Auxins

The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber

Over the last decade, genome-scale metabolic models have been increasingly used to study plant metabolic behaviour at the tissue and multi-tissue level under different environmental conditions. Quercus suber, also known as the cork oak tree, is one of the most important forest communities of the Mediterranean/Iberian region. In this work, we present the genome-scale metabolic model of the Q. suber (iEC7871). The metabolic model comprises 7871 genes, 6231 reactions, and 6481 metabolites across eight compartments. Transcriptomics data was integrated into the model to obtain tissue-specific models for the leaf, inner bark, and phellogen, with specific biomass compositions. The tissue-specific models were merged into a diel multi-tissue metabolic model to predict interactions among the three tissues at the light and dark phases. The metabolic models were also used to analyse the pathways associated with the synthesis of suberin monomers, namely the acyl-lipids, phenylpropanoids, isoprenoids, and flavonoids production. The models developed in this work provide a systematic overview of the metabolism of Q. suber, including its secondary metabolism pathways and cork formation.

Do Opposites Attract? Auxin-Abscisic Acid Crosstalk: New Perspectives

Plants are constantly exposed to a variety of different environmental stresses, including drought, salinity, and elevated temperatures. These stress cues are assumed to intensify in the future driven by the global climate change scenario which we are currently experiencing. These stressors have largely detrimental effects on plant growth and development and, therefore, put global food security in jeopardy. For this reason, it is necessary to expand our understanding of the underlying mechanisms by which plants respond to abiotic stresses. Especially boosting our insight into the ways by which plants balance their growth and their defense programs appear to be of paramount importance, as this may lead to novel perspectives that can pave the way to increase agricultural productivity in a sustainable manner. In this review, our aim was to present a detailed overview of different facets of the crosstalk between the antagonistic plant hormones abscisic acid (ABA) and auxin, two phytohormones that are the main drivers of plant stress responses, on the one hand, and plant growth, on the other.

The MdAux/IAA2 Transcription Repressor Regulates Cell and Fruit Size in Apple Fruit

Auxin plays an important role in regulating plant development, and Auxin/indole acetic acid (Aux/IAA) is a type of auxin-responsive gene and plays an important role in auxin signaling; to date, although 29 Aux/IAA proteins have been reported in Abrabidopsis thaliana, only parts of the Aux/IAA family gene functions have been identified. We previously reported that a bud sport of ‘Longfeng’ (LF) apple (Malus domestica), named ‘Grand longfeng’ (GLF), which showed a larger fruit size than LF, has lower expression of MdAux/IAA2. In this study, we identified the function of the MdAux/IAA2 gene in apple fruit size difference using Agrobacterium-mediated genetic transformation. Overexpression of MdAux/IAA2 decreased the apple flesh callus increment and caused a smaller globular cell size. In addition, overexpression of MdAux/IAA2 in GLF fruit resulted in the reduction of apple fruit size, weight, and cell size, while silencing MdAux/IAA2 in LF apple fruit resulted in an increase in apple fruit weight and cell size. We suggest that the high auxin content depressed the expression of MdAux/IAA2, and that the downregulated expression of MdAux/IAA2 led to the formation of GLF. Our study suggests a mechanism for fruit size regulation in plants and we will explore the transcription factors functioning in this process in the future.

Integration of genomics, transcriptomics and metabolomics identifies candidate loci underlying fruit weight in loquat

Fruit weight is an integral part of fruit-quality traits and directly influences commodity values and economic returns of fruit crops. Despite its importance, the molecular mechanisms underlying fruit weight remain understudied, especially for perennial fruit tree crops such as cultivated loquat (Eriobotrya japonica Lindl.). Auxin is known to regulate fruit development, whereas its role and metabolism in fruit development remain obscure in loquat. In this study, we applied a multi-omics approach, integrating whole-genome resequencing-based quantitative trait locus (QTL) mapping with an F1 population, population genomics analysis using germplasm accessions, transcriptome analysis, and metabolic profiling to identify the genomic regions potentially associated with fruit weight in loquat. We identified three major loci associated with fruit weight, supported by both QTL mapping and comparative genomic analysis between small- and big-fruited loquat cultivars. Comparison between two genotypes with contrasting fruit weight performance through transcriptomic and metabolic profiling revealed an important role of auxin in regulating fruit development, especially at the fruit enlarging stage. The multi-omics approach identified two homologs of ETHYLENE INSENSITIVE 4 (EjEIN4) and TORNADO 1 (EjTRN1) as promising candidates controlling fruit weight. Moreover, three single nucleotide polymorphism (SNP) markers were closely associated with fruit weight. Results from this study provided insights from multiple perspectives into the genetic and metabolic controls of fruit weight in loquat. The candidate genomic regions, genes, and sequence variants will facilitate understanding the molecular basis of fruit weight and lay a foundation for future breeding and manipulation of fruit weight in loquat.

