Conclusions

The rapid improvement of MS, protein separation techniques, and novel methods like sample preparation and comparison has widened the spectra of potential applications for proteomics. In addition, these technologies offer the opportunity to analyze protein expression profiles and to analyze the proteins involved in signaling pathways. At present, the plant defense proteome has been directed at a simple approach. In the future, it can be directed to an entire set of approaches all along the pathogenic signaling pathway. A suite of advanced technologies have recently been describing with coupling of these methods to high-resolution proteome analysis methods, such as nLC-MS/MS, which promises the emergence of qualitative studies of whole pro-teomes. Different approaches to protein isolation selected for a distinct subset of the proteome (e.g., acid, basic, LMW and HMW), along with different separation and detection methods, have provided unique advantages in plant proteomics. As we described above, prefractionation, sequential extraction, LCM, 2D-DIGE, and MS highly offer a valuable result in plant and can achieve a high efficiency of low-abundance protein. Currently, a number of defense responsive proteins have been identified by proteome studies, and almost all of these are employing similar approaches like classic 2-DGE and protein extraction methods in Arabiposis, rice, pea, wheat, and maize. Not as expected, however, the greatest number of proteins identified so far typically belongs to the PR family proteins, ROS-related proteins, and metabolic enzymes, implying that the demand for enriched protein samples or pathogen target-specific tissues (HR and vascular bundle) using technologies described above will continue to rise. Interestingly, PR proteins and ROS-related proteins are common factors that are induced by all biotic stresses including bacteria and fungus, indicating that these could be used as defense/stress-related marker proteins. It is notable that PBZ1, APX, and SOD induced by pathogens are known to have many isoforms showing different pIs on 2D gels in plants inoculated with pathogen and in LMM [8, 30]. However, it still remains as to how these different isoforms were regulated on their biological activity.

FIGURE 40.4. 2-DGE analyses of secreted proteome from rice suspension cultured cell incubated in vitro in the absence (control) or presence (pathogen) of rice blast fungus. Black arrows indicate the differentially induced proteins compared to the noninoculated sample (control). Gels are stained with silver nitrate.

FIGURE 40.4. 2-DGE analyses of secreted proteome from rice suspension cultured cell incubated in vitro in the absence (control) or presence (pathogen) of rice blast fungus. Black arrows indicate the differentially induced proteins compared to the noninoculated sample (control). Gels are stained with silver nitrate.

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