bluuebunny/crossref_metadata_2025_split huggingface dataset:
TheArabidopsis HKT1Gene Homolog Mediates Inward Na+ Currents inXenopus laevisOocytes and Na+ Uptake inSaccharomyces cerevisiae
Authors: Uozumi Nobuyuki , Kim Eugene J. , Rubio Francisco , Yamaguchi Takao , Muto Shoshi , Tsuboi Akio , Bakker Evert P. , Nakamura Tatsunosuke , Schroeder Julian I. 
Published: July 2002

AbstractThe Na+-K+ co-transporter HKT1, first isolated from wheat, mediates high-affinity K+ uptake. The function of HKT1 in plants, however, remains to be elucidated, and the isolation of HKT1 homologs from Arabidopsis would further studies of the roles of HKT1 genes in plants. We report here the isolation of a cDNA homologous to HKT1 from Arabidopsis (AtHKT1) and the characterization of its mode of ion transport in heterologous systems. The deduced amino acid sequence of AtHKT1 is 41% identical to that of HKT1, and the hydropathy profiles are very similar.AtHKT1 is expressed in roots and, to a lesser extent, in other tissues. Interestingly, we found that the ion transport properties of AtHKT1 are significantly different from the wheat counterpart. As detected by electrophysiological measurements, AtHKT1 functioned as a selective Na+ uptake transporter inXenopus laevis oocytes, and the presence of external K+ did not affect the AtHKT1-mediated ion conductance (unlike that of HKT1). When expressed in Saccharomyces cerevisiae, AtHKT1 inhibited growth of the yeast in a medium containing high levels of Na+, which correlates to the large inward Na+ currents found in the oocytes. Furthermore, in contrast to HKT1, AtHKT1 did not complement the growth of yeast cells deficient in K+ uptake when cultured in K+-limiting medium. However, expression ofAtHKT1 did rescue Escherichia colimutants carrying deletions in K+ transporters. The rescue was associated with a less than 2-fold stimulation of K+uptake into K+-depleted cells. These data demonstrate that AtHKT1 differs in its transport properties from the wheat HKT1, and that AtHKT1 can mediate Na+ and, to a small degree, K+ transport in heterologous expression systems.
Characterization and Expression of DNA Sequences Encoding Putative Type-II Metallothioneins in the Seagrass Posidonia oceanica
Authors: Giordani Tommaso , Natali Lucia , Maserti Bianca Elena , Taddei Sonia , Cavallini Andrea 
Published: July 2002

Abstract
Posidonia oceanica is a marine phanerogam, largely widespread in the Mediterranean sea, representing an important food substrate for many marine organisms. A progressive reduction ofP. oceanica meadows has been reported, due to anthropogenic coastal activity. Studying mechanisms by which this species responds to environmental stresses, three DNA sequences putatively encoding metallothioneins (MTs) have been isolated, by PCR. Two sequences, Pomt2a (accession no. AJ249603) andPomt2b (accession no. AJ249602), show high similarities with genes encoding type-II MTs and are interrupted by two and one intron, respectively. The third sequence, Pomt2c(accession no. AJ249604), is supposed to be a pseudogene, originated by retrotranscription of the Pomt2b mRNA. These sequences belong to a multigene family with at least five members. Northern hybridizations indicated that MT transcripts accumulation is constitutive and seasonally regulated. MT encoding RNAs increase after rhyzome harvesting and (at a lesser extent) after 15 d of cultivation in an aquarium. As for animal MTs, transcripts accumulation is observed also after exposure to trace metals such as copper and cadmium. In the case of copper, the effect depends on concentration. Finally, taking into consideration the great interest in studying the biogeochemical cycle of mercury in the Mediterranean basin and sinceP. oceanica is commonly considered a bioindicator of this metal, the effect of mercury treatments on the accumulation of MT transcripts has been analyzed: in only a few experiments a small increase in the level of transcripts was recorded, suggesting that MTs are not key elements in the mercury accumulation by this species.
Essential Role of Caffeoyl Coenzyme A O-Methyltransferase in Lignin Biosynthesis in Woody Poplar Plants
Authors: Zhong Ruiqin , Morrison W. Herbert , Himmelsbach David S. , Poole Farris L. , Ye Zheng-Hua 
Published: July 2002

