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proteorhodopsin phototrophy

traitmech:000036 · CLASS · REVIEWED

A light-harvesting metabolism in which a retinal-containing membrane protein (proteorhodopsin) acts as a light-driven proton pump, generating proton motive force without chlorophyll-based reaction centers. Widespread among marine bacterioplankton.

Proteorhodopsin pumps protons under illumination, generating PMF

Evidence-backed causal sketch linking retinal-based proteorhodopsin light-driven proton pumping to proton motive force without chlorophyll-based reaction centers.

Proteorhodopsin pumps protons under illumination, generating PMF Interactive directed graph showing evidence-backed causal relationships for proteorhodopsin phototrophy.

Edge evidence

  • proteorhodopsin enables proteorhodopsin phototrophy RO:0002327

    The retinal-binding pump realizes proteorhodopsin phototrophy.

    • DOI:10.1126/science.289.5486.1902 Béjà et al. identified proteorhodopsin as a retinal-binding light-driven proton pump.
  • proteorhodopsin phototrophy enables proton motive force RO:0002327

    Light-driven proton pumping by proteorhodopsin generates PMF.

    • DOI:10.1038/35081051 Béjà et al. support proteorhodopsin as a widespread light-energy capture system in marine bacteria.
  • light-driven proton pumping generates proton motive force biolink:produces

    Light-driven proton pumping by proteorhodopsin drives PMF generation.

    • DOI:10.4014/jmb.2410.10034 Oh 2024: "PR drives PMF generation".
  • proton motive force enables ATP production RO:0002327

    PR-mediated proton transport generates a membrane potential sufficient for ATP production.

    • DOI:10.1007/s12275-024-00125-0 Lee 2024: "PR-mediated proton transport could generate a sufficient membrane potential for ATP production".
  • proteorhodopsin phototrophy does not produce NAD(P)H METPO:2000222

    Proteorhodopsin phototrophy cannot generate NAD(P)H for anabolic metabolism; ATP-only energy module.

    • DOI:10.4014/jmb.2410.10034 Oh 2024: "PR can never be harnessed to generate NAD(P)H for anabolic metabolism".
  • all-trans retinal required for proteorhodopsin

    Functional proteorhodopsin requires all-trans retinal bound via a Schiff base to a central lysine.

    • DOI:10.1038/s41467-024-50960-3 Hirschi 2024: "Functional proteorhodopsin requires insertion of all-trans retinal by formation of a Schiff base with a central lysine".
  • beta-carotene cleaved to produce all-trans retinal

    Beta-carotene is cleaved by dioxygenase into retinal, an essential element of functional PR.

    • DOI:10.34133/2022/9782712 Jing 2022: "beta-carotene can be cleaved by dioxygenase into retinal, which is an important element in functional PR".

Provenance

Source
METPO (2025-11-25)
Definition source
DOI:10.1126/science.289.5486.1902

Parent traits (1)

Synonyms (1)

  • rhodopsin-based phototrophy RELATED_SYNONYM · DOI:10.1038/35081051

kg-microbe context

Matched 1 kg-microbe node via parent_proxy.

  • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

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).

Curation history

  1. · PROPOSED_FROM_RESEARCH · claude

    Proposed candidate METABOLISM trait (proteorhodopsin phototrophy) from literature research to fill the light-driven-energy gap.

  2. · CURATED_CAUSAL_GRAPH · claude

    Added evidence-backed causal graph (proteorhodopsin light-driven proton pump) with METPO node grounding and RO predicate groundings; promoted PROPOSED to REVIEWED.

  3. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1D7QWW9×1).

  4. · ENRICH_CAUSAL_GRAPH · claude

    Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces×1, RO:0002327×1).

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:13392×1, CHEBI:17579×1).

  7. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000222×1).