pta

UniProt ID: Q88PS4
Organism: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
Review Status: DRAFT
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Gene Description

Phosphate acetyltransferase (phosphotransacetylase; Pta, EC 2.3.1.8) is a cytoplasmic enzyme of central carbon metabolism that catalyzes the reversible transfer of an acetyl group between coenzyme A and inorganic phosphate (acetyl-CoA + phosphate = acetyl phosphate + CoA). Together with acetate kinase (AckA), Pta constitutes the AckA-Pta pathway that interconverts acetyl-CoA, the energy-rich intermediate acetyl phosphate, and acetate, sitting at the acetate node linking glycolysis/pyruvate dehydrogenase-derived acetyl-CoA to acetate overflow metabolism, energy conservation via substrate-level phosphorylation, and acetyl phosphate signaling. In Pseudomonas putida KT2440 the enzyme is encoded by pta (locus PP_0774); phosphotransacetylase activity is measurable in cell-free extracts and is abolished by disruption of pta, and acetyl phosphate generated by Pta can feed heterologous AckA to produce acetate and ATP. The KT2440 protein is unusually large (695 aa) and bipartite, with an N-terminal CobB/CobQ-like region (P-loop NTPase / DRTGG) preceding the C-terminal phosphate acetyltransferase catalytic domain that carries the substrate-binding site; the enzyme is predicted to assemble into a homohexamer.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005737 cytoplasm
IEA
GO_REF:0000044 		ACCEPT
Summary: Cytoplasmic localization for a soluble central-metabolism enzyme acting on acetyl-CoA, acetyl phosphate, and inorganic phosphate.
Reason: Consistent with the UniProt subcellular location (Cytoplasm) and with enzyme activity being routinely assayed in soluble cell-free extracts. Pta has no membrane-targeting or signal/transit features; cytoplasmic localization is appropriate.
GO:0008959 phosphate acetyltransferase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: Precise molecular function term matching EC 2.3.1.8 and RHEA:19521 (acetyl-CoA + phosphate = acetyl phosphate + CoA); this is the core catalytic activity of Pta.
Reason: This is the exact, well-supported molecular function of the gene product. Although the GOA evidence is IEA, the assignment is anchored to InterPro:IPR016475 (proteobacterial phosphate acetyltransferase signature), EC 2.3.1.8, and RHEA:19521, and is independently confirmed in P. putida KT2440 where phosphotransacetylase activity is detected in cell-free extracts and lost upon pta disruption. Core function.
GO:0016407 acetyltransferase activity
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: General parent of the precise phosphate acetyltransferase activity already annotated.
Reason: GO:0016407 is a broad ancestor of GO:0008959 (phosphate acetyltransferase activity), which is already annotated with a specific evidence trail. The general term adds no information beyond the precise term and is an InterPro2GO over-generalization.
GO:0016746 acyltransferase activity
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: Very general acyltransferase parent of the precise phosphate acetyltransferase activity.
Reason: GO:0016746 (transferring acyl groups) is an even broader ancestor of GO:0008959. It is redundant with, and far less informative than, the specific phosphate acetyltransferase activity term. Over-annotation from InterPro2GO mapping.
GO:0006085 acetyl-CoA biosynthetic process
IEA
GO_REF:0000041 		ACCEPT
Summary: Pathway-level process annotation reflecting the UniPathway mapping for acetyl-CoA biosynthesis from acetate (acetyl-CoA from acetate, step 2/2).
Reason: Pta catalyzes the second step of the acetyl-CoA-from-acetate route (AckA forms acetyl phosphate from acetate; Pta converts acetyl phosphate to acetyl-CoA), consistent with the UniPathway UPA00340/UER00459 mapping in the UniProt record. The reaction is reversible, so in overflow metabolism Pta also runs in the acetyl-CoA-consuming direction toward acetate; the biosynthetic-process term captures one valid physiological direction and is supported by the pathway annotation. Reasonable, retain.

Core Functions

Catalyzes the reversible transfer of an acetyl group between coenzyme A and inorganic phosphate (acetyl-CoA + phosphate = acetyl phosphate + CoA), the Pta half of the AckA-Pta acetate pathway.

Molecular Function:
phosphate acetyltransferase activity
Supporting Evidence:
  • file:PSEPK/pta/pta-deep-research-falcon.md
    Phosphotransacetylase (Pta) catalyzes the reversible transfer of an acetyl group between CoA and inorganic phosphate (acetyl-CoA + Pi = acetyl-phosphate + CoA); in P. putida KT2440 Pta activity is detected in cell-free extracts and abolished in a pta::mini-Tn5 mutant.

Interconverts acetyl-CoA, acetyl phosphate, and (with acetate kinase) acetate at the acetate node of central carbon metabolism, contributing to acetyl-CoA biosynthesis from acetate and to acetate overflow/energy metabolism.

Molecular Function:
phosphate acetyltransferase activity
Directly Involved In:
acetyl-CoA biosynthetic process
Supporting Evidence:
  • file:PSEPK/pta/pta-deep-research-falcon.md
    Acetyl-phosphate generated by native Pta can feed heterologous AckA to produce acetate and ATP by substrate-level phosphorylation; ackA/pta is depicted as an acetate-to-acetyl-CoA assimilation route in KT2440.

