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Transcriptomic profile of amiR-bpm and Col-0

ABSTRACT: The Jasmonate pathway regulators MYC2, MYC3 and MYC4 are central nodes in plant signaling networks integrating environmental and developmental signals to fine-tune jasmonate defenses and plant growth. Hence, their activity needs to be tightly regulated in order to optimize plant fitness. Among the increasing number of mechanisms regulating MYCs activity, protein stability is arising as a major player. However, how the levels of MYCs proteins are modulated is still poorly understood. Here, we report that MYC2, MYC3 and MYC4 are targets of BPM proteins, which act as substrate adaptors of CUL3-based E3 ubiquitin ligases. Reduction-of-function of CUL3BPM in amiR-bpm lines, bpm235 triple mutants and cul3ab double mutants enhances MYC2 and MYC3 stability and accumulation, and potentiates plant responses to JA such as root-growth inhibition, and MYC-regulated gene expression. BPM3 protein is stabilized by JA, suggesting a new negative feed-back regulatory mechanism to control MYCs activity. Our results uncover a new layer for JA-pathway regulation by CUL3BPM–mediated degradation of MYC TFs.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE131037 | GEO | 2020/02/09

REPOSITORIES: GEO

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CUL3(BPM) E3 ubiquitin ligases regulate MYC2, MYC3 and MYC4 stability and JA responses

Project description:The Jasmonate pathway regulators MYC2, MYC3 and MYC4 are central nodes in plant signaling networks integrating environmental and developmental signals to fine-tune jasmonate defenses and plant growth. Hence, their activity needs to be tightly regulated in order to optimize plant fitness. Among the increasing number of mechanisms regulating MYCs, protein stability is arising as a major player. However, how the levels of MYCs proteins are modulated is still poorly understood. Here, we report that MYC2, MYC3 and MYC4 are targets of BPM proteins, which act as substrate adaptors of CUL3-based E3 ubiquitin ligases. Reduction-of-function of CUL3(BPM) in amiR-bpm lines, bpm235 triple mutants and cul3ab double mutants enhance MYC2 and MYC3 stability and accumulation, and potentiates plant responses to JA such a root-growth inhibition, and MYC-regulated gene expression. BPM3 protein is stabilized by JA, suggesting a new negative feedback regulatory mechanism to control MYCs activity. Our results uncover a new layer for JA-pathway regulation by CUL3(BPM)-mediated degradation of MYC TFs.

2021-03-19 | PXD013906 | Pride

Transcriptomic profile of bpm2,3,5 triple mutant and Col-0

Project description:The Jasmonate pathway regulators MYC2, MYC3 and MYC4 are central nodes in plant signaling networks integrating environmental and developmental signals to fine-tune jasmonate defenses and plant growth. Hence, their activity needs to be tightly regulated in order to optimize plant fitness. Among the increasing number of mechanisms regulating MYCs activity, protein stability is arising as a major player. However, how the levels of MYCs proteins are modulated is still poorly understood. Here, we report that MYC2, MYC3 and MYC4 are targets of BPM proteins, which act as substrate adaptors of CUL3-based E3 ubiquitin ligases. Reduction-of-function of CUL3BPM in amiR-bpm lines, bpm235 triple mutants and cul3ab double mutants enhances MYC2 and MYC3 stability and accumulation, and potentiates plant responses to JA such as root-growth inhibition, and MYC-regulated gene expression. BPM3 protein is stabilized by JA, suggesting a new negative feed-back regulatory mechanism to control MYCs activity. Our results uncover a new layer for JA-pathway regulation by CUL3BPM–mediated degradation of MYC TFs.

2020-02-09 | GSE131024 | GEO

The JA-pathway MYC transcription factors regulate photomorphogenic responses by modulating the expression of HY5 and PIF targets

