Regulatory network of microRNA399 and PHO2 by systemic signaling

Recently, we showed that microRNA399s (miR399s) control inorganic phosphate (Pi) homeostasis by regulating the expression of PHO2 encoding a ubiquitin-conjugating E2 enzyme 24. Arabidopsis (Arabidopsis thaliana) plants overexpressing miR399 or the pho2 mutant overaccumulate Pi in shoots. The association of Pi translocation and coexpression of miR399s and PHO2 in vascular tissues suggests their involvement in long-distance signaling. In this study, we used reciprocal grafting between wild-type and miR399-overexpressing transgenic plants to dissect the systemic roles of miR399 and PHO2. Arabidopsis rootstocks overexpressing miR399 showed high accumulation of Pi in the wild-type scions because of reduced PHO2 expression in the rootstocks. Although miR399 precursors or expression was not detected, we found a small but substantial amount of mature miR399 in the wild-type rootstocks grafted with transgenic scions, which indicates the movement of miR399 from shoots to roots. Suppression of PHO2 with miR399b or c was less efficient than that with miR399f. Of note, findings in grafted Arabidopsis were also discovered in grafted tobacco (Nicotiana benthamiana) plants. The analysis of the pho1 mutant provides additional support for systemic suppression of PHO2 by the movement of miR399 from Pi-depleted shoots to Pi-sufficient roots. We propose that the long-distance movement of miR399s from shoots to roots is crucial to enhance Pi uptake and translocation during the onset of Pi deficiency. Moreover, PHO2 small interfering RNAs mediated by the cleavage of miR399s may function to refine the suppression of PHO2. The regulation of miR399 and PHO2 via long-distance communication in response to Pi deficiency is discussed.     

The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis

It has been reported that some double-stranded RNA (dsRNA) binding proteins interact with small RNA biogenesis-related RNase III enzymes. However, their biological significance is poorly understood. Here we examine the relationship between the Arabidopsis microRNA- (miRNA) producing enzyme DCL1 and the dsRNA binding protein HYL1. In the hyl1-2 mutant, the processing steps of miR163 biogenesis were partially impaired; increased accumulation of pri-miR163 and reduced accumulation of short pre-miR163 and mature miR163 as well as misplaced cleavages in the stem structure of pri-miR163 were detected. These misplaced cleavages were similar to those previously observed in the dcl1-9 mutant, in which the second double-stranded RNA binding domain of the protein was disrupted. An immunoprecipitation assay using Agrobacterium-mediated transient expression in Nicotiana benthamiana showed that HYL1 was able to form a complex with wild-type DCL1 protein, but not with the dcl1-9 mutant protein. We also examined miR164b and miR166a biogenesis in hyl1-2 and dcl1-9. Increased accumulation of pri-miRNAs and reduced accumulation of pre-miRNAs and mature miRNAs were detected. Misplaced cleavage on pri-miR164b was observed only in dcl1-9 but not in hyl1-2, whereas not on pri-miR166a in either mutant. These results indicate that HYL1 has a function in assisting efficient and precise cleavage of pri-miRNA through interaction with DCL1.     

A Role for Arabidopsis miR399f in Salt,Drought, and ABA Signaling

MiR399f plays a crucial role in maintaining phosphate homeostasis in Arabidopsis thaliana. Under phosphate starvation conditions, AtMYB2, which plays a role in plant salt and drought stress responses, directly regulates the expression of miR399f. In this study, we found that miR399f also participates in plant responses to abscisic acid (ABA), and to abiotic stresses including salt and drought. Salt and ABA treatment induced the expression of miR399f, as confirmed by histochemical analysis of promoter-GUS fusions. Transgenic Arabidopsis plants overexpressing miR399f (miR399f-OE) exhibited enhanced tolerance to salt stress and exogenous ABA, but hypersensitivity to drought. Our in silico analysis identified ABF3 and CSP41b as putative target genes of miR399f, and expression analysis revealed that mRNA levels of ABF3 and CSP41b decreased remarkably in miR399f-OE plants under salt stress and in response to treatment with ABA. Moreover, we showed that activation of stress-responsive gene expression in response to salt stress and ABA treatment was impaired in miR399f-OE plants. Thus, these results suggested that in addition to phosphate starvation signaling, miR399f might also modulates plant responses to salt, ABA, and drought, by regulating the expression of newly discovered target genes such as ABF3 and CSP41b.     

Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis

The hnRNP-like glycine-rich RNA-binding protein AtGRP7 regulates pre-mRNA splicing in Arabidopsis. Here we used small RNA-seq to show that AtGRP7 also affects the miRNA inventory. AtGRP7 overexpression caused a significant reduction in the level of 30 miRNAs and an increase for 14 miRNAs with a minimum log₂ fold change of ±0.5. Overaccumulation of several pri-miRNAs including pri-miR398b, pri-miR398c, pri-miR172b, pri-miR159a and pri-miR390 at the expense of the mature miRNAs suggested that AtGRP7 affects pri-miRNA processing. Indeed, RNA immunoprecipitation revealed that AtGRP7 interacts with these pri-miRNAs in vivo. Mutation of an arginine in the RNA recognition motif abrogated in vivo binding and the effect on miRNA and pri-miRNA levels, indicating that AtGRP7 inhibits processing of these pri-miRNAs by direct binding. In contrast, pri-miRNAs of selected miRNAs that were elevated or not changed in response to high AtGRP7 levels were not bound in vivo. Reduced accumulation of miR390, an initiator of trans-acting small interfering RNA (ta-siRNA) formation, also led to lower TAS3 ta-siRNA levels and increased mRNA expression of the target AUXIN RESPONSE FACTOR4. Furthermore, AtGRP7 affected splicing of pri-miR172b and pri-miR162a. Thus, AtGRP7 is an hnRNP-like protein with a role in processing of pri-miRNAs in addition to its role in pre-mRNA splicing.     

Long-distance movement and differential targeting of microRNA399s

We have previously demonstrated that miR399s control phosphate (Pi) homeostasis by regulating the expression of a ubiquitin-conjugating E2 enzyme (UBC24/PHO2) in Arabidopsis. Changes in miR399-dependent PHO2 gene expression modulate Pi uptake, allocation and remobilization. More recently, we provided evidence that miR399s are able to move in the phloem stream and across grafting junctions from the scions overexpressing miR399 to the wild-type rootstocks. Movement of miR399s serves as a long-distance signal to report and balance the Pi status between shoots and roots. Of note, results from grafting experiments indicate that miR399b is less efficient in cleaving the PHO2 mRNA than is miR399f, despite the similar mobility of the two miR399s. We propose that nucleotide 13 of miR399s, which gives rise to the sequence variation among different miR399 species, could be involved in regulating the abundance of PHO2 mRNA through sequence complementarity to the target sequences of PHO2 mRNA and mimicking target sequence of At4/IPS1 noncoding RNAs.Key words: phosphate, microRNA399, PHO2, UBC24, long-distance movement, At4/IPS1     

Morphological and photosynthetic responses of riparian plant Distylium chinense seedlings to simulated Autumn and Winter flooding in Three Gorges Reservoir Region of the Yangtze River, China

