A combinatorial TIR1/AFB-Aux/IAA co-receptor system for differential sensing of auxin

Transcriptional Tuning: How Auxin Strikes Unique Chords in Gene Regulation

Auxin is a central regulator of plant growth, development, and responses to environmental cues. How a single phytohormone mediates such a diverse array of developmental responses has remained a longstanding question in plant biology. Somehow, perception of the same auxin signal can lead to divergent responses in different organs, tissues, and cell types. These responses are primarily mediated by the nuclear auxin signaling pathway, composed of ARF transcription factors, Aux/IAA repressors, and TIR1/AFB auxin receptors, which act together to regulate auxin-dependent transcriptional changes. Transcriptional specificity likely arises through the functional diversity within these signaling components, forming many coordinated regulatory layers to generate unique transcriptional outputs. These layers include differential binding affinities for cis-regulatory elements, protein-protein interaction-specificity, subcellular localization, co-expression patterns, and protein turnover. In this review, we explore the experimental evidence of functional diversity within auxin signaling machinery and discuss how these differences could contribute to transcriptional output specificity.

BTB/POZ-MATH proteins regulate Arabidopsis seedling development by promoting auxin-independent degradation of the Aux/IAA protein IAA10

After germination, seedlings undergo etiolated development (skotomorphogenesis), enabling them to grow toward the soil surface. In Arabidopsis (Arabidopsis thaliana), etiolated seedlings exhibit rapid hypocotyl elongation, apical hook formation, and closed cotyledons to protect the meristem. In this study, we found that high-order mutants in the BPM (BTB/POZ-MATH) gene family displayed defects in seedling development, characterized by a shorter hypocotyl, early apical hook opening, and opened cotyledons in the dark. BPM1, BPM2, BPM4, and BPM5 exhibited distinct expression patterns and subcellular localization in etiolated seedlings. In a hypocotyl segment assay, the bpm mutants showed defects in auxin response, indicating impaired auxin signaling in the hypocotyl. Expression of the auxin reporter DR5:GFP was also altered in the bpm1,4,5 mutant in various tissues compared with the wild type. Furthermore, yeast 2-hybrid, bimolecular fluorescence complementation, and co-immunoprecipitation assay analyses showed that BPM1 interacts with IAA10. Experiments in protoplasts indicated that BPM1 promotes IAA10 ubiquitylation and degradation, which was supported by greater IAA10 protein accumulation in the bpm1,4,5 mutant background. In addition, IAA10 overexpression resulted in phenotypes similar to those of the bpm mutants, indicating that the BPMs may target the Aux/IAA proteins for ubiquitylation and degradation. Overall, our findings shed light on the key roles of the BPMs in auxin signaling during seedling development.

Transport of phenoxyacetic acid herbicides by PIN-FORMED auxin transporters

Auxins are a group of phytohormones that control plant growth and development. Their crucial role in plant physiology has inspired development of potent synthetic auxins that can be used as herbicides. Phenoxyacetic acid derivatives are a widely used group of auxin herbicides in agriculture and research. Despite their prevalence, the identity of the transporters required for distribution of these herbicides in plants is both poorly understood and the subject of controversial debate. Here we show that PIN-FORMED auxin transporters transport a range of phenoxyacetic acid herbicides across the membrane. We go on to characterize the molecular determinants of substrate specificity using a variety of different substrates as well as protein mutagenesis to probe the binding site. Finally, we present cryogenic electron microscopy structures of Arabidopsis thaliana PIN8 bound to either 2,4-dichlorophenoxyacetic acid or 4-chlorophenoxyacetic acid. These structures represent five key states from the transport cycle, allowing us to describe conformational changes associated with the transport cycle. Overall, our results reveal that phenoxyacetic acid herbicides use the same export machinery as endogenous auxins and exemplify how transporter binding sites undergo transformations that dictate substrate specificity. These results provide a foundation for future development of novel synthetic auxins and for precision breeding of herbicide-resistant crop plants.

Analysis of the Genes from Gibberellin, Jasmonate, and Auxin Signaling Under Drought Stress: A Genome-Wide Approach in Castor Bean (Ricinus communis L.)

Castor bean (Ricinus communis L.) can tolerate long periods of dehydration, allowing the investigation of gene circuits involved in drought tolerance. Genes from gibberellins, jasmonates, and auxin signaling are important for crosstalk in the developmental and environmental adaptation process to drought conditions. However, the genes related to these signals, as well as their transcription profiles under drought, remain poorly characterized in the castor bean. In the present work, genes from gibberellins, jasmonates, and auxin signaling were identified and molecularly characterized. These analyses allowed us to identify genes encoding receptors, inhibitory proteins, and transcription factors from each signaling pathway in the castor bean genome. Chromosomal distribution, gene structure, evolutionary relationships, and conserved motif analyses were performed. Expression analysis through RNA-seq and RT-qPCR revealed that gibberellins, jasmonates, and auxin signaling were modulated at multiple levels under drought, with notable changes in specific genes. The gibberellin receptor RcGID1c was downregulated in response to drought, and RcDELLA3 was strongly repressed, whereas its homologues were not, reinforcing the suggestion of a nuanced regulation of gibberellin signaling during drought. Considering jasmonate signaling, the downregulation of the transcription factor RcMYC2 aligned with the drought tolerance observed in mutants lacking this gene. Altogether, these analyses have provided insights into hormone signaling in the castor bean, unveiling transcriptional responses that enhance our understanding of high drought tolerance in this plant. This knowledge opens avenues for identifying potential candidate genes suitable for genetic manipulation in biotechnological approaches.

Synthetic deconvolution of an auxin-dependent transcriptional code

How developmental signals program gene expression in space and time is still poorly understood. Here, we addressed this question for the plant master regulator, auxin. Transcriptional responses to auxin rely on a large multigenic transcription factor family, the auxin response factors (ARFs). We deconvoluted the complexity of ARF-regulated transcription using auxin-inducible synthetic promoters built from cis-element pair configurations differentially bound by ARFs. We demonstrate using cellular systems that ARF transcriptional properties are not only intrinsic but also depend on the cis-element pair configurations they bind to, thus identifying a bi-layer ARF/cis-element transcriptional code. Auxin-inducible synthetic promoters were expressed differentially in planta showing at single-cell resolution how this bi-layer code patterns transcriptional responses to auxin. Combining cis-element pair configurations in synthetic promoters created distinct patterns, demonstrating the combinatorial power of the auxin bi-layer code in generating diverse gene expression patterns that are not simply a direct translation of auxin distribution.

A circadian clock RD29A is an esterase, relaying PGPR stimuli via RD29B and OPDA signaling in priming plant drought tolerance

Drought is a critical limiting factor to crop production. Efforts to combat this problem through genetic engineering have been difficult to implement without growth tradeoffs. Hence, we recently identified two drought-responsive genes, Response to Desiccation (RD)29A and RD29B, which convey plant growth-promoting rhizobacteria-mediated induced systemic tolerance (IST). IST primes enhanced drought tolerance in plants and, concomitantly, promote their growth and productivity. However, the role and activity of RD29s are largely unknown. In this study, we unravel the autonomous, yet intertwined functions and modes of RD29s. RD29A is a circadian clock esterase and RD29B is a constitutive transcriptional regulator, controlling the oscillatory cycle and induction of RD29A expressions in response to IST-inducing PGPR, Paenibacillus polymyxa CR1. A diurnal peak of RD29A activity then facilitates cellular multitasking, allowing plants to concomitantly run "growth and defense" machineries via perhaps time-sharing of limited energy resources to each operation one by one. In line with these findings, the transient overexpression of Arabidopsis RD29s led to the reconstitution of IST in Solanum lycopersicum and Nicotiana benthamiana. On the contrary, RD29A can relay two different hormone, abscisic acid (ABA) and 12-oxo-phytodienoic acid (OPDA), signaling through distinct cis-regulatory, DRE/ABRE, and TGA elements, respectively. Together, RD29s coordinates general and/or systemic defense processes against various environmental constraints including drought and wounding. We hence conclude that RD29s are unique contenders that uncouple critical aspects of plant defenses; OPDA and ABA crosstalk, IST development, and growth and defense coordination, in shaping the optimal phenomes of plant varieties under different ecological conditions.

