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‣ Heat shock-triggered Ca2+ mobilization accompanied by pectin methylesterase activity and cytosolic Ca2+ oscillation are crucial for plant thermotolerance

Wu, Hui-Chen; Jinn, Tsung-Luo
Fonte: Landes Bioscience Publicador: Landes Bioscience
Tipo: Artigo de Revista Científica
Português
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Apoplastic Ca2+ concentration controls membrane permeability, cell wall stabilization and cell integrity; however, little is known about its role in thermotolerance in plants. Here, we report that the acquired thermotolerance of etiolated rice seedlings (Oryza sativa) was abolished by an exogenously supplied Ca2+ chelator, EGTA, related to increased cellular content leakage during heat shock (HS) treatment. Thermotolerance was restored by the addition of Ca2+ during EGTA incubation. Pectin methylesterase (EC 3.1.1.11), a cell-wall remodeling enzyme, was activated in response to HS and its elevated activity was related to the recovery of the HS-released Ca2+ concentration. EGTA interfered with the capability of HS to increase oscillation of [Ca2+]cyt content. We assume that heat-activated PME activity is involved in cell-wall localized Ca2+. The removal of apoplastic Ca2+ might participate in HS signaling to induce HS protein expression and cell-wall remodeling to retain plasma membrane integrity, prevent cellular content leakage and confer thermoprotection.

‣ Addition of Genes for Cellobiase and Pectinolytic Activity in Escherichia coli for Fuel Ethanol Production from Pectin-Rich Lignocellulosic Biomass▿

Edwards, Meredith C.; Henriksen, Emily DeCrescenzo; Yomano, Lorraine P.; Gardner, Brian C.; Sharma, Lekh N.; Ingram, Lonnie O.; Doran Peterson, Joy
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /08/2011 Português
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Ethanologenic Escherichia coli strain KO11 was sequentially engineered to contain the Klebsiella oxytoca cellobiose phosphotransferase genes (casAB) as well as a pectate lyase (pelE) from Erwinia chrysanthemi, yielding strains LY40A (casAB) and JP07 (casAB pelE), respectively. To obtain an effective secretion of PelE, the Sec-dependent pathway out genes from E. chrysanthemi were provided on a cosmid to strain JP07 to construct strain JP07C. Finally, oligogalacturonide lyase (ogl) from E. chrysanthemi was added to produce strain JP08C. E. coli strains LY40A, JP07, JP07C, and JP08C possessed significant cellobiase activity in cell lysates, while only strains JP07C and JP08C demonstrated extracellular pectate lyase activity. Fermentations conducted by using a mixture of pure sugars representative of the composition of sugar beet pulp (SBP) showed that strains LY40A, JP07, JP07C, and JP08C were able to ferment cellobiose, resulting in increased ethanol production from 15 to 45% in comparison to that of KO11. Fermentations with SBP at very low fungal enzyme loads during saccharification revealed significantly higher levels of ethanol production for LY40A, JP07C, and JP08C than for KO11. JP07C ethanol yields were not considerably higher than those of LY40A; however...

‣ Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization

Wang, Junmei; Tingjun, Hou
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 12/07/2011 Português
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Molecular mechanical force field (FF) methods are useful in studying condensed phase properties. They are complementary to experiment and can often go beyond experiment in atomic details. Even a FF is specific for studying structures, dynamics and functions of biomolecules, it is still important for the FF to accurately reproduce the experimental liquid properties of small molecules that represent the chemical moieties of biomolecules. Otherwise, the force field may not describe the structures and energies of macromolecules in aqueous solutions properly. In this work, we have carried out a systematic study to evaluate the General AMBER Force Field (GAFF) in studying densities and heats of vaporization for a large set of organic molecules that covers the most common chemical functional groups. The latest techniques, such as the particle mesh Ewald (PME) for calculating electrostatic energies, and Langevin dynamics for scaling temperatures, have been applied in the molecular dynamics (MD) simulations. For density, the average percent error (APE) of 71 organic compounds is 4.43% when compared to the experimental values. More encouragingly, the APE drops to 3.43% after the exclusion of two outliers and four other compounds for which the experimental densities have been measured with pressures higher than 1.0 atm. For heat of vaporization...

