SpoVD is a sporulation-specific class B penicillin-binding protein (PBP) that functions as a D,D-transpeptidase essential for spore cortex peptidoglycan synthesis during Stage V of sporulation. It works as a cognate pair with SpoVE (a SEDS-family glycosyltransferase) to polymerize and crosslink cortex peptidoglycan at the outer forespore membrane. SpoVD is expressed exclusively in the mother cell compartment under sigmaE control with SpoIIID repression. The protein contains an N-terminal transmembrane helix, a PBP dimerization domain, a catalytic transpeptidase domain with the conserved active-site serine, and a unique C-terminal PASTA domain. Disruption of spoVD results in cortex-less, heat-sensitive spores (asporogenous phenotype). Unlike FtsI (septum) or MrdA (elongation), SpoVD is dedicated exclusively to sporulation and does not participate in vegetative cell wall synthesis or cell shape regulation.
Definition: Catalysis of the crosslinking of peptidoglycan peptide stems via D,D-transpeptidation, forming peptide cross-bridges between adjacent glycan strands. The reaction involves cleavage of a D-Ala-D-Ala bond and formation of a new peptide bond.
Justification: Currently only GO:0071972 (peptidoglycan L,D-transpeptidase activity) exists. D,D-transpeptidases like SpoVD, FtsI, and MrdA are distinct enzymes with different substrate specificities and are major contributors to peptidoglycan crosslinking.
Parent term: aminoacyltransferase activity
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: SpoVD localizes to the cell membrane during sporulation. UniProt annotates SpoVD as a peripheral membrane protein associated with the cell membrane, and SpoVD accumulates at the outer forespore membrane during cortex synthesis. Reason: The plasma membrane annotation is correct. SpoVD is membrane-associated via its N-terminal transmembrane region and localizes to the outer forespore membrane during Stage V sporulation. The IBA annotation from phylogenetic inference is consistent with experimental localization. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000771406 · PANTHER:PTN000771406 SUPPORTS TRANSFER Ancestral bacterial class B PBP node conserving N-terminal transmembrane/membrane-tethering architecture across MrdA, FtsI, and SpoVD. UniProtKB:P0AD65 · mrdA SUPPORTS TRANSFER E. coli PBP2 (MrdA) inner-membrane class B penicillin-binding protein; membrane localization is conserved in B. subtilis SpoVD. Supporting Evidence: UniProt:Q03524 Cell membrane {ECO:0000269|PubMed:8289242}; Peripheral membrane protein file:BACSU/spoVD/spoVD-deep-research-falcon.md SpoVD accumulates at the outer forespore membrane during the defined window of cortex synthesis (T2.5–T4.5) |
| GO:0008658 penicillin binding | IBA GO_REF:0000033 | ACCEPT | Summary: SpoVD is a sporulation-specific penicillin-binding protein. The original characterization by Daniel et al. 1994 demonstrated penicillin-binding activity. UniProt describes it as "Sporulation-specific penicillin-binding protein" and it belongs to the transpeptidase family with the characteristic beta-lactam binding domain (InterPro IPR001460). Reason: Core molecular function of SpoVD. Penicillin binding is experimentally demonstrated and consistent with the transpeptidase domain architecture. This is a defining feature of class B PBPs like SpoVD. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000771406 · PANTHER:PTN000771406 SUPPORTS TRANSFER Ancestral bacterial class B PBP node conserving the beta-lactam-binding transpeptidase domain. UniProtKB:P0AD65 · mrdA SUPPORTS TRANSFER E. coli PBP2 (MrdA) class B penicillin-binding protein with experimentally established beta-lactam binding. UniProtKB:P0AD68 · ftsI SUPPORTS TRANSFER E. coli PBP3 (FtsI) divisome class B penicillin-binding protein with experimentally established beta-lactam binding. Supporting Evidence: PMID:8289242 Expression of spoVD in E. coli leads to the synthesis of a membrane-associated protein of the size expected for SpoVD, which can bind labelled penicillin UniProt:Q03524 Sporulation-specific penicillin-binding protein |
