Abscisic acid regulates root elongation through the activities of auxin and ethylene in Arabidopsis thaliana

Surviving the stress: Understanding the molecular basis of plant adaptations and uncovering the role of mycorrhizal association in plant abiotic stresses

Environmental stresses severely impair plant growth, resulting in significant crop yield and quality loss. Among various abiotic factors, salt and drought stresses are one of the major factors that affect the nutrients and water uptake by the plants, hence ultimately various physiological aspects of the plants that compromises crop yield. Continuous efforts have been made to investigate, dissect and improve plant adaptations at the molecular level in response to drought and salinity stresses. In this context, the plant beneficial microbiome presents in the rhizosphere, endosphere, and phyllosphere, also referred as second genomes of the plant is well known for its roles in plant adaptations. Exploration of beneficial interaction of fungi with host plants known as mycorrhizal association is one such special interaction that can facilitates the host plants adaptations. Mycorrhiza assist in alleviating the salinity and drought stresses of plants via redistributing the ion imbalance through translocation to different parts of the plants, as well as triggering oxidative machinery. Mycorrhiza association also regulates the level of various plant growth regulators, osmolytes and assists in acquiring minerals that are helpful in plant's adaptation against extreme environmental stresses. The current review examines the role of various plant growth regulators and plants' antioxidative systems, followed by mycorrhizal association during drought and salt stresses.

Hydrotropism mechanisms and their interplay with gravitropism

Plants partly optimize their water recruitment from the growth medium by directing root growth toward a moisture source, a phenomenon termed hydrotropism. The default mechanism of downward growth, termed gravitropism, often functions to counteract hydrotropism when the water-potential gradient deviates from the gravity vector. This review addresses the identity of the root sites in which hydrotropism-regulating factors function to attenuate gravitropism and the interplay between these various factors. In this context, the function of hormones, including auxin, abscisic acid, and cytokinins, as well as secondary messengers, calcium ions, and reactive oxygen species in the conflict between these two opposing tropisms is discussed. We have assembled the available data on the effects of various chemicals and genetic backgrounds on both gravitropism and hydrotropism, to provide an up-to-date perspective on the interactions that dictate the orientation of root tip growth. We specify the relevant open questions for future research. Broadening our understanding of root mechanisms of water recruitment holds great potential for providing advanced approaches and technologies that can improve crop plant performance under less-than-optimal conditions, in light of predicted frequent and prolonged drought periods due to global climate change.

Abscisic acid biosynthesis is necessary for full auxin effects on hypocotyl elongation

In concert with other phytohormones, auxin regulates plant growth and development. However, how auxin and other phytohormones coordinately regulate distinct processes is not fully understood. In this work, we uncover an auxin-abscisic acid (ABA) interaction module in Arabidopsis that is specific to coordinating activities of these hormones in the hypocotyl. From our forward genetics screen, we determine that ABA biosynthesis is required for the full effects of auxin on hypocotyl elongation. Our data also suggest that ABA biosynthesis is not required for the inhibitory effects of auxin treatment on root elongation. Our transcriptome analysis identified distinct auxin-responsive genes in root and shoot tissues, which is consistent with differential regulation of growth in these tissues. Further, our data suggest that many gene targets repressed upon auxin treatment require an intact ABA pathway for full repression. Our results support a model in which auxin stimulates ABA biosynthesis to fully regulate hypocotyl elongation.

A mulberry 9-cis-epoxycarotenoid dioxygenase gene MaNCED1 is involved in plant growth regulation and confers salt and drought tolerance in transgenic tobacco

The phytohormone abscisic acid (ABA) is vital in regulating root elongation, seed germination, and abiotic stress responses in plants. Conversely, the mechanisms of ABA in mulberry root growth, seed germination, and abiotic stress responses are poorly understood. Here, we reported that exogenous ABA and drought treatment inhibited the growth of mulberry seedlings but significantly increased the ratio of root/stem. Inhibition of ABA synthesis by fluridone and sodium tungstate resulted in the decrease of root/stem ratio. We also showed that the expression of MaNCED1 in the root was strongly induced by drought and salt stress. Increasing the expression of MaNCED1 in tobacco using overexpression leads to increased root elongation and reduced seed germination. Compared with the wild type, the accumulation of H2O2 and MDA was reduced, while the POD activity and proline content was increased in the transgenic plants after drought and salt treatment. Further studies revealed increased resistance to drought and salt stress in MaNCED1 overexpressed tobaccos. Meanwhile, the auxin and ethylene signal pathway-related gene expression levels increased in MaNCED1 overexpressed tobaccos. This study demonstrated the roles of mulberry MaNCED1 in regulating plant development and abiotic stress responses. It gave further insights into the coordinated regulation of ABA, auxin, and ethylene in seed growth and germination.

Abscisic acid promotes auxin biosynthesis to inhibit primary root elongation in rice

Soil compaction is a global problem causing inadequate rooting and poor yield in crops. Accumulating evidence indicates that phytohormones coordinately regulate root growth via regulating specific growth processes in distinct tissues. However, how abscisic acid (ABA) signaling translates into auxin production to control root growth during adaptation to different soil environments is still unclear. In this study, we report that ABA has biphasic effects on primary root growth in rice (Oryza sativa) through an auxin biosynthesis-mediated process, causing suppression of root elongation and promotion of root swelling in response to soil compaction. We found that ABA treatment induced the expression of auxin biosynthesis genes and auxin accumulation in roots. Conversely, blocking auxin biosynthesis reduced ABA sensitivity in roots, showing longer and thinner primary roots with larger root meristem size and smaller root diameter. Further investigation revealed that the transcription factor basic region and leucine zipper 46 (OsbZIP46), involved in ABA signaling, can directly bind to the YUCCA8/rice ethylene-insensitive 7 (OsYUC8/REIN7) promoter to activate its expression, and genetic analysis revealed that OsYUC8/REIN7 is located downstream of OsbZIP46. Moreover, roots of mutants defective in ABA or auxin biosynthesis displayed the enhanced ability to penetrate compacted soil. Thus, our results disclose the mechanism in which ABA employs auxin as a downstream signal to modify root elongation and radial expansion, resulting in short and swollen roots impaired in their ability to penetrate compacted soil. These findings provide avenues for breeders to select crops resilient to soil compaction.

The nitrification inhibitor 1,9-decanediol from rice roots promotes root growth in Arabidopsis through involvement of ABA and PIN2-mediated auxin signaling

1,9-decanediol (1,9-D) is a biological nitrification inhibitor secreted in roots, which effectively inhibits soil nitrifier activity and reduces nitrogen loss from agricultural fields. However, the effects of 1,9-D on plant root growth and the involvement of signaling pathways in the plant response to 1,9-D have not been investigated. Here, we report that 1,9-D, in the 100-400 μM concentration range, promotes primary root length in Arabidopsis seedlings at 3d and 5d, by 10.1%-33.3% and 6.9%-32.6%, and, in a range of 50-200 μM, leads to an increase in the number of lateral roots. 150 μM 1,9-D was found optimum for the positive regulation of root growth. qRT-PCR analysis reveals that 1,9-D can significantly increase AtABA3 gene expression and that a mutation in ABA3 results in insensitivity of root growth to 1,9-D. Moreover, through pharmacological experiments, we show that exogenous addition of ABA (abscisic acid) with 1,9-D enhances primary root length by 23.5%-63.3%, and an exogenous supply of 1,9-D with the ABA inhibitor Flu reduces primary root length by 1.0%-14.3%. Primary root length of the pin2/eir1-1 is shown to be insensitive to both exogenous addition of 1,9-D and ABA, indicating that the auxin carrier PIN2/EIR1 is involved in promotion of root growth by 1,9-D. These results suggest a novel for 1,9-D in regulating plant root growth through ABA and auxin signaling.