Unresolved roles of Aux/IAA proteins in auxin responses

Aux/IAA proteins are well-known as key components of the nuclear auxin signaling pathway, repressing gene transcription when present and enabling gene activation upon their degradation. In this review, we explore the additional roles of Aux/IAA proteins in the known auxin perception pathways-the TIR1/AFBs nuclear as well as in the emerging cytoplasmic and apoplastic pathways. We summarize recent advances in understanding the regulation of Aux/IAA protein stability at the post-translational level, a critical factor in auxin-regulated transcriptional output. We further highlight the roles of auxin-nondegradable non-canonical Aux/IAAs in auxin-mediated transcription and their involvement in apoplastic auxin signalling. Additionally, we discuss the importance of Aux/IAAs for the adenylate cyclase activity of TIR1/AFB receptors and speculate on their involvement in the cytoplasmic auxin pathway. Using Arabidopsis root as a model, this work underscores the central role of Aux/IAA proteins in mediating auxin-driven developmental processes and environmental responses. Key questions for future research are proposed to further unravel the dynamic roles of Aux/IAAs in auxin signaling networks.

Design, Synthesis, and Herbicidal Evaluation of Novel Synthetic Auxin Herbicides Containing 6-Indolylpyridine Oxime Ester/Amine

In this study, a series of 6-indolylpyridine oxime ester/amide derivatives were synthesized as novel synthetic auxin herbicides (SAHs) for postemergence herbicidal applications. At 30 g ai/ha, compounds 9q, 9u, 9v and 9w demonstrated inhibition rates of 90 to 100% against weeds Echinochloa crus-galli (EC) and Digitaria sanguinalis (DS). Even at a reduced 7.5 g ai/ha, these compounds maintained over 90% inhibition against four broadleaf weeds, with effects comparable to those of commercial herbicides halauxifen-methyl (HAM), indolauxipyr (IND) and indolauxipyr-cyanomethyl (INC). Crop sensitivity tests confirmed the suitability of compounds 9w and 9u for application in wheat and rice fields at 30 g ai/ha. Molecular docking analysis revealed that compound 9w formed significant hydrogen bonding and π-π stacking interactions with key amino acid residues. Additionally, half maximal inhibitory concentration (IC50) values of compounds 9u and 9w for IAA in vitro inhibition activity were 6.153 and 4.389 μM, respectively, outperforming HAM (9.061 μM). Compounds 9u and 9w show promising potential as lead candidates for novel SAHs.

A point mutation in IAA34 confers resistance to the auxin herbicide 2,4-D in Sisymbrium orientale

BACKGROUND

Sisymbrium orientale has evolved resistance to 2,4-D in Australia due to a 27 bp deletion in SoIAA2. However, one population of Sisymbrium orientale resistant to 2,4-D (R1) did not contain the SoIAA2Δ27, suggesting another 2,4-D resistance mechanism was present in this population. Here, we reported a novel target-site resistance mechanism of 2,4-D in the R1 population.

RESULTS

R1 is resistant to 2,4-D, 2-methyl-4-chlorophenoxyacetic acid (MCPA), and fluroxypyr with increased tolerance to dicamba, triclopyr and picloram. The 2,4-D resistance level for R1 is lower than resistant populations containing a 27 bp deletion in IAA2. 2,4-D resistance in R1 was due to a single dominant gene. Pretreatment of R1 with the P450 inhibitor malathion did not reduce resistance to 2,4-D. We identified a point mutation, Leu 175 Pro, in SoIAA34 in R1, but not in three susceptible (S) populations. This mutation was present (either homozygous or heterozygous) in all 2,4-D resistant plants in a segregating F2 population generated from a cross between S and R1 plants. Transgenic Arabidopsis plants expressing SoIAA34-R had significantly greater root length and dry mass than the wild-type (WT) or transgenic Arabidopsis plants carrying SoIAA34-S under 2,4-D treatment.

CONCLUSION

We confirmed resistance to 2,4-D in the R1 population was controlled by a single dominant locus. Further, we verified that the Leu 175 Pro mutation in SoIAA34 is responsible for the 2,4-D resistance in R1. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Plant PI-PLC signaling in stress and development

Phosphoinositide-specific phospholipase C (PI-PLC) signaling is involved in various plant stress and developmental responses. Though several aspects of this lipid signaling pathway are conserved within animals and plants, clear differences have also emerged. While animal PLC signaling is characterized by the hydrolysis of PIP2 and production of IP3 and DAG as second messengers to activate Ca2+ and PKC signaling, plant PI-PLCs seem to predominantly use PIP as substrate and convert IP2 and DAG into inositolpolyphosphates and phosphatidic acid (PA) as plant second messengers. Sequencing of multiple plant genomes confirmed that plant PLC signaling evolved differently from animals, lacking homologs of the IP3 gated-Ca2+ channel, PKC and TRP channels, and with PLC enzymes resembling the PLCζ subfamily, which lacks the conserved PH domain that binds PIP2. With emerging tools in plant molecular biology, data analyses, and advanced imaging, plant PLC signaling is ready to gain momentum.

Mechanisms of Increase of Winter Wheat Frost Resistance Under Tebuconazole Treatment at Early Stage of Growth: Role of Hormone- and Reactive Oxygen Species-Mediated Signaling Pathways

1, 2, 4-triazole derivatives, including tebuconazole, have been reported to show positive physiological effects in cereals apart from fungicidal activity and to increase plants' tolerance against temperature stress. This study investigates the mechanisms of increasing frost resistance of etiolated winter wheat (Triticum aestivum L., "Irkutskaya" variety) seedlings by tebuconazole-based seed dresser "Bunker" (1.5 μL g-1 of seeds) and tebuconazole (30 μg g-1 of seeds). To identify ABA-dependent and ABA-independent pathways of frost resistance, we used fluridone (FLD, 5 mg L-1), an inhibitor of endogenous abscisic acid (ABA) synthesis. FLD effectively inhibited the accumulation of carotenoids in the shoots and prevented the formation of carotenoids caused by the "Bunker" and tebuconazole. In non-hardened seedlings, FLD stimulated coleoptile and first leaf growth, but did not suppress the growth inhibitory effects of "Bunker" and tebuconazole. In shoots of hardened seedlings, FLD reduced the retarding effect of tebuconazole. Regardless of seedling age, temperature, and the protectant treatment, FLD had no effect on the sugar content in the shoots. FLD did not essentially influence frost resistance induced by "Bunker" and tebuconazole in cold-hardened seedlings. Fluridone increased H2O2 content and guaiacol peroxidase activity under control conditions (both with tebuconazole and without tebuconazole) and during cold hardening (in seedlings from seeds treated with tebuconazole). ABA levels in cold-hardened seedlings treated with FLD alone, tebuconazole alone, or a combination of the two were two to three times lower than in untreated hardened seedlings. Changes in indole-3-acetic and salicylic acids in response to FLD and tebuconazole treatment indicate complex interactions with signaling cellular systems. Our results suggest that tebuconazole activates ABA-independent pathways more strongly than ABA-dependent pathways in enhancing frost resistance. The potential mechanisms of tebuconazole action in plant cells are discussed.

A novel mutation in SoIAA20 confers cross-resistance to 2,4-Dichlorophenoxyacetic acid and other auxinic herbicides in Sonchus oleraceus

BACKGROUND

2,4-Dichlorophenoxyacetic acid (2,4-D) and other auxinic herbicides are important for weed control in cropping systems globally. Weeds with resistance to 2,4-D and other auxinic herbicides have evolved, including several populations of Sonchus oleraceus from multiple sites in Australia. We report the underlying mechanism in these populations that gives rise to auxinic herbicide resistance.

RESULTS

We studied a total of three susceptible and eight resistant Sonchus oleraceus populations. All resistant populations had a deletion of three amino acids flanking the degron sequence of an Aux/IAA gene, SoIAA20, which was not found in the three susceptible populations. The eight populations with the resistant allele were also resistant to dicamba, fluroxypyr and clopyralid. The resistant plants also had reduced movement of 2,4-D out of the treated tissues compared to susceptible plants.

