EGLN1 / PHD2

evidence_span

{"source_cache": "artifacts/hbot-research/12912907.abstract.txt", "locator": "Indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "db0613321b1804356dbb60637bba0616eaaaeab041f63a095ecfcaeac3ec780e", "start_char": 0, "end_char": 1190, "text_sha256": "db0613321b1804356dbb60637bba0616eaaaeab041f63a095ecfcaeac3ec780e"}

experimental_model

Short interfering RNA silencing of each HIF prolyl-hydroxylase in human cells

exposure

PHD1, PHD2 and PHD3 silencing in normoxia and after brief hypoxia

limitations

A silencing study assigning distinct roles. It establishes which isoform sets the resting level, not the oxygen concentration at which each acts.

nutrient_topic

Hyperbaric oxygen research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. · Hyperbaric oxygen therapy

organism

Human cells

plain_language

One enzyme is the thermostat: it destroys the low-oxygen signal whenever oxygen is present.

primary_references

[hbot-p12912907] HIF prolyl-hydroxylase 2 is the key oxygen sensor setting low steady-state levels of HIF-1alpha in normoxia. (2003). https://pubmed.ncbi.nlm.nih.gov/12912907/ DOI: 10.1093/emboj/cdg392

tissue_or_cell_type

Cytosol

Hyperbaric oxygen: the exposure, its reactive species, the signals they carry, and the nutrient-dependent enzymes that handle them (2026-09-19) · lines 933–944

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Short interfering RNA silencing of each HIF prolyl-hydroxylase in human cells · source_derived_draft · unverified_draft

### hbot-phd2-oxygen-sensor Silencing PHD2 alone was sufficient to stabilise and activate HIF-1alpha in normoxia in every human cell type investigated, while silencing PHD1 or PHD3 had no effect on HIF-1alpha stability, making PHD2 the critical oxygen sensor setting the low steady-state level of HIF-1alpha. Condition category: normal nutrient_topic: Hyperbaric oxygen research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. plain_language: One enzyme is the thermostat: it destroys the low-oxygen signal whenever oxygen is present. organism: Human cells tissue_or_cell_type: Cytosol experimental_model: Short interfering RNA silencing of each HIF prolyl-hydroxylase in human cells limitations: A silencing study assigning distinct roles. It establishes which isoform sets the resting level, not the oxygen concentration at which each acts. exposure: PHD1, PHD2 and PHD3 silencing in normoxia and after brief hypoxia evidence_span: {"source_cache": "artifacts/hbot-research/12912907.abstract.txt", "locator": "Indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "db0613321b1804356dbb60637bba0616eaaaeab041f63a095ecfcaeac3ec780e", "start_char": 0, "end_char": 1190, "text_sha256": "db0613321b1804356dbb60637bba0616eaaaeab041f63a095ecfcaeac3ec780e"} [hbot-p12912907] HIF prolyl-hydroxylase 2 is the key oxygen sensor setting low steady-state levels of HIF-1alpha in normoxia. (2003). https://pubmed.ncbi.nlm.nih.gov/12912907/ DOI: 10.1093/emboj/cdg392

cross_nutrient

true

evidence_location

Figure 2C

experimental_model

Recombinant human PHD enzymes; HIF-1 alpha 556–574 peptide hydroxylation detected by VHL/elongin B/C binding; HPLC of reaction ascorbate

exposure

10 µM FeSO4, 0.5 mM 2-oxoglutarate, pH 7.5, room temperature, 1 h; ascorbate omission/titration and GSH titration; standard ascorbate 2 mM. Ascorbate measured before and after 1 h.

limitations

Minor air oxidation remained possible; result does not exclude ascorbate consumption during uncoupled or oxidative-damage reactions.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Homo sapiens protein

plain_language

Vitamin C was not used up once for every hydroxylation event in this enzyme assay.

primary_references

[c-reg-nytko] Vitamin C is dispensable for oxygen sensing in vivo. (2011). https://pubmed.ncbi.nlm.nih.gov/21346252/ DOI: 10.1182/blood-2010-09-307637

tissue_or_cell_type

Cell-free

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1159–1171

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Recombinant human PHD enzymes; HIF-1 alpha 556–574 peptide hydroxylation detected by VHL/elongin B/C binding; HPLC of reaction ascorbate · source_derived_draft · unverified_draft

