Effects of the cucumber mosaic virus 2a protein on aphid–plant interactions in Arabidopsis thaliana

The cucumber mosaic virus (CMV) 2a RNA-dependent RNA polymerase protein has an additional function in Arabidopsis thaliana, which is to stimulate feeding deterrence (antixenosis) against aphids. Antixenosis is thought to increase the probability that aphids, after acquiring CMV particles from brief probes of an infected plant's epidermal cells, will be discouraged from settling and instead will spread inoculum to neighbouring plants. The amino acid sequences of 2a proteins encoded by a CMV strain that induces antixenosis in A. thaliana (Fny-CMV) and one that does not (LS-CMV) were compared to identify residues that might determine the triggering of antixenosis. These data were used to design reassortant viruses comprising Fny-CMV RNAs 1 and 3, and recombinant CMV RNA 2 molecules encoding chimeric 2a proteins containing sequences derived from LS-CMV and Fny-CMV. Antixenosis induction was detected by measuring the mean relative growth rate and fecundity of aphids (Myzus persicae) confined on infected and on mock-inoculated plants. An amino acid sequence determining antixenosis induction by CMV was found to reside between 2a protein residues 200 and 300. Subsequent mutant analysis delineated this to residue 237. We conjecture that the Fny-CMV 2a protein valine-237 plays some role in 2a protein-induced antixenosis.     

Polyploids as a “model system” for the study of heterosis

Heterosis research over the past century has focused primarily on diploid plants and animals. This is despite the fact that most heterotic organisms contain polyploid events in their recent and/or ancient past and various important crop species are heterotic polyploids. We present an argument for the study of heterosis within polyploid systems and give examples of how their study can improve current hypotheses and generate new ones. Polyploid systems allow experiments not possible in diploids but the insights gained must be incorporated into models to explain heterosis at all levels.     

AraPPISite: a database of fine-grained protein–protein interaction site annotations for Arabidopsis thaliana

Knowledge about protein interaction sites provides detailed information of protein–protein interactions (PPIs). To date, nearly 20,000 of PPIs from Arabidopsis thaliana have been identified. Nevertheless, the interaction site information has been largely missed by previously published PPI databases. Here, AraPPISite, a database that presents fine-grained interaction details for A. thaliana PPIs is established. First, the experimentally determined 3D structures of 27 A. thaliana PPIs are collected from the Protein Data Bank database and the predicted 3D structures of 3023 A. thaliana PPIs are modeled by using two well-established template-based docking methods. For each experimental/predicted complex structure, AraPPISite not only provides an interactive user interface for browsing interaction sites, but also lists detailed evolutionary and physicochemical properties of these sites. Second, AraPPISite assigns domain–domain interactions or domain–motif interactions to 4286 PPIs whose 3D structures cannot be modeled. In this case, users can easily query protein interaction regions at the sequence level. AraPPISite is a free and user-friendly database, which does not require user registration or any configuration on local machines. We anticipate AraPPISite can serve as a helpful database resource for the users with less experience in structural biology or protein bioinformatics to probe the details of PPIs, and thus accelerate the studies of plant genetics and functional genomics. AraPPISite is available at http://systbio.cau.edu.cn/arappisite/index.html.     

Omnivores as plant bodyguards—A model of the importance of plant quality

The importance of omnivores in ecological systems is increasingly being recognized, not least due to their intensified use as biocontrol agents in crop production. We model a simple plant–herbivore–omnivore (predator) system to explore the effects of plant suitability as food for omnivores on the outcome of omnivore–herbivore interactions. The model predicts that increasing plant suitability relative to herbivore suitability for the omnivore will catalyze the extinction of herbivores or omnivores, depending on the relative growth rate of omnivores feeding solely on plants or herbivores. When omnivore growth is higher on plants, either the omnivore or the herbivore goes extinct. When omnivore growth is higher on herbivores, the possible consequences are extinction, stable coexistence, and limit cycles, depending on the combination of species properties. Our results suggest that plants in some situations may evolve towards becoming more suitable to omnivores to escape detrimental herbivores and that breeders could manipulate crop suitability to omnivore species to reach a desired outcome of omnivore–herbivore interactions.     

