Search results for: transmembrane%20voltage
19 On the Prediction of Transmembrane Helical Segments in Membrane Proteins Based on Wavelet Transform
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The prediction of transmembrane helical segments (TMHs) in membrane proteins is an important field in the bioinformatics research. In this paper, a new method based on discrete wavelet transform (DWT) has been developed to predict the number and location of TMHs in membrane proteins. PDB coded as 1KQG was chosen as an example to describe the prediction of the number and location of TMHs in membrane proteins by using this method. To access the effect of the method, 80 proteins with known 3D-structure from Mptopo database are chosen at random as the test objects (including 325 TMHs), 308 of which can be predicted accurately, the average predicted accuracy is 96.3%. In addition, the above 80 membrane proteins are divided into 13 groups according to their function and type. In particular, the results of the prediction of TMHs of the 13 groups are satisfying.Keywords: discrete wavelet transform, hydrophobicity, membrane protein, transmembrane helical segments
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 136718 Alternative Splicingof an Arabidopsis Gene, At2g24600, Encoding Ankyrin-Repeat Protein
Authors: H. Sakamoto, S. Kurosawa, M. Suzuki, S. Oguri
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In Arabidopsis, several genes encoding proteins with ankyrin repeats and transmembrane domains (AtANKTM) have been identified as mediators of biotic and abiotic stress responses. It has been known that the expression of an AtANKTM gene, At2g24600, is induced in response to abiotic stress and that there are four splicing variants derived from this locus. In this study, by RT-PCR and sequencing analysis, an unknown splicing variant of the At2g24600 transcript was identified. Based on differences in the predicted amino acid sequences, the five splicing variants are divided into three groups. The three predicted proteins are highly homologous, yet have different numbers of ankyrinrepeats and transmembrane domains. It is generally considered that ankyrin repeats mediate protein-protein interaction and that the number oftransmembrane domains affects membrane topology of proteins. The protein variants derived from the At2g24600 locus may have different molecular functions each other.
Keywords: Alternative splicing, ankyrin repeats, transmembrane domains, Arabidopsis.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 186717 On the Prediction of Transmembrane Helical Segments in Membrane Proteins
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The prediction of transmembrane helical segments (TMHs) in membrane proteins is an important field in the bioinformatics research. In this paper, a method based on discrete wavelet transform (DWT) has been developed to predict the number and location of TMHs in membrane proteins. PDB coded as 1F88 was chosen as an example to describe the prediction of the number and location of TMHs in membrane proteins by using this method. One group of test data sets that contain total 19 protein sequences was utilized to access the effect of this method. Compared with the prediction results of DAS, PRED-TMR2, SOSUI, HMMTOP2.0 and TMHMM2.0, the obtained results indicate that the presented method has higher prediction accuracy.Keywords: hydrophobicity, membrane protein, transmembranehelical segments, wavelet transform
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 151916 Using Reverse Osmosis Membrane for Chromium Removal from Aqueous Solution
Authors: S. A. Mousavi Rad, S. A. Mirbagheri, T. Mohammadi
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In this paper, removal of chromium(VI) from aqueous solution has been researched using reverse osmosis. The influence of transmembrane pressure and feed concentration on permeate flux, water recovery, permeate concentration, and salt rejection was studied. The results showed that according to the variation of transmembrane pressure and feed concentration, the permeate flux and salt rejection were in the range 19.17 to 58.75 l/m2.min and 99.51 to 99.8 %, respectively. The highest permeate flux, 58.75 l/m2.min, and water recovery, 42.47 %, were obtained in the highest pressure and the lowest feed concentration. On the other hand, the lowest permeate concentration, 0.01 mg/l, and the highest salt rejection, 99.8 %, were obtained in the highest pressure and the lowest feed concentration.Keywords: solution, Chromium, Removal, Reverse osmosis.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 253415 Separation of Polyphenolics and Sugar by Ultrafiltration: Effects of Operating Conditions on Fouling and Diafiltration
Authors: Diqiao S. Wei, M. Hossain, Zaid S. Saleh
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Polyphenolics and sugar are the components of many fruit juices. In this work, the performance of ultra-filtration (UF) for separating phenolic compounds from apple juice was studied by performing batch experiments in a membrane module with an area of 0.1 m2 and fitted with a regenerated cellulose membrane of 1 kDa MWCO. The effects of various operating conditions: transmembrane pressure (3, 4, 5 bar), temperature (30, 35, 40 ºC), pH (2, 3, 4, 5), feed concentration (3, 5, 7, 10, 15 ºBrix for apple juice) and feed flow rate (1, 1.5, 1.8 L/min) on the performance were determined. The optimum operating conditions were: transmembrane pressure 4 bar, temperature 30 ºC, feed flow rate 1 – 1.8 L/min, pH 3 and 10 Brix (apple juice). After performing ultrafiltration under these conditions, the concentration of polyphenolics in retentate was increased by a factor of up to 2.7 with up to 70% recovered in the permeate and with approx. 20% of the sugar in that stream.. Application of diafiltration (addition of water to the concentrate) can regain the flux by a factor of 1.5, which has been decreased due to fouling. The material balance performed on the process has shown the amount of deposits on the membrane and the extent of fouling in the system. In conclusion, ultrafiltration has been demonstrated as a potential technology to separate the polyphenolics and sugars from their mixtures and can be applied to remove sugars from fruit juice.Keywords: Fouling, membrane, polyphenols, ultrafiltration.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 333014 Response Surface Methodology Approach to Defining Ultrafiltration of Steepwater from Corn Starch Industry
