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cell shape

METPO:1000666 · CLASS · REVIEWED

A phenotype that describes the characteristic three-dimensional morphological form of a microbial cell, determined by cell wall structure, cytoskeletal elements, and environmental factors.

Bacterial cell-shape morphogenesis mechanism

Evidence-backed causal sketch linking cell shape to peptidoglycan synthesis, PBPs, MreB, FtsZ, crescentin, and localized wall growth.

Bacterial cell-shape morphogenesis mechanism Interactive directed graph showing evidence-backed causal relationships for cell shape.

Edge evidence

  • peptidoglycan cell wall regulates cell shape RO:0002211

    The peptidoglycan wall has a primary role in maintaining bacterial cell shape.

    • DOI:10.1038/nrmicro1205 primary role in maintaining cell shape Review supports peptidoglycan wall as central to cell shape.
  • penicillin-binding proteins catalyzes peptidoglycan synthesis biolink:catalyzes

    PBPs synthesize and remodel peptidoglycan during growth and division.

    • DOI:10.1038/nrmicro1205 carry out the reactions for synthesis and remodelling Supports PBPs in peptidoglycan synthesis/remodeling.
  • peptidoglycan synthesis causes cell shape biolink:causes

    Spatial regulation of wall synthesis determines growth morphology.

    • DOI:10.1038/nrmicro2677 peptidoglycan synthesis to bacterial growth and morphology Review supports regulated peptidoglycan synthesis as a determinant of morphology.
  • MreB positions peptidoglycan synthesis

    MreB helps organize or position peptidoglycan synthesis machinery.

    • DOI:10.1038/nrmicro2677 positions peptidoglycan biosynthesis machineries Supports MreB in spatial organization of cell-wall synthesis.
  • FtsZ regulates cell shape RO:0002211

    FtsZ controls division-associated shape generation and septal wall synthesis.

    • DOI:10.1038/nrmicro1205 FtsZ is essential for cell division Supports FtsZ as a shape-related cytoskeletal protein through cell division.
  • crescentin contributes to cell shape RO:0002326

    Crescentin contributes to curved-rod cell shape in representative bacteria.

    • DOI:10.1038/nrmicro1205 crescentin is required for the curved-rod shape Supports crescentin as a cell-shape determinant in Caulobacter.
  • Rod complex (elongasome) shapes peptidoglycan architecture

    The rod complex (elongasome) determines the overall shape and dense architecture of peptidoglycan.

    • DOI:10.1002/mbo3.1385 Rod complex may be a determinant for the whole shape of peptidoglycan and its highly dense structure.
  • peptidoglycan architecture regulates cell shape RO:0002211

    Peptidoglycan wall architecture underlies cell shape.

    • DOI:10.1002/mbo3.1385 Peptidoglycan determines cell shape (broad bacterial claim).
  • MreB organizes rod shape

    MreB coordinates with PG synthases to organize cell-wall synthesis for rod shape.

    • DOI:10.1042/bsr20221664 MreB coordinates with PG synthases and is linked to rod shape.
  • A22 (MreB inhibitor) disrupts rod shape

    A22 reduces MreB filaments, causing loss of rod shape and lysis.

    • DOI:10.1128/jb.00433-22 A22 reduces MreB filaments leading to loss of rod shape and lysis.
  • cardiolipin / increased lipid order inhibits MreB RO:0002212

    Increased lipid order or cardiolipin interferes with MreB assembly.

    • DOI:10.1128/jb.00433-22 Increased lipid order or cardiolipin interferes with MreB assembly.
  • flotillins promotes cell wall synthesis RO:0002213

    Flotillins promote MreB activity and cell-wall synthesis via membrane organization.

    • DOI:10.1128/jb.00433-22 Absence of flotillins downregulates MreB activity and cell wall synthesis.

Provenance

Source
METPO (2025-11-25)
Author
Luke Wang
Definition source
DOI:10.1038/nrmicro1205

Parent traits (1)

Children (34)

Synonyms (2)

  • Morphology.cell morphology.cell shape RELATED_SYNONYM · metpo.owl
  • cell_shape RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000666 [-5.052, -3.981, -3.909, -0.718, …]

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).

Deep research

Generated by just research-trait; source: research/traits/morphology/cell_shape-deep-research-falcon.md

Unreviewed literature output — not curated TraitMech content Ontology identifiers suggested below have not been resolved against their ontologies, and some are known to be wrong. Check any CURIE against the source before using it. 
# Curation report: microbial cell shape

## Target and scope

- **Trait:** cell shape
- **Trait CURIE:** **METPO:1000666**
- **Category / kind / status:** MORPHOLOGY / CLASS / REVIEWED
- **Parent:** METPO:1000059

This trait should represent the characteristic three-dimensional geometry of an individual microbial cell—e.g., coccus, straight rod, curved/vibrioid, helical, filamentous/branched, or archaeal disk/polyhedral form. In bacteria, the immediate load-bearing determinant is usually the peptidoglycan (PG) sacculus; shape emerges from the spatial and temporal pattern of PG synthesis, cross-linking, cleavage, and repair rather than merely from the presence of PG. MreB/elongasome or DivIVA/polar-growth systems organize these reactions, while specialized modules generate curvature, helicity, branches, or stalks (teeseling2017determinantsofbacterial pages 3-4, kysela2016diversitytakesshape pages 4-5, shlosman2023allostericactivationof pages 1-2).

