Polar auxin transport: controlling where and how much

Humic acid improves wheat growth by modulating auxin and cytokinin biosynthesis pathways

Humic acids have been widely used for centuries to enhance plant growth and productivity. The beneficial effects of humic acids have been attributed to different functional groups and phytohormone-like compounds enclosed in macrostructure. However, the mechanisms underlying the plant growth-promoting effects of humic acids are only partially understood. We hypothesize that the bio-stimulatory effect of humic acids is mainly due to the modulation of innate pathways of auxin and cytokinin biosynthesis in treated plants. A physiological investigation along with molecular characterization was carried out to understand the mechanism of bio-stimulatory effects of humic acid. A gene expression analysis was performed for the genes involved in auxin and cytokinin biosynthesis pathways in wheat seedlings. Furthermore, Arabidopsis thaliana transgenic lines generated by fusing the auxin-responsive DR5 and cytokinin-responsive ARR5 promoter to ß-glucuronidase (GUS) reporter were used to study the GUS expression analysis in humic acid treated seedlings. This study demonstrates that humic acid treatment improved the shoot and root growth of wheat seedlings. The expression of several genes involved in auxin (Tryptophan Aminotransferase of Arabidopsis and Gretchen Hagen 3.2) and cytokinin (Lonely Guy3) biosynthesis pathways were up-regulated in humic acid-treated seedlings compared to the control. Furthermore, GUS expression analysis showed that bioactive compounds of humic acid stimulate endogenous auxin and cytokinin-like activities. This study is the first report in which using ARR5:GUS lines we demonstrate the biostimulants activity of humic acid.

IAR4 mutation enhances cadmium toxicity by disturbing auxin homeostasis in Arabidopsis thaliana

Cadmium (Cd) is highly toxic to plants, but the targets and modes of toxicity remain unclear. We isolated a Cd-hypersensitive mutant of Arabidopsis thaliana, Cd-induced short root 2 (cdsr2), in the background of the phytochelatin synthase-defective mutant cad1-3. Both cdsr2 and cdsr2 cad1-3 displayed shorter roots and were more sensitive to Cd than their respective wild type. Using genomic resequencing and complementation, IAR4 was identified as the causal gene, which encodes a putative mitochondrial pyruvate dehydrogenase E1α subunit. cdsr2 showed decreased pyruvate dehydrogenase activity and NADH content, but markedly increased concentrations of pyruvate and alanine in roots. Both Cd stress and IAR4 mutation decreased auxin level in the root tips, and the effect was additive. A higher growth temperature rescued the phenotypes in cdsr2. Exogenous alanine inhibited root growth and decreased auxin level in the wild type. Cadmium stress suppressed the expression of genes involved in auxin biosynthesis, hydrolysis of auxin-conjugates and auxin polar transport. Our results suggest that auxin homeostasis is a key target of Cd toxicity, which is aggravated by IAR4 mutation due to decreased pyruvate dehydrogenase activity. Decreased auxin level in cdsr2 is likely caused by increased auxin-alanine conjugation and decreased energy status in roots.

Genome-wide analysis of PIN genes in cultivated peanuts (Arachis hypogaea L.): identification, subcellular localization, evolution, and expression patterns

BACKGROUND

Auxin is an important hormone in plants and the PIN-FORMED (PIN) genes are essential to auxin distribution in growth and developmental processes of plants. Peanut is an influential cash crop, but research into PIN genes in peanuts remains limited.

RESULTS

In this study, 16 PIN genes were identified in the genome of cultivated peanut, resolving into four subfamilies. All PIN genes were predicted to be located in the plasma membrane and a subcellular location experiment confirmed this prediction for eight of them. The gene structure, cis-elements in the promoter, and evolutionary relationships were elucidated, facilitating our understanding of peanut PINs and their evolution. In addition, the expression patterns of these PINs in various tissues were analyzed according to a previously published transcriptome dataset and qRT-PCR, which gave us a clear understanding of the temporal and spatial expression of PIN genes in different growth stages and different tissues. The expression trend of homologous genes was similar. AhPIN2A and AhPIN2B exhibited predominant expression in roots. AhPIN1A-1 and AhPIN1B-1 displayed significant upregulation following peg penetration, suggesting a potential close association with peanut pod development. Furthermore, we presented the gene network and gene ontology enrichment of these PINs. Notably, AhABCB19 exhibited a co-expression relationship with AhPIN1A and AhPIN1B-1, with all three genes displaying higher expression levels in peanut pegs and pods. These findings reinforce their potential role in peanut pod development.

CONCLUSIONS

This study details a comprehensive analysis of PIN genes in cultivated peanuts and lays the foundation for subsequent studies of peanut gene function and phenotype.

Functional analysis of auxin derived from a symbiotic mycobiont

The biosynthesis of auxin or indole-3-acetic acid by microorganisms has a major impact on plant-microbe interactions. Several beneficial microbiota are known to produce auxin, which largely influences root development and growth in the host plants. Akin to findings in rhizobacteria, recent studies have confirmed the production of auxin by plant growth-promoting fungi too. Here, we show that Penicillium citrinum isolate B9 produces auxin as deduced by liquid chromatography tandem-mass spectrometry analysis. Such fungal auxin is secreted and contributes directly to enhanced root and shoot development and overall plant growth in Arabidopsis thaliana. Furthermore, auxin production by P. citrinum likely involves more than one tryptophan-dependent pathway. Using auxin biosynthesis inhibitor L-Kynurenine, we show that the indole-3-pyruvate pathway might be one of the key biosynthetic routes involved in such auxin production. Confocal microscopy of the DR5rev:GFP Arabidopsis reporter line helped demonstrate that P. citrunum B9-derived auxin is biologically active and is able to significantly enhance auxin signaling in roots during such improved root growth and plant development. Furthermore, the phenotypic growth defects arising from impaired auxin signaling in Arabidopsis taa1 mutant or upon L-Kynurenine treatment of wild-type Arabidopsis seedlings could be significantly alleviated by fungus B9-derived auxin, thus suggesting its positive role in plant growth promotion. Collectively, our results provide clear evidence that the production of auxin is one of the main mechanisms involved in induction of the beneficial plant growth by P. citrinum.

Cytokinin-inducible response regulator SlRR6 controls plant height through gibberellin and auxin pathways in tomato

Plant height is a key agronomic trait regulated by several phytohormones such as gibberellins (GAs) and auxin. However, little is known about how cytokinin (CK) participates in this process. Here, we report that SlRR6, a type-A response regulator in the CK signaling pathway, positively regulates plant height in tomato. SlRR6 was induced by exogenous kinetin and GA3, but inhibited by indole-3-acetic acid (IAA). Knock out of SlRR6 reduced tomato plant height through shortening internode length, while overexpression of SlRR6 caused taller plants due to increased internode number. Cytological observation of longitudinal stems showed that both knock out and overexpression of SlRR6 generated larger cells, but significantly reduced cell numbers in each internode. Further studies demonstrated that overexpression of SlRR6 enhanced GA accumulation and lowered IAA content, along with expression changes in GA- and IAA-related genes. Exogenous paclobutrazol and IAA treatments restored the increased plant height phenotype in SlRR6-overexpressing lines. Yeast two-hybrid, bimolecular fluorescence complementation, and co-immunoprecipitation assays showed that SlRR6 interacts with a small auxin up RNA protein, SlSAUR58. Moreover, SlSAUR58-overexpressing plants were dwarf with decreased internode length. Overall, our findings establish SlRR6 as a vital component in the CK signaling, GA, and IAA regulatory network that controls plant height.

