Distinctive expression patterns and roles of the miRNA393/TIR1 homolog module in regulating flag leaf inclination and primary and crown root growth in rice (Oryza sativa)

? MicroRNA (miRNA)-mediated regulation of auxin signaling components plays a critical role in plant development. miRNA expression and functional diversity contribute to the complexity of regulatory networks of miRNA/target modules. ? This study functionally characterizes two members of the rice (Oryza sativa) miR393 family and their target genes, OsTIR1 and OsAFB2 (AUXIN SIGNALING F-BOX), the two closest homologs of Arabidopsis TRANSPORT INHIBITOR RESPONSE 1 (TIR1). ? We found that the miR393 family members possess distinctive expression patterns, with miR393a expressed mainly in the crown and lateral root primordia, as well as the coleoptile tip, and miR393b expressed in the shoot apical meristem. Transgenic plants overexpressing miR393a/b displayed a severe phenotype with hallmarks of altered auxin signaling, mainly including enlarged flag leaf inclination and altered primary and crown root growth. Furthermore, OsAFB2- and OsTIR1-suppressed lines exhibited increased inclination of flag leaves at the booting stage, resembling miR393-overexpressing plants. Moreover, yeast two-hybrid and bimolecular fluorescence complementation assays showed that OsTIR1 and OsAFB2 interact with OsIAA1. ? Expression diversification of miRNA393 implies the potential role of miRNA regulation during species evolution. The conserved mechanisms of the miR393/target module indicate the fundamental importance of the miR393-mediated regulation of auxin signal transduction in rice.     

The microRNA miR393 re-directs secondary metabolite biosynthesis away from camalexin and towards glucosinolates

flg22 treatment increases levels of miR393, a microRNA that targets auxin receptors. Over-expression of miR393 renders plants more resistant to biotroph pathogens and more susceptible to necrotroph pathogens. In contrast, over-expression of AFB1, an auxin receptor whose mRNA is partially resistant to miR393 degradation, renders the plant more susceptible to biotroph pathogens. Here we investigate the mechanism by which auxin signalling and miR393 influence plant defence. We show that auxin signalling represses SA levels and signalling. We also show that miR393 represses auxin signalling, preventing it from antagonizing SA signalling. In addition, over-expression of miR393 increases glucosinolate levels and decreases the levels of camalexin. Further studies on pathogen interactions in auxin signalling mutants revealed that ARF1 and ARF9 negatively regulate glucosinolate accumulation, and that ARF9 positively regulates camalexin accumulation. We propose that the action of miR393 on auxin signalling triggers two complementary responses. First, it prevents suppression of SA levels by auxin. Second, it stabilizes ARF1 and ARF9 in inactive complexes. As a result, the plant is able to mount a full SA response and to re-direct metabolic flow toward the most effective anti-microbial compounds for biotroph resistance. We propose that miR393 levels can fine-tune plant defences and prioritize resources.     

Differential regulation of microRNAs in response to osmotic,salt and cold stresses in wheat

MicroRNAs (miRNAs) are tiny non-coding regulatory molecules that modulate plant’s gene expression either by cleaving or repressing their mRNA targets. To unravel the plant actions in response to various environmental factors, identification of stress related miRNAs is essential. For understanding the regulatory behaviour of various abiotic stresses and miRNAs in wheat genotype C-306, we examined expression profile of selected conserved miRNAs viz. miR159, miR164, miR168, miR172, miR393, miR397, miR529 and miR1029 tangled in adapting osmotic, salt and cold stresses. The investigation revealed that two miRNAs (miR168, miR397) were down-regulated and miR172 was up-regulated under all the stress conditions. However, miR164 and miR1029 were up-regulated under cold and osmotic stresses in contrast to salt stress. miR529 responded to cold alone and does not change under osmotic and salt stress. miR393 showed up-regulation under osmotic and salt, and down-regulation under cold stress indicating auxin based differential cold response. Variation in expression level of studied miRNAs in presence of target genes delivers a likely elucidation of miRNAs based abiotic stress regulation. In addition, we reported new stress induced miRNAs Ta-miR855 using computational approach. Results revealed first documentation that miR855 is regulated by salinity stress in wheat. These findings indicate that diverse miRNAs were responsive to osmotic, salt and cold stress and could function in wheat response to abiotic stresses.     

