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PubMed2000

Analysis of the G-overhang structures on plant telomeres: evidence for two distinct telomere architectures.

Telomeres are highly conserved structures essential for maintaining the integrity of eukaryotic genomes. In yeast, ciliates and mammals, the G-rich strand of the telomere forms a 3' overhang on the chromosome terminus. Here we investigate the architecture of telomeres in the dicot plants Silene latifolia and Arabidopsis thaliana using the PENT (primer extension/nick translation) assay. We show that both Arabidopsis and Silene telomeres carry G-overhangs longer than 20-30 nucleotides. However, in contrast to yeast and ciliate telomeres, only half of the telomeres in Silene seedlings possess detectable G-overhangs. PENT reactions using a variety of primers and reaction conditions revealed that the remaining fraction of Silene telomeres carries either no overhangs or overhangs less than 12 nucleotides in length. G-overhangs were observed in Silene seeds and leaves, tissues that lack telomerase activity. These findings suggest that incomplete DNA replication of the lagging strand, rather than synthesis by telomerase, is the primary mechanism for G-overhang synthesis in plants. Unexpectedly, we found that the fraction of telomeres with detectable G-overhangs decreased from 50% in seedlings to 35% in leaves. The difference may reflect increased susceptibility of the G-overhangs to nuclease attack in adult leaves, an event that could act as a precursor for the catabolic processes accompanying leaf senescence

Base Sequence↗
PubMed1992

Ascaris hemoglobin gene: plant-like structure reflects the ancestral globin gene.

Animal globin genes have two introns at strictly conserved positions, while plant globin genes have both of these as well as an additional, central intron. It has been proposed that a common ancestor gene had three introns, one of which was subsequently lost from animal but not plant globin genes. We have elucidated the cDNA sequence and gene structure of a hemoglobin from the parasitic nematode Ascaris suum and found a plant-like central intron, providing strong evidence for a three-intron ancestor of modern globin genes.

Amino Acid Sequence↗
PubMedDate not supplied

Sliding-layer conformational change limited by the quaternary structure of plant RuBisCO.

RuBisCO, D-ribulose-1,5-bisphosphate carboxylase-oxygenase (EC 4.1.1.39), converts carbon dioxide to sugar in the first step of photosynthesis. In plants and some bacteria, this enzyme has an L8S8 structure, where L is the large catalytic subunit and S is the small subunit of unknown function. The molecule resembles a keg 105 A along the 4-fold axis and 132 A in diameter at the widest point of the keg. Here we describe the quaternary structure of RuBisCO from N. tabacum, the first L8S8 type known from an X-ray crystallographic study at near-atomic resolution (3 A). The structure shows that all eight L subunits are elongated along the 4-fold axis so that the molecule cannot be simply described as layers of subunits, as it had been from studies by electron microscopy. The structure, with its elongated and interdigitated L subunits, is evidence against a large, sliding-layer conformational change in plant RuBisCO, as proposed recently in Nature for the same enzyme from Alcaligenes eutrophus.

Amino Acid Sequence↗
PubMed2003

The crystal structure of plant sulfite oxidase provides insights into sulfite oxidation in plants and animals.

The molybdenum cofactor (Moco) containing sulfite oxidase (SO) from Arabidopsis thaliana has recently been identified and biochemically characterized. The enzyme is found in peroxisomes and believed to detoxify excess sulfite that is produced during sulfur assimilation, or due to air pollution. Plant SO (PSO) is homodimeric and homologous to animal SO, but contains only a single Moco domain without an additional redox center. Here, we present the first crystal structure of a plant Moco enzyme, the apo-state of Arabidopsis SO at 2.6 A resolution. The overall fold and coordination of the Moco are similar to chicken SO (CSO). Comparisons of conserved surface residues and the charge distribution in PSO and CSO reveal major differences near the entrance to both active sites reflecting different electron acceptors. Arg374 has been identified as an important substrate binding residue due to its conformational change when compared to the sulfate bound structure of CSO.

Amino Acid Sequence↗
PubMed2004

Structural basis for herbicidal inhibitor selectivity revealed by comparison of crystal structures of plant and mammalian 4-hydroxyphenylpyruvate dioxygenases.