‣ Pectin Methylesterase Genes Influence Solid Wood Properties of Eucalyptus pilularis1[C][W][OA]

Sexton, Timothy R.; Henry, Robert J.; Harwood, Chris E.; Thomas, Dane S.; McManus, Luke J.; Raymond, Carolyn; Henson, Michael; Shepherd, Mervyn
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
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This association study of Eucalyptus pilularis populations provides empirical evidence for the role of Pectin Methylesterase (PME) in influencing solid wood characteristics of Eucalyptus. PME6 was primarily associated with the shrinkage and collapse of drying timber, which are phenotypic traits consistent with the role of pectin as a hydrophilic polysaccharide. PME7 was primarily associated with cellulose and pulp yield traits and had an inverse correlation with lignin content. Selection of specific alleles in these genes may be important for improving trees as sources of high-quality wood products. A heterozygote advantage was postulated for the PME7 loci and, in combination with haplotype blocks, may explain the absence of a homozygous class at all single-nucleotide polymorphisms investigated in this gene.

‣ In Vitro-Selected Drug-Resistant Varicella-Zoster Virus Mutants in the Thymidine Kinase and DNA Polymerase Genes Yield Novel Phenotype-Genotype Associations and Highlight Differences between Antiherpesvirus Drugs

Andrei, G.; Topalis, D.; Fiten, P.; McGuigan, C.; Balzarini, J.; Opdenakker, G.; Snoeck, R.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /03/2012 Português
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Varicella zoster virus (VZV) is usually associated with mild to moderate illness in immunocompetent patients. However, older age and immune deficiency are the most important risk factors linked with virus reactivation and severe complications. Treatment of VZV infections is based on nucleoside analogues, such as acyclovir (ACV) and its valyl prodrug valacyclovir, penciclovir (PCV) as its prodrug famciclovir, and bromovinyldeoxyuridine (BVDU; brivudin) in some areas. The use of the pyrophosphate analogue foscarnet (PFA) is restricted to ACV-resistant (ACVr) VZV infections. Since antiviral drug resistance is an emerging problem, we attempt to describe the contributions of specific mutations in the viral thymidine kinase (TK) gene identified following selection with ACV, BVDU and its derivative BVaraU (sorivudine), and the bicyclic pyrimidine nucleoside analogues (BCNAs), a new class of potent and specific anti-VZV agents. The string of 6 Cs at nucleotides 493 to 498 of the VZV TK gene appeared to function as a hot spot for nucleotide insertions or deletions. Novel amino acid substitutions (G24R and T86A) in VZV TK were also linked to drug resistance. Six mutations were identified in the “palm domain” of VZV DNA polymerase in viruses selected for resistance to PFA...

‣ Methanol May Function as a Cross-Kingdom Signal

Dorokhov, Yuri L.; Komarova, Tatiana V.; Petrunia, Igor V.; Kosorukov, Vyacheslav S.; Zinovkin, Roman A.; Shindyapina, Anastasia V.; Frolova, Olga Y.; Gleba, Yuri Y.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 26/04/2012 Português
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Recently, we demonstrated that leaf wounding results in the synthesis of pectin methylesterase (PME), which causes the plant to release methanol into the air. Methanol emitted by a wounded plant increases the accumulation of methanol-inducible gene mRNA and enhances antibacterial resistance as well as cell-to-cell communication, which facilitates virus spreading in neighboring plants. We concluded that methanol is a signaling molecule involved in within-plant and plant-to-plant communication. Methanol is considered to be a poison in humans because of the alcohol dehydrogenase (ADH)-mediated conversion of methanol into toxic formaldehyde. However, recent data showed that methanol is a natural compound in normal, healthy humans. These data call into question whether human methanol is a metabolic waste product or whether methanol has specific function in humans.

