Yazar "Tombuloğlu, Hüseyin" seçeneğine göre listele
Listeleniyor 1 - 14 / 14
Sayfa Başına Sonuç
Sıralama seçenekleri
Öğe Assessment of genetic diversity and phylogenetic relationships of endangered endemic plant Barbarea integrifolia DC. (Brassicaceae) in Turkey(Tubitak Scientific & Technical Research Council Turkey, 2014) Filiz, Ertuğrul; Osma, Etem; Kandemir, Ali; Tombuloğlu, Hüseyin; Tombuloğlu, Güzin; Birbilener, Seda; Aydın, MehtapBarbarea integrifolia DC. ( Brassicaceae) is an endangered and endemic species located in Erzincan and Gumushane provinces of Turkey. In total, 27 individuals from 2 natural populations were assessed using the random amplified polymorphic DNA polymerase chain reaction ( RAPD- PCR) method coupled with sequence analysis of the internal transcribed spacer ( ITS1) rDNA region. Genetic accuracy of RAPD- PCR was tested with 25 RAPD primers, and it resulted in 115 clear and reproducible DNA fragments from 13 RAPD primers. Among these, 76 ( 66.1%) fragments were found to be polymorphic. According to the ITS1 analysis of B. integrifolia populations, the plants exhibited a relatively poor genetic diversity. In total, 60 ITS1 nucleotide sequences from the GenBank database with 2 newly identified ITS1 sequences from the Turkish populations were used to construct a maximum- likelihood tree. The lengths of ITS1 sequences of B. integrifolia were found to be 268 bp for population I and 271 bp for population II. ITS1 sequences of B. integrifolia species showed 97% sequence identity. Phylogenetic analysis revealed that Barbarea species were monophyletic and showed high bootstrap values. B. integrifolia had closer relationships with Cardamineae taxa, including Cardamine, Rorippa, and Armoracia. On the contrary, allied genus Nasturtium species were separated from Cardamineae taxa. The genetic information obtained from this study could be used for the development of conservation strategies not only for B. integrifolia but also for rare and endangered plant species.Öğe Assessment of miRNA expression profile and differential expression pattern of target genes in cold-tolerant and cold-sensitive tomato cultivars(Taylor & Francis Ltd, 2015) Koç, İbrahim; Filiz, Ertuğrul; Tombuloğlu, HüseyinMircroRNAs (miRNAs) are small non-coding RNAs about 21 nt in length. These short transcripts regulate developmental and stress responses in plants. Cold stress is one of the most restraining abiotic factors adversely affecting the plant yield. In the present study, some cold stress-related miRNAs (miR167, miR169, miR172, miR393 and miR397) in tomato (Solanum lycopersicum) were assessed at early time points (0, 1, 4 and 16 h) of cold exposure. Relative expression of miRNAs was measured by stem-loop quantitative reverse transcription polymerase chain reaction. The results showed that miR167, miR169, miR172 and miR393 were activated in the early time points of cold treatment. Especially, miR172 was found to have highest expression level. Furthermore, target genes of selected miRNAs were identified and their expression profiles were assessed between cold-sensitive and cold-tolerant cultivars of tomato. It was found that inferred expression patterns of target genes were differentiated between the cultivars. Analysis of cis-acting elements showed that miRNAs had stress-responsive elements. Meanwhile, since no miR393 sequence is available, putative miR393 sequence and its secondary structure were predicted in tomato. These results may provide a framework for further analysis in terms of understanding the response of miRNAs against cold stress in tomato.