Bacterial Rod complex peptidoglycan polymerization and crosslinking

A lateral cell-wall synthesis module for the bacterial Rod complex in which the SEDS glycosyltransferase RodA polymerizes lipid II-derived glycan strands and the class B penicillin-binding protein MrdA/PBP2 forms 4-3 peptide crosslinks. The RodA-MrdA synthase pair is the elongasome counterpart of the septal FtsW-FtsI pair and supports rod-shape maintenance. Precursor lipid II synthesis, MreB-guided spatial control, class A PBP backup polymerases, and turnover/remodeling reactions are outside this focused module.

MODULE:bacterial_rod_complex_peptidoglycan_transpeptidationDRAFTCONCRETEBiological Processmodules/bacterial_rod_complex_peptidoglycan_transpeptidation.yaml
peptidoglycan biosynthetic processGO:0009252 regulation of cell shapeGO:0008360
GO:0009252
peptidoglycan biosynthetic process
Defines peptidoglycan synthesis from lipid II.
GO:0008360
regulation of cell shape
Defines the rod-shape outcome supported by the Rod complex.
file:genes/ECOLI/mrdA/mrdA-ai-review.yaml
ECOLI mrdA gene review
The completed E. coli mrdA review grounds MrdA as the PBP2 D,D-transpeptidase of the lateral-wall Rod complex.
file:genes/ECOLI/mrdB/mrdB-ai-review.yaml
ECOLI mrdB gene review
The completed E. coli mrdB review grounds RodA/MrdB as the SEDS-family lateral-wall peptidoglycan glycosyltransferase.
PMID:3009484
Peptidoglycan synthetic activities in membranes of Escherichia coli caused by overproduction of penicillin-binding protein 2 and rodA protein.
Supports the paired requirement for RodA and MrdA/PBP2 in peptidoglycan synthesis.
PMID:27525505
SEDS proteins are a widespread family of bacterial cell wall polymerases.
Establishes the SEDS protein family as peptidoglycan glycosyltransferases.
PMID:37620344
Structural basis of peptidoglycan synthesis by E. coli RodA-PBP2 complex.
Establishes the E. coli RodA-PBP2 complex architecture.

The completed mrdB and mrdA ECOLI reviews cover the lateral-wall SEDS/bPBP synthase pair. This module is intentionally separate from the FtsW/FtsI septal synthase module because the two SEDS/bPBP pairs have distinct cellular roles and are regulated by different morphogenetic systems.

3Nodes
2Parts
0Variant Sets
0Variants
2Annotons
1Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:bacterial_rod_complex_peptidoglycan_transpeptidation deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

2 gene-function check(s) reflected in core functions · 0 conflict(s) · 0 evidence or coverage gap(s) (2 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
roda_glycosyltransferase E. coli RodA
UniProtKB:P0ABG7
Gene 		peptidoglycan glycosyltransferase activity
GO:0008955 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mrda_dd_transpeptidase E. coli MrdA
UniProtKB:P0AD65
Gene 		peptidoglycan D,D-transpeptidase activity
GO:0009002 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).

Gene-review completeness (2/2 grounded genes reviewed)

2 complete review(s) · 1 with deep research · 0 missing review · 1 reviewed but lacking deep research

Gene Review Complete Deep research
mrdA P0AD65 ✓ ✓ ✓
mrdB P0ABG7 ✓ ✓ ✗

Details

Context
bacteriaNCBITaxon:2
Bacterial Rod complex peptidoglycan synthesisBiological Processbacterial_rod_complex_peptidoglycan_transpeptidation
peptidoglycan biosynthetic processGO:0009252 regulation of cell shapeGO:0008360
Context
bacteriaNCBITaxon:2

Connections

RodA polymerizes nascent lateral-wall glycan strands that MrdA/PBP2 crosslinks through D,D-transpeptidation in the same Rod complex.
Part 1: lateral-wall glycan polymerization
RodA lateral-wall glycan polymerizationReactionroda_glycan_polymerization

Annotons

RodA peptidoglycan glycosyltransferase
roda_glycosyltransferase
Participant: Gene Product: E. coli RodA
Gene Product:
E. coli RodAUniProtKB:P0ABG7

Function

peptidoglycan glycosyltransferase activityGO:0008955
Substrates: lipid II
Products: lateral-wall peptidoglycan glycan strand

Processes

peptidoglycan biosynthetic processGO:0009252

Locations

plasma membraneGO:0005886

Rod-complex SEDS-family glycan polymerase that works with MrdA/PBP2 during lateral peptidoglycan synthesis.

Part 2: lateral-wall 4-3 peptide crosslinking
MrdA lateral-wall D,D-transpeptidationReactionmrda_dd_transpeptidation

Annotons

MrdA/PBP2 D,D-transpeptidase
mrda_dd_transpeptidase
Participant: Gene Product: E. coli MrdA
Gene Product:
E. coli MrdAUniProtKB:P0AD65

Function

peptidoglycan D,D-transpeptidase activityGO:0009002
Substrates: lateral-wall peptidoglycan pentapeptide donor stem meso-diaminopimelate acceptor stem
Products: D-Ala-mDAP 4-3-crosslinked lateral-wall peptidoglycan D-alanine

Processes

peptidoglycan biosynthetic processGO:0009252 regulation of cell shapeGO:0008360

Locations

plasma membraneGO:0005886

Rod-complex class B PBP that forms lateral-wall 4-3 peptide crosslinks. GO:0009002 is the closest existing term; a more exact D,D-transpeptidase term is still needed.