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Öğe Abiotic stress-induced regulation of antioxidant genes in different Arabidopsis ecotypes: microarray data evaluation(Taylor & Francis Ltd, 2019) Filiz, Ertuğrul; Özyiğit, İbrahim İlker; Saraçoğlu, İbrahim Adnan; Uras, Mehmet Emin; Şen, Uğur; Yalçın, BahattinAlthough stresses induce generation of reactive oxygen species (ROS), which are highly reactive and toxic, and cause severe damage to cellular components; plants have very efficient enzymatic ROS-scavenging mechanisms. Despite the substantial knowledge produced about these enzymes, we still have limited knowledge regarding their expression patterns in relation to the stress type, duration and strength. Thus, taking advantage of microarray data, this work evaluated the abiotic stresses (salt, cold, heat and light) induced regulation of six antioxidant enzymes, superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), glutathione peroxidase (GPX), monodehydroascorbate reductase (MDHAR) and dehydroascorbate reductase (DHAR), in 10 natural Arabidopsis ecotypes. The expression profiles of 36 genes encoding six enzymatic antioxidants including CSD1-3, FSD1-3, MSD1-2, CAT1-3, APX1-6, APXT, APXS, GPX1-8, MDAR1-5 and DHAR1-4 were investigated. In particular, FSD1, FSD2, CSD1 and CSD2 genes coding for SOD; CAT2 and CAT3 for CAT; APX3-6, APXT and APXS for APX; GPX1, GPX2, GPX5, GPX6 and GPX7 for GPX; MDAR2-4 for MDHAR; and DHAR1 and DHAR3 for DHAR families appeared to be more differentially expressed under given stress conditions. Primarily, high light as well as salt and cold stresses considerably up-regulated the gene expression, whereas cold stress significantly led to the down-regulation of genes. The overall expression pattern of ecotypes suggested that the studied Arabidopsis genotypes had different stress tolerance.Öğe Analysis of EST-SSRs in silver birch (Betula pendula Roth.)(Northeast Forestry Univ, 2016) Filiz, Ertuğrul; Doğan, İlhan; Özyiğit, İbrahim İlkerSimple sequence repeats (SSRs) defined as sequence repeat units between 1 and 6 bp occur abundantly in both coding and non-coding regions in eukaryotic genomes and these repeats can affect gene expression. In this study, ESTs (expressed sequence tags) of Betula pendula (silver birch) were analyzed for in silico mining of EST-SSRs, protein annotation, open reading frames (ORFs), designing primers, and identifying codon repetitions. In B. pendula, the frequency of ESTs containing SSRs was 7.8 % with an average of 1SSR/4. 78 kb of EST sequences. A total of 188 SSRs was identified by using MISA software and di-nucleotide SSR motifs (65.9 %) were found to be the most abundant type of repeat motif followed by tri- (27.1 %), tetra- (4.8 %), and penta- (2.2 %) motifs. Based on ORF analysis, 175 of 178 sequences were predicted as ORFs and the most frequent SSRs were detected in 5' UTR (58.43 %), followed by in ORF (31.46 %) and in 3' UTR (8.43 %). 102 of 178 ESTs were annotated as ribosomal protein, transport protein, membrane protein, carrier protein, binding protein, and transferase protein. For a total of 102 SSRs (57.3 %) with significant matches, a set of 102 primers (100 %) with forward and reverse strands was designed by using Primer3 software. Serine (Ser, 19.6 %) was predominant in putative encoded amino acids and most of amino acids showed nonpolar (35.3 %) nature. Our data provide resources for B. pendula and can be useful for in silico comparative analyses of Betulaceae species, including SSR mining.Öğe Application of data analysis in cold stress: a case study of Nicotiana benthamiana(Tubitak Scientific & Technical Research Council Turkey, 2015) Koç, İbrahim; Çalışkaner, Zihni Onur; Filiz, ErtuğrulCold stress is a major environmental factor in plant life cycles. Nicotiana benthamiana, which belongs to the family Solanaceae, is one of the most commonly used model species in plant-microbe interaction studies. In total, 5205 differentially expressed genes were identified under cold stress in N. benthamiana. Of these, 5029 were upregulated and 176 were downregulated within four time periods (4 h, 12 h, 24 h, and 48 h). The common up- and downregulated genes were identified as 692 and 6, respectively. The functional annotations of these genes were studied and these common genes involved in protein, RNA, miscellaneous enzyme families, signaling, stress, lipid, and carbohydrate metabolisms were enriched by using MapMan ontology. In addition, a total of 22 cold-inducible transcription factors were enriched, including subsets of the zinc finger family, bHLH, E2F/DP, bZIP, SET domain, GRAS, MYB, ARF, CO-like, Homeobox, and DOF zinc finger family members. Our findings will pave the way for understanding the expression of cold-inducible genes as a response to cold stress in Nicotiana species. This study will also be a valuable resource for crop improvement studies under abiotic stress conditions for Nicotiana plants.