Genetic Analysis of Plant Salt Tolerance Using Arabidopsis

USING ARABIDOPSIS FOR GENETIC ANALYSIS OF SALT TOLERANCE

The last decade has seen tremendous successes of genetic analysis using the Arabidopsis model system. The power of Arabidopsis genetics has been well recognized in dissecting developmental programs, hormonal, and environmental responses, including light regulation and plant-pathogen interactions. Mutational analysis is especially suited for making inroads to study complex systems because each component can be specifically mutated to reveal its effect on the entire system. Furthermore, genetic analysis has been very successful in elucidating salt stress responses in the budding yeast (Saccharomyces cerevisiae; for review, see Zhu et al., 1997). The application of Arabidopsis genetics on plant salt tolerance studies is beginning to shed light on novel tolerance mechanisms operating in plants.

Doubts may still exist about the validity of Arabidopsis as a model organism for salt tolerance studies. Since Arabidopsis is not a particularly salt tolerant plant species, the question arises as to whether it has evolved salt tolerance genes. This question is best answered by years of physiological studies with salt adaptation of glycophytic plants as well as cell cultures (Hasegawa et al., 1994), particularly during the period from 1970 through the 1980s. Although few significant mechanistic advances were made, one consistent theme that emerged from these studies was that salt-sensitive plants do have salt tolerance genes. Cell cultures derived from many different glycophytes were made salt tolerant with relative ease by gradual adaptation to higher levels of NaCl. For example, a salt-sensitive tobacco cell culture was adapted to grow over tens of thousands of generations in medium containing near seawater-level NaCl (Hasegawa et al., 1994). Salt-sensitive plants were similarly adapted to grow in the presence of high salinity. New crop varieties have not been obtained by salt adaptation, mainly because adapted plants and cells, although they survive well under high salinity, grow very slowly even without salt stress. Nevertheless, these studies illustrate that all plants have in their genomes genes for salt tolerance. Without adaptation, the salt tolerance genes may not be properly expressed to confer salt tolerance.

Salt tolerance genes in halophytes may have evolved from genes in glycophytes that were adapted to low levels of salt stress, a common environmental factor for most plants because Na⁺is one of the most abundant soil cations. Even at a typically low concentration of <1 mm, Na⁺ could accumulate to high levels inside plants because the large volume of transpirational flow of water through plants. Accumulation of Na⁺ to toxic levels may not occur because of salt tolerance genes that regulate the fluxes of Na⁺. This evolutionary argument is supported by much research showing that many agronomic traits in crop species are controlled by genes that have isologs or paralogs in Arabidopsis despite an apparent lack of those agronomic traits in this model plant. For example, although Arabidopsis does not have the fruit-ripening responses typically observed in tomato, the ethylene receptor for tomato fruit ripening is the same type of molecule that mediates the triple responses to ethylene in Arabidopsis (Wilkinson et al., 1995). Therefore, glycophytes such as Arabidopsis can be expected to have salt tolerance genes that are not very different from those of halophytes. This notion is also supported by recent findings that wild tomato strains that have very small fruits are a source of genes for increasing fruit size even in cultivars that have larger fruits (Tanksley and McCouch, 1997).

ECOTYPE DIFFERENCES AND QUANTITATIVE TRAIT LOCI

Quantitative trait loci (QTL) analysis has progressed to a point where it is technically feasible to clone some of the genes involved in a particular quantitative trait. This is especially true of some major QTLs that in practice can be treated as Mendelian loci. For agronomic traits such as flowering time, plant and seed sizes, and disease resistance, ecotype differences have been used to map the responsible QTLs in Arabidopsis (Alonso-Blanco and Koornneef, 2000).

Commonly used Arabidopsis ecotypes, such as Columbia, Landsberg erecta, Ws, and C24, differ only slightly in salt tolerance. Recombinant inbred lines are publicly available for some of the ecotype pairs. However, mapping salt tolerance QTLs in common Arabidopsis ecotypes would be difficult because the differences between these ecotypes are small. A comprehensive survey of the hundreds of Arabidopsis accessions will be necessary to use the natural variations to identify salt tolerance determinants. In addition, several close relatives of Arabidopsis are extremely salt tolerant and are true halophytes. For example, Thellungiella halophila (Thellungiellais a synonym for Arabidopsis), endemic to the coastal lands of eastern China, can survive seawater-level salinity and complete its life cycle in the presence of 300 mm NaCl. T. halophila is very similar to Arabidopsis in terms of growth, development, and also in DNA sequence (H. Zhang and J.-K. Zhu, unpublished data). Such halophytic Arabidopsis relatives could be exploited in the future for salt tolerance studies through QTL or mutational analyses.

