Browsing by Author "Öz U."

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    Comprehensive analysis of secondary metabolite biosynthetic gene clusters in Helianthus annuus L.: A bioinformatics approach
    (Elsevier B.V., 2024) Öz U.
    Plant secondary metabolite gene clusters are regions within the plant genome that encode enzymes and proteins involved in the biosynthesis of secondary metabolites. Helianthus annuus L. is a significant oilseed plant with economic importance. This study aims to comprehensively identify secondary metabolite biosynthetic gene clusters within H. annuus using bioinformatics tools, shedding light on the functions of the enzymes involved. In this study, the plantiSMASH software was utilized to predict secondary metabolite biosynthetic gene clusters in H. annuus. The results from plantiSMASH were analyzed to identify the biosynthetic gene clusters for secondary metabolites on each chromosome. The biological and molecular functions of the enzymes within these clusters were predicted using data from the relevant articles. According to the obtained data, H. annuus lacks a biosynthetic gene cluster on chromosomes four, seven, and fifteen. The identified gene clusters in this plant are polyketide, saccharide, saccharide-terpene, alkaloid, putative, and terpene. The enzyme categories found in secondary metabolite biosynthetic gene clusters include Methyltransferase, Ketosynthase, Glycosyltransferase, BAHD acyltransferase, Dioxygenase, CoA-ligase, Epimerase, PRISE enzymes, Prenyltransferase, Oxidoreductase, Aminotransferase, Copper amine oxidase, Cytochrome P450, Terpene synthase, and Pictet-Spengler enzyme (Bet v1). This comprehensive analysis provides a foundation for further investigations into the biosynthesis of secondary metabolites in H. annuus, offering valuable insights for researchers exploring the medicinal and pharmaceutical potential of this plant species. © 2024 SAAB
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    In silico genome-wide analysis of Citrus sinensis (L.) Osbeck NHX and KEA genes and their roles in abiotic stress
    (Springer Science and Business Media Deutschland GmbH, 2024) Öz U.
    Citrus sinensis (L.) Osbeck is a valuable plant belonging to the Rutaceae family. Stress is induced in plants by abiotic factors such as drought, salinity, and temperature. The monovalent cation proton antiporter (CPA) superfamily, which includes the K+efflux antiporter (KEA) and Na+/H+exchanger (NHX) genes, plays a crucial role in the regulation of physiological events. This study aims to identify the KEA and NHX genes of C. sinensis and elucidate the roles of these genes in the response to abiotic stress. For this purpose, phylogenetic structure, distribution of chromosomes, gene duplications, gene and protein structures, cis-acting elements, functional gene ontologies, targeted miRNAs, and in silico PCR primer searches were performed using CsNHX and CsKEA sequences. Two KEA and fifty-five NHX were identified as a result of the analysis. Nine of the fifty-five genes (CsNHX5, CsNHX11, CsNHX12, CsNHX17, CsNHX27, CsNHX28, CsNHX47,CsNHX48, and CsNHX55) have been identified as playing a role in the stress response. On the phylogenetic tree, NHX genes were observed to be divided into three distinct clusters. The existence of multiple segmental and tandem duplications in the CsNHX genes has been demonstrated. Stress-related motifs were identified in the promoter regions of CsKEA and CsNHX by cis-acting element analysis, while stress-related miRNAs were identified by miRNA analysis. Consequently, KEA genes are responsible for transport, but they may also play a role in abiotic stress, as they contain cis-acting elements involved in the stress response and are targeted by miRNAs associated with stress. In addition, it has been determined that CsNHX5, which plays a role in the stress response, has the potential to be used in future transgenic plant production studies as it satisfies the PCR in silico criteria. © The Author(s), under exclusive licence to Botanical Society of Sao Paulo 2024.