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PubMed2006

Bottom-up regulation of plant community structure in an aridland ecosystem.

We conducted a long-term rodent exclosure experiment in native grass- and shrub-dominated vegetation to evaluate the importance of top-down and bottom-up controls on plant community structure in a low-productivity aridland ecosystem. Using multiple regressions and analysis of covariance, we assessed how bottom-up precipitation pulses cascade through vegetation to affect rodent populations, how rodent populations affect plant community structure, and how rodents alter rates of plant community change over time. Our findings showed that bottom-up pulses cascade through the system, increasing the abundances of plants and rodents, and that rodents exerted no control on plant community structure and rate of change in grass-dominated vegetation, and only limited control in shrub-dominated vegetation. These results were discussed in the context of top-down effects on plant communities across broad gradients of primary productivity. We conclude that bottom-up regulation maintains this ecosystem in a state of low primary productivity that constrains the abundance of consumers such that they exert limited influence on plant community structure and dynamics.

Animals↗

PubMed2006

Atomic structure of plant glutamine synthetase: a key enzyme for plant productivity.

Plants provide nourishment for animals and other heterotrophs as the sole primary producer in the food chain. Glutamine synthetase (GS), one of the essential enzymes for plant autotrophy catalyzes the incorporation of ammonia into glutamate to generate glutamine with concomitant hydrolysis of ATP, and plays a crucial role in the assimilation and re-assimilation of ammonia derived from a wide variety of metabolic processes during plant growth and development. Elucidation of the atomic structure of higher plant GS is important to understand its detailed reaction mechanism and to obtain further insight into plant productivity and agronomical utility. Here we report the first crystal structures of maize (Zea mays L.) GS. The structure reveals a unique decameric structure that differs significantly from the bacterial GS structure. Higher plants have several isoenzymes of GS differing in heat stability and catalytic properties for efficient responses to variation in the environment and nutrition. A key residue responsible for the heat stability was found to be Ile-161 in GS1a. The three structures in complex with substrate analogues, including phosphinothricin, a widely used herbicide, lead us to propose a mechanism for the transfer of phosphate from ATP to glutamate and to interpret the inhibitory action of phosphinothricin as a guide for the development of new potential herbicides.

Adenosine Triphosphate↗

PubMed2004

Effects of acetic acid treatment on plant chromosome structures analyzed by atomic force microscopy.

Acetic acid treatment has been frequently used to remove cellular contaminants from plant chromosome samples for structural analyses by scanning electron microscopy and atomic force microscopy (AFM). We evaluated the effects of various concentrations of acetic acid treatments on barley chromosome structures by using AFM. The long-term 45% acetic acid treatment significantly damaged the chromosome structures, although the treatment effectively removed the cellular contaminants. On the other hand, the treatment with 15% acetic acid could not obtain sufficiently clean chromosome samples and the chromosome surface structures could not be observed. In contrast, we obtained clean chromosome preparation without severe damage by using an intermediate concentration (30%) of acetic acid treatment. In the centromeric region, we could observe fiber structures with a width of 100 nm, which were composed of ca. 50-nm granules and aligned to the axes of chromosomes. Thus, AFM analysis of chromosomes appropriately treated with acetic acid will provide important insights into the organization of higher-order structures of plant chromosomes.

Acetic Acid↗

PubMed1978

Mutagenicity of plant flavonoids: structural requirements for mutagenic activity in Salmonella typhimurium.