Advances in the study of the function and mechanism of the action of flavonoids in plants under environmental stresses

MAIN CONCLUSION

This review summarizes the anti-stress effects of flavonoids in plants and highlights its role in the regulation of polar auxin transport and free radical scavenging mechanism. As secondary metabolites widely present in plants, flavonoids play a vital function in plant growth, but also in resistance to stresses. This review introduces the classification, structure and synthetic pathways of flavonoids. The effects of flavonoids in plant stress resistance were enumerated, and the mechanism of flavonoids in plant stress resistance was discussed in detail. It is clarified that plants under stress accumulate flavonoids by regulating the expression of flavonoid synthase genes. It was also determined that the synthesized flavonoids are transported in plants through three pathways: membrane transport proteins, vesicles, and bound to glutathione S-transferase (GST). At the same time, the paper explores that flavonoids regulate polar auxin transport (PAT) by acting on the auxin export carrier PIN-FORMED (PIN) in the form of ATP-binding cassette subfamily B/P-glycoprotein (ABCB/PGP) transporter, which can help plants to respond in a more dominant form to stress. We have demonstrated that the number and location of hydroxyl groups in the structure of flavonoids can determine their free radical scavenging ability and also elucidated the mechanism by which flavonoids exert free radical removal in cells. We also identified flavonoids as signaling molecules to promote rhizobial nodulation and colonization of arbuscular mycorrhizal fungi (AMF) to enhance plant-microbial symbiosis in defense to stresses. Given all this knowledge, we can foresee that the in-depth study of flavonoids will be an essential way to reveal plant tolerance and enhance plant stress resistance.

Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization

In maize, intrinsic hormone activities and sap fluxes facilitate organogenesis patterning and plant holistic development; these hormone movements should be a primary focus of developmental biology and agricultural optimization strategies. Maize (Zea mays) is an important crop plant with distinctive life history characteristics and structural features. Genetic studies have extended our knowledge of maize developmental processes, genetics, and molecular ecophysiology. In this review, the classical life cycle and life history strategies of maize are analyzed to identify spatiotemporal organogenesis properties and develop a definitive understanding of maize development. The actions of genes and hormones involved in maize organogenesis and sex determination, along with potential molecular mechanisms, are investigated, with findings suggesting central roles of auxin and cytokinins in regulating maize holistic development. Furthermore, investigation of morphological and structural characteristics of maize, particularly node ubiquity and the alternate attachment pattern of lateral organs, yields a novel regulatory model suggesting that maize organ initiation and subsequent development are derived from the stimulation and interaction of auxin and cytokinin fluxes. Propositions that hormone activities and sap flow pathways control organogenesis are thoroughly explored, and initiation and development processes of distinctive maize organs are discussed. Analysis of physiological factors driving hormone and sap movement implicates cues of whole-plant activity for hormone and sap fluxes to stimulate maize inflorescence initiation and organ identity determination. The physiological origins and biogenetic mechanisms underlying maize floral sex determination occurring at the tassel and ear spikelet are thoroughly investigated. The comprehensive outline of maize development and morphogenetic physiology developed in this review will enable farmers to optimize field management and will provide a reference for de novo crop domestication and germplasm improvement using genome editing biotechnologies, promoting agricultural optimization.

Screening of protonstatin-1 (PS-1) analogs for improved inhibitors of plant plasma membrane H+-ATPase activity

We previously identified protonstatin-1 (PS-1) as a selective inhibitor of plasma membrane H⁺-ATPase (PM H⁺-ATPase) activity and used it as a tool to validate the chemiosmotic model for polar auxin transport. Here, to obtain compounds with higher affinity than PS-1 for PM H⁺-ATPase, we synthesized 34 PS-1 analogs and examined their ability to inhibit PM H⁺-ATPase activity. The 34 analogs showed varying inhibitory effects on the activity of this enzyme. The strongest effect was observed for the small molecule PS-2, which was approximately five times stronger than PS-1. Compared to PS-1, PS-2 was also a stronger inhibitor of auxin uptake as well as acropetal and basipetal polar auxin transport in Arabidopsis thaliana seedlings. Because PS-2 is a more potent inhibitor of PM H⁺-ATPase than PS-1, we believe that this compound could be used as a tool to study the functions of this key plant enzyme.

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.

Division of cortical cells is regulated by auxin in Arabidopsis roots

The root cortex transports water and nutrients absorbed by the root epidermis into the vasculature and stores substances such as starch, resins, and essential oils. The cortical cells are also deeply involved in determining epidermal cell fate. In Arabidopsis thaliana roots, the cortex is composed of a single cell layer generated by a single round of periclinal division of the cortex/endodermis initials. To further explore cortex development, we traced the development of the cortex by counting cortical cells. Unlike vascular cells, whose number increased during the development of root apical meristem (RAM), the number of cortical cells did not change, indicating that cortical cells do not divide during RAM development. However, auxin-induced cortical cell division, and this finding was confirmed by treatment with the auxin transport inhibitor N-1-naphthylphthalamic acid (NPA) and examining transgenic plants harboring CO2::ΔARF5, in which cortical expression of truncated AUXIN RESPONSE FACTOR5 (ΔARF5) induces auxin responses. NPA-induced cortical auxin accumulation and CO2::ΔARF5-mediated cortical auxin response induced anticlinal and periclinal cell divisions, thus increasing the number of cortical cells. These findings reveal a tight link between auxin and cortical cell division, suggesting that auxin is a key player in determining root cortical cell division.

Testing the polar auxin transport model with a selective plasma membrane H+ -ATPase inhibitor

Auxin is unique among plant hormones in that its function requires polarized transport across plant cells. A chemiosmotic model was proposed to explain how polar auxin transport is derived by the H⁺ gradient across the plasma membrane (PM) established by PM H⁺ -adenosine triphosphatases (ATPases). However, a classical genetic approach by mutations in PM H⁺ -ATPase members did not result in the ablation of polar auxin distribution, possibly due to functional redundancy in this gene family. To confirm the crucial role of PM H⁺ -ATPases in the polar auxin transport model, we employed a chemical genetic approach. Through a chemical screen, we identified protonstatin-1 (PS-1), a selective small-molecule inhibitor of PM H⁺ -ATPase activity that inhibits auxin transport. Assays with transgenic plants and yeast strains showed that the activity of PM H⁺ -ATPases affects auxin uptake as well as acropetal and basipetal polar auxin transport. We propose that PS-1 can be used as a tool to interrogate the function of PM H⁺ -ATPases. Our results support the chemiosmotic model in which PM H⁺ -ATPase itself plays a fundamental role in polar auxin transport.

Advances in Citrus Flowering: A Review

Citrus are polycarpic and evergreen species that flower once in spring or several times a year depending on the genotype and the climatic conditions. Floral induction is triggered by low temperature and water-deficit stress and occurs 2-3 months before bud sprouting, whereas differentiation takes place at the same time as sprouting. The induced buds develop single flowers or determinate inflorescences, so that vegetative growth is required at the axillary buds to renew the polycarpic habit. The presence of fruits inhibits sprouting and flower induction from nearby axillary buds in the current season. In some species and cultivars, this results in low flowering intensity the following spring, thus giving rise to alternate bearing. A number of key flowering genes act in the leaf (CiFT3, CcMADS19, etc.) or in the bud (CsLFY, CsTFL1, etc.) to promote or inhibit both flowering time and reproductive meristem identity in response to these climatic factors, the fruit dominance, or the age of the plant (juvenility). The expression of some of these genes can be modified by gibberellin treatments, which reduce bud sprouting and flowering in adult trees, and constitute the main horticultural technique to control flowering in citrus. This review presents a comprehensive view of all aspects of the flowering process in citrus, converging the research published during the past half century, which focused on plant growth regulators and the nutritional source-sink relationships and guided research toward the study of gene transcription and plant transformation, and the advances made with the development of the tools of molecular biology published during the current century.