Öğe Aromatic amino acids biosynthesis genes identification and expression analysis under salt and drought stresses in Solanum lycopersicum L.(Elsevier, 2019) Filiz, Ertuğrul; Çetin, Durmuş; Akbudak, M. AydınAromatic amino acids (AAA), phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp), are essential molecules in the plant metabolism. In this study, three AAA biosynthesis genes, chorismate synthase (CS), chorismate mutase (CM) and anthranilate synthase (AS), were identified in genome-wide scale in tomato (Solanum lycopersicum) genome. Also, bioinformatics analyses including sequence and phylogenetic analyses, predicted microRNAs targeting, digital expression and co-expression analyses and seconder and tertiary structure analyses of AAA proteins were performed. The expressions of AAA genes under drought and salt stresses were evaluated using Real Time-quantitative PCR (RT-qPCR). The promotor sequence analyses of the genes showed the presence of diverse cis-regularity elements, including light responsive, hormone responsiveness, heat stress responsiveness and elicitor-responsive elements. Based on the digital expression data, CS1 is more consistently expressed over CM1 and ASA1 through developmental stages in tomato. Co-expression network analyses revealed complex interactions between AAA genes and genes in other metabolic pathways. The expressions of AAA genes fluctuated between 0.93-2.23 fold under drought and salt stresses. Over all, it can be proposed that data obtained from this study could contribute to identification and functions of AAA genes under abiotic stress conditions for plants, particularly tomato.Öğe Assessment of chloroplast microsatellite from pine family (Pinaceae) by using bioinformatics tools(Natl Inst Science Communication-Niscair, 2014) Filiz, Ertuğrul; Koç, İbrahimMicrosatellites, also known as simple sequence repeats (SSRs), are repeating sequences of 2-6 base pairs of DNA and affect chromatin organization, regulation of gene activity, DNA repair, DNA recombination, etc. Chloroplast DNA (cpDNA) has been used extensively in plant studies at different taxonomic levels. Therefore, the aim of this study Was to understand the distrubution of microsatellites in the coding and non-coding regions of organellar genomes (cpDNAs) of Major species of pine family (Pinaceae), viz., Cathaya argyrophylla, Cedrus deodara, Larix decidua, Picea morrisonicola, P. sitchensis, Pinus contorta, P. gerardiana, P. koraiensis, P. krempfii, P. lambertiana, P. monophylla, P. nelsonii, P. thunbergii, Pseudotsuga sinensis var. wilsoniana. 1623 cpSSRs were identified in pine species with an average frequency of 9.79 cpSSR per kb, of which 584 (22.5%) were in genic regions. Mononucleotide repeats were the most abundant cpSSRs (52.4%) in these species, followed by trinucleotide SSRs (37.3%), dinucleotide (5%), tetranucleotide (3.9%), pentanucleotide (0.8%), and hexanucleotide (0.6%). As expected, trinucleotide repeats are more common in coding regions, while other repeat motifs are abundant in non-coding cpDNA. G+C content of these species have closely similar frequency, ranging from 31.67 to 38.80%. Our analyses suggest that plastome database can be used for comparative genomics in different plant species.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 genetic diversity in natural European hophornbeam (Ostrya carpinifolia Scop.) populations in Turkey(Taylor & Francis Ltd, 2016) Kulaç, Şemsettin; Filiz, Ertuğrul; Çiçek, Emrah; Değermenci, Zerrin; Vatansever, RecepGenetic diversity is a crucial component for plant survivability and fitness in terms of adaptation, genetic stability and variability. In this study, a total of 160 genotypes were investigated using 12 random amplified polymorphic DNA (RAPD) primers to understand the genetic structure and diversity of nine naturally distributed Ostrya carpinifolia populations in Turkey. Twelve RAPD primers yielded 111 clearly identifiable DNA bands, of which 71 bands were found to be polymorphic (64%). Observed number of alleles (Na), effective number of alleles (Ne) and Nei's gene diversity (h) were found as 2, 1.53 and 0.32, respectively. Total genetic variation (H-T), within-population genetic variation (H-S) and Nei's genetic differentiation coefficient (G(ST)) were found as 0.32, 0.09 and 0.70, respectively. Genetic diversity analysis (AMOVA) revealed highly significant (P < 0.001) genetic variations among and within populations. 