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At least 811 records · Page 45Linked to original sources
PubMed2005

Self-thinning and community persistence in a simple size-structured dynamical model of plant growth.

This paper presents a size-structured dynamical model of plant growth. The model takes the form of a partial differential-integral equation and includes the effects of self- shading by leaves. Closed form solutions are presented for the equilibrium size density distribution. Analytic conditions are derived for community persistence, and the self-thinning exponent is obtained as a function of species characteristics and environmental conditions.

Computer Simulation↗
PubMed1994

Computer-assisted predictions of the secondary structure in the plant virus single-stranded DNA genome.

Coconut foliar decay virus (CFDV) contains the single-stranded circular DNA molecules of 1291 nucleotides which were found to replicate autonomously in the cells of the diseased palms. The special features of the CFDV DNA sequence, including putative secondary structure and the distribution of the inverted repeat motifs, are investigated with computer-assisted prediction methods. It is evident that the structural principle of the branched series of long and short double helixes interspersed by short non-helical regions is existed for CFDV virion DNA. The total degree of base pairing is near 62%. We have also predicted the presence of several sequence elements formed by inverted repeat motifs which are potentially capable of binding the eukaryotic transcriptional regulatory factors.

Base Sequence↗
PubMed1981

Immunofluorescence microscopy of organized microtubule arrays in structurally stabilized meristematic plant cells.

Cells were prepared for indirect immunofluorescence microscopy after paraformaldehyde fixation of multicellular root apices and brief incubation in cell wall-digesting enzymes. This allowed subsequent separation of the tissue into individual cells or short files of cells which were put onto coverslips coated with polylysine. Unlike spherical protoplasts made from living tissues, these preparations retain the same polyhedral shape as the cells from which they are derived. Cellular contents, including organized arrays of microtubules, are likewise structurally stabilized. Antibodies to porcine brain tubulin react with all types of microtubule array known to occur in plant meristematic cells, namely, interphase cortical microtubules, pre-prophase bands, the mitotic spindle, and phragmoplast microtubules. The retention of antigenicity in permeabilized, isolated, stabilized cells from typical, wall-enclosed plant cells has much potential for plant immunocytochemistry, and in particular should facilitate work on the role of microtubules in the morphogenesis of organized plant tissues.

Chromosomes↗
PubMed1993

Cloning and characterization of the major hepatic glutathione S-transferase from a marine teleost flatfish, the plaice (Pleuronectes platessa), with structural similarities to plant, insect and mammalian Theta class isoenzymes.

A cDNA clone (PLGSTA) of 896 bp, containing an open reading frame encoding a 225-amino-acid polypeptide of M(r) 25,723, was isolated from a cDNA library constructed in lambda gt11 from the liver of a marine teleost flatfish, the plaice (Pleuronectes platessa). The identification of this cDNA as that coding for the subunit of the major cytosolic glutathione S-transferase of plaice liver, GST-A, was supported by its heterologous expression in and purification of its protein product from Escherichia coli. The recombinant-derived protein exhibited identical M(r) and immunoreactivity and a similar substrate specificity to GST-A previously isolated from plaice liver. Comparison of the deduced amino acid sequence of the plaice GST-A polypeptide with the primary structures of GSTs from other Phyla revealed that it showed the greatest similarity to plant, insect and mammalian Theta class GSTs. Southern blot analysis of plaice DNA hybridized to the PLGSTA cDNA showed a banding pattern indicative of the presence of a single gene. Northern blot analysis of a variety of plaice tissues showed hybridizing bands of approx. 1100 nucleotides in all tissues tested, with the highest relative amounts in liver and intestinal mucosa. A marked increase in hybridization intensity was observed in hepatic RNA samples from plaice treated with trans-stilbene oxide, suggesting that GST-A is induced by epoxides in this species.

Amino Acid Sequence↗
PubMed2003

Liquid chromatography with ultraviolet absorbance-mass spectrometric detection and with nuclear magnetic resonance spectroscopy: a powerful combination for the on-line structural investigation of plant metabolites.