Öğe Characterization of wound-induced serine protease inhibitor (wip1) genes and proteins in Turkish maize varieties(Maik Nauka/Interperiodica/Springer, 2014) Filiz, Ertuğrul; Tombuloğlu, Hüseyin; Koç, İbrahim; Osma, EtemProtease inhibitors (PIs) are generally small proteins that have been identified in plants. The wip1 gene codes for wound-induced protein, which is similar to serine PIs of the Bowman-Birk family (BBIs). In this study, we analyzed 10 wip1 genes of Turkish maize varieties to understand the structure and characteristics of the wip1 genes and proteins in maize. We found that genetic variability of wip1 genes was higher (pi: 0.0173) than reported in previous studies. Tajima's D value was found to be positive (1.73), suggesting over-dominant selection in these loci. According to phylogenetic analysis of wip1 proteins, monocot and dicot BBIs were separated independently, and Turkish varieties were clustered with each other generally. The 3D structures of wip1 proteins indicated that several wip1 proteins had structural divergence in active loops, containing various numbers of cysteine residues ranging between 7 and 9. Particularly, Cys74 was identified in Kocbey and Gozdem varieties, whereas Cys98 was only in the Gozdem variety. Also, a critical serine residue (Ser98) was observed in two varieties - Antbey and Batem Efe. These results can contribute to understanding the role of wip1 genes and corresponding proteins in maize.Öğe Comparative analysis of embryo surrounding region (Esr-6) genes in Turkish maize varieties: sequencing and modeling(Soc Botanica Sao Paulo, 2016) Tombuloğlu, Hüseyin; Aydın, Mehtap; Filiz, ErtuğrulDefensins are cysteine-rich small proteins found in plants and animals. Esr-6 (embryo surrounding region-6), which is a kind of plant defensin gene, plays an important role in nutrition, defense, and signaling of embryo. In this study, Esr-6 genes in three Turkish maize varieties (TMVs) such as Safak, Sakarya, and Seker were sequenced and characterized. Open reading frame (ORF) and protein length of Esr-6 was found as 324 bp and 111 amino acids, respectively. All TMVs contained gamma-thionin family (PF00304) domain, and subcellular localizations were predicted as extracellular. Predicted signal peptide, mature protein, and acidic pro-domain were identified in all TMVs. Four most conserved motifs were identified, but only motif 1 was found to be related with gamma-thionin family. Eight conserved cysteine residues, which are the characteristics of defensins, were detected in all TMVs. In phylogenetic analysis, Esr-6 proteins were clearly diverged from other plant defensins with the highest bootstrap value (100 %). Predicted 3D structures of Esr-6 proteins were similar to each other, including one a-helix and two beta-sheets. Conserved cysteine residues, including Cys51, Cys55, Cys66, Cys73, Cys75, and Cys79, were detected in 3D structures of all TMVs. Our study showed that Esr-6 genes and their product are well conserved among TMVs.Öğe Comparative analysis of plant lycopene cyclases(Elsevier Sci Ltd, 2015) Koç, İbrahim; Filiz, Ertuğrul; Tombuloğlu, HüseyinCarotenoids are essential isoprenoid pigments produced by plants, algae, fungi and bacteria. Lycopene cyclase (LYC) commonly cyclize carotenoids, which is an important branching step in the carotenogenesis, at one or both end of the backbone. Plants have two types of LYC (beta-LCY and epsilon-LCY). In this study, plant LYCs were analyzed. Based on domain analysis, all LYCs accommodate lycopene cyclase domain (Pf05834). Furthermore, motif analysis indicated that motifs were conserved among the plants. On the basis of phylogenetic analysis, beta-LCYs and epsilon-LCYs were classified in beta and & groups. Monocot and dicot plants separated from each other in the phylogenetic tree. Subsequently, Oryza sativa Japonica Group and Zea mays of LYCs as monocot plants and Vitis vinifera and Solanum lycopersicum of LYCs as dicot plants were analyzed. According to nucleotide diversity analysis of beta-LCYand epsilon-LCYgenes, nucleotide diversities were found to be pi: 0.30 and pi: 0.25, respectively. The result highlighted beta-LCY genes showed higher nucleotide diversity than a-LCYgenes. LYCs interacting genes and their co-expression partners were also predicted using String server. The obtained data suggested the importance of LYCs in carotenoid metabolism. 