Ibrahim Ilker Ozyigit

Identification and Comparative Analysis of H2O2-Scavenging Enzymes (Ascorbate Peroxidase and Glutathione Peroxidase) in Selected Plants Employing Bioinformatics Approaches.

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.

Use of Pyracantha coccinea Roem. as a possible biomonitor for the selected heavy metals

In this study, copper, iron, manganese and nickel levels of branches and leaves of Pyracantha coccinea Roem. (firethorn) were measured for determining the heavy metal pollution in Mugla Province. Plant samples were collected from 34 different localities in four different areas of Mugla Province, during 2006 vegetation period. Unwashed and washed leaf samples and unwashed branch samples were subjected to analysis and copper, iron, manganese and nickel concentrations of samples were measured by inductively coupled plasma optical emission spectrometry. The obtained data were analyzed with “statistical package for the social sciences” statistics program. As a result of measurements, the highest average and lowest values and their collected stations were as follows; the highest average (5.89 ± 0.04 μg/g dw) and the lowest (5.20 ± 0.03 μtg/g dw) values of copper were measured near highways. The average highest iron value (9.53 ±1.68 μtg/g dw) was in industrial area while the lowest was near highways (1.73 ± 0.54 μtg/g dw). The highest value of magnesium accumulation (1.00 ± 0.16 μtg/gdw) was measured near highways. The lowest value was determined in urban area (0.40 ± 0.14 μtg/g dw). The average highest level of nickel was in industrial area while the lowest was determined in urban area. The values were 14.34 ± 1.59 μtg/g and 4.05 ± 0.51 μtg/g dw. As a result, it was proven that P. coccinea could be used as a biomonitor species for some of these heavy metals especially for copper and nickel.

INFLUENCE OF ALUMINUM ON MINERAL NUTRIENT UPTAKE AND ACCUMULATION IN URTICA PILULIFERA L.

Pollutants can have detrimental effects on living organisms. They can cause toxicity, damaging cells, tissues and organs because of their high concentrations or activities. Plants provide a useful system for screening and monitoring environmental pollutants. Among pollutants, aluminum is considered as a primary growth limiting factor for plants resulting in decreased plant growth and development. Although considered to be a non-essential and highly toxic metal ion for growth and development, aluminum (Al) is easily absorbed by plants. Urticaceae family members have high nutrient requirements demonstrated by leaves containing high levels of calcium (Ca), iron (Fe), magnesium (Mg), and nitrogen (N). Urtica pilulifera is one of the important traditional medicinal plants in Turkey. In this study, U. pilulifera was used as a bioindicator to investigate the possible differences in the absorption and accumulation of mineral nutrients at different levels of the Al exposure and examine the mineral nutrition composition of U. pilulifera under Al stress. Also, some growth parameters (leaf-stem fresh and dry weights, root dry weights, stem lengths and leaf surface area) were investigated. U. pilulifera seedlings were grown for two months in growth-room conditions and watered with spiked Hoagland solution, which contained 0, 100, and 200 μM aluminium chloride (AlCl3). It was observed that macro- and micro-nutritional status of roots and leaves was altered by Al exposure. The concentrations of some macro- and micronutrients were reduced while concentrations of others were increased by excess of Al. Some macro- and micronutrients were increased at low level of Al whereas reductions were observed at high level of Al, and vice versa. The patterns were dependent on the macro- or micronutrient and the plant part.

Callus induction and plant regeneration from mature embryos of sunflower

Callus development and efficient shoot and root organogenesis were obtained from five different sunflower (Helianthus annuus L.) genotypes: Trakya 80, Trakya 129, Trakya 259, Trakya 2098, and Viniimk 8931, which are commercially important for Turkey. Plant tissue culture systems were established on Murashige and Skoog (MS) media supplemented with various plant growth regulators using mature embryos of sunflower. For callus induction MS + 1 mg/l 2,4-D, for shoot regeneration MS + 1 mg/l benzyladenine and 0.5 mg/l α-naphthaleneacetic acid were used. Callus induction ratios were around 80–92% in all tested genotypes. The Trakya 259 genotype gave the best shoot regeneration response (44%). All regenerated shoots were rooted on MS medium supplemented with 1 mg/l indolyl-3-butyric acid and on MS medium without any hormones. Mature embryos could be an alternative source for indirect plant regeneration and gene transfer systems for different sunflower genotypes.

Assessment of Cd-induced genotoxic damage in Urtica pilulifera L. using RAPD-PCR analysis

ABSTRACT Plants can be used as biological indicators in assessing the damage done by bioaccumulation of heavy metals and their negative impact on the environment. In the present research, Roman nettle (Urtica pilulifera L.) was employed as a bioindicator for cadmium (Cd) pollution. The comparisons between unexposed and exposed plant samples revealed inhibition of the root growth (∼25.96% and ∼45.92% after treatment with 100 and 200 µmol/L Cd concentrations, respectively), reduction in the total soluble protein quantities (∼53.92% and ∼66.29% after treatment with 100 and 200 µmol/L Cd concentrations, respectively) and a gradual genomic instability when the Cd concentrations were increased. The results indicated that alterations in randomly amplified polymorphic DNA (RAPD) profiles, following the Cd treatments, included normal band losses and emergence of new bands, when compared to the controls. Also, the obtained data from F1 plants, utilized for analysis of genotoxicity, revealed that DNA alterations, occurring in parent plants due to Cd pollution, were transmitted to the next generation.

