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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, Recep
Genetic 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.
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, Ertuğrul
The 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.
Bioinformatics database resources for plant transcription factors
(Springer International Publishing, 2017) Filiz, Ertuğrul; Vatansever, Recep; Özyiğit, İbrahim İlker
[No abstract available]
Comparative analyses of pathogenesis-related protein-10 (PR10) in plants
(Natl Inst Science Communication-Niscair, 2017) Özyiğit, İbrahim İlker; Vatansever, Recep; Filiz, Ertuğrul
In 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.
Comparative analyses of squalene synthase (SQS) proteins in poplar and pine by using bioinformatics tools
(Springer Heidelberg, 2016) Filiz, Ertuğrul; Özyiğit, İbrahim İlker; Vatansever, Recep
Squalene 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.
Comparative and phylogenetic analysis of zinc transporter genes/proteins in plants
(Tubitak Scientific & Technical Research Council Turkey, 2016) Vatansever, Recep; Özyiğit, İbrahim İlker; Filiz, Ertuğrul
Zinc 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.
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 İlker
In 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.
Essential and Beneficial Trace Elements in Plants, and Their Transport in Roots: a Review
(Springer, 2017) Vatansever, Recep; Özyiğit, İbrahim İlker; Filiz, Ertuğrul
The 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.
Genome-wide analysis of iron-regulated transporter 1 (IRT1) genes in plants
(Korean Soc Horticultural Science, 2015) Vatansever, Recep; Filiz, Ertuğrul; Özyiğit, İbrahim İlker
Iron (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.
Genome-wide exploration of metal tolerance protein (MTP) genes in common wheat (Triticum aestivum): insights into metal homeostasis and biofortification
(Springer, 2017) Vatansever, Recep; Filiz, Ertuğrul; Eroğlu, Seçkin
Metal transport process in plants is a determinant of quality and quantity of the harvest. Although it is among the most important of staple crops, knowledge about genes that encode for membrane-bound metal transporters is scarce in wheat. Metal tolerance proteins (MTPs) are involved in trace metal homeostasis at the sub-cellular level, usually by providing metal efflux out of the cytosol. Here, by using various bioinformatics approaches, genes that encode for MTPs in the hexaploid wheat genome (Triticum aestivum, abbreviated as Ta) were identified and characterized. Based on the comparison with known rice MTPs, the wheat genome contained 20 MTP sequences; named as TaMTP1-8A, B and D. All TaMTPs contained a cation diffusion facilitator (CDF) family domain and most members harbored a zinc transporter dimerization domain. Based on motif, phylogeny and alignment analysis, A, B and D genomes of TaMTP3-7 sequences demonstrated higher homology compared to TaMTP1, 2 and 8. With reference to their rice orthologs, TaMTP1s and TaMTP8s belonged to Zn-CDFs, TaMTP2s to Fe/Zn-CDFs and TaMTP3-7s to Mn-CDFs. Upstream regions of TaMTP genes included diverse cis-regulatory motifs, indicating regulation by developmental stage, tissue type and stresses. A scan of the coding sequences of 20 TaMTPs against published miRNAs predicted a total of 14 potential miRNAs, mainly targeting the members of most diverged groups. Expression analysis showed that several TaMTPs were temporally and spatially regulated during the developmental time-course. In grains, MTPs were preferentially expressed in the aleurone layer, which is known as a reservoir for high concentrations of iron and zinc. The work identified and characterized metal tolerance proteins in common wheat and revealed a potential involvement of MTPs in providing a sink for trace element storage in wheat grains.
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, Nermin
Silicon (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.
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
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Genome-Wide Identification and Comparative Analysis of Copper Transporter Genes in Plants
(Springer Heidelberg, 2017) Vatansever, Recep; Özyiğit, İbrahim İlker; Filiz, Ertuğrul
Copper (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.
Genome-wide identification and expression analysis of sulfate transporter (SULTR) genes in potato (Solanum tuberosum L.)