40 compounds structurally related to the plant flavonol quercetin were tested for mutagenic activity in Salmonella typhimurium strain TA98. 10 flavonols, quercetin, myricetin, rhamnetin, galangin, kaempferol, tamarixetin, morin, 3'-O-methylquercetin, 7,4'-di-O-methylquercetin and 5,7-di-O-methyl-quercetin, exhibited unequivocal mutagenic activity. 4 compounds, quercetin, myricetin, rhamnetin and 5,7-di-O-methylquercetin, were active without metabolic activation, although metabolic activation markedly enhanced their activity. All 4 have free hydroxyl groups at the 3' and 4' positions of the B ring. The other active compounds required an in vitro rat-liver metabolizing system for significant activity. Structural features which appear essential for mutagenic activity in this strain are a basic flavanoid ring structure with (1) a free hydroxyl group at the 3 position, (2) a double bond at the 2, 3 position, (3) a keto group at the 4 position, and (4) a structure which permits the proton of the 3-hydroxyl group to tautomerise to a 3-keto compound. The data are consistent with the requirement for a B ring structure that permits oxidation to quininoid intermediates. Free hydroxyl groups in the B ring are not essential for activity if a rat-liver metabolic activating system is employed. Data from 12 compounds which differ only at the essential sites described above indicate that the structural requirements for mutagenicity in strain TA100 are the same as those for activity in strain TA98. Based on the above structural requirements, a metabolic pathway for flavonol activation to DNA-reactive species is proposed.

Animals↗

PubMed2006

Flavonoids from Pyrrosia petiolosa (Christ) Ching.

A new kaempferol glycoside, kaempferol-3-O-beta-D-glucopyranoside-7-O-alpha-L-arabinofuranoside (1), was isolated from the EtOH extract of Pyrrosiapetiolosa together with six known flavonoids already reported from the same plant. Structural elucidation was performed by means of physico-chemical methods including MS, and 1D and 2D NMR spectroscopy.

China↗

PubMed2006

Plasticity in the composition of the light harvesting antenna of higher plants preserves structural integrity and biological function.

Arabidopsis plants in which the major trimeric light harvesting complex (LHCIIb) is eliminated by antisense expression still exhibit the typical macrostructure of photosystem II in the granal membranes. Here the detailed analysis of the composition and the functional state of the light harvesting antennae of both photosystem I and II of these plants is presented. Two new populations of trimers were found, both functional in energy transfer to the PSII reaction center, a homotrimer of CP26 and a heterotrimer of CP26 and Lhcb3. These trimers possess characteristic features thought to be specific for the native LHCIIb trimers they are replacing: the long wavelength form of lutein and at least one extra chlorophyll b, but they were less stable. A new population of loosely bound LHCI was also found, contributing to an increased antenna size for photosystem I, which may in part compensate for the loss of the phosphorylated LHCIIb that can associate with this photosystem. Thus, the loss of LHCIIb has triggered concerted compensatory responses in the composition of antennae of both photosystems. These responses clearly show the importance of LHCIIb in the structure and assembly of the photosynthetic membrane and illustrate the extreme plasticity at the level of the composition of the light harvesting system.

Arabidopsis↗

PubMed1990

New model of tertiary structure of plant 5S rRNA is confirmed by digestions with alpha-sarcin.

The cytotoxin alpha-sarcin was employed to test the model of secondary and tertiary structures of plant 5S rRNAs, which we recently proposed [(1990) Int. J. Biol. Macromol. (in press)]. alpha-Sarcin is a novel ribonuclease that hydrolyzes phosphodiester bonds adjacent to purines in nucleic acids. The digestion pattern obtained for lupin and wheat germ 5S rRNAs strongly suggests the existence of tertiary interactions between residues C34, C35, C36, A37 and G85, G86, G87, U88 as previously proposed. The results on the secondary structure of plant 5S rRNA are in line with a previously proposed model.

Base Sequence↗

PubMed1999

Novel structures of plant lectins and their complexes with carbohydrates.

Several novel structures of legume lectins have led to a thorough understanding of monosaccharide and oligosaccharide specificity, to the determination of novel and surprising quaternary structures and, most importantly, to the structural identification of the binding site for adenine and plant hormones. This deepening of our understanding of the structure/function relationships among the legume lectins is paralleled by advances in two other plant lectin families - the monocot lectins and the jacalin family. As the number of available crystal structures increases, more parallels between plant and animal lectins become apparent.

