Auxin homeostasis: the DAO of catabolism

OsMYB14, an R2R3-MYB Transcription Factor, Regulates Plant Height through the Control of Hormone Metabolism in Rice

Plant growth must be regulated throughout the plant life cycle. The MYB TF family is one of the largest TF families and is involved in metabolism, lignin biosynthesis and developmental processes. Here, we showed that OsMYB14, a rice R2R3-MYB TF, was expressed in leaves and roots, especially in rice culm and panicles, and that it localized to the nucleus. Overexpression of OsMYB14 (OsMYB14-ox) in rice resulted in a 30% reduction in plant height compared to that of the wild type (WT), while the height of the osmyb14-ko mutant generated using the CRISPR/Cas9 system was not significantly different. Microscopic observations of the first internode revealed that the cell size did not differ significantly among the lines. RNA-seq analysis revealed that genes associated with plant development, regulation, lipid metabolism, carbohydrate metabolism, and gibberellin and auxin metabolic processes were downregulated in the OsMYB14-ox line. Hormone quantitation revealed that inactive GA19 accumulated in OsMYB14-ox but not in the WT or knockout plants, suggesting that GA20 generation was repressed. IAA and IAA-Asp accumulated in OsMYB14-ox and osmyb14-ko, respectively. Indeed, real-time PCR analysis revealed that the expression of OsGA20ox1, encoding Gibberellin20 oxidase 1, and OsGH3-2, encoding IAA-amido synthetase, was downregulated in OsMYB14-ox and upregulated in osmyb14-ko. A protein binding microarray (PBM) revealed the presence of a consensus DNA-binding sequence, the ACCTACC-like motif, in the promoters of the OsGA20ox1 and GA20ox2 genes. These results suggest that OsMYB14 may act as a negative regulator of biological processes affecting plant height in rice by regulating GA biosynthesis and auxin metabolism.

Integrated analysis of the transcriptome and metabolome reveals the molecular mechanism regulating cotton boll abscission under low light intensity

BACKGROUND

Cotton boll shedding is one of the main factors adversely affecting the cotton yield. During the cotton plant growth period, low light conditions can cause cotton bolls to fall off prematurely. In this study, we clarified the regulatory effects of low light intensity on cotton boll abscission by comprehensively analyzing the transcriptome and metabolome.

RESULTS

When the fruiting branch leaves were shaded after pollination, all of the cotton bolls fell off within 5 days. Additionally, H2O2 accumulated during the formation of the abscission zone. Moreover, 10,172 differentially expressed genes (DEGs) and 81 differentially accumulated metabolites (DAMs) were identified. A KEGG pathway enrichment analysis revealed that the identified DEGs and DAMs were associated with plant hormone signal transduction and flavonoid biosynthesis pathways. The results of the transcriptome analysis suggested that the expression of ethylene (ETH) and abscisic acid (ABA) signaling-related genes was induced, which was in contrast to the decrease in the expression of most of the IAA signaling-related genes. A combined transcriptomics and metabolomics analysis revealed that flavonoids may help regulate plant organ abscission. A weighted gene co-expression network analysis detected two gene modules significantly related to abscission. The genes in these modules were mainly related to exosome, flavonoid biosynthesis, ubiquitin-mediated proteolysis, plant hormone signal transduction, photosynthesis, and cytoskeleton proteins. Furthermore, TIP1;1, UGT71C4, KMD3, TRFL6, REV, and FRA1 were identified as the hub genes in these two modules.

CONCLUSIONS

In this study, we elucidated the mechanisms underlying cotton boll abscission induced by shading on the basis of comprehensive transcriptomics and metabolomics analyses of the boll abscission process. The study findings have clarified the molecular basis of cotton boll abscission under low light intensity, and suggested that H2O2, phytohormone, and flavonoid have the potential to affect the shedding process of cotton bolls under low light stress.

Gibberellic Acid Inhibits Dendrobium nobile-Piriformospora Symbiosis by Regulating the Expression of Cell Wall Metabolism Genes

Orchid seeds lack endosperms and depend on mycorrhizal fungi for germination and nutrition acquisition under natural conditions. Piriformospora indica is a mycorrhizal fungus that promotes seed germination and seedling development in epiphytic orchids, such as Dendrobium nobile. To understand the impact of P. indica on D. nobile seed germination, we examined endogenous hormone levels by using liquid chromatography-mass spectrometry. We performed transcriptomic analysis of D. nobile protocorm at two developmental stages under asymbiotic germination (AG) and symbiotic germination (SG) conditions. The result showed that the level of endogenous IAA in the SG protocorm treatments was significantly higher than that in the AG protocorm treatments. Meanwhile, GA3 was only detected in the SG protocorm stages. IAA and GA synthesis and signaling genes were upregulated in the SG protocorm stages. Exogenous GA3 application inhibited fungal colonization inside the protocorm, and a GA biosynthesis inhibitor (PAC) promoted fungal colonization. Furthermore, we found that PAC prevented fungal hyphae collapse and degeneration in the protocorm, and differentially expressed genes related to cell wall metabolism were identified between the SG and AG protocorm stages. Exogenous GA3 upregulated SRC2 and LRX4 expression, leading to decreased fungal colonization. Meanwhile, GA inhibitors upregulated EXP6, EXB16, and EXP10-2 expression, leading to increased fungal colonization. Our findings suggest that GA regulates the expression of cell wall metabolism genes in D. nobile, thereby inhibiting the establishment of mycorrhizal symbiosis.

The YABBY gene SHATTERING1 controls activation rather than patterning of the abscission zone in Setaria viridis

Abscission is predetermined in specialized cell layers called the abscission zone (AZ) and activated by developmental or environmental signals. In the grass family, most identified AZ genes regulate AZ anatomy, which differs among lineages. A YABBY transcription factor, SHATTERING1 (SH1), is a domestication gene regulating abscission in multiple cereals, including rice and Setaria. In rice, SH1 inhibits lignification specifically in the AZ. However, the AZ of Setaria is nonlignified throughout, raising the question of how SH1 functions in species without lignification. Crispr-Cas9 knockout mutants of SH1 were generated in Setaria viridis and characterized with histology, cell wall and auxin immunofluorescence, transmission electron microscopy, hormonal treatment and RNA-Seq analysis. The sh1 mutant lacks shattering, as expected. No differences in cell anatomy or cell wall components including lignin were observed between sh1 and the wild-type (WT) until abscission occurs. Chloroplasts degenerated in the AZ of WT before abscission, but degeneration was suppressed by auxin treatment. Auxin distribution and expression of auxin-related genes differed between WT and sh1, with the signal of an antibody to auxin detected in the sh1 chloroplast. SH1 in Setaria is required for activation of abscission through auxin signaling, which is not reported in other grass species.

Transcriptome analysis reveals differentially expressed genes involved in somatic embryogenesis and podophyllotoxin biosynthesis of Sinopodophyllum hexandrum (Royle) T. S. Ying

Sinopodophyllum hexandrum (Royle) T. S. Ying, an important source of podophyllotoxin (PTOX), has become a rare and endangered plant because of over-harvesting. Somatic embryogenesis (SE) is the main way of seedling rapid propagation and germplasm enhancement, but the regeneration of S. hexandrum has not been well established, and the PTOX biosynthesis abilities at different SE stages remain unclear. Therefore, it is extremely important to elucidate the SE mechanism of S. hexandrum and clarify the biosynthesis variation of PTOX. In this study, the transcriptomes of S. hexandrum at different SE stages were sequenced, the contents of PTOX and 4'-demethylepipodophyllotoxin were assayed, and the transcript expression patterns were validated by qRT-PCR. The results revealed that plant hormone (such as auxins, abscisic acid, zeatin, and gibberellins) related pathways were significantly enriched among different SE stages, indicating these plant hormones play important roles in SE of S. hexandrum; the expression levels of a series of PTOX biosynthesis related genes as well as PTOX and 4'-demethylepipodophyllotoxin contents were much higher in embryogenic callus stage than in the other stages, suggesting embryogenic callus stage has the best PTOX biosynthesis ability among different SE stages. This study will contribute to germplasm conservation and fast propagation of S. hexandrum, and facilitate the production of PTOX.