Endogenous Auxin Content Contributes to Larger Size of Apple Fruit

Fruit size is an important economic trait that is controlled by multiple genes. However, the regulatory mechanism for fruit size remains poorly understood. A bud sport variety of "Longfeng" (LF) apple (Malus domestica) was identified and named "Grand Longfeng" (GLF). The fruit size of GLF is larger than that of LF, and both varieties are diploid. We found that the cell size in GLF fruit was larger than that of LF. Then, we compared the fruit transcriptomes of the two varieties using RNA-Seq technology. A total of 1166 differentially expressed genes (DEGs) were detected between GLF and LF fruits. The KEGG analysis revealed that the phytohormone pathway was the most enriched, in which most of the DEGs were related to auxin signaling. Moreover, the endogenous auxin levels of GLF fruit were higher than those of LF. The expressions of auxin synthetic genes, including MdTAR1 and MdYUCCA6, were higher in GLF fruit than LF. Collectively, our findings suggest that auxin plays an important role in fruit size development.

Endogenous Auxin Content Contributes to Larger Size of Apple Fruit

Fruit size is an important economic trait that is controlled by multiple genes. However, the regulatory mechanism for fruit size remains poorly understood. A bud sport variety of "Longfeng" (LF) apple (Malus domestica) was identified and named "Grand Longfeng" (GLF). The fruit size of GLF is larger than that of LF, and both varieties are diploid. We found that the cell size in GLF fruit was larger than that of LF. Then, we compared the fruit transcriptomes of the two varieties using RNA-Seq technology. A total of 1166 differentially expressed genes (DEGs) were detected between GLF and LF fruits. The KEGG analysis revealed that the phytohormone pathway was the most enriched, in which most of the DEGs were related to auxin signaling. Moreover, the endogenous auxin levels of GLF fruit were higher than those of LF. The expressions of auxin synthetic genes, including MdTAR1 and MdYUCCA6, were higher in GLF fruit than LF. Collectively, our findings suggest that auxin plays an important role in fruit size development.

Late stage trifluoromethylthiolation strategies for organic compounds

Substitution by the CF3S group allows for an increase in lipophilicity and electron-withdrawing properties along with an improvement in the bioavailability of medicinal targets; consequently, the late stage introduction of CF3S moieties into medicinal scaffolds is a sought-after strategy in synthetic organic chemistry. Different newly-developed electrophilic and nucleophilic reagents are used to effect the trifluoromethylthiolation of (hetero)aromatic compounds, aliphatic compounds (alkyl, alkenyl, alkynyl substrates), the trifluoromethylthiolation at the α- and β-carbonyl positions, and heteroatoms (N- and S-). Such reactions can involve homolytic substitutions, or functional-group substitutions (ipso). Addition reactions of electrophilic reagents to double and triple bonds followed by ring-cyclizations will be shown to yield relevant CF3S-substituted heteroaromatic compounds with relevant pharmacological action.