Abstract
Caffeoyl coenzyme A O-methyltransferase (CCoAOMT) has recently been shown to participate in lignin biosynthesis in herbacious tobacco plants. Here, we demonstrate that CCoAOMT is essential in lignin biosynthesis in woody poplar (Populus tremula × Populus alba) plants. In poplar stems, CCoAOMT was found to be expressed in all lignifying cells including vessel elements and fibers as well as in xylem ray parenchyma cells. Repression of CCoAOMT expression by the antisense approach in transgenic poplar plants caused a significant decrease in total lignin content as detected by both Klason lignin assay and Fourier-transform infrared spectroscopy. The reduction in lignin content was the result of a decrease in both guaiacyl and syringyl lignins as determined by in-source pyrolysis mass spectrometry. Fourier-transform infrared spectroscopy indicated that the reduction in lignin content resulted in a less condensed and less cross-linked lignin structure in wood. Repression of CCoAOMT expression also led to coloration of wood and an elevation of wall-bound p-hydroxybenzoic acid. Taken together, these results indicate that CCoAOMT plays a dominant role in the methylation of the 3-hydroxyl group of caffeoyl CoA, and the CCoAOMT-mediated methylation reaction is essential to channel substrates for 5-methoxylation of hydroxycinnamates. They also suggest that antisense repression of CCoAOMT is an efficient means for genetic engineering of trees with low lignin content.
Purification and Characterization of Two Voltage-Dependent Anion Channel Isoforms from Plant Seeds
Authors: Abrecht Helge , Wattiez Ruddy , Ruysschaert Jean-Marie , Homblé Fabrice 
Published: July 2002

Abstract
Mitochondria were isolated from imbibed seeds of lentil (Lens culinaris) and Phaseolus vulgaris. We copurified two voltage-dependent anion channel from detergent solubilized mitochondria in a single purification step using hydroxyapatite. The two isoforms from P. vulgaris were separated by chromatofocusing chromatography in 4m urea without any loss of channel activity. Channel activity of each isoform was characterized upon reconstitution into diphytanoyl phosphatidylcholine planar lipid bilayers. Both isoforms form large conductance channels that are slightly anion selective and display cation selective substates.
Association of Spectrin-Like Proteins with the Actin-Organized Aggregate of Endoplasmic Reticulum in the Spitzenkörper of Gravitropically Tip-Growing Plant Cells
Authors: Braun Markus 
Published: July 2002

Abstract
Spectrin-like epitopes were immunochemically detected and immunofluorescently localized in gravitropically tip-growing rhizoids and protonemata of characean algae. Antiserum against spectrin from chicken erythrocytes showed cross-reactivity with rhizoid proteins at molecular masses of about 170 and 195 kD. Confocal microscopy revealed a distinct spherical labeling of spectrin-like proteins in the apices of both cell types tightly associated with an apical actin array and a specific subdomain of endoplasmic reticulum (ER), the ER aggregate. The presence of spectrin-like epitopes, the ER aggregate, and the actin cytoskeleton are strictly correlated with active tip growth. Application of cytochalasin D and A23187 has shown that interfering with actin or with the calcium gradient, which cause the disintegration of the ER aggregate and abolish tip growth, inhibits labeling of spectrin-like proteins. At the beginning of the graviresponse in rhizoids the labeling of spectrin-like proteins remained in its symmetrical position at the cell tip, but was clearly displaced to the upper flank in gravistimulated protonemata. These findings support the hypothesis that a displacement of the Spitzenkörper is required for the negative gravitropic response in protonemata, but not for the positive gravitropic response in rhizoids. It is evident that the actin/spectrin system plays a role in maintaining the organization of the ER aggregate and represents an essential part in the mechanism of gravitropic tip growth.
ANT1, an Aromatic and Neutral Amino Acid Transporter in Arabidopsis
Authors: Chen Lishan , Ortiz-Lopez Adriana , Jung Alan , Bush Daniel R. 
Published: July 2002