| GO:0071555 cell wall organization | IBA GO_REF:0000033 | MODIFY | Summary: SpoVD crosslinks peptidoglycan during spore cortex assembly. While spore cortex peptidoglycan synthesis is a form of cell wall assembly, the parent term GO:0071555 (cell wall organization) is overly broad and does not distinguish sporulation-specific spore wall assembly and peptidoglycan biosynthesis from vegetative cell wall organization. Reason: SpoVD does not participate in vegetative cell wall organization; it functions exclusively in mother-cell-directed synthesis and crosslinking of the modified peptidoglycan layer (cortex) of the developing endospore. This overly broad parent term is refined with MODIFY to GO:0042244 (spore wall assembly, an is_a descendant of GO:0071555 via GO:0070726 cell wall assembly and part_of GO:0070590 spore wall biogenesis -> GO:0030435 sporulation resulting in formation of a cellular spore, with no taxon constraint excluding Bacteria) and the lateral replacement GO:0009252 (peptidoglycan biosynthetic process, in the sibling GO:0009273 peptidoglycan-based cell wall biogenesis branch and already accepted on this gene). Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000771406 · PANTHER:PTN000771406 SUPPORTS TRANSFER Ancestral class B PBP node PTN000771406 propagates the broad parent term GO:0071555 across both vegetative PBPs (MrdA/FtsI) and the sporulation-specific cortex synthase SpoVD. UniProtKB:P0AD65 · mrdA SUPPORTS TRANSFER E. coli MrdA (PBP2) is a vegetative elongasome peptidoglycan transpeptidase, whereas B. subtilis SpoVD is specialized for endospore cortex peptidoglycan biosynthesis and spore wall assembly (GO:0042244, GO:0009252). Proposed replacements: spore wall assembly peptidoglycan biosynthetic process Supporting Evidence: PMID:8289242 spoVD seems instead to have a specialized role in the morphogenesis of the spore cortex, which is a modified form of peptidoglycan file:BACSU/spoVD/spoVD-deep-research-falcon.md SpoVD is a D,D‑transpeptidase that cross-links peptide stems in the nascent cortex PG |
| GO:0004180 carboxypeptidase activity | IEA GO_REF:0000043 | MODIFY | Summary: This annotation derives from UniProtKB keyword mapping. While EC 3.4.16.4 (serine-type D-Ala-D-Ala carboxypeptidase) is assigned to SpoVD, GO:0004180 is a broad parent term relative to GO:0009002 (serine-type D-Ala-D-Ala carboxypeptidase activity) already annotated on the gene. Reason: GO:0004180 (carboxypeptidase activity) is an overly general parent term. Per GO review guidelines, a true but general term is refined with MODIFY to the specific supported descendant GO:0009002 (serine-type D-Ala-D-Ala carboxypeptidase activity), which is already accepted on this gene. Proposed replacements: serine-type D-Ala-D-Ala carboxypeptidase activity Supporting Evidence: UniProt:Q03524 Reaction=Preferential cleavage: (Ac)2-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Duplicate annotation of GO:0005886 (plasma membrane) with different evidence code. This IEA annotation is based on UniProtKB subcellular location vocabulary mapping. The IBA annotation with the same GO term is already present and reviewed above. Reason: Duplicate of the IBA annotation for plasma membrane. Both annotations are correct - SpoVD is membrane-associated. The IEA provides independent computational support for the IBA phylogenetic inference. Duplicates with different evidence codes are acceptable in GO. Supporting Evidence: UniProt:Q03524 Cell membrane {ECO:0000269|PubMed:8289242}; Peripheral membrane protein |
| GO:0006508 proteolysis | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: This annotation derives from the "Protease" keyword in UniProt. While SpoVD has peptidase-like activity (cleaving D-Ala-D-Ala bonds), calling it "proteolysis" is misleading. SpoVD is a transpeptidase that crosslinks peptidoglycan peptide stems - its primary function is transpeptidation, not protein degradation. The substrate is peptidoglycan precursors, not proteins. Reason: Proteolysis implies protein degradation, which is not SpoVD's function. SpoVD cleaves D-Ala-D-Ala bonds in peptidoglycan precursors as part of transpeptidation, not to degrade proteins. This annotation is technically derived from the EC 3.4.16.4 classification but creates a misleading impression of the biological function. The term is too general and potentially misleading for a peptidoglycan transpeptidase. Supporting Evidence: file:BACSU/spoVD/spoVD-deep-research-falcon.md SpoVD is a D,D‑transpeptidase that cross-links peptide stems in the nascent cortex PG |
| GO:0008233 peptidase activity | IEA GO_REF:0000043 | MODIFY | Summary: General peptidase activity annotation from UniProt keyword mapping. SpoVD cleaves D-Ala-D-Ala bonds in service of transpeptidation for peptidoglycan crosslinking, which is captured more specifically by GO:0009002. Reason: GO:0008233 (peptidase activity) is an overly general parent term. Per GO review guidelines, this broad term is refined with MODIFY to the specific supported descendant GO:0009002 (serine-type D-Ala-D-Ala carboxypeptidase activity), which is already accepted on this gene. Proposed replacements: serine-type D-Ala-D-Ala carboxypeptidase activity Supporting Evidence: UniProt:Q03524 Belongs to the transpeptidase family |