‣ The Absolute Free Energy of Binding of Avidin/Biotin Revisited

General, Ignacio J.; Dragomirova, Ralitsa; Meirovitch, Hagai
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
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The binding of biotin to avidin is one of the strongest in nature with absolute free energy of binding, ΔA0 = −20.4 kcal/mol. Therefore, this complex became a target for a large number of computational studies, which all, however, are based on approximate techniques or simplified models and have led to a wide range of results Therefore, ΔA0 is calculated here by rigorous statistical mechanical methods and models that consider long-range electrostatics. (1) We apply our method, “hypothetical scanning molecular dynamics with thermodynamic integration” (HSMD-TI) to avidin-biotin modeled by periodic boundary conditions with Particle Mesh Ewald (PME). (2) We apply the double decoupling method (DDM) to this system modeled by the Spherical Solvent Boundary Potential (SSBP) and the Generalized Solvent Boundary Potential (GSBP). The corresponding results for neutral biotin, ΔA0=−29.1±0.8 and −25.2±0.5 kcal/mol are significantly lower than the experimental value; we also provide the result for a charged biotin, ΔA0 = −32.6±0.8 kcal/mol. It is plausible to suggest that this disagreement with the experiment may stem from ignoring the (positive) contribution of a mobile loop that changes its structure upon ligand binding.

‣ Postharvest Analysis of Lowland Transgenic Tomato Fruits Harboring hpRNAi-ACO1 Construct

Behboodian, Bita; Mohd Ali, Zainon; Ismail, Ismanizan; Zainal, Zamri
Fonte: The Scientific World Journal Publicador: The Scientific World Journal
Tipo: Artigo de Revista Científica
Publicado em 31/07/2012 Português
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The plant hormone, ethylene, is an important regulator which involved in regulating fruit ripening and flower senescence. In this study, RNA interference (RNAi) technology was employed to silence the genes involved in ethylene biosynthetic pathway. This was achieved by blocking the expression of specific gene encoding the ACC oxidase. Initially, cDNA corresponding to ACO1 of lowland tomato cultivar (MT1), which has high identity with ACO1 of Solanum lycopersicum in GenBank, was cloned through RT-PCR. Using a partial coding region of ACO1, one hpRNAi transformation vector was constructed and expressed ectopically under the 35S promoter. Results showed that transgenic lines harboring the hpRNA-ACO1 construct had lower ethylene production and a longer shelf life of 32 days as compared to 10 days for wild-type fruits. Changes in cell wall degrading enzyme activities were also investigated in cases where the transgenic fruits exhibited reduced rates of firmness loss, which can be associated with a decrease in pectin methylesterase (PME) and polygalacturonase (PG) activities. However, no significant change was detected in both transgenic and wild-type fruits in terms of β-galactosidase (β-Gal) activity and levels of total soluble solid...

‣ Revisiting Molecular Dynamics on a CPU/GPU system: Water Kernel and SHAKE Parallelization

Ruymgaart, A. Peter; Elber, Ron
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Português
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We report Graphics Processing Unit (GPU) and Open-MP parallel implementations of water-specific force calculations and of bond constraints for use in Molecular Dynamics simulations. We focus on a typical laboratory computing-environment in which a CPU with a few cores is attached to a GPU. We discuss in detail the design of the code and we illustrate performance comparable to highly optimized codes such as GROMACS. Beside speed our code shows excellent energy conservation. Utilization of water-specific lists allows the efficient calculations of non-bonded interactions that include water molecules and results in a speed-up factor of more than 40 on the GPU compared to code optimized on a single CPU core for systems larger than 20,000 atoms. This is up four-fold from a factor of 10 reported in our initial GPU implementation that did not include a water-specific code. Another optimization is the implementation of constrained dynamics entirely on the GPU. The routine, which enforces constraints of all bonds, runs in parallel on multiple Open-MP cores or entirely on the GPU. It is based on Conjugate Gradient solution of the Lagrange multipliers (CG SHAKE). The GPU implementation is partially in double precision and requires no communication with the CPU during the execution of the SHAKE algorithm. The (parallel) implementation of SHAKE allows an increase of the time step to 2.0fs while maintaining excellent energy conservation. Interestingly...

