Histochemistry and composition of the cell walls of styles of Nicotiana alata Link et Otto

The cell walls of styles of Nicotiana alata Link et Otto (ornamental tobacco; Solanaceae) were analysed chemically and examined histochemically. Cell-wall preparations were obtained from whole styles and from isolated transmitting-tissue cells. The style epidermal cells were shown histochemically to have thick, lignified secondary walls. These walls probably constituted a large proportion of the cell-wall preparation from whole styles as analysis of whole-style walls indicated that the major polysaccharides were xylans and cellulose, which are typical of lignified secondary walls of Magnoliopsida (dicotyledons). Lignification of the style epidermal walls was also demonstrated histochemically in 10 other species (5 genera including Nicotiana) of the sub-family Cestroideae of the Solanaceae, but not in 15 species (9 genera) of the sub-family Solanoideae of the Solanaceae, nor in 3 other species of dicotyledons and 2 species of Liliopsida (monocotyledons). Analysis of the cell-wall preparation from isolated transmitting-tissue cells of N. alata indicated that these contained cellulose, xyloglucans, and pectic polysaccharides, which is typical of primary cell walls of dicotyledons. However, the analysis indicated that the walls also contained an unusually high proportion of Type II arabinogalactans. Staining of the transmitting-tissue cell-wall preparation with β-glucosyl Yariv reagent, a histochemical reagent specific for arabinogalactan proteins, confirmed their presence, which may be related to the role of these cells in secreting the stylar extracellular matrix.     

Epigenetic natural variation in Arabidopsis thaliana

Cytosine methylation of repetitive sequences is widespread in plant genomes, occurring in both symmetric (CpG and CpNpG) as well as asymmetric sequence contexts. We used the methylation-dependent restriction enzyme McrBC to profile methylated DNA using tiling microarrays of Arabidopsis Chromosome 4 in two distinct ecotypes, Columbia and Landsberg erecta. We also used comparative genome hybridization to profile copy number polymorphisms. Repeated sequences and transposable elements (TEs), especially long terminal repeat retrotransposons, are densely methylated, but one third of genes also have low but detectable methylation in their transcribed regions. While TEs are almost always methylated, genic methylation is highly polymorphic, with half of all methylated genes being methylated in only one of the two ecotypes. A survey of loci in 96 Arabidopsis accessions revealed a similar degree of methylation polymorphism. Within-gene methylation is heritable, but is lost at a high frequency in segregating F₂ families. Promoter methylation is rare, and gene expression is not generally affected by differences in DNA methylation. Small interfering RNA are preferentially associated with methylated TEs, but not with methylated genes, indicating that most genic methylation is not guided by small interfering RNA. This may account for the instability of gene methylation, if occasional failure of maintenance methylation cannot be restored by other means.     

Cell-Wall Carbohydrates of the Endosperm of the Seed of Gleditsia triacanthos

The endosperm of the seed of Gleditsia triacanthos L. contains 18.55% of its dry weight as nonreserve, cell-wall carbohydrates. Of this carbohydrate material, comprising mainly mannose, galactose, and glucose, 76.1% was of low-molecular weight or highly hydrophilic. Mannose, galactose, and glucose were also the major sugar components of the polysaccharides extracted with alkali (23.1% of the cell-wall), while the same sugars, with minor amounts of arabinose, form the residues. Methylation analysis of the polysaccharides and the borate-sodium hydroxide residue indicate that the cell walls are built up on a network of galactomannans, with high Man/Gal ratios, reinforced with minor amounts of cellulose.     