In order to discover new bioactive compounds from plant sources which could become new leads or new drugs, extracts should be submitted at the same time to chemical screening and to various biological or pharmacological targets. Metabolite profiling using hyphenated techniques such as LC/UV, LC/MS and more recently LC/NMR, quickly provides plenty of structural information, leading to a partial or a complete on-line de novo structure determination of the natural products of interest. As a complement to this approach, bioassays performed after LC/microfractionation of the extracts allow efficient localisation of the bioactive LC-peaks in the chromatograms. The combination of metabolite profiling and LC/bioassays provides the possibility of distinguishing between already known bioactive compounds (dereplication) and new molecules directly in crude plant extracts. Thus, the tedious isolation of compounds of low interest can be avoided and targeted isolation of new bioactive products or constituents presenting novel or unusual spectroscopic features can be undertaken. Several examples of rapid localisation of bioactive compounds, based on post-chromatographic bioautographic testing of LC/NMR microfractions and subsequent on-line identification will be illustrated. Application of hyphenated techniques for the efficient characterisation of labile constituents or constituents difficult to separate at the preparative scale will also be mentioned. The possibilities and limitations of LC/UV/NMR/MS and LC/bioassay as well as future development expected in this field will be discussed.

Chromatography, Liquid↗
PubMed2004

The X-ray structure of the plant like 5-aminolaevulinic acid dehydratase from Chlorobium vibrioforme complexed with the inhibitor laevulinic acid at 2.6 A resolution.

5-Aminolaevulinic acid dehydratase (ALAD), an early enzyme of the tetrapyrrole biosynthesis pathway, catalyses the dimerisation of 5-aminolaevulinic acid to form the pyrrole, porphobilinogen. ALAD from Chlorobium vibrioforme is shown to form a homo-octameric structure with 422 symmetry in which each subunit adopts a TIM-barrel fold with a 30 residue N-terminal arm extension. Pairs of monomers associate with their arms wrapped around each other. Four of these dimers interact principally via their arm regions to form octamers in which each active site is located on the surface. The active site contains two invariant lysine residues (200 and 253), one of which (Lys253) forms a Schiff base link with the bound substrate analogue, laevulinic acid. The carboxyl group of the laevulinic acid forms hydrogen bonds with the side-chains of Ser279 and Tyr318. The structure was examined to determine the location of the putative active-site magnesium ion, however, no evidence for the metal ion was found in the electron density map. This is in agreement with previous kinetic studies that have shown that magnesium stimulates but is not required for activity. A different site close to the active site flap, in which a putative magnesium ion is coordinated by a glutamate carboxyl and five solvent molecules may account for the stimulatory properties of magnesium ions on the enzyme.

Allosteric Site↗
PubMed1998

Three-dimensional structure of the plant photosystem II reaction centre at 8 A resolution.

Photosystem II is a multisubunit enzyme complex involved in plant photosynthesis. It uses solar energy to catalyse the breakdown of water to reducing equivalents and molecular oxygen. Native photosystem II comprises more than 25 different subunits, and has a relative molecular mass of more than 600K. Here we report the three-dimensional structure of a photosystem II subcomplex, containing the proteins D1, D2, CP47 and cytochrome b-559, determined by electron crystallography. This CP47 reaction centre, which has a relative molecular mass of 160K, can perform light-mediated energy and electron-transfer reactions but is unable to oxidize water. The complex contains 23 transmembrane alpha-helices, of which 16 have been assigned to the D1, D2 and CP47 proteins. The arrangement of these helices is remarkably similar to that of the helices in the reaction centres of purple bacteria and of plant photosystem I, indicating a common evolutionary origin for these assemblies. The map suggests that redox cofactors in the D1-D2 complex are located in positions analogous to those in the bacterial reaction centre, but the distance between the chlorophylls corresponding to the bacterial 'special pair' is significantly larger.

Biological Evolution↗
PubMed2003

Studies on the structure of the plant wax nonacosan-10-ol, the main component of epicuticular wax conifers.

The main component presents in the epicuticular waxes of needles of Pinus halepensis and the most of conifers, the secondary alcohol nonacosan-10-ol, has been investigated by X-ray diffraction and differential scanning calorimetry. The results obtained from these physical techniques permitted to establish a definitive structural model of the molecular arrangement of this wax, basically in good agreement with the model formulated by other authors from theoretical formulations. Biological implications of the proposed structure have been also formulated.

Calorimetry↗
PubMed2003

The interactions between plant growth, vegetation structure and soil processes in semi-natural acidic and calcareous grasslands receiving long-term inputs of simulated pollutant nitrogen deposition.

