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cell width large

METPO:1000890 · CLASS · REVIEWED

A cell-width phenotype in which the shorter cell dimension exceeds approximately 0.9 micrometers.

Large cell-width by elevated wall-radius set-point

DOI-backed graph linking nutrient-rich growth conditions and an elevated MreB-driven wall-radius set-point to wide rods (>0.9 μm).

Large cell-width by elevated wall-radius set-point Interactive directed graph showing evidence-backed causal relationships for cell width large.

Edge evidence

  • rich growth conditions shifts Rod-complex peptidoglycan synthesis

    Rich growth conditions shift Rod-complex activity toward a larger radius set-point.

    • DOI:10.1126/science.aaa1313 cell size scales with growth rate Supports growth-rate-dependent enlargement of cell radius.
  • Rod-complex peptidoglycan synthesis confers cell width large METPO:2007700

    Elevated Rod-complex activity yields a wide rod radius.

    • DOI:10.1146/annurev-cellbio-101011-155745 MreB-directed peptidoglycan synthesis Supports lateral PG synthesis as the producer of the wide cell radius.
  • cell width large is a cell width rdfs:subClassOf

    Large cell width is a quantitative bin of the cell-width phenotype.

    • DOI:10.1146/annurev-cellbio-101011-155745 MreB-directed peptidoglycan synthesis Supports large width as a value within the regulated cell-width distribution.
  • RodA-PBP2 allosteric activation positively regulates peptidoglycan polymerization and crosslinking RO:0002213

    Allosteric structural opening of RodA-PBP2 activates coupled PG polymerization and crosslinking.

    • DOI:10.1038/s41467-023-39037-9 "Structural opening couples the activation of polymerization and crosslinking and is essential in vivo."
  • RodA-PBP2 elongasome complex mediates lateral sidewall peptidoglycan insertion

    Activated RodA-PBP2 elongasome synthesizes and inserts new PG at lateral wall sites.

    • DOI:10.1073/pnas.2215237120 "The elongasome... synthesizing and inserting new PG material at dispersed sites in the lateral cell wall."
  • lateral sidewall peptidoglycan insertion contributes to Rod-complex peptidoglycan synthesis RO:0002326

    Lateral sidewall PG insertion is the Rod-complex-driven wall-elongation process that sets rod radius.

    • DOI:10.1146/annurev-cellbio-101011-155745 Lateral PG insertion is the MreB/Rod-complex activity governing rod radius.
  • MreB cytoskeletal filaments orients circumferential peptidoglycan insertion

    MreB filaments orient peptidoglycan insertion perpendicular to the long cell axis, controlling rod radius.

    • DOI:10.1073/pnas.2301987120 "MreB filaments are thought to orient it orthogonally to the long cell axis" guiding PG insertion perpendicular to the long axis.
  • Rod-complex circumferential rotation enables even peptidoglycan distribution RO:0002327

    Rotation of the Rod complex around the circumference enables evenly distributed PG insertion.

    • DOI:10.1002/mbo3.1385 "the Rod complex rotates perpendicularly to the long axis of the cell... allowing the insertion of peptidoglycan... in an evenly distributed manner."
  • MreC-MreD balance regulates PBP2 transpeptidase activity RO:0002211

    The balance between MreC and MreD determines PBP2 synthase activity.

    • DOI:10.1002/mbo3.1385 "the balance between MreC and MreD determines the activity of PBP2"
  • Lipid II required for peptidoglycan polymerization and crosslinking

    Lipid II is the substrate required for peptidoglycan polymerization by Rod/elongasome synthases.

    • DOI:10.3390/biom13050720 "GTases and TPases utilize the disaccharide pentapeptide of Lipid-II as a substrate for PG polymerization and synthesis of the PG layer."

Provenance

Source
METPO (2025-11-25)
Definition source
DOI:10.1146/annurev-cellbio-101011-155745

Parent traits (1)

Synonyms (1)

  • W_>0.9 RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000890 [+0.641, -3.918, -1.937, +4.002, …]

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_width_large-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-focused research report: **cell width large**

## 1. Trait scope

**Trait:** “cell width large”  
**Identifier:** `METPO:1000890`  
**Category:** morphology; **term kind:** class; **mapping:** reviewed  
**Operational definition:** the shorter dimension of a microbial cell exceeds approximately **0.9 μm**.

This is best treated as an **assay-observed morphological state**, not as a pathway or intrinsic taxonomic property. For rods, width should be measured perpendicular to the longitudinal axis, preferably from segmented, exponentially growing single cells under specified medium, temperature, osmolarity, and imaging conditions. A population should instantiate the class only when its representative statistic—ideally median or mean single-cell width—crosses the threshold, rather than merely containing occasional cells wider than 0.9 μm.

