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this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.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 AlgD, encoded by algD / PP_1288 in Pseudomonas putida strain KT2440, and is annotated as GDP-mannose 6-dehydrogenase (GDP-mannose dehydrogenase; GMD, EC 1.1.1.132). In a KT2440-focused deletion/transcriptome study, genes PP_1277–PP_1288 are treated as the alginate-associated cluster, and PP_1288 is explicitly annotated as algD (GDP-mannose 6-dehydrogenase) under an “AlgD operon” heading, linking this locus unambiguously to alginate biosynthesis in KT2440. (gulez2014colonymorphologyand pages 6-8, gulez2014colonymorphologyand pages 2-4)
Because algD is also heavily studied in Pseudomonas aeruginosa (clinical mucoid strains), literature from P. aeruginosa is used below only as homolog-based enzymology/structural context, while KT2440 locus/operon assignment and stress-responsive expression are supported directly by P. putida studies. (gulez2014colonymorphologyand pages 6-8, gulez2012transcriptomedynamicsof pages 2-4)
AlgD (GDP-mannose 6-dehydrogenase; GMD) is a cytosolic enzyme in the UDP-glucose/GDP-mannose dehydrogenase family that catalyzes the precursor-forming step for bacterial alginate biosynthesis. (serrato2024bacterialalginatebiosynthesis pages 6-8, gheorghita2023pseudomonasaeruginosabiofilm pages 7-8)
Reaction (core definition): AlgD catalyzes the irreversible oxidation of GDP-mannose to GDP-mannuronate (GDP-mannuronic acid; GDP-ManA), supplying the activated uronic-acid building block used for polymer formation. (serrato2024bacterialalginatebiosynthesis pages 6-8, gheorghita2023pseudomonasaeruginosabiofilm pages 7-8, hulen2023thegdpmannosedehydrogenase pages 1-3)
Cofactor/electron acceptor: The reaction is NAD+-dependent, and activity is commonly monitored by NADH formation (A340). (hulen2023thegdpmannosedehydrogenase pages 14-15, hulen2023thegdpmannosedehydrogenase pages 5-8)
Recent reviews describe bacterial alginate biosynthesis as beginning in the cytoplasm with the precursor pathway (AlgA/AlgC/AlgD) that yields GDP-mannuronate, after which polymerization/export/modification steps are executed by multi-protein complexes spanning the inner membrane, periplasm, and outer membrane. Within this framework, AlgD is positioned as part of the cytosolic precursor synthesis module supplying GDP-mannuronate. (serrato2024bacterialalginatebiosynthesis pages 6-8, gheorghita2023pseudomonasaeruginosabiofilm pages 7-8, gheorghita2023pseudomonasaeruginosabiofilm pages 4-5)
A KT2440 transcriptome study under controlled matric potentials organizes PP_1277–PP_1288 as an “AlgD operon” (alginate synthesis region) and identifies PP_1288 = algD = GDP-mannose 6-dehydrogenase. In that same table/description, algD is described as the first gene in the alginate synthesis operon. (gulez2014colonymorphologyand pages 6-8)
Interpretation: For KT2440, this supports that algD/PP_1288 is genetically embedded in an alginate biosynthetic locus and should be primarily interpreted as an alginate precursor-synthesis enzyme, rather than a general carbohydrate catabolic dehydrogenase. (gulez2014colonymorphologyand pages 6-8, gulez2014colonymorphologyand pages 2-4)
In KT2440, alginate-related genes show stress-responsive expression under water limitation. Specifically, algD/PP_1288 is reported as significantly induced under water-limited conditions, with a reported log2 fold-change of 3.26 in wild type at 0.4 MPa matric potential in the cited transcriptome comparison. (gulez2014colonymorphologyand pages 6-8)
Complementary KT2440 data indicate that during matric (water) stress, expression of alginate-related genes (including algB and genes within the algD operon) can be transiently upregulated early during stress exposure, consistent with induction of alginate/EPS programs as part of the response. (gulez2012transcriptomedynamicsof pages 2-4)