The Germin-like protein OsGER4 is involved in promoting crown root development under exogenous jasmonic acid treatment in rice

In rice (Oryza sativa L.), crown roots (CRs) have many important roles in processes such as root system expansion, water and mineral uptake, and adaptation to environmental stresses. Phytohormones such as auxin, cytokinin, and ethylene are known to control CR initiation and development in rice. However, the role of jasmonic acid (JA) in CR development remained elusive. Here, we report that JA promotes CR development by regulating OsGER4, a rice Germin-like protein. Root phenotyping analysis revealed that exogenous JA treatment induced an increase in CR number in a concentration-dependent manner. A subsequent genome-wide association study and gene expression analyses pinpointed a strong association between the Germin-like protein OsGER4 and the increase in CR number under exogenous JA treatment. The ProGER4::GUS reporter line showed that OsGER4 is a hormone-responsive gene involved in various stress responses, mainly confined to epidermal and vascular tissues during CR primordia development and to vascular bundles of mature crown and lateral roots. Notable changes in OsGER4 expression patterns caused by the polar auxin transport inhibitor NPA support its connection to auxin signaling. Phenotyping experiments with OsGER4 knockout mutants confirmed that this gene is required for CR development under exogenous JA treatment. Overall, our results provide important insights into JA-mediated regulation of CR development in rice.

Auxin and abscisic acid antagonistically regulate ascorbic acid production via the SlMAPK8-SlARF4-SlMYB11 module in tomato

Ascorbic acid (AsA) is a multifunctional phytonutrient that is essential for the human diet as well as plant development. While much is known about AsA biosynthesis in plants, how this process is regulated in tomato (Solanum lycopersicum) fruits remains unclear. Here, we found that auxin treatment inhibited AsA accumulation in the leaves and pericarps of tomato. The auxin response factor gene SlARF4 is induced by auxin to mediate auxin-induced inhibition of AsA accumulation. Specifically, SlARF4 transcriptionally inhibits the transcription factor gene SlMYB11, thereby modulating AsA accumulation by regulating the transcription of the AsA biosynthesis genes l-galactose-1-phosphate phosphatase, l-galactono-1,4-lactone dehydrogenase, and dehydroascorbate. By contrast, abscisic acid (ABA) treatment increased AsA accumulation in tomato under drought stress. ABA induced the expression of the mitogen-activated protein kinase gene SlMAPK8. We demonstrate that SlMAPK8 phosphorylates SlARF4 and inhibits its transcriptional activity, whereas SlMAPK8 phosphorylates SlMYB11 and activates its transcriptional activity. SlMAPK8 functions in ABA-induced AsA accumulation and drought stress tolerance. Moreover, ABA antagonizes the effects of auxin on AsA biosynthesis. Therefore, auxin- and ABA-induced regulation of AsA accumulation is mediated by the SlMAPK8-SlARF4-SlMYB11 module in tomato during fruit development and drought stress responses, shedding light on the roles of phytohormones in regulating AsA accumulation to mediate stress tolerance.

An Arabidopsis pre-RNA processing8a (prp8a) missense allele restores splicing of a subset of mis-spliced mRNAs

Eukaryotic precursor mRNAs often harbor noncoding introns that must be removed prior to translation. Accurate splicing of precursor messenger RNA depends on placement and assembly of small nuclear ribonucleoprotein (snRNP) sub-complexes of the spliceosome. Yeast (Saccharomyces cerevisiae) studies established a role in splice-site selection for PRE-RNA PROCESSING8 (PRP8), a conserved spliceosome scaffolding protein of the U5 snRNP. However, analogous splice-site selection studies in multicellular eukaryotes are lacking. Such studies are crucial for a comprehensive understanding of alternative splicing, which is extensive in plants and animals but limited in yeast. In this work, we describe an Arabidopsis (Arabidopsis thaliana) prp8a mutant that modulates splice-site selection. We isolated prp8a-14 from a screen for suppressors of pex14-6, which carries a splice-site mutation in the PEROXIN14 (PEX14) peroxisome biogenesis gene. To elucidate Arabidopsis PRP8A function in spliceosome fidelity, we combined prp8a-14 with various pex14 splice-site mutations and monitored the double mutants for physiological and molecular consequences of dysfunctional and functional peroxisomes that correspond to impaired and recovered splicing, respectively. prp8a-14 restored splicing and PEX14 function to alleles with mutations in the exonic guanine of the 5'-splice site but did not restore splicing or function to alleles with mutations in the intronic guanine of 5'- or 3'-splice sites. We used RNA-seq to reveal the systemic impact of prp8a-14 and found hundreds of differentially spliced transcripts and thousands of transcripts with significantly altered levels. Among differentially spliced transcripts, prp8a-14 significantly altered 5'- and 3'-splice-site utilization to favor sites resulting in shorter introns. This study provides a genetic platform for probing splicing in plants and hints at a role for plant PRP8 in splice-site selection.

The Indole-3-Acetamide-Induced Arabidopsis Transcription Factor MYB74 Decreases Plant Growth and Contributes to the Control of Osmotic Stress Responses

The accumulation of the auxin precursor indole-3-acetamide (IAM) in the ami1 mutant has recently been reported to reduce plant growth and to trigger abiotic stress responses in Arabidopsis thaliana. The observed response includes the induction of abscisic acid (ABA) biosynthesis through the promotion of NCED3 expression. The mechanism by which plant growth is limited, however, remained largely unclear. Here, we investigated the transcriptional responses evoked by the exogenous application of IAM using comprehensive RNA-sequencing (RNA-seq) and reverse genetics approaches. The RNA-seq results highlighted the induction of a small number of genes, including the R2R3 MYB transcription factor genes MYB74 and MYB102. The two MYB factors are known to respond to various stress cues and to ABA. Consistent with a role as negative plant growth regulator, conditional MYB74 overexpressor lines showed a considerable growth reduction. RNA-seq analysis of MYB74 mutants indicated an association of MYB74 with responses to osmotic stress, water deprivation, and seed development, which further linked MYB74 with the observed ami1 osmotic stress and seed phenotype. Collectively, our findings point toward a role for MYB74 in plant growth control and in responses to abiotic stress stimuli.

Divergence in the ABA gene regulatory network underlies differential growth control

The phytohormone abscisic acid (ABA) is a central regulator of acclimation to environmental stress; however, its contribution to differences in stress tolerance between species is unclear. To establish a comparative framework for understanding how stress hormone signalling pathways diverge across species, we studied the growth response of four Brassicaceae species to ABA treatment and generated transcriptomic and DNA affinity purification and sequencing datasets to construct a cross-species gene regulatory network (GRN) for ABA. Comparison of genes bound directly by ABA-responsive element binding factors suggests that cis-factors are most important for determining the target loci represented in the ABA GRN of a particular species. Using this GRN, we reveal how rewiring of growth hormone subnetworks contributes to stark differences in the response to ABA in the extremophyte Schrenkiella parvula. Our study provides a model for understanding how divergence in gene regulation can lead to species-specific physiological outcomes in response to hormonal cues.

