91 4. DISCUSSION 4.1: Na + /H + Antiporter (SbNHX1) gene from Salicornia brachiata In plants, the uptake and translocation of cations from the soil play an essential role in plant nutrition, signal transduction, growth, and development. Potassium (K + ) and sodium (Na + ) are important as K + is an essential macronutrient and the most abundant inorganic cation in plant cells, whereas Na + toxicity is a principal component of the deleterious effects associated with salinity stress. The genome of Arabidopsis thaliana appears to encode 984 membrane transport proteins, 67% of which are secondary active transporters (Nagata et al 2008). The plant membrane transporters are multigene families, whose members often exhibit overlapping expression patterns and a high degree of sequence homology. The highest sequence homology among NHXs occurs in the N-terminal part that forms the membrane pore, whereas C-terminal domains are more dissimilar. In mammals, ameloride competitively inhibits Na + /H + exchange with K + of 1-100 M depending on the cell type restricted manner (Counillon and Pouyssegur 2000). SbNHX1 shows the presence of this motif which is highly conserved in yeast and plant NHX genes (Gaxiola et al 1999; Yokoi et al 2002). NHX proteins may therefore readily be identified by the presence of the following consensus sequence for the ameloride (sodium) binding site: FFXXLLPPI, where X may be any amino acid. The tonoplast NHX members constitute a very diverse group. This family is divided into Class-I and Class-II groups (Pardo et al 2006) that share only 20-25% identity. The SbNHX1 gene showed higher similarity with Class-I type NHX genes of halophytes. The sequences of Class-I members are very divergent from other IC-NHE/NHX sequences and have been identified in monocotyledonous and dicotyledonous angiosperms, gymnosperms as well as the moss Physcomitrella patens
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91
4. DISCUSSION
4.1: Na+/H
+ Antiporter (SbNHX1) gene from Salicornia brachiata
In plants, the uptake and translocation of cations from the soil play an essential
role in plant nutrition, signal transduction, growth, and development. Potassium (K+)
and sodium (Na+) are important as K
+ is an essential macronutrient and the most
abundant inorganic cation in plant cells, whereas Na+ toxicity is a principal component
of the deleterious effects associated with salinity stress. The genome of Arabidopsis
thaliana appears to encode 984 membrane transport proteins, 67% of which are
secondary active transporters (Nagata et al 2008). The plant membrane transporters are
multigene families, whose members often exhibit overlapping expression patterns and
a high degree of sequence homology. The highest sequence homology among NHXs
occurs in the N-terminal part that forms the membrane pore, whereas C-terminal
domains are more dissimilar. In mammals, ameloride competitively inhibits Na+/H
+
exchange with K+
of 1-100 M depending on the cell type restricted manner
(Counillon and Pouyssegur 2000). SbNHX1 shows the presence of this motif which is
highly conserved in yeast and plant NHX genes (Gaxiola et al 1999; Yokoi et al 2002).
NHX proteins may therefore readily be identified by the presence of the following
consensus sequence for the ameloride (sodium) binding site: FFXXLLPPI, where X
may be any amino acid. The tonoplast NHX members constitute a very diverse group.
This family is divided into Class-I and Class-II groups (Pardo et al 2006) that share
only 20-25% identity. The SbNHX1 gene showed higher similarity with Class-I type
NHX genes of halophytes. The sequences of Class-I members are very divergent from
other IC-NHE/NHX sequences and have been identified in monocotyledonous and
dicotyledonous angiosperms, gymnosperms as well as the moss Physcomitrella patens
92
(Rodríguez-Rosales et al 2009). The Class-I type of NHX isoforms have shown
vacuolar membrane localization except in one case where the AtNHX1 antibody
showed the cross reactivity with plasma membrane and not tonoplast in Thellungiella
(Vera-Estrella et al 2005), which appears to be a unique feature of this Class.
