Saccharomyces cerevisiae S288c. 1093 aa. Alternative name ART1. SGD:S000000913.
UniProt domain map: APSES/KilA-N HTH DNA-binding domain (37-147, HTH 71-92), four
central ankyrin repeats, conserved C-terminal Swi6-binding region; Cdk1 phosphosites at
Ser255 and Ser806 recorded from the Holt et al. 2009 phosphoproteome.
SBF DNA-binding subunit. Swi4 is the sequence-specific DNA-binding subunit of SBF
(SCB-binding factor), the Swi4-Swi6 heterodimer that drives the Start (G1/S)
transcriptional program. The discovery papers identified the "cell-cycle box" of the HO
promoter and the two SWI genes that act through it
PMID:3542227
PMID:2649246,
and cloning of SWI4 placed the protein physically in that complex
PMID:2689885.
SCB elements and the division of labour with Swi6. The DNA-recognition function sits
in Swi4, the regulatory function in Swi6
PMID:1465410
PMID:8423776.
The N-terminal domain suffices for SCB recognition in vitro
PMID:10490612,
the SCB consensus is CA/GCGAAA
PMID:20641022,
and protein-binding microarrays recover the same motif class
PMID:19111667.
Swi4 and Mbp1 are the alternative DNA-binding subunits of the sister complexes SBF and MBF
PMID:10490612.
C-terminal auto-inhibition relieved by Swi6. Full-length Swi4 does not bind SCBs alone
because its C terminus folds back onto the DNA-binding domain; Swi6 binding to that C
terminus releases it
PMID:10490612.
The inhibitory contact is intramolecular: Swi4 is monomeric and SBF is a 1:1 heterodimer
PMID:10490612
PMID:10490612.
The C terminus is necessary and sufficient for Swi6 association and dispensable for DNA binding
PMID:8423776,
and overproduced Swi4 can bypass Swi6 for HO transcription
PMID:8423776.
Localization. Swi4 is nuclear at every cell-cycle stage, in contrast to Swi6
PMID:10490612
PMID:10490612.
ChIP-chip and ChIP-PCR place it on promoter chromatin
PMID:12464632
PMID:12464632.
Whi5 repression and Start. SBF sits on G1/S promoters in early G1 bound by the
corepressor Whi5, which is removed by Cln3-Cdc28 phosphorylation (the Rb/E2F analogy)
PMID:15210110
PMID:15210110
PMID:15210111.
The essential output of SBF (with MBF) is G1 cyclin transcription
PMID:1832338
PMID:1832338
PMID:10490612.
Shut-off after G1 involves mitotic Clb2-Cdc28 binding the Swi4 ankyrin repeats
(Siegmund and Nasmyth 1996, not in the publication cache; taken from the deep-research
synthesis)
[file:yeast/SWI4/SWI4-deep-research-falcon.md "Four ankyrin repeats mediate protein interactions, including association with mitotic Clb2–Cdc28/Cdk1."].
Slt2/Mpk1 cell-wall-integrity pathway. Independently of Start, Swi4 is the
transcription factor engaged non-catalytically by the CWI MAP kinase Mpk1 (Slt2) and its
pseudokinase paralog Mlp1: activated Mpk1 docks on Swi4, confers DNA binding without
Swi6, and Swi6 is recruited afterwards
PMID:18268013
PMID:18268013
PMID:20641022.
Reporter genes for this branch (FKS2, CHA1, YKR013w, YLR042c) are induced by several
cell-wall stresses, heat being the strongest
PMID:20641022
PMID:20641022
PMID:20641022.
Other regulation (orientation only, from the deep-research file). Whi5 and Swi6
phosphorylation are partly redundant routes to SBF activation, Bck2 gives a
Cln3-independent input, and during meiotic entry SBF is silenced jointly by Whi5 and a
long undecoded SWI4 transcript isoform (LUTI) that represses the canonical promoter
(Su et al. 2024). None of this is used to grade an annotation.
Full text cached: PMID:10490612 (Baetz and Andrews 1999), PMID:12464632 (Horak 2002),
PMID:20641022 (Kim and Levin 2010), PMID:21179020 (Lambert 2010), PMID:37968396
(Michaelis 2023). Abstract only: PMID:3542227, PMID:2649246, PMID:2689885, PMID:1832338,
PMID:1465410, PMID:8423776, PMID:18268013, PMID:16429126, PMID:19111667, PMID:25112483.
Every quote in the review YAML is from the cached text; for abstract-only papers the
claims used are all in the abstract. The SBF-complex IDA from PMID:1832338 rests on
full-text gel-shift data that is not cached and is deferred to the SGD curator.
35 GOA rows, 35 rows in existing_annotations. Tally: ACCEPT 24, MODIFY 4, REMOVE 6,
KEEP_AS_NON_CORE 1.