Dopamine Inhibits Arabidopsis Growth through Increased Oxidative Stress and Auxin Activity

Like some bacterial species and all animals, plants synthesize dopamine and react to its exogenous applications. Despite dopamine’s widespread presence and activity in plants, its role in plant physiology is still poorly understood. Using targeted experimentation informed by the transcriptomic response to dopamine exposure, we identify three major effects of dopamine. First, we show that dopamine causes hypersensitivity to auxin indole-3-acetic acid by enhancing auxin activity. Second, we show that dopamine increases oxidative stress, which can be mitigated with glutathione. Third, we find that dopamine downregulates iron uptake mechanisms, leading to a decreased iron content—a response possibly aimed at reducing DA-induced oxidative stress. Finally, we show that dopamine-induced auxin sensitivity is downstream of glutathione biosynthesis, indicating that the auxin response is likely a consequence of DA-induced oxidative stress. Collectively, our results show that exogenous dopamine increases oxidative stress, which inhibits growth both directly and indirectly by promoting glutathione-biosynthesis-dependent auxin hypersensitivity.

ABA-responsive AREB1/ABI3-1/ABI5 cascade regulates IAA oxidase gene SlDAO2 to inhibit hypocotyl elongation in tomato

Hypocotyl elongation is dramatically influenced by environmental factors and phytohormones. Indole-3-acetic acid (IAA) plays a prominent role in hypocotyl elongation, whereas abscisic acid (ABA) is regarded as an inhibitor through repressing IAA synthesis and signalling. However, the regulatory role of ABA in local IAA deactivation remains largely uncharacterized. In this study, we confirmed the antagonistic interplay of ABA and IAA during the hypocotyl elongation of tomato (Solanum lycopersicum) seedlings. We identified an IAA oxidase enzyme DIOXYGENASE FOR AUXIN OXIDATION2 (SlDAO2), and its expression was induced by both external and internal ABA signals in tomato hypocotyls. Moreover, the overexpression of SlDAO2 led to a reduced sensitivity to IAA, and the knockout of SlDAO2 alleviated the inhibitory effect of ABA on hypocotyl elongation. Furthermore, an ABA-responsive regulatory SlAREB1/SlABI3-1/SlABI5 cascade was identified to act upstream of SlDAO2 and to precisely control its expression. SlAREB1 directly bound to the ABRE present in the SlDAO2 promoter to activate SlDAO2 expression, and SlABI3-1 enhanced while SlABI5 inhibited the activation ability of SlAREB1 by directly interacting with SlAREB1. Our findings revealed that ABA might induce local IAA oxidation and deactivation via SlDAO2 to modulate IAA homoeostasis and thereby repress hypocotyl elongation in tomato.

High-throughput interspecies profiling of acidic plant hormones using miniaturised sample processing

BACKGROUND

Acidic phytohormones are small molecules controlling many physiological functions in plants. A comprehensive picture of their profiles including the active forms, precursors and metabolites provides an important insight into ongoing physiological processes and is essential for many biological studies performed on plants.

RESULTS

A high-throughput sample preparation method for liquid chromatography-tandem mass spectrometry determination of 25 acidic phytohormones classed as auxins, jasmonates, abscisates and salicylic acid was optimised. The method uses a small amount of plant tissue (less than 10 mg fresh weight) and acidic extraction in 1 mol/L formic acid in 10% aqueous methanol followed by miniaturised purification on reverse phase sorbent accommodated in pipette tips organised in a 3D printed 96-place interface, capable of processing 192 samples in one run. The method was evaluated in terms of process efficiency, recovery and matrix effects as well as establishing validation parameters such as accuracy and precision. The applicability of the method in relation to the amounts of sample collected from distantly related plant species was evaluated and the results for phytohormone profiles are discussed in the context of literature reports.

CONCLUSION

The method developed enables high-throughput profiling of acidic phytohormones with minute amounts of plant material, and it is suitable for large scale interspecies studies.

Expression analysis of PIN family genes in Chinese hickory reveals their potential roles during grafting and salt stress

Grafting is an effective way to improve Chinese hickory while salt stress has caused great damage to the Chinese hickory industry. Grafting and salt stress have been regarded as the main abiotic stress types for Chinese hickory. However, how Chinese hickory responds to grafting and salt stress is less studied. Auxin has been proved to play an essential role in the stress response through its re-distribution regulation mediated by polar auxin transporters, including PIN-formed (PIN) proteins. In this study, the PIN gene family in Chinese hickory (CcPINs) was identified and structurally characterized for the first time. The expression profiles of the genes in response to grafting and salt stress were determined. A total of 11 CcPINs with the open reading frames (ORFs) of 1,026-1,983 bp were identified. Transient transformation in tobacco leaves demonstrated that CcPIN1a, CcPIN3, and CcPIN4 were localized in the plasma membrane. There were varying phylogenetic relationships between CcPINs and homologous genes in different species, but the closest relationships were with those in Carya illinoinensis and Juglans regia. Conserved N- and C-terminal transmembrane regions as well as sites controlling the functions of CcPINs were detected in CcPINs. Five types of cis-acting elements, including hormone- and stress-responsive elements, were detected on the promoters of CcPINs. CcPINs exhibited different expression profiles in different tissues, indicating their varied roles during growth and development. The 11 CcPINs responded differently to grafting and salt stress treatment. CcPIN1a might be involved in the regulation of the grafting process, while CcPIN1a and CcPIN8a were related to the regulation of salt stress in Chinese hickory. Our results will lay the foundation for understanding the potential regulatory functions of CcPIN genes during grafting and under salt stress treatment in Chinese hickory.

Fourteen Stations of Auxin

Auxin has always been at the forefront of research in plant physiology and development. Since the earliest contemplations by Julius von Sachs and Charles Darwin, more than a century-long struggle has been waged to understand its function. This largely reflects the failures, successes, and inevitable progress in the entire field of plant signaling and development. Here I present 14 stations on our long and sometimes mystical journey to understand auxin. These highlights were selected to give a flavor of the field and to show the scope and limits of our current knowledge. A special focus is put on features that make auxin unique among phytohormones, such as its dynamic, directional transport network, which integrates external and internal signals, including self-organizing feedback. Accented are persistent mysteries and controversies. The unexpected discoveries related to rapid auxin responses and growth regulation recently disturbed our contentment regarding understanding of the auxin signaling mechanism. These new revelations, along with advances in technology, usher us into a new, exciting era in auxin research.

Beyond Photoprotection: The Multifarious Roles of Flavonoids in Plant Terrestrialization

Plants evolved an impressive arsenal of multifunctional specialized metabolites to cope with the novel environmental pressures imposed by the terrestrial habitat when moving from water. Here we examine the multifarious roles of flavonoids in plant terrestrialization. We reason on the environmental drivers, other than the increase in UV-B radiation, that were mostly responsible for the rise of flavonoid metabolism and how flavonoids helped plants in land conquest. We are reasonably based on a nutrient-deficiency hypothesis for the replacement of mycosporine-like amino acids, typical of streptophytic algae, with the flavonoid metabolism during the water-to-land transition. We suggest that flavonoids modulated auxin transport and signaling and promoted the symbiosis between plants and fungi (e.g., arbuscular mycorrhizal, AM), a central event for the conquest of land by plants. AM improved the ability of early plants to take up nutrients and water from highly impoverished soils. We offer evidence that flavonoids equipped early land plants with highly versatile “defense compounds”, essential for the new set of abiotic and biotic stressors imposed by the terrestrial environment. We conclude that flavonoids have been multifunctional since the appearance of plants on land, not only acting as UV filters but especially improving both nutrient acquisition and biotic stress defense.