The cDNA of Na+/H
+antiporter gene from Salicornia brachiata named SbNHX1
(accession number: EU448383) is 2,110 bp, consisting of a 3' – noncoding stretch of
427 bp. The open reading frame of SbNHX1 gene is 1,683 bp, encoding a polypeptide
of 560 amino acid residues with an estimated molecular mass 62.44 kDa and
isoelectric point 6.83. Amino acids blast showed the presence of a conserved NHE
(Na+/H
+ exchanger) domain. Prediction of topology of membrane spanning domains
revealed the presence of 11 strong transmembrane domains in SbNHX1, similar to
other halophyte plants like Salicornia europaea, Suaeda japonica, and
Mesembryanthemum crystallinum checked by TMpred analysis. Whereas, Salicornia
bigelovii, Kalidium foliate, Atriplex gmelini and Chenopodium glaucum have 12
transmembrane domains. The variation in the number of transmembrane domain is
intriguing and it seems plausible that these regions may be pertinent to antiporter
function. It has been suggested that glycosylation plays an important role in the proper
biosynthetic processing of transporter proteins in yeast and ScNHX1 is reported to be a
glycoprotein (Wells and Rao 2001). The putative glycosylation sites seem to be well
conserved in SbNHX1. This is the first report so far to demonstrate glycosylation of
plant NHX. In addition to glycosylation sites, several putative phosphorylation,
myristolyation sites and leucine zipper pattern are also predicted in SbNHX1.
None of the biochemical approaches has lead to the identification of the proteins
of the NHX antiporter family responsible for antiport activity. It is now clear that the
situation is much more complex than originally anticipated, with a total of at least 44
93
sequences with homology to Na+/H
+ or K
+/H
+ antiporters identified in the Arabidopsis
genome, some of which are expressed in tonoplast, plasma membrane or internal
membranes of the endosomal pathway (Sze et al 2004). Sequence homology of
AtNHX1 with amiloride sensitive animal NHE antiporters suggests that this is the
protein responsible for the amiloride sensitive and salt stress induced specific Na+/ H
+
antiport found in tonoplast vesicles (Apse et al 1999). The activity of AtNHX1 was
assayed in vacuolar membranes obtained from transgenic Arabidopsis overexpressing
the protein (Apse et al 1999). Na+/H
+ antiport activity could be measured in the
transgenic plants, showing a Km of 7 mM for Na+ whilst activity in wild type plants
was very low. Disruption of AtNHX1 resulted in an even lower Na+/H
+ exchange
activity (Apse et al 2003). Although at first suggested to be specific for Na+, later
studies have shown that AtNHX1 expressed in plants also catalyzes K+/H
+ antiport,
albeit with lower affinity (Apse et al 1999; Zhang and Blumwald 200; Apse et al
2003). The fact that null mutants in AtNHX1 or lines overexpressing the gene have
substantially altered total antiporter activity, indicate that AtNHX1 is the major
contributor to vacuolar Na+/H
+ or K
+/H
+ antiporter activity, in spite of the presence of
5 more NHX isoforms and other proteins of the CPA1 and CPA2 family in
Arabidopsis. To be able to evaluate the structure-function relationships of the plant
NHX antiporters in more detail, avoiding interference with other plant antiporters, a
more convenient system is provided by heterologous expression in yeast. Darley et al
(2000) showed that AtNHX1 activity could be measured in vacuolar membrane
vesicles obtained from a Saccharomyces cerevisiae yeast strain in which the only
endogenous NHX isoform ScNHX1 gene was disrupted. The activity of the plant
enzyme appeared to be slightly higher than that of the endogenous yeast protein, with
Km values of 11 and 16 mM for Na+ respectively, whilst no antiport activity could be
94
detected in vesicles obtained from the strain not expressing yeast or plant antiporter.
The antiport appeared also electroneutral as judged from experiments with the
membrane potential probe Oxonol V, and was shown to be sensitive to amiloride.
Using a similar yeast strain, Yamaguchi et al (2003) found that K+/H
+ antiport activity
was about two times higher than Na+/H
+ antiport activity in vacuolar vesicles obtained
from a yeast strain overexpressing the AtNHX1 protein, whilst Km values for K+ and
Na+ where 12 and 24 mM respectively. The discrepancies between specificity
measurements in plant or yeast could be due to plant specific regulatory mechanisms
not present in the heterologous system. In support of this observation it was found that,
removal of the C-terminal domain increases the Na+/H
+ antiport activity, whilst
binding of the AtCaM15 protein has the opposite effect (Yamaguchi et al 2003; 2005).