References

GO_REF:0000002
Gene Ontology annotation through association of InterPro records with GO terms
GO_REF:0000041
Gene Ontology annotation based on UniPathway vocabulary mapping
GO_REF:0000044
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
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
file:PSEPK/pta/pta-deep-research-falcon.md
Deep research report on P. putida KT2440 pta (Q88PS4 / PP_0774)

Deep Research

Falcon

(pta-deep-research-falcon.md)
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 22 citations 3 artifacts 2026-06-11T22:08:18.459362
Edison artifact artifact-00 (text/markdown)
## Context ID: pqac-00000010 Figure 1 from the document provides a schematic diagram of the metabolic pathway for succinate production from acetate in *Pseudomo (image/png)
## Context ID: pqac-00000011 In accordance with your request, I have provided crops of Figure 1 and Figure 2 from page 3. Figure 1 shows the metabolism of *P. p (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: Functional annotation of pta (UniProt Q88PS4; locus PP_0774) in Pseudomonas putida KT2440

Scope and identity verification (critical disambiguation)

The target protein is phosphate acetyltransferase / phosphotransacetylase (Pta, EC 2.3.1.8) encoded by pta with ordered locus name PP_0774 in Pseudomonas putida strain KT2440. This identity is directly supported by a KT2440 study that maps the pta locus as PP0774 and experimentally measures phosphotransacetylase activity that is abolished by a pta::mini-Tn5 disruption, confirming that PP_0774 encodes the functional Pta enzyme in this organism (nikel2013engineeringananaerobic pages 6-7, nikel2013engineeringananaerobic pages 7-8). Recent KT2440 metabolic-engineering papers also use the same gene symbol pta to denote phosphotransacetylase in acetate/acetyl-phosphate/acetyl-CoA interconversion (mutyala2023citratesynthaseoverexpression pages 1-3, bruinsma2023increasingcellularfitness pages 2-5).

1) Key concepts and current understanding

1.1 Enzyme definition and reaction

Phosphotransacetylase (Pta) catalyzes the reversible transfer of an acetyl group between CoA and inorganic phosphate:

  • Acetyl-CoA + Pi ⇄ acetyl-phosphate (AcP) + CoA

In P. putida KT2440, Pta is experimentally described as catalyzing phosphorylation of acetyl-CoA (generated by the native pyruvate dehydrogenase complex) to yield acetyl-phosphate and free CoA (nikel2013engineeringananaerobic pages 6-7). In broader bacterial acetate metabolism, the AckA–Pta pair is widely treated as a reversible two-step route connecting acetate and acetyl-CoA via acetyl-phosphate, contrasting with the Acs route (acetyl-CoA synthetase), which is typically considered irreversible and more ATP-expensive (kutscha2020microbialupgradingof pages 3-6).

1.2 Pathway context in central metabolism

Pta sits at a key junction (“acetate node”) connecting:

  • Acetyl-CoA (central carbon precursor feeding TCA cycle, glyoxylate shunt, biosynthesis)
  • Acetyl-phosphate (energy-rich intermediate; also implicated in global regulation and non-enzymatic lysine acetylation in many bacteria)
  • Acetate (overflow/fermentation end product in many organisms; also a C2 carbon source)

A 2023 P. putida study on acetate-to-succinate bioconversion depicts acetate assimilation to acetyl-CoA through both ackA/pta and acs, placing pta explicitly as a component of acetate assimilation into central metabolism (mutyala2023citratesynthaseoverexpression media afd2fae1).

1.3 Cellular localization

No retrieved P. putida KT2440 study directly measured Pta subcellular localization. However, the enzyme’s role as a soluble central-metabolism catalyst acting on acetyl-CoA, acetyl-phosphate, and Pi implies a cytosolic localization; this inference is consistent with the experimental use of cell-free extracts for Pta activity quantification in KT2440 (nikel2013engineeringananaerobic pages 6-7).

2) Experimental evidence in P. putida KT2440 (most authoritative for functional annotation)

2.1 Direct enzymatic activity and gene-dependence (loss-of-function)

Nikel & de Lorenzo (2013) quantified specific Pta activity in cell-free extracts of P. putida KT2440 grown aerobically on glucose minimal medium, and found that:

  • Pta activity increased 2.2-fold at the transition from log phase to stationary phase.
  • A pta::mini-Tn5 mutant showed no significant detectable Pta activity, indicating activity depends on an intact pta gene.
  • Pta activity in P. putida was lower than in E. coli BW25113 under similar conditions; E. coli peaked at 12.5 ± 0.9 U mg protein⁻¹ at onset of stationary phase (nikel2013engineeringananaerobic pages 6-7).

This provides strong organism-specific evidence that PP_0774 encodes an active phosphotransacetylase.

2.2 Functional coupling to acetate kinase via acetyl-phosphate (pathway complementation)

In the same KT2440 work, the authors introduced ackA from E. coli to test whether acetyl-phosphate generated by native Pta can fuel acetate kinase to generate ATP by substrate-level phosphorylation under anoxic incubation. Key data:

  • Upon inducing heterologous AckA, acetate kinase activity reached 17.8 ± 1.3 U mg protein⁻¹ (nikel2013engineeringananaerobic pages 7-8).
  • The strain secreted up to 12.9 ± 0.6 mM acetate, while control supernatants remained < 1 mM (nikel2013engineeringananaerobic pages 7-8).
  • Expressing ackA in a pta::mini-Tn5 background eliminated the acetate-secretion phenotype (reverted to control-like), confirming acetate production depended on acetyl-phosphate derived from the native Pta reaction (nikel2013engineeringananaerobic pages 7-8).

