csy3 / Cas7f (Q02MM1) — Pseudomonas aeruginosa UCBPP-PA14 — curation notes

Deep research was unavailable in this environment (no provider API keys), so this file
is my own literature journal. Every assertion carries an inline PMID plus a verbatim
quote from the cached record in publications/.

What this protein is

PA14_33310, 342 aa, "CRISPR-associated protein Csy3" = Cas7f, the backbone subunit.
Six copies polymerise along the crRNA:
PMID:32170016, matching UniProt's stoichiometry
Csy1(1),Csy2(1),Csy3(6),Cas6/Csy4(1)-crRNA(1) and
PMID:32170016. A Csy3(6)·Cas6f(1)·crRNA(1) subcomplex also forms (UniProt
SUBUNIT), which is consistent with the IntAct Csy3–Cas6f pair behind GOA's two
GO:0005515 rows (Q02MM1–Q02MM2, NbExp=12). Original PA14 biochemistry:
PMID:21536913.

What Cas7f does

Binds and kinks the crRNA, non-sequence-specifically.
PMID:32170016 — backbone, not bases:
PMID:32170016. The kinking is the functional point, since it segments the guide:
PMID:32170016.

Pins the crRNA:target-DNA heteroduplex. This is the step that makes the backbone an
active participant in target verification rather than a scaffold:
PMID:28985564. The structures are of the PA14 complex:
PMID:28985564.

Carries the DNA-binding surface of the backbone.
PMID:32170016.

The anti-CRISPR connection

Cas7f is the principal anti-CRISPR target surface of this system, which is why the
module calls it "the surface bound by AcrIF8 and related inhibitors":
PMID:32170016 — and the
inhibitors compete for the very residues above:
PMID:32170016. This is consistent
with the completed phage-side review genes/BPZF4/AcrF8/AcrF8-ai-review.yaml, which
records AcrIF8 contacting both the Cas7f backbone and the crRNA.

In vivo

Csy3 is required for spacer acquisition — a gene-specific deletion, which is the
grounding for the CACAO IMP:
PMID:26586803, in a system where
PMID:26586803.

Csy3 is not in the strict-requirement class for crRNA accumulation:
PMID:21398535 — so its GO:0043571 annotation is earned by the
acquisition phenotype, not by a crRNA-biogenesis phenotype.

Curation decisions

• Both GO:0005515 protein binding rows (IPI, partner Cas6f) → MODIFY to
  GO:0005198 structural molecule activity. Cas7f is the structural element: six
  copies interlock thumb-into-palm through roughly 2,000 Ų interfaces, and the spiral
  they form runs from the Cas6f head to the Cas8f–Cas5f tail, which is the contact this
  IntAct record samples. Holding the complex together is the whole of what this
  subunit's protein–protein contacts do.

Aspect correction (follow-up). My first pass proposed
part_of GO:0032991 protein-containing complex as the replacement, reasoning from the
E. coli comparator where all five Cascade subunits carry exactly that. That was wrong
in form: these GOA rows carry qualifier: enables, so they are molecular-function
rows, and a gene product cannot enable a cellular component. However
well-supported complex membership is, it cannot be expressed by swapping a CC term
into an enables MF row. The E. coli reviews were not making this mistake — their
GOA already contained separate part_of GO:0032991 rows, which they MODIFY to
GO:1990904; their enables GO:0005515 rows went to GO:0005198 instead.
Reconciled to the same convention:

• MODIFY the enables rows to GO:0005198 structural molecule activity ("the
  action of a molecule that contributes to the structural integrity of a complex").
  Aspect-correct, and none of its 22 children fits a non-ribosomal ribonucleoprotein,
  so the parent is the right level. Each row is backed by the verbatim structural
  quote naming the contact this subunit actually makes.
• Carry complex membership on its own NEW part_of GO:1990904 ribonucleoprotein complex row. PA14 has no part_of complex row for any Csy subunit, unlike all
  five E. coli Cascade subunits, so this is a real missing annotation rather than a
  reformulation. GO:1990904 rather than the bare GO:0032991 root because the
  60-nt crRNA is an integral component, not a ligand.
• core_functions[].in_complex → GO:1990904 for the same reason.
• Added a proposed_new_terms entry for a "CRISPR RNA-guided surveillance
  complex" CC term under GO:1990904, identical in substance to the one the five
  E. coli Cascade reviews carry, so the two systems request one term rather than two.
  GO's entire CRISPR vocabulary is five BP terms (GO:0099048, GO:0043571,
  GO:0098672 and the obsolete GO:0110132/GO:0110133); ComplexPortal models the
  type I-E complex as CPX-1005, GO does not.
• GO:0043571 maintenance of CRISPR repeat elements, IMP,
  acts_upstream_of_or_within_positive_effect → ACCEPT. A clean csy3 deletion
  abolishes spacer acquisition. The hedged qualifier is appropriate: the requirement
  runs through complex integrity rather than through a Csy3 catalytic step.

Gaps identified (missing annotations)

• GO:0003723 RNA binding (NEW, IDA, PMID:32170016). Comparator: casC (Cas7e,
  Q46899) carries GO:0003723 by IDA (PMID:25103409), as do casA, casD and casE. The
  eleven-residue crRNA-backbone contact set is directly resolved here.
• GO:0071667 DNA/RNA hybrid binding (NEW, IDA, PMID:28985564). Comparator: this is
  precisely the term casC carries by IDA from PMID:25123481 — the Cas7 subunit of E.
  coli Cascade — and casD carries it too. The β-hairpin threading that pins the
  RNA:DNA heteroduplex is the same mechanism. Of all the proposals in this gene set,
  this is the one with the tightest subunit-to-subunit comparator match.
• GO:0099048 CRISPR-cas system (NEW, IDA). Comparator: all five E. coli Cascade
  subunits carry it by IDA (PMID:18703739); no PA14 Csy subunit does. Cas7f does work in
  the "target interference" stage named in the term's definition — it presents the guide
  in segments and holds the heteroduplex — rather than merely being required for it.
  Checked via QuickGO that GO:0099048 is not an ancestor or descendant of
  GO:0043571 or GO:0051607.

Not proposed, and why

• GO:0003677 DNA binding. The lysine-rich patch is described as critical for DNA
  binding by the Csy complex, which is a contributes-to statement about the complex,
  not a demonstration that isolated Cas7f binds DNA. Comparator: E. coli casC does
  not carry a DNA-binding term either — it carries GO:0071667, which is what I propose.
  The complex-level dsDNA-binding activity is captured in core_functions as a
  contributes_to_molecular_function instead.
• GO:0051607 defense response to virus. No csy3 allele has been assayed for phage
  resistance, and the PA14 locus-level evidence is contested (see cas3-notes.md).
• No molecular-function term exists for crRNA-guided target recognition; recorded as an
  ontology gap in modules/crispr_cas_adaptive_immunity.yaml and
  modules/anti_crispr_suppression.yaml, and raised in suggested_questions rather
  than filled with an ill-fitting id.