2007 differential expression of the tfiiia regulatory

Differential Expression of the TFIIIA Regulatory
Pathway in Response to Salt Stress between
Medicago truncatula Genotypes1[W]
´
Laura de Lorenzo, Francisco Merchan, Sandrine Blanchet, Manuel Megıas, Florian Frugier,
Martin Crespi*, and Carolina Sousa
´ ´
Institut des Sciences du Vegetal, Centre National de la Recherche Scientifique, F–91198 Gif-sur-Yvette cedex,
´ ´
France (L.d.L., F.M., S.B., F.F., M.C.); and Departamento de Microbiologıa y Parasitologıa, Facultad de
Farmacia, Universidad de Sevilla, 41012 Seville, Spain (L.d.L., F.M., M.M., C.S.)

Soil salinity is one of the most significant abiotic stresses for crop plants, including legumes. These plants can establish root
symbioses with nitrogen-fixing soil bacteria and are able to grow in nitrogen-poor soils. Medicago truncatula varieties show
diverse adaptive responses to environmental conditions, such as saline soils. We have compared the differential root growth of
two genotypes of M. truncatula (108-R and Jemalong A17) in response to salt stress. Jemalong A17 is more tolerant to salt stress
than 108-R, regarding both root and nodulation responses independently of the nitrogen status of the media. A dedicated
macroarray containing 384 genes linked to stress responses was used to compare root gene expression during salt stress in
these genotypes. Several genes potentially associated with the contrasting cellular responses of these plants to salt stress were
identified as expressed in the more tolerant genotype even in the absence of stress. Among them, a homolog of the abiotic
stress-related COLD-REGULATEDA1 gene and a TFIIIA-related transcription factor (TF), MtZpt2-1, known to regulate the
former gene. Two MtZpt2 TFs (MtZpt2-1 and MtZpt2-2) were found in Jemalong A17 plants and showed increased expression
in roots when compared to 108-R. Overexpression of these TFs in the sensitive genotype 108-R, but not in Jemalong A17, led to
increased root growth under salt stress, suggesting a role for this pathway in the adaptive response to salt stress of these M.
truncatula genotypes.

Maintaining crop yields under adverse stress envi- stresses, such as nutritional disorders and oxidative
ronmental conditions is a major challenge in modern stress (Zhu, 2001). Legumes, like most crop plants, are
agriculture. To meet this goal, it is necessary to under- susceptible to salinity (Duzan et al., 2004; Chinnusamy
stand the contrasting adaptations of plants to growth et al., 2005). These plants are widely grown for grain
in stressed conditions. Salinity is one of the major and forage purposes, their world-wide economic im-
abiotic stresses that affects crop productivity and portance being second only to grasses (Graham and
quality and has been described as one of the most Vance, 2003). In addition, legumes can establish root
serious threats to agriculture and the natural status of symbioses with nitrogen-fixing soil bacteria, enabling
the environment (Chinnusamy et al., 2005). Increased the plants to grow in nitrogen-poor soils. This ability to
salinization of arable land is expected to have devas- colonize soils where other plants cannot thrive makes
tating global effects, resulting in a 30% land loss within the study of legumes and their symbioses important
the next 25 years and up to 50% by the year 2050 for agriculture. The establishment of successful sym-
(Wang et al., 2003). biosis involves an elaborate exchange of molecular
Plant responses to salt stress are diverse and include signals (Limpens and Bisseling, 2003). In the plant
modifications of root system architecture, activation host, root nodule organogenesis is regulated by di-
of stress-induced transcriptional programs, and bio- verse hormonal, metabolic, and environmental condi-
chemical adaptations, as well as plant growth inhibi- ´
tions (Crespi and Galvez, 2000), and this interaction is
tion. Salinity imposes ionic, osmotic, and secondary specifically affected in saline soils (Arrese-Igor et al.,
1999; Zahran, 1999).
1
This work was supported by the Spanish Department of Edu- The problem of salinity has been approached
cation and Science (a university professor training grant to L.d.L. through better management practices and the intro-
and a postdoctoral grant to F.M.), and by the ‘‘Grain Legumes’’ FP6 duction of salt-tolerant varieties in the affected areas.
European Economic Community project. Unfortunately, these approaches are generally uneco-
* Corresponding author; e-mail crespi@isv.cnrs-gif.fr. nomical and difficult to implement on a large scale.
The author responsible for distribution of material integral to the
findings presented in this article in accord with the policy described
However, major progress could be achieved through
in the Instructions for Authors (www.plantphysiol.org) is: Martin genetic improvement (Walia et al., 2005). Various le-
Crespi (crespi@isv.cnrs-gif.fr). gumes, such as the model legume Medicago truncatula,
[W]
The online version of this article contains Web-only data. show a large diversity of varieties adapted to vary-
www.plantphysiol.org/cgi/doi/10.1104/pp.107.106146 ing environmental conditions, including saline soils
Plant Physiology, December 2007, Vol. 145, pp. 1521–1532, www.plantphysiol.org Ó 2007 American Society of Plant Biologists 1521

de Lorenzo et al.

