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Öğe Ammonium transporter 1 (AMT1) gene family in tomato (Solanum lycopersicum L.): Bioinformatics, physiological and expression analyses under drought and salt stresses(Academic Press Inc Elsevier Science, 2020) Filiz, Ertugrul; Akbudak, M. AydinNitrogen (N) is an essential macronutrient for plants, and mainly taken from the soil as ammonium (NH+4). It is particularly transported into the plants by AMmonium Transporters (AMTs), which are plasma membrane proteins. In the present study, genome-wide identification, physiological and expression analyses of tomato (Solanum lycopersicum L.) ammonium transporters 1 (SlAMT1) genes under drought and salt stresses were performed. Sequence analyses revealed the presence of variations in SlAMT1s at nucleotide and protein levels. While all the SlAMT1s comprise an ammonium transporter domain (PF00909), the numbers of their transmembrane helices were found to be diverse. Digital expression analyses proved that SlAMT1-3 gene had different expression patterns compared to the others, suggesting its functional diversities. The expression analyses revealed that SlAMT1 genes were 0.16 and 5.94 -fold down-regulated under drought and salt stresses, respectively. The results suggested that expression of SlAMT1 genes were adversely affected by abiotic stress conditions.Öğe Antimicrobial peptides Snakin/GASA gene family in sorghum (Sorghum bicolor): Genome-wide identification and bioinformatics analyses(Elsevier, 2020) Filiz, Ertugrul; Kurt, FiratAntimicrobial 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.Öğe The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses(Mdpi, 2020) Faraji, Sahar; Filiz, Ertugrul; Kazemitabar, Seyed Kamal; Vannozzi, Alessandro; Palumbo, Fabio; Barcaccia, Gianni; Heidari, ParvizMembers of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs in the durum wheat (Triticum turgidum ssp. durum) genome, which resulted in the identification of 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had the highest number of TtAP2s/ERFs. Furthermore, a duplication assay of TtAP2s/ERFs demonstrated that 70 duplicated gene pairs had undergone purifying selection. According to RNA-seq analysis, the highest expression levels in all tissues and in response to stimuli were associated with DRF and ERF subfamily genes. In addition, the results revealed that TtAP2/ERF genes have tissue-specific expression patterns, and most TtAP2/ERF genes were significantly induced in the root tissue. Additionally, 13 TtAP2/ERF genes (six ERFs, three DREBs, two DRFs, one AP2, and one RAV) were selected for further analysis via qRT-PCR of their potential in coping with drought and salinity stresses. The TtAP2/ERF genes belonging to the DREB subfamily were markedly induced under both drought-stress and salinity-stress conditions. Furthermore, docking simulations revealed several residues in the pocket sites of the proteins associated with the stress response, which may be useful in future site-directed mutagenesis studies to increase the stress tolerance of durum wheat. This study could provide valuable insights for further evolutionary and functional assays of this important gene family in durum wheat.Öğe Characterization of ZmSnRK1 genes and their response to aphid feeding, drought and cold stress(Springer, 2024) Akbudak, M. Aydin; Yildiz, Kubra; Cetin, Durmus; Filiz, Ertugrul; Yukselbaba, Utku; Srivastava, VibhaThe SnRK1 complex in plants regulates metabolism in response to environmental stresses and glucose depletion, for stress adaptation and energy homeostasis. Through phosphorylation of various targets, SnRK1 orchestrates intricate regulatory mechanisms involved in autophagy, nutrient remobilization, and TOR activity inhibition, showcasing its pivotal role in coordinating plant metabolism and stress responses. The present study aimed to identify members of the SnRK1 gene family in the maize genome and characterize them using bioinformatics and expression analyses under aphid feeding, drought, and cold stress. The focus of the study was to conduct a comprehensive analysis towards determining gene diversity of ZmSnRK1 genes, constructing intricate 3D structures, and identifying stress-related cis-elements. Four SnRK1 genes were identified, which were named ZmSnRK1.1, ZmSnRK1.2, ZmSnRK1.3, and ZmSnRK1.4. The SnRK1 proteins were found to have a distribution of conserved motifs; however, the distinction between monocots and dicots in the phylogenetic tree was clearly demonstrated. Analysis of the promoter region revealed that the ZmSnRK1 genes contain stress-related cis-elements. Compared to the control, ZmSnRK1.3 significantly upregulated in response to aphid feeding and cold stress, while ZmSnRK1.2 showed elevated expression under drought conditions. The expression of the other two genes under these treatments was generally unperturbed. The findings of this study are poised to establish a valuable scientific foundation for future research on the roles of the SnRK1 gene family in plants, providing valuable insights for enhancing genetic resilience to stress and optimizing yield traits.