Functional implication for KT2440: These findings support a model in which KT2440 increases alginate pathway activity under water limitation, consistent with the role of alginate as an EPS that can contribute to hydrated microenvironments in soil-like conditions. (gulez2014colonymorphologyand pages 6-8, gulez2012transcriptomedynamicsof pages 2-4)
Direct localization experiments for Q88NC4 in KT2440 were not identified in the retrieved texts. However, multiple authoritative descriptions of the pathway place AlgD function in the cytoplasmic precursor synthesis stage (GDP-mannuronate generation), upstream of membrane/periplasmic polymerization and export. This strongly supports a cytosolic localization/function for AlgD in KT2440 by pathway conservation. (serrato2024bacterialalginatebiosynthesis pages 6-8, gheorghita2023pseudomonasaeruginosabiofilm pages 7-8, gheorghita2023pseudomonasaeruginosabiofilm pages 4-5)
A 2023 focused article on P. aeruginosa GMD (AlgD) summarizes that the enzyme performs a two-step, four-electron oxidation of the C-6 alcohol of GDP-mannose to the uronic acid product, and is mechanistically similar to UDP-glucose dehydrogenase. The enzyme is described as having an N-terminal domain that binds NAD+ and GDP-mannose, and a C-terminal domain containing an essential catalytic cysteine (reported as Cys268 in that article). (hulen2023thegdpmannosedehydrogenase pages 14-15)
The same source reports evidence for a “half-oxidation” intermediate and tight association with nucleotide-like ligands, consistent with a multi-step oxidative mechanism and strong ligand interactions. (hulen2023thegdpmannosedehydrogenase pages 1-3, hulen2023thegdpmannosedehydrogenase pages 8-11)
A 2023 high-authority review on P. aeruginosa biofilm exopolysaccharides places AlgD structurally as a two-domain enzyme and notes a solved structure (cited in that review) supporting a domain-swapped dimer; the review also discusses the possibility (not yet experimentally confirmed) that AlgA/AlgC/AlgD may form a cytoplasmic subcomplex to facilitate precursor channeling. (gheorghita2023pseudomonasaeruginosabiofilm pages 7-8)
A separate 2023 focused source likewise describes GMD as functioning as a domain-swapped dimer, with earlier reports of higher-order assemblies under some conditions (e.g., hexamer formation upon overexpression). (hulen2023thegdpmannosedehydrogenase pages 1-3, hulen2023thegdpmannosedehydrogenase pages 3-5)
Relevance to Q88NC4: These structural conclusions are not KT2440-specific measurements but are important for functional annotation because Q88NC4 belongs to the same dehydrogenase family and is expected to share the conserved catalytic architecture and oligomeric behavior. (gheorghita2023pseudomonasaeruginosabiofilm pages 7-8, hulen2023thegdpmannosedehydrogenase pages 14-15)
No KT2440-specific kinetic constants were identified in the retrieved full texts. For P. aeruginosa GMD (AlgD), a 2023 focused article reports:
- Strong negative cooperativity for GDP-mannose with two apparent substrate-binding regimes: Km ≈ 13 µM (high affinity) and Km ≈ 3 mM (low affinity). (hulen2023thegdpmannosedehydrogenase pages 1-3, hulen2023thegdpmannosedehydrogenase pages 5-8)
- Apparent Km for NAD+ ≈ 0.36 mM. (hulen2023thegdpmannosedehydrogenase pages 5-8)
These quantitative features are consistent with the enzyme’s described dimeric/allosteric behavior and can guide expectations for Q88NC4, but they should be treated as homolog-derived until measured for KT2440 AlgD specifically. (hulen2023thegdpmannosedehydrogenase pages 1-3, hulen2023thegdpmannosedehydrogenase pages 3-5)
A 2023 focused article describes multiple substrate-analog inhibitor strategies targeting AlgD/GMD and reports quantitative inhibition examples:
- A GDP-mannose analog inhibitor (AM5′ASG) achieved ~90% inhibition at 0.5 mM (and ~98% at 1 mM). (hulen2023thegdpmannosedehydrogenase pages 11-14)
- In vivo phenotypic linkage: M5′ASG at 0.1 mM increased P. aeruginosa sensitivity to tobramycin by 55%, supporting AlgD inhibition as a potential anti-mucoidy/anti-tolerance adjuvant strategy. (hulen2023thegdpmannosedehydrogenase pages 15-17)
