Model Plant Species For The Genomicsbased Studies

2.1. Arabidopsis

Nearly twenty years ago, plant biologists were looking for a model organism suitable for detailed analysis using the combined tools of genetics and molecular biology. Plants with effective protocols for regeneration in culture (such as Petunia and tomato) were logical candidates, particularly for studies involving Agrobacterium- mediated cell transformation. However, attention gradually shifted towards Arabidopsis, a small weed in the mustard family that was first chosen as a model genetic organism in Europe and later studied in detail in the United States (Redei, 1975). The shift towards Arabidopsis gained momentum in early 1980s with the release of a detailed genetic map and publications stressing upon the value of Arabidopsis for research in plant physiology, biochemistry and development (Meinke et al. 1998). Research with Arabidopsis has provided valuable insights into all aspects of modern biology (Rhee et al. 2003, Bevan and Walsh 2005). In several cases, long-standing questions in plant physiology and biochemistry have been resolved through genetic and molecular analysis of Arabidopsis mutants. In this regard, a special mention needs to be made for the discovery of novel SOS (Salt Overly Sensitive) pathway candidates for signaling under osmotic stress. It is through the combination of genetics, mutations, physiology, biochemistry and molecular biology tools, that we have been been able to get some insight into this signaling cascade (Chinnusamy et al. 2004). With the availability of completely sequenced and annotated genome (Arabidopsis Genome Initiative 2000), Arabidopsis has turned out to be a wonderful tool for the analysis of salt responsive transcriptomes. Among the various transcript platforms available for this plant, the most complete set is the one which includes the 70mer oligonucleotides representing approximately 26,000 DNA elements, representing the known as well as hypothetical coding regions (http://www.ag.arizona.edu/microarray). Another widely-used platform is the Affymatrix GeneChip with approximately 22,000 genes. Both these platforms have been well exploited for analysis of salt stress responsive transcriptome. Analysis has indicated a highly similar trend in gene regulation patterns, where approximately 80% of the transcripts respond similarly, indicating the comparable usefulness of these platforms (Ma et al. 2006). Recent study suggested that the Arabidopsis salt stress response could be categorized into segments distinct from others such as pathogens, cold stress or even ABA application (Ma et al. 2006). Kreps et al. (2002) accomplished analysis of transcriptome changes in response to salinity, osmotic and cold stress using the GeneChip microarray with probe sets for approximately 8,100 genes. This analysis indicated that about 30% of the transcriptome is sensitive to regulation by common stress conditions.

Rice has slowly emerged as a model system for monocot studies for reasons such as follows: (1) this species has a compact genome of 430 MB size with ~37 K genes, (2) its complete nuclear genome sequence has been determined (Goff et al. 2002, Yu et al. 2002, IRGSP 2005), (3) its complete chloroplast genome sequence has been determined, (4) ~28,000 rice full-length cDNA have been isolated and sequenced, (5) large number of ESTs have been isolated and sequenced in this species, (6) work on making of knockout mutants for every single gene in this species is in progress, (7) production of transgenics by Agrobacterium with high-frequency is demonstrated and (8) detailed molecular marker maps have been constructed. Employing diverse methods, stable genetic transformation of rice is a reality (Bajaj and Mohanty 2005). Availability of complete genome sequence of rice has generated a new spurge of interest. Transcriptome analysis of salt stress response in rice has been carried out using microarray and macroarray based methods by several groups (Table 1). Two types of arrays have been made available for genomic studies in rice, namely oligonucleotides array as well as cDNA array. There are numerous examples wherein detailed studies have been taken in rice using these approaches. Analysis of salt stress-inducible ESTs from salt tolerant rice cultivar Dee-geo-woo-gen revealed several proteins showing homology to proteins functional for detoxification, stress response and signal transduction in plants (Shiozaki et al. 2005). Comparative analysis between different rice genotypes has also been attempted employing salinity tolerant (CSR27 and Pokkali) and sensitive (PB1) cultivars of rice (Sahi et al. 2003). This study highlighted that genes such as SalT, glycine rich RNA binding proteins, ADP ribosylation factor, NADP dependent malic enzyme, Mub ubiquitin fusion protein, tumor suppressor genes, wound inducible genes, ethylene response element binding protein, alanine aminotransferase, copper chaperone, aspartate aminotrans-ferase, ripening regulated protein, metallothionine and Zn finger transcription factor are important constituents of the rice salt stress response. In another study of almost similar nature, comparative analysis between salt-sensitive rice cultivar IR64 and naturally salt tolerant Pokkali revealed several ESTs specifically induced in higher amounts in the stress tolerant Pokkali rice (Pareek et al. unpublished). Importantly, homologous genes from cultivated and wild species of rice have also shown differential response. For example, the PclNOI gene from local wild salinity resistant rice (Porteresia) has been found to possess a short stretch (37 amino acids) which seems to make the protein more tolerant towards salinity stress (Ghosh-Dastidar et al. 2006). This wild homologue has been tested in a range of species and usefulness of the same has been shown (Das-Chatterjee et al. 2006). Overexpression of a serine-rich-protein from Porteresia (PcSrp) in yeast and finger millet improves salinity tolerance (Mahalakshmi et al. 2006).