(http://www.noble.org/medicago/ecotypes.html). In to different salt stress conditions. Root length was
recent years, M. truncatula has been recognized as an measured after 5 d of growth on a rich medium
excellent legume model in view of its small, diploid ge- ¨
(Fahraeus; Truchet et al., 1985) containing various
nome, self fertility, and short life cycle, as well as avail- concentrations of NaCl (Fig. 1). Root length of M.
ability of various genomic and genetic tools (Barker truncatula 108-R was significantly reduced after NaCl
et al., 1990; Bell et al., 2001; Young et al., 2005). All these treatments in the range of 90 to 150 mM, as compared
traits make M. truncatula suitable for identifying genes with plants grown without salt (Kruskal and Wallis
that could improve agronomic performances such as test, P , 0.01; n 5 20; Fig. 1A). However, root length in
abiotic stress resistance (Cook, 1999). Jemalong A17 was negatively affected by salinity only
Stress responses involve alterations in gene expres- at 150 mM (Kruskal and Wallis test, P , 0.01; n 5 20;
sion (Tester and Davenport, 2003), suppressive sub- Fig. 1A). Altogether, we could identify a differential
tractive hybridizations, and array technologies using response to salt stress between the 108-R and Jemalong
cDNAs or oligonucleotides are increasingly being A17 genotypes. As shown in Figure 1B, M. truncatula
used to monitor global gene expression changes in Jemalong A17 grew well at high salinity levels (120 mM
various plants in response to abiotic stresses (Ozturk NaCl), while 108-R plants grew more slowly under
et al., 2002; Seki et al., 2002; Bartels and Sunkar, 2005). these salt conditions. Similarly, salt treatment re-
However, few reports analyzed differences in gene duced the root dry weight more noticeably for the
expression between salt-sensitive and salt-tolerant variety 108-R already after a 60 mM NaCl treatment,
genotypes in plants (Walia et al., 2005). Although whereas it was only significantly affected at 150 mM
such genes are useful in the dissection of genotype- in Jemalong A17 (Kruskal and Wallis test, P , 0.01;
specific regulatory pathways and mechanisms of salt n 5 20; Fig. 1C, left). No significant differences were,
tolerance, they usually represent only a fraction of all however, found for leaf dry weight biomass of each
salt-regulated genes, and isolating them is a challeng- variety and in all treatments, suggesting greater salt
ing task. The mechanisms underlying the genotype- sensitivity of the root than of the aerial part at this
dependent difference in expression of such genes are early postgermination stage (Fig. 1C, middle). The
largely unknown. ratio of root dry weight to leaf dry weight (as per-
Two genotypes (108-R and Jemalong A17) were centage of control) reveals the relative effects of
shown to have a different adaptation to salt stress increasing NaCl concentration for each genotype
(Merchan et al., 2003). We have developed, in the M. (Fig. 1C, right). As expected, ratio values for M.
truncatula 108-R genotype, a dedicated macroarray truncatula 108-R were significantly reduced with in-
containing genes linked to salt stress and recovery creased salt treatments (60–150 mM NaCl; Kruskal
responses in roots (Merchan et al., 2007). Here, we and Wallis test, P , 0.01; n 5 20). In contrast, this ratio
aimed to identify genes involved in genotype-specific was constant for the tolerant genotype, at least up to
regulatory pathways and mechanisms of salt acclima- 120 mM NaCl. These results suggest that root dry
tion. A comparison of molecular and physiological weight is significantly different between the two
responses to salt stress in sensitive and tolerant M. genotypes at medium and high salt concentrations
truncatula genotypes (108-R and Jemalong A17, re- (60–150 mM).
spectively) was performed. Expression analysis using Root growth performance was also assessed on a
the dedicated macroarray revealed several genes po- low-nitrogen medium (‘‘i’’; Blondon, 1964) to exam-
tentially associated with the contrasting responses to ine the impact of the medium on the range of vari-
salt stress in these plants. Among them, we identified ability for salinity tolerance between these two
a homolog of the COLD-REGULATEDA1 (CorA1; genotypes of M. truncatula. At the same salinity
MtCorA1; Laberge et al., 1993) gene, which is a putative concentration, root length of 108-R was even more
target of MtZpt2 transcription factors (TFs; Merchan significantly affected by salt treatment when com-
et al., 2007). Accordingly, these TFs showed higher ex- pared with the results obtained in the rich medium.
pression levels in the tolerant variety. Overexpression This difference is likely to be a consequence of min-
of MtZpt2-1 or MtZpt2-2 in roots of the salt-sensitive imal nutrient capacity of the ‘‘i’’ medium that may
variety allowed significant increase in root growth potentiate salt stress effects on growth. Statistically
specifically under salt stress conditions, suggesting a significant differences between 108-R and Jemalong
role of these pathways in the differential adaptive A17 genotypes were found for all assayed salinity
response to salt stress of these M. truncatula genotypes. conditions (Fig. 1D). M. truncatula 108-R growth was
already reduced by more than 50% at 90 mM of salt,
and an NaCl concentration of 150 mM nearly abol-
RESULTS ished root growth. This negative effect of salt on root
Evaluation of Salt Stress Growth Responses of Two growth was less pronounced in Jemalong A17, in agree-
M. truncatula Genotypes ment with the results obtained on rich (Fahraeus) ¨
medium (Fig. 1A).
We have examined root growth and dry weight These various parameters allowed us to monitor the
biomass in two genotypes of the model legume effects of salt treatments on plant growth and further
M. truncatula (108-R and Jemalong A17) in response revealed differential root growth responses between
1522 Plant Physiol. Vol. 145, 2007

Differential Salt Stress Responses in Legume

Figure 1. Effect of NaCl on root growth and dry weight of two M. truncatula genotypes. Root length and dry weight biomass under
different salt stress conditions were evaluated in an in vitro system. Germinated seedlings were grown on vertical Fahraeus or ‘‘i’’
¨
medium plates for 5 d in the presence of different NaCl concentrations (0, 30, 60, 90, 120, and 150 mM). A, Relative root length of
each variety at 5 d.a.g. in in vitro conditions with Fahraeus medium is shown as percentage of control root growth without salt. B,
¨
Representative pictures taken 5 d after transfer of the seedlings to 0, 30, and 120 mM NaCl on Fahraeus medium. C, Relative dry
¨

Plant Physiol. Vol. 145, 2007 1523

de Lorenzo et al.

the two genotypes. Plants grown in low-nitrogen turbations in the nodulation process and in nodule
medium were more affected by salinity even though, functionality could explain the decrease in plant
independently of the growth medium, the Jemalong growth under saline conditions. The contrasting root
A17 genotype had a greater ability to tolerate salt physiological responses of the two genotypes to salt
stress conditions than 108-R. treatments may be partially responsible for their dif-
ferent ability to interact with Rhizobium under stress
conditions. Nevertheless, independently of the nitro-
Effects of Salt Stress on the Rhizobial Symbiotic gen status (either from added combined nitrogen or
Interaction in M. truncatula 108-R and Jemalong through symbiotic fixation), the Jemalong A17 geno-
A17 Genotypes type is more tolerant to salt stress than 108-R.

