Root architecture remodeling induced by phosphate starvation

Rice chromatin protein OsHMGB1 is involved in phosphate homeostasis and plant growth by affecting chromatin accessibility

Although phosphorus is one of the most important essential elements for plant growth and development, the epigenetic regulation of inorganic phosphate (Pi) signaling is poorly understood. In this study, we investigated the biological function and mode of action of the high-mobility-group box 1 protein OsHMGB1 in rice (Oryza sativa), using molecular and genetic approaches. We determined that OsHMGB1 expression is induced by Pi starvation and encodes a nucleus-localized protein. Phenotypic analysis of Oshmgb1 mutant and OsHMGB1 overexpression transgenic plants showed that OsHMGB1 positively regulates Pi homeostasis and plant growth. Transcriptome deep sequencing and chromatin immunoprecipitation followed by sequencing indicated that OsHMGB1 regulates the expression of a series of phosphate starvation-responsive (PSR) genes by binding to their promoters. Furthermore, an assay for transposase-accessible chromatin followed by sequencing revealed that OsHMGB1 is involved in maintaining chromatin accessibility. Indeed, OsHMGB1 occupancy positively correlated with genome-wide chromatin accessibility and gene expression levels. Our results demonstrate that OsHMGB1 is a transcriptional facilitator that regulates the expression of a set of PSR genes to maintain Pi homeostasis in rice by increasing the chromatin accessibility, revealing a key epigenetic mechanism that fine-tune plant acclimation responses to Pi-limited environments.

Effects of Phosphate Shortage on Root Growth and Hormone Content of Barley Depend on Capacity of the Roots to Accumulate ABA

Although changes in root architecture in response to the environment can optimize mineral and water nutrient uptake, mechanisms regulating these changes are not well-understood. We investigated whether P deprivation effects on root development are mediated by abscisic acid (ABA) and its interactions with other hormones. The ABA-deficient barley mutant Az34 and its wild-type (WT) were grown in P-deprived and P-replete conditions, and hormones were measured in whole roots and root tips. Although P deprivation decreased growth in shoot mass similarly in both genotypes, only the WT increased primary root length and number of lateral roots. The effect was accompanied by ABA accumulation in root tips, a response not seen in Az34. Increased ABA in P-deprived WT was accompanied by decreased concentrations of cytokinin, an inhibitor of root extension. Furthermore, P-deficiency in the WT increased auxin concentration in whole root systems in association with increased root branching. In the ABA-deficient mutant, P-starvation failed to stimulate root elongation or promote branching, and there was no decline in cytokinin and no increase in auxin. The results demonstrate ABA’s ability to mediate in root growth responses to P starvation in barley, an effect linked to its effects on cytokinin and auxin concentrations.

Identification and Expression Analysis of GRAS Transcription Factors to Elucidate Candidate Genes Related to Stolons, Fruit Ripening and Abiotic Stresses in Woodland Strawberry (Fragaria vesca)

The cultivated strawberry (Fragaria × ananassa), an allo-octoploid with non-climacteric fleshy fruits, is a popular Rosaceae horticultural crop worldwide that is mainly propagated via stolons during cultivation. Woodland strawberry (Fragaria vesca), one of the four diploid progenitor species of cultivated strawberry, is widely used as a model plant in the study of Rosaceae fruit trees, non-climacteric fruits and stolons. One GRAS transcription factor has been shown to regulate stolon formation; the other GRAS proteins in woodland strawberry remain unknown. In this study, we identified 54 FveGRAS proteins in woodland strawberry, and divided them into 14 subfamilies. Conserved motif analysis revealed that the motif composition of FveGRAS proteins was conserved within each subfamily, but diverged widely among subfamilies. We found 56 orthologous pairs of GRAS proteins between woodland strawberry and Arabidopsis thaliana, 47 orthologous pairs between woodland strawberry and rice and 92 paralogous pairs within woodland strawberry. The expression patterns of FveGRAS genes in various organs and tissues, and changes therein under cold, heat and GA₃ treatments, were characterized using transcriptomic analysis. The results showed that 34 FveGRAS genes were expressed with different degrees in at least four organs, including stolons; only a few genes displayed organ-specific expression. The expression levels of 16 genes decreased, while that of four genes increased during fruit ripening; FveGRAS54 showed the largest increase in expression. Under cold, heat and GA₃ treatments, around half of the FveGRAS genes displayed increased or decreased expression to some extent, suggesting differing functions of these FveGRAS genes in the responses to cold, heat and GAs. This study provides insight into the potential functions of FveGRAS genes in woodland strawberry. A few FveGRAS genes were identified as candidate genes for further study, in terms of their functions in stolon formation, fruit ripening and abiotic stresses.

