The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
The target protein is correctly identified as 3-dehydroquinate synthase (DHQS) encoded by aroB in Pseudomonas putida KT2440. A KT2440 transcriptomics study explicitly maps the locus tag PP_5078 to aroB and describes it as 3-dehydroquinate synthase (“3-dehydroquinate synthase (aroB) (PP_5078)”). (lopezlara2020influenceofrehydration pages 2-4). Independent KT2440 metabolic-engineering literature also refers to aroB as encoding the native 3-dehydroquinate synthase in the shikimate pathway. (ling2022muconicacidproduction pages 1-2). Authoritative pathway reviews define AroB/DHQS as EC 4.2.3.4 and place it within the sugar phosphate cyclase superfamily, consistent with the UniProt-provided family/domain context. (derrer2013theshikimatepathway pages 3-4, derrer2013theshikimatepathway pages 4-5).
The shikimate pathway is a conserved biosynthetic route (present in bacteria, fungi, algae, and plants but absent in animals) that converts central-carbon precursors into chorismate, the branch-point precursor for aromatic amino acids and many specialized metabolites. (shende2024theshikimatepathway pages 3-4).
AroB/DHQS (3-dehydroquinate synthase) catalyzes the second step of the pathway: conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) into 3-dehydroquinate (DHQ), which is the first carbocyclic product (and a key intermediate) of the shikimate pathway. (derrer2013theshikimatepathway pages 3-4, shende2024theshikimatepathway pages 3-4, maeda2012theshikimatepathway pages 7-8).
Across authoritative reviews, DHQS is described as catalyzing:
- Substrate: DAHP (a sugar phosphate; often described as the pyranose form)
- Product: 3-dehydroquinate (DHQ) (carbocyclic intermediate)
- Phosphate: phosphate chemistry is integral; phosphate is eliminated during the mechanism and inorganic phosphate is discussed as a product/activator in mechanistic descriptions. (dev2012structureandfunction pages 2-4, derrer2013theshikimatepathway pages 3-4).
The enzyme’s functional specificity is therefore primarily for DAHP within the shikimate pathway (i.e., it is not a broad-spectrum cyclase in this context but a dedicated shikimate-pathway enzyme). (derrer2013theshikimatepathway pages 3-4, shende2024theshikimatepathway pages 3-4).
DHQS is widely characterized as an enzyme with an unusually complex, multi-step catalytic cascade occurring in a single active site:
- It uses NAD+ catalytically (transient reduction to NADH and reoxidation back to NAD+), and requires a divalent metal ion, typically described as Co2+ or Zn2+. (derrer2013theshikimatepathway pages 3-4, dev2012structureandfunction pages 2-4, maeda2012theshikimatepathway pages 7-8, derrer2013theshikimatepathway pages 4-5).
- Mechanistic steps described in reviews include an ordered sequence of alcohol oxidation, phosphate elimination, carbonyl reduction, ring opening, and intramolecular aldol condensation/cyclization to yield DHQ. (dev2012structureandfunction pages 2-4, derrer2013theshikimatepathway pages 3-4, shende2024theshikimatepathway pages 3-4).
A high-level mechanistic consensus is that the enzyme initiates a redox-triggered cascade that yields the carbocycle while suppressing side reactions (“shunt” reactions). (shende2024theshikimatepathway pages 3-4).
While not specific to P. putida KT2440, bacterial DHQS enzymes share conserved chemistry and cofactor usage; thus kinetic data from well-studied bacterial homologs provide useful bounds on expected catalytic behavior. For Mycobacterium tuberculosis DHQS, a review summarizes reported values KM(DAHP) = 6.3 µM, KM(NAD+) = 70 µM, and kcat ≈ 0.63 s−1, and also notes EDTA sensitivity with best restoration by Co2+ (and partial support by other divalent cations, with Zn often present). (nunes2020mycobacteriumtuberculosisshikimate pages 10-12).
Given the direct PP_5078→aroB mapping and the conserved reaction, aroB (PP_5078) in KT2440 is best annotated as a cytosolic metabolic enzyme of the shikimate pathway catalyzing DAHP → DHQ. (lopezlara2020influenceofrehydration pages 2-4, derrer2013theshikimatepathway pages 3-4, shende2024theshikimatepathway pages 3-4).