The formation of nitrogen-fixing nodules results
from the symbiotic interaction between legumes and Gene Expression Profiles of M. truncatula 108-R and
rhizobia, a process sensitive to salinity at several Jemalong A17
stages (initiation, development, and function of nod-
ules; Garg and Gupta, 2000). To study the effect of Transcriptional profiling of selected salt stress-
salinity on the nodulation capacity in these two related genes is useful for the assessment and com-
Medicago genotypes, plants were grown in the pres- parison of gene expression on a comprehensive scale
ence of different NaCl concentrations and subse- across genotypes. To reveal molecular mechanisms
quently inoculated with Sinorhizobium meliloti strain that may sustain the contrasting salt tolerance re-
¨
2011 (able to grow up to 300 mM NaCl; Ruberg et al., sponses in roots of both genotypes, we performed a
2003). Three weeks after inoculation, these plants were comparative analysis of expression profiles using a salt
assessed to determine their nodule number. A nega- stress dedicated macroarray containing 384 genes
tive effect on nodule formation was clearly observed in (Merchan et al., 2007). Gene expression analysis was
both varieties at high salt concentration in the medium performed using samples from roots of 108-R and
(Fig. 2A; Kruskal and Wallis test, P , 0.05; n 5 20). Jemalong A17 after 0 or 4 d of salt stress (150 mM NaCl
Salinity decreased nodule number in the 108-R geno- on ‘‘i’’ medium, referred to as ‘‘4i’’ and ‘‘4n,’’ respec-
type at 60 mM NaCl by more than 50% versus only tively). This concentration and time was previously
20% in Jemalong A17. In contrast, the latter genotype used for the analysis of recovery responses in M.
reaches a similar reduction level only at 120 mM NaCl. truncatula (Merchan et al., 2003, 2007) and represent
These results correlated with the differential root a condition that does not permanently affect root
growth sensitivity to salt stress of these genotypes. A growth. Both varieties under these conditions can
drastic reduction in the total number of nodules was fully recover their root growth after changing into a
observed at 150 mM NaCl although to a lesser extent for normal medium. We directed our experimental design
Jemalong A17 (Fig. 2A). In addition, salinity reduced to detect genes differentially regulated between the
nodule size and differentiation in both varieties, as two genotypes in control and stressed conditions (Fig.
evidenced by the appearance of white nodules without 3A). Four different treatments were used: untreated
high leghemoglobin content (data not shown). These 108-R plants (R0), 108-R plants treated with 150 mM
perturbations of the nodulation process could explain NaCl for 4 d (R4), untreated Jemalong A17 plants (J0),
the decrease in plant growth under saline conditions. and Jemalong A17 plants treated with 150 mM NaCl
The effects of salinity on the dry weight of both for 4 d (J4). To identify statistically significant differ-
108-R roots and leaves are very significant already at entially expressed genes between genotypes during
60 mM NaCl in contrast to what is observed for the salt treatments, we used a Student’s t test based on two
Jemalong A17 variety (Fig. 2B). In nodulated plants, a biological replicates and four technical replicates (e.g.
major effect of salt in the aerial part was observed in quadruplicated probes on macroarray) and retained
contrast to recently germinated seedlings. The effect in genes with P values , 0.01.
root and leaf dry weights correlated with the reduction Most of the genes were similarly regulated in these
in nodule number under salt stress, with 108-R being genotypes, because approximately one-half of the
significantly more affected than Jemalong A17. Per- spots on the dedicated macroarray (e.g. about 150

Figure 1. (Continued.)
weights of roots and leaves from M. truncatula 108-R and Jemalong A17 after 15 d of growth in Fahraeus medium submitted to
¨
different salt stress treatments. Results are shown as percentage of control without salt. Ratio (right) represents root dry weight/leaf
dry weight to evaluate the effect of salinity on dry weight biomass of the plants. D, Relative root growth (%) of the two M. truncatula
varieties grown under nonstressed and salt-stressed conditions in ‘‘i’’ medium for 5 d. Values indicated with different letters indicate
statistically significant differences (P , 0.01), whereas those marked with the same letters show statistically similar values. IC,
Interval of confidence (a 5 0.01). Columns labeled with an asterisk are significantly different (P , 0.01) within a given salinity level.
In both cases, the Kruskal and Wallis test has been used. A representative example out of two biological experiments is shown.



Figure 2. Effect of salt stress on nodulation in M. truncatula 108-R and Jemalong A17. Seeds of the two genotypes were
germinated on water agar plates, and seedlings were grown in the greenhouse in the presence of different NaCl concentrations
(0, 30, 60, 90, 120, and 150 mM). The inoculation with S. meliloti strain 2011 was made 9 d.a.g.. Nodule number and root and
leaf dry weights were determined at 30 d.a.g. (21 d.p.i.). A, The effect of salt concentration on nodulation of M. truncatula 108-R
and Jemalong A17 by S. meliloti strain 2011 is measured as percentage of the total nodule number 21 d.p.i. observed in control
(without salt) conditions. B, Relative dry weights (%) of root system and aerial part of M. truncatula 108-R and Jemalong A17
genotypes at 30 d.a.g. under different salt stress conditions. IC, Interval of confidence (a 5 0.05). Columns labeled with an
asterisk are significant differences (P , 0.05) between genotypes within a given salinity level. Statistical comparisons were
performed using the Kruskal and Wallis test. A representative example out of two biological experiments is shown.

