The identification and characterization of specific ARF-Aux/IAA regulatory modules in plant growth and development.
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ABSTRACT:
SUBMITTER: Krogan NT
PROVIDER: S-EPMC4622990 | biostudies-other | 2015
REPOSITORIES: biostudies-other
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Project description:The phytohormone auxin plays a pivotal role in the regulation of plant growth and development, including vascular differentiation and tree growth. The auxin/indole-3-acetic acid (Aux/IAA) and auxin response transcription factor (ARF) genes are key components of plant auxin signaling. To gain more insight into the regulation and functional features of Aux/IAA and ARF genes during these processes, we identified 38 AUX/IAA and 34 ARF genes in the genome of Salix suchowensis and characterized their gene structures, conserved domains, and encoded amino acid compositions. Phylogenetic analysis of some typical land plants showed that the Aux/IAA and ARF genes of Salicaceae originated from a common ancestor and were significantly amplified by the ancestral eudicot hexaploidization event and the "salicoid" duplication that occurred before the divergence of poplar and willow. By analyzing dynamic transcriptome profiling data, some Aux/IAA and ARF genes were found to be involved in the regulation of plant growth, especially in the initial plant growth process. Additionally, we found that the expression of several miR160/miR167-ARFs was in agreement with canonical miRNA-ARF interactions, suggesting that miRNAs were possibly involved in the regulation of the auxin signaling pathway and the plant growth process. In summary, this study comprehensively analyzed the sequence features, origin, and expansion of Aux/IAA and ARF genes, and the results provide useful information for further studies on the functional involvement of auxin signaling genes in the plant growth process.
| S-EPMC8188177 | biostudies-literature
Project description: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/AFB functionality, 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.
| S-EPMC6442611 | biostudies-literature
Project description:Lateral roots (LRs) are derived from a parental root and contribute to water and nutrient uptake from the soil. Auxin/indole-3-acetic acid protein (AUX/IAA; IAA) and auxin response factor (ARF)-mediated signaling are essential for LR formation. Lysigenous aerenchyma, a gas space created by cortical cell death, aids internal oxygen transport within plants. Rice (Oryza sativa) forms lysigenous aerenchyma constitutively under aerobic conditions and increases its formation under oxygen-deficient conditions; however, the molecular mechanisms regulating constitutive aerenchyma (CA) formation remain unclear. LR number is reduced by the dominant-negative effect of a mutated AUX/IAA protein in the iaa13 mutant. We found that CA formation is also reduced in iaa13 We have identified ARF19 as an interactor of IAA13 and identified a lateral organ boundary domain (LBD)-containing protein (LBD1-8) as a target of ARF19. IAA13, ARF19, and LBD1-8 were highly expressed in the cortex and LR primordia, suggesting that these genes function in the initiation of CA and LR formation. Restoration of LBD1-8 expression recovered aerenchyma formation and partly recovered LR formation in the iaa13 background, in which LBD1-8 expression was reduced. An auxin transport inhibitor suppressed CA and LR formation, and a natural auxin stimulated CA formation in the presence of the auxin transport inhibitor. Our findings suggest that CA and LR formation are both regulated through AUX/IAA- and ARF-dependent auxin signaling. The initiation of CA formation lagged that of LR formation, which indicates that the formation of CA and LR are regulated differently by auxin signaling during root development in rice.