Exogenous GA3 promotes flowering in Paphiopedilum callosum (Orchidaceae) through bolting and lateral flower development regulation

Paphiopedilum orchids have a high ornamental value, and their flower abundance and timing are both key horticultural traits regulated by phytohormones. All one-flowered Paphiopedilum have additional lateral buds in the apical bract that fail to develop. In this study, an exogenous gibberellin (GA₃) application promoted flowering of Pathiopedilum callosum by inducing its early bolting instead of the floral transition of dominant flowers. Applying GA₃ effectively promoted lateral flower differentiation, resulting in a two-flowered inflorescence. GA-promoted lateral flower formation involved GA interacting with indole-3-acetic acid (IAA) and cytokinins (CTKs), given the decreased CTK content and downregulated expression of CTK synthesis genes, the increased IAA content and downregulated expression of IAA degradation, and the upregulated expression of transport genes. Further, GA acted via PcDELLA, PcTCP15, and PcXTH9 expressed in stage 5 to promote bolting, and via expression of PcAP3, PcPI, and PcSEP to promote flowering. This study provides insight into mechanisms regulating flower development of P. callosum.

Structural and biochemical basis for the substrate specificity of Pad-1, an indole-3-pyruvic acid aminotransferase in auxin homeostasis

Phytohormone indole-3-acetic acid (IAA) plays a vital role in regulating plant growth and development. Tryptophan-dependent IAA biosynthesis participates in IAA homeostasis by producing IAA via two sequential reactions, which involve a conversion of tryptophan to indole-3-pyruvic acid (IPyA) by tryptophan aminotransferase (TAA1) followed by the irreversible formation of IAA in the second reaction. Pad-1 from Solanaceae plants regulates IAA levels by catalyzing a reverse reaction of the first step of IAA biosynthesis. Pad-1 is a pyridoxal phosphate (PLP)-dependent aminotransferase, with IPyA as the amino acceptor and l-glutamine as the amino donor. Currently, the structural and functional basis for the substrate specificity of Pad-1 remains poorly understood. In this study, we carried out structural and kinetic analyses of Pad-1 from Solanum melongena. Pad-1 is a homodimeric enzyme, with coenzyme PLP present between a central large α/β domain and a protruding small domain. The active site of Pad-1 includes a vacancy near the phosphate group (P-side) and the 3'-O (O-side) of PLP. These features are distinct from those of TAA1, which is homologous in an overall structure with Pad-1 but includes only the P-side region in the active site. Kinetic analysis suggests that P-side residues constitute a binding pocket for l-glutamine, and O-side residues of Phe124 and Ile350 are involved in the binding of IPyA. These studies illuminate distinct differences in the active site between Pad-1 and TAA1, and provide structural and functional insights into the substrate specificity of Pad-1.

Spatiotemporal auxin distribution in Arabidopsis tissues is regulated by anabolic and catabolic reactions under long-term ammonium stress

BACKGROUND

The plant hormone auxin is a major coordinator of plant growth and development in response to diverse environmental signals, including nutritional conditions. Sole ammonium (NH₄⁺) nutrition is one of the unique growth-suppressing conditions for plants. Therefore, the quest to understand NH₄⁺-mediated developmental defects led us to analyze auxin metabolism.

RESULTS

Indole-3-acetic acid (IAA), the most predominant natural auxin, accumulates in the leaves and roots of mature Arabidopsis thaliana plants grown on NH₄⁺, but not in the root tips. We found changes at the expressional level in reactions leading to IAA biosynthesis and deactivation in different tissues. Finally, NH₄⁺ nutrition would facilitate the formation of inactive oxidized IAA as the final product.

CONCLUSIONS

NH₄⁺-mediated accelerated auxin turnover rates implicate transient and local IAA peaks. A noticeable auxin pattern in tissues correlates with the developmental adaptations of the short and highly branched root system of NH₄⁺-grown plants. Therefore, the spatiotemporal distribution of auxin might be a root-shaping signal specific to adjust to NH₄⁺-stress conditions.

The main oxidative inactivation pathway of the plant hormone auxin

Inactivation of the phytohormone auxin plays important roles in plant development, and several enzymes have been implicated in auxin inactivation. In this study, we show that the predominant natural auxin, indole-3-acetic acid (IAA), is mainly inactivated via the GH3-ILR1-DAO pathway. IAA is first converted to IAA-amino acid conjugates by GH3 IAA-amidosynthetases. The IAA-amino acid conjugates IAA-aspartate (IAA-Asp) and IAA-glutamate (IAA-Glu) are storage forms of IAA and can be converted back to IAA by ILR1/ILL amidohydrolases. We further show that DAO1 dioxygenase irreversibly oxidizes IAA-Asp and IAA-Glu into 2-oxindole-3-acetic acid-aspartate (oxIAA-Asp) and oxIAA-Glu, which are subsequently hydrolyzed by ILR1 to release inactive oxIAA. This work established a complete pathway for the oxidative inactivation of auxin and defines the roles played by auxin homeostasis in plant development.

Characterization of phytohormone and transcriptome profiles during protocorm-like bodies development of Paphiopedilum

BACKGROUND

Paphiopedilum, commonly known as slipper orchid, is an important genus of orchid family with prominent horticultural value. Compared with conventional methods such as tillers and in vitro shoots multiplication, induction and regeneration of protocorm-like bodies (PLBs) is an effective micropropagation method in Paphiopedilum. The PLB initiation efficiency varies among species, hybrids and varieties, which leads to only a few Paphiopedilum species can be large-scale propagated through PLBs. So far, little is known about the mechanisms behind the initiation and maintenance of PLB in Paphiopedilum.

RESULTS

A protocol to induce PLB development from seed-derived protocorms of Paphiopedilum SCBG Huihuang90 (P. SCBG Prince × P. SCBG Miracle) was established. The morphological characterization of four key PLB developmental stages showed that significant polarity and cell size gradients were observed within each PLB. The endogenous hormone level was evaluated. The increase in the levels of indoleacetic acid (IAA) and jasmonic acid (JA) accompanying the PLBs differentiation, suggesting auxin and JA levels were correlated with PLB development. Gibberellic acid (GA) decreased to a very low level, indicated that GA inactivation may be necessary for shoot apical meristem (SAM) development. Comparative transcriptomic profiles of four different developmental stages of P. SCBG Huihuang90 PLBs explore key genes involved in PLB development. The numbers of differentially expressed genes (DEGs) in three pairwise comparisons (A vs B, B vs C, C vs D) were 1455, 349, and 3529, respectively. KEGG enrichment analysis revealed that DEGs were implicated in secondary metabolite metabolism and photosynthesis. DEGs related to hormone metabolism and signaling, somatic embryogenesis, shoot development and photosynthesis were discussed in detail.

CONCLUSION

This study is the first report on PLB development in Paphiopedilum using transcriptome sequencing, which provides useful information to understand the mechanisms of PLB development.