In bacteria, the shikimate pathway supplies chorismate, which supports aromatic amino acid biosynthesis and numerous downstream aromatic metabolites. (shende2024theshikimatepathway pages 3-4). In P. putida, this central role underpins why aroB is frequently targeted in metabolic engineering to raise flux to aromatic products. (ling2022muconicacidproduction pages 1-2, camposmagana2024combinatorialengineeringreveals pages 1-4).
No retrieved source provided a direct experimental subcellular localization assay for KT2440 AroB (e.g., fractionation, microscopy tagging). However, the enzyme acts on soluble cytosolic metabolites (DAHP, NAD+, divalent cations), and DHQS is treated in the literature as a soluble, intracellular (cytosolic) enzyme of central metabolism. This inference is consistent with the enzyme’s chemistry and its use in intracellular pathway engineering. (derrer2013theshikimatepathway pages 3-4, dev2012structureandfunction pages 2-4, ling2022muconicacidproduction pages 1-2).
In a KT2440 desiccation/rehydration transcriptome study, aroB (PP_5078) is reported among genes in an overrepresented amino-acid biosynthesis functional group and is described as upregulated during resuscitation after desiccation. (lopezlara2020influenceofrehydration pages 2-4). The same excerpt links this group to aromatic amino acid biosynthesis (phenylalanine/tyrosine), consistent with increased demand for shikimate-pathway flux during recovery. (lopezlara2020influenceofrehydration pages 2-4).
A 2024 Natural Product Reports review (“The shikimate pathway: gateway to metabolic diversity”) explicitly highlights that mechanistic proposals for DHQS are informed by high-resolution crystal structures of DHQS in complex with metals, nicotinamide cofactors, and substrate-based inhibitors, and summarizes DHQS as a multi-step enzyme stabilizing intermediates and minimizing off-pathway reactions. (shende2024theshikimatepathway pages 3-4). This consolidates the current understanding that DHQS is not merely a simple cyclase but a tightly choreographed redox-enabled cyclization catalyst.
A 2024 bioRxiv preprint applying combinatorial Design-of-Experiments (DoE) to P. putida shikimate and pABA pathways identifies aroB expression as a significant limiting factor for para-aminobenzoic acid (pABA) production. (camposmagana2024combinatorialengineeringreveals pages 1-4). Quantitatively, from 14 representative strains spanning a theoretical 512-combination design space, the authors report 2–186.2 mg/L pABA in the initial screen and 232.1 mg/L after a second engineering round guided by modeling. (camposmagana2024combinatorialengineeringreveals pages 1-4). A peer-reviewed continuation (2025) reports the same workflow and titers and again identifies aroB as a critical bottleneck (included here for completeness beyond the user’s 2024 window). (camposmagana2025combinatorialengineeringpinpoints pages 1-2).
This line of work supports an expert interpretation that, in P. putida, DHQS capacity can constrain carbon throughput through the shikimate node when production goals demand high chorismate-derived flux.
In 2024, Corynebacterium crenatum was engineered for L-tyrosine production by, among other interventions, overexpressing aroB/aroD/aroE. Reported titers reached 6.42 g/L in shake flasks and 34.6 g/L in fed-batch fermentation, with the mixed carbon-source strategy giving 16.9% higher L-tyrosine than glucose alone in flask conditions. (yang2024metabolicengineeringof pages 1-3). While not P. putida, this is relevant as a recent demonstration of real-world pathway design where increasing flux through the DAHP→DHQ→shikimate segment (including DHQS) is part of achieving industrially relevant aromatic amino acid titers.
A prominent implementation is muconic acid production in engineered P. putida KT2440. In this Nature Communications study (published Aug 2022; still actively cited as an implementation benchmark), the authors state that overexpression of aroB encoding the native 3-dehydroquinate synthase enabled efficient muconic acid production from mixed sugars. (ling2022muconicacidproduction pages 1-2). They report 33.7 g/L muconate, 0.18 g/L/h productivity, and 46% molar yield (reported as 92% of maximum theoretical yield). (ling2022muconicacidproduction pages 1-2). These data demonstrate industrially relevant titers/productivities and position aroB as a concrete intervention point in deployed strain designs.
pABA is described as a widely used industrial intermediate, and the 2024 DoE study in P. putida provides a quantitative example showing that systematic tuning of shikimate-pathway gene expression can move pABA titers across two orders of magnitude, with aroB identified as a key bottleneck. (camposmagana2024combinatorialengineeringreveals pages 1-4).