‣ PME aiming for quality, originality and peer recognition

Peeraer, Griet
Fonte: Bohn Stafleu van Loghum Publicador: Bohn Stafleu van Loghum
Tipo: Artigo de Revista Científica
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‣ Isolation and Expression analysis of OsPME1, encoding for a putative Pectin Methyl Esterase from Oryza sativa (subsp. indica)

Kanneganti, Vydehi; Gupta, Aditya Kumar
Fonte: Springer-Verlag Publicador: Springer-Verlag
Tipo: Artigo de Revista Científica
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Pectin Methyl Esterases (PMEs) play an essential role during plant development by affecting the mechanical properties of the plant cell walls. Recent studies indicated that PMEs play important role in pollen tube development. In this study, we isolated a 1.3 kb cDNA clone from rice panicle cDNA library. It contained a 1038 bp of open reading frame (ORF) encoding for a putative pectin methyl esterase of 345 aminoacids with a 20 aminoacid signal peptide and was hence designated as OsPME1 (Oryza sativaPectin Methyl Esterase 1). It contained the structural arrangement GXYXE and GXXDFIF, found in the active groups of all PMEs. OsPME1 gene product shared varying identities, ranging from 52 % to 33 % with PMEs from other plant species belonging to Brassicaceae, Fabaceae, Amaranthaceae and Funariaceae. Southern blot analysis indicated that PME1 exists as a single copy in the rice genome. Expression pattern analysis revealed that OsPME1 is expressed only in pollen grains, during the later stages of their development and was also regulated by various abiotic stress treatments and phytohormones. Functional characterization of this pollen specific PME from rice would enable us to understand its role in pollen development.

‣ Effect of calcium on cold storage and post-storage quality of peach

Gupta, Navjot; Jawandha, Sukhjit Kaur; Gill, Parmpal Singh
Fonte: Springer-Verlag Publicador: Springer-Verlag
Tipo: Artigo de Revista Científica
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Peach (Prunus persica) fruits of cv. ‘Earli Grande’ were treated with CaCl2 (4 and 6%) and stored at 0–2 °C and 85–90% RH for 21 days followed by storage at ambient conditions (28–30 °C, 65–70% RH) for 72 h. CaCl2 at 6% effectively in reduced spoilage, physiological loss in weight (PLW) effectively reduced and maintained fruit firmness, palatability rating, acidity, vitamin A content and pectin methyl estrase (PME) activity during storage. Results revealed that peach fruits harvested at optimum stage followed by post-harvest dip in 6% CaCl2 solution for 10 min can be stored for 3 weeks in cold storage (0–2 °C, 85–90% RH) with post-storage shelf-life of 3 days at ambient conditions (28–30 °C, 65–70% RH) with acceptable edible quality of fruits.

‣ A Protein•Protein Interaction Platform Involved in Recruitment of GLD-3 to the FBF•fem-3 mRNA Complex

Wu, Joann; Campbell, Zachary T.; Menichelli, Elena; Wickens, Marvin; Williamson, James R.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
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The Pumilio and FBF (PUF) family of RNA-binding proteins interacts with protein partners to post-transcriptionally regulate mRNAs in eukaryotes. The interaction between PUF family member fem-3binding factor (FBF) and germline development defective-3 protein (GLD-3) promotes spermatogenesis in Caenorhabditis elegans by increasing expression of the fem-3 mRNA. Defined here in these studies is the molecular basis for this critical interaction. A 10 amino acid region within GLD-3 is required for FBF binding, while a 7 amino acid loop in FBF between PUF repeats 7 and 8 is necessary for GLD-3 binding. These short sequences are conserved, as other FBF-bindingproteins bear sequences similar to those in GLD-3 and other C. elegans PUF proteins contain sequences similar to those in FBF. The FBF-binding region of GLD-3 forms a ternary complex with FBF on the point mutation element (PME) in the fem-3 3’ untranslated region (UTR) and formation of this GLD-3•FBF complex does not impact the RNA-binding activity of FBF. These data raise the possibility of alternative models involving the formation of a GLD-3•FBF•RNA complex in the regulation of germline mRNAs.

