Cbh1 (CENP-B homolog 1; SPAC9E9.10c) is a 514-residue nuclear, sequence-specific DNA-binding protein of fission yeast and one of three S. pombe CENP-B-like proteins (with Abp1 and Cbh2). It has an N-terminal CENP-B-type helix-turn-helix DNA-binding domain followed by a region derived from a pogo-like DDE transposase; the fission-yeast CENP-B-like proteins arose by domestication of a pogo-like transposase independently of mammalian CENP-B, and no transposase or nuclease catalytic activity has been shown for Cbh1. Purified Cbh1 binds centromeric K-type repeat DNA and the replication origin ARS3002 at a TA-rich consensus (PyPuATATPyPuTA), and in vivo it associates with centromeric K-repeat chromatin and with non-centromeric chromatin, including the long terminal repeats of Tf2 retrotransposons where it colocalizes with Abp1. Cbh1 is not essential, but it acts redundantly with Abp1: loss of both proteins causes severe slow growth, abnormal morphology, very frequent chromosome missegregation, reduced Swi6/HP1 at centromeric heterochromatin and genome instability at replication forks paused at retrotransposon LTRs. These observations place Cbh1 as an auxiliary DNA-binding factor that helps organize centromeric heterochromatin and repetitive DNA, with Abp1 as the dominant family member.
Summary: Correct centromeric location; the gene already carries the more specific PomBase term GO:0000779 condensed chromosome, centromeric region from two IDA rows.
Reason: Cbh1 binds centromeric K-type repeat DNA in vitro and associates with centromeric K-repeat chromatin in vivo, so a centromeric location is right. The term is a parent of GO:0000779 condensed chromosome, centromeric region, which PomBase curators assigned from the same direct experiments (PMID:10733588, PMID:9237993); the electronic row is refined to that term rather than kept as a separate, less specific assertion.
Cbh protein specifically interacts in vitro with the K-type repeat DNA, which is essential for centromere function.
GO:0000779 condensed chromosome, centromeric region
IDA PMID:10733588 Fission yeast homologs of human CENP-B have redundant functi...
ACCEPT
Summary: Epitope-tagged Cbh1 associates with centromeric K-repeat chromatin in vivo.
Reason: Direct chromatin-association evidence on the target protein itself. The centromere is where Cbh1's best-characterized DNA-binding activity is exercised; the cached record is abstract-only, and the curator who read the full text made the annotation.
The fission yeast proteins Abp1, Cbh1, and Cbh2 are homologs of the human protein CENP-B that bind to centromeric alpha-satellite DNA and associate with centromeric heterochromatin.
GO:0000779 condensed chromosome, centromeric region
IDA PMID:9237993 Purification and characterization of a CENP-B homologue prot...
ACCEPT
Summary: Purified Cbh1 binds the centromeric K-type repeat; the curator inferred centromeric location from this direct binding study.
Reason: Consistent with the in vivo chromatin association (PMID:10733588). The location is supported for the target protein itself, and the curator read the full paper, which is abstract-only in our cache.
Summary: Cbh1 associates with centromeric and non-centromeric chromatin, including Tf2 retrotransposon LTRs.
Reason: Chromatin is the right compartment for a sequence-specific DNA-binding protein that is found by ChIP both at centromeric K repeats and at non-centromeric sites; ChIP-seq places Cbh1 with Abp1 and Sap1 at Tf2 LTRs and solo LTRs. Chromatin is not entailed by the centromeric term, because much of Cbh1's occupancy is outside centromeres.
Summary: True but far less specific than the measured activity, sequence-specific binding of centromeric K-type repeat DNA.
Reason: The InterPro mapping (from the DDE-superfamily transposase-derived domain) is correct only at the level of nucleic acid binding. Cbh1's binding has been measured directly, with a DNase I footprint consensus, so the row is refined to the experimentally supported descendants. GO:0019237 centromeric DNA binding is already on the gene by IDA; GO:1990837 sequence-specific double-stranded DNA binding covers its parent activity, which also accounts for binding of the non-centromeric ARS3002 origin DNA.
The Cbh-binding consensus sequence was determined by DNase I footprinting assays as PyPuATATPyPuTA, featuring an inverted repeat of the first four nucleotides.
Summary: Sound PAINT inference of DNA binding for this pogo-transposase-derived clade; the gene's own direct evidence supports a more specific, sequence-specific DNA-binding term.
Reason: The IBA node PTN002712198 was seeded by Cbh1 itself, its paralog Abp1 (SPBC1105.04c) and budding-yeast Pdc2 (SGD:S000002488); the target appearing among the donors is expected, because its own IDA rows ground the node. DNA binding is ancestral to the whole family, which descends from pogo-like transposases whose CENP-B-type HTH binds DNA. Note that Pdc2 is not orthologous to the S. pombe CENP-B-like proteins (PMID:17940212), so only the family-wide, generic DNA binding should be read across that node, not any subfamily-specific specificity. For Cbh1 itself the activity is measured, so the term is refined to the gene's IDA-supported centromeric DNA binding and its sequence-specific parent.
Propagation Review
Root cause:NO FAILURE CORE
Sources checked:
PANTHER:PTN002712198 · PTN002712198 SUPPORTS TRANSFER
Generic DNA binding is ancestral to the pogo-transposase-derived family and is correctly inherited by Cbh1; the MODIFY only refines it to the gene's own measured specificity.
PomBase:SPAC9E9.10c · cbh1 (target itself) SUPPORTS TRANSFER
The target's own IDA DNA-binding evidence is one of the descendant evidences grounding the node; expected, not circular.
