Water deficit or dehydration is the most crucial environmental factor that limits crop productivity and influences geographical distribution of many crop plants. It is suggested that dehydration-responsive changes in expression of proteins may lead to cellular adaptation against water deficit conditions. Most of the earlier understanding of dehydration-responsive cellular adaptation has evolved from transcriptome analyses. By contrast, comparative analysis of dehydration-responsive proteins, particularly proteins in the subcellular fraction, is limiting. In plants, cell wall or extracellular matrix (ECM) serves as the repository for most of the components of the cell signaling process and acts as a frontline defense. Thus, we have initiated a proteomics approach to identify dehydrationresponsive ECM proteins in a food legume, chickpea. Several commercial chickpea varieties were screened for the status of dehydration tolerance using different physiological and biochemical indexes. Dehydration-responsive temporal changes of ECM proteins in JG-62, a relatively tolerant variety, revealed 186 proteins with variance at a 95% significance level statistically. The comparative proteomics analysis led to the identification of 134 differentially expressed proteins that include predicted and novel dehydration-responsive proteins. This study, for the first time, demonstrates that over a hundred ECM proteins, presumably involved in a variety of cellular functions, viz. cell wall modification, signal transduction, metabolism, and cell defense and rescue, impinge on the molecular mechanism of dehydration tolerance in plants.

The circadian clock provides adaptive advantages to an organism, resulting in increased fitness and survival. The phosphorylation events that regulate circadian-dependent signaling and the processes which post-translationally respond to clock-gated signals are largely unknown. To better elucidate post-translational events tied to the circadian system we carried out a survey of circadianregulated protein phosphorylation events in Arabidopsis seedlings. A large-scale mass spectrometry-based quantitative phosphoproteomics approach employing TiO2-based phosphopeptide enrichment techniques identified and quantified 1586 phosphopeptides on 1080 protein groups. A total of 102 phosphopeptides displayed significant changes in abundance, enabling the identification of specific patterns of response to circadian rhythms. Our approach was sensitive enough to quantitate oscillations in the phosphorylation of low abundance clock proteins (EARLY FLOWERING4; ELF4 and PSEUDORESPONSE REGULATOR3; PRR3) as well as other transcription factors and kinases. During constant light, extensive cyclic changes in phosphorylation status occurred in critical regulators, implicating direct or indirect regulation by the circadian system. These included proteins influencing transcriptional regulation, translation, metabolism, stress and phytohormones-mediated responses. We validated our analysis using the elf4 -211 allele, in which an S45L transition removes the phosphorylation herein identified. We show that removal of this phosphorylatable site diminishes interaction with EARLY FLOWERING3 (ELF3), a key partner in a tripartite evening complex required for circadian cycling. elf4 -211 lengthens period, which increases with increasing temperature, relative to the wild type, resulting in a more stable temperature compensation of circadian period over a wider temperature range. Molecular

Water deficit or dehydration is the most crucial environmental constraint on plant growth and development and crop productivity. It has been postulated that plants respond and adapt to dehydration by altering their cellular metabolism and by activating various defense machineries. The nucleus, the regulatory hub of the eukaryotic cell, is a dynamic system and a repository of various macromolecules that serve as modulators of cell signaling dictating the cell fate decision. To better understand the molecular mechanisms of dehydration-responsive adaptation in plants, we developed a comprehensive nuclear proteome of rice. The proteome was determined using a sequential method of organellar enrichment followed by two-dimensional electrophoresis-based protein identification by LC-ESI-MS/MS. We initially screened several commercial rice varieties and parental lines and established their relative dehydration tolerance. The differential display of nuclear proteins in the tolerant variety under study revealed 150 spots that showed changes in their intensities by more than 2.5-fold. The proteomics analysis led to the identification of 109 differentially regulated proteins presumably involved in a variety of functions, including transcriptional regulation and chromatin remodeling, signaling and gene regulation, cell defense and rescue, and protein degradation. The dehydration-responsive nuclear proteome revealed a coordinated response involving both regulatory and functional proteins, impinging upon the molecular mechanism of dehydration adaptation. Furthermore a comparison between the dehydrationresponsive nuclear proteome of rice and that of a legume, the chickpea, showed an evolutionary divergence in dehydration response comprising a few conserved proteins, whereas most of the proteins may be involved in cropspecific adaptation. These results might help in understanding the spectrum of nuclear proteins and the biological processes they control under dehydration as well as having implications for strategies to improve dehydration tolerance in plants. Molecular

The extracellular matrix (ECM) or cell wall is a dynamic system and serves as the first line mediator in cell signaling to perceive and transmit extra- and intercellular signals in many pathways. Although ECM is a conserved compartment ubiquitously present throughout evolution, a compositional variation does exist among different organisms. ECM proteins account for 10% of the ECM mass, however, comprise several hundreds of different molecules with diverse functions. To understand the function of ECM proteins, we have developed the cell wall proteome of a crop legume, chickpea (Cicer arietinum). This comprehensive overview of the proteome would provide a basis for future comparative proteomic efforts for this important crop. Proteomic analyses revealed new ECM proteins of unknown functions vis-à-vis the presence of many known cell wall proteins. In addition, we report here evidence for the presence of unexpected proteins with known biochemical activities, which have never been associated with ECM.

Nuclear proteins constitute a highly organized, complex network that plays diverse roles during cellular development and other physiological processes. The yeast nuclear proteome corresponds to about one-fourth of the total cellular proteins, suggesting the involvement of the nucleus in a number of diverse functions. In an attempt to understand the complexity of plant nuclear proteins, we have developed a proteome reference map of a legume, chickpea, using two-dimensional gel electrophoresis (2-DE). Approximately, 600 protein spots were detected, and LC-ESI-MS/MS analyses led to the identification of 150 proteins that have been implicated in a variety of cellular functions. The largest percentage of the identified proteins was involved in signaling and gene regulation (36%), while 17% were involved in DNA replication and transcription. The chickpea nuclear proteome indicates the presence of few new nuclear proteins of unknown functions vis-à-vis many known resident proteins. To the best of our knowledge, this is the first report of a nuclear proteome of an unsequenced genome.