A high degree of selectivity toward the target site of the pest organism is a desirable attribute for new safer agrochemicals. To assist in the design of novel herbicides, we determined the crystal structures of the herbicidal target enzyme 4-hydroxyphenylpyruvate dioxygenase (HPPD; EC 1.13.11.27) from the plant Arabidopsis thaliana with and without an herbicidal benzoylpyrazole inhibitor that potently inhibits both plant and mammalian HPPDs. We also determined the structure of a mammalian (rat) HPPD in complex with the same nonselective inhibitor. From a screening campaign of over 1000 HPPD inhibitors, six highly plant-selective inhibitors were found. One of these had remarkable (>1600-fold) selectivity toward the plant enzyme and was cocrystallized with Arabidopsis HPPD. Detailed comparisons of the plant and mammalian HPPD-ligand structures suggest a structural basis for the high degree of plant selectivity of certain HPPD inhibitors and point to design strategies to obtain potent and selective inhibitors of plant HPPD as agrochemical leads.

4-Hydroxyphenylpyruvate Dioxygenase↗
PubMed2003

Plant sphingolipids: structural diversity, biosynthesis, first genes and functions.

In mammals and Saccharomyces cerevisiae, sphingolipids have been a subject of intensive research triggered by the interest in their structural diversity and in mammalian pathophysiology as well as in the availability of yeast mutants and suppressor strains. More recently, sphingolipids have attracted additional interest, because they are emerging as an important class of messenger molecules linked to many different cellular functions. In plants, sphingolipids show structural features differing from those found in animals and fungi, and much less is known about their biosynthesis and function. This review focuses on the sphingolipid modifications found in plants and on recent advances in the functional characterization of genes gaining new insight into plant sphingolipid biosynthesis. Recent studies indicate that plant sphingolipids may be also involved in signal transduction, membrane stability, host-pathogen interactions and stress responses.

Animals↗
PubMed1998

Permeabilized Arabidopsis protoplasts provide new insight into the chromatin structure of plant alcohol dehydrogenase genes.

New data from permeabilized protoplasts have expanded our view of the 5'DNase I hypersensitive area of the Arabidopsis Adh gene derived from nuclei. DNase I hypersensitivity analyses conducted with permeabilized protoplasts from Arabidopsis cell cultures indicates that there are four distinct sites of hypersensitivity centered around positions -425, -325, -200, and -60. The hypersensitive site at -200 coincides with an in vitro hypersensitive site created by purified transcription factors bound to a G-box element. The G-box is a functional cis element that plays a role in the signal transduction of hypoxia and other stresses in Adh. The data presented in this paper support the notion that G-box-related elements may also play a role in defining chromatin structure. The new Arabidopsis data are discussed within the context of what is known about the chromatin structures and regulation of two other plant Adh genes; maize Adh1 and Adh2. The chromatin of the maize Adh1 promoter is divided into a region that is constitutively hypersensitive to DNase I (-700 to -160) and an inducibly hypersensitive region (-140 and -40). There are several sequence elements within the hypersensitive regions bound by proteins in vivo. The anaerobic response element is the most well characterized and functions in the detection of hypoxia. The maize Adh2 gene promoter is constitutively hypersensitive to DNase I, with the exception of a small region that extends to include the TATA box as the gene becomes active. Several cis elements in the Adh2 promoter are bound by factors in vivo. One, at -160, is a functional element that acts as an activator in vascular tissue. The overall goal of our research with the Adh genes from maize and Arabidopsis is to gain further insight into the relationships between the regulation of gene transcription and chromatin structure in plants as it is clear that all the necessary components that characterize regulated gene activity may not be found simply by elucidating the linear sequence of nucleotides that lie 5' to the protein coding regions and finding proteins capable of binding the promoter in vitro.

Alcohol Dehydrogenase↗
PubMed1989

Two-dimensional structure of plant light-harvesting complex at 3.7 A [corrected] resolution by electron crystallography.

The structure of the light-harvesting chlorophyll a/b-protein complex has been determined at 3.7 A resolution in projection by electron diffraction, electron microscopy and image analysis. Diffraction patterns and high-resolution spotscan images of two-dimensional crystals stabilized with tannin were recorded at low temperature. Phases of structure factors were obtained directly by image processing, after correction of the images for lattice distortions, defocus and beam tilt. Amplitudes were measured by electron diffraction. The projection map shows the detailed structure of the trimeric complex, suggesting the positions of two domains of potential structural and functional homology, of one membrane-spanning alpha-helix approximately perpendicular to the membrane plane and of several tightly bound lipid molecules.

