identifier: traitmech:000588 label: phototaxis definition: A motile phenotype in which active locomotion is directionally biased toward or away from a light source in response to illumination. definition_source: DOI:10.1105/tpc.108.057919 trait_category: PHYSIOLOGY term_kind: CLASS mapping_status: PROPOSED parent_traits: - METPO:1000702 evidence: - reference: DOI:10.7554/eLife.12620 snippet: the majority of motile cells switched direction within about 1 min, and then moved directly towards the light source notes: '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.' - reference: DOI:10.1105/tpc.108.057919 snippet: Chlamydomonas cells with low CHR2 content exhibit photophobic and phototactic responses that strictly depend on the availability of CHR1. notes: 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. - reference: DOI:10.1093/dnares/dss024 snippet: ‘PCC-M and PCC-P’ are strains that both exhibit the native positive phototaxis, whereas ‘PCC-N’ strain shows negative phototaxis. notes: 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. canonical_examples: - taxon_id: NCBITaxon:1148 taxon_label: Synechocystis sp. PCC 6803 reference: DOI:10.7554/eLife.12620 note: '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: - discussion_id: phototaxis-direction-and-mapping-boundaries prompt: Preserve directional scope and resolve phenotype-level mappings. kind: CURATION_TODO status: OPEN rationale: 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. posed_by: codex posed_date: '2026-10-04' - discussion_id: phototaxis-mechanism-and-optical-provenance prompt: Ground causal branches without promoting optical models to facts. kind: CURATION_TODO status: OPEN rationale: '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.' posed_by: codex posed_date: '2026-10-04' curation_history: - timestamp: '2026-10-04T05:21:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: 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. llm_assisted: true