Authors: Zita I. Šereš, Ljubica P. Dokić, Dragana M. Šoronja Simović, Cecilia Hodur, Zsuzsanna Laszlo, Ivana Nikolić, Nikola Maravić
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In this work the concentration of steepwater from corn starch industry is monitored using ultrafiltration membrane. The aim was to examine the conditions of ultrafiltration of steepwater by applying the membrane of 2.5nm. The parameters that vary during the course of ultrafiltration, were the transmembrane pressure, flow rate, while the permeate flux and the dry matter content of permeate and retentate were the dependent parameter constantly monitored during the process. Experiments of ultrafiltration are conducted on the samples of steepwater, which were obtained from the starch wet milling plant „Jabuka“ Pancevo. The procedure of ultrafiltration on a single-channel 250mm lenght, with inner diameter of 6.8mm and outer diameter of 10mm membrane were carried on. The membrane is made of a-Al2O3 with TiO2 layer obtained from GEA (Germany). The experiments are carried out at a flow rate ranging from 100 to 200lh-1 and transmembrane pressure of 1-3 bars. During the experiments of steepwater ultrafiltration, the change of permeate flux, dry matter content of permeate and retentate, as well as the absorbance changes of the permeate and retentate were monitored. The experimental results showed that the maximum flux reaches about 40lm-2h-1. For responses obtained after experiments, a polynomial model of the second degree is established to evaluate and quantify the influence of the variables. The quadratic equitation fits with the experimental values, where the coefficient of determination for flux is 0.96. The dry matter content of the retentate is increased for about 6%, while the dry matter content of permeate was reduced for about 35-40%, respectively. During steepwater ultrafiltration in permeate stays 40% less dry matter compared to the feed.
Keywords: Ultrafiltration, steepwater, starch industry, ceramic membrane.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 210013 Immobilized Liquid Membrane for Propylene- Propane Separation
Authors: Maryam TakhtRavanchi, Tahereh Kaghazchi, Ali Kargari
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Separation of propylene-propane mixture using immobilized liquid membrane was investigated. The effect of transmembrane pressure and carrier concentration on membrane separation performance was studied. It was observed that for 30:70 (vol. %) propylene-propane mixture, at pressure of 120kPa and carrier concentration of 20wt. %, a separation factor of 474 was obtained.Keywords: Facilitated Transport, Immobilized Liquid Membrane, Propylene-Propane Separation, Silver Nitrate.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 195312 ICAM-2, A Protein of Antitumor Immune Response in Mekong Giant Catfish (Pangasianodon gigas)
Authors: Jiraporn Rojtinnakorn
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ICAM-2 (intercellular adhesion molecule 2) or CD102 (Cluster of Differentiation 102) is type I transmembrane glycoproteins, composing 2-9 immunoglobulin-like C2-type domains. ICAM-2 plays the particular role in immune response and cell surveillance. It is concerned in innate and specific immunity, cell survival signal, apoptosis, and anticancer. EST clone of ICAM-2, from P. gigas blood cell EST libraries, showed high identity to human ICAM-2 (92%) with conserve region of ICAM N-terminal domain and part of Ig superfamily. Gene and protein of ICAM-2 has been founded in mammals. This is the first report of ICAM-2 in fish
Keywords: ICAM-2, CD102, Pangasianodon gigas, antitumor.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 177511 Edible Oil Industry Wastewater Treatment by Microfiltration with Ceramic Membrane
Authors: Zita Šereš, Dragana Šoronja Simović, Ljubica Dokić, Lidietta Giorno, Biljana Pajin, Cecilia Hodur, Nikola Maravić
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Membrane technology is convenient for separation of suspended solids, colloids and high molecular weight materials that are present. The idea is that the waste stream from edible oil industry, after the separation of oil by using skimmers is subjected to microfiltration and the obtained permeate can be used again in the production process. The wastewater from edible oil industry was used for the microfiltration. For the microfiltration of this effluent a tubular membrane was used with a pore size of 200 nm at transmembrane pressure in range up to 3 bar and in range of flow rate up to 300 L/h. Box–Behnken design was selected for the experimental work and the responses considered were permeate flux and chemical oxygen demand (COD) reduction. The reduction of the permeate COD was in the range 40-60% according to the feed. The highest permeate flux achieved during the process of microfiltration was 160 L/m2h.
