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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 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 Bioinformatics database resources for plant transcription factors(Springer International Publishing, 2017) Filiz, Ertuğrul; Vatansever, Recep; Özyiğit, İbrahim İlker[No abstract available]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.Öğe COMPARATIVE ANALYSIS OF MATURE AND PREPROPROTEIN FORM OF THIONINS IN SOME PLANT SPECIES; BIOINFORMATICS APPROACHES(Parlar Scientific Publications (P S P), 2019) Özyiğit, İbrahim İlker; Filiz, Ertuğrul; Saraçoğlu, İbrahim Adnan; Yalçın, BahattinThionins are one of the most important antimicrobial peptides in broad-range plant defense. A number of studies are present regarding the structural and biological role of mature thionins but preproprotein forms of these molecules have not been extensively studied. Thus, this study aimed to comparatively analyze a total of 56 thionin preproprotein sequences from 14 different plant species. Analyses of primary, secondary and tertiary structures of these forms revealed that preproproteins with "gamma-thionin domain" were relatively shorter and more basic than proteins with "thionin domain" structure. In addition, members of "thionin domain" were more similar to each other than that of "gamma-thionin domain" forms. Sub-cellular localizations of these forms were predicted as extracellular. Structural superposition of precursor and mature thionins showed that a large portion of precursor sequences are cleaved to form a functional protein. Although precursor forms demonstrated the significant structural divergence in modelled species, functional mature forms showed a structural pattern in alpha-helices; two alpha-helix proteins included the "thionin domain" family while one a-helix proteins contained the "gamma-thionin domain" family. Results of this study will become valuable theoretical knowledge and provide insight in terms of further understanding the formation of mature functional thionins thereby their biological roles.Öğe Comparative and phylogenetic analysis of zinc transporter genes/proteins in plants(Tubitak Scientific & Technical Research Council Turkey, 2016) Vatansever, Recep; Özyiğit, İbrahim İlker; Filiz, ErtuğrulZinc is an important catalytic element for more than 300 enzymes and plays a structural role in the stabilization of many proteins. Protein domain analysis showed that identified Zn transporter proteins belong to the ZIP protein family (PF02535). Zn transporter sequences were found to have similar molecular weights (33.1-51.4 kDa) and amino acid lengths (306-478 amino acids) with 5.31-8.92 pI values. Subcellular localization of Zn transporters was predicted as the plasma membrane. They had 6-9 putative transmembrane domains with a variable region between TM-3 and TM-4, which could contain a potential histidine-rich metal-binding domain. Moreover, alignment analysis showed that the TM-2, -4, and -5 domains could be potential metal-binding sites because they contain highly conserved His residues. Based on a homology search, the retrieved sequences were identified as corresponding homologs of either Arabidopsis thaliana or Oryza sativa. Phylogenetic analysis also supported that A. thaliana and O. sativa sequences could be used as a reference/benchmark to identify Zn transporter homologs in various plant species. The findings of this study will be valuable theoretical knowledge for feature studies in terms of understanding the gene and protein features of Zn transporters in various plants.Öğe Dissecting a co-expression network of basic helix-loop-helix (bHLH) genes from phosphate (Pi)-starved soybean (Glycine max)(Elsevier B.V., 2017) Filiz, Ertuğrul; Vatansever, Recep; Özyiğit, İbrahim İlkerIn this work, a co-expression network-based approach was employed in analysis of basic helix-loop-helix (bHLH) transcription factor genes in soybean (Glycine max). bHLHs as regulatory agents modulate many complex associations related with regular metabolic functions and various stress factors. Co-expression networks are versatile resources to understand complex associations from functional aspects. Using a microarray data from phosphate (Pi)-starved soybean, a co-expression network of bHLH genes was constructed. A network was established with 253 nodes (bHLH genes) interconnecting 1763 edges (association) and then the network was dissected into 13 distinct clusters to extensively investigate the correlations. Each cluster was individually analyzed with emphasis on seed genes, which could be used as marker/reference genes in development of plant lines with enhanced stress tolerance. The seed genes were involved in very diverse metabolic processes, including stress modulation, metal homeostasis, hormone response and developmental roles. Our network-based clustering approach provides new insight in understanding many uncharacterized plant bHLHs. © 2016 Elsevier B.V.