To evaluate the tolerance of riparian plant Distylium chinense in Three Gorges Reservoir Region to anti-season flooding, a simulation flooding experiment was conducted during Autumn and Winter, and morphology and photosynthesis of D. chinense seedlings and their recovery growth after soil drainage were analyzed in different duration of flooding and flooding depth. The seedlings were submitted to four treatments: (1) 40 seedlings unflooded and watered daily as control (Unflooded, CK); (2) 120 seedlings flooded at 1 cm above the ground level (F-1 cm); (3) 120 seedlings flooded at 12 cm above the ground level (F-12 cm) and (4) 120 seedlings completely submerged with 2 m water depth (F-2 m, top of plants at 2 m below water surface). The flooding survival, plant height, stem diameter, adventitious roots, stem lenticels, epicormic shoots, chlorophyll content and photosynthesis parameters were determined at 0, 15, 30, 90 days in flooding stress and 15, 60 days after soil drainage. The results showed that the survival of the seedlings subjected to flooding was 100% for all repeated measurements in all treatments. Adventitious roots, hypertrophied lenticels and stem hypertrophy were observed in the seedlings flooded for more than 15 d, and increased with the prolonged flooding duration, while disappeared after the soil was drained. Flooding duration and flooding depth showed significant individual and interactive effects on leaf chlorophyll a (Chl a), chlorophyll b (Chl b), and their ratio, chlorophyll (a + b), the net photosynthesis rate (P_n), transpiration rate (T_r), stomatal conductance (C_s), and inter-cellular CO₂ concentration (C_i) of D. chinense seedlings (P < 0.01). After 15 days of flooding, there was no significant decrease in P_n of the flooded seedlings as compared with that of the control seedlings. P_n of the flooded seedlings was significantly lower than that of the control seedlings after 30 days of flooding (P < 0.05), whereas P_n showed no significant difference among seedlings from three flooding depths. After 90 days of flooding, P_n of the F-2 m flooded seedlings was significantly lower than that of the controls, F-1 cm and F-12 cm flooded seedlings (P < 0.05), but still maintained high photosynthetic capacity. P_n of the F-1 cm and F-12 cm flooded seedlings rose gradually after soil drainage, while, it was significantly lower than that of the control seedlings after 15 days of recovery (P < 0.05). After 60 days of recovery, P_n of all seedlings flooded with different depths showed no significant difference as compared with that of the control seedlings and new leaves grew out in the F-2 m flooded seedlings. The effect of all flooding treatments on Gs, T_r, Chl a, Chl b, Chl a/Chl b and chl (a + b) was basically the same as their effect on P_n, while the effect of all flooding treatments on C_i was quite the contrary. Correlation analysis showed that P_n was positively relative with Gs, T_r, Chl a, Chl b and chl (a + b) (P < 0.05) and significantly negative with C_i (P < 0.05). Therefore, the present study demonstrates that D. chinense has high survival and good recovery growth after long-term flooding in anti-season flooding and could be taken as an excellent candidate species in the re-vegetation of water-level-fluctuation areas in Three Gorges Reservoir Region.     

Morphological and photosynthetic responses of riparian plant Distylium chinense seedlings to simulated Autumn and Winter flooding in Three Gorges Reservoir Region of the Yangtze River, China

To evaluate the tolerance of riparian plant Distylium chinense in Three Gorges Reservoir Region to anti-season flooding, a simulation flooding experiment was conducted during Autumn and Winter, and morphology and photosynthesis of D. chinense seedlings and their recovery growth after soil drainage were analyzed in different duration of flooding and flooding depth. The seedlings were submitted to four treatments: (1) 40 seedlings unflooded and watered daily as control (Unflooded, CK); (2) 120 seedlings flooded at 1 cm above the ground level (F-1 cm); (3) 120 seedlings flooded at 12 cm above the ground level (F-12 cm) and (4) 120 seedlings completely submerged with 2 m water depth (F-2 m, top of plants at 2 m below water surface). The flooding survival, plant height, stem diameter, adventitious roots, stem lenticels, epicormic shoots, chlorophyll content and photosynthesis parameters were determined at 0, 15, 30, 90 days in flooding stress and 15, 60 days after soil drainage. The results showed that the survival of the seedlings subjected to flooding was 100% for all repeated measurements in all treatments. Adventitious roots, hypertrophied lenticels and stem hypertrophy were observed in the seedlings flooded for more than 15 d, and increased with the prolonged flooding duration, while disappeared after the soil was drained. Flooding duration and flooding depth showed significant individual and interactive effects on leaf chlorophyll a (Chl a), chlorophyll b (Chl b), and their ratio, chlorophyll (a + b), the net photosynthesis rate (P_n), transpiration rate (T_r), stomatal conductance (C_s), and inter-cellular CO₂ concentration (C_i) of D. chinense seedlings (P < 0.01). After 15 days of flooding, there was no significant decrease in P_n of the flooded seedlings as compared with that of the control seedlings. P_n of the flooded seedlings was significantly lower than that of the control seedlings after 30 days of flooding (P < 0.05), whereas P_n showed no significant difference among seedlings from three flooding depths. After 90 days of flooding, P_n of the F-2 m flooded seedlings was significantly lower than that of the controls, F-1 cm and F-12 cm flooded seedlings (P < 0.05), but still maintained high photosynthetic capacity. P_n of the F-1 cm and F-12 cm flooded seedlings rose gradually after soil drainage, while, it was significantly lower than that of the control seedlings after 15 days of recovery (P < 0.05). After 60 days of recovery, P_n of all seedlings flooded with different depths showed no significant difference as compared with that of the control seedlings and new leaves grew out in the F-2 m flooded seedlings. The effect of all flooding treatments on Gs, T_r, Chl a, Chl b, Chl a/Chl b and chl (a + b) was basically the same as their effect on P_n, while the effect of all flooding treatments on C_i was quite the contrary. Correlation analysis showed that P_n was positively relative with Gs, T_r, Chl a, Chl b and chl (a + b) (P < 0.05) and significantly negative with C_i (P < 0.05). Therefore, the present study demonstrates that D. chinense has high survival and good recovery growth after long-term flooding in anti-season flooding and could be taken as an excellent candidate species in the re-vegetation of water-level-fluctuation areas in Three Gorges Reservoir Region.     