Chlorophyll↗
PubMed2003

Crystal structure of plant photosystem I.

Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on Earth. The conversion of sunlight into chemical energy is driven by two multisubunit membrane protein complexes named photosystem I and II. We determined the crystal structure of the complete photosystem I (PSI) from a higher plant (Pisum sativum var. alaska) to 4.4 A resolution. Its intricate structure shows 12 core subunits, 4 different light-harvesting membrane proteins (LHCI) assembled in a half-moon shape on one side of the core, 45 transmembrane helices, 167 chlorophylls, 3 Fe-S clusters and 2 phylloquinones. About 20 chlorophylls are positioned in strategic locations in the cleft between LHCI and the core. This structure provides a framework for exploration not only of energy and electron transfer but also of the evolutionary forces that shaped the photosynthetic apparatus of terrestrial plants after the divergence of chloroplasts from marine cyanobacteria one billion years ago.

Amino Acid Sequence↗
PubMed1989

The kinetics of ligand binding to plant hemoglobins. Structural implications.

The rates of reaction of oxygen, carbon monoxide, and nitric oxide with 14 plant hemoglobins have been determined by relaxation and stopped-flow methods. The combination rates for oxygen lie between 0.12 and 0.26 x 10(9)/M.s, for carbon monoxide between 0.01 and 0.07 x 10(9)/M.s, and for nitric oxide between 0.12 and 0.25 x 10(9)/M.s. The dissociation velocities for oxygen range from 5 to 25/s, and for CO from 0.005 to 0.011 s. The oxygen dissociation constants range only from 36 to 78 nM. Nanosecond relaxation experiments show large differences between the proteins. Five have known primary structures which correlate closely with the nanosecond relaxations and less immediately with the millisecond reactions. The relevant amino acid substitutions are concentrated in the C-E interhelical region.

Amino Acid Sequence↗
PubMed2001

Variability and genetic structure of plant virus populations.

Populations of plant viruses, like all other living beings, are genetically heterogeneous, a property long recognized in plant virology. Only recently have the processes resulting in genetic variation and diversity in virus populations and genetic structure been analyzed quantitatively. The subject of this review is the analysis of genetic variation, its quantification in plant virus populations, and what factors and processes determine the genetic structure of these populations and its temporal change. The high potential for genetic variation in plant viruses, through either mutation or genetic exchange by recombination or reassortment of genomic segments, need not necessarily result in high diversity of virus populations. Selection by factors such as the interaction of the virus with host plants and vectors and random genetic drift may in fact reduce genetic diversity in populations. There is evidence that negative selection results in virus-encoded proteins being not more variable than those of their hosts and vectors. Evidence suggests that small population diversity, and genetic stability, is the rule. Populations of plant viruses often consist of a few genetic variants and many infrequent variants. Their distribution may provide evidence of a population that is undifferentiated, differentiated by factors such as location, host plant, or time, or that fluctuates randomly in composition, depending on the virus.

Gene Frequency↗
PubMed1978

Glycoprotein Synthesis in Plants: II. Structure of the Mannolipid Intermediate.

This paper reports the purification and structural determination of the mannolipid shown previously (Ericson and Delmer 1977 Plant Physiol 59: 341-347) to serve as an intermediate in glycoprotein synthesis in cotyledons of Phaseolus vulgaris. The mannolipid was purified by chromatography in organic solvents on diethylaminoethyl-cellulose, followed by repeated steps of deacylation and rechromatography on Sephadex LH-20. Binding and elution behavior on diethylaminoethyl-cellulose was consistent with the presence of a monophosphate residue. Lability of the mannolipid to mild acid treatment as well as its resistance to hot phenol treatment or catalytic hydrogenation are consistent with the structure of a polyprenol having a saturated alpha-residue. After methanolysis, the chloroform-methanol-soluble portion of the mannolipid was analyzed by mass spectrometry. The fragmentation pattern obtained was nearly identical to that obtained from standard dolichol-phosphate. An intense ion at m/e 69 represented the omega-terminal isoprenoid residue, and repeating fragments separated by 68 mass units were observed up to m/e of > 1,200. All evidence supports the conclusion that the mannolipid is dolichol-monophosphate-mannose and thus provides further support for the concept that the processes involved in the glycosylation of protein in higher plants are similar to those known to occur in the animal kingdom.