Editing of the OsACS locus alters phosphate deficiency-induced adaptive responses in rice seedlings

Phosphate (Pi) deficiency severely influences the growth and reproduction of plants. To cope with Pi deficiency, plants initiate morphological and biochemical adaptive responses upon sensing low Pi in the soil, and the plant hormone ethylene plays a crucial role during this process. However, how regulation of ethylene biosynthesis influences the Pi-induced adaptive responses remains unclear. Here, we determine the roles of rice 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS), the rate-limiting enzymes in ethylene biosynthesis, in response to Pi deficiency. Through analysis of tissue-specific expression of OsACS in response to Pi deficiency and OsACS mutants generated by CRISPR/Cas9 [clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9] genome editing, we found that two members of the OsACS family, i.e. OsACS1 and OsACS2, are involved but differed in their importance in controlling the remodeling of root system architecture, transcriptional regulation of Pi starvation-induced genes, and cellular phosphorus homeostasis. Interestingly, in contrast to the known inhibitory role of ethylene on root elongation, both OsACS mutants, especially OsACS1, almost fail to promote lateral root growth in response to Pi deficiency, demonstrating a stimulatory role for ethylene in lateral root development under Pi-deficient conditions. Together, this study provides new insights into the roles of ethylene in Pi deficiency response in rice seedlings and the isoform-specific function of OsACS genes in this process.

Blue Light Regulates Phosphate Deficiency-Dependent Primary Root Growth Inhibition in Arabidopsis

Plants have evolved mechanisms to improve utilization efficiency or acquisition of inorganic phosphate (Pi) in response to Pi deficiency, such as altering root architecture, secreting acid phosphatases, and activating the expression of genes related to Pi uptake and recycling. Although many genes responsive to Pi starvation have been identified, transcription factors that affect tolerance to Pi deficiency have not been well characterized. We show here that the ectopic expression of B-BOX32 (BBX32) and the mutation of ELONGATED HYPOCOTYL 5 (HY5), whose transcriptional activity is negatively regulated by BBX32, resulted in the tolerance to Pi deficiency in Arabidopsis. The primary root lengths of 35S:BBX32 and hy5 plants were only slightly inhibited under Pi deficient condition and the fresh weights were significantly higher than those of wild type. The Pi deficiency-tolerant root phenotype of hy5 was similarly observed when grown on the medium without Pi. In addition, a double mutant, hy5 slr1, without lateral roots, also showed a long primary root phenotype under phosphate deficiency, indicating that the root phenotype of hy5 does not result from an increase of external Pi uptake. Moreover, we found that blue light may regulate Pi deficiency-dependent primary root growth inhibition through activating peroxidase gene expression, suggesting the Pi-deficiency tolerant root phenotype of hy5 may be due to blockage of blue light responses. Altogether, this study points out light quality may play an important role in the regulation of Pi deficiency responses. It may contribute to regulate plant growth under Pi deficiency through proper illumination.

AtSPX1 affects the AtPHR1-DNA-binding equilibrium by binding monomeric AtPHR1 in solution

Phosphorus is an essential macronutrient for plant growth and is deficient in ∼50% of agricultural soils. The transcription factor phosphate starvation response 1 (PHR1) plays a central role in regulating the expression of a subset of phosphate starvation-induced (PSI) genes through binding to a cis-acting DNA element termed P1BS (PHR1-binding sequences). In Arabidopsis and rice, activity of AtPHR1/OsPHR2 is regulated in part by their downstream target SPX (Syg1, Pho81, Xpr1) proteins through protein-protein interaction. Here, we provide kinetic and affinity data for interaction between AtPHR1 and P1BS sites. Using surface plasmon resonance, a tandem P1BS sequence showed ∼50-fold higher affinity for MBPAtdPHR1 (a fusion protein comprising the DNA-binding domain and coiled-coil domain of AtPHR1 fused to maltose-binding protein) than a single site. The affinity difference was largely reflected in a much slower dissociation rate from the 2× P1BS-binding site, suggesting an important role for protein co-operativity. Injection of AtSPX1 in the presence of phosphate or inositol hexakisphosphate (InsP6) failed to alter the MBPAtdPHR1-P1BS dissociation rate, while pre-mixing of these two proteins in the presence of either 5 mM Pi or 500 µM InsP6 resulted in a much lower DNA-binding signal from MBPAtdPHR1. These data suggest that, in the Pi-restored condition, AtSPX1 can bind to monomeric AtPHR1 in solution and therefore regulate PSI gene expression by tuning the AtPHR1-DNA-binding equilibrium. This Pi-dependent regulation of AtPHR1-DNA-binding equilibrium also generates a negative feedback loop on the expression of AtSPX1 itself, providing a tight control of PSI gene expression.