Öğe DNA fingerprinting and assessment of some physiological changes in Al-induced Bryophyllum daigremontianum clones(Springer, 2019) Özyiğit, İbrahim İlker; Kaval, Ali; Çakır, Ernaz Altundağ; Vardar, FilizAluminum (Al) is one of the most important stress factors that reduce plant productivity in acidic soils. Present work thereby analyzed Al-induced genomic alterations in Bryophyllum daigremontianum clones using RAPD and ISSR markers, and investigated responding changes in photosynthetic pigment (chlorophyll a, b, a/b, total chlorophyll and carotenoid) contents and total soluble protein amounts in plant leaves. The main reason for the use of bulbiferous spurs originated clone plants was to increase reliability and acceptability of RAPD and ISSR techniques in DNA fingerprinting. Raised 40 clone plants were divided into five separate groups each with eight individuals and each experimental group was watered with 0 (control), 0 (acid control), 50, 100 and 200 mu M AlCl3-containing Hoagland solutions on alternate days for two and a half months. All plant soils except control group were sprayed with 0.2% sulfuric acid following watering days and this contributed acidic characteristic (pH 4.8) to soil structure. Increase in Al concentrations were accompanied by an increase in total soluble protein amounts, a decrease in photosynthetic pigment contents, and with appearance, disappearance and intensity changes at RAPD and ISSR band profiles. Out of tested RAPD1-25 and ISSR1-15 primers, RAPD8, RAPD9, ISSR2 and ISSR7 primers produced reproducible band profiles that were distinguishable between treatment and control groups. Findings showed that RAPD and ISSR fingerprints have been useful biomarkers for investigation of plant genotoxicity, especially in clone plants. Moreover, if these fingerprints are integrated with other physiological parameters they could become more powerful tools in ecotoxicology.Öğe Essential and Beneficial Trace Elements in Plants, and Their Transport in Roots: a Review(Springer, 2017) Vatansever, Recep; Özyiğit, İbrahim İlker; Filiz, ErtuğrulThe essentiality of 14 mineral elements so far have been reported in plant nutrition. Eight of these elements were known as micronutrients due to their lower concentrations in plants (usually a100 mg/kg/dw). However, it is still challenging to mention an exact number of plant micronutrients since some elements have not been strictly proposed yet either as essential or beneficial. Micronutrients participate in very diverse metabolic processes, including from the primary and secondary metabolism to the cell defense, and from the signal transduction to the gene regulation, energy metabolism, and hormone perception. Thus, the attempt to understand the molecular mechanism(s) behind their transport has great importance in terms of basic and applied plant sciences. Moreover, their deficiency or toxicity also caused serious disease symptoms in plants, even plant destruction if not treated, and many people around the world suffer from the plant-based dietary deficiencies or metal toxicities. In this sense, shedding some light on this issue, the 13 mineral elements (Fe, B, Cu, Mn, Mo, Si, Zn, Ni, Cl, Se, Na, Al, and Co), required by plants at trace amounts, has been reviewed with the primary focus on the transport proteins (transporters/channels) in plant roots. So, providing the compiled but extensive information about the structural and functional roles of micronutrient transport genes/proteins in plant roots.Öğe GENETIC DIVERSITY AND PHYLOGENETIC ANALYSES OF TURKISH RICE VARIETIES REVEALED BY ISSR MARKERS AND CHLOROPLAST trnL-F REGION(Parlar Scientific Publications (P S P), 2018) Filiz, Ertuğrul; Uras, Mehmet Emin; Özyiğit, İbrahim İlker; Şen, Uğur; Güngör, HüseyinA set of 17 Turkish rice (Oryza sativa L.) varieties (TRVs) were characterized using inter simple sequence repeat (ISSR) markers to study genetic diversity. Also, the sequences of trnL((UAA))-F-(GAA) intergenic spacer (IGS) regions were used to evaluate the phylogenetic relationships of TRVs. According to ISSR data, the observed number of alleles (Na), effective number of alleles (Ne), Nei's gene diversity (h), Shannon's information index (I), and overall polymorphism were found as 1.62, 1.38, 0.22, 0.32, and 61.7%, respectively. The genetic distance values were identified between 1.732and 4.583, and replicon size varied from 200 bp to 1600 bp. The ISSR-UPGMA (unweighted pair group method with arithmetic mean) similarity tree and PCA (principal component analysis) exhibited different cluster topologies based on pedigree. All trnL-F regions were found as 306 bp in length, and GC content was found between 34.31% and 34.97%. The nucleotide diversities were found as pi: 0.00954 and theta: 0.03595, while Tajima's D was found as -0.382. The phylogenetic analyses revealed that trnL-F sequences are effective molecular tools in resolving phylogenetic relationships. Consequently, our findings could be useful in planning future Turkish rice breeding strategies for general rice germplasm improvement.