These results functionally validate the acetyl-CoA → acetyl-phosphate direction of the Pta reaction in KT2440 under the tested conditions and establish that the acetyl-phosphate pool can be tapped for energy generation if an AckA step is present.

2.3 Energetic consequences under anoxic incubation (physiology)

Under 24 h anoxic incubation:

  • ATP/ADP ratio in the AckA-expressing strain was 6.2 ± 0.8, a 1.3-fold increase vs. vector control (nikel2013engineeringananaerobic pages 7-8).
  • Adenylate energy charge (AEC) decreased to 0.28 ± 0.04 in control but remained ~0.62–0.69 in the AckA-expressing strain, consistent with improved cellular energy state (nikel2013engineeringananaerobic pages 7-8).

Although this is not a direct pta knockout phenotype under all conditions, it is strong pathway-level evidence for Pta’s ability to supply acetyl-phosphate in KT2440.

3) Recent developments and latest research (prioritizing 2023–2024)

3.1 2023: Carbon-conserving phosphoketolase shunt that relies on Pta

Bruinsma et al. (published Jan 2023) engineered P. putida KT2440 to express a phosphoketolase (Xfpk) that produces acetyl-phosphate from sugar phosphates. The study explicitly states that acetyl-phosphate is converted by Pta to acetyl-CoA in this engineered route (bruinsma2023increasingcellularfitness pages 2-5). Quantitative highlights:

  • In cell-free extract assays, Xfpk variants produced 1.26 and 1.19 mM AcP/OD600 (control 0.80 mM), while the selected B. breve Xfpk produced 36.25 mM AcP/OD600 (~30-fold higher) (bruinsma2023increasingcellularfitness pages 2-5).
  • On glycerol, Xfpk increased specific growth rate 0.12 → 0.18 h⁻¹ (+44.3%) and max OD600 4.4 → 6.6 (+50%) (bruinsma2023increasingcellularfitness pages 2-5).
  • Acetyl-CoA-derived product yields increased: flaviolin reporter yield +38.5% and mevalonate yield 0.011 → 0.015 mol/mol (+25.9%) (bruinsma2023increasingcellularfitness pages 2-5).
  • On engineered xylose metabolism, growth rate increased 0.02 → 0.05 h⁻¹ (+167%) and final OD600 increased 5.73 → 7.4 (+30.2%) (bruinsma2023increasingcellularfitness pages 5-6).

Interpretation: while this work does not directly perturb pta, it provides modern applied evidence that Pta-mediated conversion of acetyl-phosphate to acetyl-CoA is an enabling step for carbon-conserving acetyl-CoA supply in P. putida bioproduction (bruinsma2023increasingcellularfitness pages 2-5).

3.2 2023: Acetate-to-succinate conversion pathway explicitly includes ackA/pta

Mutyala et al. (received Apr 13 2023; published Jul 17 2023) studied succinate production from acetate under microaerobic conditions and presents a pathway schematic in which acetate is assimilated to acetyl-CoA via ackA/pta and acs, then routed through central metabolism toward succinate (mutyala2023citratesynthaseoverexpression media afd2fae1). Key quantitative results:

  • gltA overexpression showed ~50% improvement in succinate production.
  • At pH 7.5, succinate accumulated to 4.73 ± 0.6 mM in 36 h, reported as ~400% higher than wild type.
  • Overall yield was 9.5% of maximum theoretical yield on acetate minimal medium (mutyala2023citratesynthaseoverexpression pages 1-3).

Interpretation: this provides recent, application-oriented evidence that the pta node is considered part of acetate assimilation architecture in KT2440, relevant to bio-based production from C2 feedstocks (mutyala2023citratesynthaseoverexpression media afd2fae1).

3.3 2024: Systems metabolic engineering context (electrogenic anaerobic P. putida)

A 2024 dissertation on electrogenic anaerobic P. putida emphasizes that KT2440 is strictly aerobic and discusses constraints in anaerobic energy conservation, citing that P. putida lacks parts of classical acetate fermentation energy generation (AckA-Pta ATP-generating step) (weimer2024systemsmetabolicengineering pages 1-8). While this source did not yield extractable pta-specific quantitative outcomes in the retrieved sections, it situates Pta in broader discussions of P. putida energy metabolism engineering (weimer2024systemsmetabolicengineering pages 1-8).

4) Regulation and systems-level roles (expert synthesis from authoritative sources)

4.1 Growth-phase dependence and possible acetyl-CoA overflow control

In KT2440, Pta activity was growth-phase dependent (2.2-fold increase into stationary phase), consistent with a role in responding to changing acetyl-CoA availability during transitions in metabolic state (nikel2013engineeringananaerobic pages 6-7). This is compatible with the idea (demonstrated extensively in other bacteria) that the acetate/acetyl-phosphate node contributes to balancing carbon flux and CoA availability.