A 2023 article in Antibiotics argues that GDP-mannose dehydrogenase (AlgD/GMD) is an “old and new” target to reduce mucoidy-associated antibiotic tolerance, highlighting mechanistic understanding (two-step oxidation, dimeric behavior) and inhibitor development as actionable routes. (Published Nov 2023; https://doi.org/10.3390/antibiotics12121649) (hulen2023thegdpmannosedehydrogenase pages 1-3, hulen2023thegdpmannosedehydrogenase pages 15-17)
KT2440 studies under soil-relevant water limitation conditions support the practical interpretation of alginate as a protective EPS under matric stress, with algD/PP_1288 strongly induced under water limitation (quantified above). This provides an evidence-backed link between algD function (GDP-mannuronate production) and an ecological implementation: stress-adaptive EPS production in drying soil microenvironments. (gulez2014colonymorphologyand pages 6-8, gulez2012transcriptomedynamicsof pages 2-4)
In mucoid Pseudomonas contexts, AlgD activity supports alginate production, which is frequently implicated in persistence and tolerance. The 2023 focused article provides proof-of-concept that chemical inhibition of GMD can substantially inhibit enzyme activity in vitro and can increase antibiotic susceptibility in vivo (tobramycin example). These are concrete steps toward anti-biofilm adjuvant strategies targeting alginate precursor biosynthesis. (hulen2023thegdpmannosedehydrogenase pages 11-14, hulen2023thegdpmannosedehydrogenase pages 15-17)
High confidence (KT2440-specific):
- algD corresponds to PP_1288 and encodes GDP-mannose 6-dehydrogenase in the KT2440 alginate-associated operon/cluster (PP_1277–PP_1288). (gulez2014colonymorphologyand pages 6-8, gulez2014colonymorphologyand pages 2-4)
- algD is upregulated under water limitation with a reported log2FC 3.26. (gulez2014colonymorphologyand pages 6-8)
Moderate confidence (pathway-conserved inference):
- Cytosolic localization and role in the precursor-synthesis stage (supported by pathway descriptions in authoritative reviews; not directly localized in KT2440 here). (serrato2024bacterialalginatebiosynthesis pages 6-8, gheorghita2023pseudomonasaeruginosabiofilm pages 7-8)
Not established for KT2440 in retrieved texts (requires targeted enzymology):
- KT2440-specific kinetic parameters, oligomerization state, and inhibitor susceptibility. The quantitative kinetics/inhibitor data summarized above are from P. aeruginosa homolog work and should not be assumed identical for Q88NC4 without direct testing. (hulen2023thegdpmannosedehydrogenase pages 1-3, hulen2023thegdpmannosedehydrogenase pages 5-8, hulen2023thegdpmannosedehydrogenase pages 11-14)
| Item | Summary statement | Key evidence citations |
|---|---|---|
| Gene/protein | algD in Pseudomonas putida KT2440 maps to PP_1288 and is annotated as GDP-mannose 6-dehydrogenase; deletion analyses place PP_1277–PP_1288 as the alginate-associated cluster in this strain. | (gulez2014colonymorphologyand pages 6-8, gulez2014colonymorphologyand pages 2-4) |
| Enzyme name | AlgD is the GDP-mannose 6-dehydrogenase (GMD) that supplies the activated uronic-acid precursor used for alginate biosynthesis. | (gulez2014colonymorphologyand pages 6-8, serrato2024bacterialalginatebiosynthesis pages 6-8, gheorghita2023pseudomonasaeruginosabiofilm pages 4-5) |
| EC | The reviewed AlgD/GMD enzyme is identified as EC 1.1.1.132. | (hulen2023thegdpmannosedehydrogenase pages 1-3) |
| Reaction | AlgD catalyzes the irreversible oxidation of GDP-mannose to GDP-mannuronic acid (GDP-mannuronate), a key precursor-forming step in bacterial alginate biosynthesis. | (serrato2024bacterialalginatebiosynthesis pages 6-8, gheorghita2023pseudomonasaeruginosabiofilm pages 7-8, hulen2023thegdpmannosedehydrogenase pages 1-3) |
| Cofactor | The enzyme is NAD+-dependent; assays monitor NADH formation during GDP-mannose oxidation, and a reviewed value for apparent Km(NAD+) ≈ 0.36 mM is reported for P. aeruginosa GMD. | (hulen2023thegdpmannosedehydrogenase pages 14-15, hulen2023thegdpmannosedehydrogenase pages 5-8) |