69.94% of total variation was observed among populations while 26.69% was within populations. Gene flow value was calculated as 0.21 (Nm < 0.5), which could homogenize the genetic structure of a population. Two geographically isolated populations demonstrated high gene diversity and polymorphic loci ratio, indicating a relationship between geographic distribution of populations and eco-geographic factors. The findings of this study will pave the way for understanding the genetic diversity between inter- and intra-populations of O. carpinifolia species, as well as they would provide valuable information for management, conservation and utilization of in situ and ex situ Ostrya germplasms.Öğe Assessment of genetic variations of silver lime (Tilia tomentosa Moench.) by RAPD markers in urban and forest ecosystems(Taylor & Francis Ltd, 2015) Filiz, Ertuğrul; Birbilener, Seda; Özyiğit, İbrahim İlker; Kulaç, Şemsettin; Oruç, Fatma Çiğdem SakinoğluIn the present study, the genetic diversity analysis of Tilia tomentosa plants was performed by using random amplified polymorphic DNA (RAPD) primers. Twenty eight plant samples, collected from urban (25 members) and forest (3 members) ecosystems, were used in this study. A total of 53 bands were obtained from eight RAPD primers, of which 48 (90.6%) were polymorphic. The percentage of polymorphic loci (P) was found to be 94.29%, the observed number of alleles (Na) was 1.94, the effective number of alleles (Ne) was 1.60, Nei's gene diversity (h) was 0.34 and Shannon's information index (I) was 0.50. Unweighted pair group method with arithmetic mean (UPGMA) cluster analysis revealed two major groups. Members of the urban and forest ecosystems showed high genetic similarity (28%-92%) and they did not separate from each other in UPGMA tree. Furthermore, urban and forest genotypes clustered together in principal component analysis.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 Assessment of the genetic relationship of Turkish olives (Olea europaea subsp europaea) cultivars based on cpDNA trnL-F regions(Univ Zagreb, Fac Science, Div Biology, 2018) Kaya, Ergün; Vatansever, Recep; Filiz, ErtuğrulThe olive tree (Olea europaea L.) is one of the major cultivated species in the world, and Mediterranean countries produce about 90% of world cultivated olives. In this study, the genetic relationship of seven Turkish olive cultivars was investigated using non-coding trnL-F regions in chloroplastic genome. Cultivars demonstrated a similar sequence length of 330-340 bp with an average 35.26% G+C content. Variable (polymorphic/segregating), parsimony informative and total numbers of the insertion or the deletion of bases in the DNA (indel sites) were 4, 3, and 28, respectively. Nucleotide diversities p and. were found as 0.00631 and 0.00644 respectively, while Tajima's D was -0.786. cpDNA trnL-F regions of sequenced Turkish olive cultivars had a low level of genetic variations, and these non-coding regions were strictly conserved in all analyzed cultivars. Geographically distant shared more sequence similarities than relatively close cultivars. The phylogenetic analyses indicated that the biogeographic distribution of cultivars does not demonstrate any association inferring cultivar source. These results indicate the possibility of germplasm exchanges among countries or that some indel mutations contribute to variations of the Turkish olive gene pool. Thus, the authorities should develop the necessary programs to preserve the purity of native germplasms.