sporulation
METPO:1000870 · CLASS · REVIEWED
A phenotype that is relating to an organism's ability to form dormant, stress-resistant endospores.
Sporulation Spo0A and sigma-factor morphogenesis
Edge evidence
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nutrient limitation
activates
Spo0A phosphorelay
RO:0002213Starvation and stress signals feed into Spo0A activation.
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DOI:10.1016/S1369-5274(00)00141-7steps that lead to activation of Spo0A
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Spo0A phosphorelay
initiates
asymmetric septation
Spo0A-dependent transcription initiates the morphological program that includes asymmetric septation.
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DOI:10.1146/annurev.genet.30.1.297activation of these sigma factors to landmark events in morphogenesis
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asymmetric septation
establishes
compartment-specific sigma factors
Asymmetric septation establishes mother-cell and forespore compartments with distinct sigma-factor programs.
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DOI:10.1128/MMBR.67.4.526-560.2003Compartmentalization of Gene Expression
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compartment-specific sigma factors
regulates
forespore maturation
RO:0002211Sequential sigma-factor activity drives forespore development.
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DOI:10.1128/MMBR.67.4.526-560.2003forespore- and mother cell-specific transcription factors
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forespore maturation
has output
endospore
RO:0002234Forespore maturation produces a dormant endospore.
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DOI:10.1146/annurev.genet.30.1.297within which a spore is produced
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endospore
manifests as
sporulation
METPO:2007400Endospore production manifests the sporulation phenotype.
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DOI:10.1038/nrmicro2921production of a highly resistant dormant cell type known as the spore
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asymmetric septation
has output
mother cell and forespore
RO:0002234Asymmetric division produces distinct mother-cell and forespore compartments.
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DOI:10.1038/s41467-024-51654-6
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SpoIIIE
mediates
chromosome translocation
SpoIIIE translocates the chromosome into the forespore after asymmetric septation.
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DOI:10.1038/s41467-024-51654-6
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forespore engulfment
creates
cell-within-a-cell state
biolink:producesEngulfment of the forespore by the mother cell creates a cell-within-a-cell state.
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DOI:10.1038/s41467-024-51654-6
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sigma F
activates
sigma E
RO:0002213Forespore sigma F drives activation of mother-cell sigma E.
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DOI:10.1016/j.jbc.2024.107905
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sigma G
drives
spore DNA protection
Late forespore sigma G drives spore DNA protection during maturation.
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DOI:10.1038/s41467-024-51654-6
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sigma K
controls
spore coat and cortex
RO:0002211Mother-cell sigma K controls spore coat and cortex maturation.
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DOI:10.1038/s41467-024-51654-6
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spore coat and cortex
confers
heat and chemical resistance
Deposition of cortex, coat and exosporium confers heat and chemical resistance.
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DOI:10.1038/s42003-024-06521-x
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Provenance
- Source
- METPO (2025-11-25)
- Definition source
- DOI:10.1146/annurev.genet.30.1.297
Parent traits (1)
Synonyms (2)
- General.keywords
- Physiology and metabolism.spore formation.spore formation
kg-microbe context
Matched 1 kg-microbe node via direct_metpo.