Reduced Soybean Water Stress Tolerance by miR393a-Mediated Repression of GmTIR1 and Abscisic Acid Accumulation

MicroRNA393 (miR393) has been shown to regulate plant water stress tolerance through an auxin signaling pathway. However, its role in soybean (Glycine max [L.] Merr.) has not yet been reported. Here, we examined the expression pattern of miR393 family members and their target gene GmTIR1 in water-stressed roots. Subsequently, we analyzed the functions of miR393 in the regulation of water stress tolerance and its relationship with GmTIR1 and abscisic acid (ABA) using a transgenic hairy root assay. Under water stress, miR393 family genes exhibited diverse expression patterns. Overexpression and knockdown analysis demonstrated that miR393a reduced water stress tolerance as measured by root vigor, net photosynthetic rate (Pn), and relative water content (RWC). Moreover, miR393a also caused down-regulation of GmTIR1A and GmTIR1B expression, an early decrease in hydrogen peroxide (H₂O₂) levels, early and late declines in ABA content and antioxidant activities, and a late elevation of H₂O₂ and malondialdehyde (MDA) concentrations in stressed hairy roots. However, overexpression and RNAi analyses showed that GmTIR1A and GmTIR1B triggered an early increase in H₂O₂, a rise in antioxidant activities during the early and late stages, a late decline in H₂O₂ and MDA contents, and a rise in root vigor, Pn, and RWC under water stress. Similarly, exogenously supplied ABA caused early H₂O₂ accumulation, early and late increases in antioxidant capacity, and a late decrease in oxidative damage in stressed miR393a-overexpressing roots. Therefore, our study presents a valuable model in which miR393a prevents early GmTIR1- and ABA-dependent increases in H₂O₂ and thus triggers a rise in antioxidant capacity, root vigor, RWC, and Pn, consequently decreasing water stress tolerance.

     

A late embryogenesis abundant protein HVA1 regulated by an inducible promoter enhances root growth and abiotic stress tolerance in rice without yield penalty

Regulation of root architecture is essential for maintaining plant growth under adverse environment. A synthetic abscisic acid (ABA)/stress‐inducible promoter was designed to control the expression of a late embryogenesis abundant protein (HVA1) in transgenic rice. The background of HVA1 is low but highly inducible by ABA, salt, dehydration and cold. HVA1 was highly accumulated in root apical meristem (RAM) and lateral root primordia (LRP) after ABA/stress treatments, leading to enhanced root system expansion. Water‐use efficiency (WUE) and biomass also increased in transgenic rice, likely due to the maintenance of normal cell functions and metabolic activities conferred by HVA1 which is capable of stabilizing proteins, under osmotic stress. HVA1 promotes lateral root (LR) initiation, elongation and emergence and primary root (PR) elongation via an auxin‐dependent process, particularly by intensifying asymmetrical accumulation of auxin in LRP founder cells and RAM, even under ABA/stress‐suppressive conditions. We demonstrate a successful application of an inducible promoter in regulating the spatial and temporal expression of HVA1 for improving root architecture and multiple stress tolerance without yield penalty.     

Microtubule dynamics in relation to osmotic stress-induced ABA accumulation in Zea mays roots

Microtubules play important roles in many physiological processes such as plant responses to drought stress. Abscisic acid (ABA) accumulates significantly in plants in response to drought conditions, which has been considered as a major response for plants to enhance drought tolerance. In this work, the focus was on the possible roles of microtubules in the induction of ABA biosynthesis in the roots of Zea mays when subjected to osmotic stress. The dynamic changes of microtubules in response to the stress were investigated by immunofluorescence staining, enzyme-linked immunosorbent assay, and a pharmacological approach. Disruption and stabilization of microtubules both significantly stimulated ABA accumulation in maize root cells, although this stimulation was markedly lower than that caused by osmotic stress. Cells in which the microtubule stability had been changed did not respond further to osmotic stress in terms of ABA biosynthesis. However, treatment with both a microtubule de-stabilizer and a stabilizer enhanced the sensitivity of cells to osmotic stress in terms of ABA accumulation. It is suggested that both osmotic stress and changes in microtubule dynamics would trigger maize root cells to biosynthesize ABA, and interactions between osmotic stress and microtubule dynamics would have an effect on ABA accumulation in root cells, although the exact mechanism is not clear at present.     

