Research ArticleResearch Article

Three Functional Transporters for Constitutive, Diurnally Regulated, and Starvation-Induced Uptake of Ammonium into Arabidopsis Roots

Sonia Gazzarrini, Laurence Lejay, Alain Gojon, Olaf Ninnemann, Wolf B. Frommer, Nicolaus von Wirén

Published May 1999. DOI: https://doi.org/10.1105/tpc.11.5.937

Abstract

Ammonium and nitrate are the prevalent nitrogen sources for growth and development of higher plants. 15N-uptake studies demonstrated that ammonium is preferred up to 20-fold over nitrate by Arabidopsis plants. To study the regulation and complex kinetics of ammonium uptake, we isolated two new ammonium transporter (AMT) genes and showed that they functionally complemented an ammonium uptake–deficient yeast mutant. Uptake studies with 14C-methylammonium and inhibition by ammonium yielded distinct substrate affinities between ≤0.5 and 40 μM. Correlation of gene expression with 15NH4+ uptake into plant roots showed that nitrogen supply and time of day differentially regulated the individual carriers. Transcript levels of AtAMT1;1, which possesses an affinity in the nanomolar range, steeply increased with ammonium uptake in roots when nitrogen nutrition became limiting, whereas those of AtAMT1;3 increased slightly, with AtAMT1;2 being more constitutively expressed. All three ammonium transporters showed diurnal variation in expression, but AtAMT1;3 transcript levels peaked with ammonium uptake at the end of the light period, suggesting that AtAMT1;3 provides a link between nitrogen assimilation and carbon provision in roots. Our results show that high-affinity ammonium uptake in roots is regulated in relation to the physiological status of the plant at the transcriptional level and by substrate affinities of individual members of the AMT1 gene family.

INTRODUCTION

Unlike most other organisms, plants are restricted to their habitats, creating potential problems when nutritional conditions become limiting. To cope with nutrient deficiencies, higher plants have developed a variety of adaptations that enable them to respond to their internal nutritional status as well as to the external availability of nutrients. In response to both, root architecture and/or transport properties are altered, leading either to a higher utilization of internalized nutrients or to enhanced nutrient acquisition at the level of nutrient mobilization or uptake (Marschner, 1995). Because nitrogen is quantitatively the most important mineral nutrient for plants, nitrogen deficiencies occur in almost all habitats at least during certain growth phases.

Among the different responses to nitrogen deficiency, altered root architecture and increased root surface have been frequently observed and seem to play key roles in the early adaptation to nitrogen deficiency (Marschner et al., 1986). A potential signal transduction intermediate has been identified recently in the MADS box gene ANR1 from Arabidopsis that is required for the induction of lateral root growth in nitrate-rich root zones (Zhang and Forde, 1998). Thus, sensors and signal transduction cascades are required to link nutrient availability with physiological responses. On the other hand, several physiological and molecular studies have shown that nitrogen deficiency induces an enhanced capacity for nitrogen uptake by increasing NH4+ and NO3− uptake rates, which are regulated at the level of membrane transport (reviewed in von Wirén et al., 1997b). Consequently, NH4+ and NO3− transporter genes provide an important molecular target to regulate the nitrogen stress response in plants. Higher uptake rates of NH4+ versus NO3−, as found in this study with Arabidopsis, confirm a preferential uptake of the reduced nitrogen form, emphasizing that there is a larger capacity for high-affinity NH4+ uptake compared with NO3−, irrespective of the nitrogen nutritional status of the plant.

For the physiological characterization of NH4+ uptake in plants, an extended series of short-term uptake studies has been undertaken in which roots were supplied mostly with 13N- or 15N-labeled NH4+. Regarding concentration-dependent uptake kinetics, multiphasic patterns have been observed with at least two kinetically distinct components in NH4+ uptake: a low-affinity nonsaturable and a high-affinity saturable component (Ullrich et al., 1984; Wang et al., 1993). The first NH4+ transporter (AMT) genes were identified from yeast and Arabidopsis by functional complementation of a yeast mutant defective in high-affinity ammonium uptake (Marini et al., 1994; Ninnemann et al., 1994). A role of the plant genes in NH4+ nutrition is supported by the finding that NH4+ transporters are preferentially expressed in root hairs (Lauter et al., 1996), which make up >70% of the root surface and play a central role in nutrient uptake (Marschner, 1995).