2.3. Common Ice Plant

Salinity-tolerant model plants have been proposed to be an important resource of salt-stress associated genes with a hope that such investigations will enable future molecular dissections of salt-tolerance mechanisms in important crop plants (Vinocur and Altman 2005). Mesembryanthemum crystallinum (the common ice plant - known so because of the icy look due to enlarged bladder cells of leaf epidermis) has been a system of choice with selected laboratories for salt stress-related studies. This facultative halophyte has an inherent unique capability to quickly switch from normal C3 mode to CAM mode of photosynthesis upon exposure to salinity. CAM is a plastic adaptation of photosynthetic carbon fixation found in about 6% of angiosperm species that limits evaporative water loss and photorespiration, and improves water use efficiency under stress conditions (Cushman and Borland 2002, Dodd et al. 2002). Large numbers of reports highlight how this change in photosynthesis behavior is accomplished based on single-gene analysis (Niewiadomska et al. 1999). The ice plant has been used extensively as a system to investigate responses towards salinity stress such as sodium accumulation and partitioning within the cell, potassium uptake, water channels, carbon, nitrogen and amino acid metabolism and transport, and reactive oxygen scavenging mechanisms (Kore-eda et al. 2004 and references therein). In recent years, transcriptome analysis has been carried out in this species for the comprehensive genomic analysis of the salt stress-regulated genes (Kore-eda et al. 2004).

3. SALT STRESS-RELATED TRANSCRIPTOME CHANGES IN ARABIDOPSIS, RICE AND COMMON ICE PLANT

A. thaliana and O. sativa are believed to have shared a common ancestor ~150 to 200 million years ago. With the availability of (1) whole genome sequence in rice and Arabidopsis and (2) wealth of information on ESTs and transcriptome changes in Arabidopsis, rice and common ice plant, it becomes a challenge to find out the key components of the stress response pathways operative in these model systems. However, current knowledge is still largely restricted to individual genes and pathways, and the unifying picture remains hidden. The understanding of the salinity stress will be greatly enhanced by identifying the convergent and divergent pathways between salinity and other stress responses and nodes of signaling convergence (Ma et al. 2006). We manually scored the salinity-induced transcriptome changes of A. thaliana, O. sativa and M. crystallinum as revealed through microarray studies available from the published literature, in this study. Our aim was to underscore the commonalities and differences in gene expression profiles in these three genera. Those gene expression changes which were unique to a given species were ignored in the further analysis, considering that such genes might be important for species-specific functions. We emphasized for this study, genes that show alterations in two or all the three species undertaken. This category of genes was thought to be important because such genes might be related to generic functions related to salt stress response and reflect the "commoneome". The above analysis enabled us to broadly put the salt stress related gene expression profile alterations into three categories:

(1) Class I - including genes for which no major change in levels was detected,

(2) Class II - including genes which showed major up-regulation upon stress treatment and

(3) Class III - including genes which showed down-regulation upon stress treatment.

The "Class II" category of genes appear most important for governing salt stress response, considering that such genes might be associated with specific changes in gene expression and thus might represent genes associated with the induced tolerance response. Table 2 presents list of Class II and III genes noted in this study. These genes belong to categories related to diverse functions ranging from stress perception to the effector response. Overall, we find that A. thaliana and O. sativa shared more overlapping patterns in gene expression as compared to M. crystallinum.

Table 2. Up- and down-regulated genes in rice, Arabidopsis and ice Plant

Only those candidates have been selected which show response common in at least two of the salinity related transcriptome. This analysis included both salinity up-regulated (+) and down-regulated (-) genes. Artificial grouping of these genes has also been done to reflect their possible physiological role

Gene notation Up-regulated genes

Rice Arabidopsis Ice Plant

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