Indole-3-butyric acid induces lateral root formation via peroxisome-derived indole-3-acetic acid and nitric oxide

Nitric oxide: An emerging warrior of plant physiology under abiotic stress

The natural environment of plants comprises a complex set of various abiotic stresses and their capability to react and survive under this anticipated changing climate is highly flexible and involves a series of balanced interactions between signaling molecules where nitric oxide becomes a crucial component. In this article, we focussed on the role of nitric oxide (NO) in various signal transduction pathways of plants and its positive impact on maintaining cellular homeostasis under various abiotic stresses. Besides this, the recent data on interactions of NO with various phytohormones to control physiological and biochemical processes to attain abiotic stress tolerance have also been considered. These crosstalks modulate the plant's defense mechanism and help in alleviating the negative impact of stress. While focusing on the diverse functions of NO, an effort has been made to explore the functions of NO-mediated post-translational modifications, such as the N-end rule pathway, tyrosine nitration, and S-nitrosylation which revealed the exact mechanism and characterization of proteins that modify various metabolic processes in stressed conditions. Considering all of these factors, the present review emphasizes the role of NO and its interlinking with various phytohormones in maintaining developmental processes in plants, specifically under unfavorable environments.

Deciphering peroxisomal reactive species interactome and redox signalling networks

Plant peroxisomes are highly dynamic organelles with regard to metabolic pathways, number and morphology and participate in different metabolic processes and cell responses to their environment. Peroxisomes from animal and plant cells house a complex system of reactive oxygen species (ROS) production associated to different metabolic pathways which are under control of an important set of enzymatic and non enzymatic antioxidative defenses. Nitric oxide (NO) and its derivate reactive nitrogen species (RNS) are also produced in these organelles. Peroxisomes can regulate ROS and NO/RNS levels to allow their role as signalling molecules. The metabolism of other reactive species such as carbonyl reactive species (CRS) and sulfur reactive species (SRS) in peroxisomes and their relationship with ROS and NO have not been explored in depth. In this review, we define a peroxisomal reactive species interactome (PRSI), including all reactive species ROS, RNS, CRS and SRS, their interaction and effect on target molecules contributing to the dynamic redox/ROS homeostasis and plasticity of peroxisomes, enabling fine-tuned regulation of signalling networks associated with peroxisome-dependent H₂O₂. Particular attention will be paid to update the information available on H₂O₂-dependent peroxisomal retrograde signalling and to discuss a specific peroxisomal footprint.

Nitric Oxide Acts as a Key Signaling Molecule in Plant Development under Stressful Conditions

Nitric oxide (NO), a colorless gaseous molecule, is a lipophilic free radical that easily diffuses through the plasma membrane. These characteristics make NO an ideal autocrine (i.e., within a single cell) and paracrine (i.e., between adjacent cells) signalling molecule. As a chemical messenger, NO plays a crucial role in plant growth, development, and responses to biotic and abiotic stresses. Furthermore, NO interacts with reactive oxygen species, antioxidants, melatonin, and hydrogen sulfide. It regulates gene expression, modulates phytohormones, and contributes to plant growth and defense mechanisms. In plants, NO is mainly produced via redox pathways. However, nitric oxide synthase, a key enzyme in NO production, has been poorly understood recently in both model and crop plants. In this review, we discuss the pivotal role of NO in signalling and chemical interactions as well as its involvement in the mitigation of biotic and abiotic stress conditions. In the current review, we have discussed various aspects of NO including its biosynthesis, interaction with reactive oxygen species (ROS), melatonin (MEL), hydrogen sulfide, enzymes, phytohormones, and its role in normal and stressful conditions.

Auxin Crosstalk with Reactive Oxygen and Nitrogen Species in Plant Development and Abiotic Stress

The phytohormone auxin acts as an important signaling molecule having regulatory functions during the growth and development of plants. Reactive oxygen species (ROS) are also known to perform signaling functions at low concentrations; however, over-accumulation of ROS due to various environmental stresses damages the biomolecules and cell structures and leads to cell death, and therefore, it can be said that ROS act as a double-edged sword. Nitric oxide (NO), a gaseous signaling molecule, performs a wide range of favorable roles in plants. NO displays its positive role in photomorphogenesis, root growth, leaf expansion, seed germination, stomatal closure, senescence, fruit maturation, mitochondrial activity and metabolism of iron. Studies have revealed the early existence of these crucial molecules during evolution. Moreover, auxin, ROS and NO together show their involvement in various developmental processes and abiotic stress tolerance. Redox signaling is a primary response during exposure of plants to stresses and shows a link with auxin signaling. This review provides updated information related to crosstalk between auxin, ROS and NO starting from their evolution during early Earth periods and their interaction in plant growth and developmental processes as well as in the case of abiotic stresses to plants.

New Paradigms in Brassinosteroids, Strigolactones, Sphingolipids, and Nitric Oxide Interaction in the Control of Lateral and Adventitious Root Formation

The root system is formed by the primary root (PR), which forms lateral roots (LRs) and, in some cases, adventitious roots (ARs), which in turn may produce their own LRs. The formation of ARs is also essential for vegetative propagation in planta and in vitro and for breeding programs. Root formation and branching is coordinated by a complex developmental network, which maximizes the plant's ability to cope with abiotic stress. Rooting is also a response caused in a cutting by wounding and disconnection from the donor plant. Brassinosteroids (BRs) are steroid molecules perceived at the cell surface. They act as plant-growth-regulators (PGRs) and modulate plant development to provide stress tolerance. BRs and auxins control the formation of LRs and ARs. The auxin/BR interaction involves other PGRs and compounds, such as nitric oxide (NO), strigolactones (SLs), and sphingolipids (SPLs). The roles of these interactions in root formation and plasticity are still to be discovered. SLs are carotenoid derived PGRs. SLs enhance/reduce LR/AR formation depending on species and culture conditions. These PGRs possibly crosstalk with BRs. SPLs form domains with sterols within cellular membranes. Both SLs and SPLs participate in plant development and stress responses. SPLs are determinant for auxin cell-trafficking, which is essential for the formation of LRs/ARs in planta and in in vitro systems. Although little is known about the transport, trafficking, and signaling of SPLs, they seem to interact with BRs and SLs in regulating root-system growth. Here, we review the literature on BRs as modulators of LR and AR formation, as well as their crosstalk with SLs and SPLs through NO signaling. Knowledge on the control of rooting by these non-classical PGRs can help in improving crop productivity and enhancing AR-response from cuttings.

Sorting Nexin1 negatively modulates phosphate uptake by facilitating Phosphate Transporter1;1 degradation in Arabidopsis

High-affinity phosphate (Pi) transporters (PHTs) PHT1;1 and PHT1;4 are necessary for plant root Pi uptake especially under Pi-deficient conditions, but how their protein stability is modulated remains elusive. Here, we identified a Ttransfer DNA insertion mutant of Sorting Nexin1 (SNX1), which had more Pi content and less anthocyanin accumulation than the wild type under deficient Pi. By contrast, the snx1-2 mutant displayed higher sensitivity to exogenous arsenate in terms of seed germination and root elongation, revealing higher Pi uptake rates. Further study showed that SNX1 could co-localize and interact with PHT1;1 and PHT1;4 in vesicles and at the plasma membrane. Genetic analysis showed that increased Pi content in the snx1-2 mutant under low Pi conditions could be extensively compromised by mutating PHT1;1 in the double mutant snx1-2 pht1;1, revealing that SNX1 is epistatic to PHT1;1. In addition, SNX1 negatively controls PHT1;1 protein stability; therefore, PHT1;1 protein abundance in the plasma membrane was increased in the snx1-2 mutant compared with the wild type under either sufficient or deficient Pi. Together, our study (i) identifies SNX1 as a key modulator of the plant response to low Pi and (ii) unravels its role in the modulation of PHT1;1 protein stability, PHT1;1 accumulation at the plasma membrane, and root Pi uptake.

Prohibitin 3 gives birth to a new lateral root primordium

This article comments on: Li S, Li Q, Tian X, Mu L, Ji M, Wang X, Li N, Liu F, Shu J, Crawford NM, Wang Y. 2022. PHB3 regulates lateral root primordia formation via NO-mediated degradation of AUXIN/INDOLE-3-ACETIC ACID proteins. Journal of Experimental Botany 73,4034–4045.