Öğe Barley molybdenum cofactor sulfurase (MCSU): sequencing, modeling, and its comparison to other higher plants(Tubitak Scientific & Technical Research Council Turkey, 2015) Filiz, Ertuğrul; Distelfeld, Assaf; Fahima, Tzion; Metin, Özge Karakaş; Nevo, Eviatar; Song, Weining; Uncuoğlu, Ahu AltınkutMolybdenum cofactor sulfurases (MCSUs) are important enzymes for plant development and response to environmental queues, including processes such as nitrogen metabolism and regulation of the abscisic acid levels in plant tissues. We cloned and sequenced MCSU gene from barley and performed in silico comparison with rice, tomato, and Arabidopsis. Physico-chemical properties and subcellular predictions were found to be similar in different plant species. All MCSUs had three critical domains: aminotransferase class-V (Pfam: PF00266), MOSC N-terminal beta barrel (Pfam: PF03476), and MOSC (Pfam: PF03473). Secondary structure analysis revealed that random coils were the most abundant, followed by alpha-helices and extended strands. Predicted binding sites of MCSUs were different in barley and Arabidopsis, whereas rice and tomato showed the same pattern. A conserved triple-cysteine motif was detected in all MCSUs with cys438-cys440-cys445, cys431-cys433-cys438, cys428-cys430-cys435, and cys425-cys427-cys432 in barley, rice, Arabidopsis, and tomato, respectively. Furthermore, a 3D structure analysis indicated that structural divergences were present in all MCSUs, even in the core domain structure. Phylogenetic analysis of MCSUs revealed that monocot-dicot divergence was clearly observed with high bootstrap values. The results of this study will contribute to the understanding of MCSU genes and proteins in plants. The data of this study will also constitute a scientific basis for wet-lab and in silico studies of MCSUs.Öğe Bioinformatical Analyses of cinnamyl alcohol dehydrogenase (CAD) proteins from higher plant species(2019) Filiz, Ertuğrul; Kurt, FıratCinnamyl alcohol dehydrogenase (CAD) (EC 1.1.1.195) is an enzyme functioning in the reduction of variousphenylpropenyl aldehyde derivatives which are precursors in lignin and lignan production. Species-specific CADgenes have been extensively identified in recent years. In this study, we used bioinformatics tools to characterizeand classify plant CADs. The amino acid and nucleotide sequences of 16 CADs from different plant species wereused to compare their physiological properties, phylogeny, and conserved motifs. For this purpose, sequence,phylogenetical, structural analyses of proteins were conducted using various servers. All plant CADs had thecharacteristic alcohol dehydrogenase (PF08240) and zinc-binding dehydrogenase domains (PF00107). Accordingto the physicochemical analysis, it was revealed that the most of plant CADs (81.25%) were in acidic character.Sequence length (aa) and molecular weight (kDa) of CAD proteins were found in range of 356 -367 and 38.6-40.5respectively. The highest sequence similarities were found between Sorghum bicolor and Zea mays (95.3%),Panicum virgatum and Sorghum bicolor (90.9%), and Oryza sativa and Zea mays (87.1%) respectively. PlantCADs showed divergent exon-intron structures in which exon numbers were ranged from two to six. Four monocotspecies (S. bicolor, P. virgatum, Z. mays, and O. sativa) have four exons, whereas Brachypodium distachyoncontains only two exons. Phylogenetic analysis revealed that the CAD proteins mainly divided into two groups.The highest bootstrap values were found as follows: Fragaria vesca-Prunus persica clade (100%), Glycine maxMedicago truncatula (81%), and S. bicolor-Z. mays (72%). The 3D structures of plant CADs showed that Oryzaand Vitis had the most divergent structures when compared to the other plant species. Eventually, the datarepresented here contribute to studies aiming at evaluating the plant CADs extensively and at identifying new CADgenes in other plants.Öğe Bioinformatics database resources for plant transcription factors(Springer International Publishing, 2017) Filiz, Ertuğrul; Vatansever, Recep; Özyiğit, İbrahim İlker[No abstract available]Öğe Biological Network Analyses of WRKY Transcription Factor Family in Soybean (Glycine max) under Low Phosphorus Treatment(Korean Society of Crop Science, 2020) Kurt, Fırat; Filiz, ErtuğrulWRKY transcription factor (TF) is plant specific genes and play essential roles involved in biotic and abiotic stress tolerance. Gene co-expression network (GCN) analysis is effective tool for the interpretation of transcriptomic data. In this study, a co-expression network of 152 WRKY genes using publicly available microarray data (GSE78242) was constructed under low phosphate (Pi) treatment in soybean (Glycine max). A total of 149 nodes and 641 edges were obtained from CGN and seven seed genes were identified. Particularly, Glyma.19G094100 and Glyma.16G054400 seed genes (orthologue to Arabidopsis WRKY75) were found to have a direct connection to P deficiency. Promotor analyses of seed genes revealed the variations in the number of cis-regulatory elements (CREs) ranging from 80 to 137 with a total of 835 CREs. The methylation profile of Glyma.04G218700 (orthologue to Arabidopsis WRKY51) was found higher than other seed genes. As a result, our findings can be used as a scientific basis to cope with P deficiency in soybean as well as abiotic stress tolerance. In addition, these findings of this study may prove the crop improvement studies in future, especially genetically engineered soybean plants. © 2020, Korean Society of Crop Science and Springer.