Characterization of embryo and protocorm development of Paphiopedilum spicerianum

Paphiopedilum spicerianum (P. spicerianum) is a rare orchid species with high ornamental value. Asymbiotic germination is the most efficient propagation method for conservation and commercial purposes because clonal propagation is very difficult and the separation of native species of Paphiopedilum through aseptic seeding is uncommon owing to their conservatism. However, a high protocorm developmental arresting rate during the asymbiotic germination is the major obstacle for seedling establishment. The fundamental understanding of embryo and protocorm developmental mechanisms will guide the development of an effective propagation method. The morphological and physiological characterization of the key developmental process of embryos and protocorms shows that the mature seeds of P. spicerianum consist of a spherical embryo without an endosperm. Seed coats become heavily lignified once the embryo is mature. Embryo cell size is relatively uniform, and significant structure polarity and cell size gradients occur at the early protocorm stage. The high level of auxin and cytokinin accumulation at the early stage of embryo development and protocorm stage may help to facilitate cell division. The transcriptome profiles of protocorms at three different developmental stages were compared to explore the regulatory mechanism of protocorm development. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that differentially expressed genes were implicated in secondary metabolite metabolism, plant hormone signal transduction and photosynthesis. The temporal expression patterns of candidate genes related to embryo and shoot development were analyzed to reveal their roles in protocorm development: in the early stage of protocorm development, embryonic development related genes such as SERKs and BBM1 were active, while in the late stage of protocorm, shoot apical meristem related genes such as WOX8, CLAVATA2, CUC2, and SCR were active.

Genome-Wide Analysis, Modeling, and Identification of Amino Acid Binding Motifs Suggest the Involvement of GH3 Genes during Somatic Embryogenesis of Coffea canephora

Auxin plays a central role in growth and plant development. To maintain auxin homeostasis, biological processes such as biosynthesis, transport, degradation, and reversible conjugation are essential. The Gretchen Hagen 3 (GH3) family genes codify for the enzymes that esterify indole-3-acetic acid (IAA) to various amino acids, which is a key process in the induction of somatic embryogenesis (SE). The GH3 family is one of the principal families of early response to auxin genes, exhibiting IAA-amido synthetase activity to maintain optimal levels of free auxin in the cell. In this study, we carried out a systematic identification of the GH3 gene family in the genome of Coffea canephora, determining a total of 18 CcGH3 genes. Analysis of the genetic structures and phylogenetic relationships of CcGH3 genes with GH3 genes from other plant species revealed that they could be clustered in two major categories with groups 1 and 2 of the GH3 family of Arabidopsis. We analyzed the transcriptome expression profiles of the 18 CcGH3 genes using RNA-Seq analysis-based data and qRT-PCR during the different points of somatic embryogenesis induction. Furthermore, the endogenous quantification of free and conjugated indole-3-acetic acid (IAA) suggests that the various members of the CcGH3 genes play a crucial role during the embryogenic process of C. canephora. Three-dimensional modeling of the selected CcGH3 proteins showed that they consist of two domains: an extensive N-terminal domain and a smaller C-terminal domain. All proteins analyzed in the present study shared a unique conserved structural topology. Additionally, we identified conserved regions that could function to bind nucleotides and specific amino acids for the conjugation of IAA during SE in C. canephora. These results provide a better understanding of the C. canephora GH3 gene family for further exploration and possible genetic manipulation.

DIOXYGENASE FOR AUXIN OXIDATION 1 catalyzes the oxidation of IAA amino acid conjugates

Together with auxin transport, auxin metabolism is a key determinant of auxin signaling output by plant cells. Enzymatic machinery involved in auxin metabolism is subject to regulation based on numerous inputs, including the concentration of auxin itself. Therefore, experiments characterizing altered auxin availability and subsequent changes in auxin metabolism could elucidate the function and regulatory role of individual elements in the auxin metabolic machinery. Here, we studied auxin metabolism in auxin-dependent tobacco BY-2 cells. We revealed that the concentration of N-(2-oxindole-3-acetyl)-l-aspartic acid (oxIAA-Asp), the most abundant auxin metabolite produced in the control culture, dramatically decreased in auxin-starved BY-2 cells. Analysis of the transcriptome and proteome in auxin-starved cells uncovered significant downregulation of all tobacco (Nicotiana tabacum) homologs of Arabidopsis (Arabidopsis thaliana) DIOXYGENASE FOR AUXIN OXIDATION 1 (DAO1), at both transcript and protein levels. Auxin metabolism profiling in BY-2 mutants carrying either siRNA-silenced or CRISPR-Cas9-mutated NtDAO1, as well as in dao1-1 Arabidopsis plants, showed not only the expected lower levels of oxIAA, but also significantly lower abundance of oxIAA-Asp. Finally, ability of DAO1 to oxidize IAA-Asp was confirmed by an enzyme assay in AtDAO1-producing bacterial culture. Our results thus represent direct evidence of DAO1 activity on IAA amino acid conjugates.

The role of quercetin in plants

Flavonoids are a special category of hydroxylated phenolic compounds having an aromatic ring structure. Quercetin is aspecial subclass of flavonoid. It is a bioactive natural compound built upon the flavon structure nC6(ring A)-C3(ring C)-C6(ring B). Quercetin facilitates several plant physiological processes, such as seed germination, pollen growth, antioxidant machinery, and photosynthesis, as well as induces proper plant growth and development. Quercetin is a powerful antioxidant, so it potently provides plant tolerance against several biotic and abiotic stresses. This review highlights quercetin's role in increasing several physiological and biochemical processes under stress and non-stress environments. Additionally, this review briefly assesses quercetin's role in mitigating biotic and abiotic stresses (e.g., salt, heavy metal, and UV stress). The biosynthesis of flavonoids, their signaling pathways, and quercetin's role in plant signaling are also discussed.

Production of Indole Auxins by Enterobacter sp. Strain P-36 under Submerged Conditions

Bioactive compounds produced by plant growth-promoting bacteria through a fermentation process can be valuable for developing innovative second-generation plant biostimulants. The purpose of this study is to investigate the biotechnological potential of Enterobacter on the production of auxin—a hormone with multiple roles in plant growth and development. The experiments were carried in Erlenmeyer flasks and a 2-L fermenter under batch operating mode. The auxin production by Enterobacter sp. strain P-36 can be doubled by replacing casein with vegetable peptone in the culture medium. Cultivation of strain P36 in the benchtop fermenter indicates that by increasing the inoculum size 2-fold, it is possible to reduce the fermentation time from 72 (shake flask cultivation) to 24 h (bioreactor cultivation) and increase the auxin volumetric productivity from 6.4 to 17.2 mg [IAAequ]/L/h. Finally, an efficient storage procedure to preserve the bacterial auxin was developed. It is noteworthy that by sterilizing the clarified fermentation broth by filtration and storing the filtrated samples at +4 °C, the level of auxin remains unchanged for at least three months.

Altered Root Growth, Auxin Metabolism and Distribution in Arabidopsis thaliana Exposed to Salt and Osmotic Stress

Salt and osmotic stress are the main abiotic stress factors affecting plant root growth and architecture. We investigated the effect of salt (100 mM NaCl) and osmotic (200 mM mannitol) stress on the auxin metabolome by UHPLC-MS/MS, auxin distribution by confocal microscopy, and transcript levels of selected genes by qRT-PCR in Arabidopsis thaliana ecotype Columbia-0 (Col-0) and DR5rev::GFP (DR5) line. During long-term stress (13 days), a stability of the auxin metabolome and a tendency to increase indole-3-acetic acid (IAA) were observed, especially during salt stress. Short-term stress (3 h) caused significant changes in the auxin metabolome, especially NaCl treatment resulted in a significant reduction of IAA. The data derived from auxin profiling were consistent with gene expressions showing the most striking changes in the transcripts of YUC, GH3, and UGT transcripts, suggesting disruption of auxin biosynthesis, but especially in the processes of amide and ester conjugation. These data were consistent with the auxin distribution observed in the DR5 line. Moreover, NaCl treatment caused a redistribution of auxin signals from the quiescent center and the inner layers of the root cap to the epidermal and cortical cells of the root elongation zone. The distribution of PIN proteins was also disrupted by salt stress; in particular, PIN2 was suppressed, even after 5 min of treatment. Based on our results, the DR5 line was more sensitive to the applied stresses than Col-0, although both lines showed similar trends in root morphology, as well as transcriptome and metabolome parameters under stress conditions.