Silicon induces adventitious root formation in rice under arsenate stress with involvement of nitric oxide and indole-3-acetic acid

Arsenic (As) negatively affects plant development. This study evaluates how the application of silicon (Si) can favor the formation of adventitious roots in rice under arsenate stress (AsV) as a mechanism to mitigate its negative effects. The simultaneous application of AsV and Si up-regulated the expression of genes involved in nitric oxide (NO) metabolism, cell cycle progression, auxin (IAA, indole-3-acetic acid) biosynthesis and transport, and Si uptake which accompanied adventitious root formation. Furthermore, Si triggered the expression and activity of enzymes involved in ascorbate recycling. Treatment with L-NAME (NG-nitro L-arginine methyl ester), an inhibitor of NO generation, significantly suppressed adventitious root formation, even in the presence of Si; however, supplying NO in the growth media rescued its effects. Our data suggest that both NO and IAA are essential for Si-mediated adventitious root formation under AsV stress. Interestingly, TIBA (2,3,5-triiodobenzoic acid), a polar auxin transport inhibitor, suppressed adventitious root formation even in the presence of Si and SNP (sodium nitroprusside, an NO donor), suggesting that Si is involved in a mechanism whereby a cellular signal is triggered and that first requires NO formation, followed by IAA biosynthesis.

Peroxisomes as redox-signaling nodes in intracellular communication and stress responses

Peroxisomes are redox nodes playing a diverse range of roles in cell functionality and in the perception of and responses to changes in their environment.

Nitric Oxide Alters the Pattern of Auxin Maxima and PIN-FORMED1 During Shoot Development

Hormone patterns tailor cell fate decisions during plant organ formation. Among them, auxins and cytokinins are critical phytohormones during early development. Nitric oxide (NO) modulates root architecture by the control of auxin spatial patterns. However, NO involvement during the coordination of shoot organogenesis remains unclear. Here, we explore the effect of NO during shoot development by using a phenotypic, cellular, and genetic analysis in Arabidopsis thaliana and get new insights into the characterization of NO-mediated leaf-related phenotypes. NO homeostasis mutants are impaired in several shoot architectural parameters, including phyllotactic patterns, inflorescence stem elongation, silique production, leaf number, and margin. Auxin distribution is a key feature for tissue differentiation and need to be controlled at different levels (i.e., synthesis, transport, and degradation mechanisms). The phenotypes resulting from the introduction of the cue1 mutation in the axr1 auxin resistant and pin1 backgrounds exacerbate the relationship between NO and auxins. Using the auxin reporter DR5:GUS, we observed an increase in auxin maxima under NO-deficient mutant backgrounds and NO scavenging, pointing to NO-ASSOCIATED 1 (NOA1) as the main player related to NO production in this process. Furthermore, polar auxin transport is mainly regulated by PIN-FORMED 1 (PIN1), which controls the flow along leaf margin and venations. Analysis of PIN1 protein levels shows that NO controls its accumulation during leaf development, impacting the auxin mediated mechanism of leaf building. With these findings, we also provide evidence for the NO opposite effects to determine root and shoot architecture, in terms of PIN1 accumulation under NO overproduction.

Comparative Transcriptome Analysis Provides New Insights into the Molecular Regulatory Mechanism of Adventitious Root Formation in Ramie (Boehmeria nivea L.)

The occurrence of adventitious roots is necessary for the survival of cuttings. In this study, comparative transcriptome analysis between two ramie (Boehmeria nivea L.) varieties with different adventitious root (AR) patterns was performed by mRNA-Seq before rooting (control, CK) and 10 days water-induced adventitious rooting (treatment, T) to reveal the regulatory mechanism of rooting. Characterization of the two ramie cultivars, Zhongzhu No 2 (Z2) and Huazhu No 4 (H4), indicated that Z2 had a high adventitious rooting rate but H4 had a low rooting rate. Twelve cDNA libraries of the two varieties were constructed, and a total of 26,723 genes were expressed. In the non-water culture condition, the number of the distinctive genes in H4 was 2.7 times of that in Z2, while in the water culture condition, the number of the distinctive genes in Z2 was nearly 2 times of that in H4. A total of 4411 and 5195 differentially expressed genes (DEGs) were identified in the comparison of H4CK vs. H4T and Z2CK vs. Z2T, respectively. After the water culture, more DEGs were upregulated in Z2, but more DEGs were downregulated in H4. Gene ontology (GO) functional analysis of the DEGs indicated that the polysaccharide metabolic process, carbohydrate metabolic process, cellular carbohydrate metabolic process, cell wall macromolecule metabolic process, and photosystem GO terms were distinctively significantly enriched in H4. Simultaneously, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that photosynthesis, photosynthesis antenna proteins, and starch and sucrose metabolism pathways were distinctively significantly enriched in H4. Moreover, KEGG analysis showed that jasmonic acid (JA) could interact with ethylene to regulate the occurrence and number of AR in Z2. This study reveals the transcriptomic divergence of two ramie varieties with high and low adventitious rooting rates, and provides insights into the molecular regulatory mechanism of AR formation in ramie.

Jasmonates, Ethylene and Brassinosteroids Control Adventitious and Lateral Rooting as Stress Avoidance Responses to Heavy Metals and Metalloids

Developmental and environmental signaling networks often converge during plant growth in response to changing conditions. Stress-induced hormones, such as jasmonates (JAs), can influence growth by crosstalk with other signals like brassinosteroids (BRs) and ethylene (ET). Nevertheless, it is unclear how avoidance of an abiotic stress triggers local changes in development as a response. It is known that stress hormones like JAs/ET and BRs can regulate the division rate of cells from the first asymmetric cell divisions (ACDs) in meristems, suggesting that stem cell activation may take part in developmental changes as a stress-avoidance-induced response. The root system is a prime responder to stress conditions in soil. Together with the primary root and lateral roots (LRs), adventitious roots (ARs) are necessary for survival in numerous plant species. AR and LR formation is affected by soil pollution, causing substantial root architecture changes by either depressing or enhancing rooting as a stress avoidance/survival response. Here, a detailed overview of the crosstalk between JAs, ET, BRs, and the stress mediator nitric oxide (NO) in auxin-induced AR and LR formation, with/without cadmium and arsenic, is presented. Interactions essential in achieving a balance between growth and adaptation to Cd and As soil pollution to ensure survival are reviewed here in the model species Arabidopsis and rice.

Functional Characterization of GhACX3 Gene Reveals Its Significant Role in Enhancing Drought and Salt Stress Tolerance in Cotton

The acyl-coenzyme A oxidase 3 (ACX3) gene involved in the β-oxidation pathway plays a critical role in plant growth and development as well as stress response. Earlier on, studies focused primarily on the role of β-oxidation limited to fatty acid breakdown. However, ACX3 peroxisomal β-oxidation pathways result in a downstream cascade of events that act as a transduction of biochemical and physiological responses to stress. A role that is yet to be studied extensively. In this study, we identified 20, 18, 22, 23, 20, 11, and 9 proteins in Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum, G. darwinii, G. arboretum, and G. raimondii genomes, respectively. The tetraploid cotton genome had protein ranging between 18 and 22, while diploids had between 9 and 11. After analyzing the gene family evolution or selection pressure, we found that this gene family undergoes purely segmental duplication both in diploids and tetraploids. W-Box (WRKY-binding site), ABRE, CAAT-Box, TATA-box, MYB, MBS, LTR, TGACG, and CGTCA-motif are abiotic stress cis-regulatory elements identified in this gene family. All these are the binding sites for abiotic stress transcription factors, indicating that this gene is essential. Genes found in G. hirsutum showed a clear response to drought and salinity stress, with higher expression under drought and salt stress, particularly in the leaf and root, according to expression analysis. We selected Gh_DO1GO186, one of the highly expressed genes, for functional characterization. We functionally characterized the GhACX3 gene through overexpression and virus-induced gene silencing (VIGS). Overexpression of this gene enhanced tolerance under stress, which was exhibited by the germination assay. The overexpressed seed growth rate was faster relative to control under drought and salt stress conditions. The survival rate was also higher in overexpressed plants relative to control plants under stress. In contrast, the silencing of the GhACX3 gene in cotton plants resulted in plants showing the stress susceptibility phenotype and reduced root length compared to control. Biochemical analysis also demonstrated that GhACX3-silenced plants experienced oxidative stress while the overexpressed plants did not. This study has revealed the importance of the ACX3 family during stress tolerance and can breed stress-resilient cultivar.