It was proposed that in plants, in normal conditions AtNHX1 functions in K+
accumulation, but that salt stress would activate the Na+/H
+ exchange mode, releasing
interacting partners like CaM15 from the C-terminal domain. Overexpression of
AtNHX1 would also induce mainly Na+/H
+ antiporter mode due to lack of interacting
partners. In yeast, the enzyme would be present in the unactivated K+/H
+ antiporter
mode. However, differences in expression levels for the mutant enzymes might also
have affected the results (Yamaguch et al 2003). More importantly, it was shown that
the main contributor to Na+/H
+ and K
+/H
+ antiport activity in the yeast vacuolar
vesicles is the Vnx1 protein, a protein with homology to Ca2+/H
+ and Ca2
+/Na
+
antiporters (Cagnac et al 2007). The earlier reports describing AtNHX1 activity in
yeast should thus be reconsidered as they have been affected by this major background
activity. Finally, ScNHX1 was shown to be involved in protein targeting and
prevacuolar/vacuolar biogenesis (Bowers et al 2000; Brett et al 2005) which
complicates the obtention of comparable vacuolar membrane preparations from wild
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type and ScNHX1 null mutants. For these reasons, the use of membrane vesicles or
intact vacuoles in which many unidentified ion transporters are still functional is not
ideal for structure function studies on the plant NHX antiporters. In this respect,
heterologous expression in yeast also facilitates protein purification using suitable
affinity tags. To avoid interference with other ion transporters such purified protein
can be reconstituted in artificial liposomes. Finally, the encapsulation of impermeant
pH indicator dyes inside the proteoliposomes during reconstitution, permits real
quantitative measurement of pH within the range of responsiveness of the dye. Using
this approach it was shown that the AtNHX1 protein catalyzes both Na+/H
+ and K
+/H
+
antiport with similar affinity of about 40 mM (Venema et al 2002). This antiport could
be inhibited by the amiloride analogs EIPA and benzamil.
The protein sequence of 85-LFFIYLLPPI-94 in SbNHX1 is highly conserved. In
mammals, this region was identified as the binding site of amiloride, which inhibits the
eukaryotic Na+/H
+ exchanger. These features confirm that the SbNHX1 is a
vacuolartype Na+/H
+ antiporter. The analysis of SbNHX1 showed four potential N-
glycosylation sites, nine N-myristoylation sites predicted by PPsearch. Further, there
are fifteen protein kinase phosphorylation sites of casein kinase II (8 sites) and Protein
kinase C (7 sites) and a Leucine zipper pattern were also found in the SbNHX1. The
predicted secondary structure using the PSIPRED protein structure prediction server
and reveals a structure of 24 coils, 22 alpha-helices and 5 beta-strands. To investigate
the molecular evolution and phylogenetic relationships among Na+/H
+ Antiporters in
plants, Na+/H
+ antiporter protein sequences from both glycophytes and halophytes
were aligned and phylogenetic tree was constructed. SbNHX1 gets clustered with
halophytes within the Class-I type of NHX proteins.
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Topological analysis and structure-function studies have so far only been
performed with the AtNHX1 protein. Hydropathy analysis of NHX indicates a domain
organization similar to NHE isoforms, suggesting that structural features are conserved
across the families. Typically, 12 hydrophobic regions that potentially constitute
transmembrane helices are predicted in the conserved hydrophobic N-terminal domain,
with a divergent hydrophilic C-terminal domain that would be involved in regulatory
interactions. To date, two different topological models are proposed (Yamaguch et al;
2003; Sato et al; 2005). Detailed in vitro translation experiments indicate that AtNHX1
topology closely resembles the model proposed for human NHE1 (Wakabayashi et al;
2000; Sato et al; 2005), with 11 transmembrane helices and an intramembraneous loop
corresponding to hydrophobic region (Sze 1983). The plant NHX isoforms, contrary
to most intracellular NHX isoforms of other organisms lack the first H1 hydrophobic
stretch that in NHE1 or NHE6 were shown to represent an N-terminal signal peptide
required for endoplasmic reticulum insertion (Sato et al; 2005). Even so, the first
transmembrane helix of AtNHX1, corresponding to transmembrane helix 2 in NHE1,
is inserted in the same orientation into the membrane, whilst the C-terminus is exposed
to the cytoplasm (Sato et al; 2005). Hydrophobic region 9 has a very similar topology
as compared to the characteristic H10 loop in the human NHE1 isoform, and wouldn’t
cross the membrane completely (Wakabayashi et al 2000; Sato et al 2005).