Chemical Biology in Auxin Research

Molecular genetic and structural studies have revealed the mechanisms of fundamental components of key auxin regulatory pathways consisting of auxin biosynthesis, transport, and signaling. Chemical biology methods applied in auxin research have been greatly expanded through the understanding of auxin regulatory pathways. Many small-molecule modulators of auxin metabolism, transport, and signaling have been generated on the basis of the outcomes of genetic and structural studies on auxin regulatory pathways. These chemical modulators are now widely used as essential tools for dissecting auxin biology in diverse plants. This review covers the structures, primary targets, modes of action, and applications of chemical tools in auxin biosynthesis, transport, and signaling.

Auxin metabolic network regulates the plant response to metalloids stress

Metalloids are among the major pollutants posing a risk to the environment and global food security. Plant roots uptake these toxic metalloids from the soil along with other essential minerals. Plants respond to metalloid stress by regulating the distribution and levels of various endogenous phytohormones. Recent research showed that auxin is instrumental in mediating resilience to metalloid-induced stress in plants. Exogenous supplementation of the auxin or plant growth-promoting micro-organisms (PGPMs) alleviates metalloid uptake, localization, and accumulation in the plant tissues, thereby improving plant growth under metalloid stress. Moreover, auxin triggers various biological responses such as the production of enzymatic and non-enzymatic antioxidants to combat nitro-oxidative stress induced by the metalloids. However, an in-depth understanding of the auxin stimulated molecular and physiological responses to the metalloid toxicity needs to be investigated in future studies. The current review attempts to provide an update on the recent advances and the current state-of-the-art associated with auxin and metalloid interaction, which could be used as a start point to develop biotechnological tools and create an eco-friendly environment.

Quantitative analysis of auxin metabolites in lychee flowers

To investigate the modulation of endogenous indole-3-acetic acid (IAA) level by biosynthesis and inactivation during floral development, IAA and its metabolites were analyzed by LC-ESI/MS/MS in Lychee (Litchi chinensis Sonn.) flowers. In the bloomed flowers, the level of free IAA was higher in males than in females. In contrast, the total sum level of IAA metabolites was higher in females than in males, suggesting a higher biosynthetic activity of IAA in the females before the bloom. A detailed time-course analysis from the bud stage to the developing flower stage showed higher levels of IAA in females than males. The major metabolites were oxidized IAA in both sexes. The results suggest that IAA is involved in the maturation of female floral tissues in lychee, and oxidative metabolism plays an essential role in controlling the free IAA levels therein.

The apple gene responsible for columnar tree shape reduces the abundance of biologically active gibberellin

Ectopic expression of the apple 2-oxoglutarate-dependent dioxygenase (DOX, 2ODD) gene, designated MdDOX-Co, is thought to cause the columnar shape of apple trees. However, the mechanism underlying the formation of such a unique tree shape remains unclear. To solve this problem, we demonstrated that Arabidopsis thaliana overexpressing MdDOX-Co contained reduced levels of biologically active gibberellin (GA) compared with wild type. In summary: (i) with biochemical approaches, the gene product MdDOX-Co was shown to metabolize active GA A₄ (GA₄ ) to GA₅₈ (12-OH-GA₄ ) in vitro. MdDOX-Co also metabolized its precursors GA₁₂ and GA₉ to GA₁₁₁ (12-OH-GA₁₂ ) and GA₇₀ (12-OH-GA₉ ), respectively; (ii) Of the three 12-OH-GAs, GA₅₈ was still active physiologically, but not GA₇₀ or GA₁₁₁ ; (iii) Arabidopsis MdDOX-Co OE transformants converted exogenously applied deuterium-labeled (d₂ )-GA₁₂ to d₂ -GA₁₁₁ but not to d₂ -GA₅₈ , whereas transformants converted applied d₂ -GA₉ to d₂ -GA₅₈ ; (iv) GA₁₁₁ is converted poorly to GA₇₀ by GA 20-oxidases in vitro when GA₁₂ is efficiently metabolized to GA₉ ; (v) no GA₅₈ was detected endogenously in MdDOX-Co OE transformants. Overall, we conclude that 12-hydroxylation of GA₁₂ by MdDOX-Co prevents the biosynthesis of biologically active GAs in planta, resulting in columnar phenotypes.

Crystal structure of the indole-3-acetic acid-catabolizing enzyme DAO1 from Arabidopsis thaliana

Indole-3-acetic acid (IAA), the major form of the plant hormone auxin, regulates almost every aspect of plant growth and development. Therefore, auxin homeostasis is an essential process in plants. Different metabolic routes are involved in auxin homeostasis, but the catabolic pathway has remained elusive until recent studies identified DIOXYGENASE FOR AUXIN OXIDATION (DAO) from rice and Arabidopsis thaliana. DAO, a member of the 2-oxoglutarate/Fe(II)-dependent oxygenase (2ODO) family, constitutes a major enzyme for IAA catabolism. This enzyme catalyzes, with the cosubstrate 2-oxoglutarate, the conversion of IAA into 2-oxoindole-3-acetic acid, a functionally inactive oxidative product of IAA. Here, we report a crystal structure of the unliganded DAO1 from A. thaliana (AtDAO1) and its complex with 2-oxoglutarate. AtDAO1 is structurally homologous with members of the 2ODO family but exhibits unique features in the prime substrate IAA binding site. We provide structural analyses of a putative binding site for IAA, supporting possible structural determinants for the substrate specificity of AtDAO1 toward IAA.

Evolution of GA Metabolic Enzymes in Land Plants

Gibberellins (GAs) play key roles in various developmental processes in land plants. We studied the evolutionary trends of GA metabolic enzymes through a comprehensive homology search and phylogenetic analyses from bryophytes to angiosperms. Our analyses suggest that, in the process of evolution, plants were able to acquire GA metabolic enzymes in a stepwise manner and that the enzymes had rapidly diversified in angiosperms. As a good example of their rapid diversification, we focused on the GA-deactivating enzyme, GA 2-oxidase (GA2ox). Although the establishment of a GA system first occurred in lycophytes, its inactivation system mediated by GA2oxs was established at a much later time: the rise of gymnosperms and the rise of angiosperms through C19-GA2ox and C20-GA2ox development, respectively, as supported by the results of our direct examination of their enzymatic activities in vitro. Based on these comprehensive studies of GA metabolic enzymes, we discuss here that angiosperms rapidly developed a sophisticated system to delicately control the level of active GAs by increasing their copy numbers for their survival under different challenging environments.

YUCCA-Mediated Biosynthesis of the Auxin IAA Is Required during the Somatic Embryogenic Induction Process in Coffea canephora

Despite the existence of considerable research on somatic embryogenesis (SE), the molecular mechanism that regulates the biosynthesis of auxins during the SE induction process remains unknown. Indole-3-acetic acid (IAA) is an auxin that is synthesized in plants through five pathways. The biosynthetic pathway most frequently used in this synthesis is the conversion of tryptophan to indol-3-pyruvic acid (IPA) by tryptophan aminotransferase of Arabidopsis (TAA) followed by the conversion of IPA to IAA by enzymes encoded by YUCCA (YUC) genes of the flavin monooxygenase family; however, it is unclear whether YUC-mediated IAA biosynthesis is involved in SE induction. In this study, we report that the increase of IAA observed during SE pre-treatment (plants in MS medium supplemented with 1-naphthaleneacetic acid (NAA) 0.54 µM and kinetin (Kin) 2.32 µM for 14 days) was due to its de novo biosynthesis. By qRT-PCR, we demonstrated that YUC gene expression was consistent with the free IAA signal found in the explants during the induction of SE. In addition, the use of yucasin to inhibit the activity of YUC enzymes reduced the signal of free IAA in the leaf explants and dramatically decreased the induction of SE. The exogenous addition of IAA restored the SE process in explants treated with yucasin. Our findings suggest that the biosynthesis and localization of IAA play an essential role during the induction process of SE in Coffea canephora.