Bradyrhizobium japonicum IRAT FA3 Alters Arabidopsis thaliana Root Architecture via Regulation of Auxin Efflux Transporters PIN2, PIN3, PIN7, and ABCB19

Beneficial rhizobacteria can stimulate changes in plant root development. Although root system growth is mediated by multiple factors, the regulated distribution of the phytohormone auxin within root tissues plays a principal role. Auxin transport facilitators help to generate the auxin gradients and maxima that determine root structure. Here, we show that the plant-growth-promoting rhizobacterial strain Bradyrhizobium japonicum IRAT FA3 influences specific auxin efflux transporters to alter Arabidopsis thaliana root morphology. Gene expression profiling of host transcripts in control and B. japonicum-inoculated roots of the wild-type A. thaliana accession Col-0 confirmed upregulation of PIN2, PIN3, PIN7, and ABCB19 with B. japonicum and identified genes potentially contributing to a diverse array of auxin-related responses. Cocultivation of the bacterium with loss-of-function auxin efflux transport mutants revealed that B. japonicum requires PIN3, PIN7, and ABCB19 to increase lateral root development and utilizes PIN2 to reduce primary root length. Accelerated lateral root primordia production due to B. japonicum was not observed in single pin3, pin7, or abcb19 mutants, suggesting independent roles for PIN3, PIN7, and ABCB19 during the plant-microbe interaction. Our work demonstrates B. japonicum's influence over host transcriptional reprogramming during plant interaction with this beneficial microbe and the subsequent alterations to root system architecture.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Targeted protein degradation and regulation with molecular glue: past and recent discoveries

The evolution in research and clinical settings of targeted therapies has been inspired by the progress of cancer chemotherapy to use small molecules and monoclonal antibodies for targeting specific disease-associated genes and proteins for noninfectious chronic diseases. In addition to conventional protein inhibition and activation strategies as drug discovery modalities, new methods of targeted protein degradation and regulation using molecular glues have become an attractive approach for drug discovery. Mechanistically, molecular glues trigger interactions between the proteins that originally did not interact by forming ternary complexes as protein-protein interaction (PPI) modulators. New molecular glues and their mechanisms of action have been actively investigated in the past decades. An immunomodulatory imide drug, thalidomide, and its derivatives have been used in the clinic and are a class of molecular glue that induces degradation of several neo-substrates. In this review, we summarize the development of molecular glues and share our opinions on the identification of novel molecular glues in an attempt to promote the concept and inspire further investigations.

Actin Isovariant ACT7 Modulates Root Thermomorphogenesis by Altering Intracellular Auxin Homeostasis

High temperature stress is one of the most threatening abiotic stresses for plants limiting the crop productivity world-wide. Altered developmental responses of plants to moderate-high temperature has been shown to be linked to the intracellular auxin homeostasis regulated by both auxin biosynthesis and transport. Trafficking of the auxin carrier proteins plays a major role in maintaining the cellular auxin homeostasis. The intracellular trafficking largely relies on the cytoskeletal component, actin, which provides track for vesicle movement. Different classes of actin and the isovariants function in regulating various stages of plant development. Although high temperature alters the intracellular trafficking, the role of actin in this process remains obscure. Using isovariant specific vegetative class actin mutants, here we demonstrate that ACTIN 7 (ACT7) isovariant plays an important role in regulating the moderate-high temperature response in Arabidopsis root. Loss of ACT7, but not ACT8 resulted in increased inhibition of root elongation under prolonged moderate-high temperature. Consistently, kinematic analysis revealed a drastic reduction in cell production rate and cell elongation in act7-4 mutant under high temperature. Quantification of actin dynamicity reveals that prolonged moderate-high temperature modulates bundling along with orientation and parallelness of filamentous actin in act7-4 mutant. The hypersensitive response of act7-4 mutant was found to be linked to the altered intracellular auxin distribution, resulted from the reduced abundance of PIN-FORMED PIN1 and PIN2 efflux carriers. Collectively, these results suggest that vegetative class actin isovariant, ACT7 modulates the long-term moderate-high temperature response in Arabidopsis root.

Triggering Bimodal Radial Stem Growth in Pinus sylvestris at a Drought-Prone Site by Manipulating Stem Carbon Availability

A bimodal radial growth (RG) pattern, i.e., growth peaks in spring and autumn, was repeatedly found in trees in the Mediterranean regions, where summer drought causes reduction or cessation of cambial activity. In a dry inner Alpine valley of the Eastern Alps (Tyrol, Austria, 750 m asl), Pinus sylvestris shows unimodal RG with onset and cessation of cambial activity in early April and late June, respectively. A resumption of cambial activity after intense summer rainfall was not observed in this region. In a field experiment, we tested the hypothesis that early cessation of cambial activity at this drought-prone site is an adaptation to limited water availability leading to an early and irreversible switch of carbon (C) allocation to belowground. To accomplish this, the C status of young P. sylvestris trees was manipulated by physical blockage of phloem transport (girdling) 6 weeks after cessation of cambial cell division. Influence of manipulated C availability on RG was recorded by stem dendrometers, which were mounted above the girdling zone. In response to blockage of phloem flow, resumption of cambial activity was detected above girdling after about 2 weeks. Although the experimentally induced second growth surge lasted for the same period as in spring (c. 2 months), the increment was more than twice as large due to doubling of daily maximum RG rate. After girdling, wood anatomical traits above girdling no longer showed any significant differences between earlywood and latewood tracheids indicating pronounced effects of C availability on cell differentiation. Below girdling, no reactivation of cambial activity occurred, but cell wall thickness of last formed latewood cell was reduced due to lack of C supply after girdling. Intense RG resumption after girdling indicates that cessation of cambial activity can be reversed by manipulating C status of the stem. Hence, our girdling study yielded strong support for the hypothesis that belowground organs exert high C sink strengths on the drought-prone study site. Furthermore, this work highlights the need of in-depth experimental studies in order to understand the interactions between endogenous and exogenous factors on cambial activity and xylem cell differentiation more clearly.

N-acetylglucosaminyltransferase II Is Involved in Plant Growth and Development Under Stress Conditions

Alpha-1,6-mannosyl-glycoprotein 2-β-N-acetylglucosaminyltransferase [EC 2.4.1.143, N-acetylglucosaminyltransferase II (GnTII)] catalyzes the transfer of N-acetylglucosamine (GlcNAc) residue from the nucleotide sugar donor UDP-GlcNAc to the α1,6-mannose residue of the di-antennary N-glycan acceptor GlcNAc(Xyl)Man₃(Fuc)GlcNAc₂ in the Golgi apparatus. Although the formation of the GlcNAc₂(Xyl)Man₃(Fuc)GlcNAc₂ N-glycan is known to be associated with GnTII activity in Arabidopsis thaliana, its physiological significance is still not fully understood in plants. To address the physiological importance of the GlcNAc₂(Xyl)Man₃(Fuc)GlcNAc₂ N-glycan, we examined the phenotypic effects of loss-of-function mutations in GnTII in the presence and absence of stress, and responsiveness to phytohormones. Prolonged stress induced by tunicamycin (TM) or sodium chloride (NaCl) treatment increased GnTII expression in wild-type Arabidopsis (ecotype Col-0) but caused severe developmental damage in GnTII loss-of-function mutants (gnt2-1 and gnt2-2). The absence of the 6-arm GlcNAc residue in the N-glycans in gnt2-1 facilitated the TM-induced unfolded protein response, accelerated dark-induced leaf senescence, and reduced cytokinin signaling, as well as susceptibility to cytokinin-induced root growth inhibition. Furthermore, gnt2-1 and gnt2-2 seedlings exhibited enhanced N-1-naphthylphthalamic acid-induced inhibition of tropic growth and development. Thus, GnTII's promotion of the 6-arm GlcNAc addition to N-glycans is important for plant growth and development under stress conditions, possibly via affecting glycoprotein folding and/or distribution.