Shaping the root system architecture in plants for adaptation to drought stress

Root system architecture plays an important role in plant adaptation to drought stress. The root system architecture (RSA) consists of several structural features, which includes number and length of main and lateral roots along with the density and length of root hairs. These features exhibit plasticity under water-limited environments and could be critical to developing crops with efficient root systems for adaptation under drought. Recent advances in the omics approaches have significantly improved our understanding of the regulatory mechanisms of RSA remodeling under drought and the identification of genes and other regulatory elements. Plant response to drought stress at physiological, morphological, biochemical, and molecular levels in root cells is regulated by various phytohormones and their crosstalk. Stress-induced reactive oxygen species play a significant role in regulating root growth and development under drought stress. Several transcription factors responsible for the regulation of RSA under drought have proven to be beneficial for developing drought tolerant crops. Molecular breeding programs for developing drought-tolerant crops have been greatly benefitted by the availability of quantitative trait loci (QTLs) associated with the RSA regulation. In the present review, we have discussed the role of various QTLs, signaling components, transcription factors, microRNAs and crosstalk among various phytohormones in shaping RSA and present future research directions to better understand various factors involved in RSA remodeling for adaptation to drought stress. We believe that the information provided herein may be helpful in devising strategies to develop crops with better RSA for efficient uptake and utilization of water and nutrients under drought conditions.

Salicylic Acid in Root Growth and Development

In plants, salicylic acid (SA) is a hormone that mediates a plant’s defense against pathogens. SA also takes an active role in a plant’s response to various abiotic stresses, including chilling, drought, salinity, and heavy metals. In addition, in recent years, numerous studies have confirmed the important role of SA in plant morphogenesis. In this review, we summarize data on changes in root morphology following SA treatments under both normal and stress conditions. Finally, we provide evidence for the role of SA in maintaining the balance between stress responses and morphogenesis in plant development, and also for the presence of SA crosstalk with other plant hormones during this process.

Mechanisms of Abscisic Acid-Mediated Drought Stress Responses in Plants

Drought is one of the major constraints to rain-fed agricultural production, especially under climate change conditions. Plants evolved an array of adaptive strategies that perceive stress stimuli and respond to these stress signals through specific mechanisms. Abscisic acid (ABA) is a premier signal for plants to respond to drought and plays a critical role in plant growth and development. ABA triggers a variety of physiological processes such as stomatal closure, root system modulation, organizing soil microbial communities, activation of transcriptional and post-transcriptional gene expression, and metabolic alterations. Thus, understanding the mechanisms of ABA-mediated drought responses in plants is critical for ensuring crop yield and global food security. In this review, we highlighted how plants adjust ABA perception, transcriptional levels of ABA- and drought-related genes, and regulation of metabolic pathways to alter drought stress responses at both cellular and the whole plant level. Understanding the synergetic role of drought and ABA will strengthen our knowledge to develop stress-resilient crops through integrated advanced biotechnology approaches. This review will elaborate on ABA-mediated drought responses at genetic, biochemical, and molecular levels in plants, which is critical for advancement in stress biology research.

Molecular and Physiological Perspectives of Abscisic Acid Mediated Drought Adjustment Strategies

Drought is the most prevalent unfavorable condition that impairs plant growth and development by altering morphological, physiological, and biochemical functions, thereby impeding plant biomass production. To survive the adverse effects, water limiting condition triggers a sophisticated adjustment mechanism orchestrated mainly by hormones that directly protect plants via the stimulation of several signaling cascades. Predominantly, water deficit signals cause the increase in the level of endogenous ABA, which elicits signaling pathways involving transcription factors that enhance resistance mechanisms to combat drought-stimulated damage in plants. These responses mainly include stomatal closure, seed dormancy, cuticular wax deposition, leaf senescence, and alteration of the shoot and root growth. Unraveling how plants adjust to drought could provide valuable information, and a comprehensive understanding of the resistance mechanisms will help researchers design ways to improve crop performance under water limiting conditions. This review deals with the past and recent updates of ABA-mediated molecular mechanisms that plants can implement to cope with the challenges of drought stress.

A perspective on cell proliferation kinetics in the root apical meristem

Organogenesis in plants is primarily postembryonic and relies on a strict balance between cell division and cell expansion. The root is a particularly well-suited model to study cell proliferation in detail since the two processes are spatially and temporally separated for all the different tissues. In addition, the root is amenable to detailed microscopic analysis to identify cells progressing through the cell cycle. While it is clear that cell proliferation activity is restricted to the root apical meristem (RAM), understanding cell proliferation kinetics and identifying its parameters have required much effort over many years. Here, we review the main concepts, experimental settings, and findings aimed at obtaining a detailed knowledge of how cells proliferate within the RAM. The combination of novel tools, experimental strategies, and mathematical models has contributed to our current view of cell proliferation in the RAM. We also discuss several lines of research that need to be explored in the future.

Addressing Research Bottlenecks to Crop Productivity

Asymmetry of investment in crop research leads to knowledge gaps and lost opportunities to accelerate genetic gain through identifying new sources and combinations of traits and alleles. On the basis of consultation with scientists from most major seed companies, we identified several research areas with three common features: (i) relatively underrepresented in the literature; (ii) high probability of boosting productivity in a wide range of crops and environments; and (iii) could be researched in 'precompetitive' space, leveraging previous knowledge, and thereby improving models that guide crop breeding and management decisions. Areas identified included research into hormones, recombination, respiration, roots, and source-sink, which, along with new opportunities in phenomics, genomics, and bioinformatics, make it more feasible to explore crop genetic resources and improve breeding strategies.

Abscisic Acid Regulates the Root Growth Trajectory by Reducing Auxin Transporter PIN2 Protein Levels in Arabidopsis thaliana

The root is in direct contact with soil. Modulation of root growth in response to alterations in soil conditions is pivotal for plant adaptation. Extensive research has been conducted concerning the adjustment of root elongation and architecture in response to environmental factors. However, little is known about the modulation of the root growth trajectory, as well as its hormonal mechanism. Here we report that abscisic acid (ABA) participated in controlling root growth trajectory. The roots upon ABA treatment or from ABA-accumulation double mutant cyp707a1,3 exhibit agravitropism-like growth pattern (wavy growth trajectory). The agravitropism-like phenotype is mainly ascribed to the compromised shootward transportation of auxin since we detected a reduced fluorescence intensity of auxin reporter DR5:VENUS in the root epidermis upon exogenous ABA application or in the endogenous ABA-accumulation double mutant cyp707a1,3. We then tried to decipher the mechanism by which ABA suppressed shootward auxin transport. The membrane abundance of PIN2, a facilitator of shootward auxin transport, was significantly reduced following ABA treatment and in cyp707a1,3. Finally, we revealed that ABA reduced the membrane PIN2 intensity through suppressing the PIN2 expression rather than accelerating PIN2 degradation. Ultimately, our results suggest a pivotal role for ABA in the root growth trajectory and the hormonal interactions orchestrating this process.

Mutagenomics: A Rapid, High-Throughput Method to Identify Causative Mutations from a Genetic Screen

Genetic screens are powerful tools to dissect complex biological processes, but a rate-limiting step is often the cloning of targeted genes. Here, we present a strategy, "mutagenomics," to identify causal mutations from a screen in a high throughput fashion in the absence of backcrossing. Mutagenomics is initiated by sequencing the genomes of the mutants identified, which are then subjected to a three-stage pipeline. The first stage identifies sequence changes in genes previously linked to the targeted pathway. The second stage uses heuristics derived from a simulation strategy to identify genes that are represented by multiple independent alleles more often than expected by chance. The third stage identifies candidate genes for the remaining lines by sequencing multiple lines of common descent. Our simulations indicate that sequencing as few as three to four sibling lines generally results in fewer than five candidate genes. We applied mutagenomics to a screen for Arabidopsis (Arabidopsis thaliana) mutants involved in the response to the phytohormone cytokinin. Mutagenomics identified likely causative genes for many of the mutant lines analyzed from this screen, including 13 alleles of the gene encoding the ARABIDOPSIS HIS KINASE4 cytokinin receptor. The screen also identified 1-AMINOCYCLOPROPANE-1-CARBOXYLATE (ACC) SYNTHASE7, an ACC synthase homolog involved in ethylene biosynthesis, and ELONGATED HYPOCOTYL5 (HY5), a master transcriptional regulator of photomorphogenesis. HY5 was found to mediate a subset of the transcriptional response to cytokinin. Mutagenomics has the potential to accelerate the pace and utility of genetic screens in Arabidopsis.