(Springer, 2016) Vatansever, Recep; Koç, İbrahim; Özyiğit, İbrahim İlker; Şen, Uğur; Uras, Mehmet Emin; Anjum, Naser A.; Filiz, Ertuğrul
Solanum tuberosum genome analysis revealed 12 StSULTR genes encoding 18 transcripts. Among genes annotated at group level ( StSULTR I-IV), group III members formed the largest SULTRs-cluster and were potentially involved in biotic/abiotic stress responses via various regulatory factors, and stress and signaling proteins. Employing bioinformatics tools, this study performed genome-wide identification and expression analysis of SULTR (StSULTR) genes in potato (Solanum tuberosum L.). Very strict homology search and subsequent domain verification with Hidden Markov Model revealed 12 StSULTR genes encoding 18 transcripts. StSULTR genes were mapped on seven S. tuberosum chromosomes. Annotation of StSULTR genes was also done as StSULTR I-IV at group level based mainly on the phylogenetic distribution with Arabidopsis SULTRs. Several tandem and segmental duplications were identified between StSULTR genes. Among these duplications, Ka/Ks ratios indicated neutral nature of mutations that might not be causing any selection. Two segmental and one-tandem duplications were calculated to occur around 147.69, 180.80 and 191.00 million years ago (MYA), approximately corresponding to the time of monocot/dicot divergence. Two other segmental duplications were found to occur around 61.23 and 67.83 MYA, which is very close to the origination of monocotyledons. Most cis-regulatory elements in StSULTRs were found associated with major hormones (such as abscisic acid and methyl jasmonate), and defense and stress responsiveness. The cis-element distribution in duplicated gene pairs indicated the contribution of duplication events in conferring the neofunctionalization/s in StSULTR genes. Notably, RNAseq data analyses unveiled expression profiles of StSULTR genes under different stress conditions. In particular, expression profiles of StSULTR III members suggested their involvement in plant stress responses. Additionally, gene co-expression networks of these group members included various regulatory factors, stress and signaling proteins, and housekeeping and some other proteins with unknown functions.
Genome-Wide Identification and Expression Profiling of Ascorbate Peroxidase (APX) and Glutathione Peroxidase (GPX) Genes Under Drought Stress in Sorghum (Sorghum bicolor L.)
(Springer, 2018) Akbudak, M. Aydın; Filiz, Ertuğrul; Vatansever, Recep; Kontbay, Kübra
APX and GPX are two crucial plant antioxidant enzymes. By protein homology search, nine APX and seven GPX members were identified in Sorghum bicolor genome. They were annotated based on chromosomal localizations as SbAPX1-9 and SbGPX1-7. APXs were distributed on six Sorghum chromosomes and encoded polypeptides of 250-474 residues with characteristic "peroxidase" domain, whereas GPXs were on five chromosomes and encoded proteins of 136-232 residues characterized by a "GSHPx" domain. The first about 1-90 amino acid residues in SbAPXs and about 60-70 amino acid residues in SbGPXs from N-terminus corresponded to transit peptides, and formed the main source of sequence variations. On the other hand, APXs/GPXs appeared to be significantly conserved at the amino acid sequence level. Residues in active and/or metal binding sites of these enzymes were also revealed with inference to their Arabidopsis counterparts. The combined Sorghum-Arabidopsis APX and GPX phylogenies allowed inferring functional roles to putative Sorghum sequences at cross-species level. In digital RNA-seq data from Sorghum, APXs within sensitive genotypes were relatively more responsive to drought compared to GPXs. Differentially upregulated APX4 and downregulated GPX2 suggested that their performance was synergistic. SbAPXs/GPXs expression in drought-exposed sorghum roots and leaves were quantified by Real-Time quantitative PCR (RT-qPCR). Drought-exposed plants morphologically demonstrated reductions in stem/root elongation and size, retardation in plant growth, and erected leaves. Expressions of APXs/GPXs were mostly upregulated in aboveground parts of drought-exposed plants, e.g., leaves while they were downregulated in roots. Furthermore, APX1 and APX5 in leaves, and APX8, APX9, GPX5, and GPX6 in roots showed significant changes in expression levels; therefore, their synergetic regulation during drought should be considered.
