Auxin phytohormones control most aspects of plant development through a complex and interconnected signaling network. In the presence of auxin, AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors are targeted for degradation by the SKP1-CULLIN1-F-BOX (SCF) ubiquitin-protein ligases containing TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB). CULLIN1-neddylation is required for SCFTIR1/AFBfunctionality, as exemplified by mutants deficient in the NEDD8-activating enzyme subunit AUXIN-RESISTANT 1 (AXR1). Here, we report a chemical biology screen that identifies small molecules requiring AXR1 to modulate plant development. We selected four molecules of interest, RubNeddin 1 to 4 (RN1 to -4), among which RN3 and RN4 trigger selective auxin responses at transcriptional, biochemical, and morphological levels. This selective activity is explained by their ability to consistently promote the interaction between TIR1 and a specific subset of AUX/IAA proteins, stimulating the degradation of particular AUX/IAA combinations. Finally, we performed a genetic screen using RN4, the RN with the greatest potential for dissecting auxin perception, which revealed that the chromatin remodeling ATPase BRAHMA is implicated in auxin-mediated apical hook development. These results demonstrate the power of selective auxin agonists to dissect auxin perception for plant developmental functions, as well as offering opportunities to discover new molecular players involved in auxin responses.
Auxin critically regulates plant growth and development. Auxin-driven transcriptional responses are mediated through the AUXIN RESPONSE FACTOR (ARF) family of transcription factors. ARF protein condensation attenuates ARF activity, resulting in dramatic shifts in the auxin transcriptional landscape. Here, we perform a forward genetics screen for ARF hypercondensation, identifying an F-box protein, which we named AUXIN RESPONSE FACTOR F-BOX1 (AFF1). Functional characterization of SCFAFF1revealed that this E3 ubiquitin ligase directly interacts with ARF19 and ARF7 to regulate their accumulation, condensation, and nucleo-cytoplasmic partitioning. Mutants defective in
- Award ID(s):
- 1907098
- NSF-PAR ID:
- 10471055
- Publisher / Repository:
- Nature Publishing
- Date Published:
- Journal Name:
- Nature Communications
- Volume:
- 13
- Issue:
- 1
- ISSN:
- 2041-1723
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
-
more » « less
Summary Despite well established roles of micro
RNA s in plant development, few aspects have been addressed to understand their effects in seeds especially on lipid metabolism. In this study, we showed that overexpressing microRNA 167A (miR167OE ) in camelina (Camelina sativa ) under a seed‐specific promoter changed fatty acid composition and increased seed size. Specifically, the miR167OE seeds had a lower α‐linolenic acid with a concomitantly higher linoleic acid content than the wild‐type. This decreased level of fatty acid desaturation corresponded to a decreased transcriptional expression of the camelina fatty acid desaturase3 (Cs ) in developing seeds. MiR167 targeted the transcription factor auxin response factor (CsFAD 3ARF 8) in camelina, as had been reported previously in Arabidopsis. Chromatin immunoprecipitation experiments combined with transcriptome analysis indicated that CsARF 8 bound to promoters of camelinabZIP 67ABI 3ABI 3‐bZIP 12 pathway regulateCs expression and affect α‐linolenic acid accumulation. In addition, to decipher the miR167A‐CsFAD 3ARF 8 mediated transcriptional cascade forCs suppression, transcriptome analysis was conducted to implicate mechanisms that regulate seed size in camelina. Expression levels of many genes were altered in miR167FAD 3OE , including orthologs that have previously been identified to affect seed size in other plants. Most notably, genes for seed coat development such as suberin and lignin biosynthesis were down‐regulated. This study provides valuable insights into the regulatory mechanism of fatty acid metabolism and seed size determination, and suggests possible approaches to improve these important traits in camelina. -
more » « less
Summary Auxin is widely involved in plant growth and development. However, the molecular mechanism on how auxin carries out this work is unclear. In particular, the effect of auxin on pre‐
mRNA post‐transcriptional regulation is mostly unknown. By using a poly(A) tag (PAT ) sequencing approach,mRNA alternative polyadenylation (APA ) profiles after auxin treatment were revealed. We showed that hundreds of poly(A) site clusters (PAC s) are affected by auxin at the transcriptome level, where auxin reducesPAC distribution in 5′‐untranslated region (UTR ), but increases in the 3′UTR .APA site usage frequencies of 42 genes were switched by auxin, suggesting that auxin affects the choice of poly(A) sites. Furthermore, poly(A) signal selection was altered after auxin treatment. For example, a mutant of poly(A) signal binding proteinCPSF 30 showed altered sensitivity to auxin treatment, indicating interactions between auxin and the poly(A) signal recognition machinery. We also found that auxin activity on lateral root development is likely mediated by altered expression ofARF 7ARF 19IAA 14mRNA polyadenylation. -
The phytohormone auxin regulates nearly every aspect of plant development. Transcriptional responses to auxin are driven by the activities of the AUXIN RESPONSE FACTOR family of transcription factors. ARF19 (AT1G19220) is critical in the auxin signaling pathway and has previously been shown to undergo protein condensation to tune auxin responses in the root. However, ARF19 condensation dynamics in other organs has not yet been described. In the Arabidopsis stomatal lineage, we found that ARF19 cytoplasmic condensates are enriched in guard cells and pavement cells, terminally differentiated cells in the leaf epidermis. This result is consistent with previous studies showing ARF19 condensation in mature root tissues. Our data reveal that the sequestration of ARF19 into cytoplasmic condensation in differentiated leaf epidermal cells is similar to root-specific condensation patterns.more » « less
-
more » « less
Summary Many eukaryotic intracellular processes employ protein ubiquitylation by ubiquitin E3 ligases for functional regulation or protein quality control. In plants, the multi‐subunit Skp1–Cullin1–F‐box (SCF) complexes compose the largest group of E3 ligases whose specificity is determined by a diverse array of F‐box proteins. Although both sequence divergence and polymorphism of
F‐box genes well support a broad spectrum of SCF functions, experimental evidence is scarce due to the low number of identified SCF substrates. Taking advantage of the bridge role of Skp1 between F‐box and Cullin1 in the complex, we systematically analyzed the functional influence of a well‐characterizedArabidopsis Skp1‐Like1 (ASK1 )Ds insertion allele,ask1 , in different Arabidopsis accessions. Through 10 generations of backcrossing with Columbia‐0 (Col‐0), we partially rescued the fertility of this otherwise sterileask1 allele in Landsbergerecta , thus providing experimental evidence showing the polymorphic roles of SCF complexes. Thisask1 mutant produces twisted rosette leaves, a reduced number of petals, fewer viable pollen grains, and larger embryos and seeds compared to Col‐0. RNA‐Seq‐based transcriptome analysis ofask1 uncovered a large spectrum of SCF functions, which is greater than a 10‐fold increase compared with previous studies. We also identified its hyposensitive responses to auxin and abscisic acid treatments and enhanced far‐red light/phyA‐mediated photomorphogenesis. Such diverse roles are consistent with the 20–30% reduction of ubiquitylation events inask1 estimated by immunoblotting analysis in this work. Collectively, we conclude that ASK1 is a predominant Skp1 protein in Arabidopsis and that the fertileask1 mutant allowed us to uncover a comprehensive set of SCF functions.
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1038/s41467-022-31628-2