Physiological significance of pedospheric nitric oxide for root growth, development and organismic interactions

Nitric oxide (NO) is essential for plant growth and development, as well as interactions with abiotic and biotic environments. Its importance for multiple functions in plants means that tight regulation of NO concentrations is required. This is of particular significance in roots, where NO signalling is involved in processes, such as root growth, lateral root formation, nutrient acquisition, heavy metal homeostasis, symbiotic nitrogen fixation and root-mycorrhizal fungi interactions. The NO signal can also be produced in high levels by microbial processes in the rhizosphere, further impacting root processes. To explore these interesting interactions, in the present review, we firstly summarize current knowledge of physiological processes of NO production and consumption in roots and, thereafter, of processes involved in NO homeostasis in root cells with particular emphasis on root growth, development, nutrient acquisition, environmental stresses and organismic interactions.

Indole-3-butyric acid priming reduced cadmium toxicity in barley root tip via NO generation and enhanced glutathione peroxidase activity

Activation of GPX and enhanced NO level play a key role in IBA-mediated enhanced Cd tolerance in young barley roots. Application of exogenous indole-3-acetic acid (IAA) or an IAA precursor improves the tolerance of plants to heavy metals. However, the physiology of these tolerance mechanisms remains largely unknown. Therefore, we studied the priming effect of indole-3-butyric acid (IBA), an IAA precursor, on mild and severe cadmium (Cd) stress-induced responses in roots of young barley seedlings. IBA, similarly to mild Cd stress, significantly increased the glutathione peroxidase (GPX) activity in the apexes of barley roots, which remained elevated after the IBA pretreatment as well. IBA pretreatment-evoked high nitric oxide generation in roots effectively reduced the high superoxide level under the severe Cd stress, leading to less toxic peroxynitrite accumulation accompanied by markedly reduced Cd-induced cell death. On the other hand, the IBA-evoked changes in IAA homeostasis resulted in root growth reorientation from longitudinal elongation to radial swelling. However, the application of an IAA signaling inhibitor, following the activation of defense responses by IBA, was able to promote root growth even at high concentrations of Cd. Based on the results, it can be concluded that the application of IBA, as an effective activator of Cd tolerance mechanisms in young barley roots, and the subsequent use of an IAA signaling inhibitor for the inhibition of root morphogenic responses induced by altered auxin metabolism, results in a high degree of root Cd tolerance, helping it to withstand even the transient exposure to lethal Cd concentration without the absolute inhibition of root growth.

Nitric Oxide Cooperates With Auxin to Mitigate the Alterations in the Root System Caused by Cadmium and Arsenic

Oryza sativa L. is a worldwide food-crop frequently growing in cadmium (Cd)/arsenic (As) polluted soils, with its root-system as the first target of the pollutants. Root-system development involves the establishment of optimal indole-3-acetic acid (IAA) levels, also requiring the conversion of the IAA natural precursor indole-3-butyric acid (IBA) into IAA, causing nitric oxide (NO) formation. Nitric oxide is a stress-signaling molecule. In rice, a negative interaction of Cd or As with endogenous auxin has been demonstrated, as some NO protective effects. However, a synergism between the natural auxins (IAA and/or IBA) and NO was not yet determined and might be important for ameliorating rice metal(oid)-tolerance. With this aim, the stress caused by Cd/As toxicity in the root cells and the possible recovery by either NO or auxins (IAA/IBA) were evaluated after Cd or As (arsenate) exposure, combined or not with the NO-donor compound sodium-nitroprusside (SNP). Root fresh weight, membrane electrolyte leakage, and H2O2 production were also measured. Moreover, endogenous IAA/IBA contents, transcription-levels of OsYUCCA1 and OsASA2 IAA-biosynthetic-genes, and expression of the IAA-influx-carrier OsAUX1 and the IAA-responsive DR5::GUS construct were analyzed, and NO-epifluorescence levels were measured. Results showed that membrane injury by enhanced electrolyte leakage occurred under both pollutants and was reduced by the treatment with SNP only in Cd-presence. By contrast, no membrane injury was caused by either exogenous NO or IAA or IBA. Cd- and As-toxicity also resulted into a decreased root fresh weight, mitigated by the combination of each pollutant with either IAA or IBA. Cd and As decreased the endogenous NO-content, increased H2O2 formation, and altered auxin biosynthesis, levels and distribution in both adventitious (ARs) and mainly lateral roots (LRs). The SNP-formed NO counteracted the pollutants' effects on auxin distribution/levels, reduced H2O2 formation in Cd-presence, and enhanced AUX1-expression, mainly in As-presence. Each exogenous auxin, but mainly IBA, combined with Cd or As at 10 µM, mitigated the pollutants' effects by increasing LR-production and by increasing NO-content in the case of Cd. Altogether, results demonstrate that NO and auxin(s) work together in the rice root system to counteract the specific toxic-effects of each pollutant.

Plant Peroxisomes: A Factory of Reactive Species

Plant peroxisomes are organelles enclosed by a single membrane whose biochemical composition has the capacity to adapt depending on the plant tissue, developmental stage, as well as internal and external cellular stimuli. Apart from the peroxisomal metabolism of reactive oxygen species (ROS), discovered several decades ago, new molecules with signaling potential, including nitric oxide (NO) and hydrogen sulfide (H2S), have been detected in these organelles in recent years. These molecules generate a family of derived molecules, called reactive nitrogen species (RNS) and reactive sulfur species (RSS), whose peroxisomal metabolism is autoregulated through posttranslational modifications (PTMs) such as S-nitrosation, nitration and persulfidation. The peroxisomal metabolism of these reactive species, which can be weaponized against pathogens, is susceptible to modification in response to external stimuli. This review aims to provide up-to-date information on crosstalk between these reactive species families and peroxisomes, as well as on their cellular environment in light of the well-recognized signaling properties of H2O2, NO and H2S.

Cadmium and arsenic-induced-stress differentially modulates Arabidopsis root architecture, peroxisome distribution, enzymatic activities and their nitric oxide content

In plant cells, cadmium (Cd) and arsenic (As) exert toxicity mainly by inducing oxidative stress through an imbalance between the production of reactive oxygen species (ROS) and reactive nitrogen species (RNS), and their detoxification. Nitric oxide (NO) is a RNS acting as signalling molecule coordinating plant development and stress responses, but also as oxidative stress inducer, depending on its cellular concentration. Peroxisomes are versatile organelles involved in plant metabolism and signalling, with a role in cellular redox balance thanks to their antioxidant enzymes, and their RNS (mainly NO) and ROS. This study analysed Cd or As effects on peroxisomes, and NO production and distribution in the root system, including primary root (PR) and lateral roots (LRs). Arabidopsis thaliana wild-type and transgenic plants enabling peroxisomes to be visualized in vivo, through the expression of the 35S-cyan fluorescent protein fused to the peroxisomal targeting signal1 (PTS1) were used. Peroxisomal enzymatic activities including the antioxidant catalase, the H₂O₂-generating glycolate oxidase, and the hydroxypyruvate reductase, and root system morphology were also evaluated under Cd/As exposure. Results showed that Cd and As differently modulate these activities, however, catalase activity was inhibited by both. Moreover, Arabidopsis root system was altered, with the pollutants differently affecting PR growth, but similarly enhancing LR formation. Only in the PR apex, and not in LR one, Cd more than As caused significant changes in peroxisome distribution, size, and in peroxisomal NO content. By contrast, neither pollutant caused significant changes in peroxisomes size and peroxisomal NO content in the LR apex.