4.2 Regulatory context in Pseudomonas spp. (review-level)

A 2023 mini-review summarizing bacterial acetate metabolism reports that in some bacteria including Pseudomonas spp., ackA-pta expression under anaerobic/fermentative growth has been linked to the global anaerobic regulator Anr (Fnr homolog) and integration host factor subunit alpha (IhfA/LhfA) (hosmer2023bacterialacetatemetabolism pages 3-5). The same review notes additional acetate-node regulation (e.g., CrbS/R for acetate consumption via ACS) and emphasizes that acetate metabolism can cause intracellular acidification/respiratory inhibition and influence protein acetylation through acetyl-CoA and acetyl-phosphate pools (hosmer2023bacterialacetatemetabolism pages 3-5).

Because this is not KT2440-specific experimentation, these points should be treated as likely regulatory hypotheses rather than confirmed KT2440 regulatory facts.

5) Structure/function evidence supporting conserved Pta enzymology

A 2023 structure-function study of a bacterial Pta (TP0094 from Treponema pallidum) reports strong conservation of substrate-contacting residues and identifies likely catalytic residues (S314, R315, D321 in TP0094 numbering), and shows the enzyme is predominantly dimeric in solution (brautigam2023biophysicalandbiochemical pages 9-11). While not from P. putida, this supports the broader interpretation that Pta proteins are conserved enzymes with a stable oligomeric state and conserved active-site chemistry (brautigam2023biophysicalandbiochemical pages 9-11).

6) Current applications and real-world implementations

  1. Industrial biotechnology / cell-factory engineering: The 2023 phosphoketolase shunt work uses Pta as a key step to convert acetyl-phosphate to acetyl-CoA to improve yields of acetyl-CoA-derived products (mevalonate, malonyl-CoA-derived pigment) and growth on glycerol/xylose—feedstocks relevant to industrial fermentation (bruinsma2023increasingcellularfitness pages 2-5, bruinsma2023increasingcellularfitness pages 5-6).
  2. C2 feedstock upgrading: The acetate-to-succinate work positions acetate as an industrially relevant feedstock and directly includes ackA/pta among assimilation routes to acetyl-CoA in KT2440 (mutyala2023citratesynthaseoverexpression pages 1-3, mutyala2023citratesynthaseoverexpression media afd2fae1).
  3. Biopolymer precursor routing (mcl-PHA): A consortium/metabolic engineering study reports strengthening acetate assimilation in KT2440 by overexpressing acs and constructing an ackA-pta pathway; it cites an engineered P. putida producing 0.674 g/L mcl-PHA from acetate, suggesting practical use of the acetate node for product formation (qin2022reconstructionandoptimization pages 2-4).

7) Key statistics/data points (recent and organism-specific)

  • Pta activity in KT2440: growth-phase dependent; 2.2-fold increase from log to stationary; abolished in pta::mini-Tn5 (nikel2013engineeringananaerobic pages 6-7).
  • Acetyl-phosphate-driven acetate secretion when AckA is introduced: 12.9 ± 0.6 mM acetate secreted; AckA activity 17.8 ± 1.3 U mg protein⁻¹; requires intact pta (nikel2013engineeringananaerobic pages 7-8).
  • Engineered shunt AcP production: up to 36.25 mM AcP/OD600 in cell-free extracts (bruinsma2023increasingcellularfitness pages 2-5).
  • Growth and yield improvements in 2023 P. putida engineering (Xfpk shunt): growth rate up to +167% on xylose; mevalonate yield +25.9% on glycerol; mevalonate yield +48.7% on xylose (bruinsma2023increasingcellularfitness pages 2-5, bruinsma2023increasingcellularfitness pages 5-6).
  • Succinate from acetate (2023): 4.73 ± 0.6 mM in 36 h; 9.5% theoretical yield; ~400% vs WT at pH 7.5 (mutyala2023citratesynthaseoverexpression pages 1-3).

8) Visual evidence (figures)

  • A KT2440 acetate-to-succinate pathway schematic explicitly showing acetate assimilation routes including ackA/pta/acs is available (mutyala2023citratesynthaseoverexpression media afd2fae1).
  • A KT2440 phosphoketolase-shunt schematic depicts the engineered route producing acetyl-phosphate and its conversion toward acetyl-CoA (attributed to Pta in the text), along with an acetyl-phosphate quantification assay figure (bruinsma2023increasingcellularfitness media cac9d612, bruinsma2023increasingcellularfitness media 64ac7a49).

9) Limitations and gaps specific to this retrieval

  • No direct UniProt/InterPro record text for Q88PS4 was retrieved through the tools in this run; therefore, domain-level claims (e.g., exact InterPro accessions) are not re-cited here from primary database evidence.
  • No KT2440-specific, 2023–2024 primary study was retrieved that reports a direct pta deletion/overexpression phenotype under standard aerobic conditions beyond the 2013 work; more recent work tends to treat pta as part of pathway schematics or as an enabling step in engineered routes.

