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Öğe Comparative analysis of mature and preproprotein form of thionins in some plant species; bioinformatics approaches(Parlar Scientific Publications, 2019) Ozyigit, I. I.; Filiz, E.; Saracoglu, I. A.; Yalcin, B.Thionins are one of the most important antimicrobial peptides in broad-range plant defense. A number of studies are present regarding the structural and biological role of mature thionins but preproprotein forms of these molecules have not been extensively studied. Thus, this study aimed to comparatively analyze a total of 56 thionin preproprotein sequences from 14 different plant species. Analyses of primary, secondary and tertiary structures of these forms revealed that preproproteins with "gamma-thionin domain" were relatively shorter and more basic than proteins with "thionin domain" structure. In addition, members of "thionin domain" were more similar to each other than that of "gamma-thionin domain" forms. Sub-cellular localizations of these forms were predicted as extracellular. Structural superposition of precursor and mature thionins showed that a large portion of precursor sequences are cleaved to form a functional protein. Although precursor forms demonstrated the significant structural divergence in modelled species, functional mature forms showed a structural pattern in ?-helices; two ?-helix proteins included the "thionin domain" family while one a-helix proteins contained the "gamma-thionin domain" family. Results of this study will become valuable theoretical knowledge and provide insight in terms of further understanding the formation of mature functional thionins thereby their biological roles. © by PSPÖğe Genetic diversity and phylogenetic analyses of Turkish sweet corn (Zea mays var. saccharata) varieties using ISSR markers and chloroplast trnL-F IGS region(Academic Press, 2024) Filiz, E.; Uras, M.E.; Ozturk, N.; Gungor, H.; Ozyigit, I.I.Genetic diversity levels are critical for characterizing and utilizing germplasm collections and for making improvements related to elite germplasms. The current study investigated the genetic diversity level and phylogenetic relationships in ten Turkish sweet corn varieties (Zea mays var. saccharata) using 15 ISSR markers and trnL-F intergenic spacer regions, respectively. A total of 75 loci were identified, of which 57 (76%) were polymorphic. The highest polymorphism ratio (100%) was found using UBC811, UBC817, and UBC823 ISSR markers, while the lowest ratio (45.4%) was identified using UBC829. According to trnL-F intergenic spacer region analyses, nucleotide diversity was found as ?: 0.030 for Nei and ?: 0.036 for Watterson, respectively. In trnL-F intergenic spacer regions, several polymorphic (variable) sites were identified 28 of which 57% (16/28) were parsimony informative sites and 399 sites were invariable (monomorphic). The phylogenetic analysis revealed that two major groups were observed named groups A and B and ten sweet corn genotypes clustered along with known maize genotypes in subgroup B2 with 98% bootstrap value. Consequently, the ISSR data obtained in this study revealed that Turkish sweet corn genotypes exhibit extensive genetic diversity, and the trnL-F intergenic spacer region was successfully utilized to differentiate between maize genotypes from various origins and whole plant taxa. © Articles by the authors; Licensee UASVM and SHST, Cluj-Napoca, Romania. The journal allows the author(s) to hold the copyright/to retain publishing rights without restriction.Öğe GpEF1A: a novel lysine methyltransferase gene from Gypsophila perfoliata L. involved in boron homeostasis(Wiley, 2024) Akbudak, M. A.; Cirik, N.; Erdeger, S. N.; Filiz, E.; Dogu, S.; Bor, M.Rapid accumulation of boron (B) leads to toxicity in plant tissues, and the narrow gap between deficiency and toxicity makes it difficult to adjust essential B levels in soil for plant productivity. Therefore, understanding different aspects of B tolerance is necessary to provide new and valid solutions to B toxicity. Gypsophila perfoliata stands out as a remarkable example of a B-tolerant plant, with a natural propensity to thrive in environments such as B mines and soils enriched with high levels of B. In this study, a yeast functional screening experiment was conducted using cDNA libraries from G. perfoliata leaf and root cells for B tolerance. Ten colonies from the leaf library grew in 80 mm boric acid, while none emerged from the root library. Analysis of isolated cDNAs showed identical sequences and a unique motif related to B tolerance. The gene GpEF1A was identified in the tolerant yeast colonies, with predicted structural features suggesting its role, and RT-qPCR indicating increased expression under B stress. A regulatory role for EF1A lysine methylation was proposed in mammalian cells and fungi because of its dynamic and inducible nature under environmental constraints. This could also be relevant for plant cells, as the high similarity of the GpEF1A gene in some salt-tolerant plants might indicate the upregulation of EF1A as a conserved way to cope with abiotic stress conditions. This report represents the first instance of involvement of GpEF1A in B tolerance, and further detailed studies are necessary to understand other components of this tolerance mechanism.Öğe Selenium Toxicity and Tolerance in Plants: Insights from Omics Studies(wiley, 2023) Kiyak, A.; Uluisik, S.; Filiz, E.; Kurt, F.Selenium (Se) is a trace element that is widely available around the world and is vital for living things. Although it is an essential micronutrient for many living things, it causes serious toxicity, especially when taken in large quantities. Plants are the primary source of Se for humans and animals. The essentiality of Se for plants is controversial, but low amounts of Se are required to protect plants from various abiotic stresses such as cold, drought, desiccation, and metal stress. However, due to the accumulation of various toxic forms or nonspecific replacement of it with sulfur analogues, it damages plants by changing protein structures and by disrupting many metabolic pathways, which causes oxidative/nitrosative stress. In addition, Se acts as both as an antioxidant and a pro-oxidant depending on its amount in plants. In this chapter, it is aimed to evaluate the Se metabolism in plants with omics approaches. © 2023 John Wiley & Sons Ltd.