SALT-TOLERANT MUTANTS

Like many other cellular signaling pathways, tolerance responses to salt stress are expected to be under negative as well as positive regulation. Salt-tolerant mutants have the potential to reveal negative regulatory mechanisms that normally suppress some of the tolerance responses. Pleiotropic mutations that change ion transport characteristics, e.g. to restrict Na⁺ and/or to enhance K⁺ influx, may also result in salt tolerance. Several single gene mutations conferring salt tolerance in plants are known. These include soybean mutants that appear to exclude Cl⁻ (Abel, 1969), barley and tobacco mutants that overaccumulate Pro (Kueh and Bright, 1982; Sumaryati et al., 1992), fern mutants with altered K⁺ transport (Warne and Hickok, 1987), and several Arabidopsis mutants (Saleki et al., 1993; Werner and Finkelstein, 1995; Tsugane et al., 1999).

Saleki et al. (1993) selected three RS (for resistant to salts) mutants of Arabidopsis that are capable of germination under saline conditions. The RS mutants show enhanced tolerance to not only NaCl but also KCl, K₂SO₄, LiCl, and mannitol, indicating that the mutants are primarily osmotolerant. Similarly, therss (for resistant to salt stress) mutant identified byWerner and Finkelstein (1995) is also osmotolerant. The RSand rss mutations are all recessive. It is unclear whetherrss is allelic to either of the three RS mutants (i.e. RS17, RS19, and RS20). Although the RS and rss mutants germinate under high salinity, seedlings and mature plants are not more salt tolerant than the wild type. This implies that different salt tolerance mechanisms may operate during seed germination and subsequent plant growth. It is important to note that mutants with reduced abscisic acid (ABA) contents or sensitivities are also more tolerant to salt stress at seed germination (Koornneef et al., 1984). This can be explained because salt stress increases ABA levels, and ABA is inhibitory to germination.

An Arabidopsis mutant, pst1 (for photoautotrophic salt tolerance 1), was reported recently (Tsugane et al., 1999). The recessive pst1 mutation increases the capacity of plants to detoxify active oxygen species and thus enhances plant tolerance to oxidative stress as well as to salt stress. Oxidative stress is a secondary effect of salt stress. It is likely that pst1 is also more tolerant to other stresses such as heat, freezing, and drought, each of which can lead to oxidative stress. Consistent with this correlation between oxidative detoxification and multiple stress tolerance, plants genetically engineered to over-produce reactive oxygen-scavenging osmolytes show enhanced tolerance to salt, cold, and heat stresses (Hayashi et al., 1997). In contrast to the RSand rss mutants, pst1 is not salt tolerant during seed germination. Like the RS and RSS genes,PST1 has not yet been cloned.

sos MUTANTS

Most salt-sensitive mutants are expected to be recessive, and their dominant wild-type alleles, by definition, are necessary for salt tolerance. Salt-sensitive mutations have been instrumental in elucidating salt tolerance mechanisms in microbial model organisms such as Escherichia coli (Schuldiner and Padan, 1996) and yeast (Brewster et al., 1993; Mendoza et al., 1994), revealing essential roles of various transporters and signaling molecules for salt tolerance. It was not obvious initially whether salt-sensitive mutants could be isolated from Arabidopsis because the plant is salt sensitive to begin with, typical of most glycophytic plants. Nevertheless, Arabidopsis is capable of tolerating up to 100 mmNaCl depending on treatment duration and other conditions. Therefore, it is theoretically possible to have salt-sensitive mutations that make Arabidopsis even more sensitive. Several Arabidopsis mutants that are more sensitive to NaCl stress have been reported (Wu et al., 1996; Liu and Zhu, 1997a; Zhu et al., 1998). Since Arabidopsis is a relatively salt-sensitive species, the salt-sensitive mutants are more appropriately referred to as salt-hypersensitive mutants. Wu et al. (1996) have named Arabidopsis salt-hypersensitive mutants recovered from their genetic screen as sos for salt overly sensitive (it is easier to say sos than shs). In addition, several los and hos mutants recovered from a genetic screen for deregulated RD29-LUC expression (Ishitani et al., 1997) are more sensitive to salt stress inhibition (J.-K. Zhu, unpublished data).