Abstract
A new amino acid transporter was identified from the Arabidopsis expressed sequence tag cDNAs by expressing the cDNA in a yeast amino acid transport mutant. Transport analysis of the expressed protein in yeast showed that it transports aromatic and neutral amino acids, as well as arginine. This transporter (ANT1, aromatic and neutral transporter) also transports indole-3-acetic acid and 2,4-dichlorophenoxyacetic acid. The cDNA is 1.6 kb in length with an open reading frame that codes for a protein with 432 amino acids and a calculated molecular mass of 50 kD. Hydropathy analysis showedANT1 is an integral membrane protein with 11 putative membrane-spanning domains. Southern analysis and a BLAST search of the Arabidopsis genome database suggests that ANT1 is part of a small gene family containing at least five members. Phylogenetic comparisons with other known amino acid transporters in plants suggests that ANT1 represents a new class of amino acid transporter. RNA gel-blot analysis showed that this transporter is expressed in all organs with highest abundance in flowers and cauline leaves.
Phenol-Oxidizing Peroxidases Contribute to the Protection of Plants from Ultraviolet Radiation Stress
Authors: Jansen Marcel A.K. , van den Noort Ria E. , Tan M.Y. Adillah , Prinsen Els , Lagrimini L. Mark , Thorneley Roger N.F. 
Published: July 2002

Abstract
We have studied the mechanism of UV protection in two duckweed species (Lemnaceae) by exploiting the UV sensitivity of photosystem II as an in situ sensor for radiation stress. A UV-tolerantSpirodela punctata G.F.W. Meyer ecotype had significantly higher indole-3-acetic acid (IAA) levels than a UV-sensitive ecotype. Parallel work on Lemna gibbamutants suggested that UV tolerance is linked to IAA degradation rather than to levels of free or conjugated IAA. This linkage is consistent with a role for class III phenolic peroxidases, which have been implicated both in the degradation of IAA and the cross-linking of various UV-absorbing phenolics. Biochemical analysis revealed increased activity of a specific peroxidase isozyme in both UV-tolerant duckweed lines. The hypothesis that peroxidases play a role in UV protection was tested in a direct manner using genetically modified tobacco (Nicotiana sylvestris). It was found that increased activity of the anionic peroxidase correlated with increased tolerance to UV radiation as well as decreased levels of free auxin. We conclude that phenol-oxidizing peroxidases concurrently contribute to UV protection as well as the control of leaf and plant architecture.
NAD Malic Enzyme and the Control of Carbohydrate Metabolism in Potato Tubers
Authors: Jenner Helen L. , Winning Brenda M. , Millar A. Harvey , Tomlinson Kim L. , Leaver Christopher J. , Hill Steven A. 
Published: July 2002

Abstract
Potato (Solanum tuberosum) plants were transformed with a cDNA encoding the 59-kD subunit of the potato tuber NAD-dependent malic enzyme (NADME) in the antisense orientation. Measurements of the maximum catalytic activity of NADME in tubers revealed a range of reductions in the activity of this enzyme down to 40% of wild-type activity. There were no detrimental effects on plant growth or tuber yield. Biochemical analyses of developing tubers indicated that a reduction in NADME activity had no detectable effects on flux through the tricarboxylic acid cycle. However, there was an effect on glycolytic metabolism with significant increases in the concentration of 3-phosphoglycerate and phosphoenolpyruvate. These results suggest that alterations in the levels of intermediates toward the end of the glycolytic pathway may allow respiratory flux to continue at wild-type rates despite the reduction in NADME. There was also a statistically significant negative correlation between NADME activity and tuber starch content, with tubers containing reduced NADME having an increased starch content. The effect on plastid metabolism may result from the observed glycolytic perturbations.
Ethylene Induces Antifreeze Activity in Winter Rye Leaves
Authors: Yu Xiao-Ming , Griffith Marilyn , Wiseman Steven B. 
Published: July 2002