| S-EPMC6789968 | biostudies-literature
Project description:Auxin signaling, which is crucial for normal plant growth and development, mainly depends on ARF-Aux/IAA interactions. However, little is known regarding the regulatory effects of auxin signaling on anthocyanin metabolism in apple (Malus domestica). We investigated the functions of MdARF13, which contains a repression domain and is localized to the nucleus. This protein was observed to interact with the Aux/IAA repressor, MdIAA121, through its C-terminal dimerization domain. Protein degradation experiments proved that MdIAA121 is an unstable protein that is degraded by the 26S proteasome. Additionally, MdIAA121 stability is affected by the application of exogenous auxin. Furthermore, the overexpression of MdIAA121 and MdARF13 in transgenic red-fleshed apple calli weakened the inhibitory effect of MdARF13 on anthocyanin biosynthesis. These results indicate that the degradation of MdIAA121 induced by auxin treatment can release MdARF13, which acts as a negative regulator of the anthocyanin metabolic pathway. Additionally, yeast two-hybrid, bimolecular fluorescence complementation, and pull-down assays confirmed that MdMYB10 interacts with MdARF13. A subsequent electrophoretic mobility shift assay and yeast one-hybrid assay demonstrated that MdARF13 directly binds to the promoter of MdDFR, which is an anthocyanin pathway structural gene. Interestingly, chromatin immunoprecipitation-quantitative real-time PCR results indicated that the overexpression of MdIAA121 clearly inhibits the recruitment of MdARF13 to the MdDFR promoter. Our findings further characterized the mechanism underlying the regulation of anthocyanin biosynthesis via Aux/IAA-ARF signaling.
| S-EPMC6269505 | biostudies-literature
Project description:BackgroundAuxin/Indole-3-Acetic Acid (Aux/IAA) and Auxin Response Factor (ARF) transcription factors are key regulators of auxin responses in plants. We identified the suites of genes in the two gene families in Populus and performed comparative genomic analysis with Arabidopsis and rice.ResultsA total of 35 Aux/IAA and 39 ARF genes were identified in the Populus genome. Comparative phylogenetic analysis revealed that several Aux/IAA and ARF subgroups have differentially expanded or contracted between the two dicotyledonous plants. Activator ARF genes were found to be two fold-overrepresented in the Populus genome. PoptrIAA and PoptrARF gene families appear to have expanded due to high segmental and low tandem duplication events. Furthermore, expression studies showed that genes in the expanded PoptrIAA3 subgroup display differential expression.ConclusionThe present study examines the extent of conservation and divergence in the structure and evolution of Populus Aux/IAA and ARF gene families with respect to Arabidopsis and rice. The gene-family analysis reported here will be useful in conducting future functional genomics studies to understand how the molecular roles of these large gene families translate into a diversity of biologically meaningful auxin effects.
| S-EPMC2174922 | biostudies-literature
Project description:The coordinated action of the auxin-sensitive Aux/IAA transcriptional repressors and ARF transcription factors produces complex gene-regulatory networks in plants. Despite their importance, our knowledge of these two protein families is largely based on analysis of stabilized forms of the Aux/IAAs, and studies of a subgroup of ARFs that function as transcriptional activators. To understand how auxin regulates gene expression we generated a Physcomitrella patens line that completely lacks Aux/IAAs. Loss of the repressors causes massive changes in transcription with misregulation of over a third of the annotated genes. Further, we find that the aux/iaa mutant is blind to auxin indicating that auxin regulation of transcription occurs exclusively through Aux/IAA function. We used the aux/iaa mutant as a simplified platform for studies of ARF function and demonstrate that repressing ARFs regulate auxin-induced genes and fine-tune their expression. Further the repressing ARFs coordinate gene induction jointly with activating ARFs and the Aux/IAAs.
| S-EPMC4889330 | biostudies-literature
Project description:The Aux/IAA proteins are auxin-sensitive repressors that mediate diverse physiological and developmental processes in plants [1, 2]. There are 29 Aux/IAA genes in Arabidopsis that exhibit unique but partially overlapping patterns of expression [3]. Although some studies have suggested that individual Aux/IAA genes have specialized function, genetic analyses of the family have been limited by the scarcity of loss-of-function phenotypes [4]. Furthermore, with a few exceptions, our knowledge of the factors that regulate Aux/IAA expression is limited [1, 5]. We hypothesize that transcriptional control of Aux/IAA genes plays a central role in the establishment of the auxin-signaling pathways that regulate organogenesis, growth, and environmental response. Here, we describe a screen for transcription factors (TFs) that regulate the Aux/IAA genes. We identify TFs from 38 families, including 26 members of the DREB/CBF family. Several DREB/CBF TFs directly promote transcription of the IAA5 and IAA19 genes in response to abiotic stress. Recessive mutations in these IAA genes result in decreased tolerance to stress conditions, demonstrating a role for auxin in abiotic stress. Our results demonstrate that stress pathways interact with the auxin gene regulatory network (GRN) through transcription of the Aux/IAA genes. We propose that the Aux/IAA genes function as hubs that integrate genetic and environmental information to achieve the appropriate developmental or physiological outcome.
