Bioinformatics analysis of cucumber heat shock proteins and investigation of response to abiotic stress conditions by using omics approaches

Heat-shock proteins are a family of proteins that play an important role in organisms both under normal conditions and under conditions that stressors are effective. In plants, they have a very important place in terms of preserving the vitality and functionality of proteins, especially when exposed to stress conditions. Cucumber (Cucumis sativus) is a plant that is produced in every part of our country. Especially when it is evaluated in terms of nutritional and vitamin content, it has an important place in human diet. It is also used as a model organism in many studies. In this three-part thesis, genes belonging to 6 heat shock protein families (sHsp, Hsp40, Hsp60, Hsp70, Hsp90, Hsp100) were first identified in the cucumber genome using bioinformatic methods. Characterization of genes and proteins was then carried out. As a result of the analysis, 36 sHsp, 100 Hsp40, 28 Hsp60, 14 Hsp70, 7 Hsp90 and 17 Hsp100 genes were coded in the cucumber genome. Bioinformatics analyzes of CsHsp genes and proteins were performed to determine the molecular characterization. These include bioinformatics analyzes such as chromosomal distributions of CsHsps, gene structures, conserved motifs, phylogenetic relationships, gene ontology classifications, and identification of orthologs in different organisms. In the second part of the thesis, firstly transcriptomic data (RNA-seq) of cucumber plant were found in the related databases. Next, advanced bioinformatics analyzes of these data were performed to select genes to be expressed in real time-PCR. Changes in expression levels of selected genes in high temperature, low temperature, salinity, drought stress, and ABA application conditions were investigated. In the analyzes, root and leaf tissues of cucumber were collected at 1st, 3rd, 6th and 12th hours after stress treatment. As a result of the analyzes made, it was determined that the expression of CssHsp-08, CsHsp40-70 and CsHsp70-06 genes greatly increased in response to different stress conditions. Among these genes, the expression of the CssHsp-08 gene shows a large increase in drought, salinity, low temperature stresses and ABA application, indicating that this gene is an important gene for resistance to stress conditions. vii In the last part of the thesis, plant extracts were analyzed by GC-MS after derivatization in order to determine changes in metabolite level under the same stress conditions. The responses of amino acids, sugars, sugar alcohols and TCA cyclic elements to stress factors were evaluated. As a result of the analyzes made, it is noteworthy that the accumulation of the amino acids determined in the leaf, especially at high temperature, and the amino acids determined at the root, are more in the face of drought. When we compare the amounts of saturated fatty acids with the amounts of fatty acids containing polyunsaturated bonds, salinity, drought and ABA applications, but higher amounts of saturated fatty acids were found in high temperature and low temperature applications. It has also been observed that for most of the applied stress factors, sucrose accumulates in both tissues. Our work is important for the understanding of the structure, organization, evolution and expression profiles of the family of heat shock proteins, which is an important family, and will be beneficial in terms of measures to be taken against possible future food problems. In addition, our work is fundamental to the use of omics approaches to understanding plant stress mechanisms and has yielded important information.