spots) showed similar detectable signals for 108-R and Differences in Gene Regulation between
Jemalong A17 hybridization, validating the use of the the Salt-Sensitive and Salt-Tolerant
array for both genotypes. These included internal M. truncatula Genotypes
constitutive controls for gene expression analysis
such as tubulin, elongation factor, and actin genes The differential expression patterns that may lead to
used for array normalization (Merchan et al., 2007). In the increased salt tolerance of Jemalong A17 plants in
Jemalong A17, expression of 14 genes was altered after comparison to 108-R were tested in two ways. First, a
a salt stress: four genes (1.4% of the 280 stress-related comparison of expression profiles under normal
genes present in the array; Merchan et al., 2007) growth conditions between the salt-sensitive and the
induced and 10 (3.6%) down-regulated (J0 versus J4; salt-tolerant varieties (J0 versus R0) revealed 38 genes
Fig. 3B). In contrast, in the salt-sensitive genotype, up-regulated in Jemalong A17 roots relative to 108-R
transcript levels of 63 genes were altered by the salt roots (Supplemental Table S1). In contrast, only five
treatment. Among them, 23 genes (8.2%) were up- genes were more expressed in the sensitive genotype
regulated and 40 (14.3%) down-regulated at 4n (R0 in the same conditions. This large gene activation
versus R4; Fig. 3B). Surprisingly, no gene was induced observed in Jemalong A17 under control growth con-
in common between 108-R and Jemalong A17 after a ditions may account for its relatively lower levels of
salt stress but three genes were down-regulated in gene regulation by salt stress when compared to 108-R.
both genotypes (Fig. 3C). We found six salt-inducible genes in 108-R that were
We can conclude that the tolerant and sensitive common with those up-regulated in Jemalong A17
varieties have a different regulation of their transcrip- in control conditions (Supplemental Table S1, genes
tome in response to salt stress. marked in yellow), confirming that abiotic stress-related

de Lorenzo et al.

genes for the 108-R genotype are expressed at higher
levels in the tolerant genotype in the absence of stress.
Second, intrinsic differences between the two geno-
types after a salt stress were searched (J4 versus R4).
Direct comparison of gene induction/repression be-
tween the two varieties after 4 d of salt stress detected
large differences in expression patterns between the
individual genotypes. This may be particularly rele-
vant for genes whose levels of expression in control
conditions are not the same for each genotype. This
comparison allowed the detection of 118 differentially
expressed genes that were classified into two groups:
(1) those genes that are up-regulated in 108-R at 4n
of salt (six genes); and (2) those genes that are up-
regulated in Jemalong A17 at 4n (112 genes; Supple-
mental Table S2). These latter genes could be of interest
in determining the differential tolerance to salt stress
of these M. truncatula varieties. For this reason, these
genes were further characterized. Sorting of the genes
up-regulated at 4n in Jemalong A17 into functional
categories (according to Journet et al., 2002) revealed
that four categories were overrepresented: signal trans-
duction and posttranslational regulation (16.9%),
abiotic stimuli and development (11.6%), protein syn-
thesis and processing (11.6%), and hormone and sec-
ondary metabolism (11.6%), whereas a significant
proportion could not be assigned (unknown function,
24.1%; Fig. 3D). Among those classes underrepre-
sented, we found genes linked to the cell cycle (0%)
and to DNA synthesis and chromatin (0.9%) in corre-
lation with the reduction of meristem activity induced
by salt stress.
Among the 112 differentially expressed genes up-
regulated in Jemalong A17 roots under salt stress, five
genes showing different levels of induction in the
tolerant variety were randomly selected to validate the
changes detected on macroarrays using real-time re-
verse transcription (RT)-PCR on independent biolog-
ical samples (Supplemental Table S2, genes indicated
in yellow). One codes for a homolog to a ADP-
ribosylation factor (MtADPr, TC67888); one has homol-
ogy to a dormancy-associated protein (MtDor, TC85295),
another codes for a cold-inducible CORA protein
Figure 3. Gene expression profiles of M. truncatula 108-R and Jema- (MtCorA1, TC68022), a fourth matches the sequence of
long A17. A, Experimental design is based on series of pairwise
a dehydrin-related protein (MtDehyd, TC76699), and the
comparisons. Four d.a.g. seedlings from different genotypes (R for
108-R and J for Jemalong A17) were grown for 4 d without (0 mM; R0
fifth is MtHP2, a His-containing phosphotransfer pro-
and J0) or with (R4 and J4) 150 mM NaCl. Two biological and four
´
tein potentially related to cytokinin signaling (Gonzalez-
technical replicates were available for each gene, for each physiolog- Rizzo et al., 2006). The expression patterns revealed
ical condition, and for each genotype. B, The histogram shows the total using real-time RT-PCR followed the same trends seen
number of transcripts up- or down-regulated in 108-R (left bars) and in macroarrays (Fig. 4A). Interestingly, we previously
Jemalong A17 (right bars) in response to salinity stress at a level of P , relate that a homolog of the CorA1 (Laberge et al., 1993)
0.01. C, Venn diagrams illustrating the number of genes up-regulated or gene could be a target of TFIIIA-like C2H2 zinc finger
down-regulated under salinity stress in either or both genotypes of M. TF, MtZpt2-1 and MtZpt2-2 (Merchan et al., 2007; Sup-
truncatula (108-R, left, and Jemalong A17, right). D, Distribution of plemental Fig. S1). Indeed, the other potential target
differentially expressed genes into functional categories according to
gene, Fpf1 (Kania et al., 1997), as well as the MtZpt2-1
BLASTN hits (based on Journet et al., 2002; Merchan et al., 2007).
Percentages were calculated from the total number of differentially
TF, were found to be up-regulated in the tolerant
expressed genes from Jemalong A17 (112 genes). variety (Supplemental Table S2, genes indicated in
light blue). Hence, we tested whether the MtZpt2 TF
may be differentially regulated between these geno-
types. Real-time RT-PCR showed that both TFs were


