Browsing by Author "Horuz, Erdoğan"

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    Pubmed
    Comparative bioinformatics analysis and abiotic stress responses of expansin proteins in Cucurbitaceae members: watermelon and melon.
    (2023-03-01T00:00:00Z) İncili, Çınar Yiğit; Arslan, Büşra; Çelik, Esra Nurten Yer; Ulu, Ferhat; Horuz, Erdoğan; Baloglu, Mehmet Cengiz; Çağlıyan, Ebrar; Burcu, Gamze; Bayarslan, Aslı Ugurlu; Altunoglu, Yasemin Celik
    Watermelon and melon are members of the Cucurbitaceae family including economically significant crops in the world. The expansin protein family, which is one of the members of the cell wall, breaks down the non-covalent bonds between cell wall polysaccharides, causing pressure-dependent cell expansion. Comparative bioinformatics and molecular characterization analysis of the expansin protein family were carried out in the watermelon (Citrullus lanatus) and melon (Cucumis melo) plants in the study. Gene expression levels of expansin family members were analyzed in leaf and root tissues of watermelon and melon under ABA, drought, heat, cold, and salt stress conditions by quantitative real-time PCR analysis. After comprehensive searches, 40 expansin proteins (22 ClaEXPA, 14 ClaEXPLA, and 4 ClaEXPB) in watermelon and 43 expansin proteins (19 CmEXPA, 15 CmEXPLA, 3 CmEXPB, and 6 CmEXPLB) in melon were identified. The greatest orthologous genes were identified with soybean expansin genes for watermelon and melon. However, the latest divergence time between orthologous genes was determined with poplar expansin genes for watermelon and melon expansin genes. ClaEXPA-04, ClaEXPA-09, ClaEXPB-01, ClaEXPB-03, and ClaEXPLA-13 genes in watermelon and CmEXPA-12, CmEXPA-10, and CmEXPLA-01 genes in melon can be involved in tissue development and abiotic stress response of the plant. The current study combining bioinformatics and experimental analysis can provide a detailed characterization of the expansin superfamily which has roles in growth and reaction to the stress of the plant. The study ensures detailed data for future studies examining gene functions including the roles in plant growth and stress conditions.
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    Pubmed
    Comparative genomic analysis of expansin superfamily gene members in zucchini and cucumber and their expression profiles under different abiotic stresses.
    (2021-12-01T00:00:00Z) Arslan, Büşra; İncili, Çınar Yiğit; Ulu, Ferhat; Horuz, Erdoğan; Bayarslan, Aslı Ugurlu; Öçal, Mustafa; Kalyoncuoğlu, Elif; Baloglu, Mehmet Cengiz; Altunoglu, Yasemin Celik
    Zucchini and cucumber belong to the Cucurbitaceae family, a group of economical and nutritious food plants that is consumed worldwide. Expansin superfamily proteins are generally localized in the cell wall of plants and are known to possess an effect on cell wall modification by causing the expansion of this region. Although the whole genome sequences of cucumber and zucchini plants have been resolved, the determination and characterization of expansin superfamily members in these plants using whole genomic data have not been implemented yet. In the current study, a genome-wide analysis of zucchini () and cucumber () genomes was performed to determine the expansin superfamily genes. In total, 49 and 41 expansin genes were identified in zucchini and cucumber genomes, respectively. All expansin superfamily members were subjected to further bioinformatics analysis including gene and protein structure, ontology of the proteins, phylogenetic relations and conserved motifs, orthologous relations with other plants, targeting miRNAs of those genes and in silico gene expression profiles. In addition, various abiotic stress responses of zucchini and cucumber expansin genes were examined to determine their roles in stress tolerance. and from cucumber and from zucchini can be candidate genes for abiotic stress response and tolerance in addition to their roles in the normal developmental processes, which are supported by the gene expression analysis. This work can provide new perspectives for the roles of expansin superfamily genes and offers comprehensive knowledge for future studies investigating the modes of action of expansin proteins.
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    Pubmed
    HSF and Hsp Gene Families in sunflower: a comprehensive genome-wide determination survey and expression patterns under abiotic stress conditions.
    (2023-05-08T00:00:00Z) Ceylan, Yusuf; Altunoglu, Yasemin Celik; Horuz, Erdoğan
    Sunflowers belong to the Asteraceae family, which comprises nutrimental and economic oilseed plants. Heat shock proteins (Hsps) are protein families vital for all organisms' growth and survival. Besides the ordinary conditions, the expression of these proteins ascends during abiotic stress factors such as high temperature, salinity, and drought. Using bioinformatics approaches, the current study identified and analyzed HSF and Hsp gene family members in the sunflower (Helianthus annuus L.) plant. HSF, sHsp, Hsp40, Hsp60, Hsp70, Hsp90, and Hsp100 domains were analyzed in the sunflower genome, and 88, 72, 192, 52, 85, 49, and 148 genes were identified, respectively. The motif structures of the proteins in the same phylogenetic tree were similar, and the α-helical form was dominant in all the protein families except for sHsp. The estimated three-dimensional structure of 28 sHsp proteins was determined as β-sheets. Considering protein-protein interactions, the Hsp60-09 protein (38 interactions) was found to be the most interacting protein. The most orthologous gene pairs (58 genes) were identified between Hsp70 genes and Arabidopsis genes. The expression analysis of selected genes was performed under high temperature, drought, and high temperature-drought combined stress conditions in two sunflower cultivars. In stress conditions, gene expressions were upregulated for almost all genes in the first half and first hours at large. The expressions of HanHSF-45 and HanHsp70-29 genes were raised in two cultivars under high temperature and high temperature-drought combined stress conditions. This study presents a blueprint for subsequent research and delivers comprehensive knowledge of this vital protein domain.