| GO:0008360 regulation of cell shape | IEA GO_REF:0000043 | REMOVE | Summary: This annotation derives from the "Cell shape" keyword in UniProt. However, this annotation is INCORRECT for SpoVD. SpoVD is a sporulation-specific PBP that functions ONLY during spore cortex assembly. It does NOT participate in vegetative cell shape determination. Unlike MrdA (elongasome, determines rod shape) or FtsI (divisome, determines septum shape), SpoVD is dedicated exclusively to sporulation and has no role in vegetative cell morphology. Reason: SpoVD does not regulate vegetative cell shape. The "Cell shape" keyword in UniProt is erroneously applied based on homology to other PBPs (like MrdA/PBP2 and FtsI/PBP3) that do regulate cell shape. However, SpoVD is sporulation-specific and is expressed only in the mother cell during Stage V sporulation. It synthesizes spore cortex peptidoglycan, not vegetative cell wall. The disruption phenotype is asporogenous (no cortex, heat-sensitive spores), not cell shape defects. This represents an over-generalization from the PBP family. Supporting Evidence: PMID:8289242 insertional disruption of the spoVD gene has no effect on vegetative growth or division PMID:8289242 spoVD seems instead to have a specialized role in the morphogenesis of the spore cortex UniProt:Q03524 Asporogeneous; spore development starts but does not develop the spore cortex |
| GO:0008658 penicillin binding | IEA GO_REF:0000002 | ACCEPT | Summary: Duplicate annotation of GO:0008658 (penicillin binding) from InterPro mapping. The IBA annotation for the same term is already present and reviewed above. Reason: Duplicate of the IBA annotation for penicillin binding. Both are correct - SpoVD is a penicillin-binding protein. The IEA from InterPro domain mapping provides independent computational support. Duplicates with different evidence sources are acceptable. Supporting Evidence: UniProt:Q03524 Sporulation-specific penicillin-binding protein |
| GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity | IEA GO_REF:0000003 | ACCEPT | Summary: This annotation derives from EC number mapping (EC 3.4.16.4). UniProt assigns this EC to SpoVD based on the catalytic mechanism. The enzyme cleaves D-Ala-D-Ala bonds via a serine active site as part of the transpeptidation reaction for peptidoglycan crosslinking. Reason: This is the most specific molecular function term for the enzymatic activity. While the PRIMARY function is transpeptidation (crosslinking), the mechanism involves D-Ala-D-Ala cleavage via a serine active site. This term accurately captures the catalytic mechanism. Note that there is no GO term for "peptidoglycan D,D-transpeptidase activity" (only L,D exists as GO:0071972), so this carboxypeptidase term is the best available approximation. Supporting Evidence: UniProt:Q03524 Reaction=Preferential cleavage: (Ac)2-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine file:BACSU/spoVD/spoVD-deep-research-falcon.md catalytic mutants abolish heat-resistant spore formation, demonstrating transpeptidase activity is essential for cortex assembly |
| GO:0009252 peptidoglycan biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: SpoVD participates in peptidoglycan biosynthesis, specifically the crosslinking step during spore cortex assembly. UniProt pathway annotation confirms involvement in peptidoglycan biosynthesis. The annotation is correct but does not specify that this is sporulation-specific cortex peptidoglycan. Reason: Core biological process for SpoVD. The protein is essential for crosslinking peptidoglycan during spore cortex synthesis. While this term does not capture the sporulation-specific context, it accurately describes the biochemical process. Combined with GO:0030435 (sporulation), this provides appropriate functional annotation. Supporting Evidence: UniProt:Q03524 Cell wall biogenesis; peptidoglycan biosynthesis file:BACSU/spoVD/spoVD-deep-research-falcon.md SpoVD is a D,D‑transpeptidase that cross-links peptide stems in the nascent cortex PG |
| GO:0016787 hydrolase activity | IEA GO_REF:0000043 | MODIFY | Summary: Very general parent term annotation from UniProt keyword mapping. SpoVD cleaves D-Ala-D-Ala peptide stems during transpeptidation, which is captured far more specifically by GO:0009002. Reason: GO:0016787 (hydrolase activity) is an overly general parent term. Per GO review guidelines, this broad term is refined with MODIFY to the specific supported descendant GO:0009002 (serine-type D-Ala-D-Ala carboxypeptidase activity), which is already accepted on this gene. Proposed replacements: serine-type D-Ala-D-Ala carboxypeptidase activity Supporting Evidence: UniProt:Q03524 Carboxypeptidase; Cell membrane; Cell shape; Cell wall biogenesis/degradation; Hydrolase |