in several independent transgenic roots of 108-R or
Jemalong A17 genotypes to assay their salt responses.
After 3 weeks of growth in control medium, the
composite plants were transferred to a salt-containing
(100 mM NaCl) or control medium and root length was
measured 8 and 6 d after transfer in 108-R and Jema-
long A17 plants, respectively (Fig. 5). In nonsaline
conditions, the growth of MtZpt2-1 or MtZpt2-2 over-
expressing 108-R roots, as well as control roots ex-
pressing the GUS reporter gene, were not significantly
different (Fig. 5A). However, we detected for both TF-
overexpressing 108-R roots a significant increase (Stu-
dent’s t test, P , 0.01 in two independent biological
experiments; n . 25) in primary root growth com-
pared to control roots 1 week after transfer on salt
medium (Fig. 5B). These results agreed for MtZpt2-1
with our previous experiments (Merchan et al., 2007).
In contrast, Jemalong A17 roots overexpressing
MtZpt2-1 or MtZpt2-2 were not significantly affected
in their growth either in the absence or presence of salt
stress (Fig. 5, C and D, respectively), even though these
roots were effectively overexpressing the correspond-
Figure 4. Real-time RT-PCR analysis of selected genes differentially ing MtZpt2 transgene (Supplemental Fig. S2).
expressed between genotypes in response to salt stress. Specific gene We also examined whether the overexpression of
expression in the salt-tolerant (Jemalong A17) versus salt-sensitive
MtZpt2-1 or MtZpt2-2 TFs in M. truncatula 108-R and
(108-R) genotypes were analyzed in control and salt stress conditions
(4 d at 150 mM NaCl). Induction ratios were calculated between the
Jemalong A17 affected the nodulation capacity of these
salt-treated and nontreated samples. A representative example out of plants under salt stress conditions. We assayed nodu-
two biological experiments is shown, and error bars represent SD of lation capacity in control and salt stress conditions of
three technical replicates. Numbers on the x axis indicate the fold- several independent transgenic roots overexpressing
induction of gene expression in relation to the nonsalt stress condition. these genes in these two genotypes. After 3 weeks of
A, Real-time RT-PCR of five randomly selected differentially expressed growth in control medium, composite plants were
genes between genotypes: MtHP2, a His-containing phosphotransfer transferred to a salt-containing medium (100 mM
protein homolog gene (a gene involved in cytokinin signal transduc- NaCl) and inoculated with S. meliloti 2011. We deter-
tion); MtCorA1, a cold-and drought-regulated CORA protein homolog mined the total number of nodules per plant 21 d
gene; MtADPr, a gene encoding an ADP-ribosylation factor homolog
postinoculation (d.p.i.). Overexpression of either one
protein; MtDor, a gene coding for a dormancy-associated protein; and
MtDehyd, a gene encoding a dehydrin-related protein. B, Real-time
or the other MtZpt TFs did not alter significantly the
RT-PCR analysis of two genes that encode putative TFIIIA-type TFs nodulation capacity of these two genotypes under salt
(MtZpt2-1 and MtZpt2-2). stress (108-R and Jemalong A17; Supplemental Fig. S3,
A and B, respectively). Moreover, no differences in
nodulation were observed even in the absence of salt,
more expressed in the salt-tolerant Jemalong A17 geno- although the genotype-dependent differential inhibi-
type than in 108-R (Fig. 4B). These regulatory genes tory effect of salt stress on the symbiotic interaction
could then be involved in the differential response to was detected (Supplemental Fig. S3, A and B).
salt stress between these Medicago genotypes. Hence, even though the MtZpt pathway could not
be related to the different nodulation capacity of the
Role of the MtZpt Pathway in M. truncatula 108-R and genotypes either in the presence or absence of salt
Jemalong A17 Genotypes stress, their differential root growth response to salt
stress may be partially linked to the higher expression
Our previous work (Merchan et al., 2003, 2007) levels of the two MtZpt2 TFs in the tolerant variety.
demonstrated a potential role of MtZpt2 TFs in the These data suggest that the MtZpt2 pathway is acti-
adaptation of M. truncatula 108-R to salt stress, based vated in Jemalong A17.
either on stable transgenic antisense plants or on
Agrobacterium rhizogenes-transformed roots overex-
pressing MtZpt2-1 (referred as composite plants; DISCUSSION
Boisson-Dernier et al., 2001). To analyze a potential
physiological role of the MtZpt2 genes in root adapta- Soil salinity is one of the major abiotic stresses
tion of M. truncatula Jemalong A17 to salt stress, we com- reducing agricultural productivity. The direct selection
paratively overexpressed the MtZpt2-1 or MtZpt2-2 of superior salt-tolerant genotypes under field condi-
genes from Jemalong A17 under the control of the tions is hindered by the considerable influence that
constitutive 23 35S cauliflower mosaic virus promoter environmental factors have on the response of plants

de Lorenzo et al.

Figure 5. Evaluation of root growth in A. rhizogenes-transformed M. truncatula roots overexpressing MtZpt2-1 or MtZpt2-2.
Composite plants were prepared as described in Boisson-Dernier et al. (2001) using control empty vector and MtZpt2-1 or
MtZpt2-2 overexpressing constructs. After kanamycin selection of transgenic roots, composite plants were transferred to salt-
containing or control media. A representative example out of two biological experiments is shown in all cases. *, Statistically
significant differences (P , 0.01; n . 25). A and B, Growth of transgenic roots overexpressing either MtZpt2-1 or MtZpt2-2 in M.
truncatula 108-R was monitored 1 week after transfer into control (A) or a salt-containing medium (100 mM NaCl; B). The initial
position of the root apex after transfer was monitored to determine the degree of root elongation during the week. C and D, Idem
as A and B for Jemalong A17 indicating transgenic root growth in control (C) or salt-containing medium (100 mM NaCl; D).