Abstract
Antifreeze activity is induced by cold temperatures in winter rye (Secale cereale) leaves. The activity arises from six antifreeze proteins that accumulate in the apoplast of winter rye leaves during cold acclimation. The individual antifreeze proteins are similar to pathogenesis-related proteins, including glucanases, chitinases, and thaumatin-like proteins. The objective of this study was to study the regulation of antifreeze activity in response to ethylene and salicyclic acid, which are known regulators of pathogenesis-related proteins induced by pathogens. Nonacclimated plants treated with salicylic acid accumulated apoplastic proteins with no antifreeze activity. In contrast, when nonacclimated plants were exposed to ethylene, both antifreeze activity and the concentration of apoplastic protein increased in rye leaves. Immunoblotting revealed that six of the seven accumulated apoplastic proteins consisted of two glucanases, two chitinases, and two thaumatin-like proteins. The ethylene-releasing agent ethephon and the ethylene precursor 1-aminocyclopropane-1-carboxylate also induced high levels of antifreeze activity at 20°C, and this effect could be blocked by the ethylene inhibitor AgNO3. When intact rye plants were exposed to 5°C, endogenous ethylene production and antifreeze activity were detected within 12 and 48 h of exposure to cold, respectively. Rye plants exposed to drought produced both ethylene and antifreeze activity within 24 h. We conclude that ethylene is involved in regulating antifreeze activity in winter rye in response to cold and drought.
The Arabidopsis immutans Mutation Affects Plastid Differentiation and the Morphogenesis of White and Green Sectors in Variegated Plants
Authors: Aluru Maneesha R. , Bae Hanhong , Wu Dongying , Rodermel Steven R. 
Published: July 2002

Abstract
The immutans (im) variegation mutant of Arabidopsis has green and white leaf sectors due to the action of a nuclear recessive gene, IMMUTANS (IM). This gene encodes the IM protein, which is a chloroplast homolog of the mitochondrial alternative oxidase. Because the white sectors ofim accumulate the noncolored carotenoid, phytoene, IM likely serves as a redox component in phytoene desaturation. In this paper, we show that IM has a global impact on plant growth and development and is required for the differentiation of multiple plastid types, including chloroplasts, amyloplasts, and etioplasts.IM promoter activity and IM mRNAs are also expressed ubiquitously in Arabidopsis. IM transcript levels correlate with carotenoid accumulation in some, but not all, tissues. This suggests that IM function is not limited to carotenogenesis. Leaf anatomy is radically altered in the green and white sectors ofim: Mesophyll cell sizes are dramatically enlarged in the green sectors and palisade cells fail to expand in the white sectors. The green im sectors also have significantly higher than normal rates of O2 evolution and elevated chlorophyll a/b ratios, typical of those found in “sun” leaves. We conclude that the changes in structure and photosynthetic function of the green leaf sectors are part of an adaptive mechanism that attempts to compensate for a lack of photosynthesis in the white leaf sectors, while maximizing the ability of the plant to avoid photodamage.
Crystallization and initial X-ray analysis of rabbit mature sterol carrier protein 2
Authors: Choinowski Thomas , Dyer James H. , Maderegger Bernhard , Winterhalter Kaspar H. , Hauser Helmut , Piontek Klaus 
Published: July 2002

Sterol carrier protein 2 (SCP2) is a basic intracellular protein which facilitates the in vitro intermembrane transfer of cholesterol, phospholipids and glycolipids. SCP2 was expressed in Escherichia coli, purified to apparent electrophoretic homogeneity and crystallized. Single crystals were obtained by hanging-drop vapour diffusion using ammonium sulfate as precipitant. These crystals belong to space group P41212 or its enantiomorph, with unit-cell parameters a = b = 57.5, c = 86.5 Å, and have one molecule in the crystallographic asymmetric unit. Intensity data to 1.8 Å resolution were collected from native SCP2 crystals using synchrotron radiation, were processed and scaled with an R
linear = 4.9%.
Thermodynamic propensities of amino acids in the native state ensemble: Implications for fold recognition
Authors: Wrabl James O. , Larson Scott A. , Hilser Vincent J. 
Published: July 2002