Öğe Bitki biyoteknolojisinde moleküler markörler(2011) Filiz, Ertuğrul; Koç, İbrahimÖzet: Biyoteknoloji, günümüzde en popüler ve yeniliklere açık bilimsel alanların başında gelmektedir. Bitki biyoteknolojisi de bu alanlardan biridir ve bu alanda kullanılan moleküler markör teknolojileri çok önemli bir biyoteknolojik araç olarak karşımıza çıkmaktadır. Moleküler markör ile genomda herhangi bir gen bölgesi ya da gen bölgesi ile ilgili DNA parçası temsil edilmektedir. Polimer Zincir Reaksiyonunun (PCR) keşfinden sonra Çoğaltılmış Parça Uzunluk Polimorfizm (AFLP), Basit Dizi Tekrarları (SSR), Dizi İlişkili Çoğaltılmış Polimorfizm (SRAP), Tek Nükleotid Polimorfizmi (SNP) ve Basit Tekrarlı Diziler Arası Polimorfizm (ISSR) gibi yaygın olarak kullanılan çok sayıda moleküler markör teknikleri geliştirilmiştir. Bu markör teknolojileri fiziksel haritalama, gen keşfi ve etiketleme, filogenetik çalışmalar, evrimsel genetik ve genetik çeşitlilik çalışmaları gibi pek çok alanda etkin şekilde kullanılmaktadırlar. Sonuç olarak, moleküler markörler bitki biyoteknolojisi çalışmalarına çok önemli boyutlar kazandırmış, daha etkili ve hızlı bilimsel sonuçların alınmasına imkân sağlamıştır. Bu çalışmada, bitki biyoteknolojisinde kullanılan moleküler markör teknolojilerinin genel prensipleri, avantajları-dezavantajları ve uygulama alanlarından bahsedilmiştir.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 analyses of pathogenesis-related protein-10 (PR10) in plants(Natl Inst Science Communication-Niscair, 2017) Özyiğit, İbrahim İlker; Vatansever, Recep; Filiz, ErtuğrulIn the present study, we have comparatively analyzed PR10 genes and proteins from 28 plant species in order to understand the relationship (conservation or divergence) between different PR1Os in various plant species. In analyzed species, PR10 proteins were found to be small (157-166 as long and 14.3-18.2 kDa weight) and acidic (4.69-6.17) in nature. Besides, PR10 sequences had highly conserved GxGGxG motif (P-loop motif) structure at various positions. These positional variations in glycine (Gly) residues may become the result of substitution, deletions and insertions occurred during the course of PR10 evolution. In general, primary sequences of PR1Os in various plant species may have a well conserved structure. Digital expression data of tomato and maize showed that expression of PR10 genes may significantly increase in plant parts (root, lateral root and root tips) where it is more open to the mechanical perturbation and pathogenic attack, supporting the involvement of PR10 in plant defense. In phylogenetic tree, a clear monocot/polycot and dicot separation were observed. This separation could have been arising from the well conserved structure of PR10 genes of monocots and polycots than dicots. All modeled species contained the same number of beta-strands (seven) but alpha-helices varied between 2 and 4 depending on species. The results of this study will provide a theoretical reference regarding the primary, secondary and tertiary structure of PR1Os in various plant species and will support the future studies that aiming to characterize the pathogenesis-related (PR) proteins.Öğe Comparative analyses of phytochelatin synthase (PCS) genes in higher plants(Taylor & Francis Ltd, 2019) Filiz, Ertuğrul; Saraçoğlu, İbrahim Adnan; Özyiğit, İbrahim İlker; Yalçın, BahattinPlants employ various defence strategies to ameliorate the effects of heavy metal exposures, leading to re-establishment of metal homeostasis. One of the strategies includes the biosynthesis of main heavy metal detoxifying peptides phytochelatins (PCs) by phytochelatin synthase (PCS). In the present study, 14 PCS homologues were identified in the genomes of 10 selected plants. The size of these PCSs was 452-545 amino acid residues, with characteristic phytochelatin and phytochelatin_C domains. The N-terminal site of the proteins is highly conserved, whereas the C-terminal site is less