carboxydotrophic

METPO:1000633 · CLASS · REVIEWED

A trophic type in which an organism derives energy from the oxidation of carbon monoxide.

Trait evidence (2)

DOI:10.1038/nrmicro1595
Carbon monoxide (CO) supports the growth and metabolism

Review supports aerobic CO oxidation as an energy-supporting metabolism.
DOI:10.1111/j.1574-6968.1986.tb01858.x
presence of the enzyme CO dehydrogenase

Review supports CODH and CO-insensitive respiratory-chain features in aerobic carboxydotrophs.

Carboxydotrophic carbon monoxide oxidation mechanism

DOI-backed graph linking carbon monoxide, carbon monoxide dehydrogenase, respiratory electron transport, and energy conservation.

MECHANISTIC · Represents distinct aerobic molybdenum-CODH and anaerobic NiFe-CODH branches. The CooS exemplar supports the R. rubrum anaerobic branch; broad operon, CooA, RcoM, and terminal-oxidase labels are retained only with explicit review notes.

Edge evidence

carboxydotrophic uses energy substrate carbon monoxide
Carboxydotrophs use carbon monoxide to support growth or metabolism.
- DOI:10.1038/nrmicro1595 CO supports the growth and metabolism Supports carbon monoxide as an energy-supporting substrate.
carbon monoxide dehydrogenase oxidizes carbon monoxide METPO:2007803
CODH catalyzes carbon monoxide oxidation.
- DOI:10.1038/nrmicro1595 CO dehydrogenase (CODH), to oxidize CO Supports CODH-mediated CO oxidation.
molybdenum hydroxylase enzyme class for carbon monoxide dehydrogenase
Aerobic CO oxidizers use a molybdenum hydroxylase CODH.
- DOI:10.1038/nrmicro1595 use a molybdenum hydroxylase Supports molybdenum hydroxylase classification of aerobic CODH.
carbon monoxide oxidized to carbon dioxide METPO:2007405
CO oxidation yields carbon dioxide.
- DOI:10.1007/s00775-018-1541-0 oxidation of CO to CO2 Supports CO-to-CO2 conversion by CODH.
carbon monoxide dehydrogenase feeds electrons into respiratory chain METPO:2007402
CO oxidation is coupled to respiratory electron transfer.
- DOI:10.1111/j.1574-6968.1986.tb01858.x branched respiratory chain Supports respiratory-chain coupling in aerobic CO-utilizing bacteria.
respiratory chain depends on CO-insensitive terminal oxidase RO:0002502
CO-utilizing bacteria use a CO-insensitive terminal oxidase branch.
- DOI:10.1111/j.1574-6968.1986.tb01858.x CO-insensitive terminal oxidase Supports terminal oxidase adaptation for CO metabolism.
respiratory chain generates proton motive force biolink:produces
Respiratory CO oxidation conserves energy as proton motive force.
- DOI:10.1111/j.1574-6968.1986.tb01858.x pmf-driven reversed electron transfer Supports pmf involvement in aerobic carboxydotrophic energy metabolism.
proton motive force drives formation of reduced pyridine nucleotides biolink:produces
Reverse electron transfer can form reduced pyridine nucleotides.
- DOI:10.1111/j.1574-6968.1986.tb01858.x formation of reduced pyridine nucleotides Supports pmf-driven reverse electron transfer output.
Ni,Fe-carbon monoxide dehydrogenase has quality oxygen sensitivity
Ni,Fe-CODHs are oxygen sensitive, restricting them to anaerobic carboxydotrophs.
- DOI:10.1128/jb.00332-22 coo operons, which encompass O2-sensitive Ni,Fe-CODHs Ni,Fe-CODHs are noted as oxygen sensitive and associated with anaerobic carboxydotrophs.
molybdenum hydroxylase has quality oxygen tolerance
Cu,Mo-CODHs are O2-tolerant, enabling aerobic CO metabolism.
- DOI:10.1128/jb.00332-22 cox operons, which encompass O2-tolerant Cu,Mo-CODHs Cu,Mo-CODHs are O2-tolerant (aerobic CO metabolism).
CooA activates production of Ni,Fe-carbon monoxide dehydrogenase
CO-bound CooA activates transcription that produces the Ni,Fe-CODH machinery encoded in the coo operon.
- DOI:10.1128/jb.00332-22 CO binding to Fe(II) heme in the regulatory domain allosterically activates CooA to bind promoter sites upstream of the coo operon and recruit RNA polymerase (RNAP) for transcription of downstream genes CO binding to Fe(II)-heme allosterically activates promoter binding and RNAP recruitment of coo operons.
RcoM regulates production of molybdenum hydroxylase RO:0002211
RcoM regulates transcription that produces the aerobic coxSML CODH machinery.
- DOI:10.1128/jb.00332-22 CooA and RcoM each primarily regulate anaerobic and aerobic CODH expression, respectively. RcoM regulates aerobic CO oxidation and was originally identified upstream of coxMSL genes.
proton motive force powers ATP synthase METPO:2007900
The ion motive force generated by CO oxidation drives ATP synthase.
- DOI:10.1186/s40643-023-00705-9 The reduction of those electron acceptors causes the formation of an ion motive force, which leads to the synthesis of ATP Generates an ion motive force that drives ATP synthesis.
molybdenum hydroxylase coupled to reduction of dioxygen
Mo-CODH-mediated CO oxidation is coupled to O2 reduction aerobically.
- DOI:10.1128/aem.00185-23 CO oxidation by Mo-CODH was coupled with O2 reduction under aerobic conditions Mo-CODH-mediated CO oxidation supports O2 reduction aerobically.
CooA regulates production of carbon monoxide dehydrogenase RO:0002211
CO-bound CooA transcriptionally regulates production of carbon monoxide dehydrogenase and its accessory machinery.
- DOI:10.1128/jb.00332-22 Transcriptional activation leads to rapid expression of CODH and other accessory proteins Verified against the open Journal of Bacteriology article.

