MYB34 (ATR1, At5g60890) review notes

Context: part of the ARATH_SINGLE_CELL_FUNGAL project (Tang et al. 2023, PMID:37741284).

Identity

• UniProt O64399, 295 aa R2R3-MYB with two Myb HTH repeats (9-61, 62-116). It belongs to
  subgroup 12 with MYB28/29/76 (aliphatic GSL) and MYB51/MYB122 (indolic GSL).
  PMID:17420480
• Found as the dominant allele atr1D, which raises ASA1 transcription.
  PMID:9576939
  PMID:9576939

Function: indolic glucosinolate / Trp-pathway transcriptional activator

• Overexpression raises IAA and IGs. Loss of function lowers IG gene expression and IG levels.
  PMID:15579661
• In the atr1-2 mutant, IG is about 20% lower in adult leaves. Trp synthesis genes (ASA1/TSB1) are unchanged.
  PMID:15579661
• Proposed to act as a direct activator.
  PMID:15579661
• Trans-activates promoters.
  PMID:23580754
• Division of labour among the paralogs.
  PMID:24431192
  PMID:24431192
  PMID:24431192
• bHLH partners.
  PMID:25049362
  PMID:23943862 (abstract): MYC2/3/4 interact directly with GS-related MYBs.
• Brassinosteroids: BR repression of GSL is lost in myb34 (PMID:23580754).
• Sulfur deficiency: MYB34 transcript is down-regulated. This is expression only.
  PMID:17420480

Defence

• Aphid: atr1D is more resistant because of IG breakdown products.
  PMID:18346197
• Fungi: the triple mutant is more susceptible to P. cucumerina.
  PMID:26802248
• Tang et al. 2023 (full text from the user-supplied PDF; the cached copy is abstract only):
  "Three transcription factors were proposed to regulate GSL biosynthesis ... however,
  only MYB51 and MYB122 exhibited induction at infection sites" (MYB122 in the epidermis,
  MYB51 in the vasculature). MYB34 was NOT induced at C. higginsianum infection sites.
  This is consistent with MYB34 acting mainly in roots and under ABA/JA.

Annotation decisions (summary)

• GO:0000162 Trp biosynthesis (IMP, atr1D): MODIFY to GO:2000284 positive regulation of amino acid biosynthetic process. MYB34 is a TF, not a pathway enzyme.
• GO:0009759 IG biosynthesis (IMP): MODIFY to GO:0010439 regulation of glucosinolate biosynthetic process. Also added as NEW (IMP, PMID:24431192). NTR proposed: positive regulation of indole glucosinolate biosynthetic process.
• GO:0000976 x5 (ARBA + four Y1H screens): ACCEPT for the MF.
• GO:0003700 ISS, GO:0045893 IMP, nucleus x3: ACCEPT.
• GO:0005515 Y2H with uncharacterized A0A1P8BA81: REMOVE (uninformative).
• GO:0002213 defense response to insect: KEEP_AS_NON_CORE (gain of function, indirect).
• GO:0006950, GO:0051707 (ARBA), GO:0010438 S-starvation (TAS, expression only): MARK_AS_OVER_ANNOTATED.

Additional evidence (second pass, synthesizing multiple lines)

• Deep research: just deep-research-falcon ARATH MYB34 --fallback perplexity-lite. The
  wrapper hit its 600 s timeout and the perplexity-lite fallback is not available here.
  The falcon run still finished (794 s) and wrote MYB34-deep-research-falcon.md (48
  citations), and that report was used. It agrees with the primary literature: MYB34 is
  a transcriptional regulator, not an enzyme ("MYB34 is neither a biosynthetic enzyme
  nor a glucosinolate transporter"). It also points out that direct MYB34 promoter
  occupancy has not been shown by ChIP; promoter ChIP exists for MYC2 only.
• Target-promoter evidence: MYB34 trans-activates pCYP79B2 but not the camalexin-specific
  pCYP71B15 in cultured Arabidopsis cells.
  PMID:26379682
  Earlier work reports trans-activation of TSB1/CYP79B2/CYP79B3 (PMID:23580754). Four Y1H
  screens recovered MYB34 binding to promoter fragments (GOA IPI rows).
• Expression responses: MYB34 is NOT induced by elicitors, wounding or touch, unlike MYB51 and MYB122.
  PMID:26379682
  PMID:17461791
  This fits with Tang 2023 (no induction at C. higginsianum infection sites). So the Tang
  result is one of several consistent lines of evidence and is not decisive on its own.
• Camalexin: MYB34 affects camalexin only indirectly, through the IAOx supply (IAOx
  feeding rescues the triple mutant). No camalexin annotation is proposed (PMID:26379682).
• Brassinosteroid crosstalk: BES1 interacts with MYB34/51/122 and represses indolic GSL
  genes (PMID:31776183). In myb34, BR repression of GSL is lost (PMID:23580754).
• Overexpression in hig1-1 (myb51) partially rescues the IG chemotype and causes a
  high-auxin phenotype (PMID:17461791). This fits with MYB34 pushing flux into IAOx, the
  branch point shared with IAA.
• PANTHER: PTHR47994:SF5 ("F14D16.11-RELATED"), a broad plant R2R3-MYB family. GOA has no
  IBA annotations for MYB34 (or for MYB51), so there are no PAINT node placements to
  evaluate. The ortholog distribution of subgroup 12 was not analysed bioinformatically
  in this review.
• Consistency with the sibling MYB51 review (genes/ARATH/MYB51): the same choices were
  made. GO:0009759 is changed by MODIFY to GO:0010439. GO:0001228 is added as NEW (IDA,
  trans-activation). The core MF is GO:0001228 and the location is nucleus.