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    Pubmed
    Investigation of the expansin gene family in sugar beet (Beta vulgaris) by the genome-wide level and their expression responses under abiotic stresses.
    (2023-08-29) Faris Abdulkhadum Al-Mamoorı, Dima; Celik Altunoglu, Yasemin; Horuz, Erdoğan; Özkan Kök, Büşra
    Sugar beet (Beta vulgaris ssp. vulgaris) is primarily used in sugar production worldwide. Expansins are a gene family of cell wall proteins effective in regulating cell wall structure. They also participate in developmental stages, including cell and leaf growth, root development, and fruit ripening. This study comprehensively characterizes the expansin gene family members found in the sugar beet genome. In addition, in silico expression analysis of sugar beet expansin genes under variable abiotic stress conditions and expression profiles of expansin genes under combined drought and heat stresses by the qRT-PCR method were evaluated in the study. A total of 31 sugar beet expansin genes were identified. BvuEXLA-02 and BvuEXLB-02 genes can have abiotic stress tolerance roles besides their roles in normal development. Determining the properties of sugar beet expansin, family members can help enable the cellulose hydrolysis mechanism and raise plant biomass. Elucidating expression profiles of the sugar beet expansin genes under variable stress conditions can support improving plant productivity. The results of the current study may also contribute to the deep understanding of sugar beet expansin genes in the future.
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    Şeker pancarında (beta vulgaris l.) ısı şoku proteinlerinin ın sılıco analizleri ve kuraklık-sıcaklık stresinde gen ekspresyonlarının araştırılması
    (Fen Bilimleri Enstitüsü, 2022-06) Horuz, Erdoğan
    Isı şoku proteinleri (Hsp) sıcaklık, kuraklık, tuzluluk, soğuk, UV ışığı ve oksidasyon gibi birçok başka stres altında ve normal koşullarda önemli fonksiyonlara sahip proteinlerdir. Isı şoku proteinlerinin şaperonlar olarak işlev görmesinin yanında denatüre proteinlerin yeniden katlanmasına, yeni oluşan polipeptitlerin katlanmasına ve denatüre protein agregatlarının yeniden çözülmesine yardımcı olur. Şeker pancarı (Beta vulgaris L.) şeker üretiminde, alkol üretiminde, hayvan yemi ve gübre yapımında kullanılan ekonomik değeri yüksek bir bitkidir. Şeker pancarı genom dizilimi 2014 yılında belirlenmiştir ve bu genom bilgileri kullanılarak 334 (42 adet sHsp, 108 adet Hsp40, 36 adet Hsp60, 29 adet Hsp70, 13 adet Hsp90 ve 106 adet Hsp100) adet BvHsp geni saptanmıştır. BvHsp genleri kromozom üzerinde rastgele dağılım göstermiş ve en fazla BvHsp geninin kromozom 6 üzerinde olduğu belirlenmiştir. BvHsp genlerinde toplam 77 çift tandem ve 58 çift segmental duplikasyon tespit edilmiştir. Şeker pancarında 47 adet Hsp geninin intron içermediği belirlenmiştir. Şeker pancarı Hsp ailesinin evrimini anlamak için Arabidopsis, soya, çeltik ve kavak arasında sinteni analizi yapılmıştır. BvHsp genlerinde en fazla ortolog sayısı 323 çift ile soyada belirlenmiştir. Moleküler evrimsel analiz, BvHsp genlerinin evriminin negatif seleksiyona uğradığını göstermiştir. Farklı biyoinformatik yöntemler kullanılarak gen ontolojileri, hedef miRNA’ları, filogenetik ilişkileri, korunmuş motifleri, tahmini üç boyutlu protein yapıları ve açık veri tabanlarından elde edilen sıcaklık, tuz, ABA ve ışık streslerine ait transkriptom verileri kullanılarak bu genlerin ifade profilleri incelenmiştir. Ayrıca transkriptom analizi sonucunda seçilen 12 adet BvHsp geninin kuraklık, sıcaklık ve kombine strese karşı yaprak dokusundaki gen ifade düzeyleri, eş zamanlı PZR ile saptanmıştır. Seçilen bu genler arasından BvHsp70-22 ve BvHsp90-03 genlerinin kuraklık, sıcaklık ve sıcaklık-kuraklık kombine strese karşı kuraklığa hassas, dayanıklı ve yabani türde ifadelerinin büyük ölçüde arttığı belirlenmiştir. Bu genlerin kuraklık durumunda erken cevap oluşturabileceği düşünülebilir. Çalışmamız kuraklık, sıcaklık ve kombine streslere dayanıklı türlerin geliştirilmesine ve mahsülde kuraklık toleransının iyileştirilmesine katkıda bulunabilir