CONCLUSION

The paired deletion flanking the degron region of SoIAA20 likely provides resistance to 2,4-D by restricting the movement of 2,4-D from the treated tissue to the rest of the plant. We hypothesise that this deletion keeps the 2,4-D bound to the target site. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Phosphorylation of auxin signaling repressor IAA8 by heat-responsive MPKs causes defective flower development

Heat stress is a substantial and imminent threat to plant growth and development. Understanding its adverse effects on plant development at the molecular level is crucial for sustainable agriculture. However, the molecular mechanism underlying how heat stress causes developmental defects in flowers remains poorly understood. Here, we identified Indole-3-Acetic Acid 8 (IAA8), a repressor of auxin signaling, as a substrate of mitogen-activated protein kinases (MPKs) in Arabidopsis thaliana, and found that MPK-mediated phosphorylation of IAA8 inhibits flower development. MPKs phosphorylated three residues of IAA8: S74, T77, and S135. Interestingly, transgenic plants overexpressing a phospho-mimicking mutant of IAA8 (IAA8DDD OX) exhibited defective flower development due to high IAA8 levels. Furthermore, MPK-mediated phosphorylation inhibited IAA8 polyubiquitination, thereby significantly increasing its stability. Additionally, the expression of key transcription factors involved in flower development, such as bZIP and MYB genes, was significantly perturbed in the IAA8DDD OX plants. Collectively, our study demonstrates that heat stress inhibits flower development by perturbing the expression of flower development genes through the MPK-mediated phosphorylation of IAA8, suggesting that Aux/IAA phosphorylation enables plants to fine-tune their development in response to environmental stress.

BPMs regulate Arabidopsis seedling development by promoting auxin-independent degradation of the Aux/IAA protein IAA10

After germination, seedlings undergo etiolated development (skotomorphogenesis), enabling them to grow towards the soil surface. In Arabidopsis, etiolated seedlings exhibit rapid hypocotyl elongation, apical hook formation and closed cotyledons to protect the meristem. In this study, we found that high-order mutants in the BPM gene family displayed defects in seedling development, characterized by a shorter hypocotyl, early apical hook opening, and opened cotyledons in the dark. BPM1, BPM2, BPM4, and BPM5 exhibit distinct expression patterns and subcellular localization in etiolated seedlings. In a hypocotyl segment assay the bpm mutants showed defects in auxin response indicating impaired auxin signaling in the hypocotyl. Expression of the auxin reporter DR5:GFP was also altered in the bpm1,4,5 mutant in various tissues compared to the wild type. Furthermore, we showed that BPM1 and IAA10 interact in yeast two-hybrid, BiFC, and Co-IP assays. Experiments in protoplasts indicated that BPM1 promotes ubiquitylation and degradation of IAA10, and the level of IAA10 protein is greater in the bpm1,4,5 mutant. In addition, IAA10 over-expression resulted in phenotypes similar to the bpm mutants. These results indicate that the BPMs target the Aux/IAA proteins for ubiquitylation and degradation. Overall, our findings shed light on the key roles of the BPMs in auxin signaling during seedling development.

Role of TIR1/AFB family genes during grafting in Carya cathayensis

Auxins play significant roles in plant growth and development. The transporter inhibitor response1/auxin signaling F-box (TIR1/AFB) gene family encodes the auxin receptor proteins and plays an essential role in the auxin signaling pathway. Here we identified and characterized the TIR1/AFB family in Carya cathayensis (Cc) plants (named as CcTIR1/AFB). Seven CcTIR1/AFBs were identified and further confirmed by cloning. All proteins encoded by these genes conservatively contained two domains, the F-box and leucine-rich repeat (LRR) domains. The CcTIR1/AFBs were located in the nucleus. Phylogenetic analysis suggested that CcTIR1/AFBs were evenly scattered in four different subgroups. The cis-acting element analysis indicates that CcTIR1/AFBs might be activated by auxin. The spatial and temporal expression of CcTIR1/AFBs during grafting suggested that both CcAFB1 and CcAFB2 in scions and CcAFB4 in the rootstocks were significantly upregulated at 3 days after grafting, which indicated the specialization of three CcAFBs during grafting. The Y2H assay indicated that three CcAFBs were capable of interacting with CcIAA16, CcIAA27b, and CcIAA29a, among which CcAFB4 interacted strongly with CcIAA1 and CcIAA16. Our study provides the opportunity to understand the potential role of not only CcTIR1/AFBs but also special CcAFBs (CcAFB1, CcAFB2, and CcAFB4), which is a great aspect to further explore the molecular mechanism during the grafting process.

Acidic Stress Induces Cytosolic Free Calcium Oscillation, and an Appropriate Low pH Helps Maintain the Circadian Clock in Arabidopsis

Acidic stress is a formidable environmental factor that exerts adverse effects on plant growth and development, ultimately leading to a potential reduction in agricultural productivity. A low pH triggers Ca2+ influx across the plasma membrane (PM), eliciting distinct responses under various acidic pH levels. However, the underlying mechanisms by which Arabidopsis plant cells generate stimulus-specific Ca2+ signals in response to acidic stress remain largely unexplored. The experimentally induced stimulus may elicit spikes in cytosolic free Ca2+ concentration ([Ca2+]i) spikes or complex [Ca2+]i oscillations that persist for 20 min over a long-term of 24 h or even several days within the plant cytosol and chloroplast. This study investigated the increase in [Ca2+]i under a gradient of low pH stress ranging from pH 3.0 to 6.0. Notably, the peak of [Ca2+]i elevation was lower at pH 4.0 than at pH 3.0 during the initial 8 h, while other pH levels did not significantly increase [Ca2+]i compared to low acidic stress conditions. Lanthanum chloride (LaCl3) can effectively suppress the influx of [Ca2+]i from the apoplastic to the cytoplasm in plants under acid stress, with no discernible difference in intracellular calcium levels observed in Arabidopsis. Following 8 h of acid treatment in the darkness, the intracellular baseline Ca2+ levels in Arabidopsis were significantly elevated when exposed to low pH stress. A moderately low pH, specifically 4.0, may function as a spatial-temporal input into the circadian clock system. These findings suggest that acid stimulation can exert a continuous influence on intracellular calcium levels, as well as plant growth and development.

ABLs and transmembrane kinases shape extracellular auxin perception

Auxin is a key phytohormone, but the mechanism underlying apoplastic auxin perception has remained elusive. Yu et al. recently demonstrated that the interaction of two novel apoplast-localized auxin-binding protein 1 (ABP1)-like proteins, ABL1 and ABL2, with transmembrane kinases (TMKs) shapes extracellular auxin perception in both an overlapping and an ABP1-independent manner.

Slow release of a synthetic auxin induces formation of adventitious roots in recalcitrant woody plants

Clonal propagation of plants by induction of adventitious roots (ARs) from stem cuttings is a requisite step in breeding programs. A major barrier exists for propagating valuable plants that naturally have low capacity to form ARs. Due to the central role of auxin in organogenesis, indole-3-butyric acid is often used as part of commercial rooting mixtures, yet many recalcitrant plants do not form ARs in response to this treatment. Here we describe the synthesis and screening of a focused library of synthetic auxin conjugates in Eucalyptus grandis cuttings and identify 4-chlorophenoxyacetic acid-L-tryptophan-OMe as a competent enhancer of adventitious rooting in a number of recalcitrant woody plants, including apple and argan. Comprehensive metabolic and functional analyses reveal that this activity is engendered by prolonged auxin signaling due to initial fast uptake and slow release and clearance of the free auxin 4-chlorophenoxyacetic acid. This work highlights the utility of a slow-release strategy for bioactive compounds for more effective plant growth regulation.

Identification of potential auxin response candidate genes for soybean rapid canopy coverage through comparative evolution and expression analysis

Introduction

Throughout domestication, crop plants have gone through strong genetic bottlenecks, dramatically reducing the genetic diversity in today's available germplasm. This has also reduced the diversity in traits necessary for breeders to develop improved varieties. Many strategies have been developed to improve both genetic and trait diversity in crops, from backcrossing with wild relatives, to chemical/radiation mutagenesis, to genetic engineering. However, even with recent advances in genetic engineering we still face the rate limiting step of identifying which genes and mutations we should target to generate diversity in specific traits.

Methods

Here, we apply a comparative evolutionary approach, pairing phylogenetic and expression analyses to identify potential candidate genes for diversifying soybean (Glycine max) canopy cover development via the nuclear auxin signaling gene families, while minimizing pleiotropic effects in other tissues. In soybean, rapid canopy cover development is correlated with yield and also suppresses weeds in organic cultivation.