Protein and taxon examples

Graph node Protein Taxon UniProt status Role and evidence

Ni,Fe-carbon monoxide dehydrogenase

Graph node	Protein	Taxon	UniProt status	Role and evidence
Ni,Fe-carbon monoxide dehydrogenase	`UniProtKB:P31896` Carbon monoxide dehydrogenase (cooS)	Rhodospirillum rubrum `NCBITaxon:1085`	`REVIEWED` retrieved 2026-08-23 · sequence v1	NiFeS CooS enzyme catalyzing CO oxidation in the hydrogenogenic R. rubrum system; it is not used as the grounding for the umbrella CODH node. `DOI:10.1021/ja990396i` site-directed mutagenesis of the cooS gene The primary study mutagenized R. rubrum cooS and measured the resulting CODH turnover, linking this exact gene product to catalysis; UniProtKB P31896 verifies the reviewed instance. `DOI:10.1128/jb.159.2.693-699.1984` two-electron oxidation of CO to form CO2 Purified R. rubrum CODH directly catalyzed the reaction represented by the graph.

UniProtKB:P31896
Carbon monoxide dehydrogenase (cooS)

Rhodospirillum rubrum
NCBITaxon:1085

REVIEWED
retrieved 2026-08-23 · sequence v1

NiFeS CooS enzyme catalyzing CO oxidation in the hydrogenogenic R. rubrum system; it is not used as the grounding for the umbrella CODH node.

DOI:10.1021/ja990396i site-directed mutagenesis of the cooS gene The primary study mutagenized R. rubrum cooS and measured the resulting CODH turnover, linking this exact gene product to catalysis; UniProtKB P31896 verifies the reviewed instance.
DOI:10.1128/jb.159.2.693-699.1984 two-electron oxidation of CO to form CO2 Purified R. rubrum CODH directly catalyzed the reaction represented by the graph.

Provenance

Identifier source: METPO (2026-06-12)
Definition source: DOI:10.1038/nrmicro1595

Parent traits (1)

trophic type METPO:1000631

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

METPO:1000633 [-2.124, -2.915, -5.468, -0.095, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

physiology hydrogenotrophic 0.960
physiology photolithoautotrophic 0.958
physiology trophic type 0.956
physiology photoorganoheterotrophic 0.900
physiology lithoautotrophic 0.899
physiology photolithotrophic 0.884
physiology chemoautotrophic 0.871
physiology mixotrophic 0.869

Deep research

Generated by just research-trait; source: research/traits/physiology/carboxydotrophic-deep-research-falcon.md

Unreviewed literature output — not curated TraitMech content Ontology identifiers suggested below have not been resolved against their ontologies, and some are known to be wrong. Check any CURIE against the source before using it.