Binding Sites↗

PubMed2006

A comparison of experimental designs for selection in breeding trials with nested treatment structure.

Plant breeders frequently evaluate large numbers of entries in field trials for selection. Generally, the tested entries are related by pedigree. The simplest case is a nested treatment structure, where entries fall into groups or families such that entries within groups are more closely related than between groups. We found that some plant breeders prefer to plant close relatives next to each other in the field. This contrasts with common experimental designs such as the alpha-design, where entries are fully randomized. A third design option is to randomize in such a way that entries of the same group are separated as much as possible. The present paper compares these design options by simulation. Another important consideration is the type of model used for analysis. Most of the common experimental designs were optimized assuming that the model used for analysis has fixed treatment effects. With many entries that are related by pedigree, analysis based on a model with random treatment effects becomes a competitive alternative. In simulations, we therefore study the properties of best linear unbiased predictions (BLUP) of genetic effects based on a nested treatment structure under these design options for a range of genetic parameters. It is concluded that BLUP provides efficient estimates of genetic effects and that resolvable incomplete block designs such as the alpha-design with restricted or unrestricted randomization can be recommended.

Breeding↗

PubMed1998

The structure of plant vacuolar membranes according to infrared spectroscopy.

The structure of the vacuolar membrane (tonoplast) was studied in red beet roots by IR spectroscopy. The vacuolar membrane was shown to be composed of highly ordered lipids which form regions of free liquid lipid bilayer loosely bound to integral proteins. The prevalence of polar lipids in the tonoplast is responsible for the high elasticity and fluidity of the membrane. The presence of alpha-tocopherol in the tonoplast membrane accounts for a high antioxidant activity of the membrane. Integral proteins are immersed into the liquid matrix of the lipid bilayer to a different extent. Examination of the temperature effect on the kinetics of the hydrogen-deuterium exchange in integral membrane proteins showed that the efficient energy of the hydrogen exchange activation was 24 +/- 4 kcal/mol at 19-40 degrees C and increased to 54 kcal/mol at 40-50 degrees C because of the thermal denaturation of proteins. The secondary structure of integral membrane proteins is characterized by a high content of alpha-helices (53%) which decreased to 8% after the extraction of lipids.

Antioxidants↗

PubMed1979

A cytochemical and radioautographic study of the ultrastructural organization of puff-like fibrillar structures in plant interphase nuclei (Allium porrum).

Loose, fibrillar, spherical structures have been observed during recent years in interphase nuclei of both animal and plant cells. These nuclear formations have been referred to as karyosomes, fibrillar bodies, micropuffs and centromeres. In order to gain further information on the nature of these structures, a cytochemical and radioautographic investigation was undertaken using plant meristematic cells (Allium porrum). For that purpose roots were fixed with either formaldehyde or glutaraldehyde in order to carry out cytochemical tests for DNA, RNA and proteins. Certain of the preparations were also first digested with DNase, RNase or proteinase K and then stained according to different procedures. Other specimens were labelled with thymidine for high-resolution radioautographic observations. Staining with diaminobenzidine (DAB) revealed that these nuclear puff-like formations consisted partly of a loose fibrillar meshwork containing nucleic acids. Part of this fine fibrillar reticulum persisted whether the preparations were digested with DNase or RNase before staining with DAB, thus indicating that these nuclear structures contained both DNA and RNA. The fact that these formations incorporate thymidine furnished additional support for the view that they correspond to specific chromosome segments. Staining with ethanolic phosphotungstic acid or digestion of specimens with proteinase K showed that these loose fibrillar structures also consisted of proteins. Judging from their ultrastructure, their association with the chromatin reticulum as well as from their cytochemical characteristics, these nuclear formations most likely correspond to centromeres. In view of the presence of DNA within these structures, it is possible to distinguish them from other equally spherical nuclear formations, observed in certain plant species, that have generally been referred to as karyosomes or micronucleoli and that appear to consist of ribonucleoproteins.