3D modeling revealed that depicted structures were similar in O. sativa, Z mays, S. lycopersicum, and V. vinifera beta-LCYs and epsilon-LCYs. Likewise, the predicted binding sites were highly similar between O. sativa, Z mays, S. lycopersicum, and V. vinifera LCYs. Most importantly, analysis elucidated the V/IXGXGXXGXXXA motif for both type of LYC (beta-LCY and epsilon-LCY). This motif related to Rossmann fold domain and probably provides a flat platform for binding of FAD in O. sativa, Z mays, S. lycopersicum, and V vinifera beta-LCYs and epsilon-LCYs with conserved structure. In addition to lycopene cyclase domain, the V/IXGXGXXMOOCA motif can be used for exploring LYCs proteins and to annotate the function of unknown proteins containing lycopene cyclase domain. Overall results indicated that a high degree of conserved signature were observed in plant LYCs. (C) 2015 Elsevier Ltd. All rights reserved.Öğe Genome wide analysis of IQ67 domain (IQD) gene families in Brachypodium distachyon(2013) Filiz, Ertuğrul; Tombuloğlu, Hüseyin; Özyiğit, İbrahim İlkerIn plants, Ca2+ concentration is important for the regulation of developmental processes and responses against biotic and abiotic stress factors. The eukaryotic Ca2+ binding protein calmodulin (CaM: CALcium MODULating proteIN) was found in Arabidopsis which contains a characteristic plant-specific IQ67 (Ile, Glu) domain (IQD). In this study, a genome wide analysis was performed in Bracyhpodium distachyon to identify IQD genes. Using several bioinformatics tools, we determined 23 BdlQD genes which were distributed on all chromosomes and the highest gene number was detected on chromosome 2 including 12 IQD genes. 22 of the predicted proteins were considered to be basic proteins. Gene duplication analysis revealed that 8 of 23 BdlQD genes were involved in duplication event, either segmental or tandem. Phylogenetic analysis showed that two main groups were observed in joined tree with rice and Arabidopsis. Especially, monocot species (Brachypodium and rice) were grouped together with the highest bootstrap value (100%), whereas monocot and dicot species (Arabidopsis) were clustered with lower bootstrap values. Digital expression profile analysis indicated that the most of the BdlQD genes were expressed in leaves (8 genes) and flowers (6 genes), respectively. In conclusion, this comparative genomics analysis contributes to understanding IQD genes in grass species.Öğe Genome-wide analysis of IQ67 domain (IQD) gene families in Brachypodium distachyon(Southern Cross Publ, 2013) Filiz, Ertuğrul; Tombuloğlu, Hüseyin; Özyiğit, İbrahim İlkerIn plants, Ca2+ concentration is important for the regulation of developmental processes and responses against biotic and abiotic stress factors. The eukaryotic Ca2+ binding protein calmodulin (CaM: CALcium MODULating protelN) was found in Arabidopsis which contains a characteristic plant-specific IQ67 (Ile, Glu) domain (IQD). In this study, a genome wide analysis was performed in Bracyhpodium distachyon to identify IQD genes. Using several bioinformatics tools, we determined 23 BdIQD genes which were distributed on all chromosomes and the highest gene number was detected on chromosome 2 including 12 IQD genes. 22 of the predicted proteins were considered to be basic proteins. Gene duplication analysis revealed that 8 of 23 BdIQD genes were involved in duplication event, either segmental or tandem. Phylogenetic analysis showed that two main groups were observed in joined tree with rice and Arabidopsis. Especially, monocot species (Brachypodium and rice) were grouped together with the highest bootstrap value (100%), whereas monocot and dicot species (Arabidopsis) were clustered with lower bootstrap values. Digital expression profile analysis indicated that the most of the BdIQD genes were expressed in leaves (8 genes) and flowers (6 genes), respectively. In conclusion, this comparative genomics analysis contributes to understanding IQD genes in grass species.