Öğe The Conservation of VIT1-Dependent Iron Distribution in Seeds (vol 10, 907, 2019)(Frontiers Media Sa, 2020) Eroglu, Seckin; Karaca, Nur; Vogel-Mikus, Katarina; Kavcic, Anja; Filiz, Ertugrul; Tanyolac, Bahattin[Abstract Not Available]Öğe Exploration of two major boron transport genes BOR1 and NIP5;1 in the genomes of different plants(Taylor & Francis Ltd, 2020) Ozyigit, Ibrahim Ilker; Filiz, Ertugrul; Saracoglu, Ibrahim Adnan; Karadeniz, SedatBoron (B) is an essential plant micronutrient but studies regarding its transport are still limited to a few plants. This work identified two major B transport sequences in plants, NIP5;1 boric acid channel protein and BOR1 transporter. 80 BOR1 and 34 NIP5;1 homologs were identified in 18 different plant genomes. BOR1 homologs had a HCO3-transporter domain, 649-737 amino-acid residues with mainly basic nature, putative 8-11 transmembrane domains (TMDs) and 11-13 exons. NIP5;1 homologs had a MIP family domain, 294-311 amino-acid residues with basic nature, 5-6 putative TMDs and 3-5 exons. Tyrosine-based motif, acidic di-leucine motif and lysine residue, reported for polarity, vacuolar sorting and B-dependent degradation, were identified in BOR1 homologs. Two NPA motifs and an ar/R selectivity filter with AIGR residues, reportedly essential in B transport, were also found in NIP5;1 homologs. Two NPA motifs in AtNIP5;1 and OsNIP3;1 homologs were NPS and NPV, whereas in sequences homologous to AtNIP6;1 were NPA/V. Besides, ar/R selectivity filters were identified with A(N/S/T)IGR residues in NIP5;1 and NIP3;1 homologs. The BOR1 and NIP5;1 model structures were mainly conserved. Under different perturbations, Arabidopsis thaliana NIP5;1 and NIP6;1 genes demonstrated similar expression patterns although they act in different tissues, suggesting a common regulatory mechanism, whereas BOR1 showed a different expression pattern. BOR1 was substantially expressed in primary root, radicle and flower; NIP5;1 in primary root and roots, and NIP6;1 in petiole. NIP5;1, 6;1 and BOR1 expression in other plant organs implied their involvement in different pathways in addition to B uptake and its mobilization.Öğe 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, FiratTranscription 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.Öğe Genes involved in mRNA surveillance are induced in Brachypodium distachyon under cadmium toxicity(Springer, 2021) Aksoy, Emre; Uncu, Ali Tevfik; Filiz, Ertugrul; Orman, Sule; Cetin, Durmus; Akbudak, M. AydinBackground Cd accumulation in plant cells results in dramatic problems including oxidative stress and inhibition of vital enzymes. It also affects mineral uptakes by disrupting membrane permeability. Interaction among Cd and other plant nutrient elements changes the nutritional contents of crops and reduces their yield. Methods and results In the present study, Cd stress in Brachypodium distachyon led to the upregulation of some heavy metal transport genes (influx or efflux) encoding cation-efflux proteins, heavy metal-associated proteins and NRAMP proteins. The Arabidopsis orthologs of the differentially expressed B. distachyon genes (DEGs) under Cd toxicity were identified, which exhibited Bradi4g26905 was an ortholog of AtALY1-2. Detailed co-expression network and gene ontology analyses found the potential involvement of the mRNA surveillance pathway in Cd tolerance in B. distachyon. These genes were shown to be downregulated by sulfur (S) deficiency. Conclusions This is the first transcriptomic study investigating the effect of Cd toxicity in B. distachyon, a model plant for genomic studies in Poaceae (Gramineae) species. The results are expected to provide valuable information for more comprehensive research related to heavy metal toxicity in plants.