‣ Prickle1 is expressed in distinct cell populations of the central nervous system and contributes to neuronal morphogenesis

Liu, Chunqiao; Lin, Chen; Whitaker, D. Thad; Bakeri, Hirva; Bulgakov, Oleg V.; Liu, Pinghu; Lei, Jingqi; Dong, Lijin; Li, Tiansen; Swaroop, Anand
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
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Development of axons and dendrites constitutes a critical event in neuronal maturation and seems to require signaling through the planar cell polarity (PCP) pathway. Mutations in components of the PCP pathway lead to a spectrum of neurological phenotypes and disorders. For example, a missense mutation in Prickle 1 (Pk1) is associated with progressive myoclonus epilepsy (PME) in humans, and its reduced gene dosage increases sensitivity to induced seizure in mice. In an effort to unravel the role of the PCP pathway in mammalian neuronal development, we examined the expression of Pk1 in the central nervous system (CNS) using in situ hybridization (ISH) in combination with a genetic knock-in approach. We show that Pk1 transcripts are detected in the postmitotic cells of the subplate and cortical plate during mid- and late stages of cortical neurogenesis. In adult brain, Pk1 is expressed in distinct neuronal and glial cell populations, with dynamic formation of dendrites and glial processes during development. Of all the cell types in the mature retina, the highest expression of Pk1 is detected in cholinergic amacrine neurons. Knockdown of Pk1 by shRNA or dominant-negative constructs causes reduced axonal and dendritic extension in hippocampal neurons. Similarly...

‣ Pocket Mobile Echocardiography: The Next-Generation Stethoscope? A Comparison of Rapidly Acquired PME Images to Standard TTE

Liebo, Max J.; Israel, Rachel L.; Lillie, Elizabeth O.; Smith, Michael R.; Rubenson, David S.; Topol, Eric J.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 05/07/2011 Português
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‣ Cornel Iridoid Glycoside Attenuates Tau Hyperphosphorylation by Inhibition of PP2A Demethylation

Yang, Cui-cui; Kuai, Xue-xian; Li, Ya-li; Zhang, Li; Yu, Jian-chun; Li, Lin; Zhang, Lan
Fonte: Hindawi Publishing Corporation Publicador: Hindawi Publishing Corporation
Tipo: Artigo de Revista Científica
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Aim. The aim of the present study was to investigate the effect of cornel iridoid glycoside (CIG) on tau hyperphosphorylation induced by wortmannin (WT) and GF-109203X (GFX) and the underlying mechanisms. Methods. Human neuroblastoma SK-N-SH cells were preincubated with CIG (50, 100, and 200 µg/ml, resp.) for 24 h and then exposed to 10 µM WT and 10 µM GFX for 3 h after washing out CIG. Immunohistochemistry was used to observe the microtubular cytoskeleton of the cultured cells. Western blotting was used to measure the phosphorylation level of tau protein, glycogen synthase kinase 3β (GSK-3β), and protein phosphatase 2A (PP2A). The activity of PP2A was detected by a biochemical assay. Results. Preincubation of CIG significantly attenuated the WT/GFX-induced tau hyperphosphorylation at the sites of Thr205, Thr212, Ser214, Thr217, Ser396, and PHF-1 and improved the damage of morphology and microtubular cytoskeleton of the cells. CIG did not prevent the decrease in p-AKT-ser473 and p-GSK-3β-ser9 induced by WT/GFX. However, CIG significantly elevated the activity of PP2A by reducing the demethylation of PP2A catalytic subunit (PP2Ac) at Leu309 and the ratio of PME-1/LCMT in the WT/GFX-treated cells. The results suggest that CIG may be beneficial to the treatment of AD.

