bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activation Tagging Using the En-I Maize Transposon System in Arabidopsis
Authors: Marsch-Martinez Nayelli , Greco Raffaella , Van Arkel Gert , Herrera-Estrella Luis , Pereira Andy 
Published: October 2002

Abstract
A method for the generation of stable activation tag inserts was developed in Arabidopsis using the maize (Zea mays)En-I transposon system. The method employs greenhouse selectable marker genes that are useful to efficiently generate large populations of insertions. A population of about 8,300 independent stable activation tag inserts has been produced. Greenhouse-based screens for mutants in a group of plants containing about 2,900 insertions revealed about 31 dominant mutants, suggesting a dominant mutant frequency of about 1%. From the first batch of about 400 stable insertions screened in the greenhouse, four gain-in-function, dominant activation-tagged, morphological mutants were identified. A novel gain-in-function mutant calledthread is described, in which the target gene belongs to the same family as the YUCCA flavin-mono-oxygenase that was identified by T-DNA activation tagging. The high frequency of identified gain-in-function mutants in the population suggests that theEn-I system described here is an efficient strategy to saturate plant genomes with activation tag inserts. Because only a small number of primary transformants are required to generate an activation tag population, the En-I system appears to be an attractive alternative to study plant species where the present transformation methods have low efficiencies.
Overexpression of the clpP 5′-Untranslated Region in a Chimeric Context Causes a Mutant Phenotype, Suggesting Competition for a clpP-Specific RNA Maturation Factor in Tobacco Chloroplasts
Authors: Kuroda Hiroshi , Maliga Pal 
Published: October 2002

Abstract
The plastid ribosomal RNA (rrn) operon promoter was fused with DNA segments encoding the leader sequence (5′-untranslated region [UTR]) of plastid mRNAs to compare their efficiency in mediating translation of a bacterial protein neomycin phosphotransferase (NPTII) in tobacco (Nicotiana tabacum) chloroplasts. In young leaves, NPTII accumulated at 0.26% and 0.8% of the total soluble leaf protein from genes with theclpP and atpB 5′-UTR, respectively. Interestingly, expression of NPTII from the promoter with theclpP 5′-UTR (0.26% NPTII) caused a mutant (chlorotic) phenotype, whereas plants accumulating approximately 0.8% NPTII from the atpB 5′-UTR were normal green, indicating that the mutant phenotype was independent of NPTII accumulation. Low levels of monocistronic clpP mRNA and accumulation of intron-containing clpP transcripts in the chlorotic leaves suggest competition between the clpP 5′-UTR in the chimeric transcript and the native clpP pre-mRNA (ratio 16:1) for an mRNA maturation factor. Because maturation of 11 other intron-containing mRNAs was unaffected in the chlorotic leaves, it appears that the factor is clpP specific. The mutant phenotype is correlated with reduced levels (approximately 2 times) of the ClpP1 protease subunit, supporting an important role for ClpP1 in chloroplast development.
Down-Regulation of Tomato β-Galactosidase 4 Results in Decreased Fruit Softening
Authors: Smith David L. , Abbott Judith A. , Gross Kenneth C. 
Published: October 2002

AbstractTranscript abundance of the gene encoding β-galactosidase II, a β-galactosidase/exo-galactanase (EC 3.2.1.23) present during tomato (Lycopersicon esculentum) fruit ripening, was suppressed by expression of an antisense tomato β-galactosidase 4 (TBG4) cDNA driven by the cauliflower mosaic virus 35S promoter. RNA gel-blot analysis was used to evaluate TBG4 mRNA levels in transgenic fruit. All of the antisense lines had attenuated TBG4 mRNA levels in turning stage fruit; however, TBG4 mRNA suppression was unstable, and mRNA levels varied in red-ripe fruit among the lines. Suppression of TBG4 mRNA levels in antisense fruit was correlated with a reduction in extractable exo-galactanase activity against a lupin galactan. All of the antisense lines had reduced free galactose levels at mature green stage 4, but levels comparable with controls during ripening. Total cell wall galactosyl contents in the antisense fruit were not significantly different from control fruit. Whole-fruit firmness was measured using a texture analyzer and the means of the peak force measurements for four of six antisense lines were significantly higher than control fruit. One antisense line had red-ripe fruit that were 40% firmer than controls. Fruit from this antisense line also had the lowest TBG4 mRNA and exo-galactanase levels and the highest wall galactosyl content during the early stages of ripening, implicating an involvement of this gene product in cell wall modification leading to fruit softening.
Numeric Simulation of Plant Signaling Networks
Authors: Genoud Thierry , Trevino Santa Cruz Marcela B. , Métraux Jean-Pierre 
Published: October 2002