| S-EPMC5296222 | biostudies-literature
Project description:Auxin response factors (ARFs), together with auxin/indole acetic acid proteins (Aux/IAAs), are transcription factors that play key roles in regulating auxin-responsive transcription in plants. Current models for auxin signaling predict that auxin response is dependent on ARF-Aux/IAA interactions mediated by the related protein-protein interaction domain (i.e., referred to as the CTD) found in the ARF and Aux/IAA C-terminal regions. When auxin concentrations in a cell are low, ARF activators residing on the promoters of auxin response genes are thought to be inactive because of the association with dominant Aux/IAA repressors. When auxin concentrations are elevated, the Aux/IAA repressors are recruited to auxin receptors and degraded via the ubiquitin-proteasome pathway. Destruction of the Aux/IAA repressors allows the ARF activators to function in derepressing/activating auxin response genes. While this auxin signaling pathway is simple and attractive, it is unclear whether auxin-regulated gene expression is solely dependent on ARF-Aux/IAA interactions. Here we show that auxin can affect the expression of auxin response genes in a manner that is independent of the ARF activator CTD.
| S-EPMC3909085 | biostudies-literature
Project description:The phytohormone auxin controls plant growth and development via TIR1-dependent protein degradation of canonical AUX/IAA proteins, which normally repress the activity of auxin response transcription factors (ARFs). IAA33 is a non-canonical AUX/IAA protein lacking a TIR1-binding domain, and its role in auxin signaling and plant development is not well understood. Here, we show that IAA33 maintains root distal stem cell identity and negatively regulates auxin signaling by interacting with ARF10 and ARF16. IAA33 competes with the canonical AUX/IAA repressor IAA5 for binding to ARF10/16 to protect them from IAA5-mediated inhibition. In contrast to auxin-dependent degradation of canonical AUX/IAA proteins, auxin stabilizes IAA33 protein via MITOGEN-ACTIVATED PROTEIN KINASE 14 (MPK14) and does not affect IAA33 gene expression. Taken together, this study provides insight into the molecular functions of non-canonical AUX/IAA proteins in auxin signaling transduction.
| S-EPMC6939196 | biostudies-literature
Project description:The Auxin/indole-3-acetic acid (Aux/IAA) repressor genes down-regulate the auxin response pathway during many stages of plant and fruit development. In order to determine if and how Aux/IAAs participate in governing texture and hardness in stone fruit maturation, we identified 23 Aux/IAA genes in peach, confirmed by the presence of four conserved domains. In this work, we used fluorescence microscopy with PpIAA-GFP fusion reporters to observe their nuclear localization. We then conducted PCR-based differential expression analysis in "melting" and "stony hard" varieties of peach, and found that in the "melting" variety, nine PpIAAs exhibited peak expression in the S4-3 stage of fruit maturation, with PpIAA33 showing the highest (>120-fold) induction. The expression of six PpIAAs peaked in the S4-2 stage, with PpIAA14 expressed the most highly. Only PpIAA15/16 showed higher expression in the "stony hard" variety than in the "melting" variety, both peaking in the S3 stage. In contrast, PpIAA32 had the highest relative expression in buds, flowers, young and mature leaves, and roots. Our study provides insights into the expression patterns of Aux/IAA developmental regulators in response to auxin during fruit maturation, thus providing insight into their potential development as useful markers for quantitative traits associated with fruit phenotype.
| S-EPMC6801721 | biostudies-literature