vibrio shaped

METPO:1000686 · CLASS · REVIEWED

A cell shape in which an organism has a curved rod or comma morphology, characterized by a short curved cylindrical form with a single arc.

Trait evidence (1)

DOI:10.1016/j.cell.2016.12.019
V. cholerae has a characteristic curved rod morphology

Supports vibrio/comma morphology and a source-backed curvature mechanism in Vibrio cholerae.

Vibrio-shape CrvA curvature mechanism

Evidence-backed causal sketch linking vibrioid curved-rod morphology to periplasmic CrvA polymers and asymmetric peptidoglycan insertion.

NONMECHANISTIC · This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.

Edge evidence

CrvA self-assembles into periplasmic filament
CrvA forms periplasmic filaments at the inner face of cell curvature.
- DOI:10.1016/j.cell.2016.12.019 CrvA self-assembles into filaments at the inner face Supports CrvA as a periplasmic polymer at the inner curvature.
periplasmic filament patterns asymmetric peptidoglycan insertion
CrvA filaments pattern differential peptidoglycan insertion.
- DOI:10.1016/j.cell.2016.12.019 asymmetrically patterns peptidoglycan insertion Supports CrvA-dependent spatial patterning of wall insertion.
asymmetric peptidoglycan insertion causes cell-body curvature biolink:causes
Unequal peptidoglycan insertion creates more material on the outer face than the inner face, curving the cell.
- DOI:10.1016/j.cell.2016.12.019 causing more material insertions into the outer face Supports asymmetric wall insertion as the proximal cause of curvature.
cell-body curvature confers vibrio shaped METPO:2007700
Curved rod morphology produces the vibrioid/comma-shaped trait.
- DOI:10.1016/j.cell.2016.12.019 characteristic curved rod morphology Supports the observed Vibrio morphology as a curved-rod shape.
CrvB increases cell-body curvature RO:0002213
CrvB expression increases CrvA assembly and cell curvature in a dose-dependent manner.
- DOI:10.1101/2020.02.20.954503 crvB expression increased CrvA-GFP assembly as well as cell curvature in a dose-dependent manner.
CrvB colocalizes with periplasmic filament
CrvB colocalizes with CrvA in the same periplasmic inner-curve filament structure.
- DOI:10.1101/2020.02.20.954503 Both proteins localized to the same structure; CrvB-GFP filaments colocalized with periplasmic DsbA-mCherry.
VadR sRNA represses crvA mRNA
VadR sRNA is a post-transcriptional inhibitor of crvA mRNA.
- DOI:10.1038/s41467-020-19890-8 The VadR small RNA acts as a post-transcriptional inhibitor of the crvA mRNA.
crvA mRNA translated into CrvA
crvA mRNA is translated into the CrvA curvature determinant protein.
- DOI:10.1038/s41467-020-19890-8 crvA mRNA encodes the periplasmic CrvA protein that determines cell curvature.
VadR sRNA decreases cell-body curvature RO:0002212
Mutation of vadR increases cell curvature whereas overexpression has the inverse effect, indicating VadR limits curvature.
- DOI:10.1038/s41467-020-19890-8 Mutation of vadR increases cell curvature, whereas overexpression has the inverse effect.
VxrAB two-component system activates transcription of VadR sRNA
The VxrAB two-component system activates vadR transcription.
- DOI:10.1038/s41467-020-19890-8 vadR transcription is activated by the VxrAB two-component system.
cyclic di-GMP decreases cell-body curvature RO:0002212
High c-di-GMP concentrations decrease cell curvature to generate straight rods.
- DOI:10.1073/pnas.2010199117 High c-di-GMP concentrations decrease cell curvature to generate straight rods.

Provenance

Identifier source: METPO (2026-06-12)
Author: Jed Dongjin Kim-Ozaeta
Definition source: DOI:10.1016/j.cell.2016.12.019

Parent traits (1)

cell shape METPO:1000666

Synonyms (2)

vibrio RELATED_SYNONYM · metpo.owl
vibrio-shaped RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

METPO:1000686 [-5.914, -107.472, -126.065, -23.277, …]

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).

morphology swarming motility 0.342
morphology twitching motility 0.342
morphology motile 0.342
morphology spiral shaped 0.314
physiology chemoautotrophic 0.314
morphology non-spore forming 0.292
physiology lithoheterotrophic 0.290
environment non halophilic 0.284

Deep research

Generated by just research-trait; source: research/traits/morphology/vibrio_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.