Abstract
Plants have evolved an intricate signaling apparatus that integrates relevant information and allows an optimal response to environmental conditions. For instance, the coordination of defense responses against pathogens involves sophisticated molecular detection and communication systems. Multiple protection strategies may be deployed differentially by the plant according to the nature of the invading organism. These responses are also influenced by the environment, metabolism, and developmental stage of the plant. Though the cellular signaling processes traditionally have been described as linear sequences of events, it is now evident that they may be represented more accurately as network-like structures. The emerging paradigm can be represented readily with the use of Boolean language. This digital (numeric) formalism allows an accurate qualitative description of the signal transduction processes, and a dynamic representation through computer simulation. Moreover, it provides the required power to process the increasing amount of information emerging from the fields of genomics and proteomics, and from the use of new technologies such as microarray analysis. In this review, we have used the Boolean language to represent and analyze part of the signaling network of disease resistance in Arabidopsis.
Enhanced Copper Tolerance in Silene vulgaris (Moench) Garcke Populations from Copper Mines Is Associated with Increased Transcript Levels of a 2b-Type Metallothionein Gene
Authors: van Hoof Nathalie A.L.M. , Hassinen Viivi H. , Hakvoort Henk W.J. , Ballintijn Koos F. , Schat Henk , Verkleij Jos A.C. , Ernst Wilfried H.O. , Karenlampi Sirpa O. , Tervahauta Arja I. 
Published: October 2002

Abstract
Silene vulgaris (Moench) Garcke has evolved populations with extremely high levels of copper tolerance. To evaluate the role of metallothioneins (MTs) in copper tolerance in S. vulgaris, we screened a cDNA library derived from a highly copper-tolerant population using Arabidopsis-based MT probes and identified an MT2b-like gene. When expressed in yeast, this gene,SvMT2b, restored cadmium and copper tolerance in different hypersensitive strains. Northern-blot analysis and quantitative reverse transcriptase-PCR showed that plants from the copper-tolerant S. vulgaris populations had significantly higher transcript levels of SvMT2b than plants from the copper-sensitive populations, both in roots and shoots and with and without copper exposure. Southern-blot analysis suggested that the higher expression of the latter allele was caused by gene amplification. Segregating families of crosses between copper-sensitive and copper-tolerant plants exhibited a 1 to 3 segregation forSvMT2b expression. Allele-specific PCR showed that low-expression F3 plants were homozygous for the allele inherited from the copper-sensitive parent, whereas high-expression plants possessed at least one allele from the tolerant parent.SvMT2b expression did not cosegregate with copper tolerance in crosses between sensitive and tolerant plants. However, a significant cosegregation with copper tolerance did occur in families derived from crosses between moderately tolerant F3 plants with different SvMT2b genotypes. Thus, overexpression ofSvMT2b conferred copper tolerance although only within the genetic background of a copper tolerant plant.
A Novel Phytase with Sequence Similarity to Purple Acid Phosphatases Is Expressed in Cotyledons of Germinating Soybean Seedlings
Authors: Hegeman Carla E. , Grabau Elizabeth A. 
Published: October 2002

