identifier: traitmech:000120
label: sarcina arrangement
definition: A cell arrangement in which cocci divide in three perpendicular planes
  and remain attached as cubic packets of eight (sarcinae).
definition_source: DOI:10.1128/MMBR.00001-06
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000666
synonyms:
- synonym_text: cubic packet cocci
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1128/MMBR.00001-06
evidence:
- reference: DOI:10.1128/MMBR.00001-06
  notes: Young's review treats the sarcina cubic packet as a division-plane-determined
    coccal arrangement.
- reference: DOI:10.1038/ncomms4842
  notes: Three-plane division with incomplete daughter-cell separation yields cubic
    eight-cell packets.
canonical_examples:
- taxon_id: NCBITaxon:1267
  taxon_label: Sarcina ventriculi
  note: "Namesake of the sarcina (cuboidal packet-of-eight) cell arrangement from tetrad division in three planes."
  reference: PMID:27922772
causal_graphs:
- graph_id: sarcina_three_plane_division_packet
  title: Sarcina arrangement via three-plane perpendicular division
  description: Evidence-backed causal sketch linking division in three perpendicular
    planes with incomplete separation to cubic eight-cell packets.
  nodes:
  - node_id: sarcina_trait
    label: sarcina arrangement
    node_type: TRAIT
    grounding: traitmech:000120
    description: Cocci attached as cubic packets of eight (sarcinae).
  - node_id: cell_division
    label: cell division
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0051301
    description: Bacterial binary fission.
  - node_id: three_plane_perpendicular_division
    label: three perpendicular division planes
    node_type: QUALITY
    description: Successive division planes oriented along three orthogonal axes.
  - node_id: ftsz_protein
    label: FtsZ
    node_type: GENE_OR_PROTEIN
    description: Tubulin-like division protein that polymerizes at the division site.
    grounding: UniProtKB:C0LUM8
  - node_id: z_ring
    label: Z ring
    node_type: CELLULAR_LOCALIZATION
    description: Dynamic FtsZ polymer ring that marks the division site.
  - node_id: ftsa_protein
    label: FtsA
    node_type: GENE_OR_PROTEIN
    description: Actin-like protein tethering the Z ring to the cytoplasmic membrane.
    grounding: UniProtKB:A0A1M6DY20
  - node_id: cytoplasmic_membrane
    label: cytoplasmic membrane
    node_type: CELLULAR_LOCALIZATION
    description: Plasma membrane to which the divisome attaches.
  - node_id: septal_pg_remodeling
    label: septal peptidoglycan remodeling
    node_type: BIOLOGICAL_PROCESS
    description: Coordinated synthesis and hydrolysis of peptidoglycan to build the
      septal cross-wall.
  - node_id: pg_synthetases_hydrolases
    label: peptidoglycan synthetases and hydrolases
    node_type: GENE_OR_PROTEIN
    description: Enzymes that synthesize and degrade peptidoglycan during division.
  - node_id: cell_wall_synthesis_division_site
    label: cell wall synthesis at division site
    node_type: BIOLOGICAL_PROCESS
    description: FtsZ-dependent peptidoglycan synthesis localized to the division
      site.
  - node_id: septum_formation
    label: division septum formation
    node_type: BIOLOGICAL_PROCESS
    description: Formation of the division septum (cross-wall).
    grounding: GO:0000917
  - node_id: pg_hydrolases
    label: peptidoglycan hydrolases
    node_type: GENE_OR_PROTEIN
    description: Enzymes that cleave peptidoglycan bonds to enable daughter-cell separation.
  - node_id: peripheral_pg_bridge
    label: peripheral peptidoglycan bridge
    node_type: CELLULAR_LOCALIZATION
    description: Peripheral peptidoglycan connection holding daughter cells together
      after septation.