The Photosynthetic Bacterium Rhodopseudomonas palustris Strain PS3 Exerts Plant Growth-Promoting Effects by Stimulating Nitrogen Uptake and Elevating Auxin Levels in Expanding Leaves

Rhodopseudomonas palustris strain PS3, a phototrophic bacterium, was originally isolated from a paddy field located in Taipei city, Taiwan, and showed positive effects on the growth of leafy vegetables. The aim of this study was to clarify the mechanism of the beneficial effects exerted by PS3 on plants. An ineffective R. palustris strain, YSC3, isolated from a paddy field located in Yilan County, was used as the negative control for comparative analyses. We cultivated non-heading Chinese cabbage (Brassica rapa var. chinensis) in 1/2 strength Hoagland hydroponic solution, in which nitrate is the main nitrogen source. We evaluated various plant physiological responses to inoculation with different bacterial inoculants. The N use efficiency (NUE) of PS3-inoculated plants was dramatically higher than that of YSC3-inoculated plants. The nitrate uptake efficiency (NUpE) was significantly elevated in plants treated with PS3; however, no excess nitrate accumulation was observed in leaves. We also noticed that the endogenous indole-3-acetic acid (IAA) levels as well as the cell division rate in the leaves of PS3-inoculated plants were significantly higher than those in the leaves of YSC3-inoculated plants. We examined the bacterial transcription of some genes during root colonization, and found that the expression level of IAA synthesis related gene MAO was almost the same between these two strains. It suggests that the elevated endogenous IAA in the PS3-inoculated plants was not directly derived from the exogenous IAA produced by this bacterium. Taken together, we deduced that PS3 inoculation could promote plant growth by enhancing nitrate uptake and stimulating the accumulation of endogenous auxin in young expanding leaves to increase the proliferation of leaf cells during leaf development.

Integrative Analysis of the Metabolome and Transcriptome of Sorghum bicolor Reveals Dynamic Changes in Flavonoids Accumulation under Saline-Alkali Stress

With the perpetuation of soil salinization, it is imperative to improve the salt and alkaline tolerance of crops. Sorghum bicolor, a C4 crop, is often grown in semiarid areas due to its high tolerance of various abiotic stresses. Whether to improve the resistance of the sorghum itself or that of other crops, it is necessary to understand the response of sorghum under saline-alkali stress. An integrative analysis of the metabolome and transcriptome of sorghum under normal conditions and treatments of moderate and severe saline-alkali stress was performed. Among the different accumulated metabolites (DAMs) and differentially expressed genes (DEGs), flavonoid-related DAMs and DEGs were clearly changed. The level of flavonoids was increased under saline-alkali stress, and the change in flavonoids was dynamic as to whether total flavonoids or most flavonoid components accumulated more under moderate saline-alkali stress compared to severe stress. Some flavonoid metabolites were significantly correlated with the expression of flavonoid biosynthesis genes. MYB transcription factors may also contribute to the regulation of flavonoids levels. These findings present the dynamic changes and possible molecular mechanisms of flavonoids under different saline-alkali stresses and provide a foundation for future research and crop improvement.

Gravistimulation effects on Oryza sativa amino acid profile, growth pattern and expression of OsPIN genes

Gravity is an important ecological factor regulating plant growth and developmental processes. Here we used various molecular and biochemical approaches to investigate artificial and normal gravistimulation's effect on the early growth stages of rice (Oryza sativa L.) by changing the orientations of Petri dishes. Rate of amino acid formation, root and shoot growth, and OsPIN expression was significantly higher under gravistimulation compared with the control. Clinostat rotation positively affected plant growth and amino acid profile. However, under normal gravity, vertical-oriented seedlings showed high amino acid levels compared with clinostat, 90°-rotated, and control seedlings. Similarly, seedling growth significantly increased with 90°-rotated and vertical orientations. Artificial gravity and exogenous indole-3-acetic acid induced OsPIN1 expression in the roots, root shoot junction, and shoots of clinorotated seedlings. Phenyl acetic acid induced OsPIN1 expression in the roots and root shoot junction of clinorotated seedlings but not in the shoot. The current study suggests that OsPIN1 is differentially regulated and that it might be involved in the regulation of plant growth. Conversely, OsPIN2 and OsPIN3a are gravity sensors and highly induced in the roots and root shoot junctions of vertical and 90°-rotated seedlings and play an important role in stress conditions. Thus, on exposure to gravity, hormones, and UV-C radiation, these genes are highly regulated by jasmonic acid, 6-benzylaminopurine and gibberellic acid.

Gibberellins modulate local auxin biosynthesis and polar auxin transport by negatively affecting flavonoid biosynthesis in the root tips of rice

As critical signalling molecules, both gibberellin (GA) and auxin play essential roles in regulating root elongation, and many studies have been shown that auxin influences GA biosynthesis and signalling. However, the mechanism by which GA affects auxin in root elongation is still unknown. In this study, root elongation and DR5-GUS activity were analyzed in rice seedlings. Paclobutrazol-induced short root phenotypes could be partially reversed by co-treatment with IAA, and the inhibition of root elongation caused by naphthylphthalamic acid could be partially reversed when plants were co-treated with GA. DR5-GUS activity was increased in the presence of GA and was reduced at the root tip of paclobutrazol-treated seedlings, indicating that GA could regulate local auxin biosynthesis and polar auxin transport (PAT) in rice root tips. Our RNA-seq analysis showed that GA was involved in the regulation of flavonoid biosynthesis. Flavonoid accumulation level in ks1 root tips was significantly increased and negatively correlated with GA content in GA- and PAC-treated seedlings. GA also rescued the decreased DR5-GUS activity induced by quercetin in rice root tips, confirming that flavonoids act as an intermediary in GA-mediated auxin biosynthesis and PAT. Based on RNA-seq and qPCR analyses, we determined that GA regulates local auxin biosynthesis and polar auxin transport by modulating the expression of OsYUCCA6 and PIN. Our findings provide valuable new insights into the interactions between GA and auxin in the root tips of rice.

Auxin-mediated root branching is determined by the form of available nitrogen

To improve water and nutrient acquisition from the soil, plants can modulate their root system architecture. Despite the importance of changes in root architecture to exploit local nutrient patches occurring in heterogenous soils or after placed fertilization, mechanisms integrating external nutrient signals into the root developmental programme remain poorly understood. Here, we show that local ammonium supply stimulates the accumulation of shoot-derived auxin in the root vasculature and promotes lateral root emergence to build a highly branched root system. Activities of pH and auxin reporters indicate that ammonium uptake mediated by ammonium transporters acidifies the root apoplast, which increases pH-dependent import of protonated auxin into cortical and epidermal cells overlaying lateral root primordia, and subsequently promotes their emergence from the parental root. Thereby, ammonium-induced and H⁺-ATPase-mediated acidification of the apoplast allows auxin to bypass the auxin importers AUX1 and LAX3. In nitrogen-deficient plants, auxin also accumulates in the root vasculature but a more alkaline apoplast leads to retention of auxin in these tissues and prevents lateral root formation. Our study highlights the impact of externally available nitrogen forms on pH-dependent radial auxin mobility and its regulatory function in organ development.

A Conditional Mutation in SCD1 Reveals Linkage Between PIN Protein Trafficking, Auxin Transport, Gravitropism, and Lateral Root Initiation

Auxin is transported in plants with distinct polarity, defined by transport proteins of the PIN-formed (PIN) family. Components of the complex trafficking machinery responsible for polar PIN protein localization have been identified by genetic approaches, but severe developmental phenotypes of trafficking mutants complicate dissection of this pathway. We utilized a temperature sensitive allele of Arabidopsis thaliana SCD1 (stomatal cytokinesis defective1) that encodes a RAB-guanine nucleotide exchange factor. Auxin transport, lateral root initiation, asymmetric auxin-induced gene expression after gravitropic reorientation, and differential gravitropic growth were reduced in the roots of the scd1-1 mutant relative to wild type at the restrictive temperature of 25°C, but not at the permissive temperature of 18°C. In scd1-1 at 25°C, PIN1- and PIN2-GFP accumulated in endomembrane bodies. Transition of seedlings from 18 to 25°C for as little as 20 min resulted in the accumulation of PIN2-GFP in endomembranes, while gravitropism and root developmental defects were not detected until hours after transition to the non-permissive temperature. The endomembrane compartments that accumulated PIN2-GFP in scd1-1 exhibited FM4-64 signal colocalized with ARA7 and ARA6 fluorescent marker proteins, consistent with PIN2 accumulation in the late or multivesicular endosome. These experiments illustrate the power of using a temperature sensitive mutation in the gene encoding SCD1 to study the trafficking of PIN2 between the endosome and the plasma membrane. Using the conditional feature of this mutation, we show that altered trafficking of PIN2 precedes altered auxin transport and defects in gravitropism and lateral root development in this mutant upon transition to the restrictive temperature.