Abstract
Phytic acid (myo-inositol hexakisphosphate) is the major storage form of phosphorus in plant seeds. During germination, stored reserves are used as a source of nutrients by the plant seedling. Phytic acid is degraded by the activity of phytases to yield inositol and free phosphate. Due to the lack of phytases in the non-ruminant digestive tract, monogastric animals cannot utilize dietary phytic acid and it is excreted into manure. High phytic acid content in manure results in elevated phosphorus levels in soil and water and accompanying environmental concerns. The use of phytases to degrade seed phytic acid has potential for reducing the negative environmental impact of livestock production. A phytase was purified to electrophoretic homogeneity from cotyledons of germinated soybeans (Glycine max L. Merr.). Peptide sequence data generated from the purified enzyme facilitated the cloning of the phytase sequence (GmPhy) employing a polymerase chain reaction strategy. The introduction of GmPhy into soybean tissue culture resulted in increased phytase activity in transformed cells, which confirmed the identity of the phytase gene. It is surprising that the soybean phytase was unrelated to previously characterized microbial or maize (Zea mays) phytases, which were classified as histidine acid phosphatases. The soybean phytase sequence exhibited a high degree of similarity to purple acid phosphatases, a class of metallophosphoesterases.
Cloning and Characterization of a Coronatine-Regulated Tyrosine Aminotransferase from Arabidopsis
Authors: Lopukhina Anna , Dettenberg Marcus , Weiler Elmar W. , Holländer-Czytko Heike 
Published: October 2002

Abstract
In plants, the phytotoxin coronatine, which is an analog of the octadecanoids 12-oxo-phytodienoic acid and/or jasmonic acid, gives rise to a number of physiological responses similar to those of octadecanoids. To further elucidate the physiological role of these compounds, the differential RNA display technique was used to isolate a number of novel octadecanoid-inducible genes expressed in coronatine-treated Arabidopsis. Among these, a cDNA clone was identified that was similar to known tyrosine aminotransferases (TATs). The function was verified with the expressed recombinant protein. In Arabidopsis, the protein is present as a multimer of 98 kD, with a monomer of an apparent molecular mass of 47 kD. TAT mRNA could be induced within 2 h by various octadecanoids and by wounding of the plants. Accumulation of the TAT protein and a 5- to 7-fold increase in its enzymatic activity was observed 7 to 9 h after application of octadecanoids, coronatine, or wounding. The potential role of TAT in the defense response to herbivores and pathogens is discussed.
Electrodiffusional Uptake of Organic Cations by Pea Seed Coats. Further Evidence for Poorly Selective Pores in the Plasma Membrane of Seed Coat Parenchyma Cells
Authors: van Dongen Joost T. , Laan Ramon G.W. , Wouterlood Madeleine , Borstlap Adrianus C. 
Published: October 2002

Abstract
In developing seeds, the permeability of the plasma membrane of seed coat parenchyma cells is crucial for the supply of nutrients to the embryo. Here, we report characteristics of the transport of the organic cation choline and the basic amino acid l- histidine (His; cation at pH 5, electroneutral at pH 7) into isolated seed coats of pea (Pisum sativum). Supplied at sub-micromolar concentrations, choline+ accumulated in the seed coat tissue 5.1 ± 0.8-fold, His+ 2.4 ± 0.3-fold, and His0 1.3 ± 0.2-fold. Taking into consideration that at pH 5 His influxes as a cation but effluxes as a neutral molecule, these accumulations are in reasonable agreement with (electro) diffusional uptake at the prevailing membrane potential of −55 ± 3 mV. At a concentration of 100 mm, choline+ and His+, but not His0, depolarized the membrane of the parenchyma cells and neither of the substrates was accumulated. At this concentration, the relative influx (the ratio of influx and external concentration, a measure for membrane permeability) of choline and His was approximately 10 μmol g−1 fresh weight min−1 m −1, similar to that found for neutral amino acids, sucrose, glucose, and mannitol. At lower concentrations, the relative influx of choline+ and His+ increased because of increasingly more negative membrane potentials, giving rise to apparent saturation kinetics. It is suggested that transport of organic cations can proceed by a general, poorly selective pore in the plasma membrane of seed coat parenchyma cells. This pore is thought to be responsible for the unloading of a range of solutes that serve as nutrients for the embryo.
Novel Anther-SpecificmybGenes from Tobacco as Putative Regulators of Phenylalanine Ammonia-Lyase Expression
Authors: Yang Seungchan , Sweetman Justin P. , Amirsadeghi Sasan , Barghchi Medhi , Huttly Alison K. , Chung Won-Il , Twell David 
Published: October 2002