Aside from their role in uptake of NH4+, NH4+ transporters can also act as NH4+ sensors. This is of particular interest because NH4+/NH3 is not only the form of primary nitrogen assimilation or reassimilation but is also used as a signal for cell-to-cell communication in yeast (Palkova et al., 1997). In response to NH4+ availability in the growth medium, the high-affinity NH4+ transporter Mep2p from yeast generates a signal to regulate filamentous growth (Lorenz and Heitman, 1998). Thereby, regulation of MEP2 in response to nitrogen is controlled by gene transcription and is distinct from that of the other two NH4+ transporter genes MEP1 and MEP3 (Marini et al., 1997). Whether similar sensing functions of NH4+ transporters also exist in plants remains to be shown. So far, high-affinity NH4+ transport has been demonstrated only for the AMT1;1 genes from Arabidopsis and tomato (Ninnemann et al., 1994; Lauter et al., 1996). These genes belong to the same superfamily of NH4+ transporters as do the MEP genes from yeast (Marini et al., 1997). Moreover, yeast and plant NH4+ transporters also allowed the identification of homologs from bacteria and animals (Siewe et al., 1996; Marini et al., 1997).

Figure 1.
Figure 1.

Influx of 15N-Labeled NH4+ and NO3− in Arabidopsis Roots.

Plants were precultured hydroponically with a supply of 1 mM NH4NO3 or under nitrogen deficiency for 48 hr (−N). Uptake rates from 200 μM 15N-labeled NH4+ (supplied as [NH4]2SO4; open bars) or NO3− (supplied as KNO3; filled bars) solution were measured for 5 min; n = 6. Error bars indicate standard deviations. dw, dry weight.

To characterize the regulation of NH4+ transport in plants, it was our objective to isolate other members of the AMT1 gene family from Arabidopsis and to investigate their physiological contribution to NH4+ uptake by roots. In this study, we report the isolation of two full-length clones, showing that the AMT1 gene family consists of at least three members in Arabidopsis. These genes were functionally expressed in yeast for the determination of substrate affinities. In addition, their transcriptional regulation was monitored at the same as 15NH4+ influx into roots, allowing us to assign possible physiological functions to the three AMT1 genes in Arabidopsis.

RESULTS

Preferential Ammonium Uptake by Arabidopsis Roots

To examine the physiological preference of Arabidopsis roots for NH4+ versus NO3− as a nitrogen source, we grew Arabidopsis plants hydroponically without or with a supply of 1 mM NH4+NO3, and we measured influxes of NH4+ and NO3− after transfer to fresh nutrient solution containing either 200 μM 15N-labeled NH4+ or NO3−. At an adequate nitrogen nutritional status of the plants, the NH4+ uptake rate exceeded that of NO3− by >20-fold (Figure 1), whereas in nitrogen-deficient plants, NH4+ influx was still fourfold higher. This relative preference of NH4+ uptake over NO3− indicates that high-affinity transport systems for both nitrogen forms are differentially regulated and that there is a larger uptake capacity for the reduced nitrogen form irrespective of the nitrogen nutritional status.

Gene Isolation of AtAMT1;2 and AtAMT1;3

A cDNA library prepared from Arabidopsis plants was screened using AtAMT1;1 as a probe (Ninnemann et al., 1994). Two homologous cDNA clones were isolated and named AtAMT1;2 and AtAMT1;3. However, a comparison of the amino acid sequences to that of AtAMT1;1 indicated re-arrangements at the 5′ end of both clones. Intact full-length sequences were obtained by polymerase chain reaction (PCR) from a cDNA library by using primers annealing to the vector arms and primers specific for AtAMT1;2 and AtAMT1;3. The complete open reading frames of AtAMT1;2 and AtAMT1;3 encode 54.9- and 55.7-kD polypeptides of 512 and 520 amino acid residues, respectively (Figure 2). Whereas AtAMT1;3 is closely related to AtAMT1;1 with 79.4% similarity at the amino acid level, AtAMT1;2 is more distantly related, with 71.5 and 67.8% similarity to AtAMT1;1 and AtAMT1;3, respectively. Interestingly, a long serine-rich domain is located in the N terminus of AtAMT1;2. Different methods predicted 11 transmembrane helices in the deduced polypeptides of all three AMT proteins (Kyte and Doolittle, 1982; Hofmann and Stoffel, 1993; Sonnhammer et al., 1998), which is in agreement with predictions made for AMT1/MEP polypeptides from tomato, rice, and yeast (Lauter et al., 1996; Marini et al., 1997; von Wirén et al., 1997a).

Figure 2.
Figure 2.

Amino Acid Sequence Alignment of Ammonium Transporters of the AMT1 Family from Arabidopsis.

Identical residues are shown in black, and relative positions of transmembrane-spanning domains (Sonnhammer et al., 1998) are enclosed in boxes. Dashes indicate gaps. The GenBank accession numbers for the AtAMT1;2 and AtAMT1;3 cDNA sequences are AF083036 and AF083035, respectively.

To estimate the total number of AMT1 homologs in Arabidopsis, we conducted comparative DNA gel blot analysis. When genomic DNA was digested by HindIII and hybridized under low stringency with a 600-bp probe from the conserved region of AtAMT1;1, a maximum number of six bands appeared (Figure 3). A comparison to DNA gel blots hybridized under high-stringency conditions to full-length probes of the three AMT cDNAs showed that three of these six bands could be clearly assigned to AtAMT1;1, AtAMT1;2, and AtAMT1;3, which do not contain HindIII restriction sites. Thus, the other three bands most probably indicate the existence of further AMT homologs.