Keywords: Ceramic membrane, edible oil, microfiltration, wastewater.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 157610 All-or-None Principle and Weakness of Hodgkin-Huxley Mathematical Model
Authors: S. A. Sadegh Zadeh, C. Kambhampati
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Mathematical and computational modellings are the necessary tools for reviewing, analysing, and predicting processes and events in the wide spectrum range of scientific fields. Therefore, in a field as rapidly developing as neuroscience, the combination of these two modellings can have a significant role in helping to guide the direction the field takes. The paper combined mathematical and computational modelling to prove a weakness in a very precious model in neuroscience. This paper is intended to analyse all-or-none principle in Hodgkin-Huxley mathematical model. By implementation the computational model of Hodgkin-Huxley model and applying the concept of all-or-none principle, an investigation on this mathematical model has been performed. The results clearly showed that the mathematical model of Hodgkin-Huxley does not observe this fundamental law in neurophysiology to generating action potentials. This study shows that further mathematical studies on the Hodgkin-Huxley model are needed in order to create a model without this weakness.
Keywords: All-or-none, computational modelling, mathematical model, transmembrane voltage, action potential.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 12979 Structural Basis of Resistance of Helicobacterpylori DnaK to Antimicrobial Peptide Pyrrhocoricin
Authors: Musammat F. Nahar, Anna Roujeinikova
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Bacterial molecular chaperone DnaK plays an essential role in protein folding, stress response and transmembrane targeting of proteins. DnaKs from many bacterial species, including Escherichia coli, Salmonella typhimurium and Haemophilus infleunzae are the molecular targets for the insect-derived antimicrobial peptide pyrrhocoricin. Pyrrhocoricin-like peptides bind in the substrate recognition tunnel. Despite the high degree of crossspecies sequence conservation in the substrate-binding tunnel, some bacteria are not sensitive to pyrrhocoricin. This work addresses the molecular mechanism of resistance of Helicobacter pylori DnaK to pyrrhocoricin. Homology modelling, structural and sequence analysis identify a single aminoacid substitution at the interface between the lid and the β-sandwich subdomains of the DnaK substrate-binding domain as the major determinant for its resistance.
Keywords: Helicobacter pylori, molecular chaperone DnaK, pyrrhocoricin, structural biology.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 17018 The Expression of a Novel Gene Encoding an Ankyrin-Repeat Protein, DRA1, is Regulated by Drought-Responsive Alternative Splicing
Authors: H. Sakamoto, Y. Nakagawara, S. Oguri
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Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin1), whose disruption leads to increased drought-stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild-type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1is regulated in response to drought stress by alternative splicing.
Keywords: Alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 16917 The Expression of a Novel Gene Encoding an Ankyrin-Repeat Protein, DRA1, is Regulated by Drought-Responsive Alternative Splicing
Authors: H. Sakamoto, Y. Nakagawara, S. Oguri
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Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin1), whose disruption leads to increased drought-stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild-type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1is regulated in response to drought stress by alternative splicing.