Inoculation with the mycorrhizal fungus Rhizophagus irregularis modulates the relationship between root growth and nutrient content in maize (Zea mays ssp. mays L.)

Plant root systems play a fundamental role in nutrient and water acquisition. In resource-limited soils, modification of root system architecture is an important strategy to optimize plant performance. Most terrestrial plants also form symbiotic associations with arbuscular mycorrhizal fungi to maximize nutrient uptake. In addition to direct delivery of nutrients, arbuscular mycorrhizal fungi benefit the plant host by promoting root growth. Here, we aimed to quantify the impact of arbuscular mycorrhizal symbiosis on root growth and nutrient uptake in maize. Inoculated plants showed an increase in both biomass and the total content of twenty quantified elements. In addition, image analysis showed mycorrhizal plants to have denser, more branched root systems. For most of the quantified elements, the increase in content in mycorrhizal plants was proportional to root and overall plant growth. However, the increase in boron, calcium, magnesium, phosphorus, sulfur, and strontium was greater than predicted by root system size alone, indicating fungal delivery to be supplementing root uptake.

Retrograde response by reactive oxygen/nitrogen species in plants involving different cellular organelles

During oxidative and nitrosative stress conditions cellular organelles convey information to the nucleus to express specific sets of genes to withstand the stress condition and to reorganize their growth and developmental pattern. This organelle to nucleus communication is termed retrograde signaling. In the plant system chloroplast and peroxisomes are mainly involved with little involvement of mitochondria and other organelles in oxidative stress-mediated retrograde signaling. In this review, we will discuss retrograde signaling in plant systems with factors that regulate this signaling cascade.

Impact of Nitric Oxide (NO) on the ROS Metabolism of Peroxisomes

Nitric oxide (NO) is a gaseous free radical endogenously generated in plant cells. Peroxisomes are cell organelles characterized by an active metabolism of reactive oxygen species (ROS) and are also one of the main cellular sites of NO production in higher plants. In this mini-review, an updated and comprehensive overview is presented of the evidence available demonstrating that plant peroxisomes have the capacity to generate NO, and how this molecule and its derived products, peroxynitrite (ONOO⁻) and S-nitrosoglutathione (GSNO), can modulate the ROS metabolism of peroxisomes, mainly throughout protein posttranslational modifications (PTMs), including S-nitrosation and tyrosine nitration. Several peroxisomal antioxidant enzymes, such as catalase (CAT), copper-zinc superoxide dismutase (CuZnSOD), and monodehydroascorbate reductase (MDAR), have been demonstrated to be targets of NO-mediated PTMs. Accordingly, plant peroxisomes can be considered as a good example of the interconnection existing between ROS and reactive nitrogen species (RNS), where NO exerts a regulatory function of ROS metabolism acting upstream of H₂O₂.

ABCG36/PEN3/PDR8 Is an Exporter of the Auxin Precursor, Indole-3-Butyric Acid, and Involved in Auxin-Controlled Development

The PDR-type ABCG transporter, ABCG36/PDR8/PEN3, is thought to be implicated in the export of a few structurally unrelated substrates, including the auxin precursor, indole-3-butyric acid (IBA), although a clear-cut proof of transport is lacking. An outward facing, lateral root (LR) location for ABCG36 fuelled speculations that it might secrete IBA into the rhizosphere. Here, we provide strong evidence that ABCG36 catalyzes the export of IBA - but not of indole-3-acetic acid - through the plasma membrane. ABCG36 seems to function redundantly with the closely related isoform ABCG37/PDR9/PIS1 in a negative control of rootward IBA transport in roots, which might be dampened by concerted, lateral IBA export. Analyses of single and double mutant phenotypes suggest that both ABCG36 and ABCG37 function cooperatively in auxin-controlled plant development. Both seem to possess a dual function in the control of auxin homeostasis in the root tip and long-range transport in the mature root correlating with non-polar and polar expression profiles in the LR cap and epidermis, respectively.

Nitric Oxide Affects Rice Root Growth by Regulating Auxin Transport Under Nitrate Supply

Nitrogen (N) is a major essential nutrient for plant growth, and rice is an important food crop globally. Although ammonium (NH4+) is the main N source for rice, nitrate (NO3-) is also absorbed and utilized. Rice responds to NO3- supply by changing root morphology. However, the mechanisms of rice root growth and formation under NO3- supply are unclear. Nitric oxide (NO) and auxin are important regulators of root growth and development under NO3- supply. How the interactions between NO and auxin in regulating root growth in response to NO3- are unknown. In this study, the levels of indole-3-acetic acid (IAA) and NO in roots, and the responses of lateral roots (LRs) and seminal roots (SRs) to NH4+ and NO3-, were investigated using wild-type (WT) rice, as well as osnia2 and ospin1b mutants. NO3- supply promoted LR formation and SR elongation. The effects of NO donor and NO inhibitor/scavenger supply on NO levels and the root morphology of WT and nia2 mutants under NH4+ or NO3- suggest that NO3--induced NO is generated by the nitrate reductase (NR) pathway rather than the NO synthase (NOS)-like pathway. IAA levels, [3H] IAA transport, and PIN gene expression in roots were enhanced under NO3- relative to NH4+ supply. These results suggest that NO3- regulates auxin transport in roots. Application of SNP under NH4+ supply, or of cPTIO under NO3- supply, resulted in auxin levels in roots similar to those under NO3- and NH4+ supply, respectively. Compared to WT, the roots of the ospin1b mutant had lower auxin levels, fewer LRs, and shorter SRs. Thus, NO affects root growth by regulating auxin transport in response to NO3-. Overall, our findings suggest that NO3- influences LR formation and SR elongation by regulating auxin transport via a mechanism involving NO.

Root bacterial endophytes confer drought resistance and enhance expression and activity of a vacuolar H+ -pumping pyrophosphatase in pepper plants

It has been previously shown that the transgenic overexpression of the plant root vacuolar proton pumps H+ -ATPase (V-ATPase) and H+ -PPase (V-PPase) confer tolerance to drought. Since plant-root endophytic bacteria can also promote drought tolerance, we hypothesize that such promotion can be associated to the enhancement of the host vacuolar proton pumps expression and activity. To test this hypothesis, we selected two endophytic bacteria endowed with an array of in vitro plant growth promoting traits. Their genome sequences confirmed the presence of traits previously shown to confer drought resistance to plants, such as the synthesis of nitric oxide and of organic volatile organic compounds. We used the two strains on pepper (Capsicuum annuum L.) because of its high sensitivity to drought. Under drought conditions, both strains stimulated a larger root system and enhanced the leaves' photosynthetic activity. By testing the expression and activity of the vacuolar proton pumps, H+ -ATPase (V-ATPase) and H+ -PPase (V-PPase), we found that bacterial colonization enhanced V-PPase only. We conclude that the enhanced expression and activity of V-PPase can be favoured by the colonization of drought-tolerance-inducing bacterial endophytes.

Arabidopsis thaliana GH3.15 acyl acid amido synthetase has a highly specific substrate preference for the auxin precursor indole-3-butyric acid

Various phytohormones control plant growth and development and mediate biotic and abiotic stress responses. Gretchen Hagen 3 (GH3) acyl acid amido synthetases are plant enzymes that typically conjugate amino acids to indole-3-acetic acid (IAA) or jasmonic acid (JA) to inactivate or activate these phytohormones, respectively; however, the physiological and biological roles of many of these enzymes remain unclear. Using a biochemical approach, we found that the Arabidopsis thaliana GH3.15 (AtGH3.15) preferentially uses indole-3-butyric acid (IBA) and glutamine as substrates. The X-ray crystal structure of the AtGH3.15·AMP complex, modeling of IBA in the active site, and biochemical analysis of site-directed mutants provide insight on active site features that lead to AtGH3.15's preference for IBA. Assay-based in planta analysis of AtGH3.15-overexpressing lines indicated that their root elongation and lateral root density were resistant to IBA treatment but not to treatment with either IAA or JA. These findings suggest that AtGH3.15 may play a role in auxin homeostasis by modulating the levels of IBA for peroxisomal conversion to IAA. Analysis of AtGH3.15 promoter-driven yellow fluorescent protein reporter lines revealed that AtGH3.15 is expressed at significant levels in seedlings, roots, and parts of the siliques. We conclude that AtGH3.15 is unique in the GH3 protein family for its role in modifying IBA in auxin homeostasis and that it is the first GH3 protein shown to primarily modify a plant growth regulator other than IAA and JA.