Figure 3.
Figure 3.

Comparative Gel Blot Analysis of Genomic DNA from Arabidopsis Digested with NotI, PstI, or HindIII.

After transfer to nylon membranes, DNA gel blots were hybridized with a 600-bp probe from the conserved region of AtAMT1;1 and washed under low-stringency conditions in 2 × SSC and 0.1% SDS at 50°C. Alternatively, DNA gel blots were hybridized with full-length cDNAs from AtAMT1;1, AtAMT1;2, or AtAMT1;3 and washed under high-stringency conditions in 2 × SSC and 0.1% SDS at 68°C. The lengths of marker fragments in kilobases are indicated below.

Functional Expression of AtAMT1;1, AtAMT1;2, and AtAMT1;3 in a Yeast Mutant Defective in High-Affinity NH4+ Uptake

The yeast strain 31019b is defective in three endogenous NH4+ transporters (mep1, mep2, and mep3) and unable to grow on medium containing ≤5 mM NH4+ as the sole nitrogen source (Marini et al., 1997). Transformation of this strain with the yeast expression vector pFL61 expressing AtAMT1;1, AtAMT1;2, or AtAMT1;3, under the control of the constitutive yeast phosphoglycerate kinase gene promoter (Minet et al., 1992), conferred growth of 31019b down to 1 mM NH4+ as the sole nitrogen source (Figure 4). Thus, all three genes encode functional NH4+ transporters.

To determine differences in substrate affinities between the AMT proteins, we used 14C-labeled methylammonium as a substrate analog, and we measured short-term uptake in transformed yeast strains. In a range of 2 to 250 μM, 14C-methylammonium uptake rates were five to 20 times higher in AMT1-transformed cells than in cells containing the vector alone, and concentration-dependent uptake rates in all three AMT1 transformants followed saturable kinetics (Figures 5A to 5C). Determination of affinity constants after nonlinear curve fitting and subtraction of endogenous uptake activities in vector-transformed cells showed that AtAMT1;1 displayed the highest affinity (Km = 8 μM), followed closely by AtAMT1;3 (Km = 11 μM) and finally by AtAMT1;2, whose affinity was considerably lower (Km = 24 μM) (Figures 5A to 5C). Because the affinities for methylammonium do not necessarily reflect the affinity for ammonium (Venegoni et al., 1997), competition studies were performed with varying NH4+ concentrations. At a methylammonium concentration corresponding to the Km of each AMT1 transporter, a 50% inhibition by NH4+ was found at ≤0.5 μM NH4+ for AtAMT1;1 but between 25 and 40 μM for AtAMT1;2 and AtAMT1;3 (Figure 5D). These competition studies showed that the three NH4+ transporters possess distinct substrate affinities, allowing the plant to take up external NH4+ over a wide concentration range. In contrast to uptakes in AtAMT1;1, a 50% inhibition of methylammonium uptake in AtAMT1;2 and AtAMT1;3 transformants was seen at equal or higher concentrations of NH4+ relative to methylammonium. Thus, AtAMT1;2 and AtAMT1;3 provide transport systems of minor selectivity.

Organ-Dependent Expression of AtAMT1;1, AtAMT1;2, and AtAMT1;3

Total RNA extracted from stems, source leaves, sink leaves, and buds of plants grown for 5 weeks in soil culture in a greenhouse and root RNA extracted from plants grown hydroponically under axenic conditions was hybridized to gene-specific probes for all three AMTs. AtAMT1;1 transcripts were found in all organs examined (Figure 6). In contrast, expression of AtAMT1;2 was mainly confined to roots with faint signals in stems and leaves, whereas under the conditions described, AtAMT1;3 expression seemed to be exclusively restricted to roots.

Figure 4.
Figure 4.

Growth Test on Minimal Medium Containing 1 mM NH4+ as the Sole Nitrogen Source.

The yeast strain 31019b (mep1 mep2 mep3 ura3; Marini et al., 1997) was transformed with the yeast expression vector pFL61 alone (Minet et al., 1992) or pFL61 harboring the coding sequences of AtAMT1;1, AtAMT1;2, or AtAMT1;3.

Correlation between 15NH4+ Influx and AMT1 Gene Expression in Roots

Because all three AMT1 genes were strongly and preferentially expressed in roots and because the affinities for NH4+ of the AMT1 gene products differed widely, the question arose whether they play different physiological roles in roots. To examine a possible contribution of each single AMT to overall NH4+ uptake by roots, plants were grown under conditions that modulate NH4+ uptake rates, and AMT1 gene expression in roots was determined simultaneously with short-term 15NH4+ uptake rates.