Öğe Genome-wide analysis of response to low sulfur (LSU) genes in grass species and expression profiling of model grass species Brachypodium distachyon under S deficiency(Tubitak Scientific & Technical Research Council Turkey, 2016) Tombuloğlu, Hüseyin; Ablazov, Abdugaffar; Filiz, ErtuğrulSulfur (S) affects the plant life cycle and crop yield and has nutritional importance for human and animal diet. Its deficiency is one of the major problems in agriculture. However, the plant-specific LSU (response to Low SUlfur) gene family has not been extensively analyzed in major plant species such as grasses. In this study, we have performed in silico genome-wide analysis of LSU genes in 6 grass species, including Brachypodium distachyon, Sorghum bicolor, Oryza sativa, Zea mays, Triticum aestivum, and Panicum virgatum. All identified LSU genes contained one exon encoding proteins of acidic character with cytoplasmic localization. In silico analysis of cis-elements revealed that sulfur-responsive elements (SURE boxes, SUlfur Response Element, GAGAC motif) were present in all LSU genes. In phylogenetic analysis, dicot and monocot LSU genes were separated. Expression profiles of B. distachyon BdLSU1 and BdLSU2 genes were analyzed by qRT-PCR method. Two Brachypodium LSU genes demonstrated different expression patterns when subjected to 48 h of S-depletion treatment. In roots, the BdLSU2 gene was upregulated, while BdLSU1 was downregulated. In leaves, expression levels were decreased for both genes. Analysis of the BdLSU expression under drought, cold, salt, and heat stresses was carried out based on the Brachypodium stress atlas. Results showed that BdLSU genes are not specific to S limitation; indeed, they may be involved in different stress conditions by cooperating with their interacting partner proteins. The results of this study could significantly contribute to the understanding of LSU genes in plants, particularly in grass species. These results may also support plant molecular studies by aiding the understanding of the sulfur assimilation pathway.Öğe Genome-wide distribution of superoxide dismutase (SOD) gene families in Sorghum bicolor(Tubitak Scientific & Technical Research Council Turkey, 2015) Filiz, Ertuğrul; Tombuloğlu, HüseyinSuperoxide dismutases (SODs) are critical enzymes protecting cells against toxic superoxide radicals. To date, 3 types of SODs have been identified: Cu-ZnSODs, Fe-MnSODs, and NiSODs. In this study, a genome-wide analysis was performed in Sorghum bicolor to characterize SOD genes and proteins. Using several bioinformatics tools, we characterized a total of 8 SOD genes from the Sorghum genome. Gene structure, chromosomal distribution, tissue specific expression, conserved domain, and phylogenetic analyses of SOD genes were carried out. Additionally, 3-dimensional structures were determined and compared within each SbSOD protein. Chromosomal distributions revealed that the highest number of SOD genes was on chromosomes 1 and 10, with 2 members on each. Single segmental gene duplication was observed between the genes SbSOD2 and SbSOD5. Intron numbers of SbSOD genes ranged from 5 to 7. Motif analyses showed that SbSODs included 2 and 3 common motifs in Cu-ZnSOD and Fe-MnSODs, respectively. In addition, 3 functional domains were identified in SbSODs: 1) copper-zinc domain (Pfam: 00080) in Cu-ZnSOD; and 2) iron/manganese superoxide dismutases alpha-hairpin domain (Pfam: 00081) and 3) iron/manganese superoxide dismutases, C-terminal domain (Pfam: 02777) in Fe-MnSODs. Gene Ontology term enrichment analysis showed that 8 SOD genes have similar molecular functions and biological processes, and variable cellular components. Phylogenetic analysis revealed that Cu-ZnSODs (92%) and Fe-MnSODs (100%) were separated by high bootstrap values. Additionally, predicted motif structures and critical binding sites of SbSODs were found to be similar within each SOD group. The results of this study contribute to a better understanding of SOD genes and proteins in plants, especially in Sorghum taxa.Öğe Genome-wide identification and analysis of growth regulating factor genes in Brachypodium distachyon: in silico approaches(Tubitak Scientific & Technical Research Council Turkey, 2014) Filiz, Ertuğrul; Koç, İbrahim; Tombuloğlu, HüseyinGrowth-regulating factor (GRF) genes may play important roles for regulating growth and development in different plant tissues and organs. Here we report the first genome-wide analysis of the GRF gene family in Brachypodium. We performed in silico comparative analysis of GRF genes, including their structure, duplication in the genome, conserved motifs, and phylogenetic relationship. At the end of