Results and discussion

We identified genes most specifically expressed during early canopy development from the TIR1/AFB auxin receptor, Aux/IAA auxin co-receptor, and ARF auxin response factor gene families in soybean, using principal component analysis. We defined Arabidopsis thaliana and model legume species orthologs for each soybean gene in these families allowing us to speculate potential soybean phenotypes based on well-characterized mutants in these model species. In future work, we aim to connect genetic and functional diversity in these candidate genes with phenotypic diversity in planta allowing for improvements in soybean rapid canopy cover, yield, and weed suppression. Further development of this and similar algorithms for defining and quantifying tissue- and phenotype-specificity in gene expression may allow expansion of diversity in valuable phenotypes in important crops.

Genetically Encoded, Noise-Tolerant, Auxin Biosensors in Yeast

Auxins are crucial signaling molecules that regulate the growth, metabolism, and behavior of various organisms, most notably plants but also bacteria, fungi, and animals. Many microbes synthesize and perceive auxins, primarily indole-3-acetic acid (IAA, referred to as auxin herein), the most prevalent natural auxin, which influences their ability to colonize plants and animals. Understanding auxin biosynthesis and signaling in fungi may allow us to better control interkingdom relationships and microbiomes from agricultural soils to the human gut. Despite this importance, a biological tool for measuring auxin with high spatial and temporal resolution has not been engineered in fungi. In this study, we present a suite of genetically encoded, ratiometric, protein-based auxin biosensors designed for the model yeast Saccharomyces cerevisiae. Inspired by auxin signaling in plants, the ratiometric nature of these biosensors enhances the precision of auxin concentration measurements by minimizing clonal and growth phase variation. We used these biosensors to measure auxin production across diverse growth conditions and phases in yeast cultures and calibrated their responses to physiologically relevant levels of auxin. Future work will aim to improve the fold change and reversibility of these biosensors. These genetically encoded auxin biosensors are valuable tools for investigating auxin biosynthesis and signaling in S. cerevisiae and potentially other yeast and fungi and will also advance quantitative functional studies of the plant auxin perception machinery, from which they are built.

Genome-wide gene network uncover temporal and spatial changes of genes in auxin homeostasis during fruit development in strawberry (F. × ananassa)

BACKGROUND

The plant hormone auxin plays a crucial role in regulating important functions in strawberry fruit development. Although a few studies have described the complex auxin biosynthetic and signaling pathway in wild diploid strawberry (Fragaria vesca), the molecular mechanisms underlying auxin biosynthesis and crosstalk in octoploid strawberry fruit development are not fully characterized. To address this knowledge gap, comprehensive transcriptomic analyses were conducted at different stages of fruit development and compared between the achene and receptacle to identify developmentally regulated auxin biosynthetic genes and transcription factors during the fruit ripening process. Similar to wild diploid strawberry, octoploid strawberry accumulates high levels of auxin in achene compared to receptacle.

RESULTS

Genes involved in auxin biosynthesis and conjugation, such as Tryptophan Aminotransferase of Arabidopsis (TAAs), YUCCA (YUCs), and Gretchen Hagen 3 (GH3s), were found to be primarily expressed in the achene, with low expression in the receptacle. Interestingly, several genes involved in auxin transport and signaling like Pin-Formed (PINs), Auxin/Indole-3-Acetic Acid Proteins (Aux/IAAs), Transport Inhibitor Response 1 / Auxin-Signaling F-Box (TIR/AFBs) and Auxin Response Factor (ARFs) were more abundantly expressed in the receptacle. Moreover, by examining DEGs and their transcriptional profiles across all six developmental stages, we identified key auxin-related genes co-clustered with transcription factors from the NAM-ATAF1,2-CUC2/ WRKYGQK motif (NAC/WYKY), Heat Shock Transcription Factor and Heat Shock Proteins (HSF/HSP), APETALA2/Ethylene Responsive Factor (AP2/ERF) and MYB transcription factor groups.

CONCLUSIONS

These results elucidate the complex regulatory network of auxin biosynthesis and its intricate crosstalk within the achene and receptacle, enriching our understanding of fruit development in octoploid strawberries.

Comparative transcriptome analysis of differentially expressed genes and pathways in male and female flowers of Fraxinus mandshurica

Fraxinus mandshurica Rupr. (F. mandshurica) is a dioecious tree species with important ecological and application values. To delve deeper into the regulatory pathways and genes responsible for male and female flowers in F. mandshurica, we conducted transcriptome sequencing on male and female flowers at four distinct stages. The analysis revealed that the female database generated 38,319,967 reads while the male database generated 43,320,907 reads, resulting in 2930 differentially expressed genes with 1441 were up-regulated and 1489 down-regulated in males compared to females. Following an analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), four distinct pathways (hormone signal transduction, energy metabolism, flavonoid biosynthesis, and photoperiod) linked to female and male flowers were identified. Subsequently, qRT-PCR verification revealed that FmAUX/IAA, FmEIN3, and FmA-ARR genes in hormone signal transduction pathway are related to female flower development. Meanwhile, FmABF genes in hormone signal transduction pathway, FmGS and FmGDH genes in energy metabolism pathway, FmFLS genes in flavonoid biosynthesis pathway, and FmCaM, FmCRY, and FmPKA genes in photoperiod pathway are related to male flower development. This study was the first to analyze the transcriptome of male and female flowers of F. mandshurica, providing a reference for the developmental pathways and gene expression levels of male and female plants.

Comparative Transcriptome Analysis of Salt-Tolerant and -Sensitive Soybean Cultivars under Salt Stress

Soil salinity is a major limiting factor in soybean (Glycine max (L.) Merr.) yield in Xinjiang, China. Therefore, breeding soybean to tolerate highly saline soils is crucial to improve its yield. To explore the molecular mechanisms underlying the response of soybean to salt stress, we performed a comparative transcriptome analysis of root and leaf samples collected from two local soybean cultivars. The salt-tolerant cultivar 'Xin No. 9' (X9) showed higher photosynthetic activity than the salt-sensitive cultivar 'Xinzhen No. 9' (Z9) under salt stress. In total, we identified 13,180 and 13,758 differential expression genes (DEGs) in X9 and Z9, respectively, of which the number of DEGs identified in roots was much higher than that in leaves. We constructed the co-expression gene modules and conducted Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The results suggested there were distinct differences in the mechanisms of response to salt stress between the two soybean cultivars; i.e., the salt-tolerant cultivar X9 exhibited alterations in fundamental metabolism, whereas the salt-sensitive cultivar Z9 responded to salt stress mainly through the cell cycle. The possible crosstalk among phytohormone signaling, MAPK signaling, phenylpropanoid biosynthesis, starch and sucrose metabolism, and ribosome metabolism may play crucial roles in the response to salt stress in soybean. Our results offered a comprehensive understanding of the genes and pathways involved in the response to salt stress in soybean and provided valuable molecular resources for future functional studies and the breeding of soybean varieties with enhanced tolerance to salinity.

Sly-miR398b Mediates Mature Leaf Flattening by Orchestrating Auxin and H2O2 Signalling in Tomato

Leaf flattening plays a pivotal role in optimizing light capture and enhancing photosynthesis efficiency. While extensive research has clarified the molecular mechanisms governing the initial stages of leaf flattening, understanding the maintenance of this process in mature leaves remains limited. Our investigation focused on sly-miR398b in tomatoes and revealed its crucial role in maintaining leaf flattening. In situ hybridization experiments indicated predominant expression of sly-miR398b in the abaxial side. Disrupting sly-miR398b using CRISPR/Cas9 relieved its suppression on target gene (Cu/Zn-SOD, SlCSD1), elevating SlCSD1 levels specifically on the abaxial side. Consequently, this asymmetrical expression of SlCSD1 increased hydrogen peroxide (H2O2) levels in the abaxial side, hindering auxin influx genes while promoting auxin efflux gene expression. This shift reduced auxin response gene expression in the abaxial side of mature leaves compared to the adaxial side, leading to leaf epinasty in sly-miR398b mutants. Exogenous H2O2 spraying induced leaf epinasty, downregulating SlGH3.5 and upregulating SlPIN3 and SlPIN4. Remarkably, spraying with 1-naphthalacetic acid (NAA) restored leaf flattening in sly-miR398b mutants. Our findings offer novel insights into mature leaf flattening maintenance via sly-miR398b's regulation of auxin and H2O2 signalling pathways.