GO:0000082 G1/S transition, GO:0001228 activator MF, GO:0000978 cis-regulatory
DNA binding, GO:0045944 positive regulation of Pol II transcription, GO:0043565,
GO:0003677, GO:0000785 chromatin, GO:0005634 nucleus, GO:0033309 SBF (x6),
GO:0090575: ACCEPT. All follow from Swi4 being the SCB-binding, activating subunit of
SBF (quotes above). The GO:0000978 IBA carries contributes_to, which if anything
understates the case since Swi4 supplies the DNA-binding activity outright; flagged as
a suggested question, not changed. Swi4 appearing in its own WITH list on the IBA rows
is the expected marker of experimental grounding on the target, not circularity.
GO:0005737 cytoplasm (IBA, is_active_in): REMOVE. Seeded by the single donor Swi6,
whose S/G2/M cytoplasmic pool is a Swi6-specific import-control property; Swi4 is
constitutively nuclear
PMID:10490612
and the deep-research synthesis agrees
[file:yeast/SWI4/SWI4-deep-research-falcon.md "Swi4 is predominantly nuclear and was reported to remain nuclear throughout the mitotic cell cycle."].
Even for Swi6 the cytoplasm is where the inactive pool resides, so is_active_in is
not the right claim for the node. Propagation review: PROPAGATION_BAD,
COMPARTMENT_OR_COMPLEX_MISMATCH + WRONG_ORTHOLOG_OR_PARALOG.
GO:0030907 MBF transcription complex (IBA): REMOVE. The PANTHER node
PTN000917496 groups both DNA-binding paralogs (Swi4, Mbp1) with Swi6, so a
complex-identity term that distinguishes SBF from MBF cannot sit at that node. Swi4 is
in SBF, never MBF
PMID:10490612
[file:yeast/SWI4/SWI4-deep-research-falcon.md "SBF contains Swi4 plus Swi6, whereas the related MBF complex substitutes Mbp1 for Swi4 while retaining Swi6."].
The PomBase donors are correct for themselves (pombe has a single MBF); the SGD donors
are Mbp1 and Swi6, the actual MBF subunits. Six experimental GO:0033309 rows already
carry the correct complex.
GO:0042802 identical protein binding (IPI x2): REMOVE. The 1999 IntAct row is a
GST pull-down of the C-terminal 144 residues against N-terminal fragments in trans; the
authors themselves conclude Swi4 is monomeric and the contact is intramolecular
auto-inhibition
PMID:10490612
PMID:10490612
[file:yeast/SWI4/SWI4-deep-research-falcon.md "Evidence that full-length Swi4 is monomeric favors intramolecular masking rather than inhibition through Swi4 oligomerization."].
The 2010 row is bait recovery in an mChIP-MS survey; the paper never discusses a Swi4
homo-oligomer. Recording either as homomeric binding misrepresents the mechanism.
A dedicated in vivo stoichiometry experiment is proposed in suggested_experiments.
GO:0005515 protein binding with Swi6 (IPI x5): MODIFY x3, REMOVE x2. Following
the protein-binding policy: the targeted studies (Baetz and Andrews 1999, Lambert 2010,
Imamura 2014) document the obligate SBF heterodimer, so GO:0046982 protein
heterodimerization activity is proposed; the two proteome-wide surveys (Gavin 2006,
Michaelis 2023) add nothing beyond the six SBF-complex rows and are marked REMOVE.
Removal never asserts the interaction is false. Note that Lambert et al. misdescribe
MBF as Swi4-Mbp1
PMID:21179020;
MBF is Mbp1-Swi6.
GO:0006355 regulation of DNA-templated transcription (IMP, PMID:18268013): MODIFY
to GO:0045944. Sound assertion, direction-neutral root term; the evidence is
Swi4-dependent activation of FKS2 by Pol II, which the gene already carries as
GO:0045944 from the companion 2010 paper. Granularity refinement only.
GO:0034605 cellular response to heat (IMP, PMID:20641022): KEEP_AS_NON_CORE.
Swi4 genuinely executes the transcriptional output of a heat-triggered response, but
heat is one of four cell-wall stressors used interchangeably in that paper and the
process Swi4 serves is the Rlm1-independent CWI transcriptional response, not a
heat-shock program. Kept, graded non-core. For consistency the term was dropped from
the directly_involved_in list of the second core function (a KEEP_AS_NON_CORE row
should not be listed as a core process); that core function keeps GO:0045944. Whether
a CWI-signalling or fungal-type cell wall organization term is the intended
representation of the Swi4-Mpk1 branch is raised in suggested_questions.
No NEW rows. Everything the literature supports is already covered; the missing
representation of the Swi4-Mpk1 complex and of the contributes_to/enables asymmetry on
the IBA rows is raised as questions rather than asserted.
supported_by entries on the cytoplasm, MBF andfindings for the deep-research reference; checked everyexisting_annotations row against SWI4-goa.tsv (35 = 35, no placeholder text);