ParB (PA5562) is the centromere-binding component of the Pseudomonas aeruginosa ParABS chromosome-partitioning system, encoded with its partner ParA in the gidAB-parAB operon close to oriC. A 290-residue ParB/Srx-fold protein, it has an N-terminal CTP-binding (ParB_N) domain with the GERRxRA box, a central helix-turn-helix that recognises parS palindromes, and a C-terminal leucine-zipper-like dimerization domain. ParB binds the four oriC-proximal parS sites (parS1-4), hydrolyses CTP in a parS-stimulated reaction, and spreads from parS onto flanking DNA to form a large nucleoprotein complex that ParA moves during segregation of newly replicated origins. Loss of ParB, of its ability to spread or dimerize, or of all parS sites causes anucleate cells, slower growth and defective swimming and swarming motility. ParB also binds hundreds of parS half-sites across the genome, behaving as a nucleoid-associated protein, and represses genes next to parS3 and parS4; its absence changes expression of hundreds of genes.
Summary: ParB binds DNA; its defining activity is sequence-specific recognition of parS palindromes.
Reason: True but less specific than the evidence. Purified P. aeruginosa ParB binds parS-containing DNA specifically and binds all ten chromosomal parS sites with different affinities, so the informative term is sequence-specific DNA binding (GO:0043565), a descendant of DNA binding and the term used for the B. subtilis ortholog Spo0J. The non-specific DNA contacts made during spreading follow from CTP-dependent clamp closure after loading at parS, and the sequence-specific term remains the activity that defines ParB.
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.
Summary: ParB acts on the chromosome, at oriC-proximal parS sites and at half-parS sites genome-wide.
Reason: Consistent with the PAINT node and with direct P. aeruginosa data: ChIP-seq shows ParB bound in vivo at the four parS sites near oriC, where it forms a high-order nucleoprotein complex, and at hundreds of parS half-sites across the chromosome. Chromosome is the appropriate location; nucleoid-level terms would add little.
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 not part of the transcription machinery.
Reason: An electronic rule annotation that treats ParB as a transcription participant. ParB does not synthesise RNA or form part of RNA polymerase; its effects on gene expression are repression next to parS (silencing by spreading) and indirect effects of segregation defects. Those are covered by the regulation row, which is refined below. The P. putida ortholog carries no transcription terms. Unlike it, this entry has a Cro/C1-type HTH signature match (PS50943, IPR001387), which may be what triggers the UniRule; the rule's conditions were not checked, so that link is an inference.
indicating that direct ParB- parS3/parS4 interactions repress the transcription in this region
GO:0006355 regulation of DNA-templated transcription
IEA GO_REF:0000104
MODIFY
Summary: ParB represses transcription of genes adjacent to the high-affinity parS3 and parS4 sites.
Reason: Regulation is real in P. aeruginosa but its direction is known: ParB bound at parS3/parS4 represses the neighbouring promoters, and ParB overproduction silences genes placed next to parS in a parS-dependent manner. Negative regulation (GO:0045892) is the precise term. It is non-core: it follows from parS binding and spreading, and most of the transcriptome change in parB mutants is indirect.
Summary: ParB is the parS-binding, spreading component of the ParABS origin-segregation machinery.
Reason: Core process, with direct P. aeruginosa evidence. ParB does part of the work: it binds parS and spreads to form the partition complex that ParA acts on, and point mutants that bind DNA but cannot spread or dimerize phenocopy the null. parB-null and parS-null strains accumulate anucleate cells, and one oriC-proximal parS site is necessary and sufficient for segregation.
IPI PMID:21531806 Binding and spreading of ParB on DNA determine its biologica...
MODIFY
Summary: ParB self-associates, chiefly through its C-terminal dimerization domain.
Reason: The self-interaction is real (cross-linking, ultracentrifugation and two-hybrid mapping in PMID:21531806), but identical protein binding says nothing about its nature. The characterized interaction is homodimerization through the C-terminal leucine-zipper-like domain, which is required for DNA binding, spreading, ParA interaction and every in vivo function. Protein homodimerization activity (GO:0042803) states that. Higher-order oligomerization during spreading is a consequence of CTP-dependent clamping and is not a separate activity term.
Analysis confirmed the localization of the main dimerization domain in the C terminus of ParB but also mapped another self-interactive domain in the N-terminal domain.
Thus so far all the properties of ParB seem to depend on dimerization.
GO:0045881 positive regulation of sporulation resulting in formation of a cellular spore
IBA GO_REF:0000033
REMOVE
Summary: Pseudomonas aeruginosa does not sporulate; the term is inherited from B. subtilis Spo0J.