Interplay between Hormones and Several Abiotic Stress Conditions on Arabidopsis thaliana Primary Root Development

As sessile organisms, plants must adjust their growth to withstand several environmental conditions. The root is a crucial organ for plant survival as it is responsible for water and nutrient acquisition from the soil and has high phenotypic plasticity in response to a lack or excess of them. How plants sense and transduce their external conditions to achieve development, is still a matter of investigation and hormones play fundamental roles. Hormones are small molecules essential for plant growth and their function is modulated in response to stress environmental conditions and internal cues to adjust plant development. This review was motivated by the need to explore how Arabidopsis thaliana primary root differentially sense and transduce external conditions to modify its development and how hormone-mediated pathways contribute to achieve it. To accomplish this, we discuss available data of primary root growth phenotype under several hormone loss or gain of function mutants or exogenous application of compounds that affect hormone concentration in several abiotic stress conditions. This review shows how different hormones could promote or inhibit primary root development in A. thaliana depending on their growth in several environmental conditions. Interestingly, the only hormone that always acts as a promoter of primary root development is gibberellins.

Halotropism: Phytohormonal Aspects and Potential Applications

Halotropism is a sodium specific tropic movement of roots in order to obtain the optimal salt concentration for proper growth and development. Numerous results suggest that halotropic events are under the control and regulation of complex plant hormone pathway. This minireview collects some recent evidences about sodium sensing during halotropism and the hormonal regulation of halotropic responses in glycophytes. The precise hormonal mechanisms by which halophytes plant roots perceive salt stress and translate this perception into adaptive, directional growth forward increased salt concentrations are not well understood. This minireview aims to gather recently deciphered information about halotropism focusing potential hormonal aspects both in glycophytes and halophytes. Advances in our understanding of halotropic responses in different plant species could help these plants to be used for sustainable agriculture and other future applications.

Implications of Abscisic Acid in the Drought Stress Tolerance of Plants

Drought is a severe environmental constraint, which significantly affects plant growth, productivity, and quality. Plants have developed specific mechanisms that perceive the stress signals and respond to external environmental changes via different mitigation strategies. Abscisic acid (ABA), being one of the phytohormones, serves as an important signaling mediator for plants’ adaptive response to a variety of environmental stresses. ABA triggers many physiological processes, including bud dormancy, seed germination, stomatal closure, and transcriptional and post-transcriptional regulation of stress-responsive gene expression. The site of its biosynthesis and action must be clarified to understand the signaling network of ABA. Various studies have documented multiple sites for ABA biosynthesis, their transporter proteins in the plasma membrane, and several components of ABA-dependent signaling pathways, suggesting that the ABA response to external stresses is a complex networking mechanism. Knowing about stress signals and responses will increase our ability to enhance crop stress tolerance through the use of various advanced techniques. This review will elaborate on the ABA biosynthesis, transportation, and signaling pathways at the molecular level in response to drought stress, which will add a new insight for future studies.

Role of ethylene crosstalk in seed germination and early seedling development: A review

Seed germination and early seedling development are two critical phases in plant lifecycle that largely determine crop yield. Phytohormones play an essential role in governing these developmental processes; of these, ethylene (ET; C₂H₄), the smallest gaseous hormone, plays a major role via crosstalk with other hormones. Typically, the mechanism of hormone (for instance, auxin, cytokinins, ET, and gibberellins) action is determined by cellular context, revealing either synergistic or antagonistic relations. Significant progress has been made, so far, on unveiling ET crosstalk with other hormones and environmental signals, such as light. In particular, stimulatory and inhibitory effects of ET on hypocotyl growth in light and dark, respectively, and its interaction with other hormones provide an ideal model to study the growth-regulatory pathways. In this review, we aim at exploring the mechanisms of multifarious phenomena that occur via ET crosstalk during the germination of seeds (overcoming dormancy), and all through the development of seedlings. Understanding the remarkably complex mechanism of ET crosstalk that emerges from the interaction between hormones and other molecular players to modulate plant growth, remains a challenge in plant developmental biology.

Same same, but different: growth responses of primary and lateral roots

The root system architecture describes the shape and spatial arrangement of roots within the soil. Its spatial distribution depends on growth and branching rates as well as directional organ growth. The embryonic primary root gives rise to lateral (secondary) roots, and the ratio of both root types changes over the life span of a plant. Most studies have focused on the growth of primary roots and the development of lateral root primordia. Comparably less is known about the growth regulation of secondary root organs. Here, we review similarities and differences between primary and lateral root organ growth, and emphasize particularly how external stimuli and internal signals differentially integrate root system growth.

Quantitative Proteomic Analyses Identify STO/BBX24 -Related Proteins Induced by UV-B

Plants use solar radiation for photosynthesis and are inevitably exposed to UV-B. To adapt to UV-B radiation, plants have evolved a sophisticated strategy, but the mechanism is not well understood. We have previously reported that STO (salt tolerance)/BBX24 is a negative regulator of UV-B-induced photomorphogenesis. However, there is limited knowledge of the regulatory network of STO in UV-B signaling. Here, we report the identification of proteins differentially expressed in the wild type (WT) and sto mutant after UV-B radiation by iTRAQ (isobaric tags for relative and absolute quantitation)-based proteomic analysis to explore differential proteins that depend on STO and UV-B signaling. A total of 8212 proteins were successfully identified, 221 of them were STO-dependent proteins in UV-B irradiated plants. The abundances of STO-dependent PSB and LHC (light-harvesting complex) proteins in sto mutants decreased under UV-B radiation, suggesting that STO is necessary to maintain the normal accumulation of photosynthetic system complex under UV-B radiation to facilitate photosynthesis photon capture. The abundance of phenylalanine lyase-1 (PAL1), chalcone synthetase (CHS), and flavonoid synthetase (FLS) increased significantly after UV-B irradiation, suggesting that the accumulation of flavonoids do not require STO, but UV-B is needed. Under UV-B radiation, STO stabilizes the structure of antenna protein complex by maintaining the accumulation of PSBs and LHCs, thereby enhancing the non-photochemical quenching (NPQ) ability, releasing extra energy, protecting photosynthesis, and ultimately promoting the elongation of hypocotyl. The accumulation of flavonoid synthesis key proteins is independent of STO under UV-B radiation. Overall, our results provide a comprehensive regulatory network of STO in UV-B signaling.

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.

Auxin-Abscisic Acid Interactions in Plant Growth and Development

Plant hormones regulate many aspects of plant growth, development, and response to biotic and abiotic stress. Much research has gone into our understanding of individual plant hormones, focusing primarily on their mechanisms of action and the processes that they regulate. However, recent research has begun to focus on a more complex problem; how various plant hormones work together to regulate growth and developmental processes. In this review, we focus on two phytohormones, abscisic acid (ABA) and auxin. We begin with brief overviews of the hormones individually, followed by in depth analyses of interactions between auxin and ABA, focusing on interactions in individual tissues and how these interactions are occurring where possible. Finally, we end with a brief discussion and future prospects for the field.

