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coccobacillus shaped

METPO:1000688 · CLASS · REVIEWED

A cell shape intermediate between spherical cocci and elongated bacilli, typically appearing as short or plump rods.

Coccobacillus short-rod morphogenesis mechanism

Evidence-backed causal sketch linking coccobacillus shape to peptidoglycan synthesis, MreB-associated elongation, septal growth, and reduced length-to-width ratio.

Coccobacillus short-rod morphogenesis mechanism Interactive directed graph showing evidence-backed causal relationships for coccobacillus shaped.

Edge evidence

  • MreB controls peptidoglycan synthesis RO:0002211

    MreB contributes to control of peptidoglycan synthetic complexes.

    • DOI:10.1128/JB.187.1.54-64.2005 control of the peptidoglycan synthetic complexes Supports MreB involvement in shape-related PG synthesis.
  • peptidoglycan synthesis causes short-rod geometry biolink:causes

    Wall synthesis patterns determine whether cells remain rod-like or become short coccobacilli.

    • DOI:10.1128/JB.187.1.54-64.2005 conditions causing changes in cell shape Supports PG-associated shape changes to a coccobacillus state.
  • septal growth contributes to short-rod geometry RO:0002326

    Division-associated septal growth contributes to the short-rod intermediate geometry.

    • DOI:10.1128/JB.187.1.54-64.2005 role at mid-cell ... in early septation Supports a septation-linked role for MreB in representative coccobacillus-forming cells.
  • short-rod geometry confers coccobacillus shaped METPO:2007700

    Short-rod geometry produces the coccobacillus-shaped trait.

    • DOI:10.1128/JB.187.1.54-64.2005 from a rod to coccobacillus Supports the trait endpoint as a short-rod morphology.
  • RodA/PBP3 elongasome increases cell length-to-width ratio RO:0002213

    Elongasome-driven lateral wall synthesis increases the long-to-short axis ratio, opposing a coccoid shape.

    • DOI:10.1128/mBio.03235-23 This elongation depends on the SEDS/PBP pair RodA/PBP3 and is seen as an increased ratio of long to short cell axes.
  • cell length-to-width ratio determines short-rod geometry

    A reduced but non-coccoid length-to-width ratio defines the short-rod geometry of coccobacilli.

    • DOI:10.1128/mBio.03235-23 Long-to-short cell axis ratio quantifies the elongation state intermediate between coccus and rod.
  • GpsB regulates PBP2 localization RO:0002211

    GpsB regulates the localization of PBP2 between cell periphery and division septum.

    • DOI:10.1128/mBio.03235-23 a gpsB mutant shows the strongest morphological phenotype, driven by partial delocalization of PBP2 and PBP4 away from the division septum.
  • PBP2 localization controls peptidoglycan synthesis RO:0002211

    Spatial localization of PBP2 controls where peptidoglycan insertion and crosslinking occur, biasing cells toward elongation or rounding.

    • DOI:10.1128/mBio.03235-23 Increased PBP2/PBP4 at the cell periphery raises peptidoglycan insertion and crosslinking throughout the cell, impairing elongation.
  • FtsZ filament properties directs peptidoglycan synthesis RO:0002211

    FtsZ filament geometry directs asymmetric, helical patterns of cell-wall insertion.

    • DOI:10.1128/mBio.00908-16 altered FtsZ filaments direct asymmetric, helical cell-wall insertion, generating elongation; this helical pattern of wall insertion leads to elongation.
  • PBP2 (elongasome transpeptidase) required for short-rod geometry

    PBP2 transpeptidase activity within the RodA-PBP2 elongasome is required to maintain non-spherical rod/short-rod geometry.

    • DOI:10.1073/pnas.2215237120 Loss of RodA-PBP2 elongasome activity drives a rod-to-sphere transition; PBP2 transpeptidase activity is required for rod-shape maintenance.

Provenance

Source
METPO (2025-11-25)
Definition source
DOI:10.1128/JB.187.1.54-64.2005

Parent traits (1)

Synonyms (1)

  • coccobacillus RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000688 [-20.154, -47.811, +18.193, -1.988, …]

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/coccobacillus_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: coccobacillus-shaped morphology

## Executive summary

**Target:** **coccobacillus shaped** (`METPO:1000688`), morphology class, reviewed; parent `METPO:1000666`.

The trait denotes a cell whose longitudinal axis remains discernible but is only modestly longer than its width—a short, squat, or plump rod intermediate between a bacillus and a coccus. It is a geometric phenotype, not a single conserved pathway. The strongest mechanistic evidence supports at least three context-specific routes:

1. **Physiological remodeling:** *Rhodobacter sphaeroides* changes from rods during aerobic growth to coccobacilli during photoheterotrophic growth; lower light increases the spherical character.
2. **Maintenance of an intrinsic short-rod state:** in *Acinetobacter baumannii*, zinc-stabilized PBP2 and the RodA–PBP2 elongasome maintain the characteristic short, squat rod. Loss of this machinery moves cells beyond the target state toward spheres.
3. **Evolutionary reduction of elongation:** stepwise loss of `yacF` and elongasome genes can drive rod/coccobacillus-to-coccus transitions in Neisseriaceae and Moraxellaceae.

