Water-deficit or dehydration impairs almost all physiological processes and greatly influences the geographical distribution of many crop species. It has been postulated that higher plants rely mostly on induction mechanisms to maintain cellular integrity during stress conditions. Plant cell wall or extracellular matrix (ECM) forms an important conduit for signal transduction between the apoplast and symplast and acts as front-line defense, thereby playing a key role in cell fate decision under various stress conditions. To better understand the molecular mechanism of dehydration response in plants, four-week-old rice seedlings were subjected to progressive dehydration by withdrawing water and the changes in the ECM proteome were examined using two-dimensional gel electrophoresis. Dehydration-responsive temporal changes revealed 192 proteins that change their intensities by more than 2.5-fold, at one or more time points during dehydration. The proteomic analysis led to the identification of about 100 differentially regulated proteins presumably involved in a variety of functions, including carbohydrate metabolism, cell defense and rescue, cell wall modification, cell signaling and molecular chaperones, among others. The differential rice proteome was compared with the dehydration-responsive proteome data of chickpea and maize. The results revealed an evolutionary divergence in the dehydration response as well as organ specificity, with few conserved proteins. The differential expression of the candidate proteins, in conjunction with previously reported results, may provide new insight into the underlying mechanisms of the dehydration response in plants. This may also facilitate the targeted alteration of metabolic routes in the cell wall for agricultural and industrial exploitation.

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Mycobacterium tuberculosis, the causative agent of tuberculosis, accounts for 1.5 million human deaths annually worldwide. Despite efforts to eradicate tuberculosis, it still remains a deadly disease. The two best characterized strains of M. tuberculosis, virulent H37Rv and avirulent H37Ra, provide a unique platform to investigate biochemical and signaling pathways associated with pathogenicity. To delineate the biomolecular dynamics that may account for pathogenicity and attenuation of virulence in M. tuberculosis, we compared the proteome and phosphoproteome profiles of H37Rv and H37Ra strains. Quantitative phosphoproteomic analysis was performed using high-resolution Fourier transform mass spectrometry. Analysis of exponential and stationary phases of these strains resulted in identification and quantitation of 2709 proteins along with 512 phosphorylation sites derived from 257 proteins. In addition to confirming the presence of previously described M. tuberculosis phosphorylated proteins, we identified 265 novel phosphorylation sites. Quantitative proteomic analysis revealed more than five-fold upregulation of proteins belonging to virulence associated type VII bacterial secretion system in H37Rv when compared to those in H37Ra. We also identified 84 proteins, which exhibited changes in phosphorylation levels between the virulent and avirulent strains. Bioinformatics analysis of the proteins altered in their level of expression or phosphorylation revealed enrichment of pathways involved in fatty acid biosynthesis and two-component regulatory system. Our data provides a resource for further exploration of functional differences at molecular level between H37Rv and H37Ra, which will ultimately explain the molecular underpinnings that determine virulence in tuberculosis.

Water deficit or dehydration hampers plant growth and development, and shrinks harvest size of major crop species worldwide. Therefore, a better understanding of dehydration response is the key to decipher the regulatory mechanism of better adaptation. In recent years, nuclear proteomics has become an attractive area of research, particularly to study the role of nucleus in stress response. In this study, a proteome of dehydration-sensitive chickpea cultivar (ICCV-2) was generated from nuclei-enriched fractions. The LC-MS/MS analysis led to the identification of 75 differentially expressed proteins presumably associated with different metabolic and regulatory pathways. Nuclear localisation of three candidate proteins was validated by transient expression assay. The ICCV-2 proteome was then compared with that of JG-62, a tolerant cultivar. The differential proteomics and in silico analysis revealed cultivar-specific differential expression of many proteins involved in various cellular functions. The differential tolerance could be attributed to altered expression of many structural proteins and the proteins involved in stress adaptation, notably the ROS catabolising enzymes. Further, a comprehensive comparison on the abiotic stress-responsive nuclear proteome was performed using the datasets published thus far. These findings might expedite the functional determination of the dehydration-responsive proteins and their prioritisation as potential molecular targets for better adaptation.

Reversible protein phosphorylation is a ubiquitous regulatory mechanism that plays critical roles in transducing stress signals to bring about coordinated intracellular responses. To gain better understanding of dehydration response in plants, we have developed a differential phosphoproteome in a food legume, chickpea (Cicer arietinum L.). Three-week-old chickpea seedlings were subjected to progressive dehydration by withdrawing water, and the changes in the phosphorylation status of a large repertoire of proteins were monitored. The proteins were resolved by 2-DE and stained with phosphospecific fluorescent Pro-Q Diamond dye. Mass spectrometric analysis led to the identification of 91 putative phosphoproteins, presumably involved in a variety of functions including cell defense and rescue, photosynthesis and photorespiration, molecular chaperones, and ion transport, among others. Multiple sites of phosphorylation were predicted on several key elements, which include both the regulatory as well as the functional proteins. A critical survey of the phosphorylome revealed a DREPP (developmentally regulated plasma membrane protein) plasma membrane polypeptide family protein, henceforth designated CaDREPP1. The transcripts of CaDREPP1 were found to be differentially regulated under dehydration stress, further corroborating the proteomic results. This work provides new insights into the possible phosphorylation events triggered by the conditions of progressive water-deficit in plants.