Influence of the Light–Dark Cycle

When plants were grown for 6 weeks on NH4NO3-containing nutrient solution, short-term 15NH4+ influx was low at the beginning of illumination (Figure 7A). However, toward the end of the light period, 15NH4+ influx increased by a factor of 3, which was followed by a sharp decrease at the beginning of darkness. A corresponding threefold increase until the end of the light period was also observed for transcript levels of AMT1;3 (Figure 7B). Although expression of AtAMT1;1 and AtAMT1;2 was also higher during the daytime (1.5 and 1.7 times, respectively), correlation to NH4+ influx was much weaker. Therefore, it is suggested that the enhanced NH4+ influx at the end of the photoperiod was mainly brought about by transcriptional upregulation of AtAMT1;3.

Influence of Nitrogen Deficiency

Monitoring 15NH4+ influx of plants adequately supplied with nitrogen after transfer to nitrogen-free nutrient solution showed that 15NH4+ influx steeply increased, resulting in a peak after 48 to 72 hr, irrespective of whether plants were precultured with KNO3 (data not shown) or NH4NO3 (Figure 8A). The increase in NH4+ influx coincided with an increase in AtAMT1;1 transcript levels in roots, which accumulated fivefold relative to nonstarved plants within 72 hr (Figure 8B). Whereas AtAMT1;2 did not show any significant change, mRNA expression of AtAMT1;3 increased by approximately twofold. The enhanced gene expression of AtAMT1;1 and to a minor extent also of AtAMT1;3 suggested that their gene products mainly contribute to increased NH4+ influx under nitrogen deficiency.

Influence of Change of the Nitrogen Source

To differentiate between the effects of nitrogen form and nitrogen supply, plants were precultured in the presence of NH4−NO3 and then transferred to medium containing NO3 as the sole nitrogen source. As with the transfer to nitrogen-free medium, 15NH4+ influx steeply increased within 72 hr (Figure 9A). However, none of the three AMT genes responded with increased transcript levels (Figure 9B), pointing to the possiblity that increased 15NH4+ influx after transfer to NO3− could be due to regulation at the post-transcriptional level. Indeed, all three AMT genes were expressed during the experiment, pointing to a derepression in post-transcriptional regulation after the removal of NH4+ rather than an induction of AMT expression as observed under nitrogen deficiency. Alternatively, it is also possible that enhanced 15NH4+ influx was mediated by NH4+ transport proteins other than AtAMT1;1, AtAMT1;2, and AtAMT1;3.

DISCUSSION

The AMT1 Multigene Family in Plants

Several points of evidence indicate that proteins of the AMT1 gene family act as functional NH4+ transporters in plants. First, AMT1 genes belong to the MEP/AMT1 superfamily of eukaryotic and prokaryotic NH4+ transporter genes, and for the yeast genes, functional knockouts have already been characterized (Marini et al., 1994, 1997). Second, AMT1;1 genes from tomato and Arabidopsis conferred high-affinity NH4+ uptake to yeast mutants defective in NH4+ transport (Ninnemann et al., 1994; Lauter et al., 1996), which strongly suggests that AMT proteins are also targeted to the plasma membrane in plants. Moreover, biochemical characteristics of AMT-mediated transport in yeast, such as energy dependence, pH optimum, and inhibitor sensitivity to K+ (Ninnemann et al., 1994), reflect those of NH4+ uptake by intact plant roots (Wang et al., 1993, 1996). Finally, expression of AMT1;1 in tomato was found preferentially in root hairs, strongly supporting a role for AMT genes in primary NH4+ acquisition from the growth medium (Lauter et al., 1996).

Figure 5.
Figure 5.

Kinetic Analysis of AtAMT1;1, AtAMT1;2, and AtAMT1;3 in Transformed Yeast.

(A) to (C) Concentration-dependent kinetics of 14C-methylammonium uptake by yeast strain 31019b (mep1 mep2 mep3 ura3; Marini et al., 1997) transformed with pFL61 alone (filled diamonds) or pFL61 harboring the following coding sequences: AtAMT1;1 (filled squares [A]), AtAMT1;2 (filled triangles [B]), or AtAMT1;3 (filled circles [C]).

(D) The influence of increasing NH4+ concentrations on 14C-methylammonium uptake rates. Inhibition of 14C-methylammonium uptake was measured at the corresponding Km of each AMT. 100% uptake corresponds to 0.12, 0.10, and 0.24 nmol of methylammonium min−1 per 105 cells for AtAMT1;1, AEAMT1;2, and AtAMT1;3, respectively. Error bars indicate standard errors from uptake measurements with at least three independent transformants. If not visible, error bars are within the plot symbols.