A miRNA involved in phosphate-starvation response in Arabidopsis

Although microRNAs (miRNAs) have been documented to regulate development in plants and animals , the function of miRNAs in physiology is unclear. miR399 has multiple target sites in the 5' untranslated region (UTR) of a gene encoding a putative ubiquitin-conjugating enzyme (UBC) in Arabidopsis thaliana. We report here that miR399 was highly induced, whereas the target UBC mRNA was reduced by low-phosphate (Pi) stress. In transgenic plants with constitutive expression of miR399, UBC mRNA accumulation was suppressed even under high Pi. The expression of transgene UBC mRNA with 5' UTR miR399 target sites, but not the one without 5' UTR, was reduced under low-Pi condition. Furthermore, transgenic Arabidopsis plants with constitutive expression of miR399 accumulated more Pi than the wild-type, and transgenic plants expressing the UBC mRNA without 5' UTR (miRNA-deregulated) showed less inhibition of primary root growth and less induction of a Pi transporter gene by low-Pi stress than those of wild-type plants. We conclude that miR399 downregulates UBC mRNA accumulation by targeting the 5' UTR, and this regulation is important for plant responses to Pi starvation. The results suggest that miRNAs have functional roles for plants to cope with fluctuations in mineral-nutrient availability in the soil.     

The growth and phosphorus utilisation of plants in sterile media when supplied with inositol hexaphosphate, glucose 1-phosphate or inorganic phosphate

Seedlings of six temperate pasture species, three grasses and three legumes, were grown for 19–24 days in sterile agar or sand-vermiculite media, in the presence of inorganic phosphate (P_i), glucose 1-phosphate (G1P) or inositol hexaphosphate (IHP). Agar (pH 5.0) had a low IHP-sorbing capacity while IHP was almost completely sorbed in sand-vermiculite. P_i and G1P were relatively available in both media. Growth of each species was measured in relation to phosphorus (P) supply and levels of P_i supply at which shoot yields reached 90% of maximum yield (P_crit) were determined. P_crit values were generally higher for the legume species than for the grasses, and were six-fold higher for Trifolium subterraneum L. seedlings when grown in sand-vermiculite relative to agar. When supplied with G1P, seedlings of the six species grew as well as plants supplied with P_i. By contrast, IHP was a poor source of P for plant growth, even when supplied in agar at levels up to 40-fold greater than P_crit. Using the growth of T. subterraneum in the presence of IHP, it was calculated that roots released approximately 0.09 nkat phytase g^-1 root dry wt per day, over 20 days of growth. By supplementing agar containing IHP with phytase from Aspergillus niger (E.C. 3.1.3.8; 0.012 nkat plant^-1, or _∼1.3 nkat g^-1 root dry wt), sufficient P became available to enable T. subterraneum seedlings to grow as well as P_i-supplied plants. These results indicate that while pasture plants can quite effectively use P from some organic P sources (e.g. G1P), the acquisition of phytate-P is limited both by availability of substrate and the capacity of plant roots to hydrolyse available IHP. This revised version was published online in June 2006 with corrections to the Cover Date.