Influence of avocado (Persea americana) Cx-cellulase on the structural features of avocado cellulose

Avocado (Persea americana Mill.) fruit produce copious quantities of the enzyme Cx-cellulase (EC 3.2.1.4) during ripening. The possibility that Cx-cellulase is able to disrupt cellulose microfibril oranization was investigated using molecular weight (M_r), x-ray diffraction, and ultrastructural analyses of cell walls from unripe avocado fruit incubated with the purified enzyme. Results indicate that Cx-cellulase causes a downshift in the M_r of unbranched cell-wall polymers in the M_r range of 10⁶–10⁷ Da. There is an increase in the proportion of crystalline cellulose, and cellulose fibrils appear to lose cohesiveness in response to enzyme activity. We propose that Cx-cellulase attacks avocado cellulose at accessible sites in the peripheral and integral noncrystalline regions of the microfibril, resulting in a loss of cohesiveness within the fibril structure and an alteration in the binding of associated cell-wall matrix polysaccharides. The initial loss of avocado mesocarp firmness during fruit ripening may be linked to the onset of Cx-cellulase activity.Abbreviations CMC carboxymethylcellulose - DMAC dimethylacetamide - DS developmental stage - M molecular weight - XG xyloglucan     

Methylation mosaicism of 5'-(CGG)(n)-3' repeats in fragile X, premutation and normal individuals

Fragile X syndrome (FRAXA) is characterized at the molecular level by an expansion of a naturally occurring 5′-(CGG)_n-3′ repeat in the promoter and 5′-untranslated region (5′-UTR) of the fragile X mental retardation (FMR1) gene on human chromosome Xq27.3. When expanded, this region is usually hypermethylated. Inactivation of the FMR1 promoter and absence of the FMR1 protein are the likely cause of the syndrome. By using the bisulfite protocol of the genomic sequencing method, we have determined the methylation patterns in this region on single chromosomes of healthy individuals and of selected premutation carriers and FRAXA patients. In control experiments with unmethylated or M-SssI-premethylated DNAs, this protocol has been ascertained to reliably detect all cytidines or 5-methylcytidines as unmethylated or methylated nucleotides, respectively. Analyses of the DNA from FRAXA patients reveal considerable variability in the lengths of the 5′-(CGG)_n-3′ repeats and in the levels of methylation in the repeat and the 5′-UTR. In one patient (OEl) with high repeat length heterogeneity (n = 15 to >200), shorter repeats (n = 20–80) were methylated or unmethylated, longer repeats (n = 100–150) were often completely methylated, but one repeat with n = 160 proved to be completely unmethylated. This type of methylation mosaicism was observed in several FRAXA patients. In healthy females, methylated 5′-CG-3′ sequences were found in some repeats and 5′-UTRs, as expected for the sequences from one of the X chromosomes. The natural FMR1 promoter is methylation sensitive, as demonstrated by the loss of activity in transfection experiments using the unmethylated or M-SssI-premethylated FMR1 promoter fused to the luciferase gene as an activity indicator.     

Differenziamento biochimico della parete in Angiosperme e Gimnosperme

Abstract

Biochemical changes in Angiosperms and Gymnosperms cell-walls during cellular differentiation in xylem. - During differentiation of the vascular cambium in xylem cells there are changes on the biosynthesis of cell-wall polysaccharides in angiosperms and gymnosperms. Pectins are synthesized during primary growth only, whereas the synthesis of hemicelluloses and cellulose increases markedly during secondary thickening; simultaneously the synthesis of lignin begins. The cells can modulate the synthesis of cell-wall polysaccharides by an induction and repression or an activation and inactivation of certain key enzymes. It has been shown that the major control operating during xylem differentiation is exerted on polysaccharide synthases. Further controls are envisaged on the transport of nucleoside diphosphate sugars from the cytoplasmic pool to the endomembrane, on the transport of neoformed polysaccharides through the endomembrane flow, and at plasmalemma level. It has also been emphasized the role of cell-wall in autoregulating its growth and differentiation.     