Keywords: Alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 18136 The Effect of Ultrasound on Permeation Flux and Changes in Blocking Mechanisms during Dead-End Microfiltration of Carrot Juice
Authors: A. Hemmati, H. Mirsaeedghazi, M. Aboonajmi
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Carrot juice is one of the most nutritious foods that are consumed around the world. Large particles in carrot juice causing turbid appearance make some problems in the concentration process such as off-flavor due to the large particles burnt on the walls of evaporators. Microfiltration (MF) is a pressure driven membrane separation method that can clarify fruit juices without enzymatic treatment. Fouling is the main problem in the membrane process causing reduction of permeate flux. Ultrasound as a cleaning technique was applied at 20 kHz to reduce fouling in membrane clarification of carrot juice using dead-end MF system with polyvinylidene fluoride (PVDF) membrane. Results showed that application of ultrasound waves reduce diphasic characteristic of carrot juice and permeate flux increased. Evaluation of different membrane fouling mechanisms showed that application of ultrasound waves changed creation time of each fouling mechanism. Also, its behavior was changed with varying transmembrane pressure.
Keywords: Carrot juice, dead end, microfiltration, ultrasound.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 8775 Microfiltration of the Sugar Refinery Wastewater Using Ceramic Membrane with Kenics Static Mixer
Authors: Zita Šereš, Ljubica Dokić, Nikola Maravić, Dragana Šoronja–Simović, Cecilia Hodur, Ivana Nikolić, Biljana Pajin
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New environmental regulations and the increasing market preference for companies that respect the ecosystem had encouraged the industry to look after new treatments for its effluents. The sugar industry, one of the largest emitter of environmental pollutants, follows this tendency. Membrane technology is convenient for separation of suspended solids, colloids and high molecular weight materials that are present in a wastewater from sugar industry. The idea is to microfilter the wastewater, where the permeate passes through the membrane and becomes available for recycle and re-use in the sugar manufacturing process. For microfiltration of this effluent a tubular ceramic membrane was used with a pore size of 200 nm at transmembrane pressure in range of 1–3 bars and in range of flow rate of 50–150 l/h. Kenics static mixer was used for permeate flux enhancement. Turbidity and suspended solids were removed and the permeate flux was continuously monitored during the microfiltration process. The flux achieved after 90 minutes of microfiltration was in a range of 50–70 l/m2h. The obtained turbidity decrease was in the range of 50-99 % and total amount of suspended solids was removed.Keywords: Ceramic membrane, microfiltration, sugar industry, wastewater.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 18174 Study of Functional Relevant Conformational Mobility of β-2 Adrenoreceptor by Means of Molecular Dynamics Simulation
Authors: G. V. Novikov, V. S. Sivozhelezov, S. S. Kolesnikov, K. V. Shaitan
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The study reports about the influence of binding of orthosteric ligands as well as point mutations on the conformational dynamics of β-2-adrenoreceptor. Using molecular dynamics simulation we found that there was a little fraction of active states of the receptor in its apo (ligand free) ensemble corresponded to its constitutive activity. Analysis of MD trajectories indicated that such spontaneous activation of the receptor is accompanied by the motion in intracellular part of its alpha-helices. Thus receptor’s constitutive activity directly results from its conformational dynamics. On the other hand the binding of a full agonist resulted in a significant shift of the initial equilibrium towards its active state. Finally, the binding of the inverse agonist stabilized the receptor in its inactive state. It is likely that the binding of inverse agonists might be a universal way of constitutive activity inhibition in vivo. Our results indicate that ligand binding redistribute pre-existing conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux-Model) of the receptor rather than cause induced fit in it. Therefore, the ensemble of biologically relevant receptor conformations is encoded in its spatial structure, and individual conformations from that ensemble might be used by the cell in conformity with the physiological behavior.
Keywords: Seven-transmembrane receptors, constitutive activity, activation, x-ray crystallography, principal component analysis, molecular dynamics simulation.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 39053 A Novel Gene Encoding Ankyrin-Repeat Protein, SHG1, is Indispensable for Seed Germination under Moderate Salt Stress
Authors: H. Sakamoto, J. Tochimoto, S. Kurosawa, M. Suzuki, S. Oguri
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Salt stress adversely affects plant growth at various stages of development including seed germination, seedling establishment, vegetative growth and finally reproduction. Because of their immobile nature, plants have evolved mechanisms to sense and respond to salt stress. Seed dormancy is an adaptive trait that enables seed germination to coincide with favorable environmental conditions. We identified a novel locus of Arabidopsis, designated SHG1 (salt hypersensitive germination 1), whose disruption leads to reduced germination rate under moderate salt stress conditions. SHG1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. The shg1-disrupted Arabidopsis mutant died at the cotyledon stage when sown on salt-containing medium, although wild-type plants could form true leaves under the same conditions. On the other hand, this mutant showed similar phenotypes to wild-type plants when sown on medium without salt and transferred to salt-containing medium at the vegetative stage. These results suggested that SHG1 played indispensable role in the seed germination and seedling establishment under moderate salt stress conditions. SHG1 may be involved in the release of seed dormancy.