the study, 10 BdGRF genes were identified. The highest number of GRF genes was identified on chromosome 1 with 5 members, whereas the least number of genes (only 1 member) was found on chromosomes 2, 4, and 5. Of those, a single segmental duplication was observed in the Brachypodium genome. Average exon and intron numbers were determined as 3 and 4, respectively. Motif analysis showed that WRC and QLQ residues were consistent in all GRF protein sequences. Gene Ontology terms showed that 10 BdGRF proteins grouped in the same biological function, biological process, and cellular component groups. In addition, we compared the new BdGRF proteins with the other monocot and dicot GRF proteins sequences. Phylogenetic analysis revealed that GRF proteins of monocot and dicot species were clustered together in a joined tree; in particular, the monocot species (Brachypodium, maize, and rice) were grouped into the same cluster with high bootstrap values. We assume that the results of this study will provide molecular insights about GRF proteins in grass species.Öğe Genome-wide identification and expression analysis of sulphate transporter (SULTR) genes under sulfur deficiency in Brachypodium distachyon(Springer India, 2017) Tombuloğlu, Hüseyin; Filiz, Ertuğrul; Aydın, Mehtap; Koç, İbrahimSulphur is an important mineral element for plant growth and development. It involves in a number of metabolic processes with crucial functions. This study has performed a genome-wide analysis of sulfate transporter (SULTR) genes in Brachypodium distachyon. Ten putative SULTR genes were identified in Brachypodium genome. BdSULTR genes included 6-17 exons encoding a protein of 647-693 residues with basic nature. BdSULTR proteins included both sulfate_transp (PF00916) and STAS (PF01740) domains. BdSULTRs were classified into 4 groups based on the phylogenetic distribution. Promoter regions of all BdSULTR genes, except for BdSULTR3;3 and 3;5 included the SURECOREATSULTR11 elements. A considerable structural overlap was identified between superimposed SULTR1;3 and 3;1 proteins, indicating that SULTR1 members may also involve in plant stress response/tolerance like SULTR3 members. Microarray and RNA-Seq analyses also revealed the differential expression of SULTR 1 and 3 genes under different biotic/abiotic stresses. Protein-protein interaction partners of BdSULTRs were mainly related with adenylyl-sulfate kinases, 5'-adenylylsulfate reductases, ATP sulfurylases, and acyl carrier proteins. Moreover, expression profiles of identified BdSULTR genes under S-deficiency were analyzed using RT-qPCR. It was revealed that BdSULTR1;1 and 3;1 are highly expressed in plant roots as similar to tenfold and similar to fivefold, respectively, while BdSULTR2 (similar to 15-fold) and 3;1 (similar to twofold) are abundantly expressed in leaf tissues.Öğe In Silico Analysis of DREB Transcription Factor Genes and Proteins in Grasses(Springer, 2014) Filiz, Ertuğrul; Tombuloğlu, HüseyinPlants are exposed to various environmental stresses, including drought, salinity, low temperature, etc. Dehydration responsive element binding (DREB) genes, the members of AP2/ERF transcription factor family, regulate the biological processes against cold and dehydration stresses. In this study, we analyzed a total of 19 DREB transcription factor genes and proteins from 14 grass species by using bioinformatic approaches, including their physiochemical properties, conserved motif structures, homology models, and phylogenetic relationships. The domain analysis showed that all grass species contained an AP2 domain whereas some residual substitutions and/or insertions were observed in the AP2 domains of some grasses. The physiochemical analysis revealed that many DREB proteins (89.5 %) were of acidic character while the number of amino acids ranged from 213 (Aegilops speltoides subsp. speltoides) to 394 (Triticum aestivum). Based on the subcellular prediction, 16 of 19 DREB proteins were predicted to be localized in the nuclear region. According to the sequence analysis of grass DREBs, the average value of pairwise distance was found to be 0.588, while nucleotide diversity (pi) was found to be 0.435. Thus, among all DREB proteins, two most divergent ones (Oryza sativa and Avena sativa) were selected for 3D structure and protein cavity comparison. In addition, 19 DREB proteins were analyzed according to their phylogenetic relationships, and as a consequence, two main groups were observed. In this study, our analyses could be a scientific base to understand DREB genes and proteins to further wet lab studies in plants, particularly in grass species.