Peroxisomal plant metabolism - an update on nitric oxide, Ca2+ and the NADPH recycling network

Plant peroxisomes are recognized organelles that - with their capacity to generate greater amounts of H₂O₂ than other subcellular compartments - have a remarkable oxidative metabolism. However, over the last 15 years, new information has shown that plant peroxisomes contain other important molecules and enzymes, including nitric oxide (NO), peroxynitrite, a NADPH-recycling system, Ca²⁺ and lipid-derived signals, such as jasmonic acid (JA) and nitro-fatty acid (NO₂-FA). This highlights the potential for complex interactions within the peroxisomal nitro-oxidative metabolism, which also affects the status of the cell and consequently its physiological processes. In this review, we provide an update on the peroxisomal interactions between all these molecules. Particular emphasis will be placed on the generation of the free-radical NO, which requires the presence of Ca²⁺, calmodulin and NADPH redox power. Peroxisomes possess several NADPH regeneration mechanisms, such as those mediated by glucose-6-phosphate dehydrogenase (G6PDH) and 6-phosphogluconate dehydrogenase (6PGDH) proteins, which are involved in the oxidative phase of the pentose phosphate pathway, as well as that mediated by NADP-isocitrate dehydrogenase (ICDH). The generated NADPH is also an essential cofactor across other peroxisomal pathways, including the antioxidant ascorbate-glutathione cycle and unsaturated fatty acid β-oxidation, the latter being a source of powerful signaling molecules such as JA and NO₂-FA.

Roles for IBA-derived auxin in plant development

The plant hormone auxin is a central regulator of plant growth and development. Because auxin plays critical roles in cell division and cell expansion, plants use a number of cellular mechanisms to regulate auxin levels and response. Among these mechanisms is regulated input from the auxin precursor indole-3-butyric acid (IBA) toward the pool of active auxin [indole-3-acetic acid (IAA)]. In this review, we cover the mechanisms of IBA transport and conversion, and discuss specific roles for IBA-derived auxin in driving certain developmental events. We further discuss multiple open questions remaining for the IBA field.

A Role for RNS in the Communication of Plant Peroxisomes with Other Cell Organelles?

Plant peroxisomes are organelles with a very active participation in the cellular regulation of the metabolism of reactive oxygen species (ROS). However, during the last two decades peroxisomes have been shown to be also a relevant source of nitric oxide (NO) and other related molecules designated as reactive nitrogen species (RNS). ROS and RNS have been mainly associated to nitro-oxidative processes; however, some members of these two families of molecules such as H₂O₂, NO or S-nitrosoglutathione (GSNO) are also involved in the mechanism of signaling processes mainly through post-translational modifications. Peroxisomes interact metabolically with other cell compartments such as chloroplasts, mitochondria or oil bodies in different pathways including photorespiration, glyoxylate cycle or β-oxidation, but peroxisomes are also involved in the biosynthesis of phytohormones including auxins and jasmonic acid (JA). This review will provide a comprehensive overview of peroxisomal RNS metabolism with special emphasis in the identified protein targets of RNS inside and outside these organelles. Moreover, the potential interconnectivity between peroxisomes and other plant organelles, such as mitochondria or chloroplasts, which could have a regulatory function will be explored, with special emphasis on photorespiration.

Preference of Arabidopsis thaliana GH3.5 acyl amido synthetase for growth versus defense hormone acyl substrates is dictated by concentration of amino acid substrate aspartate

The GH3 family of adenylating enzymes conjugate acyl substrates such as the growth hormone indole-3-acetic acid (IAA) to amino acids via a two-step reaction of acyl substrate adenylation followed by amino acid conjugation. Arabidopsis thaliana GH3.5 was previously shown to be unusual in that it could adenylate both IAA and the defense hormone salicylic acid (SA, 2-hydroxybenzoate). Our detailed studies of the kinetics of GH3.5 on a variety of auxin and benzoate substrates provides insight into the acyl preference and reaction mechanism of GH3.5. For example, we found GH3.5 activity on substituted benzoates is not defined by the substitution position as it is for GH3.12/PBS3. Most importantly, we show that GH3.5 strongly prefers Asp as the amino acid conjugate and that the concentration of Asp dictates the functional activity of GH3.5 on IAA vs. SA. Not only is Asp used in amino acid biosynthesis, but it also plays an important role in nitrogen mobilization and in the production of downstream metabolites, including pipecolic acid which propagates defense systemically. During active growth, [IAA] and [Asp] are high and the catalytic efficiency (k_cat/K_m) of GH3.5 for IAA is 360-fold higher than with SA. GH3.5 is expressed under these conditions and conversion of IAA to inactive IAA-Asp would provide fine spatial and temporal control over local auxin developmental responses. By contrast, [SA] is dramatically elevated in response to (hemi)-biotrophic pathogens which also induce GH3.5 expression. Under these conditions, [Asp] is low and GH3.5 has equal affinity (K_m) for SA and IAA with similar catalytic efficiencies. However, the concentration of IAA tends to be very low, well below the K_m for IAA. Therefore, GH3.5 catalyzed formation of SA-Asp would occur, fine-tuning localized defensive responses through conversion of active free SA to SA-Asp. Taken together, we show how GH3.5, with dual activity on IAA and SA, can integrate cellular metabolic status via Asp to provide fine control of growth vs. defense outcomes and hormone homeostasis.

A Critical View on ABC Transporters and Their Interacting Partners in Auxin Transport

Different subclasses of ATP-binding cassette (ABC) transporters have been implicated in the transport of native variants of the phytohormone auxin. Here, the putative, individual roles of key members belonging to the ABCB, ABCD and ABCG families, respectively, are highlighted and the knowledge of their assumed expression and transport routes is reviewed and compared with their mutant phenotypes. Protein-protein interactions between ABC transporters and regulatory components during auxin transport are summarized and their importance is critically discussed. There is a focus on the functional interaction between members of the ABCB family and the FKBP42, TWISTED DWARF1, acting as a chaperone during plasma membrane trafficking of ABCBs. Further, the mode and relevance of functional ABCB-PIN interactions is diagnostically re-evaluated. A new nomenclature describing precisely the most likely ABCB-PIN interaction scenarios is suggested. Finally, available tools for the detection and prediction of ABC transporter interactomes are summarized and the potential of future ABC transporter interactome maps is highlighted.

Transcriptomics analysis of salt stress tolerance in the roots of the mangrove Avicennia officinalis

Salinity affects growth and development of plants, but mangroves exhibit exceptional salt tolerance. With direct exposure to salinity, mangrove roots possess specific adaptations to tolerate salt stress. Therefore, studying the early effects of salt on mangrove roots can help us better understand the tolerance mechanisms. Using two-month-old greenhouse-grown seedlings of the mangrove tree Avicennia officinalis subjected to NaCl treatment, we profiled gene expression changes in the roots by RNA-sequencing. Of the 6547 genes that were differentially regulated in response to salt treatment, 1404 and 5213 genes were significantly up- and down-regulated, respectively. By comparative genomics, 93 key salt tolerance-related genes were identified of which 47 were up-regulated. Upon placing all the differentially expressed genes (DEG) in known signaling pathways, it was evident that most of the DEGs involved in ethylene and auxin signaling were up-regulated while those involved in ABA signaling were down-regulated. These results imply that ABA-independent signaling pathways also play a major role in salt tolerance of A. officinalis. Further, ethylene response factors (ERFs) were abundantly expressed upon salt treatment and the Arabidopsis mutant aterf115, a homolog of AoERF114 is characterized. Overall, our results would help in understanding the possible molecular mechanism underlying salt tolerance in plants.