Regular applications of ammonium nitrate (35-140 kg N ha(-1) year(-1)) and ammonium sulphate (140 kg N ha(-1) year(-1)) to areas of acidic and calcareous grassland in the Derbyshire Peak District over a period of 6 years, have resulted in significant losses in both overall plant cover, and the abundance of individual species, associated with clear and dose-related increases in shoot nitrogen content. No overall growth response to nitrogen treatment was seen at any stage in the experiment. Phosphorus additions to the calcareous plots did however lead to significant increases in plant cover and total biomass, indicative of phosphorus limitation in this system. Clear and dose-related increases in soil nitrogen mineralization rates were also obtained, consistent with marked effects of the nitrogen additions on soil processes. High nitrification rates were seen on the calcareous plots, and this process was associated with significant acidification of the 140 kg N ha(-1) year(-1) treatments.

Ecosystem↗
PubMed1995

Structural domains of plant nuclear DNA as a constitutive component of the topoisomerase II/DNA complex.

The treatment of agarose embedded plant nuclei by strong protein denaturants was demonstrated to result in discrete self-fragmentation of intact nuclear DNA. The set of resultant DNA cleavage products involves two main types of DNA fragments sized about 50-100 kb and 300-500 kb, being of the same type in various eukaryotic representatives. The pattern of ordered DNA fragmentation has been shown to be similar both in intact nuclei and in histone-depleted ones thus suggesting that the observed DNA fragments represent preexisting DNA structural domains, corresponding to the higher levels of chromatin folding. The topoisomerase II-specific poison teniposide (VM-26) has been shown to increase the ordered DNA cleavage while the conditions stimulating the topoisomerase II-mediated reverse reaction lead to the reassociation of the cleaved DNA domains. The data presented suggest that the nuclear DNA structural domains are involved in functioning of the topoisomerase II/DNA complex, the main property of which is its ability to mediate the cleavage/reassociation reactions.

Cell Nucleus↗
PubMed1966

Structure of isolated plant Golgi apparatus revealed by negative staining.

Sucrose-gradient-purified dictyosomes of plant Golgi apparatus appear, after glutaraldehyde stabilization, as stacks of highly fenestrate and tubate cisternae when negatively stained with phosphotungstic acid, shadowed with heavy metal, or OsO(4)-stained in thin section. The tubular proliferations (diameter 200 to 400 A) extend for several microns from the central region and are united at intervals into an anastomosing network. Associated with the tubules are two kinds of vesicles which are distinguishable on the basis of texture, size, shape, and staining characteristics. One vesicle type is rough-surfaced, nearly spherical, and of uniform dimensions (diameter approximately 600 A). Metal shadowing shows that these vesicles remain spherical after drying. The other vesicle type is smooth-surfaced and varies in both size and shape. Intercisternal elements are revealed, by negative staining, on the surface of internal cisternae after fragmentation of the dictyosome. The progressive differentiation of cisternae from the forming face to the maturing face is observed in thin sections of these isolated preparations. The morphological characteristics observed in negatively stained dictyosomes indicate regions of functional specialization within the dictyosome cisternae and reveal a dictyosome structure more extensive than that envisioned from sections.

Golgi Apparatus↗
PubMed2003

Crystal structure of the plant PPC decarboxylase AtHAL3a complexed with an ene-thiol reaction intermediate.

The Arabidopsis thaliana protein AtHAL3a decarboxylates 4'-phosphopantothenoylcysteine to 4'-phosphopantetheine, a step in coenzyme A biosynthesis. Surprisingly, this decarboxylation reaction is carried out as an FMN-dependent redox reaction. In the first half-reaction, the side-chain of the cysteine residue of 4'-phosphopantothenoylcysteine is oxidised and the thioaldehyde intermediate decarboxylates spontaneously to the 4'-phosphopantothenoyl-aminoethenethiol intermediate. In the second half-reaction this compound is reduced to 4'-phosphopantetheine and the FMNH(2) cofactor is re-oxidised. The active site mutant C175S is unable to perform this reductive half-reaction. Here, we present the crystal structure of the AtHAL3a mutant C175S in complex with the reaction intermediate pantothenoyl-aminoethenethiol and FMNH(2). The geometry of binding suggests that reduction of the C(alpha)=C(beta) double bond of the intermediate can be performed by direct hydride-transfer from N5 of FMNH(2) to C(beta) of the aminoethenethiol-moiety supported by a protonation of C(alpha) by Cys175. The binding mode of the substrate is very similar to that previously observed for a pentapeptide to the homologous enzyme EpiD that introduces the aminoethenethiol-moiety as final reaction product at the C terminus of peptidyl-cysteine residues. This finding further supports our view that these homologous enzymes form a protein family of homo-oligomeric flavin-containing cysteine decarboxylases, which we have termed HFCD family.

Amino Acid Sequence↗