Protein degradation in auxin response

The signaling molecule auxin sits at the nexus of plant biology where it coordinates essentially all growth and developmental processes. Auxin molecules are transported throughout plant tissues and are capable of evoking highly specific physiological responses by inducing various molecular pathways. In many of these pathways, proteolysis plays a crucial role for correct physiological responses. This review provides a chronology of the discovery and characterization of the auxin receptor, which is a fascinating example of separate research trajectories ultimately converging on the discovery of a core auxin signaling hub that relies on degradation of a family of transcriptional inhibitor proteins-the Aux/IAAs. Beyond describing the "classical" proteolysis-driven auxin response system, we explore more recent examples of the interconnection of proteolytic systems, which target a range of other auxin signaling proteins, and auxin response. By highlighting these emerging concepts, we provide potential future directions to further investigate the role of protein degradation within the framework of auxin response.

An F-box Kelch repeat protein, PmFBK2, from Persicaria minor interacts with GID1b to modulate gibberellin signalling

The F-box protein (FBP) family plays diverse functions in the plant kingdom, with the function of many members still unrevealed. In this study, a specific FBP called PmFBK2, containing Kelch repeats from Persicaria minor, was functionally investigated. Employing the yeast two-hybrid (Y2H) assay, PmFBK2 was found to interact with Skp1-like proteins from P. minor, suggesting its potential to form an E3 ubiquitin ligase, known as the SCF complex. Y2H and co-immunoprecipitation tests revealed that PmFBK2 interacts with full-length PmGID1b. The interaction marks the first documented binding between these two protein types, which have never been reported in other plants before, and they exhibited a negative effect on gibberellin (GA) signal transduction. The overexpression of PmFBK2 in the kmd3 mutant, a homolog from Arabidopsis, demonstrated the ability of PmFBK2 to restore the function of the mutated KMD3 gene. The function restoration was supported by morphophysiological and gene expression analyses, which exhibited patterns similar to the wild type (WT) compared to the kmd3 mutant. Interestingly, the overexpression of PmFBK2 or PmGID1b in Arabidopsis had opposite effects on rosette diameter, seed weight, and plant height. This study provides new insights into the complex GA signalling. It highlights the crucial roles of the interaction between FBP and the GA receptor (GID1b) in regulating GA responses. These findings have implications for developing strategies to enhance plant growth and yield by modulating GA signalling in crops.

Low expression of auxin receptor EcAFB4 confers resistance to florpyrauxifen-benzyl in Echinochloa crus-galli (L.) P. Beauv

Echinochloa crus-galli (L.) P. Beauv is a monocotyledonous weed that seriously infests rice fields. Florpyrauxifen-benzyl, a novel synthetic auxin herbicide commercialized in China in 2018, is an herbicide for controlling E. crus-galli. However, a suspected resistant population (R) collected in 2012 showed resistance to the previously unused florpyrauxifen-benzyl. Whole-plant dose-response bioassay indicated that the R population evolved high resistance to quinclorac and florpyrauxifen-benzyl. Pretreatment with P450 inhibitors did not influence the GR50 of E. crus-galli to florpyrauxifen-benzyl. The expression of target receptor EcAFB4 was down-regulated in the R population, leading to the reduced response to florpyrauxifen-benzyl (suppresses over-production of ethylene and ABA). We verified this resistance mechanism in the knockout OsAFB4 in Oryza sativa L. The Osafb4 mutants exhibited high resistance to florpyrauxifen-benzyl and moderate resistance to quinclorac. Furthermore, DNA methylation in the EcAFB4 promoter regulated its low expression in the R population after florpyrauxifen-benzyl treatment. In summary, the low expression of the auxin receptor EcAFB4 confers target resistance to the synthetic auxin herbicide florpyrauxifen-benzyl in the R- E. crus-galli.

Transport of herbicides by PIN-FORMED auxin transporters

Auxins are a group of phytohormones that control plant growth and development 1. Their crucial role in plant physiology has inspired development of potent synthetic auxins that can be used as herbicides 2. Phenoxyacetic acid derivatives are a widely used group of auxin herbicides in agriculture and research. Despite their prevalence, the identity of the transporters required for distribution of these herbicides in plants is both poorly understood and the subject of controversial debate 3,4. Here we show that PIN-FORMED auxin transporters transport a range of phenoxyacetic acid herbicides across the membrane and we characterize the molecular determinants of this process using a variety of different substrates as well as protein mutagenesis to control substrate specificity. Finally, we present Cryo-EM structures of Arabidopsis thaliana PIN8 with 2,4-dichlorophenoxyacetic acid (2,4-D) or 4-chlorophenoxyacetic acid (4-CPA) bound. These structures represent five key states from the transport cycle, allowing us to describe conformational changes associated with substrate binding and transport across the membrane. Overall, our results reveal that phenoxyacetic acid herbicides use the same export machinery as endogenous auxins and exemplify how transporter binding sites undergo transformations that dictate substrate specificity. These results enable development of novel synthetic auxins and for guiding precision breeding of herbicide resistant crop plants.

Synthetically derived BiAux modulates auxin co-receptor activity to stimulate lateral root formation

The root system plays an essential role in plant growth and adaptation to the surrounding environment. The root clock periodically specifies lateral root prebranch sites (PBS), where a group of pericycle founder cells (FC) is primed to become lateral root founder cells and eventually give rise to lateral root primordia or lateral roots (LRs). This clock-driven organ formation process is tightly controlled by modulation of auxin content and signaling. Auxin perception entails the physical interaction of TRANSPORT INHIBITOR RESPONSE 1 (TIR1) or AUXIN SIGNALING F-BOX (AFBs) proteins with AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) repressors to form a co-receptor system. Despite the apparent simplicity, the understanding of how specific auxin co-receptors are assembled remains unclear. We identified the compound bis-methyl auxin conjugated with N-glucoside, or BiAux, in Arabidopsis (Arabidopsis thaliana) that specifically induces the formation of PBS and the emergence of LR, with a slight effect on root elongation. Docking analyses indicated that BiAux binds to F-box proteins, and we showed that BiAux function depends on TIR1 and AFB2 F-box proteins and AUXIN RESPONSE FACTOR 7 activity, which is involved in FC specification and LR formation. Finally, using a yeast (Saccharomyces cerevisiae) heterologous expression system, we showed that BiAux favors the assemblage of specific co-receptors subunits involved in LR formation and enhances AUXIN/INDOLE-3-ACETIC ACID 28 protein degradation. These results indicate that BiAux acts as an allosteric modulator of specific auxin co-receptors. Therefore, BiAux exerts a fine-tune regulation of auxin signaling aimed to the specific formation of LR among the many development processes regulated by auxin.

Enhanced Herbicide Metabolism and Target Site Mutation Enabled the Multiple Resistance to Cyhalofop-butyl, Florpyrauxifen-benzyl, and Penoxsulam in Echinochloa crus-galli

This study investigated the multiple herbicide resistance (MHR) mechanism of one Echinochloa crus-galli population that was resistant to florpyrauxifen-benzyl (FPB), cyhalofop-butyl (CHB), and penoxsulam (PEX). This population carried an Ala-122-Asn mutation in the acetolactate synthase (ALS) gene but no mutation in acetyl-CoA carboxylase (ACCase) and transport inhibitor response1 (TIR1) genes. The metabolism rate of PEX was 2-fold higher, and the production of florpyrauxifen-acid and cyhalofop-acid was lower in the resistant population. Malathion and 4-chloro-7-nitrobenzoxadiazole (NBD-Cl) could reverse the resistance, suggesting that cytochrome P450 (CYP450) and glutathione S-transferase (GST) contribute to the enhanced metabolism. According to RNA-seq and qRT-PCR validation, two CYP450 genes (CYP71C42 and CYP71D55), one GST gene (GSTT2), two glycosyltransferase genes (rhamnosyltransferase 1 and IAAGLU), and two ABC transporter genes (ABCG1 and ABCG25) were induced by CHB, FPB, and PEX in the resistant population. This study revealed that the target mutant and enhanced metabolism were involved in the MHR mechanism in E. crus-galli.

