Rice (Oryza sativa L.) is an important crop cultivated worldwide, and abiotic stresses limit its productivity. Different approaches were carried out to understand the mechanisms of rice defense responses against abiotic stresses, mainly drought. The NADPH-generating enzymes engaged in response to dehydration and salt stresses during the seedling stage of Nipponbare cultivar were analyzed. Enzyme activities of 6-phosphogluconate dehydrogenase (6PGDH), NADP-dependent aldehyde dehydrogenase, NADP-malic enzyme (NADP-ME) in leaves, and 6PGDH in roots were significantly increased in response to dehydration stress. NADP-ME and NADP-glutamate dehydrogenase activities in roots increased significantly in response to salt stress. These results suggest the involvement of NADPH-generating enzymes in plant responses to dehydration and salinity stresses, and the increased demands of NADPH in plants under abiotic stress can be furnished by enhanced activities of NADPH-producing enzymes. Also, a dehydration-induced protein was detected and identified as serine-hydroxymethyltransferase. This result indicates that serine-hydroxymethyltransferase can play a key role in regulating dehydration response in rice. Moreover, comparative proteomic analyses of CL163 (drought-tolerant), Cheniere (drought-sensitive), and Rex (moderately-drought-sensitive) rice varieties were performed. Drought-responsive proteome changes were profiled in leaves and roots at the seedling stage in response to drought stress imposed by polyethylene glycol (PEG-6000). Eighteen significantly differentially expressed proteins were identified by mass spectrometry. Elongate factor1 alpha and 17.9-kDa classI heat shock protein appear to have different expression patterns between CL163 and Cheniere, which may be attributable to the difference in drought response of the two rice varieties. Furthermore, a compendium of 103 drought resistance genes in rice was compiled to construct and analyze networks formed by associations between genes/proteins and to identify the most significant genes, biological processes/pathways. Genes were classified based on gene ontology and protein class into 26 groups. Forty-two genes were classified as transcription factors. Proteins encoded by the genes were localized in 8 subcellular locations and classified into three classes. Two pathways from KEGG whose genes were overrepresented in the compendium were identified. Gene expression, network presenting pairwise interactions between genes/proteins, and co-expression network were constructed. This study provides a systematic view of the crucial genes that can be contributing collectively to drought tolerance.

Small heat shock proteins (sHSPs) are a ubiquitous family of molecular chaperones that play a vital role in maintaining protein homeostasis in cells. They are the first line of defence against the detrimental effects of cellular stress conditions like fluctuations in temperature, pH, oxidative and osmotic potentials, heavy metal toxicity, drought and anoxia. Many sHSPs are also constitutively expressed during developmental stages of different plant tissues. Members of this family are ATP-independent chaperones, with monomeric masses varying from 12-40 kDa. A characteristic feature of sHSPs is their ability to assemble into large oligomers, ranging from dimers to 48-mers. Under stress conditions, these oligomers dissociate and/or undergo drastic conformational changes to facilitate their binding to misfolded substrate proteins in the cell. This interaction prevents the substrate from aggregating during stress. When physiological conditions are restored, the substrates are transferred to other ATP-dependent heat shock proteins for refolding. Thus sHSPs do not refold their substrates, but instead prevent them from aggregating and maintain them in a „folding-competent‟ state. The clientele of sHSPs includes proteins with a wide range of molecular masses, secondary structures and pIs. This promiscuity has led to sHSPs occupying key positions in the protein quality control network. As molecular chaperones that protect proteins, sHSPs prevent disease. Concomitantly, mutations in sHSPs have also been linked to various human diseases. Till date, high resolution crystal structures are available only for 3 sHSP oligomers. This insufficiency of structural information has hindered our understanding of the mechanism of chaperone function, the link between the oligomeric status and chaperone activity, identification of substrate binding sites and the role of the flexible terminal segments in mediating both the oligomerization and chaperone function. We undertook structural and functional characterization of plant and bacterial sHSPs in order to address some of these questions. Chapter 1 of this thesis gives an overview of the sHSP family, with special emphasis on the oligomeric assemblies of sHSPs of known structures. We highlight what we know about this family through mutational studies, what is as yet unknown, and why it is important to study this family. Chapter 2 describes our efforts at structural and functional characterization of 5 sHSPS in rice, each targeted to a different organelle. We probed the role played by the N-terminal region in mediating oligomer assembly and in the chaperone activity of the protein. Rice sHSPs displayed a wide range of hydrodynamic radii, from 4 nm to 14 nm, suggesting that their oligomeric assemblies are likely to be diverse. In chapter 3, we discuss our attempts at the structural characterization of a bacterial sHSP, Aggregation suppressing protein A, or AgsA from Salmonella enterica. We obtained a high resolution crystal structure of the dimer of the core sHSP domain. We compared this dimer with other known sHSP dimers, reported the deviations that we observed and analysed the structure to account for these differences. We used this dimer structure to successfully obtain solutions for low resolution X-ray diffraction data for oligomers of different truncated constructs of AgsA. We observed that a C-terminal truncated construct formed an octahedral 24¬mer (4.5 Å resolution), whereas a construct truncated at both termini formed a triangular bipyramidal 18-mer (7.7 Å resolution), an assembly hitherto unobserved for any sHSP. A similar 18-mer was obtained when the C-terminal truncated construct was incubated with a dipeptide prior to crystallisation (6.7 Å resolution). The cryo-EM map of the wild type protein (12 Å resolution) could be fitted with a different 18-mer. The low resolution of the data pre-empted an atomic-level description of the interfaces of the assemblies. However, our work highlights the structural plasticity of this protein and probes the sensitivity of the oligomeric assembly to minor differences in construct length.