Cell Cycle↗

PubMed1994

A myosin from a higher plant has structural similarities to class V myosins.

In plant cells, myosin is believed to be the molecular motor responsible for actin-based motility processes such as cytoplasmic streaming and directed vesicle transport. In an effort to characterize plant myosin, a cDNA encoding a myosin heavy chain was isolated from Arabidopsis thaliana. The predicted product of the MYA1 gene is 173 kDa and is structurally similar to the class V myosins. It is composed of the highly-conserved NH2-terminal "head" domain, a putative calmodulin-binding "neck" domain, an alpha-helical coiled-coil domain, and a COOH-terminal domain. Northern blot analysis shows that the Arabidopsis MYA1 gene is expressed in all the major plant tissues (flower, leaf, root, and stem). We suggest that the MYA1 myosin may be involved in a general intracellular transport process in plant cells.

Amino Acid Sequence↗

PubMed1999

Probing plant cell structure and function with viral movement proteins.

Virus-encoded movement proteins are the principal strategy by which all plant viruses counter the primary physical defense of the plant to infection - the cell wall - to produce systemic infection and disease. Our understanding of how these proteins act at the molecular and cellular level has increased enormously in the past decade and ushered in an exciting new era of plant virology as an approach to investigating plant cell structure and function. The earliest studies focused on how movement proteins interacted with plasmodesmata, and were an important element in demonstrating the dynamic nature of these intercellular channels. Current efforts are focused on the role of movement proteins in coordinating the replication of viral genomes and the vectorial movement of the progeny genomes through the infected cell, as well as into adjacent cells. Movement proteins are thus providing unique approaches to unravel the fundamental mechanisms by which macromolecular transport is directed and integrated within and between plant cells.

Cell Wall↗

PubMed1992

In vivo analysis of plant RNA structure: soybean 18S ribosomal and ribulose-1,5-bisphosphate carboxylase small subunit RNAs.

A method to investigate the structure of RNA molecules within intact plant tissues has been developed. The RNA structures are analyzed using dimethyl sulfate (DMS), which modifies substituents of adenine and cytosine residues within single-stranded regions of RNA molecules. Reactive sites are identified by primer extension analysis. Using this procedure, an analysis of the secondary structure of the cytoplasmic 18S ribosomal RNA in soybean seedling leaves has been completed. DMS modification data are in good agreement with the phylogenetic structure predicted for soybean 18S rRNA. However, there are a few notable exceptions where residues thought to be involved in double-stranded regions in all 18S rRNAs are strongly modified in soybean leaf samples. These data taken together with the phylogenetic structure suggest that alternate structures may exist in vivo. The further applicability of this technique is demonstrated by comparing the modification pattern obtained in vivo to that obtained in vitro for a particular mRNA molecule encoding the small subunit of ribulose-1,5-bisphosphate carboxylase. The results obtained are compared to a predicted minimum energy secondary structure. The data indicate that the conformation of RNA molecules within the cell may not be reflected in a structural analysis of purified mRNA molecules.

Base Composition↗

PubMed2002

Fatty acid synthase inhibitors from plants: isolation, structure elucidation, and SAR studies.

Fatty acid synthase (FAS) has been identified as a potential antifungal target. FAS prepared from Saccharomyces cerevisiae was employed for bioactivity-guided fractionation of Chlorophora tinctoria,Paspalum conjugatum, Symphonia globulifera, Buchenavia parviflora, and Miconia pilgeriana. Thirteen compounds (1-13), including three new natural products (1, 4, 12), were isolated and their structures identified by spectroscopic interpretation. They represented five chemotypes, namely, isoflavones, flavones, biflavonoids, hydrolyzable tannin-related derivatives, and triterpenoids. 3'-Formylgenistein (1) and ellagic acid 4-O-alpha-l-rhamnopyranoside (9) were the most potent compounds against FAS, with IC(50) values of 2.3 and 7.5 microg/mL, respectively. Furthermore, 43 (14-56) analogues of the five chemotypes from our natural product repository and commercial sources were tested for their FAS inhibitory activity. Structure-activity relationships for some chemotypes were investigated. All these compounds were further evaluated for antifungal activity against Candida albicans and Cryptococcus neoformans. Although there were several antifungal compounds in the set, correlation between the FAS inhibitory activity and antifungal activity could not be defined.