### Boundary cases

* **Increased length or volume without increased short-axis dimension** is not `METPO:1000890`.
* **Filamentation** caused by division inhibition is primarily a length phenotype unless width also exceeds 0.9 μm.
* **Local bulges, branches, or septal swelling** are evidence of width dysregulation but do not establish a whole-cell large-width phenotype without a defined measurement rule.
* **Rod-to-sphere conversion** often entails widening, but “spherical,” “rounded,” or “increased volume” should not automatically be mapped to `METPO:1000890`; an actual short-axis measurement is required.
* **Transient osmotic swelling, L-forms, protoplasts, and wall-less cells** should be modeled separately unless the intended graph explicitly covers these assay states.
* The 0.9-μm boundary is not universal biological evidence of abnormality: naturally broad or giant taxa may exceed it as their normal morphology.

The strongest current model is that width emerges from the **relative activities and spatial organization of peptidoglycan synthesis/remodeling systems**, rather than from MreB abundance or growth rate alone. In *Bacillus subtilis*, circumferential Rod-system synthesis narrows cells, whereas class-A penicillin-binding proteins tend to widen them; directional MreB/Rod-complex density, not a unique MreB filament geometry, predicts diameter across perturbations (dion2018celldiameterin pages 3-6, dion2018celldiameterin pages 18-19, dion2018celldiameterin pages 8-10, dion2018celldiameterin pages 1-3).

## 2. Candidate graph nodes

### Phenotypes and processes

* **cell width large** — `METPO:1000890`
* regulation of cell shape — candidate `GO:0008360`
* peptidoglycan-based cell wall — candidate `GO:0009274`
* cell-wall/peptidoglycan biosynthesis
* circumferential peptidoglycan insertion
* directional Rod-complex motion
* peptidoglycan mechanical anisotropy
* isotropic peptidoglycan insertion
* peptidoglycan hydrolysis/endopeptidase activity
* local cell widening and bulging
* spherical-cell or rounding phenotype — retain as a separate phenotype node unless width is measured
* outer-membrane load-bearing capacity

### Proteins and complexes

* **Rod complex/elongasome** — complex node containing taxon-dependent components
* **MreB**, plus *B. subtilis* homologues Mbl and MreBH
* **RodA** — SEDS-family peptidoglycan glycosyltransferase
* **PBP2/MrdA** in *E. coli*; **PBP2A/PbpH** in *B. subtilis* — class-B transpeptidases
* **MreC**, **MreD**, **RodZ** — accessory/activation and coupling components
* **class-A PBPs**, especially PBP1/PonA in *B. subtilis*
* peptidoglycan DL- and DD-endopeptidases
* **PBP5/DacA**, CwlO, FtsE, FtsX — width-related candidates from the *B. subtilis* screen
* metabolic candidates: Rpe, Pyk, PtsH, GuaA, PanD
* MinJ, YaaA, YbzH — secondary candidates requiring gene-specific mechanistic follow-up

Protein nodes should be assigned **taxon-specific UniProt accessions during implementation**. A generic “MreB” node is useful for a high-level graph, but it should not be given a single species-specific accession across *E. coli*, *B. subtilis*, and other taxa.

### Chemicals and environmental/experimental factors

* **magnesium(2+)** — candidate `CHEBI:18420`
* **A22** — MreB-polymerization antagonist; retain label-only until its exact ChEBI record is verified
* **mecillinam/amdinocillin** — PBP2-directed β-lactam; verify the chemical CURIE before curation
* nutrient-rich versus minimal medium

Showing the first 60 of 224 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_CAUSAL_GRAPH · claude

    Added DOI-backed causal graph linking rich growth conditions and elevated Rod-complex activity to large cell width (>0.9 μm).

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1, rdfs:subClassOf×1).

  4. · ENRICH_CAUSAL_GRAPH · claude

    Added 7 evidence-backed generic edges (11 new nodes) from the deep-research report.

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326×1, RO:0002327×1, RO:0002211×1).

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:27692×1).

  7. · GROUND_CAUSAL_PREDICATES · claude

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

  8. · 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.

  9. · REGROUND_CAUSAL_EDGE · claude

    Edge rod_complex_rotation -> even_pg_distribution in graph cell_width_large_setpoint_increase: retyped even_pg_distribution to BIOLOGICAL_PROCESS. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. The label reads like a quality but the description does not: 'Evenly distributed INSERTION of peptidoglycan in the cell-surface layer.' Insertion is a process, so `enables` is already the right relation and only the node type was wrong.