AbstractTwo cDNA clones (NtmybAS1 andNtmybAS2) encoding MYB-related proteins with strong sequence similarity to petunia (Petunia hybrida) PhMYB3 were isolated from a tobacco (Nicotiana tabacumcv Samsun) pollen cDNA library. Northern blot and in situ hybridization revealed that NtmybAS transcripts are specifically expressed in both sporophytic and gametophytic tissues of the anther including tapetum, stomium, vascular tissue, and developing pollen. Random binding site selection assays revealed that NtMYBAS1 bound to DNA sequences closely resembling consensus MYB binding sites MBSI and MBSIIG, with a higher affinity for MBSI. Transient expression analyses of the N-terminal MYB domain demonstrated the presence of functional nuclear localization signals, and full-length NtMYBAS1 was able to activate two different phenylalanine ammonia-lyase promoters (PALA and gPAL1) in tobacco leaf protoplasts. Similar analysis of truncated NtmybAS1cDNAs identified an essential, C-terminal trans-activation domain. Further in situ hybridization analyses demonstrated strict co-expression of NtmybAS and gPAL1 in the tapetum and stomium. Despite abundant expression ofNtmybAS transcripts in mature pollen,gPAL1 transcripts were not detectable in pollen. Our data demonstrate that NtMYBAS1 is a functional anther-specific transcription factor, which is likely to be a positive regulator ofgPAL1 expression and phenylpropanoid synthesis in sporophytic, but not in gametophytic, tissues of the anther.
A Major Light-Harvesting Polypeptide of Photosystem II Functions in Thermal Dissipation[W]
Authors: Elrad Dafna , Niyogi Krishna K. , Grossman Arthur R. 
Published: October 2002

AbstractUnder high-light conditions, photoprotective mechanisms minimize the damaging effects of excess light. A primary photoprotective mechanism is thermal dissipation of excess excitation energy within the light-harvesting complex of photosystem II (LHCII). Although roles for both carotenoids and specific polypeptides in thermal dissipation have been reported, neither the site nor the mechanism of this process has been defined precisely. Here, we describe the physiological and molecular characteristics of the Chlamydomonas reinhardtii npq5 mutant, a strain that exhibits little thermal dissipation. This strain is normal for state transition, high light–induced violaxanthin deepoxidation, and low light growth, but it is more sensitive to photoinhibition than the wild type. Furthermore, both pigment data and measurements of photosynthesis suggest that the photosystem II antenna in the npq5 mutant has one-third fewer light-harvesting trimers than do wild-type cells. The npq5 mutant is null for a gene designated Lhcbm1, which encodes a light-harvesting polypeptide present in the trimers of the photosystem II antennae. Based on sequence data, the Lhcbm1 gene is 1 of 10 genes that encode the major LHCII polypeptides in Chlamydomonas. Amino acid alignments demonstrate that these predicted polypeptides display a high degree of sequence identity but maintain specific differences in their N-terminal regions. Both physiological and molecular characterization of the npq5 mutant suggest that most thermal dissipation within LHCII of Chlamydomonas is dependent on the peripherally associated trimeric LHC polypeptides.
Genome Dynamics and Evolution of theMla(Powdery Mildew) Resistance Locus in Barley[W]
Authors: Wei Fusheng , Wing Rod A. , Wise Roger P. 
Published: October 2002

AbstractGenes that confer defense against pathogens often are clustered in the genome and evolve via diverse mechanisms. To evaluate the organization and content of a major defense gene complex in cereals, we determined the complete sequence of a 261-kb BAC contig from barley cv Morex that spans the Mla (powdery mildew) resistance locus. Among the 32 predicted genes on this contig, 15 are associated with plant defense responses; 6 of these are associated with defense responses to powdery mildew disease but function in different signaling pathways. The Mla region is organized as three gene-rich islands separated by two nested complexes of transposable elements and a 45-kb gene-poor region. A heterochromatic-like region is positioned directly proximal to Mla and is composed of a gene-poor core with 17 families of diverse tandem repeats that overlap a hypermethylated, but transcriptionally active, gene-dense island. Paleontology analysis of long terminal repeat retrotransposons indicates that the present Mla region evolved over a period of &gt;7 million years through a variety of duplication, inversion, and transposon-insertion events. Sequence-based recombination estimates indicate that R genes positioned adjacent to nested long terminal repeat retrotransposons, such as Mla, do not favor recombination as a means of diversification. We present a model for the evolution of the Mla region that encompasses several emerging features of large cereal genomes.
Energetic and entropic contributions to the interactions between like‐charged groups in cationic peptides: A molecular dynamics simulation study
Authors: Villarreal Marcos , Montich Guillermo 
Published: October 2002