Evidence summary table

Evidence type Claim (reaction/pathway/localization/regulation) Key quantitative data Organism/strain context Source and URL
Biochemical + genetic PP_0774/pta encodes active phosphotransacetylase (Pta) in P. putida KT2440; locus organization shown as PP0773–PP0774(pta)–PP0775. Pta catalyzes acetyl-CoA + Pi ⇄ acetyl-phosphate + CoA, with native activity detected in oxic glucose-grown cells and lost in a pta::mini-Tn5 mutant; activity increases at transition to stationary phase, supporting a role in acetyl-CoA/acetyl-phosphate metabolism rather than a misassigned gene. No localization experiment was reported; function is consistent with a cytosolic metabolic enzyme. Pta activity increased 2.2-fold from log to stationary phase; no significant activity in pta::mini-Tn5 mutant; E. coli comparator peaked at 12.5 ± 0.9 U mg protein⁻¹. In oxic glucose minimal medium, Δpta (E. coli) comparator showed 2.3-fold lower specific growth rate and 1.6-fold lower final biomass than parent. (nikel2013engineeringananaerobic pages 6-7) Pseudomonas putida KT2440; mini-Tn5 mutant derivative; glucose-grown cells in M9 minimal medium. Nikel & de Lorenzo 2013, Metabolic Engineering. https://doi.org/10.1016/j.ymben.2012.09.006 (nikel2013engineeringananaerobic pages 6-7)
Biochemical + engineering Native Pta-generated acetyl-phosphate in P. putida can feed heterologous AckA to produce acetate + ATP by substrate-level phosphorylation under anoxic conditions, functionally confirming the Pta → acetyl-P step in KT2440. This places Pta in the AckA-Pta acetate node linking pyruvate dehydrogenase-derived acetyl-CoA to acetyl-phosphate. Upon ackA expression from E. coli, acetate kinase activity reached 17.8 ± 1.3 U mg protein⁻¹; acetate secretion reached 12.9 ± 0.6 mM vs <1 mM in vector control; in pta::mini-Tn5 background, acetate secretion reverted to control-like levels. ATP/ADP ratio after 24 h anoxia was 6.2 ± 0.8, a 1.3-fold increase over control. AEC under anoxia fell to 0.28 ± 0.04 in control but remained ~0.62–0.69 with heterologous AckA. (nikel2013engineeringananaerobic pages 6-7, nikel2013engineeringananaerobic pages 7-8) P. putida KT2440 carrying Ptrc::ackA from E. coli MG1655; compared with pta::mini-Tn5 derivative under anoxic incubation. Nikel & de Lorenzo 2013, Metabolic Engineering. https://doi.org/10.1016/j.ymben.2012.09.006 (nikel2013engineeringananaerobic pages 6-7, nikel2013engineeringananaerobic pages 7-8)
Engineering In an engineered phosphoketolase (Xfpk) shunt, Pta converts acetyl-phosphate to acetyl-CoA in P. putida, bypassing pyruvate decarboxylation/carboxylation-associated carbon loss and improving carbon conservation into biomass and acetyl-CoA-derived products. Xfpk candidates generated 1.26, 1.19, and 36.25 mM AcP/OD600 (empty-vector control 0.80 mM); best enzyme was ~30-fold higher than weaker candidates. On glycerol, Xfpk increased growth rate 0.12 → 0.18 h⁻¹ (+44.3%) and max OD600 4.4 → 6.6 (+50%). Product yields increased: flaviolin reporter 0.002 → 0.003 (+38.5%) and mevalonate 0.011 → 0.015 mol/mol (+25.9%). On xylose, growth rate 0.02 → 0.05 h⁻¹ (+167%), final OD600 5.73 → 7.4 (+30.2%), flaviolin +49.4%, mevalonate 0.022 → 0.042 mol/mol (+48.7%). (bruinsma2023increasingcellularfitness pages 2-5, bruinsma2023increasingcellularfitness pages 5-6) P. putida KT2440-derived strains (ΔglpR, Δgcd-xylABE) expressing heterologous xfpk. Bruinsma et al. 2023, Microbial Cell Factories. https://doi.org/10.1186/s12934-022-02015-9 (bruinsma2023increasingcellularfitness pages 2-5, bruinsma2023increasingcellularfitness pages 5-6)
Pathway/physiology + application Succinate-from-acetate work places pta with ackA and acs as entry routes from acetate to acetyl-CoA/TCA-glyoxylate metabolism in P. putida. This supports functional annotation of Pta in acetate assimilation/acetyl-CoA supply, even though this study did not directly manipulate pta. gltA overexpression gave ~50% improvement in succinate production; at pH 7.5, succinate reached 4.73 ± 0.6 mM in 36 h, about ~400% of wild type; yield was 9.5% of maximum theoretical on acetate minimal medium. Figure 1 explicitly depicts ackA/pta/acs feeding acetyl-CoA from acetate. (mutyala2023citratesynthaseoverexpression pages 1-3, mutyala2023citratesynthaseoverexpression media afd2fae1) P. putida KT2440 and gltA-overexpressing derivative under microaerobic growth on acetate as sole carbon source. Mutyala et al. 2023, ACS Omega. https://doi.org/10.1021/acsomega.3c02520 (mutyala2023citratesynthaseoverexpression pages 1-3, mutyala2023citratesynthaseoverexpression media afd2fae1)
Engineering/application For acetate-based mcl-PHA production, P. putida KT2440 was engineered by strengthening acetate assimilation via acs overexpression and constructing an ackA-pta pathway, indicating practical exploitation of the Pta node to channel acetate/acetyl-phosphate toward acetyl-CoA and product formation. Engineered P. putida produced 0.674 g/L mcl-PHA from acetate; later consortium optimization reported 1.32 g/L maximum mcl-PHA from mixed glucose/xylose after further pathway engineering. The study explicitly states that in 2019 they strengthened acetate assimilation by overexpressing acs and constructing the ackA-pta pathway. (qin2022reconstructionandoptimization pages 2-4) P. putida KT2440 in monoculture and in a designed P. putida–E. coli consortium for lignocellulose conversion. Qin et al. 2022, Frontiers in Bioengineering and Biotechnology. https://doi.org/10.3389/fbioe.2022.1023325 (qin2022reconstructionandoptimization pages 2-4)
Review/regulation In Pseudomonas spp., ackA-pta expression is linked to anaerobic/fermentative regulation by Anr (Fnr homolog) and IHF/LhfA; acetate consumption is additionally controlled by CrbS/R through Acs, while CidR regulates acetate production via pyruvate:menaquinone oxidoreductase. This frames likely regulatory context for KT2440 Pta, but is not a KT2440-specific direct experiment. No direct KT2440 enzyme kinetics given; review emphasizes that acetate metabolism can impair growth via intracellular acidification/respiratory inhibition and that Ac-CoA/acetyl-phosphate can alter non-enzymatic protein acetylation. (hosmer2023bacterialacetatemetabolism pages 3-5) Review of bacteria including Pseudomonas spp.; regulatory context relevant to P. putida but not a direct KT2440 perturbation study. Hosmer et al. 2023, Emerging Topics in Life Sciences. https://doi.org/10.1042/ETLS20220092 (hosmer2023bacterialacetatemetabolism pages 3-5)