Authoritative reviews emphasize two main reasons DHQS/AroB is strategically important:
1. Pathway control point: DHQS forms the first carbocyclic intermediate and sits early in the pathway, so it can become rate-limiting when high flux is required for aromatic amino acids or downstream specialized metabolites. (shende2024theshikimatepathway pages 3-4, camposmagana2024combinatorialengineeringreveals pages 1-4).
2. Mechanistic complexity enabling inhibitor design: DHQS has well-defined cofactor and metal requirements and multi-step chemistry; high-resolution structures with cofactors/inhibitors have informed mechanistic models, making DHQS a tractable enzyme for mechanistic interrogation and (in broader contexts) inhibitor development. (shende2024theshikimatepathway pages 3-4, derrer2013theshikimatepathway pages 4-5).
A practical interpretation consistent with recent P. putida engineering results is that aroB expression/capacity often needs explicit optimization in overproduction settings (e.g., pABA), and can be part of high-performing strain architectures (e.g., muconate). (camposmagana2024combinatorialengineeringreveals pages 1-4, ling2022muconicacidproduction pages 1-2).
| Evidence type | Organism/system | Key finding | Quantitative data (if any) | Publication (authors, year) | URL/DOI |
|---|---|---|---|---|---|
| identity | Pseudomonas putida KT2440 | PP_5078 is explicitly annotated as aroB, encoding 3-dehydroquinate synthase; reported as upregulated during recovery from desiccation/rehydration, supporting the locus-to-function mapping for the target gene/protein (lopezlara2020influenceofrehydration pages 2-4) | Microarray study with triplicate analyses; numeric fold-change not given in excerpt (lopezlara2020influenceofrehydration pages 2-4) | López-Lara et al., 2020 | https://doi.org/10.1186/s13213-020-01596-3 |
| identity/pathway role | Pseudomonas putida KT2440 engineered for muconate production | The native aroB in P. putida KT2440 is identified as encoding 3-dehydroquinate synthase; overexpression improved flux to shikimate-pathway-derived muconic acid (ling2022muconicacidproduction pages 1-2) | Muconate production reached 33.7 g/L, 0.18 g/L/h, 46% molar yield (92% of theoretical maximum) in engineered strains that included aroB overexpression (ling2022muconicacidproduction pages 1-2) | Ling et al., 2022 | https://doi.org/10.1038/s41467-022-32296-y |
| mechanism | Bacterial DHQS/AroB (reviewed across taxa) | DHQS/AroB (EC 4.2.3.4) catalyzes conversion of DAHP to 3-dehydroquinate (DHQ), the second step of the shikimate pathway and first carbocyclic intermediate-forming reaction; belongs to the sugar phosphate cyclase superfamily (derrer2013theshikimatepathway pages 3-4, shende2024theshikimatepathway pages 3-4) | Reaction-level annotation; no organism-specific kinetic value in these excerpts (derrer2013theshikimatepathway pages 3-4, shende2024theshikimatepathway pages 3-4) | Derrer et al., 2013; Shende et al., 2024 | https://doi.org/10.2741/4155; https://doi.org/10.1039/d3np00037k |
| mechanism/cofactors | Bacterial DHQS/AroB (reviewed across taxa) | Catalysis requires NAD+ and a divalent metal ion; Co2+ and Zn2+ are the principal reported cofactors. Mechanism proceeds through oxidation, phosphate elimination, reduction, ring opening, and intramolecular aldol cyclization (derrer2013theshikimatepathway pages 3-4, dev2012structureandfunction pages 2-4, maeda2012theshikimatepathway pages 7-8, derrer2013theshikimatepathway pages 4-5) | Mechanistic sequence of ~5 chemical steps in one active site; catalytic NAD+ use noted (dev2012structureandfunction pages 2-4) | Dev et al., 2012; Derrer et al., 2013; Maeda & Dudareva, 2012 | https://doi.org/10.2174/157489312803900983; https://doi.org/10.2741/4155; https://doi.org/10.1146/annurev-arplant-042811-105439 |