Transcriptomic profiling and discovery of key genes involved in adventitious root formation from green cuttings of highbush blueberry (Vaccinium corymbosum L.)

BACKGROUND

Propagation of cuttings is frequently used in various plant species, including blueberry, which shows special root characteristics that may hinder adventitious root (AR) formation. AR formation is influenced by various factors, and auxin is considered to play a central role; however, little is known of the related regulatory mechanisms. In this study, a comparative transcriptome analysis of green cuttings treated with or without indole-butyric acid (IBA) was performed via RNA_seq to identify candidate genes associated with IBA-induced AR formation.

RESULTS

Rooting phenotypes, especially the rooting rate, were significantly promoted by exogenous auxin in the IBA application. Blueberry AR formation was an auxin-induced process, during which adventitious root primordium initiation (rpi) began at 14 days after cutting (DAC), root primordium (rp) was developed at 21 DAC, mature AR was observed at 28 DAC and finally outgrowth from the stem occurred at 35 DAC. Higher IAA levels and lower ABA and zeatin contents might facilitate AR formation and development. A time series transcriptome analysis identified 14,970 differentially expressed genes (DEGs) during AR formation, of which there were 7467 upregulated and 7503 downregulated genes. Of these, approximately 35 candidate DEGs involved in the auxin-induced pathway and AR formation were further identified, including 10 auxin respective genes (ARFs and SAURs), 13 transcription factors (LOB domain-containing protein (LBDs)), 6 auxin transporters (AUX22, LAX3/5 and PIN-like 6 (PIL6s)) and 6 rooting-associated genes (root meristem growth factor 9 (RGF9), lateral root primordium 1 (LRP1s), and dormancy-associated protein homologue 3 (DRMH3)). All these identified DEGs were highly upregulated in certain stages during AR formation, indicating their potential roles in blueberry AR formation.

CONCLUSIONS

The transcriptome profiling results indicated candidate genes or major regulatory factors that influence adventitious root formation in blueberry and provided a comprehensive understanding of the rooting mechanism underlying the auxin-induced AR formation from blueberry green cuttings.

YUCCA4 overexpression modulates auxin biosynthesis and transport and influences plant growth and development via crosstalk with abscisic acid in Arabidopsis thaliana

Auxin regulates a plethora of events during plant growth and development, acting in concert with other phytohormones. YUCCA genes encode flavin monooxygenases that function in tryptophan-dependent auxin biosynthesis. To understand the contribution of the YUCCA4 (YUC4) gene on auxin homeostasis, plant growth and interaction with abscisic acid (ABA) signaling, 35S::YUC4 seedlings were generated, which showed elongated hypocotyls with hyponastic leaves and changes in root system architecture that correlate with enhanced auxin responsive gene expression. Differential expression of PIN1, 2, 3 and 7 auxin transporters was detected in roots of YUC4 overexpressing seedlings compared to the wild-type: PIN1 was down-regulated whereas PIN2, PIN3 and PIN7 were up-regulated. Noteworthy, 35S::YUC4 lines showed enhanced sensitivity to ABA on seed germination and post-embryonic root growth, involving ABI4 transcription factor. The auxin reporter genes DR5::GUS, DR5::GFP and BA3::GUS further revealed that abscisic acid impairs auxin responses in 35S::YUC4 seedlings. Our results indicate that YUC4 overexpression influences several aspects of auxin homeostasis and reveal the critical roles of ABI4 during auxin-ABA interaction in germination and primary root growth.

Multi-omics analysis revealed that MAPK signaling and flavonoid metabolic pathway contributed to resistance against Meloidogyne incognita in the introgression line cucumber

Inhibiting giant cells (GCs) development is an important characteristic of introgression line cucumber IL10-1 against Meloidogyne incognita proved by our previous study, but the systematic regulatory pathways were unknown. To reveal the regulation pathways more comprehensively, in the current study, we performed a joint analysis of RNA-Seq and lable-free quantitative proteomics between the IL10-1 (resistant) and the CC3 (susceptible cucumber) after inoculation with M. incognita. The results indicated that flavonoid biosynthesis pathway was specifically enriched in IL10-1. And protein species of Csa5P590220 and Csa5P589940 associated with flavonoid biosynthesis were highly translated in IL10-1 compared with these in CC3 at 3 days post inoculation (dpi), which would resulted in the excess of flavonoids in IL10-1 roots. In addition, phosphoproteomic analysis found that phosphorylated protein species involved in MAPK signaling cascade were enhanced in IL10-1, while they were inhibited in CC3 at 3 dpi. Accordingly, we speculate that the enhanced MAPK cascade signaling plays an important role in signal transduction for IL10-1 regulating the flavonoid biosynthesis. Knowledge from the study provide important regulatory pathways and protein species of introgression line cucumber against M. incognita, which will help in efforts to improve the recognition of the resistance mechanism of plants against nematode. SIGNIFICANCE: The current approach of joint analysis in transcription level, protein level and protein phosphorylation level more comprehensively revealed the different expression patterns at the molecular level of resistant and susceptible cucumber after inoculation with M. incognita. Based on the different expression patterns, we explore the pathway of resistance regulation of resistant cucumber IL10-1. Moreover, our results are helpful for the discovery of key genes and then apply them to M. incognita-resistance breeding.

Potassium Stimulation of IAA Transport Mediated by the Arabidopsis Importer AUX1 Investigated in a Heterologous Yeast System

Auxin regulates diverse processes involved in plant growth and development. AUX1 is the first identified and most widely investigated auxin importer, and plays an important role in root gravitropism and the development of lateral root and root hair. However, the regulation of auxin transport by AUX1 is still not well understood. In this study, we examined the effect of metal ions on AUX1 transport function and found that the activity could be specifically stimulated four times by K⁺. Further experiments revealed the preference of KF on the enhancement of transport activity of AUX1 over KCl, KBr, and KI. In addition, the interaction between K⁺ and AUX1 confers AUX1 more resistant to thermal stress but more vulnerable to proteolysis. Conventional chemical modification indicated that the extracellular acidic amino acids of AUX1 play a key role in the K⁺ stimulation. Site-specific mutagenesis showed that the replacement of Asp¹⁶⁶, Asp²⁹³, and Asp³¹² of AUX1 to alanine deteriorated the K⁺-stimulated auxin transport. By contrast, when these residues were mutated to glutamate, lysine, or asparagine, only the D312E variant restored the IAA transport activity to the wild-type level. It is thus convinced that D312 is presumably the most promising residue for the K⁺ stimulation on AUX1.

In seedlings of Pinus radiata, jasmonic acid and auxin are differentially distributed on opposite sides of tilted stems affecting lignin monomer biosynthesis and composition

Plants respond to the loss of vertical growth re-orientating their affected organs. In trees, this phenomenon has received the scientific attention due to its importance for the forestry industry. Nowadays it is accepted that auxin distribution is involved in the modulation of the tilting response, but how this distribution is controlled is not fully clear. Auxin transporters that determine the spatio-temporal auxin distribution in radiate pine seedlings exposed to 45° of tilting were identified. Additionally, based on indications for an intimate plant hormone crosstalk in this process, IAA and JA contents were evaluated. The experiments revealed that expression of the auxin transporters was down-regulated in the upper half of the tilted stem, while being induced in the lower half. Moreover, transporter-coding genes were first induced at the apical zone of the stem. IAA was consistently redistributed toward the lower half, which is in accordance with the expression profile of the auxin transporters. In contrast, JA was mainly accumulated in the upper half of tilted stems. Finally, lignin content and monomeric composition were analyzed in both sides of stem and along the time course of tilting. As expected, lignin accumulation was higher at the lower half of stem at longer times of tilting. However, the most marked difference was the accumulation of the H-lignin monomer in the lower half, while the G-lignin unit was more dominant in the upper half. Here, we provide detailed insight in the distribution of IAA and JA, affecting the lignin composition during the tilting response in Pinus radiata seedlings.