Auxin-mediated responses under salt stress: from developmental regulation to biotechnological applications

As sessile organisms, plants are exposed to multiple abiotic stresses commonly found in nature. To survive, plants have developed complex responses that involve genetic, epigenetic, cellular, and morphological modifications. Among different environmental cues, salt stress has emerged as a critical problem contributing to yield losses and marked reductions in crop production. Moreover, as the climate changes, it is expected that salt stress will have a significant impact on crop production in the agroindustry. On a mechanistic level, salt stress is known to be regulated by the crosstalk of many signaling molecules such as phytohormones, with auxin having been described as a key mediator of the process. Auxin plays an important role in plant developmental responses and stress, modulating a complex balance of biosynthesis, transport, and signaling that among other things, finely tune physiological changes in plant architecture and Na+ accumulation. In this review, we describe current knowledge on auxin's role in modulating the salt stress response. We also discuss recent and potential biotechnological approaches to tackling salt stress.

Conifers exhibit a characteristic inactivation of auxin to maintain tissue homeostasis

Dynamic regulation of the concentration of the natural auxin (IAA) is essential to coordinate most of the physiological and developmental processes and responses to environmental changes. Oxidation of IAA is a major pathway to control auxin concentrations in angiosperms and, along with IAA conjugation, to respond to perturbation of IAA homeostasis. However, these regulatory mechanisms remain poorly investigated in conifers. To reduce this knowledge gap, we investigated the different contributions of the IAA inactivation pathways in conifers. MS-based quantification of IAA metabolites under steady-state conditions and after perturbation was investigated to evaluate IAA homeostasis in conifers. Putative Picea abies GH3 genes (PaGH3) were identified based on a comprehensive phylogenetic analysis including angiosperms and basal land plants. Auxin-inducible PaGH3 genes were identified by expression analysis and their IAA-conjugating activity was explored. Compared to Arabidopsis, oxidative and conjugative pathways differentially contribute to reduce IAA concentrations in conifers. We demonstrated that the oxidation pathway plays a marginal role in controlling IAA homeostasis in spruce. By contrast, an excess of IAA rapidly activates GH3-mediated irreversible conjugation pathways. Taken together, these data indicate that a diversification of IAA inactivation mechanisms evolved specifically in conifers.

A common allosteric mechanism regulates homeostatic inactivation of auxin and gibberellin

Allosteric regulation is protein activation by effector binding at a site other than the active site. Here, we show via X-ray structural analysis of gibberellin 2-oxidase 3 (GA2ox3), and auxin dioxygenase (DAO), that such a mechanism maintains hormonal homeostasis in plants. Both enzymes form multimers by interacting via GA₄ and indole-3-acetic acid (IAA) at their binding interface. Via further functional analyses we reveal that multimerization of these enzymes gradually proceeds with increasing GA₄ and IAA concentrations; multimerized enzymes have higher specific activities than monomer forms, a system that should favour the maintenance of homeostasis for these phytohormones. Molecular dynamic analysis suggests a possible mechanism underlying increased GA2ox3 activity by multimerization-GA₄ in the interface of oligomerized GA2ox3s may be able to enter the active site with a low energy barrier. In summary, homeostatic systems for maintaining GA and IAA levels, based on a common allosteric mechanism, appear to have developed independently.

Phytohormone profiles are strongly altered during induction and symptom development of the physiological ripening disorder berry shrivel in grapevine

The process of grape berry ripening follows three phases with distinct metabolic processes and complex regulations via phytohormones. The physiological ripening disorder berry shrivel (BS) is characterized by reduced sugar accumulation, low anthocyanin contents, and high acidity in affected berries. The processes leading to BS induction are unknown, but recent transcriptional data on reduced expression of switch genes hint towards a disturbed ripening onset. Herein we investigated the phytohormone composition throughout grape berry ripening in healthy and BS berries in Vitis vinifera L. cultivar Blauer Zweigelt. Thereby we hypothesize that phytohormones are key players for BS induction and suppress the expression of switch genes at veraison. The presented metabolomics and RNAseq data describe two distinct phytohormone profiles in BS berries, differing between pre- and post-veraison with a clear ethylene precursor (aminocyclopropane-1-carboxylic acid, ACC) peak before veraison. Exogenous application of ACC led to BS symptoms, while ethephone application led to berry abscission. During post-veraison, we observed high ABA-glucose ester (ABA-GE) and low indole-3-acetate aspartate (IAA-Asp) and isopentenyladenine (iP) contents in BS berries and the transcriptional induction of several phytohormone pathways. The presented descriptive data provide valuable knowledge to further decipher the role of phytohormones in BS induction and BS symptom development.

The dynamic response of the Arabidopsis root metabolome to auxin and ethylene is not predicted by changes in the transcriptome

While the effects of phytohormones on plant gene expression have been well characterized, comparatively little is known about how hormones influence metabolite profiles. This study examined the effects of elevated auxin and ethylene on the metabolome of Arabidopsis roots using a high-resolution 24 h time course, conducted in parallel to time-matched transcriptomic analyses. Mass spectrometry using orthogonal UPLC separation strategies (reversed phase and HILIC) in both positive and negative ionization modes was used to maximize identification of metabolites with altered levels. The findings show that the root metabolome responds rapidly to hormone stimulus and that compounds belonging to the same class of metabolites exhibit similar changes. The responses were dominated by changes in phenylpropanoid, glucosinolate, and fatty acid metabolism, although the nature and timing of the response was unique for each hormone. These alterations in the metabolome were not directly predicted by the corresponding transcriptome data, suggesting that post-transcriptional events such as changes in enzyme activity and/or transport processes drove the observed changes in the metabolome. These findings underscore the need to better understand the biochemical mechanisms underlying the temporal reconfiguration of plant metabolism, especially in relation to the hormone-metabolome interface and its subsequent physiological and morphological effects.

The Roles of Auxin Biosynthesis YUCCA Gene Family in Plants

Auxin plays essential roles in plant normal growth and development. The auxin signaling pathway relies on the auxin gradient within tissues and cells, which is facilitated by both local auxin biosynthesis and polar auxin transport (PAT). The TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA)/YUCCA (YUC) pathway is the most important and well-characterized pathway that plants deploy to produce auxin. YUCs function as flavin-containing monooxygenases (FMO) catalyzing the rate-limiting irreversible oxidative decarboxylation of indole-3-pyruvate acid (IPyA) to form indole-3-acetic acid (IAA). The spatiotemporal dynamic expression of different YUC gene members finely tunes the local auxin biosynthesis in plants, which contributes to plant development as well as environmental responses. In this review, the recent advances in the identification, evolution, molecular structures, and functions in plant development and stress response regarding the YUC gene family are addressed.

Auxin protects Arabidopsis thaliana cell suspension cultures from programmed cell death induced by the cellulose biosynthesis inhibitors thaxtomin A and isoxaben

BACKGROUND

Thaxtomin A (TA) is a natural cellulose biosynthesis inhibitor (CBI) synthesized by the potato common scab-causing pathogen Streptomyces scabies. Inhibition of cellulose synthesis by TA compromises cell wall organization and integrity, leading to the induction of an atypical program of cell death (PCD). These processes may facilitate S. scabies entry into plant tissues. To study the mechanisms that regulate the induction of cell death in response to inhibition of cellulose synthesis, we used Arabidopsis thaliana cell suspension cultures treated with two structurally different CBIs, TA and the herbicide isoxaben (IXB).