Defense-Related Transcriptional Reprogramming in Vitamin E-Deficient Arabidopsis Mutants Exposed to Contrasting Phosphate Availability

Vitamin E inhibits the propagation of lipid peroxidation and helps protecting photosystem II from photoinhibition, but little is known about its possible role in plant response to Pi availability. Here, we aimed at examining the effect of vitamin E deficiency in Arabidopsis thaliana vte mutants on phytohormone contents and the expression of transcription factors in plants exposed to contrasting Pi availability. Plants were subjected to two doses of Pi, either unprimed (controls) or previously exposed to low Pi (primed). In the wild type, α-tocopherol contents increased significantly in response to repeated periods of low Pi, which was paralleled by increased growth, indicative of a priming effect. This growth-stimulating effect was, however, abolished in vte mutants. Hormonal profiling revealed significant effects of Pi availability, priming and genotype on the contents of jasmonates and salicylates; remarkably, vte mutants showed enhanced accumulation of both hormones under low Pi. Furthermore, expression profiling of 1,880 transcription factors by qRT-PCR revealed a pronounced effect of priming on the transcript levels of 45 transcription factors mainly associated with growth and stress in wild-type plants in response to low Pi availability; while distinct differences in the transcriptional response were detected in vte mutants. We conclude that α-tocopherol plays a major role in the response of plants to Pi availability not only by protecting plants from photo-oxidative stress, but also by exerting a control over growth- and defense-related transcriptional reprogramming and hormonal modulation.

miRNA alterations are important mechanism in maize adaptations to low-phosphate environments

Maize is a globally important crop, and a low phosphate (LP) supply frequently limits maize yields in many areas. microRNAs (miRNAs) play important roles in plant development and environmental adaptation. In this study, spatio-temporal miRNA transcript profiling and some of the target genes in the roots and leaves of the maize inbred line Q319 were analyzed in response to LP. Complex small RNA populations were detected after LP culture, and they displayed different patterns in the roots and leaves. Differentially expressed miRNAs can be grouped into 'early' miRNAs, which respond rapidly and are often non-specific to phosphate deficiency, and 'late' miRNAs, which alter the morphology, physiology or metabolism of plants upon prolonged phosphate deficiency. miR827 and miR399-mediated posttranscriptional pathway responses to phosphate availability were conserved and species-specific in maize. Abiotic stress-related miRNAs were engaged in interactions with different signaling and/or metabolic pathways. Auxin-related miRNAs and their targets' expression may be involved in root architecture modification and upland growth retardation in maize when subjected to LP. The changes that were found in the expression of miRNAs and their target genes suggested that miRNA regulation/alterations are pivotal mechanisms in maize adaptations to LP environments. A complex regulatory mechanism involving miRNAs in response to the LP environment is present in maize.

Phytohormone regulation of root growth triggered by P deficiency or Al toxicity

Phosphorus (P) deficiency and aluminum (Al) toxicity often coexist and limit plant growth on acid soils. It has been well documented that both P deficiency and Al toxicity alter root growth, including inhibition of primary roots and promotion of lateral roots. This suggests that plants adapt to both stresses through a common regulation pathway. Although an expanding set of results shows that phytohormones play vital roles in controlling root responses to Pi starvation and Al toxicity, it remains largely unknown whether P and Al coordinately regulate root growth through interacting phytohormone biosynthesis and signal transduction pathways. This review provides a summary of recent results concerning the influences of P deficiency and Al toxicity on root growth through the action of phytohormones, most notably auxin and ethylene. The objective is to facilitate increasing insights into complex responses of plants to adverse factors common on acid soils, which can spur development of 'smart' cultivars with better root growth and higher yield on these globally distributed marginal soils.