Auxin Modulated Initiation of Lateral Roots Is Linked to Pericycle Cell Length in Maize

Auxin is essential for the regulation of root system architecture by controlling primary root elongation and lateral root (LR) formation. Exogenous auxin has been reported to inhibit primary root elongation and promote the formation of LRs. In this study, LR formation in the Zea mays primary root was quantitatively evaluated after exogenous auxin treatment by comparing the effects of auxin on two selected zones elongated either before or after auxin application. We determined two main variables in both zones: the LR density per unit of root length (LRD), and the mean phloem pericycle cell length. The total number of phloem pericycle cells (PPCs) per unit of root length was then calculated. Considering that each LR primordium is initiated from four founder cells (FCs), the percentage of PPCs (%PPC) that behave as FCs in a specific root zone was estimated by dividing the number of pericycle cells by four times the LRD. This index was utilized to describe LR initiation. Root zones elongated in the presence of a synthetic auxin (1-naphthalene acetic acid, NAA) at low concentrations (0.01 μM) showed reduced cell length and increased LRD. However, a high concentration of NAA (0.1 μM) strongly reduced both cell length and LRD. In contrast, both low and high levels of NAA stimulated LRD in zones elongated before auxin application. Analysis of the percentage of FCs in the phloem pericycle in zones elongated in the presence or absence of NAA showed that low concentrations of NAA increased the %PFC, indicating that LR initiation is promoted at new sites; however, high concentrations of NAA elicited a considerable reduction in this variable in zones developed in the presence of auxin. As these zones are composed of short pericycle cells, we propose that short pericycle cells are incapable to participate in LR primordium initiation and that auxin modulated initiation of LRs is linked to pericycle cell length.

Auxin methylation is required for differential growth in Arabidopsis

Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses.

Mitogen-Activated Protein Kinase Cascades in Plant Hormone Signaling

Mitogen-activated protein kinase (MAPK) modules play key roles in the transduction of environmental and developmental signals through phosphorylation of downstream signaling targets, including other kinases, enzymes, cytoskeletal proteins or transcription factors, in all eukaryotic cells. A typical MAPK cascade consists of at least three sequentially acting serine/threonine kinases, a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK) and finally, the MAP kinase (MAPK) itself, with each phosphorylating, and hence activating, the next kinase in the cascade. Recent advances in our understanding of hormone signaling pathways have led to the discovery of new regulatory systems. In particular, this research has revealed the emerging role of crosstalk between the protein components of various signaling pathways and the involvement of this crosstalk in multiple cellular processes. Here we provide an overview of current models and mechanisms of hormone signaling with a special emphasis on the role of MAPKs in cell signaling networks. One-sentence summary: In this review we highlight the mechanisms of crosstalk between MAPK cascades and plant hormone signaling pathways and summarize recent findings on MAPK regulation and function in various cellular processes.

UV-B Radiation Induces Root Bending Through the Flavonoid-Mediated Auxin Pathway in Arabidopsis

Ultraviolet (UV)-B radiation-induced root bending has been reported; however, the underlying mechanisms largely remain unclear. Here, we investigate whether and how auxin and flavonoids are involved in UV-B radiation-induced root bending in Arabidopsis using physiological, pharmacological, and genetic approaches. UV-B radiation modulated the direction of root growth by decreasing IAA biosynthesis and affecting auxin distribution in the root tips, where reduced auxin accumulation and asymmetric auxin distribution were observed. UV-B radiation increased the distribution of auxin on the nonradiated side of the root tips, promoting growth and causing root bending. Further analysis indicated that UV-B induced an asymmetric accumulation of flavonoids; this pathway is involved in modulating the accumulation and asymmetric distribution of auxin in root tips and the subsequent redirection of root growth by altering the distribution of auxin carriers in response to UV-B radiation. Taken together, our results indicate that UV-B radiation-induced root bending occurred through a flavonoid-mediated phototropic response to UV-B radiation.

Differential auxin transport and accumulation in the stem base lead to profuse adventitious root primordia formation in the aerial roots (aer) mutant of tomato (Solanum lycopersicum L.)

The aerial roots (aer) mutant of tomato is characterized by a profuse and precocious formation of adventitious root primordia along the stem. We demonstrated that auxin is involved in the aer phenotype but ruled out higher auxin sensitivity of mutant plants. Interestingly, polar auxin transport was altered in aer, as young seedlings showed a reduced response to an auxin transport inhibitor and higher expression of auxin export carriers SlPIN1 and SlPIN3. An abrupt reduction in transcripts of auxin efflux and influx genes in older aer hypocotyls caused a marked deceleration of auxin transport in more mature tissues. Indeed, in 20days old aer plants, the transport of labeled IAA was faster in apices than in hypocotyls, displaying an opposite trend in comparison to a wild type. In addition, auxin transport facilitators (SlPIN1, SlPIN4, SlLAX5) were more expressed in aer apices than in hypocotyls, suggesting that auxin moves faster from the upper to the lower part of the stem. Consequently, a significantly higher level of free and conjugated IAA was found at the base of aer stems with respect to their apices. This auxin accumulation is likely the cause of the aer phenotype.

Inhibitors of plant hormone transport

Here we present an overview of what is known about endogenous plant compounds that act as inhibitors of hormonal transport processes in plants, about their identity and mechanism of action. We have also summarized commonly and less commonly used compounds of non-plant origin and synthetic drugs that show at least partial 'specificity' to transport or transporters of particular phytohormones. Our main attention is focused on the inhibitors of auxin transport. The urgent need to understand precisely the molecular mechanism of action of these inhibitors is highlighted.

N-glycan containing a core α1,3-fucose residue is required for basipetal auxin transport and gravitropic response in rice (Oryza sativa)

In plants, α1,3-fucosyltransferase (FucT) catalyzes the transfer of fucose from GDP-fucose to asparagine-linked GlcNAc of the N-glycan core in the medial Golgi. To explore the physiological significance of this processing, we isolated two Oryza sativa (rice) mutants (fuct-1 and fuct-2) with loss of FucT function. Biochemical analyses of the N-glycan structure confirmed that α1,3-fucose is missing from the N-glycans of allelic fuct-1 and fuct-2. Compared with the wild-type cv Kitaake, fuct-1 displayed a larger tiller angle, shorter internode and panicle lengths, and decreased grain filling as well as an increase in chalky grains with abnormal shape. The mutant allele fuct-2 gave rise to similar developmental abnormalities, although they were milder than those of fuct-1. Restoration of a normal tiller angle in fuct-1 by complementation demonstrated that the phenotype is caused by the loss of FucT function. Both fuct-1 and fuct-2 plants exhibited reduced gravitropic responses. Expression of the genes involved in tiller and leaf angle control was also affected in the mutants. We demonstrate that reduced basipetal auxin transport and low auxin accumulation at the base of the shoot in fuct-1 account for both the reduced gravitropic response and the increased tiller angle.