PomBase:SPBC1105.04c · abp1 SUPPORTS TRANSFER
Same-subfamily (SF73) paralog with extensive direct DNA-binding evidence.
SGD:S000002488 · PDC2 SUPPORTS TRANSFER
Supports only generic DNA binding; Pdc2 is not orthologous to the S. pombe CENP-B-like proteins (PMID:17940212), so no subfamily-specific function should be read across.
Thus, the Pdc2 orthologous gene cluster appears to be derived from yet another source of pogo -like transposase than the S. pombe CENP-B-like proteins.
HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ...
ACCEPT
Summary: Genome-wide YFP localization places Cbh1 in the nucleus, consistent with its chromatin binding.
Reason: The high-throughput localization agrees with the direct chromatin-association data for Cbh1. Nucleus is the correct compartment for a chromatin-bound DNA-binding protein and is not entailed by the chromosomal terms in GO.
Next, we determined the localization of 4,431 proteins, corresponding to approximately 90% of the fission yeast proteome, by tagging each ORF with the yellow fluorescent protein.
Summary: Nuclear localization inherited from a deep node of the pogo-transposase-derived family; agrees with the direct data.
Reason: The node joins Cbh1 with mammalian CENP-B, TIGD6 and POGK. Fission-yeast and mammalian CENP-B proteins were domesticated independently from different pogo-like transposases (PMID:17940212), so subfamily-specific properties of human CENP-B must not be transferred to Cbh1. Nuclear localization, however, is a generic property of these transposase-derived DNA-binding proteins, and it is independently supported for Cbh1 by HDA and chromatin association.
Phylogenetic analysis revealed that the mammalian and fission yeast CENP-B proteins fall into 2 distinct monophyletic clades, each of which includes a different set of pogo-like transposons.
Summary: Genetic data link Cbh1 redundantly with Abp1 to centromere function, centromeric heterochromatin and genome stability, but PomBase has not assigned a biological process to Cbh1 (or to Abp1) from these papers, and the relevant papers are abstract-only in our cache.
Reason: Candidate processes exist. The abp1 cbh1 double mutant missegregates chromosomes (PMID:10733588), and loss of Cbh1 alone reduces centromeric Swi6 and silencing (PMID:12130537), which suggests a role in pericentric heterochromatin formation. Double mutants also accumulate DNA breaks at Sap1-paused forks (PMID:21151105). Most of this is redundant-pair necessity evidence. PomBase curated PMID:10733588 for both Cbh1 and Abp1 and assigned neither protein GO:0007059 chromosome segregation, and Abp1, the dominant paralog, has no centromeric heterochromatin-formation term either. Read under the do-not-add-what-curators-declined rule, the earlier proposal to replace this row with chromosome segregation is withdrawn. Whether Cbh1 itself does part of the work of heterochromatin nucleation, rather than only being required for it, cannot be settled from abstracts. The row is left undecided and the question is raised for PomBase.
In vitro assays with cell extracts with these proteins depleted allowed the specific assignments of several binding sites for them within cc2 and the K-type repeat.
The Cbh-binding consensus sequence was determined by DNase I footprinting assays as PyPuATATPyPuTA, featuring an inverted repeat of the first four nucleotides.
Core Functions
Sequence-specific binding of centromeric K-type repeat (and central-core) DNA. Cbh1 binds the centromere and contributes, redundantly with its paralog Abp1, to centromere function.
In vivo, epitope-tagged Cbhp associated with centromeric K repeat chromatin, as well as with noncentromeric regions.
Sequence-specific double-stranded DNA binding at non-centromeric sites, including the ARS3002 replication origin and Tf2 retrotransposon LTRs, where Cbh1 colocalizes with Abp1 and Sap1.
Q: PomBase has not assigned Cbh1 or Abp1 a biological process from PMID:10733588 or PMID:12130537. Is that deliberate, for example because the double-mutant phenotypes are captured as FYPO phenotypes? Or should Cbh1 carry a centromeric heterochromatin-formation term, given that Cbh1 loss alone reduces centromeric Swi6?
Q: Does Cbh1 bind Tf2 LTRs directly, or does it reach them only through Abp1? Zaratiegui et al. summarize earlier work as showing that Abp1 recruits Cbh1 to the LTRs.
Suggested Experiments
Experiment: Test whether Cbh1 occupancy at Tf2 LTRs and at centromeric K repeats depends on Abp1, using ChIP-seq of tagged Cbh1 in abp1-deleted cells, together with in vitro binding of purified Cbh1 to LTR probes.
Experiment: Replace the DDE-like region of Cbh1 with mutant versions, as was done for Abp1. This would show whether the transposase-derived region is needed for centromeric silencing and growth in an abp1 null background.
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.
Review rationale: Purified fission-yeast Cbh1 directly binds centromeric K-type repeat DNA and was characterized by DNA-binding and footprinting assays. Its in vivo centromeric-chromatin association was independently examined. These target observations directly establish nucleic acid binding. The target already has the more precise experimental centromeric DNA-binding annotation GO:0019237, which is_a DNA binding and nucleic acid binding, and the exact predicted term is already carried by InterPro mapping. The broad prediction is therefore correct but not novel and less precise.
Supporting Evidence:
PMID:9237993: "Cbh protein specifically interacts in vitro with the K-type repeat DNA, which is essential for centromere function."
PMID:10733588: "In vivo, epitope-tagged Cbhp associated with centromeric K repeat chromatin, as well as with noncentromeric regions."