# Vibrio-Shaped Microbial Trait Research Report
## TraitMech Curation Template for METPO:1000686

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## Executive Summary

This report synthesizes current mechanistic understanding of the vibrio-shaped (comma-like curved rod) morphology trait for curation into the TraitMech causal graph database. The vibrio-shaped trait (METPO:1000686) is characterized by a single-arc curvature distinguishing it from multi-arc helical morphologies and straight rods. Research identifies three distinct mechanistic modules across bacterial taxa: (1) the CrvAB periplasmic filament system in *Vibrio cholerae* regulated by c-di-GMP and stress-responsive pathways, (2) the Bd1075 LD-carboxypeptidase-mediated asymmetric peptidoglycan editing in *Bdellovibrio bacteriovorus*, and (3) the outer-membrane porin-lipoprotein elongasome-trapping complex in *Rhodospirillum rubrum* described in 2024 (fernandez2020vibriocholeraeadapts pages 1-1, nikolai2020rnamediatedcontrolof pages 1-2, banks2022asymmetricpeptidoglycanediting pages 1-2, pohl2024anoutermembrane pages 2-3, pohl2024anoutermembrane pages 1-2).

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## 1. Trait Scope and Boundaries

### 1.1 Phenotype Definition

**Vibrio-shaped morphology** (METPO:1000686) is defined as a cell shape exhibiting a curved rod or comma morphology, characterized by a short curved cylindrical form with a single arc. The trait is exemplified by *Vibrio cholerae*, which displays a "characteristic curved rod morphology" or "comma-shaped cell morphology" (nikolai2020rnamediatedcontrolof pages 1-2, fernandez2020vibriocholeraeadapts pages 1-1). The curvature represents a stable structural property encoded in the peptidoglycan cell wall architecture, as purified peptidoglycan sacculi from wild-type curved cells retain curvature ex vivo (pohl2024anoutermembrane pages 2-3).

### 1.2 Boundary Cases

**Distinction from helical morphology:** Vibrio-shaped cells possess a single arc along the cell length, contrasting with multi-arc helical spirals characteristic of *Campylobacter jejuni* and *Helicobacter pylori*, which employ distinct peptidoglycan hydrolase-based mechanisms to generate multiple turns (banks2022asymmetricpeptidoglycanediting pages 1-2).

**Straight rod state as regulatory alternative:** Vibrio-shaped cells can transition to straight rod morphology under specific regulatory or environmental conditions. In *V. cholerae*, elevated intracellular cyclic di-GMP concentrations "drive curved *V. cholerae* to adopt a straight cell morphology that is advantageous to a sessile biofilm lifestyle," demonstrating active shape modulation between curved and straight states (fernandez2020vibriocholeraeadapts pages 1-1). Deletion of curvature determinants such as *crvA* in *V. cholerae* or *bd1075* in *B. bacteriovorus* produces constitutively straight cells (nikolai2020rnamediatedcontrolof pages 1-2, banks2022asymmetricpeptidoglycanediting pages 1-2, banks2022asymmetricpeptidoglycanediting pages 10-11).

### 1.3 Taxonomic Distribution and Mechanisms

Three mechanistically distinct systems generate vibrio-shaped morphology:

1. **CrvAB periplasmic polymer module** (*Vibrio cholerae*, *NCBITaxon:666*): Periplasmic intermediate filament-like proteins forming asymmetric structures (nikolai2020rnamediatedcontrolof pages 1-2, martin2020theevolutionof pages 1-5, martin2020theevolutionof pages 5-9).

2. **Bd1075 LD-carboxypeptidase localization** (*Bdellovibrio bacteriovorus*, *NCBITaxon:959*): Asymmetric peptidoglycan hydrolysis at the outer convex face via NTF2 domain-mediated localization (banks2022asymmetricpeptidoglycanediting pages 1-2, banks2022asymmetricpeptidoglycanediting pages 10-11, banks2022asymmetricpeptidoglycanediting pages 2-4).

3. **Por39/Por41/PapS elongasome trapping** (*Rhodospirillum rubrum*, *NCBITaxon:1085*): Outer-membrane porin-lipoprotein complexes that cage elongation machinery at the outer curve, biasing peptidoglycan synthesis (pohl2024anoutermembrane pages 2-3, pohl2024anoutermembrane pages 12-13, pohl2024anoutermembrane pages 1-2).