OsTIR1 and OsAFB2 downregulation via OsmiR393 overexpression leads to more tillers, early flowering and less tolerance to salt and drought in rice

The microRNA miR393 has been shown to play a role in plant development and in the stress response by targeting mRNAs that code for the auxin receptors in Arabidopsis. In this study, we verified that two rice auxin receptor gene homologs (OsTIR1 and OsAFB2) could be targeted by OsmiR393 (Os for Oryza sativa). Two new phenotypes (increased tillers and early flowering) and two previously observed phenotypes (reduced tolerance to salt and drought and hyposensitivity to auxin) were observed in the OsmiR393-overexpressing rice plants. The OsmiR393-overexpressing rice demonstrated hyposensitivity to synthetic auxin-analog treatments. These data indicated that the phenotypes of OsmiR393-overexpressing rice may be caused through hyposensitivity to the auxin signal by reduced expression of two auxin receptor genes (OsTIR1 and OsAFB2). The expression of an auxin transporter (OsAUX1) and a tillering inhibitor (OsTB1) were downregulated by overexpression of OsmiR393, which suggested that a gene chain from OsmiR393 to rice tillering may be from OsTIR1 and OsAFB2 to OsAUX1, which affected the transportation of auxin, then to OsTB1, which finally controlled tillering. The positive phenotypes (increased tillers and early flowering) and negative phenotypes (reduced tolerance to salt and hyposensitivity to auxin) of OsmiR393-overexpressing rice present a dilemma for molecular breeding.     

miR390, Arabidopsis TAS3 tasiRNAs,and Their AUXIN RESPONSE FACTOR Targets Define an Autoregulatory Network Quantitatively Regulating Lateral Root Growth

Plants adapt to different environmental conditions by constantly forming new organs in response to morphogenetic signals. Lateral roots branch from the main root in response to local auxin maxima. How a local auxin maximum translates into a robust pattern of gene activation ensuring the proper growth of the newly formed lateral root is largely unknown. Here, we demonstrate that miR390, TAS3-derived trans-acting short-interfering RNAs (tasiRNAs), and AUXIN RESPONSE FACTORS (ARFs) form an auxin-responsive regulatory network controlling lateral root growth. Spatial expression analysis using reporter gene fusions, tasi/miRNA sensors, and mutant analysis showed that miR390 is specifically expressed at the sites of lateral root initiation where it triggers the biogenesis of tasiRNAs. These tasiRNAs inhibit ARF2, ARF3, and ARF4, thus releasing repression of lateral root growth. In addition, ARF2, ARF3, and ARF4 affect auxin-induced miR390 accumulation. Positive and negative feedback regulation of miR390 by ARF2, ARF3, and ARF4 thus ensures the proper definition of the miR390 expression pattern. This regulatory network maintains ARF expression in a concentration range optimal for specifying the timing of lateral root growth, a function similar to its activity during leaf development. These results also show how small regulatory RNAs integrate with auxin signaling to quantitatively regulate organ growth during development.     

The role of cytokinins in responses to water deficit in tobacco plants over-expressing trans-zeatin O-glucosyltransferase gene under 35S or SAG12 promoters

The impact of water deficit progression on cytokinin (CK), auxin and abscisic acid (ABA) levels was followed in upper, middle and lower leaves and roots of Nicotiana tabacum L. cv. Wisconsin 38 plants [wild type (WT)]. ABA content was strongly increased during drought stress, especially in upper leaves. In plants with a uniformly elevated total CK content, expressing constitutively the trans -zeatin O-glucosyltransferase gene ( 35S::ZOG1 ), a delay in the increase of ABA was observed; later on, ABA levels were comparable with those of WT.
As drought progressed, the bioactive CK content in leaves gradually decreased, being maintained longer in the upper leaves of all tested genotypes. Under severe stress (11 d dehydration), a large stimulation of cytokinin oxidase/dehydrogenase (CKX) activity was monitored in lower leaves, which correlated well with the decrease in bioactive CK levels. This suggests that a gradient of bioactive CKs in favour of upper leaves is established during drought stress, which might be beneficial for the preferential protection of these leaves.
During drought, significant accumulation of CKs occurred in roots, partially because of decreased CKX activity. Simultaneously, auxin increased in roots and lower leaves. This indicates that both CKs and auxin play a role in root response to severe drought, which involves the stimulation of primary root growth and branching inhibition.     

Osmotic regulation of root system architecture

Although root system architecture is known to be highly plastic and strongly affected by environmental conditions, we have little understanding of the underlying mechanisms controlling root system development. Here we demonstrate that the formation of a lateral root from a lateral root primordium is repressed as water availability is reduced. This osmotic-responsive regulatory mechanism requires abscisic acid (ABA) and a newly identified gene, LRD2. Mutant analysis also revealed interactions of ABA and LRD2 with auxin signaling. Surprisingly, further examination revealed that both ABA and LRD2 control root system architecture even in the absence of osmotic stress. This suggests that the same molecules that mediate responses to environmental cues can also be regulators of intrinsic developmental programs in the root system.     