Expression of maize calcium-dependent protein kinase (ZmCPK11) improves salt tolerance in transgenic Arabidopsis plants by regulating sodium and potassium homeostasis and stabilizing photosystem II

In plants, CALCIUM-DEPENDENT PROTEIN KINASES (CDPKs/CPKs) are involved in calcium signaling in response to endogenous and environmental stimuli. Here, we report that ZmCPK11, one of maize CDPKs, participates in salt stress response and tolerance. Salt stress induced expression and upregulated the activity of ZmCPK11 in maize roots and leaves. Activation of ZmCPK11 upon salt stress was also observed in roots and leaves of transgenic Arabidopsis plants expressing ZmCPK11. The transgenic plants showed a long-root phenotype under control conditions and a short-root phenotype under NaCl, abscisic acid (ABA) or jasmonic acid (JA) treatment. Analysis of ABA and JA content in roots indicated that ZmCPK11 can mediate root growth by regulating the levels of these phytohormones. Moreover, 4-week-old transgenic plants were more tolerant to salinity than the wild-type plants. Their leaves were less chlorotic and showed weaker symptoms of senescence accompanied by higher chlorophyll content and higher quantum efficiency of photosystem II. The expression of Na⁺ /K⁺ transporters (HKT1, SOS1 and NHX1) and transcription factors (CBF1, CBF2, CBF3, ZAT6 and ZAT10) with known links to salinity tolerance was upregulated in roots of the transgenic plants upon salt stress. Furthermore, the transgenic plants accumulated less Na⁺ in roots and leaves under salinity, and showed a higher K⁺ /Na⁺ ratio in leaves. These results show that the improved salt tolerance in ZmCPK11-transgenic plants could be due to an upregulation of genes involved in the maintenance of intracellular Na⁺ and K⁺ homeostasis and a protection of photosystem II against damage.

An Integrative Approach to Analyze Seed Germination in Brassica napus

Seed germination is a complex trait determined by the interaction of hormonal, metabolic, genetic, and environmental components. Variability of this trait in crops has a big impact on seedling establishment and yield in the field. Classical studies of this trait in crops have focused mainly on the analyses of one level of regulation in the cascade of events leading to seed germination. We have carried out an integrative and extensive approach to deepen our understanding of seed germination in Brassica napus by generating transcriptomic, metabolic, and hormonal data at different stages upon seed imbibition. Deep phenotyping of different seed germination-associated traits in six winter-type B. napus accessions has revealed that seed germination kinetics, in particular seed germination speed, are major contributors to the variability of this trait. Metabolic profiling of these accessions has allowed us to describe a common pattern of metabolic change and to identify the levels of malate and aspartate metabolites as putative metabolic markers to estimate germination performance. Additionally, analysis of seed content of different hormones suggests that hormonal balance between ABA, GA, and IAA at crucial time points during this process might underlie seed germination differences in these accessions. In this study, we have also defined the major transcriptome changes accompanying the germination process in B. napus. Furthermore, we have observed that earlier activation of key germination regulatory genes seems to generate the differences in germination speed observed between accessions in B. napus. Finally, we have found that protein-protein interactions between some of these key regulator are conserved in B. napus, suggesting a shared regulatory network with other plant species. Altogether, our results provide a comprehensive and detailed picture of seed germination dynamics in oilseed rape. This new framework will be extremely valuable not only to evaluate germination performance of B. napus accessions but also to identify key targets for crop improvement in this important process.

TRANSPORTER OF IBA1 Links Auxin and Cytokinin to Influence Root Architecture

Developmental processes that control root system architecture are critical for soil exploration by plants, allowing for uptake of water and nutrients. Conversion of the auxin precursor indole-3-butyric acid (IBA) to active auxin (indole-3-acetic acid; IAA) modulates lateral root formation. However, mechanisms governing IBA-to-IAA conversion have yet to be elucidated. We identified TRANSPORTER OF IBA1 (TOB1) as a vacuolar IBA transporter that limits lateral root formation. Moreover, TOB1, which is transcriptionally regulated by the phytohormone cytokinin, is necessary for the ability of cytokinin to exert inhibitory effects on lateral root production. The increased production of lateral roots in tob1 mutants, TOB1 transport of IBA into the vacuole, and cytokinin-regulated TOB1 expression provide a mechanism linking cytokinin signaling and IBA contribution to the auxin pool to tune root system architecture.

In Silico Roots: Room for Growth

Computational models are invaluable tools for understanding the hormonal and genetic control of root development. Thus far, models have focused on the crucial roles that auxin transport and metabolism play in determining the auxin signaling gradient that controls the root meristem. Other hormones such as cytokinins, gibberellins, and ethylene have predominantly been considered as modulators of auxin dynamics, but their underlying patterning mechanisms are currently unresolved. In addition, the effects of cell- and tissue-level growth dynamics, which induce dilution and displacement of signaling molecules, have remained unexplored. Elucidating these additional mechanisms will be essential to unravel how root growth is patterned in a robust and self-organized manner. Models incorporating growth will thus be crucial in unraveling the underlying logic of root developmental decision making.

A PEX5 missense allele preferentially disrupts PTS1 cargo import into Arabidopsis peroxisomes

The sorting of eukaryotic proteins to various organellar destinations requires receptors that recognize cargo protein targeting signals and facilitate transport into the organelle. One such receptor is the peroxin PEX5, which recruits cytosolic cargo carrying a peroxisome-targeting signal (PTS) type 1 (PTS1) for delivery into the peroxisomal lumen (matrix). In plants and mammals, PEX5 is also indirectly required for peroxisomal import of proteins carrying a PTS2 signal because PEX5 binds the PTS2 receptor, bringing the associated PTS2 cargo to the peroxisome along with PTS1 cargo. Despite PEX5 being the PTS1 cargo receptor, previously identified Arabidopsis pex5 mutants display either impairment of both PTS1 and PTS2 import or defects only in PTS2 import. Here we report the first Arabidopsis pex5 mutant with an exclusive PTS1 import defect. In addition to markedly diminished GFP-PTS1 import and decreased pex5-2 protein accumulation, this pex5-2 mutant shows typical peroxisome-related defects, including inefficient β-oxidation and reduced growth. Growth at reduced or elevated temperatures ameliorated or exacerbated pex5-2 peroxisome-related defects, respectively, without markedly changing pex5-2 protein levels. In contrast to the diminished PTS1 import, PTS2 processing was only slightly impaired and PTS2-GFP import appeared normal in pex5-2. This finding suggests that even minor peroxisomal localization of the PTS1 protein DEG15, the PTS2-processing protease, is sufficient to maintain robust PTS2 processing.