| mechanism/kinetics | Mycobacterium tuberculosis DHQS (comparative authoritative source for conserved AroB chemistry) | AroB/DHQS performs multiple transformations in one active site; kinetics and metal dependence support the conserved bacterial mechanism for DHQS enzymes (nunes2020mycobacteriumtuberculosisshikimate pages 10-12) | KM(DAHP) = 6.3 µM, KM(NAD+) = 70 µM, kcat ≈ 0.63 s⁻¹; activity abolished by EDTA and best restored by Co2+ (nunes2020mycobacteriumtuberculosisshikimate pages 10-12) | Nunes et al., 2020 | https://doi.org/10.3390/molecules25061259 |
| application | Pseudomonas putida pABA pathway engineering | Combinatorial engineering identified aroB expression as a significant limiting factor / bottleneck for para-aminobenzoic acid production in P. putida, making DHQS a practical intervention point in strain design (camposmagana2024combinatorialengineeringreveals pages 1-4, camposmagana2024combinatorialengineeringreveals pages 11-14) | Initial strain set produced 2–186.2 mg/L pABA; second round reached 232.1 mg/L (reported in related preprint/peer-reviewed continuation) (camposmagana2024combinatorialengineeringreveals pages 1-4, camposmagana2025combinatorialengineeringpinpoints pages 1-2) | Campos-Magaña et al., 2024; Campos-Magaña et al., 2025 | https://doi.org/10.1101/2024.06.17.599342; https://doi.org/10.1186/s13036-025-00553-5 |
| application | Corynebacterium crenatum metabolic engineering | Overexpression of aroB with aroD/aroE was part of a successful aromatic amino acid engineering strategy, showing broader real-world use of DHQS tuning in microbial biomanufacturing (yang2024metabolicengineeringof pages 1-3) | 6.42 g/L L-tyrosine in shake flask; 34.6 g/L in fed-batch; 16.9% higher at 3:1 glucose:mannitol vs glucose alone (yang2024metabolicengineeringof pages 1-3) | Yang et al., 2024 | https://doi.org/10.1186/s12934-024-02564-1 |
| omics | Pseudomonas putida KT2440 under desiccation/rehydration | aroB/PP_5078 was included among genes in an overrepresented amino-acid biosynthesis response, consistent with its role in aromatic amino acid precursor supply through the shikimate pathway (lopezlara2020influenceofrehydration pages 2-4) | Upregulation reported after 18 days desiccation followed by 20 min or 24 h rehydration sampling; no fold-change in excerpt (lopezlara2020influenceofrehydration pages 2-4) | López-Lara et al., 2020 | https://doi.org/10.1186/s13213-020-01596-3 |
Table: This table compiles key evidence verifying that Pseudomonas putida KT2440 PP_5078 is aroB encoding 3-dehydroquinate synthase, and summarizes its conserved reaction chemistry, cofactors, pathway role, omics support, and quantitative metabolic-engineering applications.
References
(lopezlara2020influenceofrehydration pages 2-4): Lilia I. López-Lara, Laura A. Pazos-Rojas, Lesther E. López-Cruz, Yolanda E. Morales-García, Verónica Quintero-Hernández, Jesús de la Torre, Pieter van Dillewijn, Jesús Muñoz-Rojas, and Antonino Baez. Influence of rehydration on transcriptome during resuscitation of desiccated pseudomonas putida kt2440. Annals of Microbiology, Sep 2020. URL: https://doi.org/10.1186/s13213-020-01596-3, doi:10.1186/s13213-020-01596-3. This article has 16 citations and is from a peer-reviewed journal.
(ling2022muconicacidproduction pages 1-2): Chen Ling, George L. Peabody, Davinia Salvachúa, Young-Mo Kim, Colin M. Kneucker, Christopher H. Calvey, Michela A. Monninger, Nathalie Munoz Munoz, Brenton C. Poirier, Kelsey J. Ramirez, Peter C. St. John, Sean P. Woodworth, Jon K. Magnuson, Kristin E. Burnum-Johnson, Adam M. Guss, Christopher W. Johnson, and Gregg T. Beckham. Muconic acid production from glucose and xylose in pseudomonas putida via evolution and metabolic engineering. Nature Communications, Aug 2022. URL: https://doi.org/10.1038/s41467-022-32296-y, doi:10.1038/s41467-022-32296-y. This article has 141 citations and is from a highest quality peer-reviewed journal.
(derrer2013theshikimatepathway pages 3-4): Bianca Derrer, P. Macheroux, and B. Kappes. The shikimate pathway in apicomplexan parasites: implications for drug development. Frontiers in bioscience, 18:944-69, Jun 2013. URL: https://doi.org/10.2741/4155, doi:10.2741/4155. This article has 37 citations and is from a peer-reviewed journal.