After isolation of AtAMT1;1 (Ninnemann et al., 1994), we now show that AMT1 is a multigene family consisting of at least three members in Arabidopsis (Figure 2). Full-length cDNAs were isolated for AtAMT1;2 and AtAMT1;3, with AtAMT1;3 being more closely related to AtAMT1;1. However, because low-stringency DNA gel blot analysis with a conserved AMT1 sequence resulted in a maximum of six bands (Figure 3), additional members of the AMT1 gene family might be expected. The existence of several NH4+ transporter genes in Arabidopsis suggests that membrane transport of NH4+ is a highly regulated process and emphasizes the importance of NH4+ as a main mineral nutrient in plants. This is supported by the finding that NH4+ is the preferential form for nitrogen uptake at low external concentrations (Figure 1). Therefore, we hypothesized that transporters of the AMT1 gene family are responsible for the large capacity of high-affinity NH4+ uptake in plants, and we defined their function in NH4+ transport.

Apart from a pivotal role in nutrient uptake, AMT proteins could play a role in nutrient sensing required for root growth, as in the case of the related NH4+ transporter Mep2p from yeast (Lorenz and Heitman, 1998). Thus far, no structural features were observed in the AMT1 sequences that could point to a role in nutrient sensing such as extended hydrophilic domains for protein–protein interactions, as found in RGT2/SNF3 (Özcan et al., 1996). However, because Mep2p of the AMT1/MEP superfamily acts as a sensor without showing particular structural features (Lorenz and Heitman, 1998), it is uncertain whether NH4+-sensing functions can be identified at a structural level.

Three AMT1 Transporters Expressed in Roots Show Different Affinities for Ammonium

To elucidate the possible physiological roles of AtAMT1;1, AtAMT1;2, and AtAMT1;3 at a functional and regulatory level, we expressed all three full-length clones in yeast to determine substrate affinities; on the other hand, AMT1 gene expression was related to root NH4+ uptake activity in different physiological conditions. Determination of affinity constants for 14C-methylammonium uptake by AtAMT1;1, AtAMT1;2, and AtAMT1;3 in yeast and uptake inhibition by NH4+ show that these high-affinity NH4+ transporters are differently adapted to transport at low concentrations of external NH4+. Although the calculated transport affinities ranging from ≤0.5 to 40 μM might still be subject to environmental modifications, they indicate that optimum transport capacities of the three AtAMT1 transporters cover precisely the range of NH4+ concentrations typically found in soils (Marschner, 1995).

Figure 6.
Figure 6.

Organ-Dependent Expression of AtAMT1;1, AtAMT1;2, and AtAMT1;3 in Roots, Stems, Mature Leaves, Young Leaves, and Buds of Arabidopsis.

Plants were grown under sterile conditions in liquid Murashige and Skoog medium in the growth chamber for root RNA extraction (left) or in soil culture in the greenhouse for RNA extraction from shoot organs. The gels below are shown as a loading control.

Figure 7.
Figure 7.

Correlation between NH4+ Influx and AMT Gene Expression at Different Times of Day.

(A) Time-of-day–dependent influx of 15NH4+ in Arabidopsis roots grown on 1 mM NH4NO3. Root uptake rates in 200 μM 15NH4+ were measured for 5 min; n = 12. The white bar indicates light and the black bar indicates dark conditions for plant growth. Error bars indicate standard deviations. dw, dry weight.

(B) RNA gel blot analysis of the expression of AtAMT1;1, AtAMT1;2, or AtAMT1;3. Total root RNA was extracted from plants and used as given for 15NH4+ influx studies. 25S indicates the rRNA loading control.

In yeast, two of the three MEP genes encode high-affinity NH4+ transporters (Ki of NH4+ for 14 C-methylammonium uptake 5 to 10 μM and 1 to 2 μM for Mep1p and Mep2p, respectively), whereas Mep3p possesses a much lower affinity of ≥1.4 mM (Marini et al., 1997). Whether, similar to the Mep proteins, low-affinity transporters are also included in the AMT1 gene family of Arabidopsis remains to be demonstrated. Theoretically, entry of NH4+ could also be mediated as a side activity of less specific cation channels, in particular K+ transporters and channels (Schachtman and Schroeder, 1994; White, 1996).

In uptake studies with whole plants, it has been shown that NH4+ has an inhibitory effect on low-affinity K+ uptake with the exception of growth conditions under K+ deficiency (Wang et al., 1996). This might be due to an NH4+-induced membrane depolarization, which generally decreases ion influx (Ayling, 1993), rather than through direct competition between the two ions, reinforcing the anticipation that the entry pathways of both ions might be independent. On the other hand, in patch–clamp studies with root hairs of wheat, a 15% conductance for NH4+ has been measured for inward-rectifying K+ channels (Gassmann and Schroeder, 1994), which might contribute to low-affinity NH4+ uptake in plant roots (Gassmann et al., 1993). Because NH4+ entry by K+ channels requires NH4+ concentrations above 0.1 to 1 mM (White, 1996) and average annual soil concentrations rarely rise beyond 50 μM (Marschner, 1995), the ecological significance of this transport path for field-grown plants might be restricted to periods of high nitrogen mineralization or NH4+ fertilizer application. In addition, NH4+ might be taken up into cells via diffusion of NH3, a process that gains in importance with increasing external pH. However, to significantly contribute to plant nitrogen nutrition, these pathways require external NH4+ concentrations in the millimolar range.