to salinity (Richards, 1996). Salt tolerance is a complex is an adaptive mechanism that facilitates water uptake
trait involving the function of many genes (Flowers, from deeper soil layers (Sharp et al., 1988). Similarly,
2004; Foolad, 2004). In fact, the exploitation of natural continued root growth under salt stress may provide
genetic variations and the generation of transgenic additional surfaces for sequestration of toxic ions,
plants introducing novel genes or altering expression leading to lower salt concentration, and enables reach-
levels of the existing genes are being used to improve ing soil areas with lower salt concentrations. For ex-
salt tolerance (Austin, 1993; Jain and Selvaraj, 1997; ample, salt tolerance of barley (Hordeum vulgare) was
Yeo, 1998; Hasegawa et al., 2000; Park et al., 2001; correlated with better root growth rates coupled with
Xiong and Yang, 2003; Guo et al., 2004; Davletova et al., fast growth and early flowering (Munns et al., 2000;
2005; Dana et al., 2006; Hong and Hwang, 2006). In Bartels and Sunkar, 2005). In this study, specific exper-
legumes, salt stress significantly limits productivity iments using two M. truncatula genotypes (108-R and
because of its adverse effects on the growth of the host Jemalong A17) revealed that increased primary root
plant and its symbiotic interactions. Root growth, growth after germination may be linked to their dif-
nodule development, and nitrogen-fixation efficiency ferent tolerance to salt stress. The magnitude of root
are particularly affected (Rai, 1992; Cardovilla et al., growth inhibition was mainly dependent upon the
1994). In this work, we analyze the differential adap- genotype rather than on growth media. The poor ‘‘i’’
tation to salt stress of different M. truncatula genotypes medium is probably more similar to the conditions of
(108-R and Jemalong A17) with regard to root growth the rhizosphere than is the relatively rich Fahraeus¨
and nodulation responses. Analysis of gene expression medium and was chosen for macroarray analysis be-
patterns between these genotypes allowed us to pro- cause good phenotypic variability in response to salin-
pose the implication of the TFIIIA-type TF pathway in ity was observed between these M. truncatula varieties.
the increased tolerance of Jemalong A17 to salt stress. The aerial organs also contribute to the various
Arrest of plant growth during stress conditions mechanisms aimed at postponing adverse saline ef-
depends largely on the severity of the stress (Westgate fects or tolerating salt stress. These include reduction
and Boyer, 1985; Sharp et al., 1988; Spollen et al., 1993; of water loss by increased stomatal resistance and
Munns et al., 2000; Bartels and Sunkar, 2005). How- accumulating sizeable amounts of Na1 in the vacuole
ever, continuation of root growth under drought stress (Apse et al., 1999; Steudle, 2000; Assmann and Wang,


´
2001; Zhang and Blumwald, 2001; Horie and Schroender, Comparison of EST sequences from Jemalong A17
2004). Nevertheless, in Arabidopsis (Arabidopsis thali- and 108-R revealed a high DNA sequence identity
ana), most of the genes were induced by salt stress only (90%–95%) for the large majority of transcripts, in-
in roots, not in leaves (Shisong et al., 2006). The reason dicating that the macroarray of 108-R genotype
for this might be that leaves, compared with roots, (Merchan et al., 2007) can be used for expression pro-
have a large sodium storage capacity, or it might be a filing of Jemalong A17 genes.
consequence of the relatively high concentration of The constitutive high expression of certain stress
sodium ions in roots as they perceive the salt condi- response genes in plants able to thrive in a particular
tions from the soil environment (Kreps et al., 2002; stress environment emerges as a possibly widespread
Volkov et al., 2004; Shisong et al., 2006). Under the adaptive mechanism. This would imply that rather
conditions imposed in this work, 108-R and Jemalong than the expression of particular species-specific stress-
A17 did not differ significantly in leaf dry weight after tolerance genes, it is the altered regulation of conserved
15 d of treatment. However, in nodulated plants, the genes that enables certain plants to survive in harsh
effects of salt on the aerial part were more significant, environments. For instance, in the salt cress, Thellun-
suggesting a later effect of salinity in this case. In the giella halophila, a salt-tolerant relative of the glycophyte
initial stages of growth, the aerial part may be less Arabidopsis, it was shown by comparative transcrip-
sensitive to salt stress than is the root in legumes. tome analysis that the orthologs of several well-known
In legume-Rhizobium symbiosis, the adverse effects Arabidopsis stress response genes are highly expressed
of stresses on nodule functioning vary in intensity, even under control conditions (Taji et al., 2004); simi-
depending on aspects such as plant species, rhizobial larly, the metal-tolerant Arabidopsis halleri was found to
strain, and duration and conditions of exposure to the express a number of metal-homeostasis genes at much
stressful condition (Garg and Gupta, 2000; Bouhmouch higher levels than Arabidopsis, independently of mi-
´
et al., 2005; Moron et al., 2005). Furthermore, the cronutrient status (Becher et al., 2004; Weber et al.,
number and total weight of nodules decreased in 2004). Our analysis suggests that Jemalong A17 is more
salinity treatments (Delgado et al., 1994; Merchan tolerant than 108-R to salt stress, because several stress-
et al., 2003). We showed that total nodule number in related genes are expressed under nonstressed condi-
the two M. truncatula genotypes was adversely af- tions. Jemalong A17 does not induce major changes at
fected by salt stress. The salt present in the growth the transcriptional level among the dedicated macro-
medium may inhibit the absorption of calcium, reduc- array population in response to salinity conditions as
ing the emergence and growth of roots and root hairs compared with 108-R. Additionally, gene repression
and decreasing potential infection sites (Zahran and may be moderated in the tolerant genotype, allowing
Sprent, 1986). Nodule growth has previously been growth to be achieved in the adverse conditions. In
reported to be affected by salt stress in Glycine max fact, many different functions have been identified as
(Delgado et al., 1994; Gordon et al., 1997) and Phaseolus being differentially regulated between the two geno-
vulgaris (Delgado et al., 1994; Bouhmouch et al., 2005). types in response to salt stress (more than 30% of the
It has been proposed that the inhibition of photosyn- tested genes in the macroarray). As expected, a major
thesis in plants subjected to salt stress leads to a class is linked to stress-related pathways, together with
restriction of photosynthate transport toward nodules a large class of regulatory genes (posttranscriptional
and a reduction in their size (Bekki et al., 1987). How- regulation and signal transduction). Interestingly, sev-
´
ever, Gonzalez et al. (2001) suggested that nodule eral response regulators, a cytokinin receptor, and
growth reduction is linked to the inhibition of enzymes ethylene-related and auxin-inducible genes were found
associated with Suc degradation in nodules. In nodu- (Supplemental Table S2). This further reinforces the
lated plants, both aerial and ground tissues are affected hypothesis of a cross talk between hormone- and
by salt, and complex interactions between them may environment-related signaling pathways in the control
explain the better nodulation of Jemalong A17 plants. of root growth under adverse conditions (Malamy,
Array analysis to characterize gene expression pro- 2005; Merchan et al., 2007). In addition, among those
files for large numbers of transcripts has been used to showing the largest differences, we detected a dehy-
describe the response to environmental stresses in drin-related gene and a homolog of imbibition proteins
various species, including Arabidopsis for cold, probably linked to the well-known osmotic stress com-
drought, and salt (Kreps et al., 2002; Seki et al., 2002; ponent of salt stress.
Takahashi et al., 2004), M. truncatula for recovery from TFs are crucial elements for the regulation of devel-
salt stress (Merchan et al., 2007), and rice (Oryza sativa) opment and adaptation to abiotic stresses in plants, and
for response to salt stress (Kawasaki et al., 2001). The the overexpression of specific TFs leads to increased
large number of stress-regulated genes detected in tolerance to abiotic stress, such as salt stresses (Kasuga
these studies indicates that comparative transcript et al., 1999; Winicov and Bastola, 1999; Winicov, 2000;
profiling could be applied between genotypes of the Guo et al., 2004; Kim et al., 2004; Mukhopadhyay et al.,
same species (Taji et al., 2004; Moore et al., 2005; Walia 2004; Davletova et al., 2005). We have previously stud-
et al., 2005; Weber et al., 2006). This comparative ied the MtZpt2 TFIIIA-related TFs (MtZpt2-1 and
analysis might reveal the responses shared across MtZpt2-2) in the 108-R genotype (Merchan et al., 2003,
genotypes and also identify differential responses. 2007). Gene expression patterns in antisense plants