Journal Article↗
PubMed1979

Antitumor activity of norditerpenoid dilactones in Podocarpus plants: structure-activity relationship on in vitro cytotoxicity against Yoshida sarcoma.

The in vitro cytotoxicity of norditerpenoid dilactones isolated from Podocarpus plants was determined against cultured Yoshida sarcoma cells. The dilactones involved 15 natural lactones as well as their derivatives, which include appropriate modifications necessary to the estimation of the structure-activity relationship. The unsaturated system on the B/C ring portion, the dienolide or the epoxyenolide moiety, is essential for the activity, but the gamma-lactone group on the A/B ring portion is not. Other oxygenated substituents on the skeletal carbons, such as hydroxyl, acyloxyl, or epoxide group, also show some significant effect.

Animals↗
PubMed1999

Impacts of seed and pollen flow on population genetic structure for plant genomes with three contrasting modes of inheritance.

The classical island and one-dimensional stepping-stone models of population genetic structure developed for animal populations are extended to hermaphrodite plant populations to study the behavior of biparentally inherited nuclear genes and organelle genes with paternal and maternal inheritance. By substituting appropriate values for effective population sizes and migration rates of the genes concerned into the classical models, expressions for genetic differentiation and correlation in gene frequency between populations can be derived. For both models, differentiation for maternally inherited genes at migration-drift equilibrium is greater than that for paternally inherited genes, which in turn is greater than that for biparentally inherited nuclear genes. In the stepping-stone model, the change of genetic correlation with distance is influenced by the mode of inheritance of the gene and the relative values of long- and short-distance migration by seed and pollen. In situations where it is possible to measure simultaneously Fst for genes with all three types of inheritance, estimates of the relative rates of pollen to seed flow can be made for both the short- and long-distance components of migration in the stepping-stone model.

Diploidy↗
PubMed2004

A dynamic, architectural plant model simulating resource-dependent growth.

BACKGROUND AND AIMS: Physiological and architectural plant models have originally been developed for different purposes and therefore have little in common, thus making combined applications difficult. There is, however, an increasing demand for crop models that simulate the genetic and resource-dependent variability of plant geometry and architecture, because man is increasingly able to transform plant production systems through combined genetic and environmental engineering. MODEL: GREENLAB is presented, a mathematical plant model that simulates interactions between plant structure and function. Dual-scale automaton is used to simulate plant organogenesis from germination to maturity on the basis of organogenetic growth cycles that have constant thermal time. Plant fresh biomass production is computed from transpiration, assuming transpiration efficiency to be constant and atmospheric demand to be the driving force, under non-limiting water supply. The fresh biomass is then distributed among expanding organs according to their relative demand. Demand for organ growth is estimated from allometric relationships (e.g. leaf surface to weight ratios) and kinetics of potential growth rate for each organ type. These are obtained through parameter optimization against empirical, morphological data sets by running the model in inverted mode. Potential growth rates are then used as estimates of relative sink strength in the model. These and other 'hidden' plant parameters are calibrated using the non-linear, least-square method. KEY RESULTS AND CONCLUSIONS: The model reproduced accurately the dynamics of plant growth, architecture and geometry of various annual and woody plants, enabling 3D visualization. It was also able to simulate the variability of leaf size on the plant and compensatory growth following pruning, as a result of internal competition for resources. The potential of the model's underlying concepts to predict the plant's phenotypic plasticity is discussed.

Algorithms↗
PubMed1999

EFFECTS OF PLANTS ON NEMATODE COMMUNITY STRUCTURE.

Plant-related inputs provide the resources for nematode communities. Sampling of nematode communities must be on appropriate temporal and spatial scales. Size, feeding types, food or host specificity, and chronology allow over 200 nematode species to coexist in a district. Relationships between nematode functional groups and ecological processes regulating decomposition processes have been found in field experiments. Pulse-labeling experiments have shown root-feeding nematodes to increase the flow of carbon from roots to soil microbial biomass. Soil texture is related to suitability for cropping and affects nematode communities through crop-specific infestations. Nematode diversity tends to be greatest in ecosystems with least disturbance, and bacterial-feeding nematodes make the greatest contribution to the decomposer food web in more intensively managed ecosystems. Indices of the nematode fauna reflect changes in the nematode community; these changes reflect soil and ecological processes. Understanding the role of nematodes in these processes is the key to understanding of the relationship between plants and soil nematode communities.

Journal Article↗