carbon-source memory

traitmech:000706 · CLASS · PROPOSED

A physiological phenotype in which a non-genetic cellular state established by prior carbon-source conditions persists after those conditions change and alters subsequent induction or growth responses to carbon sources.

Trait evidence (3)

DOI:10.1371/journal.pgen.1004556
Cells grown under cyclical glucose/lactose conditions thus displayed phenotypic memory of their previous metabolic adaptation.

Lambert and Kussell 2014, PMID:25255314, PMC4177670; Results / Phenotypic memory in response to sudden environmental changes, not the abstract. Primary text, actual Figure 2 and Text S1 were inspected. Repeated glucose/lactose switches demonstrate history-dependent growth; the paper distinguishes inherited protein persistence from continuing induction after stimulus removal. F3 is an engineered W3110 derivative, not an unmodified natural exemplar. Growth is a chamber-level relative elongation readout. DOI:10.1371/journal.pgen.1004793 corrects author-name typesetting, not the biological claims; the correction was read. Model predictions are not additional experimental replication. Other figures, raw data and equations were not independently reanalyzed.
DOI:10.7554/eLife.39234
past exposure to an environmental condition can shorten the time needed to adapt when the condition re-occurs

Cerulus et al. 2018, PMID:30299256, PMC6211830; scientific abstract, confirmed against NCBI full-text XML. Relevant Results, Methods, Discussion, actual Figures 1, 2, 6 and Figure 1 supplement 4 were inspected. Carbon-shift assays separate population lag from single-cell growth resumption; cells not resuming within the observation window are not thereby proved dead. Cross-sugar effects and respiratory perturbations oppose an obligatory same-sugar or sugar-specific protein-inheritance mechanism. The main AN63 series is engineered; the separately reported non-laboratory strains have unreviewed primary provenance here. Publisher article access was challenged; public figure assets were accessible. Raw data and all other supplements were not reanalyzed.
DOI:10.1016/j.cub.2007.10.044
This "galactose memory" persists for several generations

Zacharioudakis et al. 2007, PMID:17997309; directly retrieved, source-qualified MED scientific abstract only. The preceding sentence compares initial GAL activation with rapid reactivation in progeny after intervening glucose growth. This supports the induction endpoint, not a measured growth-rate benefit. Its Gal1 and cytoplasmic-factor interpretation remains assay-specific; the abstract's chromatin conclusion is not universalized. Full text, figures and strain provenance were not inspected. The index links a Comment in, not a correction or independent replication.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1371/journal.pgen.1004556

Parent traits (1)

phenotype METPO:1000059

kg-microbe context

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

Discussions and Knowledge Gaps (2)

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

Retain carbon-source history dependence without conflating its endpoints or neighboring traits.

CURATION TODO OPEN carbon-memory-scope-and-hierarchy · raised by codex · 2026-10-12

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 qualifier carbon-source bounds this curator-defined class. Unqualified cellular, metabolic, phenotypic and transcriptional memory, bistability and hysteresis are not asserted as exact synonyms. Demonstrating the phenotype requires comparing prior histories under matched test conditions and genetic background; a single diauxic transition, persistent reporter fluorescence, gene presence or a different current medium alone is insufficient. Induction kinetics and growth recovery are distinct endpoints, and one must not be substituted for the other. No fixed duration, number of divisions, benefit, particular sugar, or molecular mechanism is required. Genetic adaptation, immune memory, chemotactic temporal sensing, stress priming and stochastic bet hedging are not equivalent. METPO:1000731 nutrient adaptation is a trophic-type class locally framed as the chronic copiotroph/oligotroph axis; diauxic growth denotes sequential nutrient use, and generalist/specialist describe niche breadth. METPO:1000059 phenotype is the conservative parent pending upstream hierarchy review. This is not a sequence-feature record or a precomposed uses-carbon-source assertion.

Resolve natural strain provenance and assay-specific causal branches before adding exemplars or a graph.

KNOWLEDGE GAP OPEN carbon-memory-examples-and-mechanisms · raised by codex · 2026-10-12

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 retained observations do not establish a uniform species-wide phenotype or a common protein-resolved mechanism. Canonical taxa require primary provenance and authority-resolved taxon identity; no canonical_examples, causal_graphs or external xrefs are asserted. Source-qualified MED and Crossref records were checked on 2026-10-12. Lambert's linked correction was read and retained in evidence notes; no other linked correction or retraction was exposed by these bounded records. Publisher/full-text access limits are recorded per source, not treated as absence of notices. The pinned and current upstream METPO releases contain no exact memory class found by the ignored/hidden lexical and RDF assessment; the ontology baseline remains unchanged.

Curation history

2026-10-12T03:30:18Z · MINTED_TRAITMECH_ID · codex
Added carbon-source memory with three primary DOI-backed sources and directly checked snippets. Reserved 000706, v582 and 1065900-1065999 after ignored/hidden worktree and pending-PR checks. Endpoint, strain-provenance, mechanism and notice limits are explicit. Existing traits unchanged; timestamp is the observed UTC curation decision.

Recorded curation sessions

2026-10-12T03:32:22Z · claude-code
- CREATE — Add evidence-backed carbon-source memory
  Added one PROPOSED PHYSIOLOGY record through the dry-run-first validated writer. Three primary DOIs support non-genetic carbon-source history dependence with distinct induction and growth endpoints; all three short snippets directly matched retrieved source text. Read the Lambert author-name correction, primary full text and selected actual figures for Lambert and Cerulus, and the source-qualified Zacharioudakis abstract; full-text and provenance limits remain explicit. Ignored/hidden searches covered all 22 registered TraitMech roots, current upstream snapshots, all open/draft PR file lists, and all-state METPO discussions. Reserved traitmech:000706, v582, and the whole 1065900-1065999 block after no-collision checks against 581 cohorts and 127 CommunityMech worktrees. The temporary seeder has 399 records; 55 exact IDs absent from the 1100-record baseline remain discovery leads, not automatically accepted traits. No existing trait, protected spore_germination record, ontology mirror, snippet baseline, or prior review was edited. Canonical examples and causal graphs are intentionally unasserted pending source-specific provenance and mechanism work. Initial writer dry run and 20 focused writer tests passed; broader native validation and saved self-review follow in this branch.
Read this curation session
2026-10-12T03:35:41Z · codex
- AUDIT — Correct history actor attribution without changing the trait
  Corrects history/records/carbon_source_memory/2026-10-12T033222Z-claude-code-032113.yaml: session.actors[0].name retained the scaffolder default claude-code because --actor-name was omitted. The actual actor was codex, using model gpt-5 and agent_tool codex as already recorded. Preserve that original file unchanged as append-only provenance; this successor supplies the corrected attribution. No scientific claim, TraitRecord byte, curation_history event, or proposal changed for this correction. The current add-trait skill already requires the actual --actor-name and post-scaffold inspection, so it needs no duplicate instruction or default modification.
Read this curation session