MYB34 (ALTERED TRYPTOPHAN REGULATION 1, ATR1; At5g60890) is a nuclear R2R3-MYB transcription factor of subgroup 12, the small clade that also contains the aliphatic glucosinolate regulators MYB28, MYB29 and MYB76 and its two indolic paralogs MYB51 and MYB122. Its two N-terminal Myb-type HTH repeats bind promoter DNA, and MYB34 acts as a transcriptional activator of tryptophan-pathway and indolic glucosinolate biosynthetic genes, most strongly the tryptophan-metabolizing genes CYP79B2, CYP79B3 and CYP83B1, and more modestly the tryptophan synthesis genes ASA1 and TSB1. It was identified through the dominant atr1D allele, which disrupts an upstream ORF in the 5' leader and causes overexpression, raising indolic glucosinolate levels about ten-fold and also elevating free IAA. Loss-of-function mutants have no visible phenotype but contain modestly reduced indolic glucosinolates, and the myb34 myb51 myb122 triple mutant contains no detectable indolic glucosinolates. Among the three paralogs, MYB34 controls indolic glucosinolate production mainly in roots and young seedlings, and acts mainly under abscisic acid and jasmonate signalling, whereas MYB51 dominates in shoots and under salicylic acid and ethylene signalling. MYB34 forms complexes with the jasmonate-regulated bHLH factors MYC2, MYC3, MYC4 (bHLH04/05/06), which are required for glucosinolate gene activation. Its outputs, indolic glucosinolates and their PEN2-dependent breakdown products, contribute to defence against aphids and fungal pathogens. Unlike MYB51 and MYB122, MYB34 is not transcriptionally induced in leaf cells at sites of Colletotrichum higginsianum infection.
Definition: Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of indole glucosinolates.
Justification: GO has only the generic GO:0010439 regulation of glucosinolate biosynthetic process. The R2R3-MYB subgroup 12 regulators are split by substrate class: MYB34, MYB51 and MYB122 activate the tryptophan-derived (indolic) branch, while MYB28, MYB29 and MYB76 activate the methionine-derived (aliphatic) branch. Indole- and aliphatic-specific positive-regulation children would capture this well-established distinction.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000162 L-tryptophan biosynthetic process | IMP PMID:9576939 A Myb homologue, ATR1, activates tryptophan gene expression ... | MODIFY | Summary: Based on the dominant atr1D allele, which overexpresses ATR1/MYB34 and increases transcription of ASA1, the gene encoding the first and rate-limiting enzyme of tryptophan synthesis. MYB34 is a transcription factor that activates tryptophan-pathway genes. It does not carry out any enzymatic step of tryptophan biosynthesis. Reason: A transcription factor that raises expression of ASA1 (and, more weakly, TSB1) regulates tryptophan biosynthesis. It does not take part in the biosynthetic process itself. The phenotype comes from a gain-of-function allele. In atr1-2 loss-of-function mutants, Trp synthesis gene transcripts were not significantly changed in seedlings or adult leaves (PMID:15579661), so the Trp-synthesis effect is modest and partly redundant. GO has no tryptophan-specific regulation term. The closest existing term is positive regulation of amino acid biosynthetic process. Proposed replacements: positive regulation of amino acid biosynthetic process Supporting Evidence: PMID:9576939 ATR1 encodes a Myb-like transcription factor that modulates ASA1 expression. PMID:15579661 Steady-state transcript levels of the primary Trp synthesis genes ASA1 and TSB1 were not significantly different between wild-type and atr1-2 adult leaves |