Figure 8.
Figure 8.

Correlation between NH4+ Influx and AMT Gene Expression after Subjecting Roots to Nitrogen Deficiency.

(A) 15NH4+ influx in Arabidopsis roots after transfer of hydroponically grown plants from 1 mM NH4NO3 to nitrogen-free nutrient solution. Uptake rates in 200 μM 15NH4+ were measured for 5 min; n = 6. Error bars indicate standard deviations. dw, dry weight.

(B) RNA gel blot analysis of expression of AtAMT1;1, AtAMT1;2, or A tAMT1;3. Total root RNA was extracted from plants as used for 15NH4+ influx studies. 25S indicates rRNA loading control.

Figure 9.
Figure 9.

Correlation between NH4+ Influx and AMT Gene Expression after Transfer of Roots to NO3− as the Sole Nitrogen Source.

(A) 15NH4+ influx in Arabidopsis roots after transfer of hydroponically grown plants from 1 mM NH4NO3 to 1 mM KNO3. Uptake rates in 200 μM 15NH4+ were measured for 5 min; n = 6. Error bars indicate standard deviations. dw, dry weight; h, hour.

(B) RNA gel blot analysis for the expression of AtAMT1;1, AtAMT1;2, and AtAMT1;3. Total root RNA was extracted from plants as used for 15NH4+ influx studies. 25S indicates rRNA loading control.

AMT1 gene expression is organ dependent and differentially regulated for AtAMT1;1, AtAMT1;2, and AtAMT1;3. All three genes are highly expressed in roots (Figure 6), but expression of AtAMT1;1 and AtAMT1;2 was also found in shoot organs, being highest in mature leaves. A physiological role of NH4+ transporters in leaves is evident for NH4+ import from the vascular system across the mesophyll plasma membrane, because NH4+ concentrations in the xylem can rise to 2.6 mM under exclusive NH4+ supply or even up to 300 μM in the absence of supplied NH4+ (Cramer and Lewis, 1993). On the other hand, NH4+ transporters in mesophyll cells might be involved in the retrieval of photorespiratory NH3/NH4+. Even under ambient CO2 concentrations, the loss of photorespiratory NH3 in mitochondria (Keys et al., 1978) can lead to lethality or at least to a dramatic increase in leaf ammonia concentrations if reassimilation of NH3 is absent or inhibited, as is the case for photorespiratory mutants from barley and Arabidopsis (Somerville and Ogren, 1980; Wallsgrove et al., 1987). Because photorespiratory NH3 is likely to be reprotonated during passage to the cytosol or when released to the leaf apoplast, a reimport via NH4+ transporters such as the AMT1 gene family might be required. Therefore, it will be of particular interest to determine their cellular localization and regulation under different photorespiratory conditions.

Evidence for the Role of AtAMT1;1 in Deficiency-Induced and AtAMT1;3 in Diurnally Regulated Ammonium Uptake

High expression levels of AtAMT1;1, AtAMT1;2, and AtAMT1;3 in roots (Figure 6) suggested that all three AMT genes play a role in root NH4+ uptake from the growth medium. Moreover, evidence for different physiological functions of AtAMT1;1, AtAMT1;2, and AtAMT1;3 came from the observations that diurnal variations in 15NH4+ influx correlated with transcript levels of AtAMT1;3, whereas enhanced 15NH4+ influx after plant transfer to nitrogen-free nutrient solution closely correlated with transcriptional upregulation of AtAMT1;1 (Figures 7 and 8). Therefore, we concluded that AtAMT1;1 is mainly responsible for the enhanced capacity for NH4+ uptake under nitrogen deficiency. This is of particular physiological significance because AtAMT1;1 is the transporter with the highest substrate affinity, indicating that high nitrogen demand triggers induction of the transporter, which allows most efficient uptake even from external concentrations in the nanomolar range. An additional contribution of AtAMT1;3 to NH4+ uptake under these conditions is indicated by the smaller but significant increase in AtAMT1;3 transcript levels.

On the other hand, AtAMT1;3 transcription was strongly induced at the end of the light period, which usually coincides with high carbohydrate levels in roots required for NH4+ assimilation (Kerr et al., 1985). This suggests that transcriptional regulation of AtAMT1;3 might also be controlled by the availability of carbon skeletons in roots, thereby providing a physiological link between nitrogen and carbon metabolism in plants. However, it cannot be excluded that AtAMT1;3 is linked to diurnal regulation mediated by the circadian clock or by changes in any other metabolites. This might also be the case for both AtAMT1;1 and AtAMT1;2 transcription, which slightly decreased during the dark period (Figure 7B).