Approximately 250,000 seedlings derived from ethylmethane sulfonate-, fast neutron-, or T-DNA mutagenesis were screened using a root-bending assay (Wu et al., 1996; Zhu et al., 1998). Over 40 sosmutant lines were recovered. Allelism tests by pair-wise crosses between the mutants revealed that the mutants fall into five complementation groups, defining five salt tolerance genes:SOS1 (Wu et al., 1996), SOS2 (Zhu et al., 1998),SOS3 (Liu and Zhu, 1997a), SOS4, andSOS5 (J.-K. Zhu, unpublished data).

By comparing the growth of the sos mutants on various salts,sos1, sos2, and sos3 mutants were found to be hypersensitive to Na⁺ and Li⁺. It is interesting to note that hypersensitivity to Na⁺ in these sosmutants always seems to be linked to hypersensitivity to Li⁺, a more toxic analog of Na⁺. The sos mutants are not more sensitive to high concentrations of K⁺, Cs⁺, Mg²⁺, Ca²⁺, Cl⁻, NO₃ ⁻, or SO₄ ²⁻. The lack of hypersensitivity to Cs⁺ was unexpected and may indicate that mechanisms of Cs⁺ transport in plants are distinct from those for K⁺, Na⁺, and Li⁺.

The sos2 and sos3 mutants also do not have altered responses to osmotic stress as indicated by normal growth on mannitol media. It is interesting that sos1 seedlings appeared to be more inhibited by low to medium levels of mannitol stress. Under high mannitol stress, the growth of sos1plants did not appear different from that of wild-type plants. Furthermore, sos1 (Liu and Zhu, 1997b) as well assos2 and sos3 accumulate more Pro under NaCl stress. It appears that the extent of Pro accumulation is correlated with the levels of salt sensitivity and stress damage. Consistent with this notion, the salt-tolerant mutants rss andpst1 accumulate less Pro than the wild type under NaCl stress (Werner and Finkelstein, 1995; Tsugane et al., 1999).

Significantly, sos1, 2, and 3 mutants were found to grow poorly on agar medium depleted of K⁺. Of the three sos mutants,sos1 plants are most sensitive to Na⁺and require the highest levels of K⁺ for normal growth. Experiments using⁸⁶Rb⁺ indicated thatsos1 seedlings have reduced capacity for high affinity K⁺ uptake (Ding and Zhu, 1997). Similar uptake studies have failed to detect significant differences in high affinity K⁺ transport between wild-type plants andsos2 or sos3.

The similar spectrum of phenotypes of sos1, sos2, and sos3 suggests that the three SOS genes function in the same or related processes. Double mutants were constructed between these mutants and no additive effect was found (Liu and Zhu, 1997a; Zhu et al., 1998; Halfter et al., 2000). Based on these genetic results, we have proposed that SOS1,SOS2, and SOS3 function in the same pathway leading to Na⁺ tolerance.

SOS GENES AND A REGULATORY PATHWAY FOR PLANT SALT TOLERANCE

A REGULATORY PATHWAY FOR Na⁺TOLERANCE

Besides identifying genes and gene products, an important goal of salt stress research should be to try to connect the various gene products to learn about the pathways and networks that underlie salt stress responses. These pathways and networks are not only necessary for a comprehensive understanding of salt stress tolerance, but also form the necessary basis for rationale approaches to genetic improvement of plant salt tolerance.

After SOS3 was cloned, its gene product was used as a bait to identify its interacting proteins via the yeast two-hybrid approach (Halfter et al., 2000). A large number of related protein kinases were found to interact with SOS3. However, such interactions in the yeast two-hybrid system or in vitro may not necessarily reflect any in planta interaction or function. It was fortunate that when theSOS2 gene was cloned later, it became clear from its sequence that it belongs to the family of SOS3-interacting protein kinases. However, SOS2 was not among those protein kinases discovered by two-hybrid library screening. Even though SOS2 does interact with SOS3, the SOS2 transcript was under-represented in the two-hybrid library because of its low level of expression (Halfter et al., 2000). In fact, the interaction between SOS2 and SOS3 is stronger than that between SOS3 and any of the other protein kinases. SOS2-SOS3 interaction is mediated through the regulatory domain of SOS2.