Evaluation of different protocols for the analysis of lipophilic plant metabolites by gas chromatography–mass spectrometry using potato as a model

In the analysis of lipophilic plant metabolites by gas chromatography?Cmass spectrometry a step is required to release fatty acids and other analytes from complex molecules. Seven alternative methods were compared to the standard method of 1% H₂SO₄/50°C/16?h using Desirée and Phureja potato tubers as models. With two sodium methoxide alkali-catalysed methods (0.5?M NaOCH₃/50°C/1 and 16?h) recoveries of ferulic acids increased, long chain fatty acids and sterols decreased, 2-hydroxy acids were negligible, solanidine was absent and ??5-avenasterol isomerisation was minimal. Using a harsh alkali hydrolysis (1.0?M KOH/120°C/24?h) followed by a mild methylation (1% H₂SO₄/50°C/1.5?h), recoveries of polyunsaturated fatty acids were poor, sterols decreased but ??5-avenasterol isomerisation was minimal. With a mild alkali hydrolysis (0.5?M NaOH/100°C/5?min) followed by methylation with boron trifluoride (14%BF₃/100°C/30?min) recoveries of sterols and 2-hydroxy fatty acids were similar to the standard method and ??5-avenasterol isomerisation was high. Lower ferulic acid recoveries, absence of solanidine and overestimation of fatty alcohols were evident in both methods involving alkali hydrolysis. Three different methods using hydrochloric acid (1.00?M HCl/70°C/5?h, 0.63?M HCl/110°C/2?h and 2.00?M HCl/50°C/24?h) all gave increased recoveries of 2-hydroxy acids, ferulic acids, solanidine and sterols, although ??5-avenasterol isomerisation increased. Hydrochloric acid methods are recommended for studies requiring quantitative determinations (i.e. concentration of metabolite in sample). Either the hydrochloric acid methods or the standard sulphuric acid method are suggested for determining relative concentrations between samples, although there is a requirement for further studies.     

Genotype–environment interactions affect flower and fruit herbivory and plant chemistry of Arabidopsis thaliana in a transplant experiment

Large differences exist in flower and fruit herbivory between dune and inland populations of plants of Arabidopsis thaliana (Brassicaceae). Two specialist weevils Ceutorhynchus atomus and C. contractus (Curculionidae) and their larvae are responsible for this pattern in herbivory. We test, by means of a reciprocal transplant experiment, whether these differences reflect environmental influences or genetic variation in plant defense level. All plants suffered more damage after being transplanted to the dune site than after being transplanted to the inland site. Plants of inland origin suffered more flower and fruit herbivory than plants of dune origin when grown at the dune transplant site, but differences were much smaller at the inland site. Both flower damage by adult weevils and fruit damage by their larvae were subject to significant genotype × environment interactions. The observed pattern in herbivory is a strong indication for local adaption of plant defense to the level of herbivory by Ceutorhynchus. In order to identify the mechanism of defense, a quantitative analysis of glucosinolates was performed on the seeds with HPLC. Highly significant differences were found in glucosinolate types and total concentration. These patterns were mainly determined by the origin of the plants (dune or inland) and by a genotype × environment interaction. Herbivory was not significantly correlated to the concentration of glucosinolates in seeds. We therefore analyzed the total metabolic composition of seeds, using NMR spectroscopy and multivariate data analysis. Major differences in chemical composition were found in the water–methanol fractions: more glucosinolate and sucrose in the dune and more fatty acids, lipids and sinapoylmalate in the inland populations. We discuss which of these chemical factors could explain the marked differences in damage between populations.     

Arabidopsis, a model to study biological functions of isoprene emission?

The volatile hemiterpene isoprene is emitted from plants and can affect atmospheric chemistry. Although recent studies indicate that isoprene can enhance thermotolerance or quench oxidative stress, the underlying physiological mechanisms are largely unknown. In this work, Arabidopsis (Arabidopsis thaliana), a natural nonemitter of isoprene and the model plant for functional plant analyses, has been constitutively transformed with the isoprene synthase gene (PcISPS) from Grey poplar (Populus x canescens). Overexpression of poplar ISPS in Arabidopsis resulted in isoprene-emitting rosettes that showed transiently enhanced growth rates compared to the wild type under moderate thermal stress. The findings that highest growth rates, higher dimethylallyl diphosphate levels, and enzyme activity were detected in young plants during their vegetative growth phase indicate that enhanced growth of transgenic plants under moderate thermal stress is due to introduced PcISPS. Dynamic gas-exchange studies applying transient cycles of heat stress to the wild type demonstrate clearly that the prime physiological role of isoprene formation in Arabidopsis is not to protect net assimilation from damage against thermal stress, but may instead be to retain the growth potential or coordinated vegetative development of the plant. Hence, this study demonstrates the enormous potential but also the pitfalls of transgenic Arabidopsis (or other nonnatural isoprenoid emitters) in studying isoprene biosynthesis and its biological function(s).     

Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein–protein interaction

Dicer or Dicer-like (DCL) protein is a catalytic component involved in microRNA (miRNA) or small interference RNA (siRNA) processing pathway, whose fragment structures have been partially solved. However, the structure and function of the unique DUF283 domain within dicer is largely unknown. Here we report the first structure of the DUF283 domain from the Arabidopsis thaliana DCL4. The DUF283 domain adopts an α-β-β-β-α topology and resembles the structural similarity to the double-stranded RNA-binding domain. Notably, the N-terminal α helix of DUF283 runs cross over the C-terminal α helix orthogonally, therefore, N- and C-termini of DUF283 are in close proximity. Biochemical analysis shows that the DUF283 domain of DCL4 displays weak dsRNA binding affinity and specifically binds to double-stranded RNA-binding domain 1 (dsRBD1) of Arabidopsis DRB4, whereas the DUF283 domain of DCL1 specifically binds to dsRBD2 of Arabidopsis HYL1. These data suggest a potential functional role of the Arabidopsis DUF283 domain in target selection in small RNA processing.     

Seed–seedling conflict in conifers as a result of plant–plant interactions at the forest-tundra ecotone

Background: As the climate warms, plant interactions between shrubs and conifer seedlings may affect migration of boreal trees into alpine areas; however these interactions have not been widely tested across conifer life stages.

Aims: Determine the role of shading by Betula glandulosa shrubs on early Picea mariana recruitment in the forest-tundra ecotone of the Mealy Mountains, Labrador (Canada).

Methods: Four shrub treatments were established with varying degrees of shade (unaltered, trimmed, cleared, shaded). Emergence and growth of P. mariana in treatment plots were compared to control plots without shrubs.

Results: Seedling emergence was facilitated; seedlings beneath shrubs emerged at greater levels (16% ± 5.1%) than in the control (0.5% ± 0.3%); however, evidence of facilitation post-emergence was weak, likely due to stronger interactions with seedbed species at this stage. Vertical growth of young seedlings was greatest in control and shaded plots, but needle production significantly decreased with increased shade suggesting that seedlings may compete with shrubs for light early in life.

Conclusions: Although facilitation has been previously implicated as an important mechanism in stressful environments, our study indicates that the early life stages of some conifers at the tree line are not strongly facilitated by shrubs as has been previously suggested for adults.     

Salinity tolerance of Arabidopsis: a good model for cereals?

Arabidopsis is a glycophyte species that is sensitive to moderate levels of NaCl. Arabidopsis offers unique benefits to genetic and molecular research and has provided much information about both Na(+) transport processes and Na(+) tolerance. A compilation of data available on Na(+) accumulation and Na(+) tolerance in Arabidopsis is presented, and comparisons are made with several crop plant species. The relationship between Na(+) tolerance and Na(+) accumulation is different in Arabidopsis and cereals, with an inverse relationship often found within cereal species that is not as evident in Arabidopsis ecotypes. Results on salinity tolerance obtained in Arabidopsis should therefore be extrapolated to cereals with caution. Arabidopsis remains a useful model to study and discover plant Na(+) transport processes.     

Structure–function characterization of the recombinant aspartic proteinase A1 from Arabidopsis thaliana

Aspartic proteinases (APs) are involved in several physiological processes in plants, including protein processing, senescence, and stress response and share many structural and functional features with mammalian and microbial APs. The heterodimeric aspartic proteinase A1 from Arabidopsis thaliana (AtAP A1) was the first acid protease identified in this model plant, however, little information exists regarding its structure function characteristics. Circular dichroism analysis indicated that recombinant AtAP A1 contained an higher α-helical content than most APs which was attributed to the presence of a sequence known as the plant specific insert in the mature enzyme. rAtAP A1 was stable over a broad pH range (pH 3–8) with the highest stability at pH 5–6, where 70–80% of the activity was retained after 1 month at 37 °C. Using calorimetry, a melting point of 79.6 °C was observed at pH 5.3. Cleavage profiles of insulin β-chain indicated that the enzyme exhibited a higher specificity as compared to other plant APs, with a high preference for the Leu₁₅–Tyr₁₆ peptide bond. Molecular modeling of AtAP A1 indicated that exposed histidine residues and their interaction with nearby charged groups may explain the pH stability of rAtAP A1.     