Among all three AMT genes, AtAMT1;2 showed most stable expression levels in all experiments, possibly pointing to a role in constitutive high-affinity uptake of NH4+ at external concentrations in the micromolar to millimolar range. However, because only a few physiological conditions have been investigated, these studies provide correlative evidence for different physiological roles of the individual AMT genes on the basis that further AMT homologs did not or weakly cross-hybridized with AtAMT1;1 to AtAMT1;3. To obtain direct evidence for the physiological role of the individual NH4+ transporter genes in Arabidopsis, we identified knockout mutants by using an approach similar to that used to identify an insertion in K+ channel genes (Gaymard et al., 1998; Hirsch et al., 1998). A subsequent combination of the K+ and NH4+ transport mutants might then allow a complete overview of the genes involved in both low- and high-affinity NH4+ transport to be obtained. So far, the present data could demonstrate that both adapted substrate affinities and transcriptional regulation of AtAMT1;1, AtAMT1;2, and AtAMT1;3 allow the plant to respond differentially to varying nutritional conditions in the environment as well as within the plant.

METHODS

Library Screening and DNA and Sequence Analyses

A λ ZAPII cDNA library made from Arabidopsis thaliana seedlings (Minet et al., 1992) was screened using AtAMT1;1 (Ninnemann et al., 1994) as probe. After in vivo excision, the sequences of isolated clones were determined on both strands. To verify 5′ sequences of AtAMT1;2 and AtAMT1;3, polymerase chain reactions (PCRs) were performed with Pfu polymerase (Stratagene, La Jolla, CA) with an Arabidopsis cDNA library as template (Minet et al., 1992), using reverse primers specific for AtAMT1;2 (5′-GCGGCGAGGGAAGATGTTGAGTTA-3′) and AtAMT1;3 (5′-AGCGGCCGCGATTGCGAACGCCCA-3′) and a forward primer carrying the vector arm sequence (5′-TATTTTAGCGTAAAGGATGGGGAAA-3′). DNA sequences of AtAMT1;2 and AtAMT1;3 have DDBJ/EMBL/GenBank accession numbers AF083036 and AF083035, respectively.

Isolation of genomic DNA from seedlings and of RNA from different organs of Arabidopsis plants as well as DNA gel blot and RNA analyses were essentially performed as given in Ninnemann et al. (1994). For this purpose, Arabidopsis ecotype C24 plants were grown either in axenic culture on Murashige and Skoog medium (Difco, Augsburg, Germany) supplemented with 2% sucrose, as described by Touraine and Glass (1997), or in soil culture in the greenhouse.

Yeast Transformation and Uptake Measurements

To clone AtAMT1;2 and AtAMT1;3 into the NotI site of the yeast expression vector pFL61, we designed specific primers that included Bsp120I restriction sites, and PCR reactions were run using Pfu polymerase on the Arabidopsis cDNA library. Primers used for AtAMT1;2 and AtAMT1;3 are as follows: 5′-TCTCCCTCGGGCCCTCTCCACCATGGACACCGC-3′ and 5′-GACTCGTTTGGGCCCACTCAATTCTCC-3′; and 5′-TTTGGCGGGCCCATGTCAGGAGCTATAACATGCTCTGCGGCC-3′ and 5′-CAAACCGGGCCCTCCAAATATTTATATTTCAAAACCAAAGCCC-3′, respectively.

The yeast strain 31019b (mep1Δ mep2Δ::LEU2 mep3Δ::KanMX2 ura3; Marini et al., 1997) was transformed with pFL61 harboring the cDNA sequence of AtAMT1;1 or PCR products of AtAMT1;2 and AtAMT1;3, according to Dohmen et al. (1991). Yeast transformants were selected on nitrogen-free medium (NAA; Difco) supplemented with 0.5 mM (NH4)2SO4 and 2% glucose. For uptake measurements, yeast cells were grown to the logarithmic phase in NAA medium supplemented with 2% glucose and 500 μg/mL l-proline. Cells were harvested at OD620 nm of 0.5 to 0.7, washed, and resuspended in 20 mM sodium phosphate buffer, pH 7, to a final OD620 nm of 8. Five minutes before the uptake measurement, cells were supplemented with 100 mM glucose and incubated at 30°C. To start the reaction, we added 100 μL of this cell suspension to 100 μL of the same buffer containing different concentrations of 14C-methylammonium (2.11 Gbq/mmol; Amersham), and after 0.5, 1, 2, and 4 min, aliquots were withdrawn, diluted in 4 mL of ice-cold sodium phosphate buffer containing 100 mM methylammonium, and filtered through glass fiber filters (GF/C; Whatman International Ltd., Maidstone, UK). Filters were washed twice with 4 mL of water and analyzed by liquid scintillation spectrometry. For inhibition studies, different concentrations of NH4+ as (NH4)2SO4 were added to the 14C-methylammonium solution.