Öğe Genetic diversity and phylogenetic analysis of Robinia pseudoacacia L. populations using ISSR markers, ITS1 and trnL-F intergenic spacer sequences(Czech Academy Agricultural Sciences, 2024) Uras, Mehmet Emin; Filiz, Ertugrul; Sen, Ugur; Ozyigit, Ibrahim IlkerRobinia pseudoacacia L. is a deciduous tree planted almost all around the world for a wide variety of uses such as ornamental in urban ecosystems and forest trees in afforestation. This study aims to evaluate the genetic diversity and phylogenetic relations of R. pseudoacacia using some selected populations in Istanbul and Kocaeli cities. For this aim, molecular marker-assisted and DNA sequence-based analyses were performed. According to the results, nine of 15 inter simple sequence repeats (ISSR) primers gave clear and distinguishable bands with a total of 100 loci. The percentage of polymorphic loci (PPL) was calculated as 100% for multi-populations and ranged from 46% to 76% for single populations. Nei's gene diversity value was calculated between 0.165 and 0.251. The lowest and highest PPL were found in populations of Barbaros Boulevard and Dilovasi District, respectively. Population structure analysis showed seven different genetic structures for five populations. Internal transcribed spacer 1 region (ITS1) and trnL-F intergenic spacer region were used to examine the phylogenetic relationships of R. pseudoacacia, and both regions showed a high discriminative power at the family level. Based on the findings, R. pseudoacacia, as a forest tree residing in the urban ecosystem, may face the risk of population decline in the upcoming years due to its moderate/low genetic diversity and susceptibility to environmental pressures.Öğe Genome-wide exploration and analysis of plant stress-responsive CAMTA transcription factor genes in Brachypodium distachyon and their expression patterns under environmental challenges(Elsevier, 2024) Akbudak, M. Aydin; Cetin, Durmus; Filiz, Ertugrul; Srivastava, VibhaCalmodulin-binding transcription activators (CAMTAs) is a family of transcriptional factors, which are highly sensitive to various stressors and hormone signals. They are involved in regulating plant growth, development, stress response, and have distinct biological roles in different plant compartments. Although the gene families coding the CAMTA transcription factors have been identified and functionally characterized in many plant species, it has not been previously reported in Brachypodium distachyon, which is a model organism for genomic research in cereals and grasses. In the present study, seven novel CAMTA genes were identified in the B. distachyon genome, all of which contain the CG-1 (pfam03859) domain. Their sequence details were provided with exon numbers ranging from 10 to 13 and protein length varying from 836 to 1034 amino acid residues. All BdCAMTA proteins, except BdCAMTA1, were found to be acidic and localized to the nucleus. The BdCAMTA genes exhibit diverse responses to cold, drought, and salinity stresses, without being specific to any stress. Therefore, upcoming studies should prioritize the investigation of molecular mechanisms governing functional specificity and redundancy among individual members of CAMTA. These findings establish a valuable scientific foundation for future research concerning the roles of the CAMTA gene family in plants. (c) 2024 SAAB. Published by Elsevier B.V. All rights reserved.Öğe 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, AdnanBackground 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.Öğe Genome-wide investigation of proline transporter (ProT) gene family in tomato: Bioinformatics and expression analyses in response to drought stress(Elsevier France-Editions Scientifiques Medicales Elsevier, 2020) Akbudak, M. Aydin; Filiz, ErtugrulProline has various functions in plants, such as growth, development and stress response to biotic and abiotic factors. Therefore, proline accumulation and transport are vital for crop production in higher quality and quantity. The present study addresses genome-wide identification and bioinformatics analyses of tomato (Solanum lycopersicum) proline transporter (ProT) genes and their expression profiles under drought stress. The analyses indicated four novel ProT genes (SlProTs) in the tomato genome and their protein lengths ranged from 439 to 452 amino acid residues. All SlProTs contained a PF01490 (transmembrane amino acid transporter protein) domain and seven exons, and they had a basic p1. The phylogeny analysis proved that monocot-dicot divergence was not present and the SlProT proteins were distinct from the ProT proteins in monocots and Arabidopsis. Based on the digital expression analysis, SlProT1 and SlProT2 genes seemed to be more active than the others in response to abiotic stress conditions. However, detected by RT-qPCR, the expression levels of all SlProT genes under drought stress were similar. The promotor analyses of SlProT genes revealed that they contained many transcription factors binding sites in cis-elements, such as MYB, Dof, Hox, bZIP, bHLH, AP2/ERF and WRKY. Finally, our findings could contribute to the understanding of SlProT genes and proline metabolism in plants.