Öğe In silico comparative analysis of LEA (Late Embryogenesis Abundant) proteins in Brachypodium distachyon L.(Southern Cross Publ, 2013) Filiz, Ertuğrul; Özyiğit, İbrahim İlker; Tombuloğlu, Hüseyin; Koç, İbrahimThe Late Embryogenesis Abundant (LEA) proteins in plants are basically related with water deficiency. Recent studies showed that LEA proteins might be molecular chaperones regulating many physiological functions. In this study, LEA proteins were analyzed in model grass Brachypodium distachyon L. The data represented here may help to further analyze the FA genes in model grass Brachypodium in order to understand their functions especially under conditions of water deficiency and/or other physiological mechanisms. By using the Pfam database, proteins containing at least one LEA conserved repeat (LEA2, LEA3, LEA4, LEAS, and LEA6) were classified as LEA family members. According to these results, 36 LEA proteins were identified in B. distachyon. LEA2 repeat was found as the dominant protein among 28 members followed by LEA3 (5 members). Physicochemical analysis showed that pI values and GRAVY index ranged from 4.40 to 11.1 and 0.48 to -1.423, respectively. Many LEA proteins were considered as basic character (26 members, 72.2%), while 10 proteins (27.8%) were in acidic form. Moreover, GRAVY index revealed that 19 of the 36 sequences were considered hydrophobic (52.8%) while others were hydrophilic (47.2%). Comparative phylogenetic analysis revealed that BdLEA proteins fall into eight subgroups. They were basically divided into two main groups. Chromosomal distribution of LEA genes was determined and segmental and tandem duplications were found in eight genes which may cause expansions of LEA genes through the Brachypodium genome. These results can be helpful for the further functional analysis of LEA proteins in Brachypodium.Öğe The size of iron oxide nanoparticles determines their translocation and effects on iron and mineral nutrition of pumpkin (Cucurbita maxima L.)(Elsevier, 2022) Tombuloğlu, Hüseyin; Slimani, Yassine; Akhtar, Sultan; Alsaeed, Moneerah; Tombuloglu, Guzin; Almessiere, Munirah A.; Toprak, Muhammet S.The ability of nanoparticles (NPs) to migrate in the plant body is an important issue to ensure that the NPs reach the desired tissue and to be able to select the most efficient NPs for agricultural applications. In this study, the size impact of four different iron oxide NPs (8-10, 18-20, 20-40, and 30-50 nm referred as NP10, NP20, NP30, and NP40, respectively) on their translocation in pumpkin was elucidated. To assess the root-to-shoot trans -location, phloem sap was examined under transmission electron microscope (TEM). In addition, vibrating sample magnetometer (VSM) and inductively coupled plasma optical emission spectrophotometry (ICP-OES) analyses of stem and leaf tissues were performed to confirm size-dependent translocation. TEM and VSM analyses verified root-to-stem translocation of all tested NPs. The NPs treatment significantly altered the abundances of Mn, Cu, K, P, Al, Mg, and Na in tissues. The iron (Fe) content was abundant in plants treated with NP30 and NP20, and the lowest in plants treated with NP10 and NP40. Together with, only NP30 was found to be significantly trans -located to the leaves, where it was 393 mg/kg in DW, about 2.3 times that of control. These findings pointed out the size-dependent translocation of NPs. It seems that biological barriers in the vascular bundle appear to restrict the migration, especially for NPs with an average size of 40 nm and above in pumpkins. These findings are important for selecting the most suitable size of iron oxide NPs for use in agricultural practices.