RESULTS

The induction of cell death by TA and IXB was abrogated following pretreatment with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) and the natural auxin indole-3-acetic acid (IAA). The addition of auxin efflux inhibitors also inhibited the CBI-mediated induction of PCD. This effect may be due to intracellular accumulation of auxin. Auxin has a wide range of effects in plant cells, including a role in the control of cell wall composition and rigidity to facilitate cell elongation. Using Atomic Force Microscopy (AFM)-based force spectroscopy, we found that inhibition of cellulose synthesis by TA and IXB in suspension-cultured cells decreased cell wall stiffness to a level slightly different than that caused by auxin. However, the cell wall stiffness in cells pretreated with auxin prior to CBI treatment was equivalent to that of cells treated with auxin only.

CONCLUSIONS

Addition of auxin to Arabidopsis cell suspension cultures prevented the TA- and IXB-mediated induction of cell death. Cell survival was also stimulated by inhibition of polar auxin transport during CBI-treatment. Inhibition of cellulose synthesis perturbed cell wall mechanical properties of Arabidopsis cells. Auxin treatment alone or with CBI also decreased cell wall stiffness, showing that the mechanical properties of the cell wall perturbed by CBIs were not restored by auxin. However, since auxin's effects on the cell wall stiffness apparently overrode those induced by CBIs, we suggest that auxin may limit the impact of CBIs by restoring its own transport and/or by stabilizing the plasma membrane - cell wall - cytoskeleton continuum.

Eriodictyol can modulate cellular auxin gradients to efficiently promote in vitro cotton fibre development

BACKGROUND

Flavonoids have essential roles in flower pigmentation, fibre development and disease resistance in cotton. Previous studies show that accumulation of naringenin in developing cotton fibres significantly affects fibre growth. This study focused on determining the effects of the flavonoids naringenin, dihydrokaempferol, dihydroquerectin and eriodictyol on fibre development in an in vitro system.

RESULTS

20 μM eriodictyol treatment produced a maximum fibre growth, in terms of fibre length and total fibre units. To gain insight into the associated transcriptional regulatory networks, RNA-seq analysis was performed on eriodictyol-treated elongated fibres, and computational analysis of differentially expressed genes revealed that carbohydrate metabolism and phytohormone signaling pathways were differentially modulated. Eriodictyol treatment also promoted the biosynthesis of quercetin and dihydroquerectin in ovules and elongating fibres through enhanced expression of genes encoding chalcone isomerase, chalcone synthase and flavanone 3-hydroxylase. In addition, auxin biosynthesis and signaling pathway genes were differentially expressed in eriodictyol-driven in vitro fibre elongation. In absence of auxin, eriodictyol predominantly enhanced fibre growth when the localized auxin gradient was disrupted by the auxin transport inhibitor, triiodobenzoic acid.

CONCLUSION

Eriodictyol was found to significantly enhance fibre development through accumulating and maintaining the temporal auxin gradient in developing unicellular cotton fibres.

Auxins in potato: molecular aspects and emerging roles in tuber formation and stress resistance

The study of the effects of auxins on potato tuberization corresponds to one of the oldest experimental systems in plant biology, which has remained relevant for over 70 years. However, only recently, in the postgenomic era, the role of auxin in tuber formation and other vital processes in potatoes has begun to emerge. This review describes the main results obtained over the entire period of auxin-potato research, including the effects of exogenous auxin; the content and dynamics of endogenous auxins; the effects of manipulating endogenous auxin content; the molecular mechanisms of auxin signaling, transport and inactivation; the role and position of auxin among other tuberigenic factors; the effects of auxin on tuber dormancy; the prospects for auxin use in potato biotechnology. Special attention is paid to recent insights into auxin function in potato tuberization and stress resistance. Taken together, the data discussed here leave no doubt on the important role of auxin in potato tuberization, particularly in the processes of tuber initiation, growth and sprouting. A new integrative model for the stage-dependent auxin action on tuberization is presented. In addition, auxin is shown to differentially affects the potato resistance to biotrophic and necrotrophic biopathogens. Thus, the modern auxin biology opens up new perspectives for further biotechnological improvement of potato crops.

Overexpression of OsIAAGLU reveals a role for IAA-glucose conjugation in modulating rice plant architecture

OsIAAGLU could catalyze the reaction of IAA with glucose to generate IAA-glucose. Overexpression of OsIAAGLU in rice resulted in altered rice shoot architecture and root gravitropism. The distribution and levels of indole-3-acetic acid (IAA) within plant tissues are well known to play vital roles in plant growth and development. An important mechanism of regulating free IAA levels in monocots is formation of IAA ester conjugates. In this study, a cytosol-localized protein encoded by the rice gene of indole-3-acetic acid glucosyltransferase (OsIAAGLU) was found to catalyze the reaction of free IAA with glucose to generate IAA-glucose. Expression of OsIAAGLU could be induced by IAA and NAA. The number of tillers and leaf angle was significantly increased with a concomitant decrease in plant height and panicle length in the transgenic rice lines overexpressing OsIAAGLU compared to the wild-type (WT) plants. Phenotypes of iaaglu mutants constructed using the CRISPR/Cas9 system had no obvious differences with WT plants. Furthermore, overexpression of OsIAAGLU resulted in reduced sensitivity to IAA/NAA and altered gravitropic response of the roots in the transgenic plants. Free IAA contents in the leaves, root tips, and lamina joint of OsIAAGLU-overexpressing transgenic lines were lower than those of WT plants. These results support that OsIAAGLU could play a regulatory role in IAA homeostasis and rice architecture.

Indole-3-acetylaspartate and indole-3-acetylglutamate, the IAA-amide conjugates in the diploid strawberry achene, are hydrolyzed in growing seedlings

Indole-3-acetylaspartate and indole-3-acetylglutamate are the stored auxin amino acid conjugates of the achene of the diploid strawberry and serve as sources of auxin during seedling growth. The edible part of the strawberry, a pseudocarp, has long been known to enlarge in response to auxin produced by the developing achenes, the botanical true fruit. Auxin homeostasis involves a complex interaction between biosynthesis, conjugate formation and hydrolysis, catabolism and transport. Strawberry tissues are capable of synthesizing auxin conjugates, and transcriptome data support the expression of genes involved in IAA conjugate formation and hydrolysis throughout embryo development and subsequent seedling growth. Using a highly sensitive and selective mass spectrometric method, we identified all the low molecular weight indole-auxin amino acid conjugates in achenes of F. vesca as consisting of indole-3-acetylaspartate (IAasp) and indole-3-acetylglutamate (IAglu). In contrast to what has been proposed to occur in Arabidopsis, we determined that IAasp and IAglu are hydrolyzed by seedlings to provide a source of free IAA for growth.

A bacterial assay for rapid screening of IAA catabolic enzymes

BACKGROUND

Plants rely on concentration gradients of the native auxin, indole-3-acetic acid (IAA), to modulate plant growth and development. Both metabolic and transport processes participate in the dynamic regulation of IAA homeostasis. Free IAA levels can be reduced by inactivation mechanisms, such as conjugation and degradation. IAA can be conjugated via ester linkage to glucose, or via amide linkage to amino acids, and degraded via oxidation. Members of the UDP glucosyl transferase (UGT) family catalyze the conversion of IAA to indole-3-acetyl-1-glucosyl ester (IAGlc); by contrast, IAA is irreversibly converted to indole-3-acetyl-l-aspartic acid (IAAsp) and indole-3-acetyl glutamic acid (IAGlu) by Group II of the GRETCHEN HAGEN3 (GH3) family of acyl amido synthetases. Dioxygenase for auxin oxidation (DAO) irreversibly oxidizes IAA to oxindole-3-acetic acid (oxIAA) and, in turn, oxIAA can be further glucosylated to oxindole-3-acetyl-1-glucosyl ester (oxIAGlc) by UGTs. These metabolic pathways have been identified based on mutant analyses, in vitro activity measurements, and in planta feeding assays. In vitro assays for studying protein activity are based on producing Arabidopsis enzymes in a recombinant form in bacteria or yeast followed by recombinant protein purification. However, the need to extract and purify the recombinant proteins represents a major obstacle when performing in vitro assays.