# Curation-focused research report: carboxydotrophic

**Target trait:** `METPO:1000633`
**Category:** PHYSIOLOGY | **Term kind:** CLASS | **Mapping:** REVIEWED
**Proposed operational meaning:** an organism conserves energy from oxidation of carbon monoxide (CO), whether coupled to aerobic respiration, anaerobic respiration, hydrogenogenesis, acetogenesis, or another experimentally demonstrated energy-conserving process.

## 1. Scope and boundaries

The chemically invariant core is:

**CO + H₂O → CO₂ + 2H⁺ + 2e⁻**, catalyzed by carbon monoxide dehydrogenase (CODH). The released electrons must feed an energy-conserving system for the phenotype to qualify under the supplied definition. Aerobic organisms commonly couple CO oxidation to O₂ reduction; anaerobes can couple it to H₂ evolution, acetogenesis, methanogenesis, or anaerobic respiration. The enzyme families differ substantially: aerobic CODHs are generally Mo,Cu-containing CoxLMS enzymes, whereas anaerobic CODHs are Ni,Fe,S enzymes that may be monofunctional or associated with acetyl-CoA synthase (ACS). (bahrle2023currentstatusof pages 5-8, oelgeschlager2008carbonmonoxidedependentenergy pages 1-2, svetlitchnyi2001twomembraneassociatednifescarbon pages 1-2)

### Recommended inclusion rule

Curate `METPO:1000633` when at least one of the following is demonstrated:

1. growth with CO as an energy source;
2. CO-dependent ATP generation, ion-gradient formation, respiration, or H₂ evolution;
3. CO-dependent production of reduced electron carriers connected experimentally to energy conservation;
4. a complete mechanistic chain from CODH-catalyzed CO oxidation to a respiratory or chemiosmotic module.

CO need not be the sole carbon source. Strict “growth on CO as sole carbon and energy source” is a particularly strong assay, but it is narrower than the supplied ontology definition.

### Boundary cases

- **Carboxydovory:** some organisms oxidize low or atmospheric CO to support maintenance or respiration without fixing CO-derived CO₂ or growing autotrophically. This overlaps the supplied energy-based definition but is distinguished in the literature from classical carboxydotrophy. Represent it as a narrower assay/context rather than requiring carbon fixation in every carboxydotroph. (bahrle2023currentstatusof pages 5-8)
- **CODH gene presence alone:** not sufficient. Approximately 6% of surveyed microbial genomes were estimated to encode at least one Ni,Fe-CODH gene, but homologs may serve reversible CO₂ reduction, acetyl-CoA metabolism, or backup energy metabolism; genomic presence is therefore predictive rather than phenotypic evidence. (bahrle2023currentstatusof pages 5-8)
- **CODH/ACS-dependent carbonyl synthesis:** production and channeling of CO as an internal Wood–Ljungdahl-pathway intermediate is not necessarily energy derivation from exogenous CO.
- **CO production:** composting, heme degradation, or other CO-generating processes are outside scope unless the same organism also oxidizes CO for energy.
- **Community-level CO conversion:** a consortium may be carboxydotrophic while the responsible organism remains unresolved. Do not assign the phenotype to every community member.
- **Methanogenesis, acetogenesis, or dechlorination supported indirectly by H₂/acetate:** downstream consumers are not themselves carboxydotrophs unless direct CO oxidation is shown.

## 2. Candidate graph nodes

Identifiers below are deliberately conservative. Labels are retained where an exact ontology term was not verified.

### Trait and processes

- `METPO:1000633` — carboxydotrophic
- `METPO:1000631` — supplied parent trait
- CO oxidation / carbon-monoxide dehydrogenase reaction
- aerobic respiration
- anaerobic respiration
- hydrogenogenesis / water–gas-shift metabolism
- acetogenesis
- methanogenesis
- Calvin–Benson–Bassham (CBB) cycle
- Wood–Ljungdahl pathway (reductive acetyl-CoA pathway)
- proton- or sodium-motive-force generation
- ATP synthesis
- autotrophic growth
- reductive dechlorination — downstream community application, not part of the core trait

### Chemicals and electron carriers

- `CHEBI:17245` — carbon monoxide
- `CHEBI:16526` — carbon dioxide
- `CHEBI:15377` — water
- `CHEBI:15378` — proton
- `CHEBI:15379` — dioxygen

Showing the first 60 of 265 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Canonical examples (2)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

Carboxydothermus hydrogenoformans NCBITaxon:129958 PMID:16311624 Thermophilic hydrogenogenic CO oxidiser (CO + H2O -> CO2 + H2). Afipia/Oligotropha carboxidovorans is the aerobic CO-oxidiser model.
Rhodospirillum rubrum NCBITaxon:1085 DOI:10.1128/jb.174.16.5284-5294.1992 Canonical hydrogenogenic CO oxidizer with genetically and biochemically characterized cooS CODH and CooA-regulated coo operons.