conserved. Further, the present study also identified fully conserved Cys residues involved in heavy metal binding reported earlier. In addition, other preserved cysteines, with minor substitutions Cys(C)-> Ser(S) or Tyr(Y) or Trp(W), were also identified in the PCS sequences that might be associated with metal binding. The reported catalytic triad residues from Arabidopsis, Cys56, His162 and Asp180, are all conserved at the respective sites of PCSs. A clear monocot/dicot separation was revealed by phylogenetic analysis and was further corroborated by the exon-intron organisations of the PCS genes. Moreover, gene ontology terms, co-expression network, cis-regulatory motif and miRNA analyses indicated that the complex as well as dynamic regulation of PCSs has significant involvement in different metabolic pathways associated with signalling, defence, stress and phytohormone, in addition to metal detoxification. Moreover, variations in protein structure are suggested to confer the functional divergence in PCS proteins.Öğe Comparative analyses of squalene synthase (SQS) proteins in poplar and pine by using bioinformatics tools(Springer Heidelberg, 2016) Filiz, Ertuğrul; Özyiğit, İbrahim İlker; Vatansever, RecepSqualene synthase (SQS, EC 2.5.1.21) is a major enzyme in biosynthesis of isoprenoid (farnesyl pyrophosphate (FPP) squalene). In the present study, we have analyzed SQS enzymes of black cottonwood (Populus trichocarpa, hereafter Pt) and Masson's pine (Pinus massoniana, hereafter Pm) using bioinformatics tools. PtSQS and PmSQS sequences were found to have very similar physicochemical properties with "squalene/phytoene synthase" domain structure (PF00494). PtSQS sequence was 47.3 kDa weight and 413 amino acids long with a pI value of 6.86, while PmSQS was 46.6 kDa weight and 409 amino acids long with a pI of 7.92. Alignment of SQS protein sequences in 15 plant species showed a highly similar conserved pattern and included (DTVED81)-D-77 and (DYLED217)-D-213 motifs, which are rich in aspartic acids, for FPP binding sites. In phylogenetic tree, monocots and polycot were clearly separated from dicots with high bootstrap value (99 %). A total of 10 interaction partners were predicted for PtSQS and PmSQS proteins. Nine of them were hypothetical proteins (related with phytosterol biosynthesis), while one was putative uncharacterized protein. Similar 3D structures and identical binding sites were predicted for pine and poplar. In docking, FPP-PtSQS was found to make 8 H bonds with Asp81, Asp217, Glu80, and Gln206 residues in poplar with highest affinity while FPP-PmSQS made 7 H bonds with Arg49, Arg74, Ser48, and Val47 residues in pine with highest affinity. The results of this study will provide valuable theoretical knowledge for future studies of identification and characterization of SQS genes and proteins in various tree species and will provide an insight for studies of biotechnological manipulation of sterol biosynthesis pathway to enhance the plant stress tolerance and productivity.Öğe Comparative Analysis and Modeling of Superoxide Dismutases (SODs) in Brachypodium distachyon L.(Springer, 2014) Filiz, Ertuğrul; Koç, İbrahim; Özyiğit, İbrahim İlkerSuperoxide dismutase (SOD, EC 1.15.1.1) is an enzyme catalyzing the dismutation of superoxide radical to hydrogen peroxide and dioxygen. To date, four types of SODs - Cu/ZnSOD, MnSOD, FeSOD, and NiSOD - have been identified. In this study, SOD proteins of Brachypodium distachyon (L.) Beauv. were screened by utilization of bioinformatics approaches. According to our results, Mn/FeSODs and Cu/ZnSODs of B. distachyon were found to be in basic and acidic character, respectively. Domain analyzes of SOD proteins revealed that iron/manganese SOD and copper/zinc SOD were within studied SOD proteins. Based on the seconder structure analyzes, Mn/FeSODs and Cu/ZnSODs of B. distachyon were found as having similar sheets, turns and coils. Although helical structures were noticed in the types of Mn/FeSODs, no the type of Cu/ZnSODs were identified having helical structures. The predicted binding sites of Fe/MnSODs and Cu/ZnSODs were confirmed for having His-His-Asp-His and His-His-His-Asp-Ser residues with different positions, respectively. The 3D structure analyzes of SODs revealed that some structural divergences were observed in patterns of SODs domains. Based on phylogenetic analysis, Mn/FeSODs were found to have similarities whereas Cu/ZnSODs were clustered independently in phylogenetic tree.