Indole-3-butyric acid promotes adventitious rooting in Arabidopsis thaliana thin cell layers by conversion into indole-3-acetic acid and stimulation of anthranilate synthase activity

BACKGROUND

Indole-3-acetic acid (IAA), and its precursor indole-3-butyric acid (IBA), control adventitious root (AR) formation in planta. Adventitious roots are also crucial for propagation via cuttings. However, IBA role(s) is/are still far to be elucidated. In Arabidopsis thaliana stem cuttings, 10 μM IBA is more AR-inductive than 10 μM IAA, and, in thin cell layers (TCLs), IBA induces ARs when combined with 0.1 μM kinetin (Kin). It is unknown whether arabidopsis TCLs produce ARs under IBA alone (10 μM) or IAA alone (10 μM), and whether they contain endogenous IAA/IBA at culture onset, possibly interfering with the exogenous IBA/IAA input. Moreover, it is unknown whether an IBA-to-IAA conversion is active in TCLs, and positively affects AR formation, possibly through the activity of the nitric oxide (NO) deriving from the conversion process.

RESULTS

Revealed undetectable levels of both auxins at culture onset, showing that arabidopsis TCLs were optimal for investigating AR-formation under the total control of exogenous auxins. The AR-response of TCLs from various ecotypes, transgenic lines and knockout mutants was analyzed under different treatments. It was shown that ARs are better induced by IBA than IAA and IBA + Kin. IBA induced IAA-efflux (PIN1) and IAA-influx (AUX1/LAX3) genes, IAA-influx carriers activities, and expression of ANTHRANILATE SYNTHASE -alpha1 (ASA1), a gene involved in IAA-biosynthesis. ASA1 and ANTHRANILATE SYNTHASE -beta1 (ASB1), the other subunit of the same enzyme, positively affected AR-formation in the presence of exogenous IBA, because the AR-response in the TCLs of their mutant wei2wei7 was highly reduced. The AR-response of IBA-treated TCLs from ech2ibr10 mutant, blocked into IBA-to-IAA-conversion, was also strongly reduced. Nitric oxide, an IAA downstream signal and a by-product of IBA-to-IAA conversion, was early detected in IAA- and IBA-treated TCLs, but at higher levels in the latter explants.

CONCLUSIONS

Altogether, results showed that IBA induced AR-formation by conversion into IAA involving NO activity, and by a positive action on IAA-transport and ASA1/ASB1-mediated IAA-biosynthesis. Results are important for applications aimed to overcome rooting recalcitrance in species of economic value, but mainly for helping to understand IBA involvement in the natural process of adventitious rooting.

On plant roots logical gates

Theoretical constructs of logical gates implemented with plant roots are morphological computing asynchronous devices. Values of Boolean variables are represented by plant roots. A presence of a plant root at a given site symbolises the logical True, an absence the logical False. Logical functions are calculated via interaction between roots. Two types of two-inputs-two-outputs gates are proposed: a gate 〈x, y〉→〈xy, x+y〉 where root apexes are guided by gravity and a gate 〈x,y〉→〈x¯y,x〉 where root apexes are guided by humidity. We propose a design of binary half-adder based on the gates.

Plant peroxisomes: A nitro-oxidative cocktail

Although peroxisomes are very simple organelles, research on different species has provided us with an understanding of their importance in terms of cell viability. In addition to the significant role played by plant peroxisomes in the metabolism of reactive oxygen species (ROS), data gathered over the last two decades show that these organelles are an endogenous source of nitric oxide (NO) and related molecules called reactive nitrogen species (RNS). Molecules such as NO and H2O2 act as retrograde signals among the different cellular compartments, thus facilitating integral cellular adaptation to physiological and environmental changes. However, under nitro-oxidative conditions, part of this network can be overloaded, possibly leading to cellular damage and even cell death. This review aims to update our knowledge of the ROS/RNS metabolism, whose important role in plant peroxisomes is still underestimated. However, this pioneering approach, in which key elements such as β-oxidation, superoxide dismutase (SOD) and NO have been mainly described in relation to plant peroxisomes, could also be used to explore peroxisomes from other organisms.

Multiple roles of nitric oxide in root development and nitrogen uptake

Nitric oxide (NO) is widely recognized for its role as a signaling molecule in regulating plant developmental processes. We summarize recent work on NO generation via nitrate reductase (NR) or/and NO synthase (NOS) pathway in response to nutrient fluctuation and its regulation of plant root growth and N metabolism. The promotion or inhibition of root development most likely depends on NO concentrations and/or experimental conditions. NO plays an important role in regulating plant NR activity at posttranslational level probably via a direct interaction mechanism, thus contributing largely to N assimilation. NO also regulates N distribution and uptake in many plant species. In rice cultivar, NR-generated NO plays a pivotal role in improving N uptake capacity by increasing root growth and inorganic N uptake, representing a potential strategy for rice adaption to a fluctuating nitrate supply.

ROS homeostasis as a prerequisite for the accomplishment of plant cytokinesis

Reactive oxygen species (ROS) are emerging players in several biological processes. The present work investigates their potential involvement in plant cytokinesis by the application of reagents disturbing ROS homeostasis in root-tip cells of Triticum turgidum. In particular, the NADPH-oxidase inhibitor diphenylene iodonium, the ROS scavenger N-acetyl-cysteine, and menadione that leads to ROS overproduction were used. The effects on cytokinetic cells were examined using light, fluorescence, and transmission electron microscopy. ROS imbalance had a great impact on the cytokinetic process including the following: (a) formation of atypical "phragmoplasts" incapable of guiding vesicles to the equatorial plane, (b) inhibition of the dictyosomal and/or endosomal vesicle production that provides the developing cell plates with membranous and matrix polysaccharidic material, (c) disturbance of the fusion processes between vesicles arriving on the cell plate plane, (d) disruption of endocytic vesicle production that mediates the removal of the excess membrane material from the developing cell plate, and (e) the persistence of large callose depositions in treated cell plates. Consequently, either elevated or low ROS levels in cytokinetic root-tip cells resulted in a total inhibition of cell plate assembly or the formation of aberrant cell plates, depending on the stage of the affected cytokinetic cells. The latter failed to expand towards cell cortex and hence to give rise to complete daughter cell wall. These data revealed for the first time the necessity of ROS homeostasis for accomplishment of plant cytokinesis, since it seems to be a prerequisite for almost every aspect of this process.

Gene expression profile indicates involvement of NO in Camellia sinensis pollen tube growth at low temperature

BACKGROUND

Nitric oxide (NO) functions as a critical signaling molecule in the low-temperature stress responses in plants, including polarized pollen tube growth in Camellia sinensis. Despite this, the potential mechanisms underlying the participation of NO in pollen tube responses to low temperature remain unclear. Here, we investigate alterations to gene expression in C. sinensis pollen tubes exposed to low-temperature stress and NO using RNA-Seq technology, in order to find the potential candidate genes related to the regulation of pollen tube elongation by NO under low-temperature stress.

RESULTS

Three libraries were generated from C. sinensis cv. 'Longjingchangye' pollen tubes cultured at 25 °C (CsPT-CK) and 4 °C (CsPT-LT) or with 25 μM DEA NONOate (CsPT-NO). The number of unigenes found for the three biological replications were 39,726, 40,440 and 41,626 for CsPT-CK; 36,993, 39,070 and 39,439 for CsPT-LT; and 39,514, 38,298 and 39,061 for CsPT-NO. A total of 36,097 unique assembled and annotated sequences from C. sinensis pollen tube reads were found in a BLAST search of the following databases: NCBI non-redundant nucleotide, Swiss-prot protein, Kyoto Encyclopedia of Genes and Genomes, Cluster of Orthologous Groups of proteins, and Gene Ontology. The absolute values of log2Ratio > 1 and probability > 0.7 were used as the thresholds for significantly differential gene expression, and 766, 497 and 929 differentially expressed genes (DEGs) were found from the comparison analyses of the CK-VS-LT, CK-VS-NO and LT-VS-NO libraries, respectively. Genes related to metabolism and signaling pathways of plant hormones, transcription factors (TFs), vesicle polarized trafficking, cell wall biosynthesis, the ubiquitination machinery of the ubiquitin system and species-specific secondary metabolite pathways were mainly observed in the CK-VS-LT and CK-VS-NO libraries.