Estimation of the Fraction of Cancer Cells in a Tumor DNA Sample Using DNA Methylation

Contamination of normal cells is almost always present in tumor samples and affects their molecular analyses. DNA methylation, a stable epigenetic modification, is cell type-dependent, and different between cancer and normal cells. Here, we aimed to demonstrate that DNA methylation can be used to estimate the fraction of cancer cells in a tumor DNA sample, using esophageal squamous cell carcinoma (ESCC) as an example. First, by an Infinium HumanMethylation450 BeadChip array, we isolated three genomic regions (TFAP2B, ARHGEF4, and RAPGEFL1) i) highly methylated in four ESCC cell lines, ii) hardly methylated in a pooled sample of non-cancerous mucosae, a pooled sample of normal esophageal mucosae, and peripheral leukocytes, and iii) frequently methylated in 28 ESCCs (TFAP2B, 24/28; ARHGEF4, 20/28; and RAPGEFL1, 19/28). Second, using eight pairs of cancer and non-cancer cell samples prepared by laser capture microdissection, we confirmed that at least one of the three regions was almost completely methylated in ESCC cells, and all the three regions were almost completely unmethylated in non-cancer cells. We also confirmed that DNA copy number alterations of the three regions in 15 ESCC samples were rare, and did not affect the estimation of the fraction of cancer cells. Then, the fraction of cancer cells in a tumor DNA sample was defined as the highest methylation level of the three regions, and we confirmed a high correlation between the fraction assessed by the DNA methylation fraction marker and the fraction assessed by a pathologist (r=0.85; p<0.001). Finally, we observed that, by correction of the cancer cell content, CpG islands in promoter regions of tumor-suppressor genes were almost completely methylated. These results demonstrate that DNA methylation can be used to estimate the fraction of cancer cells in a tumor DNA sample.     

Structural analysis of arabinoxylans isolated from ball-milled switchgrass biomass

Ball-milled alcohol-insoluble residue (AIR) was prepared from switchgrass (Panicum virgatum var Alamo) and sequentially extracted with 50 mM ammonium oxalate buffer, 50 mM sodium carbonate, 1 M KOH containing 1% NaBH₄, and 4 M KOH containing 1% NaBH₄. Arabinoxylan was the most abundant component of the 1 M KOH-extracted fraction, which was treated with endoxylanase to generate oligosaccharides. Gel-permeation chromatography of these oligosaccharides produced three size-homogeneous oligosaccharide fractions with molecular weights of 678, 810, and 1074 Da, corresponding to 5, 6, and 8 pentose units, respectively. Detailed structural analysis of these oligosaccharides was performed using methylation analysis, multiple-step mass spectrometry (ESIMSⁿ), and 1D and 2D NMR spectroscopy. The preferred gas-phase fragmentation pathways were identified for these oligosaccharides, providing extensive sequence information that was completely consistent with structures determined by ab initio NMR analysis. These results demonstrate the high information content of ESIMSⁿ analysis when applied to cell-wall-derived oligosaccharides and provide standard data that will facilitate the analysis of cell-wall polysaccharide fragments with a sensitivity that is sufficient for the analysis of samples obtained from dissected tissues as well as other small samples.     

Structure of Plant Cell Walls : XXVI. The Walls of Suspension-Cultured Sycamore Cells Contain a Family of Rhamnogalacturonan-I-Like Pectic Polysaccharides

Considerable information has been obtained about the primary structures of suspension-cultured sycamore (Acer pseudoplatanus) cell-wall pectic polysaccharides, i.e. rhamnogalacturonan I, rhamnogalacturonan II, and homogalacturonan. However, these polysaccharides, which are solubilized from the walls by endo-α-1,4-polygalacturonase, account for only about half of the pectic polysaccharides known to be present in sycamore cell walls. We now report that, after exhaustive treatment with endo-α-1,4-polygalacturonase, additional pectic polysaccharides were extracted from sycamore cell walls by treatment with Na₂CO₃ at 1 and 22°C. These previously uncharacterized polysaccharides accounted for ~4% of the cell wall. Based on the glycosyl and glycosyl-linkage compositions and the nature of the products obtained by treating the quantitatively predominant NaCO₃-extracted polysaccharides with lithium metal dissolved in ethylenediamine, the polysaccharides were found to strongly resemble rhamnogalacturonan I. However, unlike rhamnogalacturonan I that characteristically had equal amounts of 2- and 2,4-linked rhamnosyl residues in its backbone, the polysaccharides extracted in Na₂CO₃ at 1°C had markedly disparate ratios of 2- to 2,4-linked rhamnosyl residues. We concluded that polysaccharides similar to rhamnogalacturonan I but with different degrees of branching are present in the walls of suspension-cultured sycamore cells.     