Antifungal Agents↗

PubMed2005

Structure of plant photosystem I revealed by theoretical modeling.

Photosystem (PS) I is a large membrane protein complex vital for oxygenic photosynthesis, one of the most important biological processes on the planet. We present an "atomic" model of higher plant PSI, based on theoretical modeling using the recent 4.4 angstroms x-ray crystal structure of PSI from pea. Because of the lack of information on the amino acid side chains in the x-ray structural model and the high cofactor content in this system, novel modeling techniques were developed. Our model reveals some important structural features of plant PSI that were not visible in the crystal structure, and our model sheds light on the evolutionary relationship between plant and cyanobacterial PSI.

Amino Acid Sequence↗

PubMed2000

Eavesdropping on insects hidden in soil and interior structures of plants.

Accelerometer, electret microphone, and piezoelectric disk acoustic systems were evaluated for their potential to detect hidden insect infestations in soil and interior structures of plants. Coleopteran grubs (the scarabaeids Phyllophaga spp. and Cyclocephala spp.) and the curculionids Diaprepes abbreviatus (L.) and Otiorhynchus sulcatus (F.) weighing 50-300 mg were detected easily in the laboratory and in the field except under extremely windy or noisy conditions. Cephus cinctus Norton (Hymenoptera: Cephidae) larvae weighing 1-12 mg could be detected in small pots of wheat in the laboratory by taking moderate precautions to eliminate background noise. Insect sounds could be distinguished from background noises by differences in frequency and temporal patterns, but insects of similarly sized species could not be distinguished easily from each other. Insect activity was highly variable among individuals and species, although D. abbreviatus grubs tended to be more active than those of O. sulcatus. Tests were done to compare acoustically predicted infestations with the contents of soil samples taken at recording sites. Under laboratory or ideal field conditions, active insects within approximately 30 cm were identified with nearly 100% reliability. In field tests under adverse conditions, the reliability decreased to approximately 75%. These results indicate that acoustic systems with vibration sensors have considerable potential as activity monitors in the laboratory and as field tools for rapid, nondestructive scouting and mapping of soil insect populations.

Acoustics↗

PubMed2002

Structural variation and functional importance of a D-loop-T-loop interaction in valine-accepting tRNA-like structures of plant viral RNAs.

Valine-accepting tRNA-like structures (TLSs) are found at the 3' ends of the genomic RNAs of most plant viruses belonging to the genera Tymovirus, Furovirus, Pomovirus and Pecluvirus, and of one Tobamovirus species. Sequence alignment of these TLSs suggests the existence of a tertiary D-loop-T-loop interaction consisting of 2 bp, analogous to those in the elbow region of canonical tRNAs. The conserved G(18).Psi(55) pair of regular tRNAs is found to covary in these TLSs between G.U (possibly also modified to G.Psi) and A.G. We have mutated the relevant bases in turnip yellow mosaic virus (TYMV) and examined the mutants for symptom development on Chinese cabbage plants and for accumulation of genetic reversions. Development of symptoms is shown to rely on the presence of either A.G or G.U in the original mutants or in revertants. This finding supports the existence and functional importance of this tertiary interaction. The fact that only G.U and A.G are accepted at this position appears to result from steric and energetic limitations related to the highly compact nature of the elbow region. We discuss the implications of these findings for the various possible functions of the valine-accepting TLS.

Base Sequence↗