| GO:0000976 transcription cis-regulatory region binding | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learning transfer of cis-regulatory region binding to an R2R3-MYB protein with two Myb-type HTH DNA-binding repeats (UniProt DNA_BIND features 37-61 and 89-112). Reason: Sequence-specific promoter binding is the expected activity of a canonical R2R3-MYB. It is supported independently by several yeast one-hybrid screens, and the cited papers describe MYB34 as trans-activating CYP79B2/CYP79B3/TSB1 promoters. Supporting Evidence: PMID:23580754 MYB34, MYB51, and MYB122, identified as regulators of the indolic glucosinolate biosynthetic pathway, exclusively trans-activate the promoters of TSB1, CYP79B2, and CYP79B3 |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:25352272 Promoter-based integration in plant defense regulation. | ACCEPT | Summary: Systematic yeast one-hybrid screen of glucosinolate pathway promoters. MYB34 bound the promoters of FMO GS-OX1 (AT1G65860) and BCAT3 (AT3G49680). Reason: Y1H gives direct evidence that MYB34 binds promoter DNA, and the bound promoters belong to glucosinolate pathway genes, which fits the known role of MYB34. The targets here are aliphatic-pathway genes, so this row supports the binding activity, not any particular target. IPI is unusual for protein-DNA Y1H data but the activity is sound. Supporting Evidence: PMID:25352272 A systematic yeast one-hybrid study was used to identify hundreds of unique potential regulatory interactions with a nearly complete complement of 21 promoters for the aliphatic glucosinolate pathway. |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:25533953 An Arabidopsis gene regulatory network for secondary cell wa... | ACCEPT | Summary: Genome-scale yeast one-hybrid network for secondary cell wall genes. MYB34 was recovered binding the same two promoters (AT1G65860, AT3G49680) that were tested in the shared Y1H resource. Reason: The DNA-binding activity is well supported and fits an R2R3-MYB. These are high-throughput Y1H interactions, and the claim accepted is the binding activity, not a role for MYB34 in cell wall synthesis. Supporting Evidence: PMID:25533953 Our Y1H approach revealed a highly interconnected regulatory network. |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:30356219 Transcriptional regulation of nitrogen-associated metabolism... | ACCEPT | Summary: Y1H-based nitrogen-associated transcriptional regulatory network. MYB34 bound the promoters of AT1G72330 (ALAAT2), AT2G25930 (ELF3) and AT2G31955 (CNX2). Reason: These Y1H interactions are further evidence that MYB34 binds promoter DNA. Whether MYB34 regulates these nitrogen-metabolism targets in planta has not been shown, so no process annotation follows from this row. The binding activity itself is sound. Supporting Evidence: PMID:30356219 Here we present a transcriptional regulatory network and twenty-one transcription factors that regulate the architecture of root and shoot systems in response to changes in nitrogen availability. |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:31806676 A PXY-Mediated Transcriptional Network Integrates Signaling ... | ACCEPT | Summary: Y1H-mapped PXY-mediated vascular transcriptional network. MYB34 bound the promoters of PHB (AT2G34710) and TMO5-like bHLH (AT3G25710). Reason: This is consistent evidence for promoter-binding activity. Any role in vascular development is untested and is not implied by this MF annotation. Supporting Evidence: PMID:31806676 we mapped a putative PXY-mediated transcriptional regulatory network comprising 690 transcription factor-promoter interactions in Arabidopsis |
| GO:0002213 defense response to insect | IMP PMID:18346197 Identification of indole glucosinolate breakdown products wi... | KEEP AS NON CORE | Summary: The atr1D overexpression mutant overproduces indole glucosinolates and is more resistant to green peach aphid (Myzus persicae). The defensive effect comes from post-ingestive breakdown products of indole glucosinolates. Reason: The phenotype is a gain-of-function effect that works through MYB34's metabolic output, the indole glucosinolates. The defence is carried out by indole glucosinolate breakdown products. The acts_upstream_of_or_within qualifier fits this indirect relationship. This is a real physiological consequence of MYB34 activity, but it is downstream and not a core function. Supporting Evidence: PMID:18346197 A defensive role for indole glucosinolates is suggested by the observation that atr1D