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## 2. Causal Graph Entities

### 2.1 Genes and Proteins

#### *Vibrio cholerae* Module

- **CrvA** (label-only; species-specific identifier): Periplasmic intermediate filament-like protein; polymerizes in periplasm; "determines cell curvature" and "decreases net growth on the minor axis relative to the major axis" (nikolai2020rnamediatedcontrolof pages 1-2, fernandez2020vibriocholeraeadapts pages 2-3, herzog2020smallregulatoryrnas pages 37-43).

- **CrvB** (label-only; species-specific identifier): Cooperates with CrvA; "promotes higher-order CrvA polymerization in dose-dependent fashion"; colocalized in periplasmic filaments at inner cell curvature (martin2020theevolutionof pages 5-9, martin2020theevolutionof pages 11-18).

- **VadR** (label-only; small regulatory RNA): Post-transcriptional inhibitor; "VadR small RNA (sRNA) as a post-transcriptional inhibitor of the *crvA* mRNA"; mutation increases curvature, overexpression decreases curvature (nikolai2020rnamediatedcontrolof pages 1-2, herzog2020smallregulatoryrnas pages 37-43).

- **VxrAB** (label-only; two-component system): Transcriptional activator; "*vadR* transcription is activated by the VxrAB two-component system" (nikolai2020rnamediatedcontrolof pages 1-2, herzog2020smallregulatoryrnas pages 37-43).

- **VpsR** (label-only; transcription factor): c-di-GMP-responsive regulator; "Loss of *vpsR* abolishes c-di-GMP-mediated curvature reduction"; "directly activates *vpsT* transcription" (fernandez2020vibriocholeraeadapts pages 2-3).

- **VpsT** (label-only; transcription factor): c-di-GMP-binding transcription factor; "VpsT overexpression can decrease curvature independently of c-di-GMP concentration" (fernandez2020vibriocholeraeadapts pages 2-3).

#### *Bdellovibrio bacteriovorus* Module

- **Bd1075** (label-only; species-specific): LD-carboxypeptidase (*EC:3.4.17.-* candidate); "exerting LD-carboxypeptidase activity upon the predator cell wall"; "localizes specifically to the outer convex face"; deletion produces straight rod morphology (banks2022asymmetricpeptidoglycanediting pages 1-2, banks2022asymmetricpeptidoglycanediting pages 10-11, banks2022asymmetricpeptidoglycanediting pages 2-4).

- **Bd1075 NTF2 domain** (nuclear transport factor 2-like domain; residues 196–304): "The NTF2 domain is necessary for proper localization" and "asymmetric targeting to the outer convex cell face" (banks2022asymmetricpeptidoglycanediting pages 1-2, banks2022asymmetricpeptidoglycanediting pages 10-11).

#### *Rhodospirillum rubrum* Module (2024)

Showing the first 60 of 454 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

Vibrio cholerae NCBITaxon:666 PMID:28086090 Comma-shaped (curved-rod) vibrio; cholera agent and the canonical Vibrio.

Curation history

2026-05-05T01:35:46.896189+00:00 · SEEDED_FROM_METPO · seed_from_metpo
imported from data/raw/metpo.owl (CLASS)
2026-05-11T18:00:00-07:00 · CURATED_WITH_LITERATURE · codex
Reviewed vibrio shape and added DOI-backed causal graph for CrvA periplasmic filaments, asymmetric peptidoglycan insertion, and curved-rod morphology.
2026-05-20T03:35:31Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1).
2026-05-20T05:49:25Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes×1).
2026-06-23T00:00:00Z · ENRICH_CAUSAL_GRAPH · claude
Added 7 evidence-backed generic edges (5 new nodes) from the deep-research report.
2026-06-24T17:21:14Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212×2, RO:0002213×1).
2026-06-24T17:23:34Z · GROUND_CAUSAL_NODES · claude
Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:49537×1).
2026-08-06T01:00:00Z · 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.
2026-08-26T03:23:00Z · REVIEW_GRAPH_PROTEIN_TAXON · claude
Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope vibrio_shaped_crvA_curvature=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (crvA, crvB, vxrAB_tcs); retyped 2 node(s) (vadR_srna->RNA, crvA_mrna->RNA).