Poplar woody taproot under bending stress: the asymmetric response of the convex and concave sides

Background and Aims Progress has been made in understanding the physiological and molecular basis of root response to mechanical stress, especially in the model plant Arabidopsis thaliana, in which bending causes the initiation of lateral root primordia toward the convex side of the bent root. In the case of woody roots, it has been reported that mechanical stress induces an asymmetric distribution of lateral roots and reaction wood formation, but the mechanisms underlying these responses are largely unknown. In the present work, the hypothesis was tested that bending could determine an asymmetric response in the two sides of the main root axis as cells are stretched on the convex side and compressed on the concave side. Methods Woody taproots of 20 seedlings were bent to an angle of 90° using a steel net. Changes in the anatomy, lignin and phytohormone content and proteome expression in the two sides of the bent root were analysed; anatomical changes, including dissimilarities and similarities to those found in poplar bent woody stem, were also considered. Key Results Compression forces at the concave side of poplar root induced the formation of reaction wood which presented a high lignin content and was associated with the induction of cambium cell activity. Auxin seemed to be the main hormone triggering lignin deposition and cell wall strengthening in the concave sides. Abscisic acid appeared to function in the water stress response induced by xylem structures and/or osmotic alterations in the compression sides, whereas gibberellins may control cell elongation and gravitropisms. Conclusions Poplar root reaction wood showed characteristics different from those produced in bent stem. Besides providing biomechanical functions, a bent root ensures water uptake and transport in the deforming condition induced by tension and compression forces by two different strategies: an increase in xylem thickness in the compressed side, and lateral root formation in the tension side.

The PIN1 family gene PvPIN1 is involved in auxin-dependent root emergence and tillering in switchgrass

Switchgrass (Panicum virgatum L.; family Poaceae) is a warm-season C4 perennial grass. Tillering plays an important role in determining the morphology of aboveground parts and the final biomass yield of switchgrass. Auxin distribution in plants can affect a variety of important growth and developmental processes, including the regulation of shoot and root branching, plant resistance and biological yield. Auxin transport and gradients in plants are mediated by influx and efflux carriers. PvPIN1, a switchgrass PIN1-like gene that is involved in regulating polar transport, is a putative auxin efflux carrier. Neighbor-joining analysis using sequences deposited in NCBI databases showed that the PvPIN1gene belongs to the PIN1 family and is evolutionarily closer to the Oryza sativa japonica group. Tiller emergence and development was significantly promoted in plants subjected toPvPIN1 RNA interference (RNAi), which yielded a phenotype similar to that of wild-type plants treated with the auxin transport inhibitor TIBA (2,3,5-triiodobenzoic acid). A transgenic approach that inducedPvPIN1 gene overexpression or suppression altered tiller number and the shoot/root ratio. These data suggest that PvPIN1plays an important role in auxin-dependent adventitious root emergence and tillering.

Modelling the emergence of polarity patterns for the intercellular transport of auxin in plants

The hormone auxin is actively transported throughout plants via protein machineries including the dedicated transporter known as PIN. The associated transport is ordered with nearby cells driving auxin flux in similar directions. Here, we provide a model of both the auxin transport and of the dynamics of cellular polarization based on flux sensing. Our main findings are: (i) spontaneous intracellular PIN polarization arises if PIN recycling dynamics are sufficiently nonlinear, (ii) there is no need for an auxin concentration gradient and (iii) ordered multi-cellular patterns of PIN polarization are favoured by molecular noise.

Different cucumber CsYUC genes regulate response to abiotic stresses and flower development

The phytohormone auxin is essential for plant growth and development, and YUCCA (YUC) proteins catalyze a rate-limiting step for endogenous auxin biosynthesis. Despite YUC family genes have been isolated from several species, systematic expression analyses of YUCs in response to abiotic stress are lacking, and little is known about the function of YUC homologs in agricultural crops. Cucumber (Cucumis sativus L.) is a world cultivated vegetable crop with great economical and nutritional value. In this study, we isolated 10 YUC family genes (CsYUCs) from cucumber and explored their expression pattern under four types of stress treatments. Our data showed that CsYUC8 and CsYUC9 were specifically upregulated to elevate the auxin level under high temperature. CsYUC10b was dramatically increased but CsYUC4 was repressed in response to low temperature. CsYUC10a and CsYUC11 act against the upregulation of CsYUC10b under salinity stress, suggesting that distinct YUC members participate in different stress response, and may even antagonize each other to maintain the proper auxin levels in cucumber. Further, CsYUC11 was specifically expressed in the male flower in cucumber, and enhanced tolerance to salinity stress and regulated pedicel and stamen development through auxin biosynthesis in Arabidopsis.

Variation in genomic methylation in natural populations of Populus simonii is associated with leaf shape and photosynthetic traits

DNA methylation, one of the best-studied types of chromatin modification, suppresses the expression of transposable elements, pseudogenes, repetitive sequences, and individual genes. However, the extent and variation of genome-wide DNA methylation in natural populations of plants remain relatively unknown. To investigate variation in DNA methylation and whether this variation associates with important plant traits, including leaf shape and photosynthesis, 20 413 DNA methylation sites were examined in a poplar association population (505 individuals) using methylation-sensitive amplification polymorphism (MSAP) technology. Calculation of epi-population structure and kinships assigned individuals into subsets (K=3), revealing that the natural population of P. simonii consists of three subpopulations. Population epigenetic distance and geographic distance showed a significant correlation (r=0.4688, P<0.001), suggesting that environmental factors may affect epigenetics. Single-marker approaches were also used to identify significant marker-trait associations, which found 1087 high-confidence DNA methylation markers associated with different phenotypic traits explaining ~5-15% of the phenotypic variance. Among these loci, 147 differentially methylated fragments were obtained by sequencing, representing 130 candidate genes. Expression analysis of six candidate genes indicated that these genes might play important roles in leaf development and regulation of photosynthesis. This study provides association analysis to study the effects of DNA methylation on plant development and these data indicate that epigenetics bridges environmental and genetic factors in affecting plant growth and development.

SPLINTS: small-molecule protein ligand interface stabilizers

Regulatory protein-protein interactions are ubiquitous in biology, and small molecule protein-protein interaction inhibitors are an important focus in drug discovery. Remarkably little attention has been given to the opposite strategy-stabilization of protein-protein interactions, despite the fact that several well-known therapeutics act through this mechanism. From a structural perspective, we consider representative examples of small molecules that induce or stabilize the association of protein domains to inhibit, or alter, signaling for nuclear hormone, GTPase, kinase, phosphatase, and ubiquitin ligase pathways. These SPLINTS (small-molecule protein ligand interface stabilizers) drive interactions that are in some cases physiologically relevant, and in others entirely adventitious. The diverse structural mechanisms employed suggest approaches for a broader and systematic search for such compounds in drug discovery.

Pin1At regulates PIN1 polar localization and root gravitropism

Root gravitropism allows plants to establish root systems and its regulation depends on polar auxin transport mediated by PIN-FORMED (PIN) auxin transporters. PINOID (PID) and PROTEIN PHOSPHATASE 2A (PP2A) act antagonistically on reversible phosphorylation of PINs. This regulates polar PIN distribution and auxin transport. Here we show that a peptidyl-prolyl cis/trans isomerase Pin1At regulates root gravitropism. Downregulation of Pin1At suppresses root agravitropic phenotypes of pp2aa and 35S:PID, while overexpression of Pin1At affects root gravitropic responses and enhances the pp2aa agravitropic phenotype. Pin1At also affects auxin transport and polar localization of PIN1 in stele cells, which is mediated by PID and PP2A. Furthermore, Pin1At catalyses the conformational change of the phosphorylated Ser/Thr-Pro motifs of PIN1. Thus, Pin1At mediates the conformational dynamics of PIN1 and affects PID- and PP2A-mediated regulation of PIN1 polar localization, which correlates with the regulation of root gravitropism.

Insights into the multifaceted application of microscopic techniques in plant tissue culture systems

Microscopic techniques remain an integral tool which has allowed for the better understanding and manipulation of in vitro plant culture systems. The recent advancements will inevitably help to unlock the long-standing mysteries of fundamental biological mechanisms of plant cells. Beyond the classical applications in micropropagation aimed at the conservation of endangered and elite commercial genotypes, plant cell, tissue and organ cultures have become a platform for elucidating a myriad of fundamental physiological and developmental processes. In conjunction with microscopic techniques, in vitro culture technology has been at the centre of important breakthroughs in plant growth and development. Applications of microscopy and plant tissue culture have included elucidation of growth and development processes, detection of in vitro-induced physiological disorders as well as subcellular localization using fluorescent protein probes. Light and electron microscopy have been widely used in confirming the bipolarity of somatic embryos during somatic embryogenesis. The technique highlights basic anatomical, structural and histological evidence for in vitro-induced physiological disorders during plant growth and development. In this review, we discuss some significant biological insights in plant growth and development, breakthroughs and limitations of various microscopic applications and the exciting possibilities offered by emergent in vivo live imaging and fluorescent protein engineering technologies.