  - node_id: daughter_cell_separation
    label: daughter-cell separation
    node_type: BIOLOGICAL_PROCESS
    description: Physical splitting of daughter cells after division.
  edges:
  - subject: three_plane_perpendicular_division
    predicate: causes
    object: sarcina_trait
    description: Three perpendicular division planes with incomplete separation yield
      cubic eight-cell packets.
    evidence:
    - reference: DOI:10.1038/ncomms4842
      notes: Three-plane division with incomplete daughter-cell separation yields
        cubic eight-cell packets.
    predicate_id: biolink:causes
  - subject: cell_division
    predicate: enables
    object: sarcina_trait
    description: Bacterial cell division underlies sarcina packet formation.
    evidence:
    - reference: DOI:10.1128/MMBR.00001-06
      notes: Young treats the sarcina cubic packet as a division-plane-determined
        coccal arrangement.
    predicate_id: RO:0002327
  - subject: ftsz_protein
    predicate: polymerizes to form
    object: z_ring
    description: FtsZ polymerizes to form the dynamic Z ring at the division site.
    evidence:
    - reference: DOI:10.1002/mbo3.1338
      notes: FtsZ polymerizes to form a dynamic structure known as the Z ring; broadly
        conserved bacterial/coccal mechanism.
  - subject: ftsa_protein
    predicate: attaches
    object: z_ring
    description: FtsA tethers the Z ring to the cytoplasmic membrane for proper divisome
      assembly.
    evidence:
    - reference: DOI:10.1002/mbo3.1338
      notes: Proper Z ring assembly requires attachment to the cytoplasmic membrane
        via interactions with FtsA; general divisome mechanism.
  - subject: ftsa_protein
    predicate: attaches Z ring to
    object: cytoplasmic_membrane
    description: FtsA attaches the Z ring to the cytoplasmic membrane.
    evidence:
    - reference: DOI:10.1002/mbo3.1338
      notes: Z ring attachment to the cytoplasmic membrane occurs via interactions
        with FtsA.
  - subject: pg_synthetases_hydrolases
    predicate: cooperate in
    object: septal_pg_remodeling
    description: PG synthetases and hydrolases work together to build the septal cross-wall.
    evidence:
    - reference: DOI:10.1002/mbo3.1338
      notes: PG synthetases and hydrolases work together to incorporate new PG into
        the existing mesh and to make the septal cross wall; general cell-wall remodeling
        principle.
  - subject: cell_wall_synthesis_division_site
    predicate: drives
    object: septum_formation
    description: FtsZ-dependent cell wall synthesis at the division site drives septum
      formation.
    evidence:
    - reference: DOI:10.1111/j.1574-6976.2007.00098.x
      notes: FtsZ-dependent cell wall synthesis is predominant; coccal cell wall synthesis
        occurs mainly at the division site, driving septation.
  - subject: pg_hydrolases
    predicate: degrade
    object: peripheral_pg_bridge
    description: Peptidoglycan hydrolases degrade the peripheral PG bridge connecting
      daughter cells.
    evidence:
    - reference: DOI:10.1002/mbo3.1338
      notes: Hydrolases likely trigger cell splitting by degrading the peripheral
        bridge, not the entire septum; general separation mechanism.
  - subject: peripheral_pg_bridge
    predicate: degradation triggers
    object: daughter_cell_separation
    description: Degradation of the peripheral PG bridge triggers daughter-cell splitting;
      incomplete separation retains packets.
    evidence:
    - reference: DOI:10.1002/mbo3.1338
      notes: Degradation of the peripheral PG bridge, together with mechanical factors,
        results in a sudden crack that separates the cells; regulated/incomplete separation
        determines packet retention.
curation_history:
- timestamp: '2026-06-08T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate MORPHOLOGY trait (sarcina / cubic-packet arrangement);
    leftover round, cell-arrangement sibling of diplococcus shaped.
  llm_assisted: true
- timestamp: '2026-06-09T15:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (three-plane perpendicular division
    → cubic packet) with GO node grounding and RO/biolink predicate groundings; promoted
    PROPOSED to REVIEWED.
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 7 evidence-backed generic edges (11 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:19Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:C0LUM8×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:34Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0000917×1).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:20Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A1M6DY20×1).
  llm_assisted: true