A facile forward-genetic screen for Arabidopsis autophagy mutants reveals twenty-one loss-of-function mutations disrupting six ATG genes

Macroautophagy is a process through which eukaryotic cells degrade large substrates including organelles, protein aggregates, and invading pathogens. Over 40 autophagy-related (ATG) genes have been identified through forward-genetic screens in yeast. Although homology-based analyses have identified conserved ATG genes in plants, only a few atg mutants have emerged from forward-genetic screens in Arabidopsis thaliana. We developed a screen that consistently recovers Arabidopsis atg mutations by exploiting mutants with defective LON2/At5g47040, a protease implicated in peroxisomal quality control. Arabidopsis lon2 mutants exhibit reduced responsiveness to the peroxisomally-metabolized auxin precursor indole-3-butyric acid (IBA), heightened degradation of several peroxisomal matrix proteins, and impaired processing of proteins harboring N-terminal peroxisomal targeting signals; these defects are ameliorated by preventing autophagy. We optimized a lon2 suppressor screen to expedite recovery of additional atg mutants. After screening mutagenized lon2-2 seedlings for restored IBA responsiveness, we evaluated stabilization and processing of peroxisomal proteins, levels of several ATG proteins, and levels of the selective autophagy receptor NBR1/At4g24690, which accumulates when autophagy is impaired. We recovered 21 alleles disrupting 6 ATG genes: ATG2/At3g19190, ATG3/At5g61500, ATG5/At5g17290, ATG7/At5g45900, ATG16/At5g50230, and ATG18a/At3g62770. Twenty alleles were novel, and 3 of the mutated genes lack T-DNA insertional alleles in publicly available repositories. We also demonstrate that an insertional atg11/At4g30790 allele incompletely suppresses lon2 defects. Finally, we show that NBR1 is not necessary for autophagy of lon2 peroxisomes and that NBR1 overexpression is not sufficient to trigger autophagy of seedling peroxisomes, indicating that Arabidopsis can use an NBR1-independent mechanism to target peroxisomes for autophagic degradation.

Abbreviations: ATG: autophagy-related; ATI: ATG8-interacting protein; Col-0: Columbia-0; DSK2: dominant suppressor of KAR2; EMS: ethyl methanesulfonate; GFP: green fluorescent protein; IAA: indole-3-acetic acid; IBA: indole-3-butyric acid; ICL: isocitrate lyase; MLS: malate synthase; NBR1: Next to BRCA1 gene 1; PEX: peroxin; PMDH: peroxisomal malate dehydrogenase; PTS: peroxisomal targeting signal; thiolase: 3-ketoacyl-CoA thiolase; UBA: ubiquitin-associated; WT: wild type

The Coordination of Ethylene and Other Hormones in Primary Root Development

The primary root is the basic component of root systems, initiates during embryogenesis and develops shortly after germination, and plays a key role in early seedling growth and survival. The phytohormone ethylene shows significant inhibition of the growth of primary roots. Recent findings have revealed that the inhibition of ethylene in primary root elongation is mediated via interactions with phytohormones, such as auxin, abscisic acid, gibberellin, cytokinins, jasmonic acid, and brassinosteroids. Considering that Arabidopsis and rice are the model plants of dicots and monocots, as well as the fact that hormonal crosstalk in primary root growth has been extensively investigated in Arabidopsis and rice, a better understanding of the mechanisms in Arabidopsis and rice will increase potential applications in other species. Therefore, we focus our interest on the emerging studies in the research of ethylene and hormone crosstalk in primary root development in Arabidopsis and rice.

Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

Drought induced changes of leaf-to-root relationships in two tomato genotypes

Water deficit triggers a dynamic and integrated cross-talk between leaves and roots. Tolerant plants have developed several physiological and molecular mechanisms to establish new cell metabolism homeostasis, avoiding and/or escaping from permanent impairments triggered by drought. Two tomato genotypes (a Southern Italy landrace called Ciettaicale and the well-known commercial cultivar Moneymaker) were investigated at vegetative stage to assess leaf and root metabolic strategies under 20 days of water deficit. Physiological and metabolic changes, in terms of ABA, IAA, proline, soluble sugars and phenols contents, occurred in both tomato genotypes under water stress. Overall, our results pointed out the higher plasticity of Ciettaicale to manage plant water status under drought in order to preserve the source-sink relationships. This aim was achieved by maintaining a more efficient leaf photosystem II (PSII) photochemistry, as suggested by chlorophyll fluorescence parameters, associated with a major investment towards root growth and activity to improve water uptake. On the contrary, the higher accumulation of carbon compounds, resulting from reduced PSII photochemistry and enhanced starch reserve mobilization, in leaves and roots of Moneymaker under drought could play a key role in the osmotic adjustment, although causing a feedback disruption of the source-sink relations. This hypothesis was also supported by the different drought-induced redox unbalance, as suggested by H₂O₂ and MDA contents. This could affect both PSII photochemistry and root activity, leading to a major involvement of NPQ and antioxidant system in response to drought in Moneymaker than Ciettaicale.

The PP2A-interactor TIP41 modulates ABA responses in Arabidopsis thaliana

Modulation of growth in response to environmental cues is a fundamental aspect of plant adaptation to abiotic stresses. TIP41 (TAP42 INTERACTING PROTEIN OF 41 kDa) is the Arabidopsis thaliana orthologue of proteins isolated in mammals and yeast that participate in the Target-of-Rapamycin (TOR) pathway, which modifies cell growth in response to nutrient status and environmental conditions. Here, we characterized the function of TIP41 in Arabidopsis. Expression analyses showed that TIP41 is constitutively expressed in vascular tissues, and is induced following long-term exposure to NaCl, polyethylene glycol and abscisic acid (ABA), suggesting a role of TIP41 in adaptation to abiotic stress. Visualization of a fusion protein with yellow fluorescent protein indicated that TIP41 is localized in the cytoplasm and the nucleus. Abolished expression of TIP41 results in smaller plants with a lower number of rosette leaves and lateral roots, and an increased sensitivity to treatments with chemical TOR inhibitors, indicating that TOR signalling is affected in these mutants. In addition, tip41 mutants are hypersensitive to ABA at germination and seedling stage, whereas over-expressing plants show higher tolerance. Several TOR- and ABA-responsive genes are differentially expressed in tip41, including iron homeostasis, senescence and ethylene-associated genes. In yeast and mammals, TIP41 provides a link between the TOR pathway and the protein phosphatase 2A (PP2A), which in plants participates in several ABA-mediated mechanisms. Here, we showed an interaction of TIP41 with the catalytic subunit of PP2A. Taken together, these results offer important insights into the function of Arabidopsis TIP41 in the modulation of plant growth and ABA responses.

A pex1 missense mutation improves peroxisome function in a subset of Arabidopsis pex6 mutants without restoring PEX5 recycling

Peroxisomes are eukaryotic organelles critical for plant and human development because they house essential metabolic functions, such as fatty acid β-oxidation. The interacting ATPases PEX1 and PEX6 contribute to peroxisome function by recycling PEX5, a cytosolic receptor needed to import proteins targeted to the peroxisomal matrix. Arabidopsis pex6 mutants exhibit low PEX5 levels and defects in peroxisomal matrix protein import, oil body utilization, peroxisomal metabolism, and seedling growth. These defects are hypothesized to stem from impaired PEX5 retrotranslocation leading to PEX5 polyubiquitination and consequent degradation of PEX5 via the proteasome or of the entire organelle via autophagy. We recovered a pex1 missense mutation in a screen for second-site suppressors that restore growth to the pex6-1 mutant. Surprisingly, this pex1-1 mutation ameliorated the metabolic and physiological defects of pex6-1 without restoring PEX5 levels. Similarly, preventing autophagy by introducing an atg7-null allele partially rescued pex6-1 physiological defects without restoring PEX5 levels. atg7 synergistically improved matrix protein import in pex1-1 pex6-1, implying that pex1-1 improves peroxisome function in pex6-1 without impeding autophagy of peroxisomes (i.e., pexophagy). pex1-1 differentially improved peroxisome function in various pex6 alleles but worsened the physiological and molecular defects of a pex26 mutant, which is defective in the tether anchoring the PEX1-PEX6 hexamer to the peroxisome. Our results support the hypothesis that, beyond PEX5 recycling, PEX1 and PEX6 have additional functions in peroxisome homeostasis and perhaps in oil body utilization.