de Lorenzo et al.

and A. rhizogenes-transformed roots overexpressing different concentrations (30, 60, 90, 120, and 150 mM). After four additional
days, plants were infected with a stationary-phase culture of wild-type
MtZpt2-1 together with transient assays revealed that Sinorhizobium meliloti strain 2011. Nodules were counted 21 d after inoculation
MtZpt2-1 may be an activator of the MtCorA1 genes in (30 d.a.g.). This experiment was conducted in a greenhouse, minimizing
108-R (Merchan et al., 2007). In this work, we found evaporation to keep the total water volume of the pots constant. Two biological
increased expression of the MtCorA1 gene in the tol- replicates per salinity treatment were performed (20 plants/genotype).
erant Jemalong A17 variety that correlated with the Fifteen and 30 d after the start of salt treatment in both types of experi-
ments (root growth comparisons and determination of nodulation capacity in
differential expression of these TFs. Overexpression these two varieties, respectively), individual plants of salt stress and nonstress
of either one or the other MtZpt2 TFs enhanced root treatments were harvested. Plants were separated into root system and aerial
growth of 108-R plants but not of Jemalong A17 part. Plant materials were dried at 60°C for 48 h and plant dry weight (under
plants under salt stress conditions. We speculate that salt stress and as a percentage of dry weight under the nonstress treatment)
was determined for individual plants of each genotype.
¨
activation of the TFIIIA Kruppel-like pathway may be
partially involved in the tolerance of Jemalong A17 to
salt stress. RNA Extraction and DNA Array Construction
In conclusion, our results demonstrate the contrast- Roots were collected after 4 d of salinity treatment at 150 mM NaCl and
ing salt tolerance at physiological and transcriptional immediately frozen in liquid nitrogen for RNA extraction (Merchan et al.,
levels between two M. truncatula genotypes. This 2007). For real-time quantitative RT-PCR experiments, total RNA was extracted
using the Total RNA Isolation kit (Macherey-Nagel). Macroarray hybridiza-
variability in salt sensitivity may be linked to the
tions were performed as described in the EMBO M. truncatula Practical Course
activation of MtZpt TFs in the tolerant Jemalong A17 manual (http://www.isv.cnrs-gif.fr/embo01/manuels/pdf/module5.pdf).
genotype and could be a potential genetic resource for DNA macroarrays were constructed as described previously in Merchan
improving the salt tolerance of M. truncatula and et al. (2007).
legume crops in selective breeding programs.
Macroarray Expression Analysis and Real-Time RT-PCR
Measurement of Transcript Level of Selected Genes
MATERIALS AND METHODS
cDNA probe labeling, hybridization of macroarrays, and quantification
Plant Material and Growth Conditions of hybridization signals were performed as described in http://www.isv.
cnrs-gif.fr/embo01/manuels/pdf/module5.pdf (Merchan et al., 2007). Ex-
Two genotypes of Medicago truncatula, 108-R (Hoffmann et al., 1997) and periments were normalized relative to expression of six housekeeping genes,
Jemalong A17 (Barker et al., 1990), were used in this work. Seeds of these whose expression was between 0.5- and 1.5-fold that of the control in all tested
varieties of M. truncatula were scarified in concentrated sulfuric acid for 8 min conditions and genotypes. These constitutive controls were selected to nor-
and rinsed three times with distilled water. The scarified seeds were surface malize all signals obtained from macroarray hybridizations (Merchan et al.,
sterilized for 20 min in bleach (12% [v/v] sodium hypochlorite). After washing 2007).
with sterilized water, seeds were sown on 1% water-agar plates and stored for For real-time RT-PCR, after DNase treatment (RQ1 RNase-free DNase,
2 d at 4°C before incubating overnight at 24°C in the dark to ensure uniform Promega), 1.5 mg of total RNA were retrotranscribed for 1 h at 42°C using the
germination. Germinated seedlings were transferred to square plates or pots SUPERSCRIPT II first-strand synthesis system (Invitrogen) and subsequently
containing appropriate medium and treatment (see below) and grown verti- denatured for 10 min at 75°C. One-tenth of the cDNAs were used as a template
cally in a growth chamber or in a greenhouse, respectively. in 10-mL PCR reactions. PCR was performed with a Light Cycler apparatus
¨
In this work, the Fahraeus and ‘‘i’’ media were used. The poor ‘‘i’’ medium and the LC FastStart DNA Master SYBR Green I (Roche Diagnostics)
(Blondon, 1964) was used for root growth and nodulation assays of seedlings. according to the manufacturer’s instructions. Gene-specific PCR primers
¨
The Fahraeus medium (Truchet et al., 1985) with added nitrogen (1 mM) was were designed according to the cDNA sequences using the PRIMER3 software
used to measure root growth and to prepare composite plants (see below). For (http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi; maximum size,