miRNA778 and SUVH6 are involved in phosphate homeostasis in Arabidopsis

microRNAs (miRNAs) play an important role in plant adaptation to phosphate (Pi) starvation. Histone methylation can remodel chromatin structure and mediate gene expression. This study identified Arabidopsis miR778, a Pi-responsive miRNA, and its target gene Su(var) 3-9 homologs 6 (SUVH6) encoding a histone H3 lysine 9 (H3K9) methyltransferase. Overexpression of miR778 moderately enhanced primary and lateral root growth, free phosphate accumulation in shoots, and accumulation of anthocyanin under Pi deficient conditions. miR778 overexpression relieved the arrest of columella cell development under Pi starvation. Conversely, transgenic plants overexpressing a miR778-target mimic (35S::MIM778), that act as a sponge and sequesters miR778, showed opposite phenotypes of 35S::miR778 plants under Pi deficiency. Expression of several Pi deficiency-responsive genes such as miR399, Phosphate Transporter (PHT1;4), Low Phosphate-Resistant1 (LPR1) and Production of Anthocyanin Pigment 1 (PAP1) were elevated in the miR778 overexpressing plants, suggesting that both miR778 and SUVH6 are involved in phosphate homeostasis in plants. This study has provided a basis for further investigation on how SUVH6 regulates its downstream genes through chromatin remodeling and DNA methylation in plants stressed by Pi deficiency.

An update on polygalacturonase-inhibiting protein (PGIP), a leucine-rich repeat protein that protects crop plants against pathogens

Polygalacturonase inhibiting proteins (PGIPs) are cell wall proteins that inhibit the pectin-depolymerizing activity of polygalacturonases secreted by microbial pathogens and insects. These ubiquitous inhibitors have a leucine-rich repeat structure that is strongly conserved in monocot and dicot plants. Previous reviews have summarized the importance of PGIP in plant defense and the structural basis of PG-PGIP interaction; here we update the current knowledge about PGIPs with the recent findings on the composition and evolution of pgip gene families, with a special emphasis on legume and cereal crops. We also update the information about the inhibition properties of single pgip gene products against microbial PGs and the results, including field tests, showing the capacity of PGIP to protect crop plants against fungal, oomycetes and bacterial pathogens.

Regulation of root morphogenesis in arbuscular mycorrhizae: what role do fungal exudates, phosphate, sugars and hormones play in lateral root formation?

BACKGROUND

Arbuscular mycorrhizae (AMs) form a widespread root-fungus symbiosis that improves plant phosphate (Pi) acquisition and modifies the physiology and development of host plants. Increased branching is recognized as a general feature of AM roots, and has been interpreted as a means of increasing suitable sites for colonization. Fungal exudates, which are involved in the dialogue between AM fungi and their host during the pre-colonization phase, play a well-documented role in lateral root (LR) formation. In addition, the increased Pi content of AM plants, in relation to Pi-starved controls, as well as changes in the delivery of carbohydrates to the roots and modulation of phytohormone concentration, transport and sensitivity, are probably involved in increasing root system branching.

SCOPE

This review discusses the possible causes of increased branching in AM plants. The differential root responses to Pi, sugars and hormones of potential AM host species are also highlighted and discussed in comparison with those of the non-host Arabidopsis thaliana.

CONCLUSIONS

Fungal exudates are probably the main compounds regulating AM root morphogenesis during the first colonization steps, while a complex network of interactions governs root development in established AMs. Colonization and high Pi act synergistically to increase root branching, and sugar transport towards the arbusculated cells may contribute to LR formation. In addition, AM colonization and high Pi generally increase auxin and cytokinin and decrease ethylene and strigolactone levels. With the exception of cytokinins, which seem to regulate mainly the root:shoot biomass ratio, these hormones play a leading role in governing root morphogenesis, with strigolactones and ethylene blocking LR formation in the non-colonized, Pi-starved plants, and auxin inducing them in colonized plants, or in plants grown under high Pi conditions.

Growth and nodulation of symbiotic Medicago truncatula at different levels of phosphorus availability

Medicago truncatula is an important model plant for characterization of P deficiency on leguminous plants at the physiological and molecular levels. Growth optimization of this plant with regard to P supply is the first essential step for elucidation of the role of P in regulation of nodulation. Hence, a study was carried out to address the growth pattern of M. truncatula hydroponically grown at different gradual increases in P levels. The findings revealed that M. truncatula had a narrow P regime, with an optimum P level (12 μM P) which is relatively close to the concentration that induces P toxicity. The accumulated P concentration (2.7 mg g(-1) dry matter), which is normal for other crops and legumes, adversely affected the growth of M. truncatula plants. Under P deficiency, M. truncatula showed a higher symbiotic efficiency with Sinorhizobium meliloti 2011 in comparison with S. meliloti 102F51, partially as a result of higher electron allocation to N2 versus H(+). The total composition of free amino acids in the phloem was significantly affected by P deprivation. This pattern was found to be almost exclusively the result of the increase in the asparagine level, suggesting that asparagine might be the shoot-derived signal that translocates to the nodules and exerts the down-regulation of nitrogenase activity. Additionally, P deprivation was found to have a strong influence on the contents of the nodule carbon metabolites. While levels of sucrose and succinate tended to decrease, a higher accumulation of malate was observed. These findings have provided evidence that N2 fixation of M. truncatula is mediated through an N feedback mechanism which is closely related to nodule carbon metabolism.

