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    Antimicrobial peptides Snakin/GASA gene family in sorghum (Sorghum bicolor): Genome-wide identification and bioinformatics analyses
    (Elsevier, 2020) Filiz, Ertugrul; Kurt, Firat
    Antimicrobial peptides (AMPs) are important biomolecules in plant innate immunity and snakins (SNs) are one of them. In this study, SN genes were first identified in sorghum (Sorghum bicolor, Sb) genome and analyzed using bioinformatical approaches. A total of 12 SbSN genes were found and peptide chain lengths were between 93 and 137 amino acids. In addition, it was found that all SN proteins contained the GASA (PF02704) domain structure, conserved cysteine residues and were basic character. According to GO annotation data, SbSN proteins were found to be commonly associated with hormone response in biological processes. When the promoter regions were examined, it was found that there were 16 types of transcription factor binding sites, proving dynamic gene regulation. According to digital expression data, SbSN genes were found to exhibit various expression profiles depending on the six tissue types. According to co-expression data consisting of 573 genes, SbSN genes were found to be positively associated with protein kinase genes and showed direct connection with them. In terms of the predicted 3D structures and surface pockets, SbSN proteins were found to exhibit structural diversity. As a result, the findings will contribute to the understanding of SN proteins in plants, particularly in sorghum plant.
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    Expression and Co-expression Analyses of WRKY, MYB, bHLH and bZIP Transcription Factor Genes in Potato (Solanum tuberosum) Under Abiotic Stress Conditions: RNA-seq Data Analysis
    (Springer, 2021) Filiz, Ertugrul; Kurt, Firat
    Transcription factors regulate gene expression depending on environmental and extracellular stimuli and signals from other cells. WRKY, MYB, bHLH and bZIP transcription factors (TFs) are one of the most important TF families in plants. Therefore, WRKY, MYB, bHLH and bZIP TFs in potato (Solanum tuberosum, St) genome under heat, salinity and drought stresses were investigated in terms of expression, co-expression and differentially expressed genes (DEGs). A total of 26,172 genes were collectively analysed in the study and four genes were identified as common DEGs, highly expressed under each abiotic stress. The salt stress was found to induce StbHLH and StMYB TFs whereas the heat stress activated StWRKY and StbZIP TFs. Moreover, the top three highly expressed genes were identified for each TF family under each stress condition. Since some of the genes were unannotated, their functional predictions including unannotated common DEGs were made based on orthologue gene comparisons in Arabidopsis. TFs involved in gene regulation along with four common DEGs were identified in co-expression analyses. As a result, 12 bHLH, 5 bZIP, 9 MYB and 14 WRKY TFs were detected in co-expression networks of the four common DEGs. Regarding DEGs, PGSC0003DMT400040149 was generally found to be involved in sulphur metabolism. PGSC0003DMT400016360 and PGSC0003DMT400007351 gene networks were found to contain more than 400 overlapping genes, suggesting that they may have roles in similar pathways in response to abiotic stress conditions in potato. Lastly, we found that MYB-bHLH cross talking may occur in response to abiotic stresses in potato. The findings are particularly important to understand roles of TFs under the mentioned stresses in potato.