AbstractAn amino acid sequence, in the context of the solvent environment, contains all of the thermodynamic information necessary to encode a three‐dimensional protein structure. To investigate the relationship between an amino acid sequence and its corresponding protein fold, a database of thermodynamic stability information was assembled that spanned 2951 residues from 44 nonhomologous proteins. This information was obtained using the COREX algorithm, which computes an ensemble‐based description of the native state of a protein. It was observed that amino acid types partitioned unequally into high, medium, and low thermodynamic stability environments. Furthermore, these distributions were reproducible and were significantly different than those expected from random partitioning. To assess the structural importance of the distributions, simple fold‐recognition experiments were performed based on a 3D‐1D scoring matrix containing only COREX residue stability information. This procedure was able to recover amino acid sequences corresponding to correct target structures more effectively than scoring matrices derived from randomized data. High‐scoring sequences were often aligned correctly with their corresponding target profiles, suggesting that calculated thermodynamic stability profiles have the potential to encode sequence information. As a control, identical fold‐recognition experiments were performed on the same database of proteins using DSSP secondary structure information in the scoring matrix, instead of COREX residue stability information. The comparable performance of both approaches suggested that COREX residue stability information and secondary structure information could be of equivalent utility in more sophisticated fold‐recognition techniques. The results of this work are a consequence of the idea that amino acid sequences fold not into single, rigidly stable structures but rather into thermodynamic ensembles best represented by a time‐averaged structure.
Fold recognition without folds
Authors: Koretke Kristin K. , Russell Robert B. , Lupas Andrei N. 
Published: July 2002

AbstractFold recognition predicts protein three‐dimensional structure by establishing relationships between a protein sequence and known protein structures. Most methods explicitly use information derived from the secondary and tertiary structure of the templates. Here we show that rigorous application of a sequence search method (PSI‐BLAST) with no reference to secondary or tertiary structure information is able to perform as well as traditional fold recognition methods. Since the method, SENSER, does not require knowledge of the three‐dimensional structure, it can be used to infer relationships that are not tractable by methods dependent on structural templates.
An improved hydrogen bond potential: Impact on medium resolution protein structures
Authors: Fabiola Felcy , Bertram Richard , Korostelev Andrei , Chapman Michael S. 
Published: July 2002

AbstractA new semi‐empirical force field has been developed to describe hydrogen‐bonding interactions with a directional component. The hydrogen bond potential supports two alternative target angles, motivated by the observation that carbonyl hydrogen bond acceptor angles have a bimodal distribution. It has been implemented as a module for a macromolecular refinement package to be combined with other force field terms in the stereochemically restrained refinement of macromolecules. The parameters for the hydrogen bond potential were optimized to best fit crystallographic data from a number of protein structures. Refinement of medium‐resolution structures with this additional restraint leads to improved structure, reducing both the free R‐factor and over‐fitting. However, the improvement is seen only when stringent hydrogen bond selection criteria are used. These findings highlight common misconceptions about hydrogen bonding in proteins, and provide explanations for why the explicit hydrogen bonding terms of some popular force field sets are often best switched off.
The HoxB1 hexapeptide is a prefolded domain: Implications for the Pbx1/Hox interaction
Authors: Slupsky Carolyn M. , Sykes David B. , Gay Grant L. , Sykes Brian D. 
Published: July 2002

AbstractHox proteins are transcriptional regulators that bind consensus DNA sequences. The DNA‐binding specificity of many of these Hox proteins is modulated by the heterodimerization with partners, such as the Pbx proteins. This cooperative heterodimerization is accomplished through a conserved hexapeptide motif found N‐terminal to the Hox DNA‐binding homeodomain. Several human leukemias have been associated with a chromosomal translocation involving either the Hox gene (i.e., NUP98/HOXA9) or the gene encoding Pbx1 (E2A/PBX1). The transforming ability of these fusion oncoproteins relies at least partially on the ability to interact with one another through this hexapeptide motif. Herein we describe NMR structural calculations of the hexapeptide of HoxB1 (Nα‐acetyl‐Thr‐Phe‐Asp‐Trp‐Met‐Lys‐amide) that has been shown to mediate binding between HoxB1 and Pbx1 and a hexapeptide consensus sequence (Nα‐acetyl‐Leu‐Phe‐Pro‐Trp‐Met‐Arg‐amide). The consensus peptide exists in two conformations caused by cis–trans isomerization of the Phe–Pro peptide bond. The structures of the HoxB1 peptide and the trans form of the consensus peptide reveal a turn very similar to that found as part of the HoxB1/Pbx1/DNA complex in the X‐ray crystal structure. This observation implies that this region is at least partially ‘preformed’ and thus ready to interact with Pbx1 and stabilize binding of Pbx1 and HoxB1 to DNA. The structural results presented here provide a starting point for synthesizing potential nonpeptide or cyclical peptide antagonists that mimic the interaction of these transcriptional cofactors resulting in a potential chemotherapeutic for certain types of leukemias.