The rôle of abscisic acid in root growth and gravireaction: A critical review

A brief account is given of the discovery of abscisic acid (ABA) in roots and root caps of higher plants as well as the techniques by which ABA may be demonstrated in these tissues. The remainder of the review is concerned with examining the rôle of ABA in the regulation of root growth. In this regard, it is well established that when ABA is supplied to roots their elongation is usually inhibited, although at low external concentrations a stimulation of growth may also be found. Fewer observations have been directed at exploring the connection between root growth and the level of naturally occurring, endogenous ABA. Nevertheless, the evidence here also suggests that ABA is an inhibitory regulator of root growth. Moreover, ABA appears to be involved in the differential growth that arises in response to a gravitational stimulus. Recent reports that deny a rôle for ABA in root gravitropism are considered inconclusive. The response of roots to osmotic stress and the changes in ABA levels which ensue, are summarised; so are the interrelations between ABA and other hormones, particularly auxin (e.g. indoleacetic acid); both are considered in the context of the root growth and development. Quantitative changes in auxin and ABA levels may together provide the root with a flexible means of regulating its growth.     

TTG1-mediated flavonols biosynthesis alleviates root growth inhibition in response to ABA

Key message

Our results demonstrate that the flavonoids biosynthetic pathway can be effectively manipulated to confer enhanced plant root growth under water-stress conditions.

Abstract

Abscisic acid (ABA) is one of most important phytohormones. It functions in various processes during the plant lifecycle. Previous studies indicate that ABA has a negative effect on root growth and branching. Auxin is another key plant growth regulator that plays an essential role in plant growth and development. In contrast to ABA, auxin is a positive regulator of root growth and development at low concentrations. This study was performed to help understand whether flavonoids can suppress the effect of ABA on lateral root growth. The recessive TRANSPARENT TESTA GLABRA 1 (ttg1) mutant was characterized on ABA and sucrose treatments. It was determined that auxin mobilization could be altered by modifying flavonoids biosynthesis, which resulted in alterations of root architecture in response to ABA treatment. Moreover, transgenic TTG1-overexpression (TTG1-OX) seedlings exhibited enhanced root length and lateral root number compared to wild-type seedlings grown under normal or stress conditions. Genetic manipulation of the flavonoids biosynthetic pathway could therefore be employed successfully for the improvement of plant root systems by overcoming the inhibition of ABA and some abiotic stresses.     

Arabidopsis ROP‐interactive CRIB motif‐containing protein 1 (RIC1) positively regulates auxin signalling and negatively regulates abscisic acid (ABA) signalling during root development

Auxin and abscisic acid (ABA) modulate numerous aspects of plant development together, mostly in opposite directions, suggesting that extensive crosstalk occurs between the signalling pathways of the two hormones. However, little is known about the nature of this crosstalk. We demonstrate that ROP‐interactive CRIB motif‐containing protein 1 (RIC1) is involved in the interaction between auxin‐ and ABA‐regulated root growth and lateral root formation. RIC1 expression is highly induced by both hormones, and expressed in the roots of young seedlings. Whereas auxin‐responsive gene induction and the effect of auxin on root growth and lateral root formation were suppressed in the ric1 knockout, ABA‐responsive gene induction and the effect of ABA on seed germination, root growth and lateral root formation were potentiated. Thus, RIC1 positively regulates auxin responses, but negatively regulates ABA responses. Together, our results suggest that RIC1 is a component of the intricate signalling network that underlies auxin and ABA crosstalk.     

MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development

Although several plant microRNAs (miRNAs) have been shown to play a role in plant development, no phenotype has yet been associated with a reduction or loss of expression of any plant miRNA. Arabidopsis thaliana miR164 was predicted to target five NAM/ATAF/CUC (NAC) domain-encoding mRNAs, including NAC1, which transduces auxin signals for lateral root emergence. Here, we show that miR164 guides the cleavage of endogenous and transgenic NAC1 mRNA, producing 3'-specific fragments. Cleavage was blocked by NAC1 mutations that disrupt base pairing with miR164. Compared with wild-type plants, Arabidopsis mir164a and mir164b mutant plants expressed less miR164 and more NAC1 mRNA and produced more lateral roots. These mutant phenotypes can be complemented by expression of the appropriate MIR164a and MIR164b genomic sequences. By contrast, inducible expression of miR164 in wild-type plants led to decreased NAC1 mRNA levels and reduced lateral root emergence. Auxin induction of miR164 was mirrored by an increase in the NAC1 mRNA 3' fragment, which was not observed in the auxin-insensitive mutants auxin resistant1 (axr1-12), axr2-1, and transport inhibitor response1. Moreover, the cleavage-resistant form of NAC1 mRNA was unaffected by auxin treatment. Our results indicate that auxin induction of miR164 provides a homeostatic mechanism to clear NAC1 mRNA to downregulate auxin signals.