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    Computational study of the plastid rRNA methyl transferase (CMAL) gene in higher plants and its role in drought and salt stresses
    (Springer, 2025) Kurt, Firat; Filiz, Ertugrul; Aydin, Adnan
    This study uses a bioinformatic approach to investigate plastid rRNA methyltransferase (CMAL) genes in four plant species (Arabidopsis thaliana, Oryza sativa, Glycine max, Zea mays). Furthermore, the gene expression levels of the CMAL gene of maize and soybean plants under drought and salt stress were investigated using RT-qPCR. We found differences between monocot and dicot CMALs, observed structural variations among species, and revealed a close evolutionary relationship between dicots and bacteria. CMAL genes show dynamic regulation in response to heat and drought stress, with maize showing tissue-specific variability. Specifically, the ZmCMAL gene in maize has a potential role in nutrient uptake and soil-related challenges, whereas AtCMAL in A. thaliana is involved in several cellular processes based on protein interactions. In a wet-lab study, ZmCMAL exhibited a fluctuating expression pattern under salt stress, with its ability to cope decreasing at higher salt concentrations. Meanwhile, GmCMAL was sensitive to both drought and salt, displaying an adaptive increase in expression as salt stress intensified. The promoter regions of CMAL genes predominantly contain cis-elements linked to abiotic stress and hormone responses, indicating their potential involvement in auxin-related pathways in cellular metabolism. These findings shed light on the regulatory role of CMAL genes in plants and their responses to stresses.
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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.