CONCLUSION

Differentially expressed unigenes related to the inhibition of C. sinensis pollen tube growth under low temperature and NO are identified in this study. The transcriptomic gene expression profiles present a valuable genomic tool to improve studying the molecular mechanisms underlying low-temperature tolerance in pollen tube.

Strigolactones are required for nitric oxide to induce root elongation in response to nitrogen and phosphate deficiencies in rice

The response of the root system architecture to nutrient deficiencies is critical for sustainable agriculture. Nitric oxide (NO) is considered a key regulator of root growth, although the mechanisms remain unknown. Phenotypic, cellular and genetic analyses were undertaken in rice to explore the role of NO in regulating root growth and strigolactone (SL) signalling under nitrogen-deficient and phosphate-deficient conditions (LN and LP). LN-induced and LP-induced seminal root elongation paralleled NO production in root tips. NO played an important role in a shared pathway of LN-induced and LP-induced root elongation via increased meristem activity. Interestingly, no responses of root elongation were observed in SL d mutants compared with wild-type plants, although similar NO accumulation was induced by sodium nitroprusside (SNP) application. Application of abamine (the SL inhibitor) reduced seminal root length and pCYCB1;1::GUS expression induced by SNP application in wild type; furthermore, comparison with wild type showed lower SL-signalling genes in nia2 mutants under control and LN treatments and similar under SNP application. Western blot analysis revealed that NO, similar to SL, triggered proteasome-mediated degradation of D53 protein levels. Therefore, we presented a novel signalling pathway in which NO-activated seminal root elongation under LN and LP conditions, with the involvement of SLs.

In Silico Analysis of Arabidopsis thaliana Peroxisomal 6-Phosphogluconate Dehydrogenase

NADPH, whose regeneration is critical for reductive biosynthesis and detoxification pathways, is an essential component in cell redox homeostasis. Peroxisomes are subcellular organelles with a complex biochemical machinery involved in signaling and stress processes by molecules such as hydrogen peroxide (H2O2) and nitric oxide (NO). NADPH is required by several peroxisomal enzymes involved in β-oxidation, NO, and glutathione (GSH) generation. Plants have various NADPH-generating dehydrogenases, one of which is 6-phosphogluconate dehydrogenase (6PGDH). Arabidopsis contains three 6PGDH genes that probably are encoded for cytosolic, chloroplastic/mitochondrial, and peroxisomal isozymes, although their specific functions remain largely unknown. This study focuses on the in silico analysis of the biochemical characteristics and gene expression of peroxisomal 6PGDH (p6PGDH) with the aim of understanding its potential function in the peroxisomal NADPH-recycling system. The data show that a group of plant 6PGDHs contains an archetypal type 1 peroxisomal targeting signal (PTS), while in silico gene expression analysis using affymetrix microarray data suggests that Arabidopsis p6PGDH appears to be mainly involved in xenobiotic response, growth, and developmental processes.

Light-modulated seminal wavy roots in rice mediated by nitric oxide-dependent signaling

Rice (Oryza sativa L.) seminal roots from germinated seeds help establish seedlings, but the seminal root growth and morphology are sensitive to environmental factors. Our previous research showed that several indica-type rice varieties such as Taichung native 1 (TCN1) showed light-induced wavy roots. Also, auxin and oxylipins are two signaling factors regulating the wavy root photomorphology. To investigate the signaling pathway, here, we found that nitric oxide (NO) was a second messenger triggering the signal transduction of light stimuli to induce the wavy morphology of seminal roots in rice. Moreover, interactions between oxylipins and phytohormones such as ethylene and auxin participating in the NO-dependent regulatory pathway of light-induced wavy roots were examined. The order of action of signaling components in the pathway was NO, oxylipins, ethylene, and auxin.

Peroxisomes sense and respond to environmental cues by regulating ROS and RNS signalling networks

BACKGROUND

Peroxisomes are highly dynamic, metabolically active organelles that used to be regarded as a sink for H2O2 generated in different organelles. However, peroxisomes are now considered to have a more complex function, containing different metabolic pathways, and they are an important source of reactive oxygen species (ROS), nitric oxide (NO) and reactive nitrogen species (RNS). Over-accumulation of ROS and RNS can give rise oxidative and nitrosative stress, but when produced at low concentrations they can act as signalling molecules.

SCOPE

This review focuses on the production of ROS and RNS in peroxisomes and their regulation by antioxidants. ROS production is associated with metabolic pathways such as photorespiration and fatty acid β-oxidation, and disturbances in any of these processes can be perceived by the cell as an alarm that triggers defence responses. Genetic and pharmacological studies have shown that photorespiratory H2O2 can affect nuclear gene expression, regulating the response to pathogen infection and light intensity. Proteomic studies have shown that peroxisomal proteins are targets for oxidative modification, S-nitrosylation and nitration and have highlighted the importance of these modifications in regulating peroxisomal metabolism and signalling networks. The morphology, size, number and speed of movement of peroxisomes can also change in response to oxidative stress, meaning that an ROS/redox receptor is required. Information available on the production and detection of NO/RNS in peroxisomes is more limited. Peroxisomal homeostasis is critical for maintaining the cellular redox balance and is regulated by ROS, peroxisomal proteases and autophagic processes.

CONCLUSIONS

Peroxisomes play a key role in many aspects of plant development and acclimation to stress conditions. These organelles can sense ROS/redox changes in the cell and thus trigger rapid and specific responses to environmental cues involving changes in peroxisomal dynamics as well as ROS- and NO-dependent signalling networks, although the mechanisms involved have not yet been established. Peroxisomes can therefore be regarded as a highly important decision-making platform in the cell, where ROS and RNS play a determining role.

Functions of Nitric Oxide (NO) in Roots during Development and under Adverse Stress Conditions

The free radical molecule, nitric oxide (NO), is present in the principal organs of plants, where it plays an important role in a wide range of physiological functions. Root growth and development are highly regulated by both internal and external factors such as nutrient availability, hormones, pattern formation, cell polarity and cell cycle control. The presence of NO in roots has opened up new areas of research on the role of NO, including root architecture, nutrient acquisition, microorganism interactions and the response mechanisms to adverse environmental conditions, among others. Additionally, the exogenous application of NO throughout the roots has the potential to counteract specific damages caused by certain stresses. This review aims to provide an up-to-date perspective on NO functions in the roots of higher plants.

Nitric oxide generated by nitrate reductase increases nitrogen uptake capacity by inducing lateral root formation and inorganic nitrogen uptake under partial nitrate nutrition in rice

Increasing evidence shows that partial nitrate nutrition (PNN) can be attributed to improved plant growth and nitrogen-use efficiency (NUE) in rice. Nitric oxide (NO) is a signalling molecule involved in many physiological processes during plant development and nitrogen (N) assimilation. It remains unclear whether molecular NO improves NUE through PNN. Two rice cultivars (cvs Nanguang and Elio), with high and low NUE, respectively, were used in the analysis of NO production, nitrate reductase (NR) activity, lateral root (LR) density, and (15)N uptake under PNN, with or without NO production donor and inhibitors. PNN increased NO accumulation in cv. Nanguang possibly through the NIA2-dependent NR pathway. PNN-mediated NO increases contributed to LR initiation, (15)NH₄(+)/(15)NO₃(-) influx into the root, and levels of ammonium and nitrate transporters in cv. Nanguang but not cv. Elio. Further results revealed marked and specific induction of LR initiation and (15)NH₄(+)/(15)NO₃(-) influx into the roots of plants supplied with NH₄(+)+sodium nitroprusside (SNP) relative to those supplied with NH₄(+) alone, and considerable inhibition upon the application of cPTIO or tungstate (NR inhibitor) in addition to PNN, which is in agreement with the change in NO fluorescence in the two rice cultivars. The findings suggest that NO generated by the NR pathway plays a pivotal role in improving the N acquisition capacity by increasing LR initiation and the inorganic N uptake rate, which may represent a strategy for rice plants to adapt to a fluctuating nitrate supply and increase NUE.