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    Genome-wide identification of serine acetyltransferase (SAT) gene family in rice (Oryza sativa) and their expressions under salt stress
    (Springer, 2021) Kurt, Firat; Filiz, Ertugrul; Aydin, Adnan
    Background Assimilation of sulfur to cysteine (Cys) occurs in presence of serine acetyltransferase (SAT). Drought and salt stresses are known to be regulated by abscisic acid, whose biosynthesis is limited by Cys. Cys is formed by cysteine synthase complex depending on SAT and OASTL enzymes. Functions of some SAT genes were identified in Arabidopsis; however, it is not known how SAT genes are regulated in rice (Oryza sativa) under salt stress. Methods and results Sequence, protein domain, gene structure, nucleotide, phylogenetic, selection, gene duplication, motif, synteny, digital expression and co-expression, secondary and tertiary protein structures, and binding site analyses were conducted. The wet-lab expressions of OsSAT genes were also tested under salt stress. OsSATs have underwent purifying selection. Segmental and tandem duplications may be driving force of structural and functional divergences of OsSATs. The digital expression analyses of OsSATs showed that jasmonic acid (JA) was the only hormone inducing the expressions of OsSAT1;1, OsSAT2;1, and OsSAT2;2 whereas auxin and ABA only triggered OsSAT1;1 expression. Leaf blade is the only plant organ where all OsSATs but OsSAT1;1 were expressed. Wet-lab expressions of OsSATs indicated that OsSAT1;1, OsSAT1;2 and OsSAT1;3 genes were upregulated at different exposure times of salt stress. Conclusions OsSAT1;1, expressed highly in rice roots, may be a hub gene regulated by cross-talk of JA, ABA and auxin hormones. The cross-talk of the mentioned hormones and the structural variations of OsSAT proteins may also explain the different responses of OsSATs to salt stress.
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    Sulfite Reductase (SiR) Gene in Rice (Oryza sativa): Bioinformatics and Expression Analyses Under Salt and Drought Stresses
    (Springer, 2021) Kurt, Firat; Filiz, Ertugrul; Aydin, Adnan
    Rice sulfite reductase (OsSiR) is important protein in reducing sulfite to sulfide. In this paper, it is aimed to shed light on OsSiR's probable structure, function, and expression using in silico methods and test its responses under drought and salt stresses. Moreover, it was also analyzed if OsSiR was structurally different from other SiR proteins. We estimated that OsSiR lacks ribbon-helix-helix DNA-binding motif allowing it to bind to DNA; therefore, it was probably localized in stroma as a non-nucleoid-type protein. Also, we found that OsSiR expression was regulated by JA in roots and by crosstalk of JA and ABA in shoots. RT-qPCR results showed that there was 20% increase in the expression of OsSiR at 3rd h of the salt treatment. However, OsSiR was downregulated when exposed to drought stress and salt stress for longer periods of time, respectively. OsSiR has a high post-translational potential because of its high phosphorylation sites. This may be originating from the most prevalent residue, Gly, facilitating its binding to phosphates in OsSiR. Our docking results showed that ligand binding residues of OsSiR (Arg159, Thr162, Gln167, and Pro501) were also active site residues of OsSiR. Both two domains of OsSiR interacted with sulfite and the number of the residues in 4Fe-4S domain (PF01077) was higher. The findings in this study are important in terms of structural and expressional studies of rice SiR (OsSiR) and can be used for SiR proteins in sorghum (Sorghum bicolor), maize (Zea mays), and foxtail millet (Setaria italica), which are closely related and highly similar to OsSiR in terms of sequence and predicted 3D structure.
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    Wall associated kinases (WAKs) gene family in tomato (Solanum lycopersicum): Insights into plant immunity
    (Elsevier, 2020) Kurt, Firat; Kurt, Baris; Filiz, Ertugrul
    Wall-associated kinases (WAKs), a subgroup of receptor-like kinases (RLKs), are localized on the cell wall and have roles in pathogen recognition and signal transduction in plants due to their interactions with pectin molecules. In this study, it was aimed at characterizing WAK genes in tomato (Solanum lycopersicum) using bioinformatics approaches. In this respect, all SlWAKs were identified as RD-kinases and all motifs in eukaryotic protein kinase (ePK) subdomains in SlWAKs were determined. Motif, sequence, and protein structure analyses showed that Solyc07g007020.2 and Solyc09g014740.2 are more distinctive proteins among SlWAKs suggesting that they may be involved in very specific pathways in plant defense system and may have different ligand selectivity. Other than that, we found that miRNAs silencing SlWAK genes are involved in various pathways and controlled with complex biological processes. Docking analyses showed that oligomeric pectin has higher binding affinity to SlWAK1. The findings are important for plant protection studies aiming at identifying roles of different WAKs in plant immune system, particularly in tomato.