Table: This table compiles organism-specific and closely relevant pathway evidence supporting functional annotation of Pseudomonas putida KT2440 pta (UniProt Q88PS4; PP_0774). It emphasizes direct biochemical/genetic support from Nikel & de Lorenzo and recent engineering studies that place Pta in acetyl-phosphate/acetyl-CoA metabolism.

References

  1. (nikel2013engineeringananaerobic pages 6-7): Pablo I. Nikel and Víctor de Lorenzo. Engineering an anaerobic metabolic regime in pseudomonas putida kt2440 for the anoxic biodegradation of 1,3-dichloroprop-1-ene. Metabolic Engineering, 15:98-112, Jan 2013. URL: https://doi.org/10.1016/j.ymben.2012.09.006, doi:10.1016/j.ymben.2012.09.006. This article has 134 citations and is from a domain leading peer-reviewed journal.

  2. (nikel2013engineeringananaerobic pages 7-8): Pablo I. Nikel and Víctor de Lorenzo. Engineering an anaerobic metabolic regime in pseudomonas putida kt2440 for the anoxic biodegradation of 1,3-dichloroprop-1-ene. Metabolic Engineering, 15:98-112, Jan 2013. URL: https://doi.org/10.1016/j.ymben.2012.09.006, doi:10.1016/j.ymben.2012.09.006. This article has 134 citations and is from a domain leading peer-reviewed journal.

  3. (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.

  4. (bruinsma2023increasingcellularfitness pages 2-5): Lyon Bruinsma, Maria Martin-Pascual, Kesi Kurnia, Marieken Tack, Simon Hendriks, Richard van Kranenburg, and Vitor A. P. Martins dos Santos. Increasing cellular fitness and product yields in pseudomonas putida through an engineered phosphoketolase shunt. Microbial Cell Factories, Jan 2023. URL: https://doi.org/10.1186/s12934-022-02015-9, doi:10.1186/s12934-022-02015-9. This article has 15 citations and is from a peer-reviewed journal.

  5. (kutscha2020microbialupgradingof pages 3-6): Regina Kutscha and Stefan Pflügl. Microbial upgrading of acetate into value-added products—examining microbial diversity, bioenergetic constraints and metabolic engineering approaches. International Journal of Molecular Sciences, 21:8777, Nov 2020. URL: https://doi.org/10.3390/ijms21228777, doi:10.3390/ijms21228777. This article has 68 citations.

  6. (mutyala2023citratesynthaseoverexpression media afd2fae1): 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.

  7. (bruinsma2023increasingcellularfitness pages 5-6): Lyon Bruinsma, Maria Martin-Pascual, Kesi Kurnia, Marieken Tack, Simon Hendriks, Richard van Kranenburg, and Vitor A. P. Martins dos Santos. Increasing cellular fitness and product yields in pseudomonas putida through an engineered phosphoketolase shunt. Microbial Cell Factories, Jan 2023. URL: https://doi.org/10.1186/s12934-022-02015-9, doi:10.1186/s12934-022-02015-9. This article has 15 citations and is from a peer-reviewed journal.

  8. (weimer2024systemsmetabolicengineering pages 1-8): ALA Weimer. Systems metabolic engineering of electrogenic anaerobic pseudomonas putida for enhanced 2-ketogluconate production. Unknown journal, 2024.