Genome-wide identification and expression profiling of EIL gene family in woody plant representative poplar (Populus trichocarpa)
(Elsevier Science Inc, 2017) Filiz, Ertuğrul; Vatansever, Recep; Özyiğit, İbrahim İlker; Uras, Mehmet Emin; Şen, Uğur; Anjum, Naser A.; Pereira, Eduarda
This study aimed to improve current understanding on ethylene-insensitive 3-like (EIL) members, least explored in woody plants such as poplar (Populus trichocarpa Torr. & Grey). Herein, seven putative EIL members were identified in P. trichocarpa genome and were roughly annotated either as EIN3-like sequence associated with ethylene pathway or EIL3-like sequences related with sulfur (S)-pathway. Motif-distribution pattern of proteins also corroborated this annotation. They were distributed on six chromosomes (chrl, 3, 4 and 8-10), and were revealed to encode a protein of 509-662 residues with nuclear localization. The presence of ethylene insensitive 3 (EIN3; PF04873) domain (covering first 80 280 residues from N-terminus) was confirmed by Hidden Markov Model-based search. The first half of EIL proteins (similar to 80-280 residues including EIN3 domain) was substantially conserved. The second half (-300-600 residues) was considerably diverged. Additionally, first half of proteins harbored acidic, praline-rich and glutamine-rich sites, and supported the essentiality of these regions in the transcriptional-activation and protein-function. Moreover, identified six segmental and one-tandem duplications demonstrated the negative or purifying selective nature of mutations. Furthermore, expression profile analysis indicated the possibility of a crosstalk between EIN3-and EIL3-like genes, and co-expression networks implicated their interactions with very diverse panels of biological molecules. (C) 2017 Elsevier Inc. All rights reserved.
Genome-wide identification of galactinol synthase (GolS) genes in Solanum lycopersicum and Brachypodium distachyon
(Elsevier Sci Ltd, 2015) Filiz, Ertuğrul; Özyiğit, İbrahim İlker; Vatansever, Recep
GoIS genes stand as potential candidate genes for molecular breeding and/or engineering programs in order for improving abiotic stress tolerance in plant species. In this study, a total of six galactinol synthase (GolS)genes/proteins were retrieved for Solanum lycopersicum and Brachypodium distachyon. GolS protein sequences were identified to include glyco_transf_8 (PF01501) domain structure, and to have a close molecular weight (36.40-39.59 kDa) and amino acid length (318-347 aa) with a slightly acidic pI (5.35-6.40). The sub-cellular location was mainly predicted as cytoplasmic. S. lycopersicum genes located on chr 1 and 2, and included one segmental duplication while genes of B. distachyon were only on chr 1 with one tandem duplication. GoIS sequences were found to have well conserved motif structures. Cis-acting analysis was performed for three abiotic stress responsive elements, including ABA responsive element (ABRE), dehydration and cold responsive elements (DRE/CRT) and low-temperature responsive element (LTRE). ABRE elements were found in all GoIS genes, except for SIGoIS4; DRE/CRT was not detected in any GoIS genes and LTRE element found in SlGolS1 and BdGolS1 genes. AU analysis in UTR and ORF regions indicated that SlGolS and BdGoIS mRNAs may have a short half-life. SlGolS3 and SlG0lS4 genes may generate more stable transcripts since they included AATTAAA motif for polyadenylation signal POLASIG2. Seconder structures of SIGolS proteins were well conserved than that of BdGolS. Some structural divergences were detected in 3D structures and predicted binding sites exhibited various patterns in GoIS proteins. (C) 2015 Elsevier Ltd. All rights reserved.
Genome-wide identification of mildew resistance locus O (MLO) genes in tree model poplar (Populus trichocarpa): powdery mildew management in woody plants
(Springer, 2018) Filiz, Ertuğrul; Vatansever, Recep
Poplars are economically important fast growing trees. They are exposed to broad range of fungal diseases like powdery mildew (PM). MLOs (mildew resistance locus O), as plant susceptibility genes, act as negative regulators and whose loss-of-functions confer complete resistance to PM disease. Herein, work identified the MLO gene family members in poplar, a woody model species. A total of 26 identified MLOs (annotated as PtMLO1-26) were distributed on 14 poplar chromosomes either individually or in groups of two to four. PtMLO genes encoded a polypeptide of 341-593 residues with a characteristic MLO domain structure. One tandem and eight segmental duplications were revealed in PtMLO genes. PtMLO proteins anchored at plasma membrane and had putative 5-9 TMDs with extracellular/cytosolic N- and C-terminuses. They were rich in leucine (9.1-12.9%), which is reported to play roles in defense response signaling. The C-terminal calmodulin-binding domain (CaMBD), reported to modulate the signaling mechanism in the defense response, was completely preserved in all PtMLOs, except PtMLO6. This domain was partially absent in PtMLO6 which is inferred to be a different MLO type or a pseudogene with a lost/impaired function in PM response. Besides, second and third cytoplasmic loops that are critical for PM-susceptibility were identified in PtMLOs. Particularly, PtMLO17, 18, 19, and 24 genes, inferred from Arabidopsis-poplar comparative phylogeny, were identified as potential candidates that may be involved in poplar-PM resistance. Notably, inductions of 14 PtMLO genes were detected in probes of microarray data such as GSE56865, GSE16417, and GSE23726 under different fungal infections indicating their involvements in plant defense. Overall, this work provided a basis for woody plant genomics for the effective and better management of poplar-PM disease.