(derrer2013theshikimatepathway pages 4-5): Bianca Derrer, P. Macheroux, and B. Kappes. The shikimate pathway in apicomplexan parasites: implications for drug development. Frontiers in bioscience, 18:944-69, Jun 2013. URL: https://doi.org/10.2741/4155, doi:10.2741/4155. This article has 37 citations and is from a peer-reviewed journal.
(shende2024theshikimatepathway pages 3-4): Vikram V. Shende, Katherine D. Bauman, and Bradley S. Moore. The shikimate pathway: gateway to metabolic diversity. Natural product reports, 41:604-648, Jan 2024. URL: https://doi.org/10.1039/d3np00037k, doi:10.1039/d3np00037k. This article has 173 citations and is from a peer-reviewed journal.
(maeda2012theshikimatepathway pages 7-8): Hiroshi Maeda and Natalia Dudareva. The shikimate pathway and aromatic amino acid biosynthesis in plants. Jun 2012. URL: https://doi.org/10.1146/annurev-arplant-042811-105439, doi:10.1146/annurev-arplant-042811-105439. This article has 1905 citations and is from a domain leading peer-reviewed journal.
(dev2012structureandfunction pages 2-4): Aditya Dev, Satya Tapas, Shivendra Pratap, and Pravindra Kumar. Structure and function of enzymes of shikimate pathway. Current Bioinformatics, 7:374-391, Nov 2012. URL: https://doi.org/10.2174/157489312803900983, doi:10.2174/157489312803900983. This article has 20 citations and is from a peer-reviewed journal.
(nunes2020mycobacteriumtuberculosisshikimate pages 10-12): José E. S. Nunes, Mario A. Duque, Talita F. de Freitas, Luiza Galina, Luis F. S. M. Timmers, Cristiano V. Bizarro, Pablo Machado, Luiz A. Basso, and Rodrigo G. Ducati. Mycobacterium tuberculosis shikimate pathway enzymes as targets for the rational design of anti-tuberculosis drugs. Molecules, 25:1259, Mar 2020. URL: https://doi.org/10.3390/molecules25061259, doi:10.3390/molecules25061259. This article has 74 citations.
(camposmagana2024combinatorialengineeringreveals pages 1-4): Marco A Campos-Magaña, Sara Moreno-Paz, Vitor AP Martins dos Santos, Luis Garcia-Morales, and Maria Suarez-Diez. Combinatorial engineering reveals shikimate pathway bottlenecks in para-aminobenzoic acid production in pseudomonas putida. bioRxiv, Jun 2024. URL: https://doi.org/10.1101/2024.06.17.599342, doi:10.1101/2024.06.17.599342. This article has 0 citations.
(camposmagana2025combinatorialengineeringpinpoints pages 1-2): Marco A Campos-Magaña, Sara Moreno-Paz, Maria Martin-Pascual, Vitor AP Martins dos Santos, Luis Garcia-Morales, and Maria Suarez-Diez. Combinatorial engineering pinpoints shikimate pathway bottlenecks in para-aminobenzoic acid production in pseudomonas putida. Journal of Biological Engineering, Sep 2025. URL: https://doi.org/10.1186/s13036-025-00553-5, doi:10.1186/s13036-025-00553-5. This article has 0 citations and is from a peer-reviewed journal.
(yang2024metabolicengineeringof pages 1-3): Gang Yang, Sicheng Xiong, Mingzhu Huang, Bin Liu, Yanna Shao, and Xuelan Chen. Metabolic engineering of corynebacterium crenatum for enhanced l-tyrosine production from mannitol and glucose. Microbial Cell Factories, Oct 2024. URL: https://doi.org/10.1186/s12934-024-02564-1, doi:10.1186/s12934-024-02564-1. This article has 7 citations and is from a peer-reviewed journal.
(camposmagana2024combinatorialengineeringreveals pages 11-14): Marco A Campos-Magaña, Sara Moreno-Paz, Vitor AP Martins dos Santos, Luis Garcia-Morales, and Maria Suarez-Diez. Combinatorial engineering reveals shikimate pathway bottlenecks in para-aminobenzoic acid production in pseudomonas putida. bioRxiv, Jun 2024. URL: https://doi.org/10.1101/2024.06.17.599342, doi:10.1101/2024.06.17.599342. This article has 0 citations.