Strigolactones activate different hormonal pathways for regulation of root development in response to phosphate growth conditions

BACKGROUND

Strigolactones (SLs) - a group of plant hormones and their derivatives - have been found to play a role in the regulation of root development, in addition to their role in suppression of lateral shoot branching: they alter root architecture and affect root-hair elongation, and SL signalling is necessary for the root response to low phosphate (Pi) conditions. These effects of SLs have been shown to be associated with differential activation of the auxin and ethylene signalling pathways.

SCOPE

The present review highlights recent findings on the activity of SLs as regulators of root development, in particular in response to low Pi stress, and discusses the different hormonal networks putatively acting with SLs in the root's Pi response.

CONCLUSIONS

SLs are suggested to be key regulators of the adaptive responses to low Pi in the root by modulating the balance between auxin and ethylene signalling. Consequently, they impact different developmental programmes responsible for the changes in root system architecture under differential Pi supply.

Understanding plant responses to phosphorus starvation for improvement of plant tolerance to phosphorus deficiency by biotechnological approaches

In both prokaryotes and eukaryotes, including plants, phosphorus (P) is an essential nutrient that is involved in various biochemical processes, such as lipid metabolism and the biosynthesis of nucleic acids and cell membranes. P also contributes to cellular signaling cascades by function as mediators of signal transduction and it also serves as a vital energy source for a wide range of biological functions. Due to its intensive use in agriculture, P resources have become limited. Therefore, it is critically important in the future to develop scientific strategies that aim to increase P use efficiency and P recycling. In addition, the biologically available soluble form of P for uptake (phosphate; Pi) is readily washed out of topsoil layers, resulting in serious environmental pollution. In addition to this environmental concern, the wash out of Pi from topsoil necessitates a continuous Pi supply to maintain adequate levels of fertilization, making the situation worse. As a coping mechanism to P stress, plants are known to undergo drastic cellular changes in metabolism, physiology, hormonal balance and gene expression. Understanding these molecular, physiological and biochemical responses developed by plants will play a vital role in improving agronomic practices, resource conservation and environmental protection as well as serving as a foundation for the development of biotechnological strategies, which aim to improve P use efficiency in crops. In this review, we will discuss a variety of plant responses to low P conditions and various molecular mechanisms that regulate these responses. In addition, we also discuss the implication of this knowledge for the development of plant biotechnological applications.

Differential regulation of two types of monogalactosyldiacylglycerol synthase in membrane lipid remodeling under phosphate-limited conditions in sesame plants

Phosphate (Pi) limitation causes drastic lipid remodeling in plant membranes. Glycolipids substitute for the phospholipids that are degraded, thereby supplying Pi needed for essential biological processes. Two major types of remodeling of membrane lipids occur in higher plants: whereas one involves an increase in the concentration of sulfoquinovosyldiacylglycerol in plastids to compensate for a decreased concentration of phosphatidylglycerol, the other involves digalactosyldiacylglycerol (DGDG) synthesis in plastids and the export of DGDG to extraplastidial membranes to compensate for reduced abundances of phospholipids. Lipid remodeling depends on an adequate supply of monogalactosyldiacylglycerol (MGDG), which is a substrate that supports the elevated rate of DGDG synthesis that is induced by low Pi availability. Regulation of MGDG synthesis has been analyzed most extensively using the model plant Arabidopsis thaliana, although orthologous genes that encode putative MGDG synthases exist in photosynthetic organisms from bacteria to higher plants. We recently hypothesized that two types of MGDG synthase diverged after the appearance of seed plants. This divergence might have both enabled plants to adapt to a wide range of Pi availability in soils and contributed to the diversity of seed plants. In the work presented here, we found that membrane lipid remodeling also takes place in sesame, which is one of the most common traditional crops grown in Asia. We identified two types of MGDG synthase from sesame (encoded by SeMGD1 and SeMGD2) and analyzed their enzymatic properties. Our results show that both genes correspond to the Arabidopsis type-A and -B isoforms of MGDG synthase. Notably, whereas Pi limitation up-regulates only the gene encoding the type-B isoform of Arabidopsis, low Pi availability up-regulates the expression of both SeMGD1 and SeMGD2. We discuss the significance of the different responses to low Pi availability in sesame and Arabidopsis.