METPO:1000870[-1.554, -2.668, -2.202, -0.616, …]
Nearest neighbors in embedding space
- morphology motility 0.840
- physiology oxidase activity 0.829
- morphology gas vesicle 0.829
- physiology chemotaxis 0.829
- environment metal tolerant 0.829
- physiology dormancy 0.829
- environment mercury tolerant 0.829
- environment ionizing radiation tolerant 0.829
Deep research
# Curation-focused research report: bacterial sporulation ## 1. Scope and recommended interpretation **Target trait:** sporulation **Trait identifier:** **`METPO:1000870`** **Category / kind / status:** MORPHOLOGY / CLASS / REVIEWED **Parent:** `METPO:1000059` For this graph, sporulation should mean the **capacity of a vegetative bacterial cell to execute endospore-forming differentiation**, culminating in a dormant endospore. In the canonical *Bacillus* sequence, starvation or nutrient limitation activates Spo0A, followed by asymmetric septation, formation of mother-cell and forespore compartments, forespore engulfment, cortex and coat assembly, core maturation, mother-cell lysis, and release of the mature spore. A recent review describes seven morphological stages and the ordered σF–σE–σG–σK program; a 2024 primary study reports that the post-septation program takes approximately six hours in *Bacillus subtilis* and becomes irreversible after asymmetric division. (m.2023sporulationstructureassembly pages 4-6, updegrove2024altruisticfeedingand pages 1-2) ### Boundaries Include: - initiation of bacterial **endospore formation**; - developmental asymmetric division and forespore morphogenesis; - compartment-specific transcription and intercellular signaling; - cortex, coat, and core maturation insofar as they are necessary to produce an endospore; - mother-cell lysis and spore release. Keep separate or model only as downstream/modifier branches: - **germination and outgrowth**, which convert a dormant spore back to vegetative growth; - **spore resistance**, persistence, and dormancy, which are products/properties of a mature spore rather than sporulation itself; - bacterial **exospore** formation, fungal sporulation, conidiation, fruiting-body development, cyst formation, and akinetes. Endospore and exospore formation involve distinct, likely independently evolved pathways despite sharing nutrient limitation and extensive envelope remodeling. (beskrovnaya2021structuralmetabolicand pages 2-3) Accordingly, the existing definition—“an organism’s ability to form dormant, stress-resistant endospores”—is appropriate, but the causal graph should terminate at **mature endospore formation/release**, with dormancy and resistance represented as downstream consequences. ## 2. Candidate nodes grouped by type ### Environmental and experimental inputs - nutrient limitation / starvation; - transition to stationary phase; - sporulation-inducing medium or nutrient downshift; - population-level glycerol signal/nutrient; - favorable nutrient influx, as an antagonist after starvation but before commitment; - heat, desiccation, radiation, disinfectants, and preservatives—**assay factors for mature-spore resistance, not primary sporulation triggers**. Starvation is strongly supported as a trigger, but the immediate biochemical input to individual Kin proteins remains context dependent. Sporulation integrates multiple environmental and metabolic cues through the phosphorylation state of Spo0A. (gohari2024theimpactof pages 1-2, updegrove2024altruisticfeedingand pages 1-2) ### Regulatory proteins and signaling modules - KinA, KinB and other sporulation-associated histidine kinases; - Spo0F, Spo0B, Spo0A, and phosphorylated Spo0A (`Spo0A~P`); - Rap phosphatases/Phr peptide regulators and Spo0E-family phosphatases; - σH/SigH; - SpoIIE, SpoIIAA, SpoIIAB, σF/SigF; - SpoIIR, SpoIIGA, pro-σE, σE/SigE; - SpoIIIA proteins and SpoIIQ transenvelope complex; - σG/SigG; - pro-σK and σK/SigK; SpoIVB–BofA–SpoIVFA–SpoIVFB should remain provisional unless separately evidenced in the target source set; - Rho transcription-termination factor; - ShfA/YabQ and ShfP/YvnB. ### Morphogenesis and envelope-remodeling entities - polar/asymmetric septum; - mother cell and forespore;
Curation history
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SEEDED_FROM_METPO · seed_from_metpo
imported from data/raw/metpo.owl (CLASS)
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CURATED_WITH_LITERATURE · codex
Added DOI-backed definition and causal graph for nutrient limitation, Spo0A phosphorelay, asymmetric septation, compartment sigma factors, forespore maturation, and endospore formation.
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GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1).
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GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400×1).
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RENAME_PREDICATE_LABELS · claude
Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives → regulates ×1.
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GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211×1).
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GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213×1).
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REMOVE_REDUNDANT_SYNONYM · claude
Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).
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ENRICH_CAUSAL_GRAPH · claude
Added 7 evidence-backed generic edges (12 new nodes) from the deep-research report.
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GROUND_CAUSAL_PREDICATES · claude
Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1, biolink:produces×1, RO:0002213×1, RO:0002211×1).
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GROUND_CAUSAL_NODES · claude
Grounded 4 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A100JQQ1×1, UniProtKB:E0J3M3×1, UniProtKB:A0A0C7NZS0×1, UniProtKB:A0A060N640×1).
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RETRACT_DEAD_UNIPROT_GROUNDINGS · claude
Retracted 3 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)
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MIGRATE_MICROBE_DOMAIN_EDGES · claude
Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to has output), issue 301. 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. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.