mutant plants, which overproduce indole glucosinolates, are more resistant to M. persicae |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | ACCEPT | Summary: Inferred from the genome-wide classification of Arabidopsis transcription factors. MYB34 is a canonical R2R3-MYB with two Myb HTH repeats, and genetic and transactivation data show it activates transcription of target genes. Reason: Correct core activity. Experimental work shows MYB34 transactivates indolic-pathway promoters (PMID:23580754, PMID:26379682) and activates ASA1 and CYP79B2/B3/CYP83B1 expression (PMID:15579661). The more specific activator term GO:0001228 is proposed as NEW for consistency with the MYB51 review. Supporting Evidence: PMID:15579661 The simplest model is that ATR1 serves as a direct transcriptional activator of both Trp synthesis genes and Trp secondary metabolism genes |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | REMOVE | Summary: Binary Y2H interaction with an uncharacterized protein (A0A1P8BA81, MTI20.21) from the phytohormone interactome map. Reason: Generic protein binding carries no functional information, and the partner is an uncharacterized protein from a high-throughput screen. The interaction may still be real. The functionally relevant MYB34 partners, the bHLH IIIe factors MYC2, MYC3, MYC4/bHLH04/05, are documented in other studies (PMID:23943862, PMID:25049362) but are not the subject of this row. Supporting Evidence: PMID:32612234 Here, we experimentally generated a systems-level map of the Arabidopsis phytohormone signalling network, consisting of more than 2,000 binary protein-protein interactions. |
| GO:0005634 nucleus | HDA PMID:14617066 Analysis of the Arabidopsis nuclear proteome and its respons... | ACCEPT | Summary: Identified in a 2D-gel/MALDI-TOF survey of the Arabidopsis nuclear proteome. Reason: Nuclear localization is expected for a DNA-binding transcription factor. The cached abstract does not list individual proteins, so we defer to the curator, who read the full dataset. Supporting Evidence: PMID:14617066 Proteomic analyses led to the identification of 184 spots corresponding to 158 different proteins implicated in a variety of cellular functions. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (Nucleus, ECO:0000305). Reason: Consistent with MYB34's role as a promoter-binding transcriptional activator. |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP sequence-based prediction of nuclear localization. Reason: Consistent with the HDA and UniProt nuclear assignments and with transcription factor function. |
| GO:0006950 response to stress | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ARBA machine-learning transfer of the very general term response to stress. Reason: Correct but uninformative. The term is an ancestor of defense response to insect (GO:0002213), which is kept for MYB34, so it is entailed rather than over-annotated. MYB34's specific roles are captured by regulation of glucosinolate biosynthetic process and the specific non-core terms. Treated the same way as the identical ARBA row on MYB122. |
| GO:0009759 indole glucosinolate biosynthetic process | IMP PMID:15579661 The Arabidopsis ATR1 Myb transcription factor controls indol... | MODIFY | Summary: In atr1-2 loss-of-function plants, CYP79B2, CYP79B3 and CYP83B1 transcripts are reduced and indolic glucosinolates fall by about 20% in adult leaves. Overexpression (atr1D, 35S-ATR1) raises indolic glucosinolate levels, by roughly an order of magnitude in atr1D. Reason: The evidence is strong, but MYB34 controls indolic glucosinolate biosynthesis by activating transcription of the biosynthetic genes. The enzymatic steps are carried out by CYP79B2/B3, CYP83B1, SUR1, UGT74B1 and SOT16. Under the participation test, a transcription factor gets the regulation term, not the biosynthetic process term. GO has no indole-specific regulation term, so the replacement is GO:0010439 regulation of glucosinolate biosynthetic process. A more specific positive-regulation term for indole glucosinolates is proposed