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    Abiotic stress-induced regulation of antioxidant genes in different Arabidopsis ecotypes: microarray data evaluation
    (Taylor & Francis Ltd, 2019) Filiz, Ertuğrul; Özyiğit, İbrahim İlker; Saraçoğlu, İbrahim Adnan; Uras, Mehmet Emin; Şen, Uğur; Yalçın, Bahattin
    Although stresses induce generation of reactive oxygen species (ROS), which are highly reactive and toxic, and cause severe damage to cellular components; plants have very efficient enzymatic ROS-scavenging mechanisms. Despite the substantial knowledge produced about these enzymes, we still have limited knowledge regarding their expression patterns in relation to the stress type, duration and strength. Thus, taking advantage of microarray data, this work evaluated the abiotic stresses (salt, cold, heat and light) induced regulation of six antioxidant enzymes, superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), glutathione peroxidase (GPX), monodehydroascorbate reductase (MDHAR) and dehydroascorbate reductase (DHAR), in 10 natural Arabidopsis ecotypes. The expression profiles of 36 genes encoding six enzymatic antioxidants including CSD1-3, FSD1-3, MSD1-2, CAT1-3, APX1-6, APXT, APXS, GPX1-8, MDAR1-5 and DHAR1-4 were investigated. In particular, FSD1, FSD2, CSD1 and CSD2 genes coding for SOD; CAT2 and CAT3 for CAT; APX3-6, APXT and APXS for APX; GPX1, GPX2, GPX5, GPX6 and GPX7 for GPX; MDAR2-4 for MDHAR; and DHAR1 and DHAR3 for DHAR families appeared to be more differentially expressed under given stress conditions. Primarily, high light as well as salt and cold stresses considerably up-regulated the gene expression, whereas cold stress significantly led to the down-regulation of genes. The overall expression pattern of ecotypes suggested that the studied Arabidopsis genotypes had different stress tolerance.
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    Comparative analyses of phytochelatin synthase (PCS) genes in higher plants
    (Taylor & Francis Ltd, 2019) Filiz, Ertuğrul; Saraçoğlu, İbrahim Adnan; Özyiğit, İbrahim İlker; Yalçın, Bahattin
    Plants employ various defence strategies to ameliorate the effects of heavy metal exposures, leading to re-establishment of metal homeostasis. One of the strategies includes the biosynthesis of main heavy metal detoxifying peptides phytochelatins (PCs) by phytochelatin synthase (PCS). In the present study, 14 PCS homologues were identified in the genomes of 10 selected plants. The size of these PCSs was 452-545 amino acid residues, with characteristic phytochelatin and phytochelatin_C domains. The N-terminal site of the proteins is highly conserved, whereas the C-terminal site is less conserved. Further, the present study also identified fully conserved Cys residues involved in heavy metal binding reported earlier. In addition, other preserved cysteines, with minor substitutions Cys(C)-> Ser(S) or Tyr(Y) or Trp(W), were also identified in the PCS sequences that might be associated with metal binding. The reported catalytic triad residues from Arabidopsis, Cys56, His162 and Asp180, are all conserved at the respective sites of PCSs. A clear monocot/dicot separation was revealed by phylogenetic analysis and was further corroborated by the exon-intron organisations of the PCS genes. Moreover, gene ontology terms, co-expression network, cis-regulatory motif and miRNA analyses indicated that the complex as well as dynamic regulation of PCSs has significant involvement in different metabolic pathways associated with signalling, defence, stress and phytohormone, in addition to metal detoxification. Moreover, variations in protein structure are suggested to confer the functional divergence in PCS proteins.
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    COMPARATIVE ANALYSIS OF MATURE AND PREPROPROTEIN FORM OF THIONINS IN SOME PLANT SPECIES; BIOINFORMATICS APPROACHES
    (Parlar Scientific Publications (P S P), 2019) Özyiğit, İbrahim İlker; Filiz, Ertuğrul; Saraçoğlu, İbrahim Adnan; Yalçın, Bahattin
    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 alpha-helices; two alpha-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.