No deep-research provider was available in this container (no API keys), so
just deep-research was not run and no -deep-research-<provider>.md file
exists for this gene. The literature below was assembled by hand from the
cached publications/PMID_*.md records, the UniProt flat file, and web
retrieval of two sources that are not in the cache (the 1976 Eur. J. Biochem.
full text and the Meijer/Horcajadas/Salas phi29 review). Every cached record
used here is abstract-only (full_text_available: false), so the
curator-deference rule applies throughout: no experimental row was removed on
the strength of an abstract.
GONUTS (gowiki.tamu.edu) was retried for this gene on 2026-11-01 and is still
down: both https://gowiki.tamu.edu/wiki/index.php/Gene:P03679 and the site
search returned HTTP 410 Gone. The CACAO row's wiki-side rationale therefore
could not be read, exactly as in batches 1–2.
86 aa (mature chain 2–86) early protein, two products from the same ORF by
alternative in-phase initiation: the 10 kDa "Long" form (P03679-1) and a 6 kDa
"Short"/delta-1 form (P03679-2) lacking residues 1–34
PMID:2526779,
PMID:2526779.
The same paper mapped gene 1 to ORF-6 by sequencing the ochre mutation in
sus1(629) PMID:2526779.
Sequence features (UniProt P03679): predicted coiled coil 38–67, hydrophobic
C-terminus, no transmembrane helix — it is a peripheral membrane protein, not
an integral one [file:BPPH2/1/1-uniprot.txt "Peripheral membrane protein"].
p1 self-polymerises into protofilament sheets resembling tubulin/FtsZ polymers
PMID:9774353, and the
authors conclude it is a structural component of a viral-encoded,
membrane-associated structure
PMID:9774353
that supplies an PMID:9774353.
Assembly determinants are mapped: the coiled-coil residues Leu46/Met53/Leu60
are required for sheet formation
PMID:11283004,
and seven single substitutions in the coiled-coil or hydrophobic region block
formation of large complexes PMID:15883018.
Membrane attachment maps to the hydrophobic C-terminus
PMID:9193003.
In infected cells p1 is membrane-associated
PMID:11032825, has a
peripheral location by immunoEM
PMID:12904294,
and assembles into membrane-associated multimers
PMID:12904294.
Those structures form independently of the rest of the replisome and are
functional: plasmid-borne p1
PMID:12904294.
The model is that PMID:12904294.
p1 binds the primer terminal protein (TP) directly — and the TP-binding and
membrane/self-assembly functions are separable, since the C-terminally truncated
p1DeltaC43 still PMID:11032825.
In membrane vesicles from infected cells p1, free TP and a little DNA polymerase
co-fractionate PMID:9193003,
giving the membrane-associated multiprotein initiation complex model.
The replisome is proposed to attach to this platform
PMID:11032825.
Host side: p1-YFP localises to midcell, colocalises with and associates with
host FtsZ PMID:23836667,
and midcell targeting is lost without FtsZ. The same paper restates the
replication phenotype PMID:23836667.
So the honest statement is: p1 is a replication protein whose loss severely
impairs (but does not formally abolish at all temperatures) viral DNA synthesis.
This matters for the choice between involved_in and
acts_upstream_of_or_within_positive_effect, and the latter — which the CACAO
row uses — is the more cautious and arguably better-fitting qualifier.
One group (Sophia University; Hirokawa/Makino lab) reports that gp1 represses
the upstream dna genes post-transcriptionally. mRNA level and integrity are
unchanged PMID:9480849,
gp1 binds RNA in vitro
PMID:9480849,
and the conclusion is that translation of
PMID:9480849.
The follow-up links self-assembly to this activity
PMID:15883018
and restates that gp1
PMID:15883018.
UniProt curates this as the RNA-binding keyword (refs 6 and 10 of the entry).
Caveat recorded for the reviewer: this is a single laboratory, the target
transcript is the phi29 dna operon mRNA, and the Salas lab's extensive p1 work
never tested it. It is cited here to justify refining the RNA-binding term to
mRNA binding and to support one new regulatory BP row, flagged as
single-provenance in the row's reason.
The CACAO row is GO:0039693 viral DNA genome replication,
acts_upstream_of_or_within_positive_effect, IMP, PMID:820555 (Carrascosa et
al. 1976). The screen predicted an adjacent-locus / one-paper-many-genes
failure: a single multi-gene mutant survey spread across many phi29 entries,
whose abstract (all that is cached) says only
PMID:820555 without naming
the six.
The prediction is wrong for this gene. The 1976 full text was retrieved
(Eur. J. Biochem. 66:229–241, DOI 10.1111/j.1432-1033.1976.tb10512.x; OCR copy
via scispace) and it names gene 1 three separate times:
So the six DNA-negative cistrons are 1, 2, 3, 5, 6 and 17, gene 1 is one of
them, and the paper individually establishes the annotated term for this gene by
a named suppressor-sensitive mutant (sus1(629)) scored for phage DNA synthesis —
a textbook IMP. The same mutant allele is the one Prieto et al. later sequenced
to prove ORF-6 = gene 1 PMID:2526779,
which independently confirms that the 1976 "sus1" is this locus and not a
neighbour. These full-text sentences are not quoted in the review's
supported_text fields, because the cached publication record is abstract-only
and quotes must be verbatim substrings of the cached source; they are recorded
here instead and summarised in the row's reason.
| Term | Evidence | Action | Note |
|---|---|---|---|
| GO:0033644 host cell membrane (EXP, IDA, IEA) | 11032825 / 12904294 / SL-0380 | ACCEPT ×3 | peripheral host-membrane location, directly shown |
| GO:0039693 viral DNA genome replication (IDA, IEA, IMP/CACAO) | 11032825 / KW-1194 / 820555 | ACCEPT ×3 | core; CACAO row verified against full text |
| GO:0003723 RNA binding (IEA KW) | GO_REF:0000043 | MODIFY → GO:0003729 mRNA binding | target is the dna operon mRNA |
| GO:0006260 DNA replication (IEA) | GO_REF:0000120 | MODIFY → GO:0039693 | lateral fix: GO:0039693 is not a descendant of GO:0006260 (checked in QuickGO), so this row asserts cellular DNA replication, which p1 does not do |
| GO:0016020 membrane (IEA InterPro) | GO_REF:0000002 | MODIFY → GO:0033644 | GO:0033644 sits under host cellular component, not under GO:0016020, so this is a lateral refinement to the host-scoped term already carried by IDA |
| GO:0016032 viral process (IEA InterPro) | GO_REF:0000002 | TOO_GENERAL | GO:0039693 is a descendant (GO:0039693 → GO:0019079 → GO:0019058 → GO:0016032) and is asserted in this review |
| GO:0017148 negative regulation of translation | NEW (IDA, 9480849) | NEW | single-lab provenance flagged in reason |
Ontology checks run against the QuickGO ancestors endpoint on 2026-11-01:
GO:0039693 ancestors include GO:0016032 but not GO:0006260;
GO:0033644 ancestors are GO:0033643/GO:0044217/GO:0018995 and do not
include GO:0016020.