Project description:Jasmonates are key regulators of the balance between defence and growth in plants. However, the molecular mechanisms by which activation of defences reduces growth are not yet understood. Here, we analyze the role of MYC transcription factors (TFs) and JA in photomorphogenic growth. We found that multiple myc mutants share light-related phenotypes with mutants of the phytochrome B photoreceptor, regarding seed germination and hypocotyl growth. Over-expression of MYC2 in a phyB background partially suppressed its long hypocotyl phenotype. We show that the activity of MYC TFs is partially independent of COI1 and that JA inhibition of hypocotyl growth acts through alteration of auxin homeostasis and is partially independent of the classical JA signalling pathway. Transcriptomic analysis of multiple myc mutants confirmed that MYCs are required for full expression of R-light regulated genes, including the master regulator HY5. ChIP-Seq analyses revealed that MYC2 and MYC3 directly bind to the promoter of HY5 and that HY5 gene expression and protein levels are compromised in multiple myc mutants. Moreover, MYC2 and MYC3 share a high amount of direct targets with PIFs, and have an opposite effect on gene expression of these targets. Altogether, our results pinpoint MYCs as photomorphogenic TFs that regulate phytochrome responses by regulating PIFs targets and activating HY5 expression. This has important implication to understand the trade-off between growth and defence, since the same TFs that activate defence responses are photomorphogenic growth regulators.

2019-07-31 | GSE114590 | GEO

Functional analysis of evening complex component LUX in Arabidopsis

Project description:Plants trigger leaf senescence to relocate energy and nutrients from aging leaves to developing tissues or storage organs to optimize the growth and reproduction under limited nutrients and energy conditions. Jasmonate signaling is one of the major endogenous hormone signals to induced leaf senescence in Arabidopsis. However, whether circadian clock will gate Jasmonate signaling to induce leaf senescence and the underlying precise mechanism is unclear. Here we find that the Evening Complex (EC) of core oscillator closely regulates leaf senescence. To identify the underlying mechanism of EC regulating leaf senescence, we conducted RNA-sequencing. Transcriptomic data reveals Evening complex extensively involves into JA signal transduction and responses. Moreover, the mutants of ELF3, ELF4 and LUX universly display the accelerated JA-induced leaf senescence phenotype, while their overexpression lines act reversely. In accordance with the transcript levels of JA immediate early induced JA-responsive gene MYC2 are up-regulated in lux mutants. Futhermore we demonstrated LUX can bind to to the promoter of MYC2 in vivo to represses its transcription. In addition, the accelerated JA-induced leaf senescence in mutants of evening complex can be overturned by myc2, myc3 and myc4 mutants redundantly. Collectively, our findings demonstrated the underlying molecular basis for circadian clock gating jasmonate signaling to induce leaf senescence through the module of evening complex to directly repressing MYC2 transcription. This novel established molecular module also refines complicated nodes between circadian clock and jasmonate signal in Arabidopsis.

2018-02-06 | GSE99290 | GEO

JA-INDUCIBLE MYC2-LIKE1 acts as a repressor and negatively regulates jasmonate signaling in Arabidopsis

Project description:Jasmonate (JA) is a plant hormone that controls trade-offs between plant growth and responses to biotic and abiotic stresses. Although recent studies uncover core mechanism for JA-induced responses in Arabidopsis thaliana, it remains elusive how plants attenuate those responses. We report here that a basic-helix-loop-helix type transcription factor named JA-INDUCIBLE MYC2-LIKE1 (JAM1) acts as a transcriptional repressor and negatively regulates JA signaling. Arabidopsis plants expressing the chimeric repressor for JAM1 exhibited a substantial reduction of JA responses, including JA-induced inhibition of root growth, accumulation of anthocyanin, and male fertility. These plants were also compromised in resistance to attack by Spodoptera exigua. Conversely, jam1-4 loss-of-function mutants showed enhanced JA responsiveness, including increased resistance to the insect attack. Competitive binding of JAM1 and MYC2 to the target sequence of MYC2 suggested negative regulation of JA signaling by JAM1 and suppression of MYC2 function. These results indicate that JAM1 plays a pivotal role in fine-tuning of JA-mediated stress responses and plant growth by negatively regulating JA signaling. Transcriptomes of ProJAM1:JAM1-SRDX, ProMYC2:MYC2-SRDX and wild-type Arabidopsis seedlings with or without jasmonic acid were compared.

2013-07-03 | E-GEOD-42552 | biostudies-arrayexpress

ChIP-Seq of Arabidopsis Transcription Factors MYC2 and MYC3

Project description:The genome-wide target genes of transcription factors MYC2 and MYC3 were determined in etiolated (dark-grown) seedlings of Arabidopsis thaliana. Chromatin immunoprecipition of MYC2 and MYC3 was performed as described in O’Malley et al (2016; doi: 10.1016/j.cell.2016.04.038), using transgenic A. thaliana expressing MYC2::YpET and MYC3::YpET fusion proteins from their native promoters, generated by recombineering (Gimenez-Ibanez et al. 2017; doi: 10.1111/nph.14354 ). Three-day old etiolated seedlings were treated with methyl JA for 2 h (as described in Schweizer et al., 2013), then harvested for ChIP-Seq.

