CLB5 (P30283, YPR120C) — curation notes

Working notes for the GO annotation review of the budding-yeast S-phase cyclin Clb5.
Inline citations are verbatim quotes from the cached publications; the deep research
file is CLB5-deep-research-falcon.md (not edited).

Identity and family

• S-phase entry cyclin-5; cyclin family, cyclin A/B subfamily; 435 aa; ~520 molecules/cell
  (UniProt P30283). Not essential. Interacts with Cdc28 (IntAct NbExp=6).
• CLB5 and CLB6 lie tail-to-tail next to CLB2 and CLB1 respectively and form a distinct pair
  of B-type cyclins PMID:8253070.

Core biology: S-phase cyclin of Cdc28

• Transcribed at Start with the G1/S program PMID:8319908; expression peaks early in the cycle
  PMID:8253070.
• Deletion phenotypes: PMID:8319908; PMID:8253070.
• The S-phase-driving kinase is Clb5/6-Cdc28, not Cln-Cdc28 PMID:8319908; ectopic CLB5 bypasses the Cln requirement PMID:8319908.
• Sic1 holds Clb-Cdc28 (not Cln-Cdc28) inactive until its Cdc34/SCF-dependent destruction
  PMID:7954792; the clb1-6 sextuple
  mutant arrests in G1 PMID:7954792.
• Origin-timing output: PMID:9734354; PMID:9734354.
• Substrate targeting (deep research, not from cached primary papers): the Clb5 hydrophobic
  patch docks RXL/Cy motifs in Sic1, Orc6 and Cdc6; Clb5 binds Sld2 and clb5 clb6 delays Sld2
  phosphorylation; origin-bound Clb5-Orc6 docking contributes to re-replication control
  (Archambault et al. 2005, doi:10.4161/cc.4.1.1402; Bloom & Cross 2007, doi:10.1038/nrm2105).

Localization and degradation

• PMID:10848575; at nuclear division the signal
  becomes diffuse PMID:10848575, coincident with destruction-box-dependent degradation
  PMID:10848575. A residual cytoplasmic pool exists PMID:10848575.
• No study reports Clb5 at the spindle pole body; the propagated MTOC IBA (node PTN007424001,
  seeded by cdc13, crs1, cyclin B1/B2, Clb2) therefore lacks target evidence.

Secondary (non-core) roles

• Spindle/SPB separation with Clb3/Clb4: PMID:8319908. Mechanism: the early Clb kinases
  inactivate APC-Hct1 in S phase PMID:11438663;
  PMID:11438663;
  PMID:11438663. Cdh1 inactivation stabilizes Cin8/Kip1/Ase1 PMID:16688214. So Clb5-Cdc28 does part of the work (Hct1
  phosphorylation), but the role is redundant and regulatory: KEEP_AS_NON_CORE for
  GO:0010696, GO:1901673 and GO:0000086.
• DNA damage response: PMID:26801641; PMID:26801641; PMID:26801641. Graded KEEP_AS_NON_CORE, as in the CLB2 review.

Meiosis

• PMID:9732268; single mutant: PMID:9732268; Clb5-Cdc28
  complexes are present in meiotic cells PMID:9732268. Clb1/3/4 cannot substitute even when expressed
  from the CLB5 promoter (DeCesare & Stuart 2012, doi:10.1534/genetics.111.134684; not cached).
  Premeiotic DNA replication rows are ACCEPTed as core because the function is Clb5/6-specific.

Curation decisions worth flagging

1. GO:0005515 protein binding (4 IPI rows, all with Cdc28): the Kuhne & Linder row is MODIFIED
   to GO:0016538 because the paper's conclusion is that Clb5 associates with the p34CDC28 kinase
   in vivo PMID:8253070; the three high-throughput rows (Uetz Y2H, Breitkreutz KPI-MS, Michaelis AE-MS)
   are REMOVED as uninformative and redundant with GO:0016538/GO:0000307, without disputing the
   interaction.
2. GO:0007089 traversing Start (IBA from PTN000808767, seeded by S. pombe cig2 = SPAPB2B4.03;
   note the CLB2 review calls this donor cdc13, but PomBase resolves SPAPB2B4.03 to cig2 and
   SPBC582.03 to cdc13): MARK_AS_OVER_ANNOTATED. Clb5 is a product of the Start program and is
   Sic1-inhibited until after Start; its role is the G1/S transition (GO:0000082, ACCEPT), not
   the transcription/G1-CDK feedback that defines Start.
3. GO:0005815 MTOC (IBA): MARK_AS_OVER_ANNOTATED for lack of any SPB localization evidence on
   Clb5 and because the SPB-separation contribution runs through nuclear Cdh1 inactivation.
4. GO:0006355 regulation of DNA-templated transcription (IMP, Schwob & Nasmyth 1993):
   UNDECIDED. The cached record is abstract-only, the Genes Dev full text returned HTTP 403,
   and the abstract mentions transcription only as an input to CLB5/CLB6 expression.
5. GO:0045740 positive regulation of DNA replication: ACCEPTed as-is rather than MODIFIED to
   GO:0006270/GO:1902975 DNA replication initiation. Comparator check (QuickGO, taxon 559292):
   DNA replication initiation is carried by ORC/MCM/Sld2/Dpb11/Cdc7/Dbf4 and by no cyclin or
   by CDC28; SGD's convention places the cyclin-CDK on the regulatory term plus G1/S transition.
6. GO:0061575 (activator activity) is used in core_functions but not added as NEW: QuickGO shows
   SGD annotates no Cln/Clb cyclin to GO:0061575 (only BUR2/CTK2/CKS1 by IBA), whereas PomBase
   (cig2, cdc13) and human (CCNB1, CCND1-3) do; adding a child of the already-carried
   GO:0016538 would be redundant, so this is left as a validator warning and a note.
7. WITH/FROM oddities: the IGI rows from PMID:8253070 and PMID:9732268 list SGD:S000006324,
   which resolves to CLB5 itself (the genetic partner in both papers is CLB6, SGD:S000003341).
   Fields left as seeded; noted in the review summaries.

Identifier resolutions used

SGD: S000000038 CLN3; S000002314 CLB3; S000003340 CLB1; S000003341 CLB6; S000004200 CLB4;
S000004812 CLN1; S000005584 ASE1; S000006177 CLN2; S000006323 CLB2; S000006324 CLB5.
PomBase: SPAPB2B4.03 cig2; SPBC582.03 cdc13; SPBC2G2.09c crs1; SPBC19F5.01c puc1; SPCC4E9.02 cig1.