mutyala2023citratesynthaseoverexpression pages 1-3): Sakuntala Mutyala, Shuwei Li, Himanshu Khandelwal, Da Seul Kong, and Jung Rae Kim. Citrate synthase overexpression of pseudomonas putida increases succinate production from acetate in microaerobic cultivation. ACS Omega, 8:26231-26242, Jul 2023. URL: https://doi.org/10.1021/acsomega.3c02520, doi:10.1021/acsomega.3c02520. This article has 13 citations and is from a peer-reviewed journal.
(dong2024modificationofglucose pages 1-2): Yue Dong, Keyao Zhai, Yatao Li, Zhen Lv, Mengyao Zhao, Tian Gan, and Yuchao Ma. Modification of glucose metabolic pathway to enhance polyhydroxyalkanoate synthesis in pseudomonas putida. Current Issues in Molecular Biology, 46:12784-12799, Nov 2024. URL: https://doi.org/10.3390/cimb46110761, doi:10.3390/cimb46110761. This article has 4 citations.
(molina‐henares2010identificationofconditionally pages 3-4): M. Antonia Molina‐Henares, Jesús De La Torre, Adela García‐Salamanca, A. Jesús Molina‐Henares, M. Carmen Herrera, Juan L. Ramos, and Estrella Duque. Identification of conditionally essential genes for growth of pseudomonas putida kt2440 on minimal medium through the screening of a genome‐wide mutant library. Environmental Microbiology, 12:1468-1485, Jun 2010. URL: https://doi.org/10.1111/j.1462-2920.2010.02166.x, doi:10.1111/j.1462-2920.2010.02166.x. This article has 89 citations and is from a domain leading peer-reviewed journal.
(dolan2022systemswidedissectionof pages 8-12): Stephen K. Dolan, Andre Wijaya, Michael Kohlstedt, Lars Gläser, Paul Brear, Rafael Silva-Rocha, Christoph Wittmann, and Martin Welch. Systems-wide dissection of organic acid assimilation in pseudomonas aeruginosa reveals a novel path to underground metabolism. Dec 2022. URL: https://doi.org/10.1128/mbio.02541-22, doi:10.1128/mbio.02541-22. This article has 18 citations and is from a domain leading peer-reviewed journal.
(favoino2024enhancedbiosynthesisof pages 2-4): Giusi Favoino, Nicolas Krink, Tobias Schwanemann, Nick Wierckx, and Pablo I. Nikel. Enhanced biosynthesis of poly(3‐hydroxybutyrate) in engineered strains of pseudomonas putida via increased malonyl‐coa availability. Microbial Biotechnology, Nov 2024. URL: https://doi.org/10.1111/1751-7915.70044, doi:10.1111/1751-7915.70044. This article has 11 citations and is from a peer-reviewed journal.
(mutyala2023citratesynthaseoverexpression pages 3-4): Sakuntala Mutyala, Shuwei Li, Himanshu Khandelwal, Da Seul Kong, and Jung Rae Kim. Citrate synthase overexpression of pseudomonas putida increases succinate production from acetate in microaerobic cultivation. ACS Omega, 8:26231-26242, Jul 2023. URL: https://doi.org/10.1021/acsomega.3c02520, doi:10.1021/acsomega.3c02520. This article has 13 citations and is from a peer-reviewed journal.
(dong2024modificationofglucose pages 5-7): Yue Dong, Keyao Zhai, Yatao Li, Zhen Lv, Mengyao Zhao, Tian Gan, and Yuchao Ma. Modification of glucose metabolic pathway to enhance polyhydroxyalkanoate synthesis in pseudomonas putida. Current Issues in Molecular Biology, 46:12784-12799, Nov 2024. URL: https://doi.org/10.3390/cimb46110761, doi:10.3390/cimb46110761. This article has 4 citations.
(mutyala2023citratesynthaseoverexpression pages 7-9): Sakuntala Mutyala, Shuwei Li, Himanshu Khandelwal, Da Seul Kong, and Jung Rae Kim. Citrate synthase overexpression of pseudomonas putida increases succinate production from acetate in microaerobic cultivation. ACS Omega, 8:26231-26242, Jul 2023. URL: https://doi.org/10.1021/acsomega.3c02520, doi:10.1021/acsomega.3c02520. This article has 13 citations and is from a peer-reviewed journal.
(mutyala2023citratesynthaseoverexpression media 7beed0b4): Sakuntala Mutyala, Shuwei Li, Himanshu Khandelwal, Da Seul Kong, and Jung Rae Kim. Citrate synthase overexpression of pseudomonas putida increases succinate production from acetate in microaerobic cultivation. ACS Omega, 8:26231-26242, Jul 2023. URL: https://doi.org/10.1021/acsomega.3c02520, doi:10.1021/acsomega.3c02520. This article has 13 citations and is from a peer-reviewed journal.
(mutyala2023citratesynthaseoverexpression media d07f77bb): Sakuntala Mutyala, Shuwei Li, Himanshu Khandelwal, Da Seul Kong, and Jung Rae Kim. Citrate synthase overexpression of pseudomonas putida increases succinate production from acetate in microaerobic cultivation. ACS Omega, 8:26231-26242, Jul 2023. URL: https://doi.org/10.1021/acsomega.3c02520, doi:10.1021/acsomega.3c02520. This article has 13 citations and is from a peer-reviewed journal.
(mutyala2023citratesynthaseoverexpression pages 9-10): Sakuntala Mutyala, Shuwei Li, Himanshu Khandelwal, Da Seul Kong, and Jung Rae Kim. Citrate synthase overexpression of pseudomonas putida increases succinate production from acetate in microaerobic cultivation. ACS Omega, 8:26231-26242, Jul 2023. URL: https://doi.org/10.1021/acsomega.3c02520, doi:10.1021/acsomega.3c02520. This article has 13 citations and is from a peer-reviewed journal.
(mutyala2023citratesynthaseoverexpression pages 4-5): Sakuntala Mutyala, Shuwei Li, Himanshu Khandelwal, Da Seul Kong, and Jung Rae Kim. Citrate synthase overexpression of pseudomonas putida increases succinate production from acetate in microaerobic cultivation. ACS Omega, 8:26231-26242, Jul 2023. URL: https://doi.org/10.1021/acsomega.3c02520, doi:10.1021/acsomega.3c02520. This article has 13 citations and is from a peer-reviewed journal.
(yang2023citratesynthaseglta pages 6-8): Qingqing Yang, Qing Yan, Bo Zhang, Li-qun Zhang, and Xiaogang Wu. Citrate synthase glta modulates the 2,4-diacetylphloroglucinol biosynthesis of pseudomonas fluorescens 2p24 and is essential for the biocontrol capacity. Journal of Agricultural and Food Chemistry, 71:11892-11901, Jul 2023. URL: https://doi.org/10.1021/acs.jafc.3c03051, doi:10.1021/acs.jafc.3c03051. This article has 8 citations and is from a highest quality peer-reviewed journal.