An outcome of SOS3 binding to SOS2 is that SOS2 protein kinase activity is activated (Halfter et al., 2000). Without SOS3, SOS2 has virtually no activity with several peptide substrates. In the presence of SOS3, SOS2 becomes capable of phosphorylating the peptides. Although the binding between SOS2 and SOS3 appears to be independent of free Ca²⁺, SOS2 phosphorylation of the peptide substrates requires Ca²⁺ (Halfter et al., 2000). It is likely that SOS3 and SOS2 always form a protein kinase complex and, in this sense, they should be considered as subunits of a multisubunit enzyme. Whether this enzyme complex contains other proteins remains to be determined.

SOS3 interaction with and activation of SOS2 kinase is very consistent with genetic evidence that the two genes are both positive regulators of salt tolerance and function in the same pathway (Zhu et al., 1998; Halfter et al., 2000). These two proteins together define a previously unknown regulatory pathway for plant Na⁺ tolerance (Fig.1). Since it is known that salt stress elicits a rise in the concentration of cytosolic-free Ca²⁺ (Läuchli, 1990; Knight et al., 1997), we anticipate that Ca²⁺ will be a direct input signal for this SOS pathway. Such a Ca²⁺ signal does not appear to be very different from that elicited by drought (Knight et al., 1997). However, specificity for Na⁺ stress might be found in subtle differences between the Ca²⁺ signals, e.g. subcellular location, frequency, and amplitude of the Ca²⁺ oscillation. The fact that thesos3 mutation (i.e. mutation in the Ca²⁺ sensor) impairs Na⁺tolerance but has no effect on osmotic stress tolerance strongly suggests the existence of a Ca²⁺ signal that is specific for Na⁺ stress (Liu and Zhu, 1998). The receptor(s) for Na⁺ stress is not known in either plants or yeasts. The connection between Na⁺sensing and the generation of a Ca²⁺ signal are equally unknown. It is even unclear whether Na⁺is sensed inside or outside the cell. In E. coli, Na⁺ appears to be sensed internally by theNhaR gene product, a transcription factor that binds to the promoter of the NhaA Na⁺/H⁺antiporter (Schuldiner and Padan, 1996). In plant cells, it is possible that Na⁺ is sensed by a transporter(s) for K⁺, Na⁺, or Ca²⁺.

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Fig. 1.

Diagram of the SOS pathway for plant Na⁺ tolerance. High Na⁺stress is sensed either externally or internally (not shown) and somehow leads to an increase of cytosolic free Ca²⁺ concentration. SOS3 binds to this Ca²⁺ and activates the protein kinase SOS2. Activated SOS3-SOS2 kinase complex is necessary for increased expression of SOS1 and perhaps other transporter genes under salt stress. The SOS3/SOS2 pathway may also regulate the activities of SOS1 and other transporters at the post-translational level. This gene expression and transporter activity regulation brings about homeostasis of ions such as Na⁺ and K⁺and consequently plant tolerance to Na⁺stress.

Based on the phenotypes of the sos2 andsos3 mutants, the output of the SOS3/SOS2 regulatory pathway is expected to be modulation of abundance and/or activity of certain K⁺ and Na⁺ transporters. Many K⁺ and Na⁺transporters have been cloned. Because there is little information about their function in Na⁺ tolerance, it is difficult to tell which ones might be regulated by the SOS pathway.

One output of the regulatory pathway is up-regulation ofSOS1 Na⁺/H⁺antiporter gene expression by salt stress (Shi et al., 2000). In thesos3-1 mutant background, no such up-regulation could be found. Mutations in SOS2 also seem to prevent NaCl induction of SOS1 transcript in the shoot but not in the root. In the root, there may be a functionally redundant SOS2-like protein kinase. How the pathway modulates SOS1 gene induction remains to be determined. If the induction is transcriptional, then a transcription factor in the pathway needs to be identified. The SOS3/SOS2 regulatory pathway may also control the expression of other genes, particularly other transporter genes. This awaits comprehensive gene expression profiling of sos2 andsos3 mutants and the wild type using DNA micro-arrays or DNA chips.