Leaf expansion in Phaseolus: transient auxin-induced growth increase

Control of leaf expansion by auxin is not well understood. Evidence from short term exogenous applications and from treatment of excised tissues suggests auxin positively influences growth. Manipulations of endogenous leaf auxin content, however, suggests that, long-term, auxin suppresses leaf expansion. This study attempts to clarify the growth effects of auxin on unifoliate (primary) leaves of the common bean (Phaseolus vulgaris) by reexamining the response to auxin treatment of both excised leaf strips and attached leaves. Leaf strips, incubated in culture conditions that promoted steady elongation for up to 48 h, treated with 10 μM NAA responded with an initial surge of elongation growth complete within 10 hours followed by insensitivity. A range of NAA concentrations from 0.1 μM to 300 μM induced increased strip elongation after 24 hours and 48 hours. Increased elongation and epinastic curvature of leaf strips was found specific to active auxins. Expanding attached unifoliates treated once with aqueous auxin α-naphthalene acetic acid (NAA) at 1.0 mM showed both an initial surge in growth lasting 4-6 hours followed by growth inhibition sustained at least as long as 24 hours post treatment. Auxin-induced inhibition of leaf expansion was associated with smaller epidermal cell area. Together the results suggest increasing leaf auxin first increases growth then slows growth through inhibition of cell expansion. Excised leaf strips, retain only the initial increased growth response to auxin and not the subsequent growth inhibition, either as a consequence of wounding or of isolation from the plant.

Genome-wide analysis of auxin transport genes identifies the hormone responsive patterns associated with leafy head formation in Chinese cabbage

Auxin resistant 1/like aux1 (AUX/LAX), pin-formed (PIN) and ATP binding cassette subfamily B (ABCB/MDR/PGP) are three families of auxin transport genes. The development-related functions of the influx and efflux carriers have been well studied and characterized in model plants. However, there is scant information regarding the functions of auxin genes in Chinese cabbage and the responses of exogenous polar auxin transport inhibitors (PATIs). We conducted a whole-genome annotation and a bioinformatics analysis of BrAUX/LAX, BrPIN, and BrPGP genes in Chinese cabbage. By analyzing the expression patterns at several developmental stages in the formation of heading leaves, we found that most auxin-associate genes were expressed throughout the entire process of leafy head formation, suggesting that these genes played important roles in the development of heads. UPLC was used to detect the distinct and uneven distribution of auxin in various segments of the leafy head and in response to PATI treatment, indicated that the formation of the leafy head depends on polar auxin transport and the uneven distribution of auxin in leaves. This study provides new insight into auxin polar transporters and the possible roles of the BrLAX, BrPIN and BrPGP genes in leafy head formation in Chinese cabbage.

Grape berry ripening delay induced by a pre-véraison NAA treatment is paralleled by a shift in the expression pattern of auxin- and ethylene-related genes

BACKGROUND

Auxins act as repressors of ripening inception in grape (véraison), while ethylene and abscisic acid (ABA) play a positive role as inducers of the syndrome. Despite the increasing amount of information made available on this topic, the complex network of interactions among these hormones remains elusive. In order to shed light on these aspects, a holistic approach was adopted to evaluate, at the transcriptomic level, the crosstalk between hormones in grape berries, whose ripening progression was delayed by applying naphtalenacetic acid (NAA) one week before véraison.

RESULTS

The NAA treatment caused significant changes in the transcription rate of about 1,500 genes, indicating that auxin delayed grape berry ripening also at the transcriptional level, along with the recovery of a steady state of its intracellular concentration. Hormone indices analysis carried out with the HORMONOMETER tool suggests that biologically active concentrations of auxins were achieved throughout a homeostatic recovery. This occurred within 7 days after the treatment, during which the physiological response was mainly unspecific and due to a likely pharmacological effect of NAA. This hypothesis is strongly supported by the up-regulation of genes involved in auxin conjugation (GH3-like) and action (IAA4- and IAA31-like). A strong antagonistic effect between auxin and ethylene was also observed, along with a substantial 'synergism' between auxins and ABA, although to a lesser extent.

CONCLUSIONS

This study suggests that, in presence of altered levels of auxins, the crosstalk between hormones involves diverse mechanisms, acting at both the hormone response and biosynthesis levels, creating a complex response network.

Inhibition of lamina outgrowth following Solanum lycopersicum AUXIN RESPONSE FACTOR 10 (SlARF10) derepression