15N-Uptake Studies

Arabidopsis seeds (ecotype Columbia C24) were germinated, and seedlings were grown hydroponically for 18 days under sterile conditions (Figures 7 and 8) according to the protocol described by Touraine and Glass (1997), with the exception that hydroponic vessels harbored seven to 10 seedlings on 60 mL of the following nutrient solution: 1 mM NH4NO3, 1 mM CaSO4, 1 mM KH2PO4, 0.5 mM MgSO4, 50 μM NaFeEDTA, 50 μM H3BO3, 12 μM MnCl2, 1 μM CuCl2, 1 μM ZnCl2, 30 nM (NH4)6Mo7O24, 10 g/L sucrose, and 0.5 g/L Mes. The pH was adjusted to 5.7. Nitrogen-free or NO3− solutions used in the experiments had the same composition as the NH4NO3 solution used for growth, except that 1 mM NH4NO3 was omitted or replaced by 1 mM KNO3, respectively. To avoid depletion, the nutrient solution was renewed twice during the first 10 days of growth and then daily in the week preceding and during the experiments.

Plants were cultivated in a growth chamber at 60% relative humidity, with a light intensity of 200 μmol m−2 sec−1 and a day–night temperature regime of 8 hr at 22°C and 16 hr at 20°C, respectively. To cultivate plants in the absence of sucrose (Figure 6), we grew plants under nonsterile conditions and a higher light intensity of 400 μmol m−2 sec−1 and a day–night temperature regime of 16 hr at 24°C and 8 hr at 20°C, respectively. To support the plants, the bottoms of Eppendorf tubes were cut and replaced by stainless steel mesh. The tubes were filled with sand and placed in plastic holders in a polystyrene raft floating on nutrient solution in a 10-L cuvette. Seeds were germinated directly on prewetted sand; after 2 weeks, plants were transferred to complete nutrient solution containing 1 mM NH4NO3 as the nitrogen source. Influx of 15NH4+ in roots was determined after transferring the plants first to 0.1 mM CaSO4 for 1 min, then to nutrient solution containing 0.2 mM 15N-labeled NH4+ (99 atom% 15N) for 5 min, and finally to 0.1 mM CaSO4 for 1 min. The influx solution was the same as used for plant growth except that 1 mM NH4NO3 was replaced by 0.1 mM (15NH4)2SO4. Roots were separated from shoots and dried for 48 hr at 70°C. 15N contents were determined by mass spectrometry using a continuous-flow isotope ratio mass spectrometer coupled with an elemented analyzer (model ANCA-MS; Europa Scientific, Crewe, UK; Clarkson et al., 1996).

RNA was extracted from roots according to Lobreaux et al. (1992). Ten or 20 μg of total RNA was electrophoresed through formaldehyde agarose gels and transferred to nylon membranes (Hybond N; Amersham). Prehybridizations were performed for 4 hr at 42°C in 50% formamide, 4 × SSPE (1 × SSPE is 0.15 M NaCl, 15 mM sodium phosphate, and 1 mM EDTA, pH 7.4), 1% sarkosyl, 10% dextran sulfate, and 100 μg/mL denatured salmon sperm DNA. Hybridizations were achieved overnight at 42°C in the same buffer containing the 32P-labeled cDNA probe representing full-length cD-NAs. Filters were washed twice in 2 × SSC (1 × SSC is 0.15 M NaCl and 0.015 M sodium citrate) and 0.1% SDS and twice in 0.1 × SSC and 0.1% SDS for 15 min at 42°C. A 25S rRNA cDNA probe was used as a reference for relative quantifications conducted with a PhosphorImager (Storm; Molecular Dynamics, Sunnyvale, CA). All correlative experiments were conducted at least two times independently and yielded similar results.

ACKNOWLEDGMENTS

We thank Wolfgang Jost (ZMBP, Tübingen, Germany) and Pascal Tillard (Biochimie et Physiologie Moléculaire des Plantes, Montpellier, France) for excellent technical assistance and Bruno André (Université Libre de Bruxelles, Brussels, Belgium) for providing the yeast mutant. This work was supported by the European Community BIOTECH4 program EURATINE.

  • Received October 9, 1998.
  • Accepted February 19, 1999.
  • Published May 1, 1999.

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Three Functional Transporters for Constitutive, Diurnally Regulated, and Starvation-Induced Uptake of Ammonium into Arabidopsis Roots
Sonia Gazzarrini, Laurence Lejay, Alain Gojon, Olaf Ninnemann, Wolf B. Frommer, Nicolaus von Wirén
The Plant Cell May 1999, 11 (5) 937-947; DOI: 10.1105/tpc.11.5.937
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