MKK4 curation notes

Session 2026-10-06, added for the stomatal_lineage_development module (where MKK4/MKK5 are representative members of the redundant MAPKK step). Fetched by accession (O80397, alias MKK4); UniProt entry verified (M2K4_ARATH, At1g51660). Falcon deep research not attempted (provider returned HTTP 402 for all other genes this session).

Key findings

• MKK4/MKK5 act downstream of YODA and upstream of MPK3/MPK6 in stomatal development PMID:17259259; loss gives clustered stomata, activation abolishes stomatal fate PMID:17259259.
• YDA phosphorylates MKK4 PMID:22307275; MAPKKK5 phosphorylates MKK4/MKK5 activation loops PMID:27679653.
• Immune MAPK cascade downstream of FLS2 PMID:11875555.
• Inflorescence architecture downstream of ERECTA PMID:23263767; floral organ abscission downstream of HAE/HSL2 PMID:18809915.
• Non-canonical chloroplast stromal import of MKK4 PMID:19516975 - kept non-core.

Curation decisions

• Core MF: MAP kinase kinase activity (GO:0004708). IDA from PMID:9878570 accepted deferring to curator (abstract only, centred on MKK2/MEK1).
• NEW: negative regulation of stomatal complex development (IGI, PMID:17259259) - MKK4 performs the phosphorylation relay step, so it does part of the work.
• Protein binding: MPK3/MPK6 rows MODIFIED to MAP kinase binding; MAPKKK5 row to MAPKKK binding; BRX, MYB73, KNAT1, TIFY8, ILK4 rows REMOVED.

2026-10-09: combined with independent review

Reconciled this review with an independent review written from the chitin-perception angle (PR 4451). Both reviews used the same GOA file (40 rows), so every row matched. Rows where the decision changed relative to this file:

• nucleus (HDA PMID:15610358, IEA GO_REF:0000044, ISM GO_REF:0000122): ACCEPT -> KEEP_AS_NON_CORE. The nuclear GFP signal is credible, but the activating MAPKKK-MKK4 step is mainly cytosolic PMID:27679653. Nucleus removed from the core_functions locations.
• pollen-pistil interaction (IGI PMID:32890733): KEEP_AS_NON_CORE -> UNDECIDED. The cached record is abstract-only, and the abstract names MKK1/2/3/7/9 + MPK3/MPK4. The WITH/FROM list is MKK1 (AT4G26070), MKK2 (AT4G29810), MKK7 (AT1G18350), MKK9 (AT1G73500), MPK3 (AT3G45640) and AT1G51660 (MKK4 itself), with no MKK3 (AT5G40440). That points to a possible MKK3/MKK4 identifier swap, but the full text cannot be checked, so the row is left UNDECIDED (not removed) and raised as a question.
• protein serine kinase activity (IEA RHEA:17989): ACCEPT -> MODIFY to GO:0004708 MAP kinase kinase activity. This is an EC 2.7.12.2 expansion artefact: MKK4 phosphorylates the Thr/Tyr of the MPK3/MPK6 activation loop, and no serine-directed substrate activity is documented.

Disagreements resolved in favour of this file:
- Protein binding IPI rows with MPK3/MPK6 or MAPKKK5 as partner (8 rows): the other review REMOVEd all 13 protein binding rows. I kept the MODIFY to GO:0051019 MAP kinase binding / GO:0031435 MAPKKK binding. The annotation-reviewer policy prefers MODIFY when the paper supports a more informative MF, these interactions are the functional docking partners of the cascade, and the MKK5 review on main makes the same choice. The other 5 rows (BRX, MYB73, KNAT1, TIFY8, ILK4/AT3G58760) are REMOVEd in both reviews.
- defense response to other organism (IBA, IEA, IMP PMID:11875555): the other review used KEEP_AS_NON_CORE; I kept ACCEPT. PRR-triggered immune signalling is one of the two principal roles of the MKK4/MKK5 pair, directly shown in PMID:11875555 and PMID:35652263, and the MKK5 review on main also ACCEPTs it.
- NEW GO:2000122 negative regulation of stomatal complex development (IGI PMID:17259259): kept. It is used by the stomatal_lineage_development module. MKK4 performs a phosphorylation step of the relay, so it does part of the work. Comparators: EPF2 carries it in GOA, and the YDA and ERECTA reviews carry it.

Additions from the other review:
- Core function evidence for the chitin branch PMID:27679653, MKK4DD specificity for MPK3/MPK6 PMID:18378893, and the YDA vs MAPKKK3/5 split PMID:35652263.
- Camalexin rests on gain-of-function evidence only PMID:18378893. As a result, no camalexin term and no cell surface PRR signalling term (GO:0002752) were added; both are raised as questions, consistent with MKK5/MPK3/MPK6.
- Activation-loop sites T-224/S-230 PMID:27679653.
- Wound-induced ethylene (Li et al. 2018, from deep research; not cached): the mkk4 knockdown has a small effect compared with mkk5. No term was added.
- Chloroplast stroma stays non-core (in vitro import into pea chloroplasts only). This is supported by a quote from the repo deep-research file, re-checked verbatim.

2026-10-15 journal: QuickGO record for the PMID:32890733 row (PR #5026 follow-up)

• Query (re-run 2026-10-15): QuickGO REST, https://www.ebi.ac.uk/QuickGO/services/annotation/search?reference=PMID:32890733&limit=200 (Accept: application/json) returned 6 annotations, all GO:0009875 pollen-pistil interaction IGI acts_upstream_of_or_within, assigned by TAIR, to MKK1 (Q94A06), MKK2 (Q9S7U9), MKK4 (O80397), MKK7 (Q9LPQ3), MKK9 (Q9FX43) and MPK3 (Q39023); none to MKK3 or MPK4. The row stays UNDECIDED.
• Full text on 2026-10-15: fetch-pmid PMID:32890733 --force cached abstract only (no PMC record); Europe PMC lists no PMCID (isOpenAccess N). Earlier attempts recorded in the review reason (Cell Press 403, bioRxiv 429) were not re-tested.