RESULTS

In this work we report a rapid, reproducible and cheap method to screen the enzymatic activity of recombinant proteins that are known to inactivate IAA. The enzymatic reactions are carried out directly in bacteria that produce the recombinant protein. The enzymatic products can be measured by direct injection of a small supernatant fraction from the bacterial culture on ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem spectrometry (UHPLC-ESI-MS/MS). Experimental procedures were optimized for testing the activity of different classes of IAA-modifying enzymes without the need to purify recombinant protein.

CONCLUSIONS

This new method represents an alternative to existing in vitro assays. It can be applied to the analysis of IAA metabolites that are produced upon supplementation of substrate to engineered bacterial cultures and can be used for a rapid screening of orthologous candidate genes from non-model species.

The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family

AUXIN RESPONSE FACTORS (ARFs) are plant-specific transcription factors (TFs) that couple perception of the hormone auxin to gene expression programs essential to all land plants. As with many large TF families, a key question is whether individual members determine developmental specificity by binding distinct target genes. We use DAP-seq to generate genome-wide in vitro TF:DNA interaction maps for fourteen maize ARFs from the evolutionarily conserved A and B clades. Comparative analysis reveal a high degree of binding site overlap for ARFs of the same clade, but largely distinct clade A and B binding. Many sites are however co-occupied by ARFs from both clades, suggesting transcriptional coordination for many genes. Among these, we investigate known QTLs and use machine learning to predict the impact of cis-regulatory variation. Overall, large-scale comparative analysis of ARF binding suggests that auxin response specificity may be determined by factors other than individual ARF binding site selection.

Auxins and Cytokinins-The Role of Subcellular Organization on Homeostasis

Plant hormones are master regulators of plant growth and development. Better knowledge of their spatial signaling and homeostasis (transport and metabolism) on the lowest structural levels (cellular and subcellular) is therefore crucial to a better understanding of developmental processes in plants. Recent progress in phytohormone analysis at the cellular and subcellular levels has greatly improved the effectiveness of isolation protocols and the sensitivity of analytical methods. This review is mainly focused on homeostasis of two plant hormone groups, auxins and cytokinins. It will summarize and discuss their tissue- and cell-type specific distributions at the cellular and subcellular levels.

Out of Shape During Stress: A Key Role for Auxin

In most abiotic stress conditions, including salinity and water deficit, the developmental plasticity of the plant root is regulated by the phytohormone auxin. Changes in auxin concentration are often attributed to changes in shoot-derived long-distance auxin flow. However, recent evidence suggests important contributions by short-distance auxin transport from local storage and local auxin biosynthesis, conjugation, and oxidation during abiotic stress. We discuss here current knowledge on long-distance auxin transport in stress responses, and subsequently debate how short-distance auxin transport and indole-3-acetic acid (IAA) metabolism play a role in influencing eventual auxin accumulation and signaling patterns. Our analysis stresses the importance of considering all these components together and highlights the use of mathematical modeling for predictions of plant physiological responses.

Maternal auxin supply contributes to early embryo patterning in Arabidopsis

The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat¹. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue². The coordinated and synchronous development of the embryo and the surrounding integuments, and the alignment of their growth axes, suggest communication between maternal tissues and the embryo. In contrast to animals, however, where a network of maternal factors that direct embryo patterning have been identified^3,4, only a few maternal mutations have been described to affect embryo development in plants^5-7. Early embryo patterning in Arabidopsis requires accumulation of the phytohormone auxin in the apical cell by directed transport from the suspensor^8-10. However, the origin of this auxin has remained obscure. Here we investigate the source of auxin for early embryogenesis and provide evidence that the mother plant coordinates seed development by supplying auxin to the early embryo from the integuments of the ovule. We show that auxin response increases in ovules after fertilization, due to upregulated auxin biosynthesis in the integuments, and this maternally produced auxin is required for correct embryo development.

Manipulation and Sensing of Auxin Metabolism, Transport and Signaling

The plant hormone auxin is involved in virtually every aspect of plant growth and development. A chemical genetic approach has greatly contributed to the identification of important genes in auxin biosynthesis, transport and signaling. Molecular genetic technologies and structural information for auxin regulatory components have accelerated the identification and characterization of many novel small molecule modulators in auxin biology. These modulators have been widely utilized to dissect auxin responses. Here we provide an overview of the structure, primary target, in planta activity and application of small molecule modulators in auxin biology.

Modulation of Phytohormone Signaling: A Primary Function of Flavonoids in Plant-Environment Interactions

The old observation that plants preferentially synthesize flavonoids with respect to the wide range of phenylpropanoid structures when exposed to high doses of UV-B radiation has supported the view that flavonoids are primarily involved in absorbing the shortest solar wavelengths in photoprotection. However, there is compelling evidence that the biosynthesis of flavonoids is similarly upregulated in response to high photosynthetically active radiation in the presence or in the absence of UV-radiation, as well as in response to excess metal ions and photosynthetic redox unbalance. This supports the hypothesis that flavonoids may play prominent roles as scavengers of reactive oxygen species (ROS) generated by light excess. These 'antioxidant' functions of flavonoids appears robust, as maintained between different life kingdoms, e.g., plants and animals. The ability of flavonoids to buffer stress-induced large alterations in ROS homeostasis and, hence, to modulate the ROS-signaling cascade, is at the base of well-known functions of flavonoids as developmental regulators in both plants and animals. There is both long and very recent evidence indeed that, in plants, flavonoids may strongly affect phytohormone signaling, e.g., auxin and abscisic acid signaling. This function is served by flavonoids in a very low (nM) concentration range and involves the ability of flavonoids to inhibit the activity of a wide range of protein kinases, including but not limited to mitogen-activated protein kinases, that operate downstream of ROS in the regulation of cell growth and differentiation. For example, flavonoids inhibit the transport of auxin acting on serine-threonine PINOID (PID) kinases that regulate the localization of auxin efflux facilitators PIN-formed (PIN) proteins. Flavonoids may also determine auxin gradients at cellular and tissue levels, and the consequential developmental processes, by reducing auxin catabolism. Recent observations lead to the hypothesis that regulation/modulation of auxin transport/signaling is likely an ancestral function of flavonoids. The antagonistic functions of flavonoids on ABA-induced stomatal closure also offer novel hypotheses on the functional role of flavonoids in plant-environment interactions, in early as well as in modern terrestrial plants. Here, we surmise that the regulation of phytohormone signaling might have represented a primary function served by flavonols for the conquest of land by plants and it is still of major significance for the successful acclimation of modern terrestrial plants to a severe excess of radiant energy.

Essential Roles of Local Auxin Biosynthesis in Plant Development and in Adaptation to Environmental Changes

It has been a dominant dogma in plant biology that the self-organizing polar auxin transport system is necessary and sufficient to generate auxin maxima and minima that are essential for almost all aspects of plant growth and development. However, in the past few years, it has become clear that local auxin biosynthesis is required for a suite of developmental processes, including embryogenesis, endosperm development, root development, and floral initiation and patterning. Moreover, it was discovered that local auxin biosynthesis maintains optimal plant growth in response to environmental signals, including light, temperature, pathogens, and toxic metals. In this article, I discuss the recent progress in auxin biosynthesis research and the paradigm shift in recognizing the important roles of local auxin biosynthesis in plant biology.

Control of Endogenous Auxin Levels in Plant Root Development

In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture.