ParB (PP_0001) is the centromere-binding protein of the Pseudomonas putida ParABS chromosome-partitioning system. Its gene lies beside its partner parA, next to oriC, where parS-like palindromes also lie. ParB is a 290-residue ParB/Srx-fold protein with an N-terminal CTP-binding domain carrying the GERRWRA box, a central helix-turn-helix for parS recognition, and a C-terminal dimerization domain. It is 79% identical to the experimentally characterized P. aeruginosa ParB, which binds parS, hydrolyses CTP in a parS-stimulated reaction and spreads onto flanking DNA to form the origin partition complex. In P. putida, the parAB genes provide partition activity: parA and parB mutations, and deletion of the whole parAB locus, raise the frequency of anucleate cells, mainly as cultures in minimal medium enter stationary phase and divide without ongoing replication. An oriC-region parS sequence stabilises an unstable plasmid in E. coli only when P. putida ParA and ParB are supplied.
Summary: ParB binds DNA; the defining activity is sequence-specific binding to parS palindromes.
Reason: True but less specific than the evidence supports. In P. putida, a parS-like sequence from the oriC-parAB region confers ParAB-dependent plasmid stability, the functional signature of ParB-parS recognition, and the curated UniProt function states that ParB binds the origin region. The 79%-identical P. aeruginosa ParB binds parS specifically (IDA in that review). Sequence-specific DNA binding (GO:0043565), a descendant of DNA binding, is the informative term.
Purified ParB binds specifically to DNA containing a putative parS sequence based on the consensus sequence found in the chromosomes of Bacillus subtilis, Pseudomonas putida, and Streptomyces coelicolor.
file:PSEPK/parB/parB-uniprot.txt
Binds to the DNA origin of replication (By similarity).
Summary: ParB is bound to the chromosome at the oriC-proximal parS region.
Reason: Consistent with the TreeGrafter inference and with the orthologous P. aeruginosa ParB, which binds parS sites near oriC in vivo and forms a nucleoprotein complex there. The P. putida parS-like sites lie in the same oriC-parAB region.
we show that ParB binds to four parS site located within 15 kb of oriC in vivo, and that this binding promotes the formation of a high order nucleoprotein complex.
Summary: ParB is the parS-binding component of P. putida chromosome partition.
Reason: Core process, supported by P. putida genetics as well as orthology. parB mutants produce anucleate cells in minimal medium at the entry into stationary phase, and P. putida ParAB reconstitutes partition of a parS-carrying plasmid in E. coli. ParB does part of the work of the process: it is the parS-bound partition complex that ParA moves.
However, in M9-minimal medium different parA and parB mutations gave between 5 and 10% anucleate cells during the transition from exponential phase to stationary phase.
One was inserted into an unstable mini-F and shown to stabilize it in E. coli in a ParAB-dependent manner.
GO:0045881 positive regulation of sporulation resulting in formation of a cellular spore
IEA GO_REF:0000118
REMOVE
Summary: Pseudomonas putida does not sporulate; the term is transferred from B. subtilis Spo0J.
Reason: The term reaches PANTHER from B. subtilis Spo0J, which antagonises Soj inhibition of the Spo0A-dependent sporulation decision. P. putida forms no spores and has no Spo0A pathway, and the parAB locus has been studied in this species precisely because it has no developmental phase. The same term is removed from the P. aeruginosa ortholog's IBA row.
Propagation Review
Root cause:PROPAGATION BAD
Failure modes:LINEAGE OR TAXON MISMATCH
Sources checked:
PANTHER:PTN002433458SUPPORTS SOURCE BUT NOT TARGET
TreeGrafter carries the positive-sporulation term inherited from the B. subtilis Spo0J-seeded IBD (PTN002121186) to non-sporulating Pseudomonas.
We have investigated the role in partition of the parAB locus of a free-living bacterium, Pseudomonas putida, not known to pass through developmental phases.
Summary: ParB is predicted to be a parS-stimulated CTPase, like its directly assayed P. aeruginosa ortholog.
Reason: The 79%-identical P. aeruginosa ParB hydrolyses CTP in a parS-stimulated reaction, measured on the purified protein. The P. putida protein has the same CTP-binding box (GERRWRA, residues 91-97) at the same position. CTP binding and hydrolysis are a conserved feature of the ParB family that ancestral reconstruction traces to early bacteria. Not in GOA, and absent from NCBI's architecture-based annotation, which names the N-terminal domain a nuclease. The P. aeruginosa source rows are themselves proposed (IDA) in the genes/PSEAE/parB review and are not yet in GOA, so this transfer depends on them being accepted.