Curation history

2026-08-23T09:11:00Z · CURATE_PROTEIN_TAXON_EXAMPLE · codex
Reviewed the aerobic and anaerobic graph branches, grounded NiFe CODH and ATP synthase, documented exact label-only dispositions including CooA, and added DOI-backed R. rubrum CooS P31896.
2026-05-05T01:35:46.868229+00:00 · SEEDED_FROM_METPO · seed_from_metpo
imported from data/raw/metpo.owl (CLASS)
2026-05-08T00:00:00-07:00 · ADDED_CAUSAL_GRAPH · codex
Added DOI-backed causal graph for CODH-mediated carbon monoxide oxidation, respiratory-chain coupling, and energy conservation.
2026-05-20T03:35:31Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000016×1).
2026-05-23T08:21:50Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces×1).
2026-05-23T21:30:07Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007405×1, METPO:2007402×1).
2026-05-24T04:38:01Z · GROUND_CAUSAL_NODES · claude
Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022904×1).
2026-05-24T04:41:04Z · GROUND_CAUSAL_NODES · claude
Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500×1).
2026-05-24T05:05:15Z · GROUND_CAUSAL_NODES · claude
Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A061JSS8×1, UniProtKB:A0A099I9V3×1).
2026-05-26T02:30:13Z · RETYPE_CAUSAL_NODES · claude
Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1.
2026-05-26T05:00:48Z · RENAME_PREDICATE_LABELS · claude
Renamed 1 causal-edge predicate label(s) to align with existing groundings: requires → depends on ×1.
2026-05-26T05:00:51Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002502×1).
2026-06-13T21:03:27Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces×1).
2026-06-23T00:00:00Z · ENRICH_CAUSAL_GRAPH · claude
Added 8 evidence-backed generic edges (9 new nodes) from the deep-research report.
2026-06-24T17:21:14Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:encodes×2, RO:0002211×1).
2026-06-24T17:21:20Z · GROUND_CAUSAL_NODES · claude
Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A415TT77×1).
2026-06-24T17:23:34Z · GROUND_CAUSAL_NODES · claude
Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15379×1).
2026-06-26T07:15:20Z · GROUND_CAUSAL_NODES · claude
Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1D7QXJ2×1, UniProtKB:A0A0D5N3T8×1).
2026-07-20T04:21:12Z · RETRACT_DEAD_UNIPROT_GROUNDINGS · claude
Retracted 4 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)
2026-08-06T02:00:00Z · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude
Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to oxidizes), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.
2026-08-07T04:00:00Z · REGROUND_CAUSAL_EDGE · claude
Re-grounded the `encodes` edge(s) from biolink:encodes to METPO:2007813, issue 342. biolink:encodes is NOT a slot in the pinned biolink 4.4.0 model, so the CURIE resolved to nothing upstream while looking like an upstream term to anyone reading this record -- the disclaimer saying otherwise lived in mappings/predicate_grounding.tsv, which is not read at the point of use. RO:0002205 (has gene product) is the nearest real term but relates a GENE to a gene product, whereas these edges relate a gene cluster or operon to a protein complex or a biosynthetic process, which its range does not admit; that mismatch is why the coinage existed. METPO:2007813 is proposed in proposals/metpo_traitmech_v9 and is a placeholder id until METPO mints it, which puts it in the same state as the rest of that cohort rather than in a category of its own.
2026-08-17T02:00:00Z · NORMALISE_NODE_SENSE · claude
One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. A third id for the same molecule, grounded CHEBI:15379 like the rest. Folded into molecular_oxygen: #384 reported two ids for oxygen, and there were four.
2026-08-22T04:26:16Z · REVIEW_UNIPROT_INSTANCE_GROUNDINGS · codex
Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).
2026-08-30T19:21:37Z · REVIEW_EVIDENCE_REFERENCE_CHURN · codex
Offline review for issue 520 retained 1 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1101/2023.01.17.524042 -> DOI:10.1128/aem.00185-23 (1 edge).
2026-08-31T06:33:04Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007900×1).
2026-08-31T10:45:00Z · CONNECT_CAUSAL_GRAPH_COMPONENTS · codex
Resolved issue #183 graph fragmentation (2 components to 1) with 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.