2019-11-28 | GSE114430 | GEO

JA-INDUCIBLE MYC2-LIKE1 acts as a repressor and negatively regulates jasmonate signaling in Arabidopsis

2013-07-03 | GSE42552 | GEO

A MYC2, MYC3, MYC4-dependent transcription factor network regulates touch responses in plants

Project description:Plants are continuously exposed to environmental triggers, including mechanical stimulation. Our results demonstrate that jasmonic acid (JA)-signalling plays a key role in very early gene expression changes, well before it leads to touch-induced developmental changes. We show that the JA-activated transcription factors MYC2/MYC3/MYC4 co-regulate touch-induced gene expression of 266 genes, many of which peak in induction around 25 minutes and then rapidly decline by 40-60 minutes. ChIP-seq shows that MYC2 dynamically binds hundreds of touch-induced promoters within 25 minutes. Promoter activation assays confirm that MYC2 directly activates these touch-induced promoters. By combining multi-omic data, we have identified a core MYC2/3/4-dependent ‘touch regulon’, containing many previously-unknown MYC2 targets like bHLH19 and ERF109. We show bHLH19 can in turn directly activate the ORA47 promoter, indicating that MYC2/3/4 initiate a hierarchical network of downstream transcription factors. Through hormone profiling we reveal the rapid touch-induced accumulation of JA/JA-isoleucine is directly controlled by MYC2/3/4 in a positive amplification loop regulating JA-biosynthesis genes.

2019-10-29 | PXD014008 | Pride

Functional conservation of jasmonate-related MYC transcription factors in Marchantia polymorpha

Project description:The lipid-derived phytohormone jasmonoyl-isoleucine (JA-Ile) regulates plant immunity, growth and development in vascular plants by activating genome-wide transcriptional reprogramming. In Arabidopsis, this is largely orchestrated by the master regulator MYC2 and related transcription factors (TFs). However, the TFs activating this pathway in basal plant lineages are currently unknown. We report the functional conservation of MYC-related TFs between the eudicot Arabidopsis thaliana and the liverwort Marchantia polymorpha, a plant belonging to one of the most basal land-plants lineages. Phylogenetic analysis suggests that MYC function first appeared in charophycean algae, and therefore predates the evolutionary appearance of any other jasmonate pathway component. Marchantia possesses two functionally interchangeable MYC genes, one in females and one in males. Similar to AtMYC2, MpMYCs showed nuclear localization, interaction with JAZ-repressors, and regulation by light. Phenotypic and molecular characterization of loss- or gain-of-function mutants demonstrated that MpMYCs are necessary and sufficient for the activation of the pathway in Marchantia, but unlike their Arabidopsis orthologs, do not regulate fertility. Our results show that despite 450 million years of independent evolution, MYCs are functionally conserved between bryophytes and eudicots. Genetic conservation in one of the most basal lineages suggests that MYC function existed in the common ancestor of land plants and evolved from a pre-existing MYC function in charophycean algae.

2019-03-19 | GSE124159 | GEO

A MYC2, MYC3, MYC4-dependent transcription factor network regulates touch responses in plants

Project description:Plants are continuously exposed to environmental triggers, including mechanical stimulation. Our results demonstrate that jasmonic acid (JA)-signalling not only plays a key role in touch-induced developmental changes, but also in the very early gene expression changes. Using multi-omics, we show that the JA-activated transcription factors MYC2/MYC3/MYC4 co-regulate touch-induced gene expression of 266 genes. MYC2/3/4 particularly activate top touch-induced genes, which peak around 25 minutes and then rapidly decline by 40-60 minutes. ChIP-seq shows that MYC2 dynamically binds hundreds of touch-induced promoters within 25 minutes. Furthermore, promoter activation assays confirm that MYC2 directly activates touch-induced promoters. By combining these data, we identified a core MYC2/3/4-dependent ‘touch regulon’, containing many previously-unknown MYC2 targets like bHLH19 and ERF109. bHLH19 can in turn directly activate the ORA47 promoter, indicating that MYC2/3/4 initiate a hierarchical network of downstream transcription factors. Finally, hormone profiling shows that the rapid touch-induced accumulation of JA/JA-isoleucine is directly controlled by MYC2/3/4 in a positive amplification loop regulating JA-biosynthesis genes.

2019-10-29 | GSE132316 | GEO

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