¨
nodulation experiments on composite plants, Fahraeus medium without 300 bp; melting temperature, 60°C). The following gene-specific primers were
nitrogen was used for optimal nodulation. used (forward and reverse, respectively): 5#-GGTTGTTTGCGAAGAAG-
GAG-3# and 5#-GTACCCCACGGTTTCAACAT-3# for TC67888 (MtADPr);
5#-GGTGTCGTCGGAGTCACAG-3# and 5#-TGGCCTTGAGAAGCTTAGGA-3#
Treatment and Evaluation of Salinity Tolerance for TC85295 (MtDor); 5#-TGTCTCAGCAGATGGCACAG-3# and 5#-CGA-
GGAGGAAGTTGATGGAG-3# for TC76699 (MtDehyd for 108-R); 5#-GAG-
Plants were grown under various salt stress conditions (0, 30, 60, 90, 120,
CGAGGAGGAAGTTGATGG-3# and 5#-TGGTGCTGGTGGAGTTGTTA-3# for
and 150 mM of sodium chloride) to elucidate differences in the root growth,
dry weight biomass, and nodulation capacity between the varieties studied. TC106659 (MtDehyd for Jemalong A17); 5#-GGCGGAGGTGGTTACAATGG-3#
NaCl is a common salt that adversely affects plant growth under natural and 5#-GGCAACAGATTCAGCAGCAC-3# for TC68024 (MtCorA1); 5#-ATA-
conditions, although a unique salt is generally not found in soils (Bernstein, GATGCGTGCCGCAGGTG-3# and 5#-GCATCTCTACAGATCCACTC-3# for
TC74018 (MtHP2); 5#-AAGTCCGGAAAAGCCGGGAGG-3# and 5#-GCACT-
1962). Different levels of NaCl were used in this study to provide a range of
TAACTCACCCACCACTGC-3# for MtZpt2-1; 5#-GGCAACGGACTTTCTAC-
root growth and nodulation responses from the control treatment and of
CTC-3# and 5#-CTCCTCCATCAGCCACCGTG-3# for MtZpt2-2. Parallel
selected varieties.
For root growth comparisons, seedlings were placed in petri dishes with reactions to amplify MtActin11 were used to normalize the amount of template
¨
the appropriate medium (poor ‘‘i’’ medium or richer Fahraeus medium), and cDNA. Synthesis of three independent cDNA preparations from the same
the position of primary root tips was marked on the petri dish every 24 h. Root RNA sample (technical duplicates) allowed us to monitor reproducibility of the
length was measured the 5th d for around 20 seedlings in petri dishes, and two assay. A representative example out of the two biological replicates performed
is shown for each figure.
replications of each treatment (20 plants/genotypes) were performed. The
experiment was conducted in a growth chamber with mean temperature 24°C
under a 16-/8-h photoperiod, and 70% of relative humidity. Statistical Analysis
For measuring the effect of salt concentration on nodulation of M.
truncatula genotypes, 2-d-old seedlings were placed in plastic pots containing Root length, dry weight, and number of nodules in the various treatments
perlite:sand (3:1, v/v) as mixed substrate (five seedlings per pot) and irrigated were tested for significant differences using a Kruskal and Wallis test (Georgin
with the appropriate medium (‘‘i’’ medium; Blondon, 1964) in the greenhouse. and Gouet, 2000) because of the low sample size (n 5 20). Statistical analysis of
Plants were grown in this medium until the 5th d after germination (d.a.g.) the macroarray data was based on a moderated Student’s t test and is de-
when salt stress treatments were initiated. The plant growth media with salt scribed in detail in Merchan et al. (2007). Genes with adjusted P values , 0.01
stress was identical to that of controls, except for the addition of NaCl at were selected as statistically significant. For composite plants, we analyzed the



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Supplemental Figure S1. Homology analysis between Zpt2 sequences. ´
Crespi M, Galvez S (2000) Molecular mechanisms in root nodule devel-
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108-R and Jemalong A17 plants. overexpressing chitinases of fungal origin show enhanced resistance to
Supplemental Figure S3. Evaluation of nodulation capacity in A. rhizogenes- biotic and abiotic stress agent. Plant Physiol 142: 722–730
transformed M. truncatula roots overexpressing MtZpt2-1 or MtZpt2-2 in Davletova S, Schlauch K, Coutu J, Mittler R (2005) The zinc-finger protein
108-R and Jemalong A17. Zat12 plays a central role in reactive oxygen and abiotic stress signaling
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tolerant and salt-sensitive genotypes grown under normal conditions and nitrogen fixation by pea, faba-bean, common bean and soybean
(J0 versus R0). plants. Soil Biol Biochem 26: 371–376
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Bradyrhizobium japonicum Nod factor by soybean [Glycine max (L.) Merr.]
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root hairs under abiotic stress conditions. J Exp Bot 55: 2641–2646
the same conditions (J4 versus R4).
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Foolad MR (2004) Recent advances in genetics of salt tolerance in tomato.
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Garg BK, Gupta IC (2000) Nodulation and symbiotic nitrogen fixation
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