‣ Processive Pectin Methylesterases: The Role of Electrostatic Potential, Breathing Motions and Bond Cleavage in the Rectification of Brownian Motions

Mercadante, Davide; Melton, Laurence D.; Jameson, Geoffrey B.; Williams, Martin A. K.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 04/02/2014 Português
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Pectin methylesterases (PMEs) hydrolyze the methylester groups that are found on the homogalacturonan (HG) chains of pectic polysaccharides in the plant cell wall. Plant and bacterial PMEs are especially interesting as the resulting de-methylesterified (carboxylated) sugar residues are found to be arranged contiguously, indicating a so-called processive nature of these enzymes. Here we report the results of continuum electrostatics calculations performed along the molecular dynamics trajectory of a PME-HG-decasaccharide complex. In particular it was observed that, when the methylester groups of the decasaccharide were arranged in order to mimic the just-formed carboxylate product of de-methylesterification, a net unidirectional sliding of the model decasaccharide was subsequently observed along the enzyme’s binding groove. The changes that occurred in the electrostatic binding energy and protein dynamics during this translocation provide insights into the mechanism by which the enzyme rectifies Brownian motions to achieve processivity. The free energy that drives these molecular motors is thus demonstrated to be incorporated endogenously in the methylesterified groups of the HG chains and is not supplied exogenously.

‣ When do microcircuits produce beyond-pairwise correlations?

Barreiro, Andrea K.; Gjorgjieva, Julijana; Rieke, Fred; Shea-Brown, Eric
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 06/02/2014 Português
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Describing the collective activity of neural populations is a daunting task. Recent empirical studies in retina, however, suggest a vast simplification in how multi-neuron spiking occurs: the activity patterns of retinal ganglion cell (RGC) populations under some conditions are nearly completely captured by pairwise interactions among neurons. In other circumstances, higher-order statistics are required and appear to be shaped by input statistics and intrinsic circuit mechanisms. Here, we study the emergence of higher-order interactions in a model of the RGC circuit in which correlations are generated by common input. We quantify the impact of higher-order interactions by comparing the responses of mechanistic circuit models vs. “null” descriptions in which all higher-than-pairwise correlations have been accounted for by lower order statistics; these are known as pairwise maximum entropy (PME) models. We find that over a broad range of stimuli, output spiking patterns are surprisingly well captured by the pairwise model. To understand this finding, we study an analytically tractable simplification of the RGC model. We find that in the simplified model, bimodal input signals produce larger deviations from pairwise predictions than unimodal inputs. The characteristic light filtering properties of the upstream RGC circuitry suppress bimodality in light stimuli...

‣ Cell wall methanol as a signal in plant immunity

Komarova, Tatiana V.; Sheshukova, Ekaterina V.; Dorokhov, Yuri L.
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 18/03/2014 Português
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Cell wall pectin forms a matrix around the cellulose–xyloglucan network that is composed of rhamnogalacturonan I, rhamnogalacturonan II, and homogalacturonan (HG), a major pectic polymer consisting of α-1,4-linked galacturonic acids. HG is secreted in a highly methyl-esterified form and selectively de-methyl-esterified by pectin methylesterases (PMEs) during cell growth and pathogen attack. The mechanical damage that often precedes the penetration of the leaf by a pathogen promotes the activation of PME, which in turn leads to the emission of methanol (MeOH), an abundant volatile organic compound, which is quickly perceived by the intact leaves of the damaged plant, and the neighboring plants. The exposure to MeOH may result in a “priming” effect on intact leaves, setting the stage for the within-plant, and neighboring plant immunity. The emission of MeOH by a wounded plant enhances the resistance of the non-wounded, neighboring “receiver” plants to bacterial pathogens and promotes cell-to-cell communication that facilitates the spread of viruses in neighboring plants.

‣ Characterization and transcript profiling of the pectin methylesterase (PME) and pectin methylesterase inhibitor (PMEI) gene families in flax (Linum usitatissimum)

Pinzón-Latorre, David; Deyholos, Michael K
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em 30/10/2013 Português
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