Comparative genomic profiling of transport inhibitor Response1/Auxin signaling F-box (TIR1/AFB) genes in eight Pyrus genomes revealed the intraspecies diversity and stress responsiveness patterns

In the genomics of plants and the phytoecosystem, Pyrus (pear) is among the most nutritious fruits and contains fiber that has great health benefits to humans. It is mostly cultivated in temperate regions and is one of the most cultivated pome fruits globally. Pears are highly subjected to biotic and abiotic stresses that affect their yield. TIR1/AFB proteins act as auxin co-receptors during the signaling of nuclear auxins and play a primary role in development-related regulatory processes and responses to biotic and abiotic stresses. However, this gene family and its members have not been explored in Pyrus genomes, and understanding these genes will help obtain useful insights into stress tolerance and ultimately help maintain a high yield of pears. This study reports a pangenome-wide investigation of TIR1/AFB genes from eight Pyrus genomes: Cuiguan (Pyrus pyrifolia), Shanxi Duli (P. betulifolia), Zhongai 1 [(P. ussuriensis × communis) × spp.], Nijisseiki (P. pyrifolia), Yunhong No.1 (P. pyrifolia), d'Anjou (P. communis), Bartlett v2.0 (P. communis), and Dangshansuli v.1.1 (P. bretschneideri). These genes were randomly distributed on 17 chromosomes in each genome. Based on phylogenetics, the identified TIR1/AFB genes were divided into six groups. Their gene structure and motif pattern showed the intraspecific structural conservation as well as evolutionary patterns of Pyrus TIR1/AFBs. The expansion of this gene family in Pyrus is mainly caused by segmental duplication; however, a few genes showed tandem duplication. Moreover, positive and negative selection pressure equally directed the gene's duplication process. The GO and PPI analysis showed that Pyrus TIR1/AFB genes are associated with abiotic stress- and development-related signaling pathways. The promoter regions of Pyrus TIR1/AFB genes were enriched in hormone-, light-, development-, and stress-related cis elements. Furthermore, publicly available RNA-seq data analysis showed that DaTIR1/AFBs have varied levels of expression in various tissues and developmental stages, fruit hardening disease conditions, and drought stress conditions. This indicated that DaTIR1/AFB genes might play critical roles in response to biotic and abiotic stresses. The DaTIR1/AFBs have similar protein structures, which show that they are involved in the same function. Hence, this study will broaden our knowledge of the TIR1/AFB gene family in Pyrus, elucidating their contribution to conferring resistance against various environmental stresses, and will also provide valuable insights for future researchers.

Carrier-based delivery system of phytohormones in plants: stepping outside of the ordinary

Climate change is increasing the stresses on crops, resulting in reduced productivity and further augmenting global food security issues. The dynamic climatic conditions are a severe threat to the sustainability of the ecosystems. The role of technology in enhancing agricultural produce with the minimum environmental impact is hence crucial. Active molecule/Plant growth regulators (PGRs) are molecules helping plants' growth, development, and tolerance to abiotic and biotic stresses. However, their degradation, leaching in surrounding soil and ground water, as well as the assessment of the correct dose of application etc., are some of the technical disadvantages faced. They can be resolved by encapsulation/loading of PGRs on polymer matrices. Micro/nanoencapsulation is a revolutionary tool to deliver bioactive compounds in an economically affordable and environmentally friendly way. Carrier-based smart delivery systems could be a better alternative to PGRs application in the agriculture field than conventional methods (e.g., spraying). The physiochemical properties and release kinetics of PGRs from the encapsulating system are being explored. Therefore, the present review emphasizes the current status of PGRs encapsulation approach and their potential benefits to plants. This review also addressed the mechanistic action of carrier-based delivery systems for release, which may aid in developing smart delivery systems with specific tailored properties in future research.

WAV E3 ubiquitin ligases mediate degradation of IAA32/34 in the TMK1-mediated auxin signaling pathway during apical hook development

Auxin regulates plant growth and development through downstream signaling pathways, including the best-known SCFTIR1/AFB-Aux/IAA-ARF pathway and several other less characterized "noncanonical" pathways. Recently, one SCFTIR1/AFB-independent noncanonical pathway, mediated by Transmembrane Kinase 1 (TMK1), was discovered through the analyses of its functions in Arabidopsis apical hook development. Asymmetric accumulation of auxin on the concave side of the apical hook triggers DAR1-catalyzed release of the C-terminal of TMK1, which migrates into the nucleus, where it phosphorylates and stabilizes IAA32/34 to inhibit cell elongation, which is essential for full apical hook formation. However, the molecular factors mediating IAA32/34 degradation have not been identified. Here, we show that proteins in the CYTOKININ INDUCED ROOT WAVING 1 (CKRW1)/WAVY GROWTH 3 (WAV3) subfamily act as E3 ubiquitin ligases to target IAA32/34 for ubiquitination and degradation, which is inhibited by TMK1c-mediated phosphorylation. This antagonistic interaction between TMK1c and CKRW1/WAV3 subfamily E3 ubiquitin ligases regulates IAA32/34 levels to control differential cell elongation along opposite sides of the apical hook.

The Role of FveAFB5 in Auxin-Mediated Responses and Growth in Strawberries

Auxin is a crucial hormone that regulates various aspects of plant growth and development. It exerts its effects through multiple signaling pathways, including the TIR1/AFB-based transcriptional regulation in the nucleus. However, the specific role of auxin receptors in determining developmental features in the strawberry (Fragaria vesca) remains unclear. Our research has identified FveAFB5, a potential auxin receptor, as a key player in the development and auxin responses of woodland strawberry diploid variety Hawaii 4. FveAFB5 positively influences lateral root development, plant height, and fruit development, while negatively regulating shoot branching. Moreover, the mutation of FveAFB5 confers strong resistance to the auxinic herbicide picloram, compared to dicamba and quinclorac. Transcriptome analysis suggests that FveAFB5 may initiate auxin and abscisic acid signaling to inhibit growth in response to picloram. Therefore, FveAFB5 likely acts as an auxin receptor involved in regulating multiple processes related to strawberry growth and development.

Auxin and carbohydrate control flower bud development in Anthurium andraeanum during early stage of sexual reproduction

BACKGROUND

Flower buds of Anthurium andraeanum frequently cease to grow and abort during the early flowering stage, resulting in prolonged planting times and increased commercialization costs. Nevertheless, limited knowledge exists of the mechanism of flower development after initiation in A. andraeanum.

RESULTS

In this study, the measurement of carbohydrate flow and intensity between leaves and flowers during different growth stages showed that tender leaves are strong sinks and their concomitant flowers are weak ones. This suggested that the tender leaves compete with their concomitant flower buds for carbohydrates during the early growth stages, potentially causing the abortion of the flower buds. The analysis of transcriptomic differentially expressed genes suggested that genes related to sucrose metabolism and auxin response play an important role during flower bud development. Particularly, co-expression network analysis found that AaSPL12 is a hub gene engaged in flower development by collaborating carbohydrate and auxin signals. Yeast Two Hybrid assays revealed that AaSPL12 can interact with AaARP, a protein that serves as an indicator of dormancy. Additionally, the application of exogenous IAA and sucrose can suppress the expression of AaARP, augment the transcriptional abundance of AaSPL12, and consequently expedite flower development in Anthurium andraeanum.

CONCLUSIONS

Collectively, our findings indicated that the combination of auxin and sugar signals could potentially suppress the repression of AaARP protein to AaSPL12, thus advancing the development of flower buds in Anthurium andraeanum.

Protein post-translational modifications in auxin signaling

Protein post-translational modifications (PTMs), such as ubiquitination, phosphorylation, and small ubiquitin-like modifier (SUMO)ylation, are crucial for regulating protein stability, activity, subcellular localization, and binding with cofactors. Such modifications remarkably increase the variety and complexity of proteomes, which are essential for regulating numerous cellular and physiological processes. The regulation of auxin signaling is finely tuned in time and space to guide various plant growth and development. Accumulating evidence indicates that PTMs play critical roles in auxin signaling regulations. Thus, a thorough and systematic review of the functions of PTMs in auxin signal transduction will improve our profound comprehension of the regulation mechanism of auxin signaling and auxin-mediated various processes. This review discusses the progress of protein ubiquitination, phosphorylation, histone acetylation and methylation, SUMOylation, and S-nitrosylation in the regulation of auxin signaling.