Öğe Investigation of PIC1 (permease in chloroplasts 1) gene's role in iron homeostasis: bioinformatics and expression analyses in tomato and sorghum(Springer, 2020) Filiz, Ertugrul; Aydin Akbudak, M.Iron (Fe) is a crucial micronutrient in plant metabolism; thus, iron homeostasis is critical for plant development. Permease in chloroplast 1 (PIC1) is the first protein determined in the chloroplast playing a role iron homeostasis. In the present study, the PIC1 gene was investigated at a genome-wide scale in four plant genomes; Arabidopsis, tomato, maize and sorghum. Based on the gene ontology database, 21 GO terms were found related to the PIC1 gene, most of which were involved in iron hemostasis and transport. The digital expression data revealed that the expression of the majority of PIC1 genes (62.5%) in Arabidopsis decreased under abiotic stress conditions. Expression profiles of tomato PIC1 (SlPIC1) and sorghum PIC1 (SbPIC1) genes were also analyzed under salt and drought stress conditions using Real Time-quantitative PCR (RT-qPCR). Our wet-lab studies demonstrated that the SbPIC1 gene was down-regulated under salt and drought stresses in all tissues, while SlPIC1 was up-regulated in all but root tissue under drought stress. Some structural variations were detected in predicted 3D structures of PIC1 proteins and the structural similarity values varied between 0.23 and 0.35. Consequently, these results may contribute to the understanding of the PIC1 gene in iron transport and homeostasis in plants.Öğe Molecular Characterization of Prunus spinosa L. (Rosaceae) Populations from theWest Black Sea Region in Turkey Using Inter-simple Sequence Repeat Polymerase Chain Reaction(Springer, 2023) Gulay, Muhammed; Sevindik, Emre; Sofyalioglu, Erengul; Cayir, Muhammed Ebrar; Filiz, ErtugrulIn this study, molecular characterization of four Prunus spinosa populations was carried out using the inter-simple sequence repeat polymerase chain reaction (ISSR-PCR) marker method. Populations were collected from Bolu, Duzce and Zonguldak provinces in Turkey. After genomic DNA (gDNA) isolation from the populations, PCR amplification was performed using 13 ISSR primers. As a result of the study, 116 polymorphic bands were obtained and the polymorphism rate was determined as 81.89%. These results were based on the genetic distance matrix obtained in the NTSYS-pc package version 2.10. The results showed that the closest genotypes were DY2 and DY4, with a similarity value of 0.2037 between them. DY4 and BM1 are found to have a similarity value of 0.5641, which indicates that they are the two genotypes that differ most from one another. The mean polymorphism information content (PIC) value was determined as 0.3507 and the mean Nei's gene diversity (H) value was determined as 0.4559. In the unweighted pair group method with arithmetic mean (UPGMA) dendrogram, 13 populations were divided into two groups. According to principal component analysis (PCA), the first three eigen values explained 55% of the total variance in the population. As a result, the polymorphism rate was found to be very high with ISSR analysis, and the UPGMA dendrogram was compatible with the geographical distribution. The results of studies on P. spinosa populations using the ISSR analysis can be beneficial for cultivar development and further studies in the future.Öğe Pathogenesis related protein-1 (PR-1) genes in tomato (Solanum lycopersicum L.): Bioinformatics analyses and expression profiles in response to drought stress(Academic Press Inc Elsevier Science, 2020) Akbudak, M. Aydin; Yildiz, Sukran; Filiz, ErtugrulThe pathogenesis-related protein 1 (PR-1) gene family play important roles in the plant metabolism in response to biotic and abiotic stresses. The present study aimed genome-wide identification and bioinformatics analyses of PR-1 genes in tomato (Solanum lycopersicum L.). The analyses resulted in the identification of 13 novel SlPR-1 genes, each of which produce a protein belonging to the CAP superfamily (PF00188). The KEGG annotation analyses revealed that the SlPR-1 proteins functioned in the environmental information processing (09130). The expression patterns of the PR-1 genes and some stress-related physiological parameters were investigated in Fusarium oxysporum sensitive and tolerant tomato varieties under drought stress. The drought stress leaded upregulation of all SlPR-1 genes, reaching up to 50 folds. The results indicate that the SlPR-1 genes play active roles in response to drought. This is the first study exhibiting the expression profiles of SlPR-1 genes under an abiotic stress, drought, in tomato.Öğe Sulfite Reductase (SiR) Gene in Rice (Oryza sativa): Bioinformatics and Expression Analyses Under Salt and Drought Stresses(Springer, 2021) Kurt, Firat; Filiz, Ertugrul; Aydin, AdnanRice 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.Öğe Wall associated kinases (WAKs) gene family in tomato (Solanum lycopersicum): Insights into plant immunity(Elsevier, 2020) Kurt, Firat; Kurt, Baris; Filiz, ErtugrulWall-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.