Auxin response factors (ARFs) are plant transcription factors that activate or repress the expression of auxin-responsive genes and accordingly, play key roles in auxin-mediated developmental processes. Here we identified and characterized the Solanum lycopersicum (tomato) ARF10 homolog (SlARF10), demonstrated that it is posttranscriptionally regulated by Sl-miR160, and investigated the significance of this regulation for tomato development. In wild-type tomato, SlARF10 is primarily expressed in the pericarp of mature and ripened fruit, showing an expression profile complementary to that of Sl-miR160. Constitutive expression of wild-type SlARF10 did not alter tomato development. However, transgenic tomato plants that constitutively expressed the Sl-miR160a-resistant version (mSlARF10) developed narrow leaflet blades, sepals and petals, and abnormally shaped fruit. During compound leaf development, mSlARF10 accumulation specifically inhibited leaflet blade outgrowth without affecting other auxin-driven processes such as leaflet initiation and lobe formation. Moreover, blade size was inversely correlated with mSlARF10 transcript levels, strongly implying that the SlARF10 protein, which was localized to the nucleus, can function as a transcriptional repressor of leaflet lamina outgrowth. Accordingly, known auxin-responsive genes, which promote cell growth, were downregulated in shoot apices that accumulated increased mSlARF10 levels. Taken together, we propose that repression of SlARF10 by Sl-miR160 is essential for auxin-mediated blade outgrowth and early fruit development.

A genomics approach to understanding the role of auxin in apple (Malus x domestica) fruit size control

BACKGROUND

Auxin is an important phytohormone for fleshy fruit development, having been shown to be involved in the initial signal for fertilisation, fruit size through the control of cell division and cell expansion, and ripening related events. There is considerable knowledge of auxin-related genes, mostly from work in model species. With the apple genome now available, it is possible to carry out genomics studies on auxin-related genes to identify genes that may play roles in specific stages of apple fruit development.

RESULTS

High amounts of auxin in the seed compared with the fruit cortex were observed in 'Royal Gala' apples, with amounts increasing through fruit development. Injection of exogenous auxin into developing apples at the start of cell expansion caused an increase in cell size. An expression analysis screen of auxin-related genes involved in auxin reception, homeostasis, and transcriptional regulation showed complex patterns of expression in each class of gene. Two mapping populations were phenotyped for fruit size over multiple seasons, and multiple quantitative trait loci (QTLs) were observed. One QTL mapped to a region containing an Auxin Response Factor (ARF106). This gene is expressed during cell division and cell expansion stages, consistent with a potential role in the control of fruit size.

CONCLUSIONS

The application of exogenous auxin to apples increased cell expansion, suggesting that endogenous auxin concentrations are at least one of the limiting factors controlling fruit size. The expression analysis of ARF106 linked to a strong QTL for fruit weight suggests that the auxin signal regulating fruit size could partially be modulated through the function of this gene. One class of gene (GH3) removes free auxin by conjugation to amino acids. The lower expression of these GH3 genes during rapid fruit expansion is consistent with the apple maximising auxin concentrations at this point.

Pseudomonas aeruginosa PAO1 virulence factors and poplar tree response in the rhizosphere

Whole-transcriptome analysis was used here for the first time in the rhizosphere to discern the genes involved in the pathogenic response of Pseudomonas aeruginosa PAO1 as well as to discern the response of the poplar tree. Differential gene expression shows that 185 genes of the bacterium and 753 genes of the poplar tree were induced in the rhizosphere. Using the P. aeruginosa transcriptome analysis, isogenic knockout mutants, and two novel plant assays (poplar and barley), seven novel PAO1 virulence genes were identified (PA1385, PA2146, PA2462, PA2463, PA2663, PA4150 and PA4295). The uncharacterized putative haemolysin repressor, PA2463, upon inactivation, resulted in greater poplar virulence and elevated haemolysis while this mutant remained competitive in the rhizosphere. In addition, disruption of the haemolysin gene itself (PA2462) reduced the haemolytic activity of P. aeruginosa, caused less cytotoxicity and reduced barley virulence, as expected. Inactivating PA1385, a putative glycosyl transferase, reduced both poplar and barley virulence. Furthermore, disrupting PA2663, a putative membrane protein, reduced biofilm formation by 20-fold. Inactivation of PA3476 (rhlI) increased virulence with barley as well as haemolytic activity and cytotoxicity, so quorum sensing is important in plant pathogenesis. Hence, this strategy is capable of elucidating virulence genes for an important pathogen.