Study on Design, Synthesis and Herbicidal Activity of Novel 6-Indazolyl-2-picolinic Acids

Thirty-eight new 4-amino-3,5-dicholo-6-(1H-indazolyl)-2-picolinic acids and 4-amino-3,5-dicholo-6-(2H-indazolyl)-2-picolinic acids were designed by scaffold hopping and synthesized to discover potential herbicidal molecules. All the new compounds were tested to determine their inhibitory activities against Arabidopsis thaliana and the root growth of five weeds. In general, the synthesized compounds exhibited excellent inhibition properties and showed good inhibitory effects on weed root growth. In particular, compound 5a showed significantly greater root inhibitory activity than picloram in Brassica napus and Abutilon theophrasti Medicus at the concentration of 10 µM. The majority of compounds exhibited a 100% post-emergence herbicidal effect at 250 g/ha against Amaranthus retroflexus and Chenopodium album. We also found that 6-indazolyl-2-picolinic acids could induce the up-regulation of auxin genes ACS7 and NCED3, while auxin influx, efflux and auxin response factor were down-regulated, indicating that 6-indazolyl-2-picolinic acids promoted ethylene release and ABA production to cause plant death in a short period, which is different in mode from other picolinic acids.

Enhanced metabolic detoxification is associated with fluroxypyr resistance in Bassia scoparia

Auxin-mimic herbicides chemically mimic the phytohormone indole-3-acetic-acid (IAA). Within the auxin-mimic herbicide class, the herbicide fluroxypyr has been extensively used to control kochia (Bassia scoparia). A 2014 field survey for herbicide resistance in kochia populations across Colorado identified a putative fluroxypyr-resistant (Flur-R) population that was assessed for response to fluroxypyr and dicamba (auxin-mimics), atrazine (photosystem II inhibitor), glyphosate (EPSPS inhibitor), and chlorsulfuron (acetolactate synthase inhibitor). This population was resistant to fluroxypyr and chlorsulfuron but sensitive to glyphosate, atrazine, and dicamba. Subsequent dose-response studies determined that Flur-R was 40 times more resistant to fluroxypyr than a susceptible population (J01-S) collected from the same field survey (LD50 720 and 20 g ae ha-1, respectively). Auxin-responsive gene expression increased following fluroxypyr treatment in Flur-R, J01-S, and in a dicamba-resistant, fluroxypyr-susceptible line 9,425 in an RNA-sequencing experiment. In Flur-R, several transcripts with molecular functions for conjugation and transport were constitutively higher expressed, such as glutathione S-transferases (GSTs), UDP-glucosyl transferase (GT), and ATP binding cassette transporters (ABC transporters). After analyzing metabolic profiles over time, both Flur-R and J01-S rapidly converted [14C]-fluroxypyr ester, the herbicide formulation applied to plants, to [14C]-fluroxypyr acid, the biologically active form of the herbicide, and three unknown metabolites. The formation and flux of these metabolites were faster in Flur-R than J01-S, reducing the concentration of phytotoxic fluroxypyr acid. One unique metabolite was present in Flur-R that was not present in the J01-S metabolic profile. Gene sequence variant analysis specifically for auxin receptor and signaling proteins revealed the absence of non-synonymous mutations affecting auxin signaling and binding in candidate auxin target site genes, further supporting our hypothesis that non-target site metabolic degradation is contributing to fluroxypyr resistance in Flur-R.

The ZmbHLH32-ZmIAA9-ZmARF1 module regulates salt tolerance in maize

The growth and productivity of maize (Zea mays), along with other crop plants, can be significantly hindered by salt stress. Nevertheless, the precise molecular mechanism underlying salt tolerance in maize has yet to be fully elucidated. Hence, it was attempted to identify ZmIAA9, a member of the maize Aux/IAA gene family, as a positive regulator of salt tolerance in maize, which was accompanied by the increased ROS detoxification and elevated transcript abundances of ROS scavenging genes. Molecular and biochemical assays have provided compelling evidence that ZmbHLH32, a transcription factor belonging to the bHLH family, was capable of binding directly to the promoter region of ZmIAA9, thereby activating its expression. This interaction between ZmbHLH32 and ZmIAA9 could be critical for the regulation of salt tolerance in maize. As expected, overexpression of ZmbHLH32 led to the enhanced salt tolerance. In contrast, decreased salt tolerance was attained after application of knockout mutants of ZmbHLH32. Furthermore, ZmARF1, which could act as a downstream of ZmIAA9, was found to physically interact with ZmIAA9 and repress the expression levels of ROS scavenging genes. Thus, our work uncovers a novel mechanism of ZmbHLH32-ZmIAA9-ZmARF1 module-mediated salt tolerance in maize, which can be exploited for breeding salt-tolerant maize varieties.

ABLs and TMKs are co-receptors for extracellular auxin

Extracellular perception of auxin, an essential phytohormone in plants, has been debated for decades. Auxin-binding protein 1 (ABP1) physically interacts with quintessential transmembrane kinases (TMKs) and was proposed to act as an extracellular auxin receptor, but its role was disputed because abp1 knockout mutants lack obvious morphological phenotypes. Here, we identified two new auxin-binding proteins, ABL1 and ABL2, that are localized to the apoplast and directly interact with the extracellular domain of TMKs in an auxin-dependent manner. Furthermore, functionally redundant ABL1 and ABL2 genetically interact with TMKs and exhibit functions that overlap with those of ABP1 as well as being independent of ABP1. Importantly, the extracellular domain of TMK1 itself binds auxin and synergizes with either ABP1 or ABL1 in auxin binding. Thus, our findings discovered auxin receptors ABL1 and ABL2 having functions overlapping with but distinct from ABP1 and acting together with TMKs as co-receptors for extracellular auxin.

Structure-activity relationship of 2,4-D correlates auxinic activity with the induction of somatic embryogenesis in Arabidopsis thaliana

2,4-dichlorophenoxyacetic acid (2,4-D) is a synthetic analogue of the plant hormone auxin that is commonly used in many in vitro plant regeneration systems, such as somatic embryogenesis (SE). Its effectiveness in inducing SE, compared to the natural auxin indole-3-acetic acid (IAA), has been attributed to the stress triggered by this compound rather than its auxinic activity. However, this hypothesis has never been thoroughly tested. Here we used a library of forty 2,4-D analogues to test the structure-activity relationship with respect to the capacity to induce SE and auxinic activity in Arabidopsis thaliana. Four analogues induced SE as effectively as 2,4-D and 13 analogues induced SE but were less effective. Based on root growth inhibition and auxin response reporter expression, the 2,4-D analogues were classified into different groups, ranging from very active to not active auxin analogues. A halogen at the 4-position of the aromatic ring was important for auxinic activity, whereas a halogen at the 3-position resulted in reduced activity. Moreover, a small substitution at the carboxylate chain was tolerated, as was extending the carboxylate chain with an even number of carbons. The auxinic activity of most 2,4-D analogues was consistent with their simulated TIR1-Aux/IAA coreceptor binding characteristics. A strong correlation was observed between SE induction efficiency and auxinic activity, which is in line with our observation that 2,4-D-induced SE and stress both require TIR1/AFB auxin co-receptor function. Our data indicate that the stress-related effects triggered by 2,4-D and considered important for SE induction are downstream of auxin signalling.

Roles of auxin pathways in maize biology

Phytohormones play a central role in plant development and environmental responses. Auxin is a classical hormone that is required for organ formation, tissue patterning, and defense responses. Auxin pathways have been extensively studied across numerous land plant lineages, including bryophytes and eudicots. In contrast, our understanding of the roles of auxin in maize morphogenesis and immune responses is limited. Here, we review evidence for auxin-mediated processes in maize and describe promising areas for future research in the auxin field. Several recent transcriptomic and genetic studies have demonstrated that auxin is a key influencer of both vegetative and reproductive development in maize (namely roots, leaves, and kernels). Auxin signaling has been implicated in both maize shoot architecture and immune responses through genetic and molecular analyses of the conserved co-repressor RAMOSA ENHANCER LOCUS2. Polar auxin transport is linked to maize drought responses, root growth, shoot formation, and leaf morphogenesis. Notably, maize has been a key system for delineating auxin biosynthetic pathways and offers many opportunities for future investigations on auxin metabolism. In addition, crosstalk between auxin and other phytohormones has been uncovered through gene expression studies and is important for leaf and root development in maize. Collectively these studies point to auxin as a cornerstone for maize biology that could be leveraged for improved crop resilience and yield.

Substrate recognition and transport mechanism of the PIN-FORMED auxin exporters

Auxins are pivotal plant hormones that regulate plant growth and transmembrane polar auxin transport (PAT) direct patterns of development. The PIN-FORMED (PIN) family of membrane transporters mediate auxin export from the plant cell and play crucial roles in PAT. Here we describe the recently solved structures of PIN transporters, PIN1, PIN3, and PIN8, and also their mechanisms of substrate recognition and transport of auxin. We compare structures of PINs in both inward- and outward-facing conformations, as well as PINs with different binding configurations for auxin. By this comparative analysis, a model emerges for an elevator transport mechanism. Central structural elements necessary for function are identified, and we show that these are shared with other distantly related protein families.