### c-reg-phd-ascorbate-not-stoichiometric HPLC showed only a small decline in ascorbate during the PHD2 peptide reaction, independent of hydroxyl-acceptor substrate, providing no evidence that coupled prolyl hydroxylation consumed ascorbate stoichiometrically. Condition category: normal nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: Vitamin C was not used up once for every hydroxylation event in this enzyme assay. organism: Homo sapiens protein tissue_or_cell_type: Cell-free experimental_model: Recombinant human PHD enzymes; HIF-1 alpha 556–574 peptide hydroxylation detected by VHL/elongin B/C binding; HPLC of reaction ascorbate limitations: Minor air oxidation remained possible; result does not exclude ascorbate consumption during uncoupled or oxidative-damage reactions. exposure: 10 µM FeSO4, 0.5 mM 2-oxoglutarate, pH 7.5, room temperature, 1 h; ascorbate omission/titration and GSH titration; standard ascorbate 2 mM. Ascorbate measured before and after 1 h. cross_nutrient: true evidence_location: Figure 2C [c-reg-nytko] Vitamin C is dispensable for oxygen sensing in vivo. (2011). https://pubmed.ncbi.nlm.nih.gov/21346252/ DOI: 10.1182/blood-2010-09-307637

evidence_access

Primary full text, recombinant methods and enzyme kinetics

experimental_model

Human PHD2 residues 181–402; NMR and enzymatic assays.

limitations

Millimolar assay exposure is relevant to local gut questions, not evidence of inhibition throughout the body at normal blood levels.

nutrient_topic

Butyrate collection; molecular form, preparation, species, exposure and manipulation remain explicit. · Butyrate

plain_language

It also directly affected an enzyme that normally marks HIF for degradation.

primary_references

Microbiota-derived butyrate is an endogenous HIF prolyl hydroxylase inhibitor. · 2021 · https://pubmed.ncbi.nlm.nih.gov/34190032/ · DOI 10.1080/19490976.2021.1938380

Butyrate: microbial production, fuel use, signaling and nutrient interactions (2026-09-19) · lines 246–252

AI-assisted research curation; primary-abstract references and experimental limitations individually identified. Not publisher full text. · supports · Human PHD2 residues 181–402; NMR and enzymatic assays. · source_derived_draft · unverified_draft

## butyrate-phd2-inhibition It also directly affected an enzyme that normally marks HIF for degradation. Butyrate bound and inhibited a recombinant human PHD2 catalytic fragment; kinetic analysis gave a noncompetitive Ki of 5.3 ± 0.5 mM relative to 2-oxoglutarate. Model: Human PHD2 residues 181–402; NMR and enzymatic assays. Limitations: Millimolar assay exposure is relevant to local gut questions, not evidence of inhibition throughout the body at normal blood levels. Evidence access: Primary full text, recombinant methods and enzyme kinetics Microbiota-derived butyrate is an endogenous HIF prolyl hydroxylase inhibitor. · 2021 · https://pubmed.ncbi.nlm.nih.gov/34190032/ · DOI 10.1080/19490976.2021.1938380

evidence_span

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experimental_model

Short interfering RNA silencing of each HIF prolyl-hydroxylase in human cells

exposure

PHD1, PHD2 and PHD3 silencing in normoxia and after brief hypoxia

limitations

A silencing study assigning distinct roles. It establishes which isoform sets the resting level, not the oxygen concentration at which each acts.

nutrient_topic

Hyperbaric oxygen research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. · Hyperbaric oxygen therapy

organism

Human cells

plain_language

The thermostat builds more of itself when oxygen is scarce, so the system resets when oxygen returns.

primary_references

[hbot-p12912907] HIF prolyl-hydroxylase 2 is the key oxygen sensor setting low steady-state levels of HIF-1alpha in normoxia. (2003). https://pubmed.ncbi.nlm.nih.gov/12912907/ DOI: 10.1093/emboj/cdg392

tissue_or_cell_type

Cytosol

Hyperbaric oxygen: the exposure, its reactive species, the signals they carry, and the nutrient-dependent enzymes that handle them (2026-09-19) · lines 946–957

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Short interfering RNA silencing of each HIF prolyl-hydroxylase in human cells · source_derived_draft · unverified_draft