Auxin and physical constraint exerted by the perianth promote androgynophore bending in Passiflora mucronata L. (Passifloraceae)

The androgynophore column, a distinctive floral feature in passion flowers, is strongly crooked or bent in many Passiflora species pollinated by bats. This is a floral feature that facilitates the adaptation to bat pollination. Crooking or bending of plant organs are generally caused by environmental stimulus (e.g. mechanical barriers) and might involve the differential distribution of auxin. Our aim was to study the role of the perianth organs and the effect of auxin in bending of the androgynophore of the bat-pollinated species Passiflora mucronata. Morpho-anatomical characterisation of the androgynophore, including measurements of curvature angles and cell sizes both at the dorsal (convex) and ventral (concave) sides of the androgynophore, was performed on control flowers, flowers from which perianth organs were partially removed and flowers treated either with auxin (2,4-dichlorophenoxyacetic acid; 2,4-D) or with an inhibitor of auxin polar transport (naphthylphthalamic acid; NPA). Asymmetric growth of the androgynophore column, leading to bending, occurs at a late stage of flower development. Removing the physical constraint exerted by perianth organs or treatment with NPA significantly reduced androgynophore bending. Additionally, the androgynophores of plants treated with 2,4-D were more curved when compared to controls. There was a larger cellular expansion at the dorsal side of the androgynophores of plants treated with 2,4-D and in both sides of the androgynophores of plants treated with NPA. This study suggests that the physical constraint exerted by perianth and auxin redistribution promotes androgynophore bending in P. mucronata and might be related to the evolution of chiropterophily in the genus Passiflora.

Isolation of developing secondary xylem specific cellulose synthase genes and their expression profiles during hormone signalling in Eucalyptus tereticornis

Cellulose synthases (CesA) represent a group of β-1, 4 glycosyl transferases involved in cellulose biosynthesis. Recent reports in higher plants have revealed that two groups of CesA gene families exist, which are associated with either primary or secondary cell wall deposition. The present study aimed at identifying developing secondary xylem specific cellulose synthase genes from Eucalyptus tereticornis, a species predominantly used in paper and pulp industries in the tropics. The differential expression analysis of the three EtCesA genes using qRT-PCR revealed 49 to 87 fold relative expression in developing secondary xylem tissues. Three full length gene sequences of EtCesA1, EtCesA2 and EtCesA3 were isolated with the size of 2940, 3114 and 3123 bp, respectively. Phytohormone regulation of all three EtCesA genes were studied by exogenous application of gibberellic acid, naphthalene acetic acid, indole acetic acid and 2, 4-epibrassinolide in internode tissues derived from three-month-old rooted cuttings. All three EtCesA transcripts were upregulated by indole acetic acid and gibberellic acid. This study demonstrates that the increased cellulose deposition in the secondary wood induced by hormones can be attributed to the upregulation of xylem specific CesAs.

The ZmCLA4 gene in the qLA4-1 QTL controls leaf angle in maize (Zea mays L.)

Maize architecture is a major contributing factor to their high level of productivity. Maize varieties with an erect-leaf-angle (LA) phenotype, which increases light harvesting for photosynthesis and grain-filling, have elevated grain yields. Although a large body of information is available on the map positions of quantitative trait loci (QTL) for LA, little is known about the molecular mechanism of these QTL. In this study, the ZmCLA4 gene, which is responsible for the qLA4-1 QTL associated with LA, was identified and isolated by fine mapping and positional cloning. The ZmCLA4 gene is an orthologue of LAZY1 in rice and Arabidopsis. Sequence analysis revealed two SNPs and two indel sites in ZmCLA4 between the D132 and D132-NIL inbred maize lines. Association analysis showed that C/T/mutation667 and CA/indel965 were strongly associated with LA. Subcellular localization verified the functions of a predicted transmembrane domain and a nuclear localization signal in ZmCLA4. Transgenic maize plants with a down-regulated ZmCLA4 RNAi construct and transgenic rice plants over-expressing ZmCLA4 confirmed that the ZmCLA4 gene located in the qLA4 QTL regulated LA. The allelic variants of ZmCLA4 in the D132 and D132-NIL lines exhibited significant differences in leaf angle. ZmCLA4 transcript accumulation was higher in D132-NIL than in D132 during all the developmental stages and was negatively correlated with LA. The gravitropic response was increased and cell shape and number at the leaf and stem junctions were altered in D132-NIL relative to D132. These findings suggest that ZmCLA4 plays a negative role in the control of maize LA through the alteration of mRNA accumulation, leading to altered shoot gravitropism and cell development. The cloning of the gene responsible for the qLA4-1 QTL provides information on the molecular mechanisms of LA in maize and an opportunity for the improvement of plant architecture with regard to LA through maize breeding.

Unexpectedly low nitrogen acquisition and absence of root architecture adaptation to nitrate supply in a Medicago truncatula highly branched root mutant

To complement N2 fixation through symbiosis, legumes can efficiently acquire soil mineral N through adapted root architecture. However, root architecture adaptation to mineral N availability has been little studied in legumes. Therefore, this study investigated the effect of nitrate availability on root architecture in Medicago truncatula and assessed the N-uptake potential of a new highly branched root mutant, TR185. The effects of varying nitrate supply on both root architecture and N uptake were characterized in the mutant and in the wild type. Surprisingly, the root architecture of the mutant was not modified by variation in nitrate supply. Moreover, despite its highly branched root architecture, TR185 had a permanently N-starved phenotype. A transcriptome analysis was performed to identify genes differentially expressed between the two genotypes. This analysis revealed differential responses related to the nitrate acquisition pathway and confirmed that N starvation occurred in TR185. Changes in amino acid content and expression of genes involved in the phenylpropanoid pathway were associated with differences in root architecture between the mutant and the wild type.

Phylogeny and molecular evolution analysis of PIN-FORMED 1 in angiosperm

PIN-FORMED 1 (PIN1) is an important secondary transporter and determines the direction of intercellular auxin flow. As PIN1 performs the conserved function of auxin transport, it is expected that the sequence and structure of PIN1 is conserved. Therefore, we hypothesized that PIN1 evolve under pervasive purifying selection in the protein-coding sequences in angiosperm. To test this hypothesis, we performed detailed evolutionary analyses of 67 PIN1 sequences from 35 angiosperm species. We found that the PIN1 sequences are highly conserved within their transmembrane regions, part of their hydrophilic regions. We also found that there are two or more PIN1 copies in some of these angiosperm species. PIN1 sequences from Poaceae and Brassicaceae are representative of the modern clade. We identified 12 highly conserved motifs and a significant number of family-specific sites within these motifs. One family-specific site within Motif 11 shows a different residue between monocots and dicots, and is functionally critical for the polarity of PIN1. Likewise, the function of PIN1 appears to be different between monocots and dicots since the phenotype associated with PIN1 overexpression is opposite between Arabidopsis and rice. The evolution of angiosperm PIN1 protein-coding sequences appears to have been primarily driven by purifying selection, but traces of positive selection associated with sequences from certain families also seem to be present. We verified this observation by calculating the numbers of non-synonymous and synonymous changes on each branch of a phylogenetic tree. Our results indicate that the evolution of angiosperm PIN1 sequences involve strong purifying selection. In addition, our results suggest that the conserved sequences of PIN1 derive from a combination of the family-specific site variations and conserved motifs during their unique evolutionary processes, which is critical for the functional integrity and stability of these auxin transporters, especially in new species. Finally, functional difference of PIN1 is likely to be present in angiosperm because the positive selection is occurred in one branch of Poaceae.