in proposed_new_terms. The myb34 myb51 myb122 triple mutant, which lacks indolic glucosinolates (PMID:24431192), confirms the regulatory role. Proposed replacements: regulation of glucosinolate biosynthetic process Supporting Evidence: PMID:15579661 However, adult leaves of atr1-2 mutant plants contained reduced transcript levels of CYP79B2 , CYP79B3 , and CYP83B1 relative to parental Ws PMID:15579661 Correspondingly, IG measurements showed approximately 20% reduced IG accumulation in atr1-2 adult leaves PMID:24431192 The myb34 myb51 myb122 triple mutant is devoid of IGs, indicating that these three MYB factors are indispensable for IG production under standard growth conditions. file:ARATH/MYB34/MYB34-deep-research-falcon.md MYB34 is neither a biosynthetic enzyme nor a glucosinolate transporter |
| GO:0010438 cellular response to sulfur starvation | TAS PMID:17420480 Omics-based identification of Arabidopsis Myb transcription ... | MARK AS OVER ANNOTATED | Summary: Hirai et al. 2007 report that MYB28, MYB29 and ATR1/MYB34 transcripts are down-regulated under sulfur deficiency. The authors suggest this shuts down glucosinolate synthesis to save sulfur. Reason: The only evidence is that MYB34 expression falls under sulfur starvation. That makes MYB34 a responsive gene. It does not show that MYB34 carries out the cellular response. No mutant evidence links MYB34 to sulfur-starvation responses, and the study's functional work concerned MYB28/MYB29 and aliphatic glucosinolates. At most, glucosinolate downregulation under S deficiency is a consequence of reduced MYB34 expression. Supporting Evidence: PMID:17420480 Under sulfur-deficiency conditions, the expression of PMG1 / Myb28 , PMG2 / Myb29 , and ATR1 / Myb34 was down-regulated, presumably to shut down GSL biosynthesis |
| GO:0045893 positive regulation of DNA-templated transcription | IMP PMID:9576939 A Myb homologue, ATR1, activates tryptophan gene expression ... | ACCEPT | Summary: The dominant atr1D allele increases ASA1 (AT5G05730) transcription, which identifies ATR1/MYB34 as a positive transcriptional regulator of tryptophan pathway genes. Reason: MYB34 is a transcriptional activator. Increased ASA1 transcription and the later demonstration that MYB34 activates CYP79B2/B3/CYP83B1 expression (PMID:15579661) support positive regulation of transcription as a core process. Supporting Evidence: PMID:9576939 One of these mutants, atr1D is dominant for increased transcription of ASA1 in specific seedling tissues. |
| GO:0051707 response to other organism | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ARBA machine-learning transfer of the broad biotic-response term. Reason: Kept as non-core because the term is an ancestor of defense response to insect (GO:0002213), which is kept for MYB34, and because MYB34 contributes to defense against Plectosphaerella in the triple mutant; the annotation is therefore entailed. It should not be read as MYB34 being transcriptionally pathogen-responsive, which the evidence below argues against. MYB34 contributes indirectly to antimicrobial and anti-herbivore defence by supporting indolic glucosinolate production. The myb34 myb51 myb122 triple mutant is more susceptible to Plectosphaerella cucumerina (PMID:26802248). MYB34 itself is not a pathogen-responsive gene. In a single-cell atlas of Colletotrichum higginsianum infection, only MYB51 and MYB122 among the three indolic regulators were induced at infection sites (PMID:37741284; full text). MYB34 is likewise not induced by silver nitrate, wounding or touch, unlike MYB51 and MYB122 (PMID:26379682, PMID:17461791). Responses to SA/ET, the main pathogen signals, act mainly through MYB51 (PMID:24431192). Supporting Evidence: PMID:24431192 MYB51 is the central regulator of IG synthesis upon SA and ET signaling PMID:26802248 MYB34/51/122 contribute to resistance toward P. cucumerina exclusively through IG biosynthesis PMID:26379682 However, the expression of MYB34 was reduced, indicating that it plays a less important role in phytoalexin regulation. PMID:17461791 Mechanical stimuli such as touch or wounding transiently induced the expression of HIG1/MYB51 but not of ATR1/MYB34 |