Rat β-glucuronidase as a reporter protein for the analysis of the plant secretory pathway

Abstract

E. coliβ-glucuronidase, a cytosolic enzyme, was found not to be a good reporter enzyme for secretion studies in plants. In this study, we chose to test and adapt an animal β-glucuronidase as a better reporter protein for the secretory pathway of plants. We modified rat β-glucuronidase to obtain secreted and vacuolar variants. Five different C-termini were produced: the original C-terminus of the rat enzyme, a 19 codon deletion (Δ19), a 15 codon deletion (Δ15) and fusions of the Δ19 or Δ15 termini with the last 6 or 7 codons of the vacuolar sorting determinant of tobacco chitinase A, respectively. The signal sequence of the rat β-glucuronidase polypeptide was replaced by the sequence encoding the signal peptide of tobacco chitinase A. In a transient expression system, the best enzymatic activity was found with β-glucuronidase having the 15 codons deletion, therefore Δ15 (secRGUS) and Δ15 + Chi (RGUS-Chi) were further evaluated and their efficiency of secretion or vacuolar targeting were tested under different conditions. To determine the correct targeting of reporter genes, we compared the localization of β-glucuronidase and of an endogenous marker, α-mannosidase. Treating cells with drugs that specifically affect different aspects of the secretory pathway also tested the validity of RGUS-based reporters. A non-specific inhibitor such as cytochalasin D and a wide range inhibitor such as BFA were compared with specific inhibitors such as wortmannin and bafilomycin A1. Finally, monensin and NH₄Cl were used to evaluate the role of vacuolar pH in correct RGUS-Chi targeting. The two new reporter proteins proved to be good tools for our studies in the transient expression system in tobacco protoplasts and for further applications.     

Accumulation of a thermostable endo-1,4-β-D-glucanase in the apoplast of Arabidopsis thaliana leaves

Plant biomass, the most abundant renewable resource on earth, is a potential source of fermentable sugars for production of alternative transportation fuels and other chemicals. Bioconversion of plant biomass to fermentable glucose involves enzymatic hydrolysis of cellulose, a major polysaccharide constituent. Because commercially available microbial cellulases are prohibitively expensive for bioethanol processes, we have investigated the feasibility of producing these enzymes in plants as a low-cost, potentially high-volume alternative to traditional production methods. We have successfully expressed the catalytic domain of a thermostable (T _opt=81 °C) endo-1,4--D-glucanase from the eubacterium, Acidothermus cellulolyticus, in the apoplast of tobacco BY-2 suspension cells and leaves of Arabidopsis thaliana plants. The apoplast-targeting cassette designed for this work consists of the cauliflower mosaic virus 35S promoter, the tobacco mosaic virus translational enhancer, the sequence encoding the tobacco Pr1a signal peptide, and the polyadenylation signal of nopaline synthase. Recombinant E1 catalytic domain was targeted to the ER by the signal peptide and secreted into the apoplast via the default pathway. Secretion of the enzyme did not detectably affect the growth rate of transgenic BY-2 cells, although the protein was enzymatically active at elevated temperatures. Similarly, transgenic plants exhibited no abnormal phenotypes correlating with expression of the enzyme. Close agreement between independent immunochemical and activity-based assays indicates that the enzyme accumulated to concentrations up to 26% of the total soluble protein in leaves of primary A. thaliana transformants. The amount of functional endoglucanase produced illustrates that plants can accumulate very large quantities of enzyme for commercial biomass conversion.     

Ribonucleotide reductase from the higher plant Arabidopsis thaliana : expression of the R2 component and characterization of its iron-radical center

 Deoxyribonucleotides synthesis has not been biochemically characterized in higher plants. From a cDNA of the small component (protein R2) of ribonucleotide reductase from Arabidopsis thaliana, an inducible overexpression plasmid has been constructed. A recombinant 78-kDa homodimeric protein containing very little iron was purified to homogeneity. Addition of ferrous iron and oxygen resulted in a protein containing 1.2 tyrosyl radicals and 4 iron atoms per dimer. Light absorption and low-temperature EPR spectra indicated close similarity of the iron-radical centers in plant and mouse R2 proteins. It is then suggested that, as in all class I eukaryotic ribonucleotide reductase, the active site of R2 component contains a μ-oxo bridged di-iron center in strong interaction with a tyrosyl radical. The stability of the radical seems, however, to be larger in the plant R2 protein, as shown by its resistance to hydroxyurea. Received: 20 March 1997 / Accepted: 5 June 1997     

Identification of a product specific β-amyrin synthase from Arabidopsis thaliana

Triterpene skeletons are produced by oxidosqualene cyclases (OSCs). The genome sequencing of Arabidopsis thaliana revealed the presence of thirteen OSC homologous genes including At1g78950, which has been revised recently as two independent ORFs, namely At1g78950 and At1g78955. The cDNA corresponding to the revised At1g78950 was obtained by RT-PCR, ligated into Saccharomyces cerevisiae expression vector pYES2, and expressed in a lanosterol synthase deficient S. cerevisiae strain. LC-MS and NMR analyses of the accumulated product in the host cells showed that the product of At1g78950 is β-amyrin, indicating that At1g78950 encodes a β-amyrin synthase (EC 5.4.99.-).