Structural features of the mucilage from the stem pith of kiwifruit (actinidia deliciosa): part I,structure of the inner core

The mucilage found in the stem pith of Actinidia deliciosa contains d-glucuronic acid, d-mannose, l-fucose, l-arabinose, and d-galactose in the molar ratios 1.0:1.5:2.0:4.0. The native, carboxyl-reduced, and partially acid-hydrolysed polysaccharides were subjected to methylation analysis. Partial acid hydrolysis of the methylated, carboxyl-reduced glucuronomannan core produced a series of methylated oligosaccharides which, as their alditol derivatives, were isolated by reverse-phase h.p.l.c. and characterised by e.i.- and f.a.b.-m.s. The data suggest that the polysaccharide contains a →4)-β-d-GlcpA-(1→2)-α-d-Manp-(1→ backbone with most of the d-mannosyl and d-glucosyluronic acid residues substituted through positions 3 with oligosaccharides containing l-arabinose, α-l-fucose, and β-d-galactose.     

Dedication

Mixed cultures derived from Boston Harbor sediments, which gave evidence of methylating tin compounds, yielded two isolates, each a Bacillus sp., which methylated CH₃SnCl₃ to form (CH₃)₃SnX in coculture. Neither organism alone gave evidence of methylation. SnCl₄ and (CH₃)₂SnCl₂ were not methylated. Transfer of either organism to filtered medium containing CH₃SnCl₃ in which the other had grown did not lead to methylation. Therefore methylation by the coculture is not simply a matter of cross‐feeding.     

Structural characterization and biological activities of two α-glucans from <Emphasis Type="Italic">Radix Paeoniae Alba</Emphasis>

Radix Paeoniae Alba is widely used in Chinese traditional medicine to treat various diseases such as gastrointestinal disorders, cancer, and other diseases. In this study, two polysaccharides RPAPW1 and RPAPW2 were isolated from Radix Paeoniae Alba by DEAE-52 cellulose chromatography and G-25 sephadex. According to physicochemical methods, NMR and methylation analysis, RPAPW1 and RPAPW2 were established to be α-glucans consisting of predominant 4-linked α- Glc residues branched at O-6 and contained trace amount of protein and uronic acid. Immunological tests indicated that RPAPW1, RPAPW2 and could promote splenocyte proliferation and RAW264.7 phagocytic activity. In vitro, RPAPW1 and RPAPW2 elicited a week reducing power, DPPH scavenging activity and could not protect the PC12 cells from H₂O₂ damage. These data implied polysaccharides RPAPW1 and RPAPW2 had the potential to be a natural immunopotentiating and antioxidant supplement for preparing functional foods and nutraceuticals.     

Development of a Novel Output Value for Quantitative Assessment in Methylated DNA Immunoprecipitation-CpG Island Microarray Analysis

In DNA methylation microarray analysis, quantitative assessment of intermediate methylation levels in samples with various global methylation levels is still difficult. Here, specifically for methylated DNA immunoprecipitation-CpG island (CGI) microarray analysis, we developed a new output value. The signal log ratio reflected the global methylation levels, but had only moderate linear correlation (r = 0.72) with the fraction of DNA molecules immunoprecipitated. By multiplying the signal log ratio using a coefficient obtained from the probability value that took account of signals in neighbouring probes, its linearity was markedly improved (r = 0.94). The new output value, Me value, reflected the global methylation level, had a strong correlation also with the fraction of methylated CpG sites obtained by bisulphite sequencing (r = 0.88), and had an accuracy of 71.8 and 83.8% in detecting completely methylated and unmethylated CGIs. Analysis of gastric cancer cell lines using the Me value showed that methylation of CGIs in promoters and gene bodies was associated with low and high, respectively, gene expression. The degree of demethylation of promoter CGIs after 5-aza-2''-deoxycytidine treatment had no association with that of induction of gene expression. The Me value was considered to be useful for analysis of intermediate methylation levels of CGIs.     