Agrobacterium rhizogenes-mediated transformation and its biotechnological applications in crops

The history of Agrobacterium-related plant biotechnology goes back for more than three decades with the discovery of molecular mechanisms of crown gall disease in plants. After 1980s, gene technologies began developing rapidly and today, related with the improved gene transfer methods, plant biotechnology has become one of the most important branches in science. Till now, the most important genes related with agricultural affairs have been utilized for cloning of plants with the deployment of different techniques used in genetic engineering. Especially, Agrobacterium tumefaciens was used extensively for transferring desired genetic materials to plants rapidly and effectively by the researchers to create transgenic plants. Recognition of the biology of Agrobacterium species and newly developed applications of their T-DNA systems has been a great step in plant biotechnology. This chapter provides the reader with extensive information on A. rhizogenes which is responsible for the development of hairy root disease in a wide range of dicotyledonous plants and its T-DNA system. This knowledge will be useful in improving utilization of crops and the formulation of new and up-graded transgenic based food products.

Long-Term Effects of Aluminum and Cadmium on Growth, Leaf Anatomy, and Photosynthetic Pigments of Cotton

Aluminum (Al) and cadmium (Cd) are two elements that contaminate soil in different ways as waste products of some industrial processes and that can be tolerated by some plant species in different concentrations. In this study, growth parameters of leaves and stems (fresh and dry weights, stem lengths, leaf surface area, and lamina thickness), anatomical changes in leaves (lower and upper epidermis, stomata and mesophyll tissue), and photosynthetic pigment contents (chlorophyll a and b, total chlorophyll, and carotenoids) were investigated in cotton (Gossypium hirsutum L. cv. Nazilli 84S), which was treated with Al and Cd for 3 months. Cotton seedlings were grown in greenhouse conditions and watered with Hoagland nutrient solutions, which contained 0, 100, and 200 μM aluminum chloride (AlCl3) and cadmium chloride (CdCl2). It was observed that reduced soil pH positively affected many parameters in cotton plants. Aluminum accumulation was greater in leaves than stems while the opposite was true for Cd accumulation. Leaves and stems of cotton plants treated with 100 and 200 μM Al and Cd showed slight growth changes; however, high concentrations of Al (200 μM) caused significant reductions in leaf area and leaf fresh weight, whereas stem fresh weight decreased with 200 μM Cd treatment. Anatomical parameters were mostly affected significantly under both concentrations of Al and Cd solutions (100 and 200 μM). The results revealed that the anatomical changes in the leaves varied in both treatments, and the long-term effect of the tested metals did not include harmful effects on anatomical structures. Moreover, the variations could be signals of tolerance or adaptive mechanisms of the leaves under the determined concentrations.

Isolation of a transcription factor DREB1A gene from Phaseolus vulgaris and computational insights into its characterization: protein modeling, docking and mutagenesis

A transcription factor DREB1A (dehydration-responsive element-binding 1A) gene was amplified and sequenced from the common bean (Phaseolus vulgaris). PvDREB1A had a 777 base pairs (bp) open reading frame encoding a protein of 225 residues. The protein sequence contained a conserved DNA-binding AP2 domain of about 60 residues and a nuclear localization signal (NLS) at N-terminus site. PvDREB1A demonstrated high homology with other DREB1 members only in AP2 domain and NLS site. The phylogenetic distribution of different DREB members showed three main groups as DREB1–3 and PvDREB1A was a member of DREB1 group. Homology modeling and secondary structure analyses revealed that PvDREB1A AP2 domain was packed into the three-stranded antiparallel beta sheets (β1–3) and an alpha helix (α1) almost parallel to these beta sheets. Moreover, DNA-binding AP2 domain of PvDREB1A and GCC-box containing double helix DNA were docked. The docking analysis showed that PvDREB1A AP2 domain could bind to the major groove of the DNA by three-stranded antiparallel beta sheets, with residues Gly86 or Thr87 in β1-sheet and Arg63 or Arg64 in β3-sheet. The docked complex also indicated that AP2 domain has a preferential for the binding of GCC stretches in the double helix DNA. A total of 36 reliably estimated hot spots residues were identified with high mutability grade but none of these residues was essential for the protein function since they are located at outside the DNA-binding AP2 domain of PvDREB1A.

Antimicrobial and antioxidant activities of medicinal plant Glycyrrhiza glabra var. glandulifera from different habitats

ABSTRACT In this study, the antimicrobial and antioxidant activities of root methanolic extracts of Glycyrrhiza glabra var. glandulifera (Waldst. & Kit.) Boiss. (Fabaceae) were investigated. Plant samples were collected from different habitats in the East Mediterranean part of Turkey. The plant extracts were evaluated for antimicrobial activities against nine bacterial and two yeast strains using disc-diffusion and minimum inhibitory concentration methods. The antioxidant activity was determined by using the DPPH (1,1-diphenyl-2-picrylhydrazyl) method. The antimicrobial assays indicated that the plant root extracts were more effective against Gram-positive bacteria than against Gram-negative ones. In addition, the extracts had higher antimicrobial effect against Candida species than against bacteria. The extracts showed good antioxidant activity, with a median inhibitory concentration (IC50) in the range of 588 ± 0.86 µg/mL to 2190 ± 1.73 µg/mL. Results indicated that different environmental conditions in each habitat might affect the contents of chemical compounds and biological activity in the natural licorice populations of. This study also supported the traditional use of licorice and as well as suggested that it may also be its beneficial role in the treatment of other infections. The obtained results indicated that different environmental conditions in each habitat might affect the contents of chemical compounds and the biological activity in the natural licorice populations.

Comparative Analysis and Modeling of Superoxide Dismutases (SODs) in Brachypodium distachyon L.

Superoxide 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.