Summary: ParB binds parS palindromes, as shown directly for its P. aeruginosa ortholog.
Reason: The replacement proposed for the electronic DNA binding row, recorded with its evidence. The 79%-identical P. aeruginosa ParB binds parS specifically as a purified protein (IDA in that review), with a parS consensus that includes the P. putida sites. In P. putida itself, an oriC-region parS-like sequence confers ParAB-dependent plasmid stability, the functional signature of ParB-parS recognition. The P. aeruginosa source rows are themselves proposed (IDA) in the genes/PSEAE/parB review and are not yet in GOA, so this transfer depends on them being accepted.
Purified ParB binds specifically to DNA containing a putative parS sequence based on the consensus sequence found in the chromosomes of Bacillus subtilis, Pseudomonas putida, and Streptomyces coelicolor.
ISM file:PSEPK/parA/parA-bioinformatics/RESULTS.md
NEW
Summary: ParB carries the conserved ParB CTP-binding box GERRWRA.
Reason: The GERRWRA box at residues 91-97 coordinates the CTP phosphates in characterized ParB CTPases and is identical in the directly assayed P. aeruginosa ParB. Recorded separately from CTPase activity because GO does not derive one from the other.
Supporting Evidence:
file:PSEPK/parA/parA-bioinformatics/RESULTS.md
ParB has the CTP-binding box GERRWRA at 91-97, which coordinates the CTP phosphates in characterized ParB CTPases.
Core Functions
ParB recognises parS palindromes in the oriC-parAB region and forms the origin partition complex on which ParA acts during chromosome segregation.
However, in M9-minimal medium different parA and parB mutations gave between 5 and 10% anucleate cells during the transition from exponential phase to stationary phase.
parS-stimulated CTP hydrolysis by the N-terminal ParB/Srx-fold domain, inferred from the directly assayed P. aeruginosa ortholog and the conserved GERRWRA CTP-binding box.
Q: Why is the P. putida par phenotype confined to division without ongoing replication (minimal medium, entry into stationary phase), when the P. aeruginosa par mutants are defective during exponential growth?
Suggested Experiments
Experiment: Measure CTP hydrolysis by purified P. putida ParB with and without an oriC-region parS DNA, and test a GERRWRA-box mutant in the anucleate-cell assay.
Hypothesis: P. putida ParB is a parS-stimulated CTPase and CTP binding is required for its partition function.
Type: enzyme assay and genetic complementation
External Prediction Reviews
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
NCBI PGAP names WP_003253185.1 "ParB/RepB/Spo0J family partition protein" from the SPARCLE CDD domain architecture 11445026 (COG1475 Spo0J region, described as containing a "ParB-like nuclease domain") and passes on one GO term, DNA binding. The identical-protein record links WP_003253185.1 to 586 assemblies of the P. putida group (2026-10-24). The term is true but less precise than the main review's sequence-specific DNA binding. The interesting result is what is missing. The protein also matches TIGR00180, whose product name is identical and which carries chromosome segregation and cytokinesis as well as DNA binding. Because the architecture wins the naming, PGAP passes on only DNA binding and drops chromosome segregation, the core process that GOA (TreeGrafter) and the main review both have. Neither the architecture nor any matched model carries the ParB CTPase activity (GO:0043273), and the CDD description of the N-terminal domain as a nuclease predates the discovery that this fold binds and hydrolyses CTP.
LSP — Less precise than existing annotation Review score: 2/2
Prediction method: NCBI PGAP · Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record · PMID:33270901
Review rationale: True but less precise. Also in GOA (InterPro2GO), where the main review MODIFIES it to sequence-specific DNA binding (GO:0043565): ParB is defined by recognition of parS palindromes, and a P. putida oriC-region parS-like site confers ParAB-dependent partition. The specific term is also recorded in the main review as a NEW row (ISO from the directly assayed P. aeruginosa ParB), so a supported, more specific annotation exists for this protein. Scored as less precise, consistent with both rows.
Supporting Evidence:
PMID:11849535: "One was inserted into an unstable mini-F and shown to stabilize it in E. coli in a ParAB-dependent manner."
PMID:15466051: "Purified ParB binds specifically to DNA containing a putative parS sequence"