Keywords: Germination, ankyrin repeat, Arabidopsis, salt tolerance.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 18842 Bone Generation through Mechanical Loading
Authors: R. S. A. Nesbitt, J. Macione, A. Debroy, S. P. Kotha
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Bones are dynamic and responsive organs, they regulate their strength and mass according to the loads which they are subjected. Because, the Wnt/β-catenin pathway has profound effects on the regulation of bone mass, we hypothesized that mechanical loading of bone cells stimulates Wnt/β-catenin signaling, which results in the generation of new bone mass. Mechanical loading triggers the secretion of the Wnt molecule, which after binding to transmembrane proteins, causes GSK-3β (Glycogen synthase kinase 3 beta) to cease the phosphorylation of β-catenin. β-catenin accumulation in the cytoplasm, followed by its transport into the nucleus, binding to transcription factors (TCF/LEF) that initiate transcription of genes related to bone formation. To test this hypothesis, we used TOPGAL (Tcf Optimal Promoter β-galactosidase) mice in an experiment in which cyclic loads were applied to the forearm. TOPGAL mice are reporters for cells effected by the Wnt/β-catenin signaling pathway. TOPGAL mice are genetically engineered mice in which transcriptional activation of β- catenin, results in the production of an enzyme, β-galactosidase. The presence of this enzyme allows us to localize transcriptional activation of β-catenin to individual cells, thereby, allowing us to quantify the effects that mechanical loading has on the Wnt/β-catenin pathway and new bone formation. The ulnae of loaded TOPGAL mice were excised and transverse slices along different parts of the ulnar shaft were assayed for the presence of β-galactosidase. Our results indicate that loading increases β-catenin transcriptional activity in regions where this pathway is already primed (i.e. where basal activity is already higher) in a load magnitude dependent manner. Further experiments are needed to determine the temporal and spatial activation of this signaling in relation to bone formation.Keywords: Bone Resorption and Formation, Mechanical Loading of Bone, Wnt Signaling Pathway & β-catenin.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 14341 Rice cDNA Encoding PROLM is Capable of Rescuing Salt Sensitive Yeast Phenotypes G19 and Axt3K from Salt Stress
Authors: Prasad Senadheera, Younousse Saidi, Frans JM Maathuis
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Rice seed expression (cDNA) library in the Lambda Zap 11® phage constructed from the developing grain 10-20 days after flowering was transformed into yeast for functional complementation assays in three salt sensitive yeast mutants S. cerevisiae strain CY162, G19 and Axt3K. Transformed cells of G19 and Axt3K with pYES vector with cDNA inserts showed enhance tolerance than those with empty pYes vector. Sequencing of the cDNA inserts revealed that they encode for the putative proteins with the sequence homologous to rice putative protein PROLM24 (Os06g31070), a prolamin precursor. Expression of this cDNA did not affect yeast growth in absence of salt. Axt3k and G19 strains expressing the PROLM24 were able to grow upto 400 mM and 600 mM of NaCl respectively. Similarly, Axt3k mutant with PROLM24 expression showed comparatively higher growth rate in the medium with excess LiCl (50 mM). The observation that expression of PROLM24 rescued the salt sensitive phenotypes of G19 and Axt3k indicates the existence of a regulatory system that ameliorates the effect of salt stress in the transformed yeast mutants. However, the exact function of the cDNA sequence, which shows partial sequence homology to yeast UTR1 is not clear. Although UTR1 involved in ferrous uptake and iron homeostasis in yeast cells, there is no evidence to prove its role in Na+ homeostasis in yeast cells. Absence of transmembrane regions in Os06g31070 protein indicates that salt tolerance is achieved not through the direct functional complementation of the mutant genes but through an alternative mechanism.Keywords: Rice seed expression, salt stress, prolamin, salinitytolerance, Oryza sativa
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1859