| Pathway/operon context | In KT2440, PP_1277–PP_1288 are presented as the AlgD operon/alginate synthesis region; algD is described as the first gene in the alginate synthesis operon and PP_1288 is functionally annotated as GDP-mannose 6-dehydrogenase. | (gulez2014colonymorphologyand pages 6-8, gulez2014colonymorphologyand pages 2-4) |
| Stress regulation evidence | Under water limitation/matric stress, alginate-related genes in KT2440 are transiently upregulated; the 2014 study reports algD/PP_1288 log2-fold change = 3.26 in WT at 0.4 MPa Ψm, supporting stress-responsive activation of alginate precursor synthesis. | (gulez2014colonymorphologyand pages 6-8, gulez2012transcriptomedynamicsof pages 2-4) |
| Structural notes | Direct KT2440 structural data were not found in this run, but reviewed AlgD/GMD homologs are described as having an N-terminal nucleotide-binding domain and C-terminal catalytic domain with an essential catalytic Cys residue, and crystal work supports a domain-swapped dimer; these features are consistent with UniProt family/domain assignment but remain inferred for Q88NC4 rather than directly demonstrated here. | (gheorghita2023pseudomonasaeruginosabiofilm pages 7-8, hulen2023thegdpmannosedehydrogenase pages 14-15, hulen2023thegdpmannosedehydrogenase pages 3-5) |
| Kinetics/inhibition data | No KT2440-specific kinetic constants were found in this run. For the well-studied P. aeruginosa homolog, GDP-mannose shows strong negative cooperativity with reported Km values of ~13 µM and ~3 mM; substrate-analog inhibitors can be potent, including AM5′ASG, which gave ~90% inhibition at 0.5 mM. These data are supportive homolog evidence, not KT2440-specific measurements. | (hulen2023thegdpmannosedehydrogenase pages 1-3, hulen2023thegdpmannosedehydrogenase pages 5-8, hulen2023thegdpmannosedehydrogenase pages 11-14) |
| Localization | The available evidence places AlgD in the cytoplasmic precursor-synthesis stage of alginate biosynthesis, alongside AlgA and AlgC, generating GDP-mannuronate before polymerization/export steps handled by membrane/periplasmic components. | (serrato2024bacterialalginatebiosynthesis pages 6-8, gheorghita2023pseudomonasaeruginosabiofilm pages 7-8, gheorghita2023pseudomonasaeruginosabiofilm pages 4-5) |
Table: This table summarizes the evidence-supported functional annotation of algD/PP_1288 (UniProt Q88NC4) in Pseudomonas putida KT2440, including confirmed KT2440-specific findings and clearly labeled homolog-based inferences where direct strain-specific data were limited.
References
(gulez2014colonymorphologyand pages 6-8): Gamze Gulez, Ali Altıntaş, Mustafa Fazli, Arnaud Dechesne, Christopher T. Workman, Tim Tolker‐Nielsen, and Barth F. Smets. Colony morphology and transcriptome profiling of pseudomonas putida kt2440 and its mutants deficient in alginate or all eps synthesis under controlled matric potentials. MicrobiologyOpen, 3:457-469, Jun 2014. URL: https://doi.org/10.1002/mbo3.180, doi:10.1002/mbo3.180. This article has 33 citations and is from a peer-reviewed journal.
(gulez2014colonymorphologyand pages 2-4): Gamze Gulez, Ali Altıntaş, Mustafa Fazli, Arnaud Dechesne, Christopher T. Workman, Tim Tolker‐Nielsen, and Barth F. Smets. Colony morphology and transcriptome profiling of pseudomonas putida kt2440 and its mutants deficient in alginate or all eps synthesis under controlled matric potentials. MicrobiologyOpen, 3:457-469, Jun 2014. URL: https://doi.org/10.1002/mbo3.180, doi:10.1002/mbo3.180. This article has 33 citations and is from a peer-reviewed journal.
(gulez2012transcriptomedynamicsof pages 2-4): Gamze Gülez, Arnaud Dechesne, Christopher T. Workman, and Barth F. Smets. Transcriptome dynamics of pseudomonas putida kt2440 under water stress. Feb 2012. URL: https://doi.org/10.1128/aem.06150-11, doi:10.1128/aem.06150-11. This article has 55 citations and is from a peer-reviewed journal.