In addition to controlling gene expression under NaCl stress, the SOS3/SOS2 pathway might be expected to regulate SOS1 and other transporter activities at the post-translational level. Regulation of activity would be faster and may be important for more rapid responses needed to cope with salt stress. Whether SOS3 and/or SOS2 directly interact with and modulate SOS1 antiport activity should be tested. Additional unidentified components in the pathway may be required for such regulations. When any of the other Na⁺ or K⁺ transporters are determined to function in Na⁺ tolerance, they would also be good candidates to directly test for gene expression or activity regulation by the SOS3/SOS2 pathway.

RELATIONSHIP WITH OTHER PATHWAYS

High concentrations of salts cause hyperosmotic as well as ionic stresses. The osmotic and ionic stresses in turn may generate secondary effects such as oxidative stress. The SOS3/SOS2 pathway mediates specifically tolerance to ionic stress, particularly Na⁺ stress. This pathway is therefore distinct from those defined by gene expression (Shinozaki and Yamaguchi-Shinozaki, 1997) or genetic analysis (Ishitani et al., 1997) for osmotic, cold, and ABA responses. It is also different from other protein kinase pathways for stress, such as CDPK, AtDBF2, or mitogen-activated protein kinase (for review, see Halfter et al., 2000). None of the other kinases function specifically in Na⁺ tolerance. Notwithstanding, the SOS3/SOS2 pathway may “cross-talk” with the other stress-signaling cascades. The SOS pathway may also interact with pathways for cell division and expansion, because it eventually regulates plant growth under salt stress.

SOS3 AND THE EFFECT OF EXTERNAL Ca²⁺

External Ca²⁺ enhances plant salt tolerance (Läuchli, 1990). High levels of extracellular Ca²⁺ exert numerous effects on plant cells, many of which may be correlated with alleviating Na toxicity. These effects include, for example, improved K and Ca²⁺nutrition, and reduced cellular Na content. Many of the effects of extracellular Ca²⁺ in relieving salt toxicity are likely achieved by activating signaling pathways for K⁺ and Na⁺ transport, which includes regulation of influx, efflux, and compartmentation of these ions. The SOS3 gene has been proposed to be involved in mediating the beneficial effect of Ca²⁺ (Liu and Zhu, 1997a, 1998). A loss-of-function mutation in this gene (i.e. sos3-1) increases the level of extracellular Ca²⁺required to relieve salt stress (Liu and Zhu, 1997a). Whereas the exact mechanism underlying the connection between extracellular Ca and the SOS3 protein, an apparently intracellular signaling molecule (Liu and Zhu, 1998), is unclear, the dramatic effect of sos3-1mutation on the Ca requirement unequivocally reveals such a connection. Na⁺ stress is known to cause Ca depletion in the extracellular space and the outer surface of the plasma membrane (Läuchli, 1990). An important function of high levels of external Ca might be to compensate for this depletion, thus ensuring Ca influx for the activation of intracellular signaling pathways that control adaptive mechanisms such as the regulation of K and Na transport. Thesos3-1 mutation is a deletion in a Ca-binding domain and it reduces Ca binding of the SOS3 protein (Ishitani et al., 2000). Increased extracellular Ca has been shown to elevate the cytosolic-free Ca to higher levels, which presumably overcomes the Ca-binding defect of sos3-1, thereby partially rescuing the mutant phenotype. It is also possible that at higher levels of external Ca, cells use an alternative signaling mechanism that by-passes the SOS3 pathway. Furthermore, Ca may also exert its protective effect against Na⁺ stress in ways that are independent of SOS3.

CONCLUSION AND PERSPECTIVES

Mutational analysis in Arabidopsis has yielded a number of single gene mutations conferring salt tolerance or hypersensitivity. Cloning and characterization of some of the SOS genes has uncovered a novel Ca-dependent protein kinase pathway for the regulation of ion homeostasis and plant salt tolerance. It is important that new mutations affecting salt tolerance continue to be isolated by using variations of existing genetic screens or completely new screens. As more mutations are discovered and cloned, gaps in the SOS pathway can be filled, and additional pathways may emerge. Increasingly, this endeavor will benefit from the use of reverse genetics as the Arabidopsis genome sequencing approaches completion and more gene knock-out lines become available and are examined under salt stress. Mutants resulting from the forward and reverse genetics should be used in genome scale gene expression profiling and proteome scale protein expression profiling, to increase our understanding of the complex topics of salt tolerance.