A comparative study of antioxidative activities of cell-wall polysaccharides

Oxidative burst in plants is elicited by biotic and abiotic stressors. Analogously to some monosaccharides which act as intracellular antioxidants, cell-wall polysaccharides may be in charge of buffering free-radical production in the extracellular compartment under pronounced prooxidative settings. Although a wide range of plant polysaccharides have been examined for their antioxidative properties, this usually has not been done in a coherent and comparative manner and against biologically relevant reactive species. Here we show that different cell-wall polysaccharides, cellulose, pectin, d-galacto-d-mannan, arabinogalactan, and xylan, exhibit distinctive antioxidative activities against the hydroxyl radical (OH)-generating Fenton reaction and superoxide. We found, using an EPR spin-trapping method, that the main carriers of ‘anti-Fenton’ activity in the plant cell wall are pectin and xylan. They most likely act by binding metal ions in such a manner to allow the Fenton reaction, after which they scavenge OH. Such a mode of action is preferred by cells resulting in a safe degradation of H₂O₂. On the other hand, the polysaccharides examined showed similar superoxide scavenging capacities. We propose that plants may employ different antioxidative characteristics of polysaccharides to regulate their redox status by modifying the composition of the cell wall.     

DNA Methylation Occurred around Lowly Expressed Genes of Plastid DNA during Tomato Fruit Development

We have analyzed DNA methylation of plastid DNA from fully ripened red fruits, green mature fruits, and green leaves of tomato (Lycopersicon esculentum var. Firstmore). Essentially identical restriction profiles were obtained between chromoplast and chloroplast DNAs by EcoRI digestion. BstNI/EcoRII and HpaII/MspI are pairs of isoschizomers that can discriminate between methylated and unmethylated DNAs. These endonucleases produced different restriction patterns of plastid DNAs from tomato fruits compared to tomato leaves. Moreover, we have found from Southern blots that methylation was not detected in DNA fragments containing certain genes that are actively expressed in chromoplasts, whereas DNA fragments bearing genes that are barely transcribed in chromoplasts are methylated.     

Aberrant DNA methylation is associated with disease progression, resistance to imatinib and shortened survival in chronic myelogenous leukemia

The epigenetic impact of DNA methylation in chronic myelogenous leukemia (CML) is not completely understood. To elucidate its role we analyzed 120 patients with CML for methylation of promoter-associated CpG islands of 10 genes. Five genes were identified by DNA methylation screening in the K562 cell line and 3 genes in patients with myeloproliferative neoplasms. The CDKN2B gene was selected for its frequent methylation in myeloid malignancies and ABL1 as the target of BCR-ABL translocation. Thirty patients were imatinib-naïve (mostly treated by interferon-alpha before the imatinib era), 30 were imatinib-responsive, 50 were imatinib-resistant, and 10 were imatinib-intolerant. We quantified DNA methylation by bisulfite pyrosequencing. The average number of methylated genes was 4.5 per patient in the chronic phase, increasing significantly to 6.2 in the accelerated and 6.4 in the blastic phase. Higher numbers of methylated genes were also observed in patients resistant or intolerant to imatinib. These patients also showed almost exclusive methylation of a putative transporter OSCP1. Abnormal methylation of a Src suppressor gene PDLIM4 was associated with shortened survival independently of CML stage and imatinib responsiveness. We conclude that aberrant DNA methylation is associated with CML progression and that DNA methylation could be a marker associated with imatinib resistance. Finally, DNA methylation of PDLIM4 may help identify a subset of CML patients that would benefit from treatment with Src/Abl inhibitors.     