(serrato2024bacterialalginatebiosynthesis pages 6-8): Rodrigo Vassoler Serrato. Bacterial alginate biosynthesis and metabolism. Biochemistry, May 2024. URL: https://doi.org/10.5772/intechopen.109295, doi:10.5772/intechopen.109295. This article has 6 citations and is from a peer-reviewed journal.
(gheorghita2023pseudomonasaeruginosabiofilm pages 7-8): Andreea A Gheorghita, Daniel J Wozniak, Matthew R Parsek, and P Lynne Howell. Pseudomonas aeruginosa biofilm exopolysaccharides: assembly, function, and degradation. FEMS microbiology reviews, Oct 2023. URL: https://doi.org/10.1093/femsre/fuad060, doi:10.1093/femsre/fuad060. This article has 91 citations and is from a domain leading peer-reviewed journal.
(hulen2023thegdpmannosedehydrogenase pages 1-3): Christian Hulen. The gdp-mannose dehydrogenase of pseudomonas aeruginosa: an old and new target to fight against antibiotics resistance of mucoid strains. Antibiotics, 12:1649, Nov 2023. URL: https://doi.org/10.3390/antibiotics12121649, doi:10.3390/antibiotics12121649. This article has 9 citations.
(hulen2023thegdpmannosedehydrogenase pages 14-15): Christian Hulen. The gdp-mannose dehydrogenase of pseudomonas aeruginosa: an old and new target to fight against antibiotics resistance of mucoid strains. Antibiotics, 12:1649, Nov 2023. URL: https://doi.org/10.3390/antibiotics12121649, doi:10.3390/antibiotics12121649. This article has 9 citations.
(hulen2023thegdpmannosedehydrogenase pages 5-8): Christian Hulen. The gdp-mannose dehydrogenase of pseudomonas aeruginosa: an old and new target to fight against antibiotics resistance of mucoid strains. Antibiotics, 12:1649, Nov 2023. URL: https://doi.org/10.3390/antibiotics12121649, doi:10.3390/antibiotics12121649. This article has 9 citations.
(gheorghita2023pseudomonasaeruginosabiofilm pages 4-5): Andreea A Gheorghita, Daniel J Wozniak, Matthew R Parsek, and P Lynne Howell. Pseudomonas aeruginosa biofilm exopolysaccharides: assembly, function, and degradation. FEMS microbiology reviews, Oct 2023. URL: https://doi.org/10.1093/femsre/fuad060, doi:10.1093/femsre/fuad060. This article has 91 citations and is from a domain leading peer-reviewed journal.
(hulen2023thegdpmannosedehydrogenase pages 8-11): Christian Hulen. The gdp-mannose dehydrogenase of pseudomonas aeruginosa: an old and new target to fight against antibiotics resistance of mucoid strains. Antibiotics, 12:1649, Nov 2023. URL: https://doi.org/10.3390/antibiotics12121649, doi:10.3390/antibiotics12121649. This article has 9 citations.
(hulen2023thegdpmannosedehydrogenase pages 3-5): Christian Hulen. The gdp-mannose dehydrogenase of pseudomonas aeruginosa: an old and new target to fight against antibiotics resistance of mucoid strains. Antibiotics, 12:1649, Nov 2023. URL: https://doi.org/10.3390/antibiotics12121649, doi:10.3390/antibiotics12121649. This article has 9 citations.
(hulen2023thegdpmannosedehydrogenase pages 11-14): Christian Hulen. The gdp-mannose dehydrogenase of pseudomonas aeruginosa: an old and new target to fight against antibiotics resistance of mucoid strains. Antibiotics, 12:1649, Nov 2023. URL: https://doi.org/10.3390/antibiotics12121649, doi:10.3390/antibiotics12121649. This article has 9 citations.
(hulen2023thegdpmannosedehydrogenase pages 15-17): Christian Hulen. The gdp-mannose dehydrogenase of pseudomonas aeruginosa: an old and new target to fight against antibiotics resistance of mucoid strains. Antibiotics, 12:1649, Nov 2023. URL: https://doi.org/10.3390/antibiotics12121649, doi:10.3390/antibiotics12121649. This article has 9 citations.