Artifacts

Edison artifact artifact-00

Citations

dolan2022systemswidedissectionof pages 8-12
mutyala2023citratesynthaseoverexpression pages 1-3
favoino2024enhancedbiosynthesisof pages 2-4
mutyala2023citratesynthaseoverexpression pages 3-4
dong2024modificationofglucose pages 5-7
mutyala2023citratesynthaseoverexpression pages 7-9
dong2024modificationofglucose pages 1-2
yang2023citratesynthaseglta pages 6-8
mutyala2023citratesynthaseoverexpression pages 9-10
mutyala2023citratesynthaseoverexpression pages 4-5
https://doi.org/10.1021/acsomega.3c02520
https://doi.org/10.3390/cimb46110761
https://doi.org/10.1128/mbio.02541-22
https://doi.org/10.1111/1751-7915.70044
https://doi.org/10.1111/j.1462-2920.2010.02166.x
https://doi.org/10.1021/acs.jafc.3c03051
https://doi.org/10.1021/acsomega.3c02520,
https://doi.org/10.3390/cimb46110761,
https://doi.org/10.1111/j.1462-2920.2010.02166.x,
https://doi.org/10.1128/mbio.02541-22,
https://doi.org/10.1111/1751-7915.70044,
https://doi.org/10.1021/acs.jafc.3c03051,