Archaea require a separate mechanistic branch: many lack PG and instead use S-layers and archaeal cytoskeletal systems. In *Haloferax volcanii*, rod and disk states are growth-condition-dependent and genetically separable, with RdfA, DdfA, volactin, and CetZ1 implicated in shape determination (brown2024mindproteinsregulate pages 1-2, schiller2024identificationofstructural pages 1-2).

### Boundary cases

Do **not** treat the following as synonymous with cell shape:

1. **Cell size**—length, width, area, or volume may change without a categorical geometry change.
2. **Cell arrangement**—chains, clusters, diplococci, or biofilm architecture describe relations among cells.
3. **Division and separation**—filamentation caused by failed septation is a shape phenotype only when the individual-cell geometry endpoint is explicitly measured; otherwise it is primarily a division phenotype.
4. **Growth mode**—lateral, polar, or zonal PG insertion is an upstream process, not the trait itself.
5. **Polarity, motility, branching, stalks, and appendages**—curate as shape only where they alter the cell body or a source explicitly links them to morphogenesis.
6. **Spheroplast, protoplast, and L-form states**—these are induced envelope-deficient states and should carry assay/environment qualifiers. The *Vibrio cholerae* recovery study is useful mechanistically but is not evidence for unperturbed vegetative morphogenesis (goudin2023recoveryofvibrio pages 1-2).
7. **Pleomorphism**—a distribution or capacity to transition among shapes; it should not be collapsed into any one terminal shape.

## Current mechanistic model

The best-supported bacterial core is:

**lipid II → PG polymerization and peptide cross-linking → patterned PG insertion/remodeling → sacculus mechanical anisotropy → cell shape.**

RodA–PBP2 provides coupled glycan polymerization/transpeptidation in the elongasome, while MreB aligns with membrane curvature and orients circumferential synthesis. Divisome synthesis, centered on FtsW–FtsI and FtsZ organization, creates septa and new poles. PG hydrolases permit controlled expansion by cleaving existing bonds; unbalanced synthesis or hydrolysis produces deformation or lysis (teeseling2017determinantsofbacterial pages 3-4, hussain2018mrebfilamentsalign pages 1-2, shlosman2023allostericactivationof pages 1-2).

This model is not universal. MreB-less Actinomycetota and Rhizobiales can elongate from poles or tips using DivIVA/polarisome or bactofilin-associated machinery. Specialized cytoskeletal or envelope-patterning systems superimpose curvature or helicity on a basal rod-building program (richter2023interactingbactofilinsimpact pages 1-2, sen2024adispensablesepiva pages 1-2, pohl2024anoutermembrane pages 1-2).

## Candidate nodes grouped by type

### Trait and morphology nodes

- **cell shape — METPO:1000666**
- rod shape
- spherical/coccoid shape
- curved or vibrioid shape
- helical shape
- filamentous/hyphal shape
- branched morphology
- disk/polyhedral shape
- pleomorphic shape transition

Child-shape CURIEs should be added only after lookup in METPO or another approved phenotype ontology; labels are safer than guessed identifiers.

### Chemicals and envelope structures

- **peptidoglycan — CHEBI:8005**
- **potassium cation — CHEBI:29103**
- lipid II — grounding should be verified against ChEBI before curation
- glycan chains and peptide cross-links
- cytoplasmic/plasma membrane
- outer membrane
- periplasm

Showing the first 60 of 260 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  2. · CURATED_WITH_LITERATURE · codex

    Reviewed cell shape trait and added DOI-backed causal graph for peptidoglycan cell wall, PBPs, MreB, FtsZ, crescentin, and localized wall growth.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211×1, RO:0002326×1).

  4. · GROUND_CAUSAL_PREDICATES · claude

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

  5. · RENAME_PREDICATE_LABELS · claude

    Renamed 1 causal-edge predicate label(s) to align with existing groundings: maintains → regulates ×1.

  6. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211×1).

  7. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009252×1).

  8. · GROUND_CAUSAL_NODES · claude

    Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1B1UYY2×1, UniProtKB:C0LUM8×1, UniProtKB:A0A2N9AY16×1).

  9. · RENAME_PREDICATE_LABELS · claude

    Renamed 1 causal-edge predicate label(s) to align with existing groundings: determines → causes ×1.

  10. · GROUND_CAUSAL_PREDICATES · claude

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

  11. · ENRICH_CAUSAL_GRAPH · claude

    Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.

  12. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211×1, RO:0002212×1, RO:0002213×1).

  13. · RETRACT_DEAD_UNIPROT_GROUNDINGS · claude

    Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)