Mutagenesis of the corresponding region in the yeast ScNHX1 protein has revealed
that several amino acids that are uniquely conserved amongst the intracellular NHX
are essential for function (Mukerjee et al 2006). Still care has to be taken with these
data, as a 3D homology model of NHE1 based on the crystal structure of NhaA gives
slightly different results, notably concerning NHE1 TM helix 9 and the
intramembraneous loop H10 (Landau et al 2007). A different membrane topology for
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the Arabidopsis AtNHX1 protein was found based on insertion mutagenesis with a
3xHA epitope (Yamaguchi et al 2003). In this model the C-terminal domain would be
exposed to the vacuolar lumen, whilst the N-terminus would be cytoplasmic. In
accordance with this topology it was found that in the yeast ScNHX1 protein some
amino acids in the C-terminal domain are N-glycosylated, which indicates that at least
part of the C-terminal domain of ScNHX1 is exposed to the endosomal lumen at some
stage (Wells et al 2001). In this new topology model of AtNHX1, which predicts only
9 transmembrane helices, hydrophobic domain 3, containing the putative amiloride
binding domain, and the hydrophobic domains 5 and 6, containing residues that are
likely involved in Na+ or H
+ binding and transport, would not cross the membrane.
This would result in several transmembrane helices being inserted in the opposite
direction in the membrane, which was related to the fact that plant NHX enzymes have
an opposite transport direction as compared to the plamsa membrane located NHE
proteins (Yamaguchi et al 2003). Whilst animal plasma membrane NHE proteins are
activated by cytoplasmic acidification, and normally catalyze entry of Na+ coupled to
the extrusion of protons (Landau et al 2007) the plant enzymes are suggested to be
involved in extrusion (to the vacuole) of Na+ or K
+, causing cytoplasmic acidification.
The related bacterial (2H+/Na
+) NhaA protein is activated by internal alkalinization
and catalyzes the entry of protons coupled to the extrusion of Na+ (Taglicht et al 1991).
Electroneutral 1:1 Cation/Proton exchangers could also be fully reversible, as was
shown for instance for amiloride sensitive Na+/H
+ exchange in mamalian cells (Paris et
al 1983) and the Schizosaccharomyces pombe plasma membrane SOD2 Na+/H
+
antiporter (Hahnenberger 1996). Detailed mutagenesis studies for the human NHE1
protein and structural resolution of individual transmembrane helices, have pinpointed
residues in transmembrane segments 4, 7 and 9 (corresponding to 3, 6 and 8 in
98
Arabidopsis AtNHX1) that could be directly involved in ion transport (Reddy et al
2008). These transmembrane regions are strongly conserved also in the intracellular
NHX family. A mechanism for ion translocation in NHE1 was proposed, based on
these mutagenesis data and an NHE1 homology model build according to the structure
of the bacterial (2H+/Na
+) antiporter NhaA (Landau et al 2007). This model shows
essential roles for P167, P168, E262, D267 and S351, which correspond to amino
acids P88, P89, E179, D185 and S271 in the Arabidopsis AtNHX1 sequence, and that
are conserved throughout the intracellular NHX family. Also most other residues in
NHE that are important for drug binding or activity, are conserved in the NHX
sequences. These data strengthen the idea that structure and functioning of the NHX
and NHE families is very similar, and that the transport direction is imposed by
regulatory domains. The activity of animal NHE proteins can be regulated by a variety
of regulatory mechanisms involving the long C-terminal tail. Preliminary experiments
have indicated that removal of the last 82 amino acids in the Arabidopsis AtNHX1
protein modifies the transport specificity of the protein, increasing especially Na+/H
+
antiport activity but not K+/H
+ antiport activity, indicating a regulatory role of this
domain (Yamaguchi et al 2003). Later it was shown, using a two-hybrid screen and
immuno precipitation assays, that the C-terminal domain interacts with a CaM-Like
protein AtCaM15 (Yamaguchi et al 2005). AtCaM15 was also found inside the
vacuole of transiently transformed Arabidopsis protoplasts and in yeast cells
expressing the protein. This localization would permit interaction with the C-terminal
domain of AtNHX1 within the vacuoles. Activity measurements using yeast vacuoles
obtained from cells expressing AtNHX1 and AtCaM15 indicated that the CaM15
binding inhibits Na+/H
+ antiport by AtNHX1, without a significant effect on the Km of
the transport reaction. AtNHX1 activity is possibly also regulated through interaction
99
with the protein kinase SOS2.82 SOS2 is the pivotal kinase of the SOS (Salt Overly
Sensitive) pathway involved in regulation of ion transport under salt stress and in
regulation of several other stress responses (Batelli et al 2007). It was reported that
amiloride sensitive specific vacuolar Na+/H
+ antiporter activity in Arabidopsis