Stability of N-acyl groups in methylated α2 → 8-linked oligosialosyl chains toward methanolysis. Analysis by chemical ionization-mass spectrometry

The stability of N-acetyl group of methylated trisaccharide of N-acetylneuraminic acid toward methanolysis under conditions used in methylation analysis was investigated. The analysis of the products obtained after a reaction sequence, methylation-methanolysis-deuterioacetylation, by chemical ionization-mass spectrometry has led to unequivocal conclusion that N-acetyl group of internal 8-O-substituted residue of the methylated oligosialosyl compound is de-N-acetylated under conditions sufficient to cleave glycosidic linkages, whereas the fully methylated nonreducing terminal residue of neuraminic acid is completely resistant to de-N-acetylation. The reaction mechanism to explain these observations is presented.     

Escherichia coli formylmethionine tRNA: methylation of specific guanine and adenine residues catalyzed by HeLa cells tRNA methylases and the effect of these methylations on its biological properties

Purified HeLa cell tRNA methylases have been used for site-specific methylations of Escherichia coli formylmethionine transfer ribonucleic acid (tRNA^fMet). Guanine-N²-methylase catalyzed the methylation of a specific guanine residue (G₂₇) and adenine-1-methylase that of a specific adenine residue (A₅₉). The combined action of both of these enzymes leads to a total incorporation of two methyl groups and results in the methylation of both G₂₇ and A₅₉.The effect of introducing additional methyl groups on the function of tRNA has been studied by a comparison in vitro of the biological properties of tRNA^fMet and enzymically methylated tRNA^fMet. It was found that none of the following properties of E. coli tRNA^fMet are altered to any significant extent by methylation: (a) rate, extent, and specificity of aminoacylation, (b) ability of methionyl-tRNA to be enzymically formylated, and (c) ability of formylmethionyl-tRNA to initiate protein synthesis in cell-free extracts of E. coli in the presence of f2 RNA as messenger. Also, the temperature versus absorbance profile of the doubly methylated tRNA^fmet was virtually identical to that of the E. coli tRNA^fMet, and enzymically methylated tRNA^fmet resembled tRNA^fMet in that both were resistant to deacylation by E. coli, N-acylaminoacyl-tRNA hydrolase.     

Pea xyloglucan and cellulose : I. Macromolecular organization

A macromolecular complex composed of xyloglucan and cellulose was obtained from elongating regions of etiolated pea (Pisum sativum L. var. Alaska) stems. Xyloglucan could be solubilized by extraction of this complex with 24% KOH-0.1% NaBH₄ or by extended treatment with endo-1,4-β-glucanase. The polysaccharide was homogeneous by ultracentrifugal analysis and gel filtration on Sepharose CL-6B, molecular weight 330,000. The structure of pea xyloglucan was examined by fragmentation analysis of enzymic hydrolysates, methylation analysis, and precipitation tests with fucose- or galactose-binding lectins. The polysaccharide was composed of equal amounts of two subunits, a nonasaccharide (glucose/xylose/galactose/fucose, 4:3:1:1) and a heptasaccharide (glucose/xylose, 4:3), which appeared to be distributed at random, but primarily in alternating sequence. The xyloglucan:cellulose complex was examined by light microscopy using iodine staining, by radioautography after labeling with [³H]fucose, by fluorescence microscopy using a fluorescein-lectin (fucose-binding) as probe, and by electron microscopy after shadowing. The techniques all demonstrated that the macromolecule was present in files of cell shapes, referred to here as cell-wall `ghosts,' in which xyloglucan was localized both on and between the cellulose microfibrils. Since the average chain length of pea xyloglucan was many times the diameter of cellulose microfibrils, it could introduce cross-links by binding to adjacent fibrils and thereby contribute rigidity to the wall.