📄 View Raw YAML

id: Q88FA4
gene_symbol: gltA
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:160488
  label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
description: >-
  gltA (PP_4194) encodes citrate synthase (EC 2.3.3.16), the enzyme that
  catalyzes the committed, first step of the tricarboxylic acid (TCA) cycle. It
  catalyzes the Claisen-type condensation of acetyl-CoA and oxaloacetate with
  hydrolysis of the resulting citryl-CoA thioester to yield citrate and free
  CoA. The protein is a 429-residue type I (large, bacterial) citrate synthase
  of the citrate synthase family (PIRSF001369; TIGR01798 cit_synth_I), typically
  assembling as a homohexamer (trimer of dimers), with the canonical His/His/Asp
  catalytic machinery (active-site residues His306 and Asp364 in this sequence).
  It is a soluble cytoplasmic enzyme. By channeling acetyl-CoA into the TCA
  cycle, GltA sits at a central node of carbon and energy metabolism, governing
  the entry of acetyl-CoA (derived from glycolysis, fatty acid oxidation, or
  acetate assimilation) into oxidative metabolism and balancing respiratory
  energy generation against the use of acetyl-CoA for biosynthesis. In
  P. putida it is central to aerobic central metabolism and acetate
  assimilation.
existing_annotations:
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: located_in
  review:
    summary: >-
      Citrate synthase is a soluble cytoplasmic enzyme; this localization is
      consistent with the enzyme class and with experimental detection of GltA
      in the soluble cell lysate fraction of P. putida KT2440.
    action: ACCEPT
    reason: >-
      Bacterial citrate synthases are soluble cytosolic enzymes with no membrane
      anchor or signal peptide; the IEA assignment is correct and informative.
- term:
    id: GO:0006099
    label: tricarboxylic acid cycle
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    summary: >-
      Citrate synthase catalyzes the entry/committed step of the TCA cycle
      (condensation of acetyl-CoA and oxaloacetate to citrate). This is the
      canonical biological process for the gene and is strongly supported by
      family membership and the UniPathway TCA assignment (UPA00223; isocitrate
      from oxaloacetate, step 1/2).
    action: ACCEPT
    reason: >-
      Core biological process of the gene; directly supported by enzyme function
      and pathway assignment.
- term:
    id: GO:0036440
    label: citrate synthase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      This is the precise molecular function of the gene product. The UniProt
      catalytic activity (RHEA:16845, EC 2.3.3.16; oxaloacetate + acetyl-CoA +
      H2O = citrate + CoA + H+), the conserved catalytic triad, and the citrate
      synthase family assignment all support citrate synthase activity as the
      core molecular function.
    action: ACCEPT
    reason: >-
      Represents the core molecular function of gltA; well supported by
      sequence, family, and pathway evidence.
- term:
    id: GO:0046912
    label: acyltransferase activity, acyl groups converted into alkyl on transfer
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      This is a broad parent class of citrate synthase activity (citrate
      synthase transfers an acetyl group with conversion to a carboxymethyl
      group). While not incorrect, it is far less informative than GO:0036440
      citrate synthase activity, which is already annotated and captures the
      precise reaction.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Redundant, less-specific ancestor of the already-annotated specific
      function GO:0036440; provides no additional information about gltA
      function.
core_functions:
- description: >-
    Citrate synthase catalyzing the committed first step of the TCA cycle,
    condensing acetyl-CoA and oxaloacetate to form citrate and CoA
  supported_by:
  - reference_id: GO_REF:0000120
    supporting_text: >-
      UniProt catalytic activity RHEA:16845 / EC 2.3.3.16 (oxaloacetate +
      acetyl-CoA + H2O = citrate + CoA + H+); citrate synthase family
      assignment.
  molecular_function:
    id: GO:0036440
    label: citrate synthase activity
  directly_involved_in:
  - id: GO:0006099
    label: tricarboxylic acid cycle
  locations:
  - id: GO:0005737
    label: cytoplasm
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:12534463
  title: Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: KT2440 genome reference (Nelson et al. 2002, Environ Microbiol) establishing the locus/gene assignment.

gltA

Gene Description

Existing Annotations Review

Core Functions

Citrate synthase catalyzing the committed first step of the TCA cycle, condensing acetyl-CoA and oxaloacetate to form citrate and CoA

References

Deep Research

Falcon

Research report: gltA (UniProt Q88FA4) in Pseudomonas putida KT2440 (PSEPK)

0) Target verification (mandatory disambiguation)

Verified identity

Notes on PP_4194 mapping

1) Key concepts and current understanding

1.1 Definition and primary biochemical function

1.2 Enzyme family/structure and regulatory features (best-available evidence)

1.3 Pathway placement and cellular role

2) Subcellular localization (where the protein functions)

3) Essentiality and fitness impact in P. putida KT2440

3.1 Evidence suggesting broad essentiality of expression

3.2 Evidence that ΔgltA can be viable under some engineered conditions

3.3 Interpretation

4) Recent developments (prioritized 2023–2024)

4.1 2023: gltA overexpression increases succinate production from acetate (microaerobic)

4.2 2024: gltA deletion as a carbon-redirection strategy for PHA overproduction

4.3 2024: gltA perturbation in malonyl‑CoA engineering (qualitative in retrieved pages)

5) Applications and real-world implementations

5.1 Bioproduction from acetate (succinate)

5.2 Bioplastics and chassis optimization (PHAs)

6) Expert interpretation and analysis (from authoritative sources)

6.1 Why gltA is a high-leverage node

6.2 Tradeoffs noted in the literature

7) Key statistics and data (recent studies)

8) Summary of evidence for functional annotation (recommended Gene Ontology-style statements)

9) Evidence table (quick reference)

References (URLs / publication dates)

Artifacts

Citations

📄 View Raw YAML