Accordingly, the best TraitMech model should represent **balanced lateral peptidoglycan elongation relative to septal growth** as the proximal shape mechanism, while keeping physiological, genetic, and evolutionary branches taxon-scoped. Peptidoglycan principally determines cell shape, and RodA/PBP2 extend the longitudinal axis by inserting lateral-wall material. (slovak2005localizationofmreb pages 1-2, micelli2023aconservedzincbinding pages 1-2)

## 1. Trait scope and boundaries

### Operational definition

Curate `METPO:1000688` when microscopy or an authoritative taxonomic description identifies cells as **coccobacilli, short rods, squat rods, or plump rods**, ideally with images or length/width measurements. The phenotype may be constitutive or conditional. In *A. baumannii*, the experimentally described wild-type state is “short, squat rods”; in *R. sphaeroides*, photoheterotrophic cells are expressly “coccobacillus shaped.” (slovak2005localizationofmreb pages 1-2, micelli2023aconservedzincbinding pages 4-6)

### Boundary cases

- **Coccus/spherical:** no sustained long axis. The spherical Δ`pbp2` phenotype in *A. baumannii* is an **out-of-class endpoint**, useful as loss-of-trait evidence but not as a positive instance of `METPO:1000688`. (micelli2023aconservedzincbinding pages 4-6)
- **Ordinary bacillus/rod:** clearly elongated cells with a larger aspect ratio. Aerobic *R. sphaeroides* is the contrasting rod state. (slovak2005localizationofmreb pages 1-2)
- **Filament:** excessive length or failed septation; not coccobacillary. Piperacillin–tazobactam-associated filamentation should not be mapped to this trait. (micelli2023aconservedzincbinding pages 4-6)
- **Localized bulging/swelling:** amdinocillin produces mid-cell bulges in *R. sphaeroides*. This is evidence about PBP2-directed side-wall elongation, but it is not itself evidence for a uniform coccobacillus phenotype. (slovak2005localizationofmreb pages 7-10)
- **Pleomorphism:** a heterogeneous population should receive the coccobacillus trait only if that state is explicitly observed and its frequency or growth condition is recorded.
- **Taxonomic label versus measured state:** calling a genus “coccobacillary” does not prove that every strain or growth condition has the same morphology.

### Recommended assay representation

Record growth phase, medium, oxygen regime, illumination, temperature, perturbation, imaging method, cell count, median length, median width, and aspect-ratio distribution. “Short rod” without measurements is acceptable but weaker. A universal numerical aspect-ratio cutoff is not supported by the retrieved literature and should not be invented.

## 2. Candidate graph nodes

### Trait and phenotype nodes

- **coccobacillus shaped** — `METPO:1000688`
- short/squat rod — label-only synonym or narrower assay description
- rod-shaped cell — label-only unless an approved METPO identifier is verified
- spherical/coccal cell — label-only contrasting phenotype
- increased cell width — label-only quantitative phenotype
- bacterial cell morphogenesis — `GO:0000902`

### Taxa

- *Acinetobacter baumannii* — `NCBITaxon:470`
- *Rhodobacter sphaeroides* — `NCBITaxon:1063`
- *Neisseria elongata* — use label-only until the intended strain-level taxon is verified
- Neisseriaceae and Moraxellaceae — label-only unless exact taxonomic CURIEs are validated during YAML curation

### Genes, proteins, and complexes

- `pbp2` / penicillin-binding protein 2 (PBP2; class-B PBP transpeptidase) — label-only; use a strain-specific UniProt identifier only after sequence verification
- `rodA` / RodA, SEDS-family peptidoglycan glycosyltransferase — label-only
- RodA–PBP2 complex — label-only complex
- elongasome/rod system — label-only cellular machinery
- `mreB`, `mreC`, `mreD`, `rodZ` — label-only
- `yacF` / ZapD — label-only; note nomenclature and taxon dependence
- `pbpC` — label-only because gene naming can be taxon-specific

Showing the first 60 of 223 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

    Added DOI-backed definition and causal graph for MreB, peptidoglycan synthesis, septal growth, and short-rod coccobacillus geometry.

  3. · GROUND_CAUSAL_PREDICATES · claude

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

  6. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes×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 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1B1UYY2×1).

  9. · ENRICH_CAUSAL_GRAPH · claude

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

  10. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211×3, RO:0002213×1).

  11. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A060RK42×1).

  12. · 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)

  13. · MIGRATE_MICROBE_DOMAIN_EDGES · claude

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