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 iron-regulated transporter 1 (IRT1) genes in plants(Korean Soc Horticultural Science, 2015) Vatansever, Recep; Filiz, Ertuğrul; Özyiğit, İbrahim İlkerIron (Fe) is an essential micronutrient required in a number of biological processes in plant species. Fe transporters are a type of broad-range metal transporter and have different families functioning in different compartments. This study focused on iron-regulated transporter 1 (IRT1), which are mainly responsible for Fe uptake from root, in 17 selected plant species with an emphasis on Brachypodium distachyon, Chlamydomonas reinhardtii, Solanum lycopersicum and Populus trichocarpa species. All IRT1 proteins were observed to belong to the ZIP (PF02535) protein family with eight transmembrane (TM) domains, and have a similar molecular weight (33.86-42.72 kDa, except for C. reinhardtii with 65.83 kDa) and amino acid length (324-408 aa, except for C. reinhardtii with 639 aa), with pI values of 5.31-7.16. The sub-cellular localization of these proteins was predicted to be the plasma membrane. Similar exon numbers were also detected with most genes having 2-3, except for C. reinhardtii (5), Physcomitrella patens (5) and Vitis vinifera (4). In a phylogenetic tree, monocot-dicot separation was not observed in main groups but some subgroups included only monocot or dicot proteins. Predicted interaction partner analysis of AtIRT1 (AT2G30080.1) pointed to main interaction partners either directly related with iron transport or that of other metal ion. The results of this study provide a theoretical reference for elucidating the structural and biological role of IRT1 genes/proteins in plant species.Öğe Genome-wide exploration of silicon (Si) transporter genes, Lsi1 and Lsi2 in plants; insights into Si-accumulation status/capacity of plants(Springer, 2017) Vatansever, Recep; Özyiğit, İbrahim İlker; Filiz, Ertuğrul; Gözükara, NerminSilicon (Si) is a nonessential, beneficial micronutrient for plants. It increases the plant stress tolerance in relation to its accumulation capacity. In this work, root Si transporter genes were characterized in 17 different plants and inferred for their Si-accumulation status. A total of 62 Si transporter genes (31 Lsi1 and 31 Lsi2) were identified in studied plants. Lsi1s were 261-324 residues protein with a MIP family domain whereas Lsi2s were 472-547 residues with a citrate transporter family domain. Lsi1s possessed characteristic sequence features that can be employed as benchmark in prediction of Si-accumulation status/capacity of the plants. Silicic acid selectivity in Lsi1s was associated with two highly conserved NPA (Asn-Pro-Ala) motifs and a Gly-Ser-Gly-Arg (GSGR) ar/R filter. Two NPA regions were present in all Lsi1 members but some Ala substituted with Ser or Val. GSGR filter was only available in the proposed high and moderate Si accumulators. In phylogeny, Lsi1s formed three clusters as low, moderate and high Si accumulators based on tree topology and availability of GSGR filter. Low-accumulators contained filters WIGR, AIGR, FAAR, WVAR and AVAR, high-accumulators only with GSGR filter, and moderate-accumulators mostly with GSGR but some with A/CSGR filters. A positive correlation was also available between sequence homology and Si-accumulation status of the tested plants. Thus, availability of GSGR selectivity filter and sequence homology degree could be used as signatures in prediction of Si-accumulation status in experimentally uncharacterized plants. Moreover, interaction partner and expression profile analyses implicated the involvement of Si transporters in plant stress tolerance.Öğe Genome-wide exploration of silicon (Si) transporter genes, Lsi1 and Lsi2 in plants; insights into Si-accumulation status/capacity of plants (vol 30, pg 185, 2017)(Springer, 2017) Vatansever, Recep; Özyiğit, İbrahim İlker; Filiz, Ertuğrul; Gözükara, Nermin…Öğe Genome-Wide Identification and Comparative Analysis of Copper Transporter Genes in Plants(Springer Heidelberg, 2017) Vatansever, Recep; Özyiğit, İbrahim İlker; Filiz, ErtuğrulCopper (Cu) transporters have primary importance in maintenance of physiological limits of Cu home-ostasis in plants. However, structural characterization of Cu transporters in many plant species is still limited. In this study, a total of 78 potential Cu transporter genes were identified from 18 different plant species. Study revealed that Cu transporters could be characterized with a CTR protein family (PF04145) domain, three putative transmembrane domains (TMDs), a single exon number, and a basic character. Met-rich motifs at N-terminal region, MXXXM motif in TMD-2, and GXXXG motif in TMD-3 could be essential for Cu transport since they were highly conserved in all analyzed species. In phylogeny, a clear distinction was observed between Cu transporter sequences of lower and higher plants. General topological features of Cu transporters in higher plants-monocots and dicots-were highly conserved compared to lower plants. Identification of Cu transporter homologous in various plant species and their comparative analysis at gene and protein levels will become valuable theoretical basis for future studies aiming to further characterization and molecular manipulation of Cu transporters.