| GO:0010439 regulation of glucosinolate biosynthetic process | IMP PMID:24431192 MYB34, MYB51, and MYB122 distinctly regulate indolic glucosi... | NEW | Summary: Analysis of myb34 single, myb34 myb51 double and myb34 myb51 myb122 triple mutants shows that MYB34 regulates indolic glucosinolate biosynthesis, mainly in roots and under ABA/JA signalling. In the absence of all three MYBs, no indolic glucosinolates are made. Reason: This is the correct process term for MYB34's core role, and it matches the MODIFY replacement for the indole glucosinolate biosynthetic process row. It passes the participation test for a regulation term: MYB34 binds and activates promoters of the biosynthetic genes. The best-characterized regulators carry the equivalent term, so this keeps MYB34 consistent with them. Supporting Evidence: PMID:24431192 MYB34 controlling biosynthesis of IGs mainly in the roots PMID:24431192 MYB34 is the key regulator upon ABA and JA signaling PMID:15579661 this work implicates ATR1 as a key homeostatic regulator of Trp metabolism |
| GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | IDA PMID:26379682 The role of MYB34, MYB51 and MYB122 in the regulation of cam... | NEW | Summary: In trans-activation assays in cultured Arabidopsis cells, p35S:MYB34 increased pCYP79B2:uidA reporter activity but did not activate the camalexin-specific pCYP71B15 or pCYP71A13 promoters. Gain of function (atr1D, 35S-ATR1) raises CYP79B2/B3/CYP83B1 transcripts. Reason: The existing annotations record only the generic DNA-binding transcription factor activity. Promoter trans-activation and gain- and loss-of-function expression data show that MYB34 activates the transcription of its targets, and no repressor activity has been reported. This matches the GO:0001228 NEW annotation in the MYB51 review. Direct in vivo occupancy of target promoters by MYB34 (ChIP) has not been shown. Supporting Evidence: PMID:26379682 The activity of pCYP79B2:uidA increased, whereas that of pCYP71B15:uidA was not affected by all three MYB factors, as demonstrated by co-expression via trans-activation assays with cultured Arabidopsis cells PMID:15579661 The simplest model is that ATR1 serves as a direct transcriptional activator of both Trp synthesis genes and Trp secondary metabolism genes |
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Download this section (compressed HTML)Q: Does MYB34 bind specific MYB-core cis-elements in the CYP79B2, CYP79B3 and CYP83B1 promoters in planta (ChIP), and are the aliphatic-pathway promoters bound in Y1H screens (FMO GS-OX1, BCAT3) also regulated by MYB34 in vivo?
Q: Why is MYB34, unlike MYB51 and MYB122, not induced at Colletotrichum higginsianum infection sites? Does its predominantly root- and ABA/JA-linked activity reflect a division of labour in which MYB34 sets basal or root indolic glucosinolate pools while MYB51/MYB122 handle localized pathogen-induced synthesis?
Q: Should the GO:0010438 sulfur-starvation and GO:0000162 tryptophan biosynthesis annotations, which rest on expression change or gain-of-function data, be retracted in favour of regulation terms?
Experiment: Profile genome-wide MYB34 occupancy with an epitope-tagged MYB34 expressed from its native promoter in roots, with and without MeJA or ABA treatment, and compare it with MYB51 occupancy.
Hypothesis: MYB34 binds directly to promoters of CYP79B2, CYP79B3, CYP83B1 and ASA1.
Type: ChIP-seq / DAP-seq
Experiment: Inoculate myb34, myb51, myb122 and higher-order mutants with Colletotrichum higginsianum and quantify indolic glucosinolates and their PEN2-dependent products at infection sites. Use single-cell or spatial transcriptomics to check whether MYB34 expression changes in any cell type.
Hypothesis: MYB34 contributes little to localized antifungal indolic glucosinolate production in leaves compared with MYB51 and MYB122.
Type: cell-type-specific genetics
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