Identification of potential Auxin Response Candidate genes for soybean rapid canopy coverage through comparative evolution and expression analysis

Glycine max, soybean, is an abundantly cultivated crop worldwide. Efforts have been made over the past decades to improve soybean production in traditional and organic agriculture, driven by growing demand for soybean-based products. Rapid canopy cover development (RCC) increases soybean yields and suppresses early-season weeds. Genome-wide association studies have found natural variants associated with RCC, however causal mechanisms are unclear. Auxin modulates plant growth and development and has been implicated in RCC traits. Therefore, modulation of auxin regulatory genes may enhance RCC. Here, we focus on the use of genomic tools and existing datasets to identify auxin signaling pathway RCC candidate genes, using a comparative phylogenetics and expression analysis approach. We identified genes encoding 14 TIR1/AFB auxin receptors, 61 Aux/IAA auxin co-receptors and transcriptional co-repressors, and 55 ARF auxin response factors in the soybean genome. We used Bayesian phylogenetic inference to identify soybean orthologs of Arabidopsis thaliana genes, and defined an ortholog naming system for these genes. To further define potential auxin signaling candidate genes for RCC, we examined tissue-level expression of these genes in existing datasets and identified highly expressed auxin signaling genes in apical tissues early in development. We identified at least 4 TIR1/AFB, 8 Aux/IAA, and 8 ARF genes with highly specific expression in one or more RCC-associated tissues. We hypothesize that modulating the function of these genes through gene editing or traditional breeding will have the highest likelihood of affecting RCC while minimizing pleiotropic effects.

Dynamic context-dependent regulation of auxin feedback signaling in synthetic gene circuits

Phytohormone auxin plays a key role in regulating plant organogenesis. However, understanding the complex feedback signaling network that involves at least 29 proteins in Arabidopsis in the dynamic context remains a significant challenge. To address this, we transplanted an auxin-responsive feedback circuit responsible for plant organogenesis into yeast. By generating dynamic microfluidic conditions controlling gene expression, protein degradation, and binding affinity of auxin response factors to DNA, we illuminate feedback signal processing principles in hormone-driven gene expression. In particular, we recorded the regulatory mode shift between stimuli counting and rapid signal integration that is context-dependent. Overall, our study offers mechanistic insights into dynamic auxin response interplay trackable by synthetic gene circuits, thereby offering instructions for engineering plant architecture.

Intrinsic disorder and conformational coexistence in auxin coreceptors

AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) transcriptional repressor proteins and the TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB) proteins to which they bind act as auxin coreceptors. While the structure of TIR1 has been solved, structural characterization of the regions of the Aux/IAA protein responsible for auxin perception has been complicated by their predicted disorder. Here, we use NMR, CD and molecular dynamics simulation to investigate the N-terminal domains of the Aux/IAA protein IAA17/AXR3. We show that despite the conformational flexibility of the region, a critical W-P bond in the core of the Aux/IAA degron motif occurs at a strikingly high (1:1) ratio of cis to trans isomers, consistent with the requirement of the cis conformer for the formation of the fully-docked receptor complex. We show that the N-terminal half of AXR3 is a mixture of multiple transiently structured conformations with a propensity for two predominant and distinct conformational subpopulations within the overall ensemble. These two states were modeled together with the C-terminal PB1 domain to provide the first complete simulation of an Aux/IAA. Using MD to recreate the assembly of each complex in the presence of auxin, both structural arrangements were shown to engage with the TIR1 receptor, and contact maps from the simulations match closely observations of NMR signal-decreases. Together, our results and approach provide a platform for exploring the functional significance of variation in the Aux/IAA coreceptor family and for understanding the role of intrinsic disorder in auxin signal transduction and other signaling systems.

A plant virus protein, NIa-pro, interacts with Indole-3-acetic acid-amido synthetase, whose levels positively correlate with disease severity

Potato virus Y (PVY) is an economically important plant pathogen that reduces the productivity of several host plants. To develop PVY-resistant cultivars, it is essential to identify the plant-PVY interactome and decipher the biological significance of those molecular interactions. We performed a yeast two-hybrid (Y2H) screen of Nicotiana benthamiana cDNA library using PVY-encoded NIa-pro as the bait. The N. benthamiana Indole-3-acetic acid-amido synthetase (IAAS) was identified as an interactor of NIa-pro protein. The interaction was confirmed via targeted Y2H and bimolecular fluorescence complementation (BiFC) assays. NIa-pro interacts with IAAS protein and consequently increasing the stability of IAAS protein. Also, the subcellular localization of both NIa-pro and IAAS protein in the nucleus and cytosol was demonstrated. By converting free IAA (active form) to conjugated IAA (inactive form), IAAS plays a crucial regulatory role in auxin signaling. Transient silencing of IAAS in N. benthamiana plants reduced the PVY-mediated symptom induction and virus accumulation. Conversely, overexpression of IAAS enhanced symptom induction and virus accumulation in infected plants. In addition, the expression of auxin-responsive genes was found to be downregulated during PVY infection. Our findings demonstrate that PVY NIa-pro protein potentially promotes disease development via modulating auxin homeostasis.

OsIPK2, a Rice Inositol Polyphosphate Kinase Gene, Is Involved in Phosphate Homeostasis and Root Development

Phosphorus (P) is a growth-limiting nutrient for plants, which is taken up by root tissue from the environment as inorganic phosphate (Pi). To maintain an appropriate status of cellular Pi, plants have developed sophisticated strategies to sense the Pi level and modulate their root system architecture (RSA) under the ever-changing growth conditions. However, the molecular basis underlying the mechanism remains elusive. Inositol polyphosphate kinase (IPK2) is a key enzyme in the inositol phosphate metabolism pathway, which catalyzes the phosphorylation of IP3 into IP5 by consuming ATP. In this study, the functions of a rice inositol polyphosphate kinase gene (OsIPK2) in plant Pi homeostasis and thus physiological response to Pi signal were characterized. As a biosynthetic gene for phytic acid in rice, overexpression of OsIPK2 led to distinct changes in inositol polyphosphate profiles and an excessive accumulation of Pi levels in transgenic rice under Pi-sufficient conditions. The inhibitory effects of OsIPK2 on root growth were alleviated by Pi-deficient treatment compared with wild-type plants, suggesting the involvement of OsIPK2 in the Pi-regulated reconstruction of RSA. In OsIPK2-overexpressing plants, the altered acid phosphatase (APase) activities and misregulation of Pi-starvation-induced (PSI) genes were observed in roots under different Pi supply conditions. Notably, the expression of OsIPK2 also altered the Pi homeostasis and RSA in transgenic Arabidopsis. Taken together, our findings demonstrate that OsIPK2 plays an important role in Pi homeostasis and RSA adjustment in response to different environmental Pi levels in plants.

Canonical and Alternative Auxin Signaling Systems in Mono-, Di-, and Tetraploid Potatoes

It has long been known that the phytohormone auxin plays a promoting role in tuber formation and stress tolerance in potatoes. Our study aimed to identify and characterize the complete sets of auxin-related genes that presumably constitute the entire auxin signaling system in potato (Solanum tuberosum L.). The corresponding genes were retrieved from sequenced genomes of the doubled monoploid S. tuberosum DM1-3-516-R44 (DM) of the Phureja group, the heterozygous diploid line RH89-039-16 (RH), and the autotetraploid cultivar Otava. Both canonical and noncanonical auxin signaling pathways were considered. Phylogenetic and domain analyses of deduced proteins were supplemented by expression profiling and 3D molecular modeling. The canonical and ABP1-mediated pathways of auxin signaling appeared to be well conserved. The total number of potato genes/proteins presumably involved in canonical auxin signaling is 46 and 108 in monoploid DM and tetraploid Otava, respectively. Among the studied potatoes, spectra of expressed genes obviously associated with auxin signaling were partly cultivar-specific and quite different from analogous spectrum in Arabidopsis. Most of the noncanonical pathways found in Arabidopsis appeared to have low probability in potato. This was equally true for all cultivars used irrespective of their ploidy. Thus, some important features of the (noncanonical) auxin signaling pathways may be variable and species-specific.