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bacillus shaped

METPO:1000667 · CLASS · REVIEWED

A cell shape characterized by an elongated, rod cylindrical morphology with relatively parallel sides and rounded ends.

Bacillus-shape rod elongation mechanism

Evidence-backed causal sketch linking bacillus morphology to MreB-organized Rod complexes, lateral peptidoglycan insertion, and FtsZ-coupled division.

Bacillus-shape rod elongation mechanism Interactive directed graph showing evidence-backed causal relationships for bacillus shaped.

Edge evidence

  • MreB interacts with Rod complex biolink:interacts_with

    MreB filaments interact with the Rod complex that elongates the cell wall.

    • DOI:10.1146/annurev-cellbio-010521-010834 MreB filaments interact with Rod complexes Supports MreB-Rod complex interaction in rod-shape regulation.
  • Rod complex directs peptidoglycan synthesis RO:0002211

    Rod complexes direct sidewall peptidoglycan synthesis.

    • DOI:10.1146/annurev-cellbio-010521-010834 Rod complexes drive cell wall insertion Supports Rod complex contribution to wall insertion.
  • peptidoglycan synthesis has output lateral cell-wall elongation RO:0002234

    Directed peptidoglycan synthesis supports cylindrical elongation.

    • DOI:10.1038/nrmicro2677 peptidoglycan synthesis to bacterial growth and morphology Supports regulated peptidoglycan synthesis as a determinant of bacterial morphology.
  • lateral cell-wall elongation regulates bacillus shaped RO:0002211

    Lateral wall elongation maintains bacillus-like rod morphology.

    • DOI:10.1016/j.tim.2011.11.004 restores its rod shape Supports MreB-associated cell-wall synthesis as important for rod shape restoration and maintenance.
  • FtsZ coordinates with peptidoglycan synthesis

    FtsZ coordinates division-associated peptidoglycan synthesis with rod-cell growth.

    • DOI:10.1038/nrmicro1205 FtsZ collaborates with penicillin binding proteins Supports FtsZ-PBP collaboration in bacterial cell-shape generation.
  • peptidoglycan cell wall determines bacillus shaped

    The peptidoglycan cell wall protects against osmotic lysis and determines cell shape.

    • DOI:10.1038/s41467-023-39037-9 PG protects bacteria against osmotic lysis and determines cell shape.
  • RodA-PBP2 synthase (Rod complex) required for bacterial cell elongation

    RodA-PBP2 is the essential synthase responsible for bacterial elongation.

    • DOI:10.1038/s41467-023-39037-9 RodA-PBP2 is an essential synthase responsible for bacterial elongation.
  • circumferential glycan strand insertion gives rise to bacillus shaped

    Elongasome inserts long glycan strands as barrel-hoop reinforcement, giving rise to a rod-shaped cell.

    • DOI:10.1038/s41467-024-49785-x Inserts long glycan strands acting as barrel-hoop-like reinforcing structures, thereby giving rise to a rod-shaped cell.
  • moenomycin inhibits class A penicillin-binding proteins RO:0002212

    Moenomycin inhibits class A penicillin-binding proteins, a family of PG synthases.

    • DOI:10.1038/s41467-023-41082-3 Moenomycin inhibits a family of PG synthases known as Class-A penicillin-binding proteins.
  • RodZ causally upstream of, negative effect spherical cell morphology

    Loss of RodZ causes cells to become spherical, indicating RodZ maintains rod shape.

    • DOI:10.3389/fmicb.2024.1400434 delta-rodZ cells were spherical (WT cells are rod-shaped); RodZ broadly implicated in rod maintenance.

Provenance

Source
METPO (2025-11-25)
Author
Anthea Guo
Definition source
DOI:10.1146/annurev-cellbio-010521-010834

Parent traits (1)

Synonyms (1)

  • bacillus RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000667 [-93.971, +37.913, +150.959, -201.986, …]

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/bacillus_shaped-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: bacillus-shaped morphology

## Trait record and scope

- **Trait:** bacillus shaped
- **Identifier:** **“METPO:1000667”**
- **Category/kind/status:** MORPHOLOGY / CLASS / REVIEWED
- **Parent:** METPO:1000666
- **Operational meaning:** a single microbial cell with an elongated cylindrical body, approximately parallel lateral sides, and rounded ends. Here, **bacillus** denotes morphology, not membership in the genus *Bacillus*.

The trait should be assigned from an observed cell-shape phenotype, ideally during a specified growth phase and condition. It is not itself a physiological capacity or growth preference. In canonical bacteria, rod shape is propagated as the peptidoglycan (PG) sacculus expands: the Rod complex directs lateral PG insertion, whereas the divisome makes septal wall. A 2023 review states that the elongasome directs lateral insertion “along the long axis, enabling cylindrical growth,” with RodA and FtsW supporting elongation and division, respectively (galinier2023recentadvancesin pages 3-5).