Auxins differentially regulate root system architecture and cell cycle protein levels in maize seedlings

Maize (Zea mays) root system architecture has a complex organization, with adventitious and lateral roots determining its overall absorptive capacity. To generate basic information about the earlier stages of root development, we compared the post-embryonic growth of maize seedlings germinated in water-embedded cotton beds with that of plants obtained from embryonic axes cultivated in liquid medium. In addition, the effect of four different auxins, namely indole-3-acetic acid (IAA), 1-naphthaleneacetic acid (NAA), indole-3-butyric acid (IBA) and 2,4-dichlorophenoxyacetic acid (2,4-D) on root architecture and levels of the heat shock protein HSP101 and the cell cycle proteins CKS1, CYCA1 and CDKA1 were analyzed. Our data show that during the first days after germination, maize seedlings develop several root types with a simultaneous and/or continuous growth. The post-embryonic root development started with the formation of the primary root (PR) and seminal scutellar roots (SSR) and then continued with the formation of adventitious crown roots (CR), brace roots (BR) and lateral roots (LR). Auxins affected root architecture in a dose-response fashion; whereas NAA and IBA mostly stimulated crown root formation, 2,4-D showed a strong repressing effect on growth. The levels of HSP101, CKS1, CYCA1 and CDKA in root and leaf tissues were differentially affected by auxins and interestingly, HSP101 registered an auxin-inducible and root specific expression pattern. Taken together, our results show the timing of early branching patterns of maize and indicate that auxins regulate root development likely through modulation of the HSP101 and cell cycle proteins.

Auxin activity: Past, present, and future

Long before its chemical identity was known, the phytohormone auxin was postulated to regulate plant growth. In the late 1800s, Sachs hypothesized that plant growth regulators, present in small amounts, move differentially throughout the plant to regulate growth. Concurrently, Charles Darwin and Francis Darwin were discovering that light and gravity were perceived by the tips of shoots and roots and that the stimulus was transmitted to other tissues, which underwent a growth response. These ideas were improved upon by Boysen-Jensen and Paál and were later developed into the Cholodny-Went hypothesis that tropisms were caused by the asymmetric distribution of a growth-promoting substance. These observations led to many efforts to identify this elusive growth-promoting substance, which we now know as auxin. In this review of auxin field advances over the past century, we start with a seminal paper by Kenneth Thimann and Charles Schneider titled "The relative activities of different auxins" from the American Journal of Botany, in which they compare the growth altering properties of several auxinic compounds. From this point, we explore the modern molecular understanding of auxin-including its biosynthesis, transport, and perception. Finally, we end this review with a discussion of outstanding questions and future directions in the auxin field. Over the past 100 yr, much of our progress in understanding auxin biology has relied on the steady and collective advance of the field of auxin researchers; we expect that the next 100 yr of auxin research will likewise make many exciting advances.

Nitric oxide mediates strigolactone signaling in auxin and ethylene-sensitive lateral root formation in sunflower seedlings

Strigolactones (SLs) play significant role in shaping root architecture whereby auxin-SL crosstalk has been observed in SL-mediated responses of primary root elongation, lateral root formation and adventitious root (AR) initiation. Whereas GR24 (a synthetic strigolactone) inhibits LR and AR formation, the effect of SL biosynthesis inhibitor (fluridone) is just the opposite (root proliferation). Naphthylphthalamic acid (NPA) leads to LR proliferation but completely inhibits AR development. The diffusive distribution of PIN1 in the provascular cells in the differentiating zone of the roots in response to GR24, fluridone or NPA treatments further indicates the involvement of localized auxin accumulation in LR development responses. Inhibition of LR formation by GR24 treatment coincides with inhibition of ACC synthase activity. Profuse LR development by fluridone and NPA treatments correlates with enhanced [Ca(2+)]cyt in the apical region and differentiating zones of LR, indicating a critical role of [Ca(2+)] in LR development in response to the coordinated action of auxins, ethylene and SLs. Significant enhancement of carotenoid cleavage dioxygenase (CCD) activity (enzyme responsible for SL biosynthesis) in tissue homogenates in presence of cPTIO (NO scavenger) indicates the role of endogenous NO as a negative modulator of CCD activity. Differences in the spatial distribution of NO in the primary and lateral roots further highlight the involvement of NO in SL-modulated root morphogenesis in sunflower seedlings. Present work provides new report on the negative modulation of SL biosynthesis through modulation of CCD activity by endogenous nitric oxide during SL-modulated LR development.

Phenotypic plasticity of the maize root system in response to heterogeneous nitrogen availability

Mineral nutrients are distributed in a non-uniform manner in the soil. Plasticity in root responses to the availability of mineral nutrients is believed to be important for optimizing nutrient acquisition. The response of root architecture to heterogeneous nutrient availability has been documented in various plant species, and the molecular mechanisms coordinating these responses have been investigated particularly in Arabidopsis, a model dicotyledonous plant. Recently, progress has been made in describing the phenotypic plasticity of root architecture in maize, a monocotyledonous crop. This article reviews aspects of phenotypic plasticity of maize root system architecture, with special emphasis on describing (1) the development of its complex root system; (2) phenotypic responses in root system architecture to heterogeneous N availability; (3) the importance of phenotypic plasticity for N acquisition; (4) different regulation of root growth and nutrients uptake by shoot; and (5) root traits in maize breeding. This knowledge will inform breeding strategies for root traits enabling more efficient acquisition of soil resources and synchronizing crop growth demand, root resource acquisition and fertilizer application during crop growing season, thereby maximizing crop yields and nutrient-use efficiency and minimizing environmental pollution.

Hypocotyl adventitious root organogenesis differs from lateral root development

Wound-induced adventitious root (AR) formation is a requirement for plant survival upon root damage inflicted by pathogen attack, but also during the regeneration of plant stem cuttings for clonal propagation of elite plant varieties. Yet, adventitious rooting also takes place without wounding. This happens for example in etiolated Arabidopsis thaliana hypocotyls, in which AR initiate upon de-etiolation or in tomato seedlings, in which AR initiate upon flooding or high water availability. In the hypocotyl AR originate from a cell layer reminiscent to the pericycle in the primary root (PR) and the initiated AR share histological and developmental characteristics with lateral roots (LRs). In contrast to the PR however, the hypocotyl is a determinate structure with an established final number of cells. This points to differences between the induction of hypocotyl AR and LR on the PR, as the latter grows indeterminately. The induction of AR on the hypocotyl takes place in environmental conditions that differ from those that control LR formation. Hence, AR formation depends on differentially regulated gene products. Similarly to AR induction in stem cuttings, the capacity to induce hypocotyl AR is genotype-dependent and the plant growth regulator auxin is a key regulator controlling the rooting response. The hormones cytokinins, ethylene, jasmonic acid, and strigolactones in general reduce the root-inducing capacity. The involvement of this many regulators indicates that a tight control and fine-tuning of the initiation and emergence of AR exists. Recently, several genetic factors, specific to hypocotyl adventitious rooting in A. thaliana, have been uncovered. These factors reveal a dedicated signaling network that drives AR formation in the Arabidopsis hypocotyl. Here we provide an overview of the environmental and genetic factors controlling hypocotyl-born AR and we summarize how AR formation and the regulating factors of this organogenesis are distinct from LR induction.

Oxidative stress and NO signalling in the root apex as an early response to changes in gravity conditions

Oxygen influx showed an asymmetry in the transition zone of the root apex when roots were placed horizontally on ground. The influx increased only in the upper side, while no changes were detected in the division and in the elongation zone. Nitric oxide (NO) was also monitored after gravistimulation, revealing a sudden burst only in the transition zone. In order to confirm these results in real microgravity conditions, experiments have been set up by using parabolic flights and drop tower. The production of reactive oxygen species (ROS) was also monitored. Oxygen, NO, and ROS were continuously monitored during normal and hyper- and microgravity conditions in roots of maize seedlings. A distinct signal in oxygen and NO fluxes was clearly detected only in the apex zone during microgravity, with no significant changes in normal and in hypergravity conditions. The same results were obtained by ROS measurement. The detrimental effect of D'orenone, disrupting the polarised auxin transport, on the onset of the oxygen peaks during the microgravity period was also evaluated. Results indicates an active role of NO and ROS as messengers during the gravitropic response, with probable implications in the auxin redistribution.