Identification and Comparative Analysis of H2O2-Scavenging Enzymes (Ascorbate Peroxidase and Glutathione Peroxidase) in Selected Plants Employing Bioinformatics Approaches
(Frontiers Media Sa, 2016) Özyiğit, İbrahim İlker; Filiz, Ertuğrul; Vatansever, Recep; Kurtoğlu, Kuaybe Y.; Koç, İbrahim; Öztürk, Münir; Anjum, Naser A.
Among major reactive oxygen species (ROS), hydrogen peroxide (H2O2) exhibits dual roles in plant metabolism. Low levels of H2O2 modulate many biological/physiological processes in plants; whereas, its high level can cause damage to cell structures, having severe consequences. Thus, steady-state level of cellular H2O2 must be tightly regulated. Glutathione peroxidases (GPX) and ascorbate peroxidase (APX) are two major ROS-scavenging enzymes which catalyze the reduction of H2O2 in order to prevent potential H2O2-derived cellular damage. Employing bioinformatics approaches, this study presents a comparative evaluation of both GPX and APX in 18 different plant species, and provides valuable insights into the nature and complex regulation of these enzymes. Herein, (a) potential GPX and APX genes/proteins from 18 different plant species were identified, (b) their exon/intron organization were analyzed, (c) detailed information about their physicochemical properties were provided, (d) conserved motif signatures of GPX and APX were identified, (e) their phylogenetic trees and 3D models were constructed, (f) protein-protein interaction networks were generated, and finally (g) GPX and APX gene expression profiles were analyzed. Study outcomes enlightened GPX and APX as major H2O2-scavenging enzymes at their structural and functional levels, which could be used in future studies in the current direction.
Identification of Differentially Expressed Genes in Chilling-Induced Potato (Solanum tuberosum L.); a Data Analysis Study
(Springer, 2015) Koç, İbrahim; Vatansever, Recep; Özyiğit, İbrahim İlker; Filiz, Ertuğrul
Cold stress, as chilling (< 20 A degrees C) or freezing (< 0 A degrees C), is one of the frequently exposed stresses in cultivated plants like potato. Under cold stress, plants differentially modulate their gene expression to develop a cold tolerance/acclimation. In the present study, we aimed to identify the overall gene expression profile of chilling-stressed (+4 A degrees C) potato at four time points (4, 8, 12, and 48 h), with a particular emphasis on the genes related with transcription factors (TFs), phytohormones, lipid metabolism, signaling pathway, and photosynthesis. A total of 3504 differentially expressed genes (DEGs) were identified at four time points of chilling-induced potato, of which 1397 were found to be up-regulated while 2107 were down-regulated. Heatmap showed that genes were mainly up-regulated at 4-, 8-, and 12-h time points; however, at 48-h time point, they inclined to down-regulate. Seventy five up-regulated TF genes were identified from 37 different families/groups, including mainly from bHLH, WRKY, CCAAT-binding, HAP3, and bZIP families. Protein kinases and calcium were major signaling molecules in cold-induced signaling pathway. A collaborated regulation of phytohormones was observed in chilling-stressed potato. Lipid metabolisms were regulated in a way, highly probably, to change membrane composition to avoid cold damage and render in signaling. A down-regulated gene expression profile was observed in photosynthesis pathway, probably resulting from chilling-induced reduced enzyme activity or light-triggered ROSs damage. The findings of this study will be a valuable theoretical knowledge in terms of understanding the chilling-induced tolerance mechanisms in cultivated potato plants as well as in other Solanum species.