Ethylene Receptors Signal via a Noncanonical Pathway to Regulate Abscisic Acid Responses

Ethylene is a gaseous plant hormone perceived by a family of receptors in Arabidopsis (Arabidopsis thaliana) including ETHYLENE RESPONSE1 (ETR1) and ETR2. Previously we showed that etr1-6 loss-of-function plants germinate better and etr2-3 loss-of-function plants germinate worse than wild-type under NaCl stress and in response to abscisic acid (ABA). In this study, we expanded these results by showing that ETR1 and ETR2 have contrasting roles in the control of germination under a variety of inhibitory conditions for seed germination such as treatment with KCl, CuSO₄, ZnSO₄, and ethanol. Pharmacological and molecular biology results support a model where ETR1 and ETR2 are indirectly affecting the expression of genes encoding ABA signaling proteins to affect ABA sensitivity. The receiver domain of ETR1 is involved in this function in germination under these conditions and controlling the expression of genes encoding ABA signaling proteins. Epistasis analysis demonstrated that these contrasting roles of ETR1 and ETR2 do not require the canonical ethylene signaling pathway. To explore the importance of receptor-protein interactions, we conducted yeast two-hybrid screens using the cytosolic domains of ETR1 and ETR2 as bait. Unique interacting partners with either ETR1 or ETR2 were identified. We focused on three of these proteins and confirmed the interactions with receptors. Loss of these proteins led to faster germination in response to ABA, showing that they are involved in ABA responses. Thus, ETR1 and ETR2 have both ethylene-dependent and -independent roles in plant cells that affect responses to ABA.

Mechanisms for Abscisic Acid Inhibition of Primary Root Growth

Abscisic acid (ABA) plays pivotal roles in plant growth and development and in responses to diverse stresses. It also modulates the growth of primary and lateral roots. Much evidence indicated that key cellular components auxin, ethylene, PLETHs, reactive oxygen species and Ca²⁺ are involved in the regulation of ABA suppression of root elongation. In this review, we summary the molecular mechanism for ABA inhibiting primary root growth, focusing on the roles of these components in Arabidopsis.

miR160 and miR166/165 Contribute to the LEC2-Mediated Auxin Response Involved in the Somatic Embryogenesis Induction in Arabidopsis

MicroRNAs are non-coding small RNA molecules that are involved in the post-transcriptional regulation of the genes that control various developmental processes in plants, including zygotic embryogenesis (ZE). miRNAs are also believed to regulate somatic embryogenesis (SE), a counterpart of the ZE that is induced in vitro in plant somatic cells. However, the roles of specific miRNAs in the regulation of the genes involved in SE, in particular those encoding transcription factors (TFs) with an essential function during SE including LEAFY COTYLEDON2 (LEC2), remain mostly unknown. The aim of the study was to reveal the function of miR165/166 and miR160 in the LEC2-controlled pathway of SE that is induced in in vitro cultured Arabidopsis explants.In ZE, miR165/166 controls the PHABULOSA/PHAVOLUTA (PHB/PHV) genes, which are the positive regulators of LEC2, while miR160 targets the AUXIN RESPONSE FACTORS (ARF10, ARF16, ARF17) that control the auxin signaling pathway, which plays key role in LEC2-mediated SE. We found that a deregulated expression/function of miR165/166 and miR160 resulted in a significant accumulation of auxin in the cultured explants and the spontaneous formation of somatic embryos. Our results show that miR165/166 might contribute to SE induction via targeting PHB, a positive regulator of LEC2 that controls embryogenic induction via activation of auxin biosynthesis pathway (Wójcikowska et al., 2013). Similar to miR165/166, miR160 was indicated to control SE induction through auxin-related pathways and the negative impact of miR160 on ARF10/ARF16/ARF17 was shown in an embryogenic culture. Altogether, the results suggest that the miR165/166- and miR160-node contribute to the LEC2-mediated auxin-related pathway of embryogenic transition that is induced in the somatic cells of Arabidopsis. A model summarizing the suggested regulatory interactions between the miR165/166-PHB and miR160-ARF10/ARF16/ARF17 nodes that control SE induction in Arabidopsis was proposed.

Crosstalk Complexities between Auxin, Cytokinin, and Ethylene in Arabidopsis Root Development: From Experiments to Systems Modeling, and Back Again

Understanding how hormones and genes interact to coordinate plant growth in a changing environment is a major challenge in plant developmental biology. Auxin, cytokinin, and ethylene are three important hormones that regulate many aspects of plant development. This review critically evaluates the crosstalk between the three hormones in Arabidopsis root development. We integrate a variety of experimental data into a crosstalk network, which reveals multiple layers of complexity in auxin, cytokinin, and ethylene crosstalk. In particular, data integration reveals an additional, largely overlooked link between the ethylene and cytokinin pathways, which acts through a phosphorelay mechanism. This proposed link addresses outstanding questions on whether ethylene application promotes or inhibits receptor kinase activity of the ethylene receptors. Elucidating the complexity in auxin, cytokinin, and ethylene crosstalk requires a combined experimental and systems modeling approach. We evaluate important modeling efforts for establishing how crosstalk between auxin, cytokinin, and ethylene regulates patterning in root development. We discuss how a novel methodology that iteratively combines experiments with systems modeling analysis is essential for elucidating the complexity in crosstalk of auxin, cytokinin, and ethylene in root development. Finally, we discuss the future challenges from a combined experimental and modeling perspective.

Disparate peroxisome-related defects in Arabidopsis pex6 and pex26 mutants link peroxisomal retrotranslocation and oil body utilization

Catabolism of fatty acids stored in oil bodies is essential for seed germination and seedling development in Arabidopsis. This fatty acid breakdown occurs in peroxisomes, organelles that sequester oxidative reactions. Import of peroxisomal enzymes is facilitated by peroxins including PEX5, a receptor that delivers cargo proteins from the cytosol to the peroxisomal matrix. After cargo delivery, a complex of the PEX1 and PEX6 ATPases and the PEX26 tail-anchored membrane protein removes ubiquitinated PEX5 from the peroxisomal membrane. We identified Arabidopsis pex6 and pex26 mutants by screening for inefficient seedling β-oxidation phenotypes. The mutants displayed distinct defects in growth, response to a peroxisomally metabolized auxin precursor, and peroxisomal protein import. The low PEX5 levels in these mutants were increased by treatment with a proteasome inhibitor or by combining pex26 with peroxisome-associated ubiquitination machinery mutants, suggesting that ubiquitinated PEX5 is degraded by the proteasome when the function of PEX6 or PEX26 is reduced. Combining pex26 with mutations that increase PEX5 levels either worsened or improved pex26 physiological and molecular defects, depending on the introduced lesion. Moreover, elevating PEX5 levels via a 35S:PEX5 transgene exacerbated pex26 defects and ameliorated the defects of only a subset of pex6 alleles, implying that decreased PEX5 is not the sole molecular deficiency in these mutants. We found peroxisomes clustered around persisting oil bodies in pex6 and pex26 seedlings, suggesting a role for peroxisomal retrotranslocation machinery in oil body utilization. The disparate phenotypes of these pex alleles may reflect unanticipated functions of the peroxisomal ATPase complex.