### Boundaries

- **Include:** straight rods and ordinary rod-length variants whose sides remain approximately parallel.
- **Curved rods:** retain rod architecture but may merit an additional curvature trait; curvature-specific modules such as CrvA, crescentin, or porin–PapS should not define the generic bacillus-shaped graph.
- **Coccobacilli/ovococci:** borderline where length-to-width ratio and parallel sidewalls are weak; require an explicit assay rule.
- **Filaments:** elongated rods without normal septation should additionally receive a filamentous phenotype; filamentation is not equivalent to ordinary bacillus shape.
- **Spheres, disks, L-forms, and pleomorphic cells:** exclude unless documenting a transition into or out of the rod state. Wall-deficient *Vibrio cholerae* spheroplasts lose rod organization and later regenerate branches of normal rod diameter, making this a useful regeneration assay rather than a constitutive trait (goudin2023recoveryofvibrio pages 1-2).
- **Archaeal rods:** phenotypically in scope but mechanistically separate. *Haloferax volcanii* lacks bacterial PG and changes between rods and disks according to growth phase and swimming state; bacterial elongasome edges must not be projected onto it (schiller2024identificationofstructural pages 1-2).
- **Noncanonical bacterial rods:** some Rhizobiales produce rods through unipolar growth without the standard MreB-mediated dispersed-growth program (williams2019mechanismsofpolar pages 57-61).

## Current mechanistic model

The strongest general model is **distributed envelope synthesis plus mechanical feedback**, not “MreB alone specifies a cylinder.” MreB filaments orient active Rod complexes approximately around the circumference; RodA polymerizes glycan and PBP2 cross-links peptide stems. This yields anisotropic sidewall expansion while septal synthesis closes and rounds the ends. MreC, MreD, RodZ, hydrolases, aPBPs, precursor supply, and envelope mechanics regulate this core process (fivenson2023arolefor pages 1-2, galinier2023recentadvancesin pages 3-5).

Recent work expands the model beyond PG alone. In Gram-negative *E. coli*, strengthening the outer membrane rescued growth and rod-shape defects of hypomorphic Rod-complex mutants and restored proper orientation of MreB-directed synthesis. Thus, rod propagation depends on the mechanical state of the whole envelope, although this result is taxon-specific (fivenson2023arolefor pages 1-2, fivenson2023arolefor media 0289c886).

## Candidate nodes grouped by type

### Trait and processes

- bacillus shaped — **METPO:1000667**
- cell morphogenesis — candidate **GO:0000902**
- regulation of cell shape — candidate **GO:0008360**
- peptidoglycan-based cell-wall biogenesis — candidate **GO:0009273**
- cell-wall organization or biogenesis — candidate **GO:0071554**
- lateral PG synthesis / cylindrical cell elongation — label-only until the project’s preferred process term is verified
- septal PG synthesis / cell division
- circumferential glycan insertion
- sacculus mechanical anisotropy
- cell diameter control
- de novo rod-shape recovery

### Complexes and cellular structures

- Rod complex / elongasome — MreB, MreC, MreD, RodZ, RodA, PBP2
- divisome — FtsZ-associated apparatus including FtsW–FtsI
- peptidoglycan sacculus
- cytoplasmic membrane
- periplasm — candidate **GO:0042597**
- Gram-negative outer membrane — candidate **GO:0009279**
- MreB cytoskeletal filaments
- FtsZ ring

### Genes and proteins

- **mreB / MreB:** actin-like organizer of circumferential Rod-complex activity
- **mreC / MreC:** Rod-complex regulator; evidence supports activation through PBP2–RodA in *E. coli*
- **mreD / MreD:** core component, but its precise causal function remains incompletely resolved

Showing the first 60 of 228 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 bacillus shape as rod-like morphology and added DOI-backed causal graph for MreB, Rod complex, peptidoglycan synthesis, lateral wall elongation, and FtsZ coupling.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1).

  4. · GROUND_CAUSAL_PREDICATES · claude

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

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

  9. · RENAME_PREDICATE_LABELS · claude

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

  10. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1).

  11. · ENRICH_CAUSAL_GRAPH · claude

    Added 5 evidence-backed generic edges (8 new nodes) from the deep-research report.

  12. · GROUND_CAUSAL_PREDICATES · claude

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

  13. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:28908×1).

  14. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:H1XNL6×1).

  15. · RETRACT_DEAD_UNIPROT_GROUNDINGS · claude

    Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)

  16. · MIGRATE_MICROBE_DOMAIN_EDGES · claude

    Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 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.

  17. · REGROUND_CAUSAL_EDGE · claude

    Re-grounded causal edge(s) off enables/RO:0002327 onto part of (biolink:part_of), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so an edge pointing at a GENE_OR_PROTEIN entailed a false type. The replacements are chosen per idiom rather than swept: a gene cluster ENCODES its product, a subunit is PART OF the complex it belongs to, and an energy source or acquired repertoire CONTRIBUTES TO the machine it powers or composes. All three declare no rdfs:domain or rdfs:range, so none can reintroduce the class of defect being removed.

  18. · REGROUND_CAUSAL_EDGE · claude

    Corrected the mreB edge from part of to interacts with (biolink:interacts_with), issue 334 review. The first pass over-claimed: the edge's own snippet says MreB filaments INTERACT WITH Rod complexes, and the target node is described as machinery associated with MreB, so parthood is not what the evidence supports. The corpus is also split on it - cell_shape.yaml types rod_complex a PATHWAY with MreB inside it, while this file types it GENE_OR_PROTEIN with MreB outside - which makes parthood exactly the kind of modelling decision this work defers elsewhere. interacts with says what the quoted sentence says and needs no such decision. The edge description was rephrased to match the predicate.