The role of Phe82 and Phe351 in auxin-induced substrate perception by TIR1 ubiquitin ligase: a novel insight from molecular dynamics simulations

It is well known that Auxin plays a key role in controlling many aspects of plant growth and development. Crystal structures of Transport inhibitor response 1 (TIR1), a true receptor of auxin, were very recently determined for TIR1 alone and in complexes with auxin and different synthetic analogues and an Auxin/Indole-3-Acetic Acid (Aux/IAA) substrate peptide. However, the dynamic conformational changes of the key residues of TIR1 that take place during the auxin and substrate perception by TIR1 and the detailed mechanism of these changes are still unclear. In the present study, various computational techniques were integrated to uncover the detailed molecular mechanism of the auxin and Aux/IAA perception process; these simulations included molecular dynamics (MD) simulations on complexes and the free enzyme, the molecular mechanics Poisson Boltzmann surface area (MM-PBSA) calculations, normal mode analysis, and hydrogen bond energy (HBE) calculations. The computational simulation results provided a reasonable explanation for the structure-activity relationships of auxin and its synthetic analogues in view of energy. In addition, a more detailed model for auxin and Aux/IAA perception was also proposed, indicating that Phe82 and Phe351 played a pivotal role in Aux/IAA perception. Upon auxin binding, Phe82 underwent conformational changes to accommodate the subsequent binding of Aux/IAA. As a result, auxin enhances the TIR1-Aux/IAA interactions by acting as a "molecular glue". Besides, Phe351 acts as a "fastener" to further improve the substrate binding. The structural and mechanistic insights obtained from the present study will provide valuable clues for the future design of promising auxin analogues.

Identification and quantitation of auxins in plants by liquid chromatography/electrospray ionization ion trap mass spectrometry

Auxin is an important phylohormone, which regulates specific physiological responses such as division, elongation and differentiation of cells. A new method using liquid chromatography/electrospray ionization ion trap mass spectrometry (LC/ESI-ITMS) has been developed for identification and quantitation of four auxins. Under the optimum conditions, four auxins (indole-3-acetic acid, indole-3-propionic acid, indole-3-butyric acid and 1-naphthylacetic acid) were completely separated and quantitated within 7 min with a minimum detection limit of 8.0 ng mL(-1) with relative standard deviations lower than 5.0%. This method also has been applied to analysis of auxins in Chinese cabbage where, even with a complicated serious background perturbation due to the natural biological matrix, the mean recoveries ranged from 77.5% to 99.8%. Finally, we discuss the MS-relevant properties of the identified auxins in detail.

Mechanism of auxin interaction with Auxin Binding Protein (ABP1): a molecular dynamics simulation study

Auxin Binding Protein 1 (ABP1) is ubiquitous in green plants. It binds the phytohormone auxin with high specificity and affinity, but its role in auxin-induced processes is unknown. To understand the proposed receptor function of ABP1 we carried out a detailed molecular modeling study. Molecular dynamics simulations showed that ABP1 can adopt two conformations differing primarily in the position of the C-terminus and that one of them is stabilized by auxin binding. This is in agreement with experimental evidence that auxin induces changes at the ABP1 C-terminus. Simulations of ligand egress from ABP1 revealed three main routes by which an auxin molecule can enter or leave the ABP1 binding site. Assuming the previously proposed orientation of ABP1 to plant cell membranes, one of the routes leads to the membrane and the other two to ABP1's aqueous surroundings. A network of hydrogen-bonded water molecules leading from the bulk water to the zinc-coordinated ligands in the ABP1 binding site was formed in all simulations. Water entrance into the zinc coordination sphere occurred simultaneously with auxin egress. These results suggest that the hydrogen-bonded water molecules may assist in protonation and deprotonation of auxin molecules and their egress from the ABP1 binding site.

New insight into the biochemical mechanisms regulating auxin transport in plants

The transport of the plant hormone auxin has been under intense investigation since its identification 80 years ago. Studies have gradually refined our understanding of the importance of auxin transport in many aspects of plant signalling and development, and the focus has intensified in recent years towards the identification of the proteins involved in auxin transport and their functional mechanism. Within the past 18 months, the field has progressed rapidly, with confirmation that several distinct classes of proteins, previously dubbed as 'putative auxin permeases' or 'auxin transport facilitators', are bona fide transporters of IAA (indol-3-ylacetic acid). In this review we will appraise the recent transport data and highlight likely future research directions, including the characterization of auxiliary proteins necessary for the regulation of auxin transporters.