AbstractThe interaction between like‐charged amino acid residues has been proposed to stabilize the folded state of peptides and proteins, and to modulate the substrate binding and the action mechanism of enzymes. We have used an alanine‐ and lysine‐based peptide as a model system to study the interaction between like charges, and we have performed a 16‐nsec molecular dynamics simulation in solution. The calculated potential of mean force for the approach of the lysine's Nζ atoms showed a minimum at a distance of 0.7 nm, in agreement with the separation probabilities obtained from analysis of protein crystal structures. The analysis of the individual energy components showed that the solvent polarization pays for the approach of the like charges and that the van der Waals energies do not contribute significantly. The entropic contributions have been divided in conformational and desolvation terms. Both terms favor the formation of the charge pair. A 10‐fold increase in counterion concentration was observed—with respect to its bulk concentration—next to the peptide charges, which helps to stabilize the peptide charges at a close distance.
Fast‐folding protein kinetics, hidden intermediates, and the sequential stabilization model
Authors: Ozkan S. Banu , Dill Ken A. , Bahar Ivet 
Published: October 2002

AbstractDo two‐state proteins fold by pathways or funnels? Native‐state hydrogen exchange experiments show discrete nonnative structures in equilibrium with the native state. These could be called hidden intermediates (HI) because their populations are small at equilibrium, and they are not detected in kinetic experiments. HIs have been invoked as disproof of funnel models, because funnel pictures appear to indicate (1) no specific sequences of events in folding; (2) a continuum, rather than a discrete ladder, of structures; and (3) smooth landscapes. In the present study, we solve the exact dynamics of a simple model. We find, instead, that the present microscopic model is indeed consistent with HIs and transition states, but such states occur in parallel, rather than along the single pathway predicted by the sequential stabilization model. At the microscopic level, we observe a huge multiplicity of trajectories. But at the macroscopic level, we observe two pathways of specific sequences of events that are relatively traditional except that they are in parallel, so there is not a single reaction coordinate. Using singular value decomposition, we show an accurate representation of the shapes of the model energy landscapes. They are highly complex funnels.
Sequence conservation in the chagasin family suggests a common trend in cysteine proteinase binding by unrelated protein inhibitors
Authors: Rigden Daniel J. , Mosolov Vladimir V. , Galperin Michael Y. 
Published: October 2002

AbstractThe recently described inhibitor of cysteine proteinases fromTrypanosoma cruzi, chagasin, was found to have close homologs in several eukaryotes, bacteria and archaea, the first protein inhibitors of cysteine proteases in prokaryotes. These previously uncharacterized 110–130 residue‐long proteins share a well‐conserved sequence motif that corresponds to two adjacent β‐strands and the short loop connecting them. Chagasin‐like proteins also have other conserved, mostly aromatic, residues, and share the same predicted secondary structure. These proteins adopt an all‐β fold with eight predicted β‐strands of the immunoglobulin type. The phylogenetic distribution of the chagasins generally correlates with the presence of papain‐like cysteine proteases. Previous studies have uncovered similar trends in cysteine proteinase binding by two unrelated inhibitors, stefin and p41, that belong to the cystatin and thyroglobulin families, respectively. A hypothetical model of chagasin–cruzipain interaction suggests that chagasin may dock to the cruzipain active site in a similar manner with the conserved NPTTG motif of chagasin forming a loop that is similar to the wedge structures formed at the active sites of papain and cathepsin L by stefin and p41.