  9. (hosmer2023bacterialacetatemetabolism pages 3-5): Jennifer Hosmer, A. McEwan, and U. Kappler. Bacterial acetate metabolism and its influence on human epithelia. Emerging Topics in Life Sciences, 8:1-13, Mar 2023. URL: https://doi.org/10.1042/etls20220092, doi:10.1042/etls20220092. This article has 107 citations.

  10. (brautigam2023biophysicalandbiochemical pages 9-11): Chad A. Brautigam, Ranjit K. Deka, Shih-Chia Tso, Wei Z. Liu, and Michael V. Norgard. Biophysical and biochemical studies support tp0094 as a phosphotransacetylase in an acetogenic energy-conservation pathway in treponema pallidum. PLOS ONE, 18:e0283952, May 2023. URL: https://doi.org/10.1371/journal.pone.0283952, doi:10.1371/journal.pone.0283952. This article has 3 citations and is from a peer-reviewed journal.

  11. (qin2022reconstructionandoptimization pages 2-4): Ruolin Qin, Yinzhuang Zhu, Mingmei Ai, and Xiaoqiang Jia. Reconstruction and optimization of a pseudomonas putida-escherichia coli microbial consortium for mcl-pha production from lignocellulosic biomass. Frontiers in Bioengineering and Biotechnology, Oct 2022. URL: https://doi.org/10.3389/fbioe.2022.1023325, doi:10.3389/fbioe.2022.1023325. This article has 28 citations.

  12. (bruinsma2023increasingcellularfitness media cac9d612): Lyon Bruinsma, Maria Martin-Pascual, Kesi Kurnia, Marieken Tack, Simon Hendriks, Richard van Kranenburg, and Vitor A. P. Martins dos Santos. Increasing cellular fitness and product yields in pseudomonas putida through an engineered phosphoketolase shunt. Microbial Cell Factories, Jan 2023. URL: https://doi.org/10.1186/s12934-022-02015-9, doi:10.1186/s12934-022-02015-9. This article has 15 citations and is from a peer-reviewed journal.

  13. (bruinsma2023increasingcellularfitness media 64ac7a49): Lyon Bruinsma, Maria Martin-Pascual, Kesi Kurnia, Marieken Tack, Simon Hendriks, Richard van Kranenburg, and Vitor A. P. Martins dos Santos. Increasing cellular fitness and product yields in pseudomonas putida through an engineered phosphoketolase shunt. Microbial Cell Factories, Jan 2023. URL: https://doi.org/10.1186/s12934-022-02015-9, doi:10.1186/s12934-022-02015-9. This article has 15 citations and is from a peer-reviewed journal.

Artifacts

Citations

  1. nikel2013engineeringananaerobic pages 6-7
  2. kutscha2020microbialupgradingof pages 3-6
  3. nikel2013engineeringananaerobic pages 7-8
  4. bruinsma2023increasingcellularfitness pages 2-5
  5. bruinsma2023increasingcellularfitness pages 5-6
  6. mutyala2023citratesynthaseoverexpression pages 1-3
  7. weimer2024systemsmetabolicengineering pages 1-8
  8. hosmer2023bacterialacetatemetabolism pages 3-5
  9. brautigam2023biophysicalandbiochemical pages 9-11
  10. qin2022reconstructionandoptimization pages 2-4
  11. https://doi.org/10.1016/j.ymben.2012.09.006
  12. https://doi.org/10.1186/s12934-022-02015-9
  13. https://doi.org/10.1021/acsomega.3c02520
  14. https://doi.org/10.3389/fbioe.2022.1023325
  15. https://doi.org/10.1042/ETLS20220092
  16. https://doi.org/10.1016/j.ymben.2012.09.006,
  17. https://doi.org/10.1021/acsomega.3c02520,
  18. https://doi.org/10.1186/s12934-022-02015-9,
  19. https://doi.org/10.3390/ijms21228777,
  20. https://doi.org/10.1042/etls20220092,
  21. https://doi.org/10.1371/journal.pone.0283952,
  22. https://doi.org/10.3389/fbioe.2022.1023325,