Reason: The only donor is B. subtilis Spo0J (P26497), where Spo0J antagonises Soj inhibition of the Spo0A-dependent sporulation decision. P. aeruginosa forms no endospores and has no Spo0A phosphorelay, so the process does not exist in the target lineage. The problem is node placement: the sporulation IBD (PTN002121186) sits on a node whose descendants include non-sporulating Gammaproteobacteria. The P. aeruginosa literature attributes the sporulation role to the B. subtilis homologue only.
Propagation Review
Root cause:PROPAGATION BAD
Failure modes:LINEAGE OR TAXON MISMATCH
Sources checked:
PANTHER:PTN002121186 · ParB family node carrying the positive-sporulation IBD SUPPORTS SOURCE BUT NOT TARGET
Seeded by B. subtilis Spo0J, where the Soj-Spo0A sporulation link is experimentally established. The node also covers non-sporulating Gammaproteobacteria such as Pseudomonas, which have no Spo0A pathway. A shallower IBD placement or a taxon constraint would fix this at source.
UniProtKB:P26497 · B. subtilis Spo0J SUPPORTS SOURCE BUT NOT TARGET
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.
IDA PMID:38843873 Inhibitor of Chromosome Segregation in Pseudomonas aeruginos...
NEW
Summary: Purified P. aeruginosa ParB hydrolyses CTP, with parS DNA stimulating the reaction.
Reason: Direct biochemical evidence on this protein: CTP hydrolysis by purified P. aeruginosa ParB follows Michaelis-Menten kinetics (KM about 44 uM), requires DNA and is fully stimulated only by parS. This is the conserved ParB CTPase that drives clamp closure and spreading, and it is not in GOA for this protein. ParB is the catalyst here, so this is an activity annotation, not a substrate role.
IDA PMID:15466051 ParB of Pseudomonas aeruginosa: interactions with its partne...
NEW
Summary: ParB binds parS palindromes specifically, in vitro and in vivo.
Reason: Direct evidence: purified ParB binds parS-containing DNA specifically, binds all ten genomic parS sites with different affinities, and binds parS1-4 in vivo (ChIP-seq). This is the replacement proposed for the electronic DNA binding row, recorded with its experimental source.
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.
IC PMID:38843873 Inhibitor of Chromosome Segregation in Pseudomonas aeruginos...
NEW
Summary: ParB binds the CTP it hydrolyses.
Reason: Curator inference from the measured CTP hydrolysis by purified ParB, which requires CTP binding, together with the conserved CTP-binding box GERRWRA. Binding was not measured separately, so the code is IC. Recorded separately because GO does not derive CTP binding from CTPase activity.
We found that the same holds true for the P. aeruginosa ParB.
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 near oriC through its central HTH domain and, as a CTP-dependent clamp, spreads onto flanking DNA to build the partition complex that ParA acts on during origin segregation.
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.
Q: Does CTP binding or hydrolysis by P. aeruginosa ParB control its occupancy of the hundreds of half-parS sites, or only spreading from the full parS1-4 sites?
Q: Which of the ParB-dependent expression changes are direct (half-parS binding near promoters) and which follow from segregation defects?
Suggested Experiments
Experiment: Compare ChIP-seq occupancy at parS1-4 and at half-parS sites for wild-type ParB and a mutant in the CTP-binding box (GERRWRA, residues 91-97).
Hypothesis: Half-parS binding does not require CTP-dependent clamping, whereas spreading from parS1-4 does.
Type: ChIP-seq
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.
P. aeruginosa PAO1 is one of NCBI's curated reference genomes, so PGAP does not annotate its assembly. The identical protein WP_003100240.1 is annotated by PGAP in other genomes (39,835 assemblies in its identical-protein record, 2026-10-24). As for the P. putida ortholog, it is named "ParB/RepB/Spo0J family partition protein" from SPARCLE architecture 11445026 and carries only DNA binding. TIGR00180, which also matches and carries chromosome segregation, does not pass on its GO because it does not name the protein. The prediction is less precise than the experimentally supported sequence-specific DNA binding. The directly measured parS-stimulated CTPase activity of this protein (PMID:38843873) has no source in PGAP.
LSP — Less precise than existing annotation Review score: 2/2
Prediction method: NCBI PGAP · Version: WP_003100240.1 record (modified 2025-01-01); GO from WP_ record · PMID:33270901
Review rationale: True but less precise. Also in GOA (combined IEA), where the main review MODIFIES it to sequence-specific DNA binding (GO:0043565), supported by direct binding of purified ParB to parS and by binding to all ten genomic parS sites.
Supporting Evidence:
PMID:15466051: "Purified ParB binds specifically to DNA containing a putative parS sequence"
PMID:25794281: "It was found that ParB binds specifically to all ten parS sites, although with different affinities."