| GO:0030435 sporulation resulting in formation of a cellular spore | IEA GO_REF:0000043 | ACCEPT | Summary: SpoVD is essential for sporulation, specifically Stage V (cortex synthesis). The gene name "spoVD" indicates Stage V sporulation involvement. Disruption results in asporogenous phenotype with failure to form spore cortex and loss of heat resistance. Reason: This is the CORE biological process for SpoVD. The protein is specifically expressed during sporulation, functions exclusively in spore cortex assembly, and is essential for forming heat-resistant spores. This annotation correctly captures the primary biological context. Supporting Evidence: PMID:8289242 spoVD seems instead to have a specialized role in the morphogenesis of the spore cortex, which is a modified form of peptidoglycan UniProt:Q03524 Asporogeneous; spore development starts but does not develop the spore cortex file:BACSU/spoVD/spoVD-deep-research-falcon.md SpoVD accumulates at the outer forespore membrane during the defined window of cortex synthesis |
| GO:0071555 cell wall organization | IEA GO_REF:0000043 | MODIFY | Summary: Duplicate annotation of GO:0071555 (cell wall organization) from UniProt keyword mapping. Like the IBA row for the same term, this parent term is overly broad and does not distinguish endospore cortex assembly from vegetative cell wall organization. Reason: Consistent with the IBA row on GO:0071555, this overly broad parent term is replaced with MODIFY by its is_a descendant GO:0042244 (spore wall assembly, via GO:0070726 cell wall assembly, with no taxon constraint excluding Bacteria) and the lateral replacement GO:0009252 (peptidoglycan biosynthetic process, already accepted on this gene). Proposed replacements: spore wall assembly peptidoglycan biosynthetic process Supporting Evidence: UniProt:Q03524 Cell wall biogenesis; peptidoglycan biosynthesis |
| GO:0034301 endospore formation | TAS PMID:8289242 The Bacillus subtilis spoVD gene encodes a mother-cell-speci... | NEW | Summary: SpoVD is specifically required for bacterial endospore formation. This term is more specific than GO:0030435 (sporulation resulting in formation of a cellular spore) and captures the bacterial endospore context explicitly. Reason: GO:0034301 (endospore formation) is more specific than GO:0030435 for B. subtilis sporulation. SpoVD is essential for endospore cortex assembly, and this term explicitly captures the bacterial endospore biology. Multiple lines of evidence from Daniel et al. 1994 support this annotation. Supporting Evidence: PMID:8289242 spoVD seems instead to have a specialized role in the morphogenesis of the spore cortex file:BACSU/spoVD/spoVD-deep-research-falcon.md catalytic mutants abolish heat-resistant spore formation, demonstrating transpeptidase activity is essential for cortex assembly |
| GO:0043594 outer endospore membrane | IDA PMID:20417640 Interactions between late-acting proteins required for pepti... | NEW | Summary: SpoVD localizes to the outer forespore membrane during cortex synthesis. Fay et al. 2010 demonstrated this localization using GFP-SpoVD fusion with quantitative fluorescence microscopy. Reason: More specific cellular component term than GO:0005886 (plasma membrane). SpoVD specifically localizes to the outer forespore membrane (equivalent to outer endospore membrane during cortex synthesis) where it synthesizes cortex peptidoglycan. This is experimentally demonstrated with quantitative microscopy. Supporting Evidence: file:BACSU/spoVD/spoVD-deep-research-falcon.md SpoVD localizes to the outer forespore membrane during cortex synthesis (GFP-SpoVD forespore/mother-cell ratio ~3.27 ± 0.76) file:BACSU/spoVD/spoVD-deep-research-falcon.md SpoVD accumulates at the outer forespore membrane during the defined window of cortex synthesis (T2.5–T4.5) PMID:20417640 We found that localization of SpoVD is dependent on SpoVE and that SpoVD protects SpoVE from in vivo proteolysis. |
Loading supporting content…
Download this section (compressed HTML)Q: What is the functional significance of the PASTA domain in SpoVD, and does it contribute to substrate recognition or localization during cortex synthesis?
Q: Are there any conditions under which SpoVD might contribute to vegetative cell wall synthesis, or is its function strictly limited to sporulation?
Experiment: Generate PASTA domain deletion mutants of SpoVD and assess localization using GFP fusions and cortex formation by electron microscopy and heat resistance assays.
Hypothesis: The PASTA domain of SpoVD is required for proper localization to the outer forespore membrane or for substrate recognition during cortex synthesis.
Type: genetic/microscopy
Experiment: Purify recombinant SpoVD and test for transpeptidase activity using synthetic peptidoglycan precursor substrates, monitoring crosslink formation by mass spectrometry.
Hypothesis: SpoVD has D,D-transpeptidase activity that can be demonstrated biochemically.
Type: biochemical
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)