📄 View Raw YAML

 
id: Q88PS4
gene_symbol: pta
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:160488
  label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
description: Phosphate acetyltransferase (phosphotransacetylase; Pta, EC 2.3.1.8) is a cytoplasmic enzyme of central carbon metabolism that catalyzes the reversible transfer of an acetyl group between coenzyme A and inorganic phosphate (acetyl-CoA + phosphate = acetyl phosphate + CoA). Together with acetate kinase (AckA), Pta constitutes the AckA-Pta pathway that interconverts acetyl-CoA, the energy-rich intermediate acetyl phosphate, and acetate, sitting at the acetate node linking glycolysis/pyruvate dehydrogenase-derived acetyl-CoA to acetate overflow metabolism, energy conservation via substrate-level phosphorylation, and acetyl phosphate signaling. In Pseudomonas putida KT2440 the enzyme is encoded by pta (locus PP_0774); phosphotransacetylase activity is measurable in cell-free extracts and is abolished by disruption of pta, and acetyl phosphate generated by Pta can feed heterologous AckA to produce acetate and ATP. The KT2440 protein is unusually large (695 aa) and bipartite, with an N-terminal CobB/CobQ-like region (P-loop NTPase / DRTGG) preceding the C-terminal phosphate acetyltransferase catalytic domain that carries the substrate-binding site; the enzyme is predicted to assemble into a homohexamer.
existing_annotations:
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: Cytoplasmic localization for a soluble central-metabolism enzyme acting on acetyl-CoA, acetyl phosphate, and inorganic phosphate.
    action: ACCEPT
    reason: Consistent with the UniProt subcellular location (Cytoplasm) and with enzyme activity being routinely assayed in soluble cell-free extracts. Pta has no membrane-targeting or signal/transit features; cytoplasmic localization is appropriate.
- term:
    id: GO:0008959
    label: phosphate acetyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: Precise molecular function term matching EC 2.3.1.8 and RHEA:19521 (acetyl-CoA + phosphate = acetyl phosphate + CoA); this is the core catalytic activity of Pta.
    action: ACCEPT
    reason: This is the exact, well-supported molecular function of the gene product. Although the GOA evidence is IEA, the assignment is anchored to InterPro:IPR016475 (proteobacterial phosphate acetyltransferase signature), EC 2.3.1.8, and RHEA:19521, and is independently confirmed in P. putida KT2440 where phosphotransacetylase activity is detected in cell-free extracts and lost upon pta disruption. Core function.
- term:
    id: GO:0016407
    label: acetyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: General parent of the precise phosphate acetyltransferase activity already annotated.
    action: MARK_AS_OVER_ANNOTATED
    reason: GO:0016407 is a broad ancestor of GO:0008959 (phosphate acetyltransferase activity), which is already annotated with a specific evidence trail. The general term adds no information beyond the precise term and is an InterPro2GO over-generalization.
- term:
    id: GO:0016746
    label: acyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: Very general acyltransferase parent of the precise phosphate acetyltransferase activity.
    action: MARK_AS_OVER_ANNOTATED
    reason: GO:0016746 (transferring acyl groups) is an even broader ancestor of GO:0008959. It is redundant with, and far less informative than, the specific phosphate acetyltransferase activity term. Over-annotation from InterPro2GO mapping.
- term:
    id: GO:0006085
    label: acetyl-CoA biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000041
  qualifier: involved_in
  review:
    summary: Pathway-level process annotation reflecting the UniPathway mapping for acetyl-CoA biosynthesis from acetate (acetyl-CoA from acetate, step 2/2).
    action: ACCEPT
    reason: Pta catalyzes the second step of the acetyl-CoA-from-acetate route (AckA forms acetyl phosphate from acetate; Pta converts acetyl phosphate to acetyl-CoA), consistent with the UniPathway UPA00340/UER00459 mapping in the UniProt record. The reaction is reversible, so in overflow metabolism Pta also runs in the acetyl-CoA-consuming direction toward acetate; the biosynthetic-process term captures one valid physiological direction and is supported by the pathway annotation. Reasonable, retain.
core_functions:
- description: Catalyzes the reversible transfer of an acetyl group between coenzyme A and inorganic phosphate (acetyl-CoA + phosphate = acetyl phosphate + CoA), the Pta half of the AckA-Pta acetate pathway.
  supported_by:
  - reference_id: file:PSEPK/pta/pta-deep-research-falcon.md
    supporting_text: Phosphotransacetylase (Pta) catalyzes the reversible transfer of an acetyl group between CoA and inorganic phosphate (acetyl-CoA + Pi = acetyl-phosphate + CoA); in P. putida KT2440 Pta activity is detected in cell-free extracts and abolished in a pta::mini-Tn5 mutant.
  molecular_function:
    id: GO:0008959
    label: phosphate acetyltransferase activity
- description: Interconverts acetyl-CoA, acetyl phosphate, and (with acetate kinase) acetate at the acetate node of central carbon metabolism, contributing to acetyl-CoA biosynthesis from acetate and to acetate overflow/energy metabolism.
  supported_by:
  - reference_id: file:PSEPK/pta/pta-deep-research-falcon.md
    supporting_text: Acetyl-phosphate generated by native Pta can feed heterologous AckA to produce acetate and ATP by substrate-level phosphorylation; ackA/pta is depicted as an acetate-to-acetyl-CoA assimilation route in KT2440.
  molecular_function:
    id: GO:0008959
    label: phosphate acetyltransferase activity
  directly_involved_in:
  - id: GO:0006085
    label: acetyl-CoA biosynthetic process
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000041
  title: Gene Ontology annotation based on UniPathway vocabulary mapping
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
  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: LOW
    correctness: VERIFIED
    review_notes: PMID matches the KT2440 genome paper cited in the UniProt record (RN [1]); establishes the genome/locus PP_0774 but does not directly characterize Pta function.
- id: file:PSEPK/pta/pta-deep-research-falcon.md
  title: Deep research report on P. putida KT2440 pta (Q88PS4 / PP_0774)
  findings: []
  reference_review:
    relevance: HIGH
    correctness: UNVERIFIED
    review_notes: Synthesizes organism-specific evidence (notably Nikel & de Lorenzo 2013, Metab Eng, doi:10.1016/j.ymben.2012.09.006) that PP_0774/pta encodes an active phosphotransacetylase. Underlying primary papers were not independently verified here (no PMID in cache); LLM-generated summary, treat quantitative details with caution.