### hbot-phd2-autoregulation PHD2 is itself upregulated by hypoxia, providing a HIF-1-dependent auto-regulatory mechanism driven by oxygen tension. Condition category: normal nutrient_topic: Hyperbaric oxygen research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. plain_language: The thermostat builds more of itself when oxygen is scarce, so the system resets when oxygen returns. organism: Human cells tissue_or_cell_type: Cytosol experimental_model: Short interfering RNA silencing of each HIF prolyl-hydroxylase in human cells limitations: A silencing study assigning distinct roles. It establishes which isoform sets the resting level, not the oxygen concentration at which each acts. exposure: PHD1, PHD2 and PHD3 silencing in normoxia and after brief hypoxia evidence_span: {"source_cache": "artifacts/hbot-research/12912907.abstract.txt", "locator": "Indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "db0613321b1804356dbb60637bba0616eaaaeab041f63a095ecfcaeac3ec780e", "start_char": 0, "end_char": 1190, "text_sha256": "db0613321b1804356dbb60637bba0616eaaaeab041f63a095ecfcaeac3ec780e"} [hbot-p12912907] HIF prolyl-hydroxylase 2 is the key oxygen sensor setting low steady-state levels of HIF-1alpha in normoxia. (2003). https://pubmed.ncbi.nlm.nih.gov/12912907/ DOI: 10.1093/emboj/cdg392

evidence_access

Primary abstract

experimental_model

Human cell experiments with beta-oxidation inhibition.

limitations

Pharmacological inhibition has limitations; the complementary purified-PHD2 assay supports a separate mechanism.

nutrient_topic

Butyrate collection; molecular form, preparation, species, exposure and manipulation remain explicit. · Butyrate

plain_language

Fuel burning was not the only way it influenced HIF.

primary_references

Microbiota-derived butyrate is an endogenous HIF prolyl hydroxylase inhibitor. · 2021 · https://pubmed.ncbi.nlm.nih.gov/34190032/ · DOI 10.1080/19490976.2021.1938380

Butyrate: microbial production, fuel use, signaling and nutrient interactions (2026-09-19) · lines 254–260

AI-assisted research curation; primary-abstract references and experimental limitations individually identified. Not publisher full text. · supports · Human cell experiments with beta-oxidation inhibition. · source_derived_draft · unverified_draft

## butyrate-hif-without-oxidation Fuel burning was not the only way it influenced HIF. Butyrate still stabilized HIF in human epithelial-cell experiments when its beta-oxidation and associated oxygen consumption were inhibited. Model: Human cell experiments with beta-oxidation inhibition. Limitations: Pharmacological inhibition has limitations; the complementary purified-PHD2 assay supports a separate mechanism. Evidence access: Primary abstract Microbiota-derived butyrate is an endogenous HIF prolyl hydroxylase inhibitor. · 2021 · https://pubmed.ncbi.nlm.nih.gov/34190032/ · DOI 10.1080/19490976.2021.1938380

evidence_access

Primary abstract

experimental_model

Human endothelial cells; released silicon in the ppm range.

limitations

Accessed abstract does not establish direct inhibitor binding; HIF PHD2 differs from collagen prolyl hydroxylase.

nutrient_topic

Silica collection; molecular form, preparation, species, exposure and manipulation remain explicit. · Silica and soluble silicon

plain_language

A biomaterial study implicated oxygen-sensing machinery.

primary_references

Promoting angiogenesis with mesoporous microcarriers through a synergistic action of delivered silicon ion and VEGF. · 2017 · https://pubmed.ncbi.nlm.nih.gov/27918936/ · DOI 10.1016/j.biomaterials.2016.11.053

Silica: soluble silicon, cellular transport and particle-specific mechanisms (2026-09-19) · lines 272–278

AI-assisted research curation; primary references, access levels and experimental limitations individually identified. Not publisher full text. · supports · Human endothelial cells; released silicon in the ppm range. · source_derived_draft · unverified_draft

## silica-microcarrier-hif A biomaterial study implicated oxygen-sensing machinery. Silicon-releasing microcarriers increased HIF1A expression and stabilization, attributed to reduced PHD2 activity in HUVECs. Model: Human endothelial cells; released silicon in the ppm range. Limitations: Accessed abstract does not establish direct inhibitor binding; HIF PHD2 differs from collagen prolyl hydroxylase. Evidence access: Primary abstract Promoting angiogenesis with mesoporous microcarriers through a synergistic action of delivered silicon ion and VEGF. · 2017 · https://pubmed.ncbi.nlm.nih.gov/27918936/ · DOI 10.1016/j.biomaterials.2016.11.053

cross_nutrient

true

evidence_location

Figure 2A–B; hydroxylation Methods

experimental_model

Recombinant human PHD enzymes; HIF-1 alpha 556–574 peptide hydroxylation detected by VHL/elongin B/C binding

exposure

10 µM FeSO4, 0.5 mM 2-oxoglutarate, pH 7.5, room temperature, 1 h; ascorbate omission/titration and GSH titration; standard ascorbate 2 mM.