An Arabidopsis kinase cascade influences auxin-responsive cell expansion

Mitogen-activated protein kinase (MPK) cascades are conserved mechanisms of signal transduction across eukaryotes. Despite the importance of MPK proteins in signaling events, specific roles for many Arabidopsis MPK proteins remain unknown. Multiple studies have suggested roles for MPK signaling in a variety of auxin-related processes. To identify MPK proteins with roles in auxin response, we screened mpk insertional alleles and identified mpk1-1 as a mutant that displays hypersensitivity in auxin-responsive cell expansion assays. Further, mutants defective in the upstream MAP kinase kinase MKK3 also display hypersensitivity in auxin-responsive cell expansion assays, suggesting that this MPK cascade affects auxin-influenced cell expansion. We found that MPK1 interacts with and phosphorylates ROP BINDING PROTEIN KINASE 1 (RBK1), a protein kinase that interacts with members of the Rho-like GTPases from Plants (ROP) small GTPase family. Similar to mpk1-1 and mkk3-1 mutants, rbk1 insertional mutants display auxin hypersensitivity, consistent with a possible role for RBK1 downstream of MPK1 in influencing auxin-responsive cell expansion. We found that RBK1 directly phosphorylates ROP4 and ROP6, supporting the possibility that RBK1 effects on auxin-responsive cell expansion are mediated through phosphorylation-dependent modulation of ROP activity. Our data suggest a MKK3 • MPK1 • RBK1 phosphorylation cascade that may provide a dynamic module for altering cell expansion.

The Biphasic Root Growth Response to Abscisic Acid in Arabidopsis Involves Interaction with Ethylene and Auxin Signalling Pathways

Exogenous abscisic acid (ABA) is known to either stimulate or inhibit root growth, depending on its concentration. In this study, the roles of ethylene and auxin in this biphasic effect of ABA on root elongation were investigated using chemical inhibitors and mutants. Inhibitors of ethylene perception and biosynthesis and an auxin influx inhibitor were all found to block the inhibitory effect of high ABA concentrations, but not the stimulatory effect of low ABA concentrations. In addition, three ethylene-insensitive mutants (etr1-1, ein2-1, and ein3-1), two auxin influx mutants (aux1-7, aux1-T) and an auxin-insensitive mutant (iaa7/axr2-1) were all insensitive to the inhibitory effect of high ABA concentrations. In the case of the stimulatory effect of low ABA concentrations, it was blocked by two different auxin efflux inhibitors and was less pronounced in an auxin efflux mutant (pin2/eir1-1) and in the iaa7/axr2-1 auxin-insensitive mutant. Thus it appears that the stimulatory effect seen at low ABA concentrations is via an ethylene-independent pathway requiring auxin signalling and auxin efflux through PIN2/EIR1, while the inhibitory effect at high ABA concentrations is via an ethylene-dependent pathway requiring auxin signalling and auxin influx through AUX1.

The PEX1 ATPase Stabilizes PEX6 and Plays Essential Roles in Peroxisome Biology

A variety of metabolic pathways are sequestered in peroxisomes, conserved organelles that are essential for human and plant survival. Peroxin (PEX) proteins generate and maintain peroxisomes. The PEX1 ATPase facilitates recycling of the peroxisome matrix protein receptor PEX5 and is the most commonly affected peroxin in human peroxisome biogenesis disorders. Here, we describe the isolation and characterization of, to our knowledge, the first Arabidopsis (Arabidopsis thaliana) pex1 missense alleles: pex1-2 and pex1-3pex1-2 displayed peroxisome-related defects accompanied by reduced PEX1 and PEX6 levels. These pex1-2 defects were exacerbated by growth at high temperature and ameliorated by growth at low temperature or by PEX6 overexpression, suggesting that PEX1 enhances PEX6 stability and vice versa. pex1-3 conferred embryo lethality when homozygous, confirming that PEX1, like several other Arabidopsis peroxins, is essential for embryogenesis. pex1-3 displayed symptoms of peroxisome dysfunction when heterozygous; this semidominance is consistent with PEX1 forming a heterooligomer with PEX6 that is poisoned by pex1-3 subunits. Blocking autophagy partially rescued PEX1/pex1-3 defects, including the restoration of normal peroxisome size, suggesting that increasing peroxisome abundance can compensate for the deficiencies caused by pex1-3 and that the enlarged peroxisomes visible in PEX1/pex1-3 may represent autophagy intermediates. Overexpressing PEX1 in wild-type plants impaired growth, suggesting that excessive PEX1 can be detrimental. Our genetic, molecular, and physiological data support the heterohexamer model of PEX1-PEX6 function in plants.

Environmental nitrate signals through abscisic acid in the root tip

Roots respond to changes in environmental nitrate with a localized stimulation of ABA levels in the root tip. This rise in ABA levels is due to the action of ER-localized β-GLUCOSIDASE 1, which releases bioactive ABA from the inactive ABA-glucose ester. The slow rise in root tip ABA levels stimulates expression of nitrate metabolic enzymes and simultaneously activates a negative feedback loop involving the protein phosphatase, ABI2, which reduces nitrate influx via the AtNPF6.3 transceptor. The rise in root-tip localized ABA also negatively regulates expression of the SCARECROW transcription factor, thus providing a sensitive mechanism for modulating root growth in response to environmental changes.

The Triple Response Assay and Its Use to Characterize Ethylene Mutants in Arabidopsis

Exposure of plants to ethylene results in drastic morphological changes. Seedlings germinated in the dark in the presence of saturating concentrations of ethylene display a characteristic phenotype known as the triple response. This phenotype is robust and easy to score. In Arabidopsis the triple response is usually evaluated at 3 days post germination in seedlings grown in the dark in rich media supplemented with 10 μM of the ethylene precursor ACC in air or in unsupplemented media in the presence of 10 ppm ethylene. The triple response in Arabidopsis consists of shortening and thickening of hypocotyls and roots and exaggeration of the curvature of apical hooks. The search for Arabidopsis mutants that fail to show this phenotype in ethylene or, vice versa, display the triple response in the absence of exogenously supplied hormone has allowed the identification of the key components of the ethylene biosynthesis and signaling pathways. Herein, we describe a simple protocol for assaying the triple response in Arabidopsis. The method can also be employed in many other dicot species, with minor modifications to account for species-specific differences in germination. We also compiled a comprehensive table of ethylene-related mutants of Arabidopsis, including many lines with auxin-related defects, as wild-type levels of auxin biosynthesis, transport, signaling, and response are necessary for the normal response of plants to ethylene.

Arabidopsis seed germination speed is controlled by SNL histone deacetylase-binding factor-mediated regulation of AUX1

Histone acetylation is known to affect the speed of seed germination, but the molecular regulatory basis of this remains ambiguous. Here we report that loss of function of two histone deacetylase-binding factors, SWI-INDEPENDENT3 (SIN3)-LIKE1 (SNL1) and SNL2, results in accelerated radicle protrusion and growth during seed germination. AUXIN RESISTANT 1 (AUX1) is identified as a key factor in this process, enhancing germination speed downstream of SNL1 and SNL2. AUX1 expression and histone H3 acetylation at lysines 9 and 18 is regulated by SNL1 and SNL2. The D-type cyclins encoding genes CYCD1;1 and CYCD4;1 display increased expression in AUX1 over-expression lines and the snl1snl2 double mutant. Accordingly, knockout of CYCD4;1 reduces seed germination speed of AUX1 over-expression lines and snl1snl2 suggesting the importance of cell cycling for radicle protrusion during seed germination. Together, our work identifies AUX1 as a link between histone acetylation mediated by SNL1 and SNL2, and radicle growth promoted by CYCD1;1 and CYCD4;1 during seed germination.

Histone acetylation influences the speed of seed germination. Here, Wang et al. show that loss of the SNL1/SNL2 histone deacetylase binding factors accelerates seed germination and provide evidence that they act by regulating the expression of AUX1 which in turn influences cell division.