membrane vesicles was lower in vesicles obtained from sos2 knockout mutants, and
that this activity could be stimulated in vitro by the addition of activated SOS2 protein
(Qui et al 2004). The activity was further inhibited by AtNHX1 antibodies. It was later
shown by tandem affinity purification and yeast two-hybrid assays that SOS2 also
interacts with several vacuolar V-ATPase subunits and that vesicles isolated from sos2
knockout mutants show considerably lower V-ATPase dependent acidification (Batelli
et al 2007). Comparison of antiport activity in vesicles obtained from wild-type and
sos2 mutant plants is thus difficult, as the V-ATPase mediated vesicle acidification and
thus driving force for the antiport is not the same in the two cases. Structural or
regulatory mechanisms have not been studied for other plant NHX isoforms. The C-
terminus of the yeast NHX1 protein was shown to interact with the small GTPase
activating protein Gyp6 (Ali et al 2004). A model was proposed in which Gyp6
functions as a negative regulator of NHX. Inhibition of NHX1 would result in a more
acidic endsosome/prevacuolar compartment limiting retrograde traffic from the
prevacuolar compartment to the trans Golgi network or Golgi compartment. Such
inhibition would be relieved upon delivery by anterograde traffic of the small GTPase
protein GTP-Ypt6, as it will compete with NHX1 for Gyp6 binding. This would result
in endosome/prevacuolar alkalinization and termination of the Ypt6 signal, stimulation
of retrograde traffic permitting reactivation of Gyp6 by Ric1/Rgp1 in the trans Golgi
network or Golgi (Ali et al 2004). The C-terminus of the human trans Golgi network
localized NHE7 protein was shown to interact with several SCAMP (secretory carrier
100
membrane protein) proteins, which would affect shutteling of NHE7 between
recycling vesicles and the trans Golgi network (Lin et al 2005). The C-terminus of the
NHE7 isoform was also shown to interact with caveolins, facilitating association of
NHE7 to caveole/lipd rafts (Lin et al 2007). The C-terminal domains of the human
isoforms NHE6, 7 and 9, but not NHE8 were found to interact with RACK1 (Receptor
for activated C Kinase 1).
4.2: Expression profiling of SbNHX1 gene
SbNHX1 gene showed very high expression with NaCl treatment. In the present
study we found a basal level of transcripts in plants without salt stress which increased
significantly with salt treatment. SbNHX1 transcripts increased gradually from 4-fold
to 12-fold by increasing the NaCl concentration up to 500 mM NaCl and thereafter
reduced. Plants were also treated at 0.5 M NaCl for different time period to see the
sequential pattern of transcript. The transcript was increased from 2 to 10 folds
concomitantly by increasing the duration treatment from 6 to 48 h, however at 72 h it
reduced further.
Involvement of NHX antiporters in maintaining ion homeostasis is indicated by
the induction of Na+/H
+ antiport activity or NHX gene expression in aerial parts or
roots of many plant species when grown in saline conditions. On comparing Melilotus
indicus, a halophyte growing up to 400 mM NaCl, with a glycophytic relative
Medicago intertexta, it was found that the halophytic species accumulated much less
Na+ and maintained higher levels of K
+. Na
+ accumulation and induction of very
similar NHX transcripts in response to salt stress were found only in the glycophytic
species, but not in the halophyte, indicating that NHX gene induction is related to the
101
includer phenotype (Zahran et al 2007). Also comparing different maize varieties
differing in salt tolerance, it was observed that NHX transcripts were only induced in
roots of a variety known to exclude Na+ from the shoot (Zörb et al 2004). Similarly, it
was observed that HvNHX1 was mostly induced in roots of the relatively salt tolerant
monocot barley, whilst in rice, OsNHX1 induction is observed in shoots, suggesting
that the high salt tolerance in barley is related to accumulation of Na+
in root cell
vacuoles in order to limit transport to the shoot (Fukuda et al 2004a; 2004b). The
expression of most of the vacuolar NHX genes is induced under NaCl treatment,
including Arabidopsis AtNHX1 and rice OsNHX1. In cotton, the GhNHX1 gene was
strongly induced by salt stress in all organs, with the highest levels occurring in leaves
(Wu et al 2004). In wheat TaNHX1 transcripts also showed increased level of
expression in the seedlings after salt treatment (Wang et al 2002). Similarly, SbNHX1
gene showed very high expression with NaCl treatment.
Regulatory genes are quite important, since they can express wide array of genes
to control the multifarious environment conditions. The transcription factors interact
with cis-elements in the promoter regions of various abiotic stress-related genes and
up-regulate the expression of many secondary responsive genes resulting in abiotic
stresses tolerance. In Arabidopsis thaliana, cis-elements and corresponding binding
proteins, with distinct type of DNA binding domains, such as AP2/ERF (apetala 2/