limitations

Alternative reductant effects vary with substrate and assay; this is not a nutritional substitution recommendation or proof of in-vivo compensation mechanism.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Homo sapiens proteins

plain_language

These oxygen-sensing enzymes could use support from glutathione when vitamin C was absent in the test tube.

primary_references

[c-reg-nytko] Vitamin C is dispensable for oxygen sensing in vivo. (2011). https://pubmed.ncbi.nlm.nih.gov/21346252/ DOI: 10.1182/blood-2010-09-307637

tissue_or_cell_type

Cell-free

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1145–1157

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Recombinant human PHD enzymes; HIF-1 alpha 556–574 peptide hydroxylation detected by VHL/elongin B/C binding · source_derived_draft · unverified_draft

### c-reg-gsh-substitutes-phd Reduced glutathione stimulated all three tested PHD isoforms in the absence of ascorbate; millimolar GSH could substitute in the peptide assay, indicating reductant redundancy in this setting. Condition category: normal nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: These oxygen-sensing enzymes could use support from glutathione when vitamin C was absent in the test tube. organism: Homo sapiens proteins tissue_or_cell_type: Cell-free experimental_model: Recombinant human PHD enzymes; HIF-1 alpha 556–574 peptide hydroxylation detected by VHL/elongin B/C binding limitations: Alternative reductant effects vary with substrate and assay; this is not a nutritional substitution recommendation or proof of in-vivo compensation mechanism. exposure: 10 µM FeSO4, 0.5 mM 2-oxoglutarate, pH 7.5, room temperature, 1 h; ascorbate omission/titration and GSH titration; standard ascorbate 2 mM. cross_nutrient: true evidence_location: Figure 2A–B; hydroxylation Methods [c-reg-nytko] Vitamin C is dispensable for oxygen sensing in vivo. (2011). https://pubmed.ncbi.nlm.nih.gov/21346252/ DOI: 10.1182/blood-2010-09-307637

cross_nutrient

true

evidence_location

Primary abstract rate/extent and substrate comparisons

experimental_model

Purified enzyme with human HIF-1 alpha-derived peptide substrate

exposure

Ascorbate versus omission/alternative reducing agents; exact concentrations and enzyme constructs not recovered from primary abstract.

limitations

Peptide hydroxylation does not directly establish HIF degradation or transcription changes in intact cells; ankyrin probe is not physiological HIF.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Human HIF-1 alpha substrate; purified recombinant hydroxylase

plain_language

Vitamin C increased the activity of an isolated oxygen-sensing proline hydroxylase.

primary_references

[c-reg-flashman] Investigating the dependence of the hypoxia-inducible factor hydroxylases (factor inhibiting HIF and prolyl hydroxylase domain 2) on ascorbate and other reducing agents. (2010). https://pubmed.ncbi.nlm.nih.gov/20055761/ DOI: 10.1042/bj20091609

tissue_or_cell_type

Cell-free

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1117–1129

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified enzyme with human HIF-1 alpha-derived peptide substrate · source_derived_draft · unverified_draft

### c-reg-phd2-ascorbate Ascorbate increased the initial rate and extent of PHD2-catalyzed hydroxylation at both tested human HIF-1 alpha prolyl sites in purified-enzyme peptide experiments. Condition category: normal nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: Vitamin C increased the activity of an isolated oxygen-sensing proline hydroxylase. organism: Human HIF-1 alpha substrate; purified recombinant hydroxylase tissue_or_cell_type: Cell-free experimental_model: Purified enzyme with human HIF-1 alpha-derived peptide substrate limitations: Peptide hydroxylation does not directly establish HIF degradation or transcription changes in intact cells; ankyrin probe is not physiological HIF. exposure: Ascorbate versus omission/alternative reducing agents; exact concentrations and enzyme constructs not recovered from primary abstract. cross_nutrient: true evidence_location: Primary abstract rate/extent and substrate comparisons [c-reg-flashman] Investigating the dependence of the hypoxia-inducible factor hydroxylases (factor inhibiting HIF and prolyl hydroxylase domain 2) on ascorbate and other reducing agents. (2010). https://pubmed.ncbi.nlm.nih.gov/20055761/ DOI: 10.1042/bj20091609