TraitMech

TraitMech › PHYSIOLOGY

phototaxis

traitmech:000588 · CLASS · PROPOSED

A motile phenotype in which active locomotion is directionally biased toward or away from a light source in response to illumination.

Trait evidence (3)

  • DOI:10.7554/eLife.12620
    the majority of motile cells switched direction within about 1 min, and then moved directly towards the light source

    Results, first subsection, Figure 1c-d and methods; publisher version 2, posted 2022-04-22, originally published 2016-02-09 (PMID:26858197). Version-specific full text: https://cdn.elifesciences.org/articles/12620/elife-12620-v2.xml. Figure 1 and both optical figure supplements visually inspected. Motile Synechocystis sp. PCC 6803 PCC-M cells on agarose move toward oblique RGB illumination (470/525/625 nm, equal intensity; 10 micromol photons per square metre per second). The projected white-light intensity gradient does not produce significant directional bias in this experiment. Cells were sampled from moving colony fronts; analysis excludes immotile cells. These observations are separate from torA-gfp optical reporter assays and from the proposed PixJ1-to-pilus signaling model. They do not establish one universal directional-sensing mechanism.

  • DOI:10.1105/tpc.108.057919
    Chlamydomonas cells with low CHR2 content exhibit photophobic and phototactic responses that strictly depend on the availability of CHR1.

    Abstract exact-matched at Europe PMC (PMID:18552201). The PMC introduction distinguishes directional swimming toward or away from light from transient photophobic reversal; the beginning of Results identifies the cell-wall-deficient CW2 strain. Evidence concerns Chlamydomonas reinhardtii under the stated receptor-content conditions, not every algal strain or a universal CHR1 requirement. Xenopus ion-conductance assays are heterologous. Remaining full-text sections and supplements were not inspected; no natural algal exemplar or complete protein-resolved pathway is inferred.

  • DOI:10.1093/dnares/dss024
    ‘PCC-M and PCC-P’ are strains that both exhibit the native positive phototaxis, whereas ‘PCC-N’ strain shows negative phototaxis.

    Results, section 3.1, exact-matched to Europe PMC full-text XML (PMID:23069868). Methods trace PCC-M to the Shestakov laboratory in 1993 and maintenance of motile colonies, matching the Schuergers study. The strain descends from the original PCC isolate but has undergone laboratory microevolution; it is not asserted genetically identical to the original isolate. Discussion also reports no blue-light phototaxis for PCC-M. This supports a substrain-qualified exemplar, not a statement that every PCC 6803 lineage or illumination gives the same response.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1105/tpc.108.057919

Parent traits (1)

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Canonical examples (1)

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

  • Synechocystis sp. PCC 6803 NCBITaxon:1148 DOI:10.7554/eLife.12620 Motile wild-type PCC-M substrain, not the torA-gfp reporter. Figure 1c-d shows positive phototaxis on agarose under oblique RGB illumination after sampling moving colony fronts. Independent provenance: DOI:10.1093/dnares/dss024, Methods 2.1 and Results 3.1; PCC-M retains native positive phototaxis but has laboratory sequence differences and lacks blue-light phototaxis in the cited comparison. NCBI:1148 was resolved at NCBI on 2026-10-04; it is species-level, not a PCC-M-specific accession. No universal substrain, wavelength or sign claim.

Discussions and Knowledge Gaps (2)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Preserve directional scope and resolve phenotype-level mappings.

CURATION TODO OPEN phototaxis-direction-and-mapping-boundaries · raised by codex · 2026-10-04

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

Positive and negative responses are directional cases, not a requirement to exhibit both or a permanent sign. Speed changes alone (photokinesis), light sensing alone and phototrophic energy conservation do not establish this trait. A photophobic response can participate in phototaxis but is not an exact synonym. METPO:1000241 is obsolete with no replacement or definition; do not revive it or assert a replaces relation without upstream review. External biological-process terms are not automatically equivalent to this organismal disposition; verify scope before adding xrefs or lexical synonyms.

Ground causal branches without promoting optical models to facts.

CURATION TODO OPEN phototaxis-mechanism-and-optical-provenance · raised by codex · 2026-10-04

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

The cyanobacterial PixJ1/response-regulator/pilus branch is a proposed model in Schuergers Figure 5; causal edges and eligible taxon-paired protein accessions require additional primary checks. Native algal signaling must be separated from heterologous conductance and cell-wall-deficient strains. Version 2 optical supplement graphics also differ from their captions: Figure 3 supplement 1 labels a 60x objective versus 100x in text, and Figure 4 supplement 1 labels 633 nm versus 625 nm in text. Do not silently reconcile these parameters or use them to quantify a mechanistic graph. Figure 1 phenotype evidence is retained independently. No NONMECHANISTIC graph is used to bypass protein-grounding requirements.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added phototaxis with three primary DOI citations and exact snippets. Ignored-and-hidden searches found no exact live trait; the obsolete METPO class is not reused. Reserved METPO:1054200 in v465. Verified publisher version 2, optical supplements and PCC-M provenance; added a substrain-qualified NCBI-resolved canonical example. Deferred ungrounded protein branches and recorded source discrepancies.