bluuebunny/crossref_metadata_2025_split huggingface dataset:
Independent Action of ELF3 and phyB to Control Hypocotyl Elongation and Flowering Time
Authors: Reed Jason W. , Nagpal Punita , Bastow Ruth M. , Solomon Keely S. , Dowson-Day Mandy J. , Elumalai Rangasamy P. , Millar Andrew J. 
Published: July 2002

Abstract
Light regulates various aspects of plant growth, and the photoreceptor phytochrome B (phyB) mediates many responses to red light. In a screen for Arabidopsis mutants with phenotypes similar to those ofphyB mutants, we isolated two new elf3mutants. One has weaker morphological phenotypes than previously identified elf3 alleles, but still abolishes circadian rhythms under continuous light. Like phyB mutants,elf3 mutants have elongated hypocotyls and petioles, flower early, and have defects in the red light response. However, we found that elf3 mutations have an additive interaction with a phyB null mutation, with phyA orhy4 null mutations, or with a PHYB overexpression construct, and that an elf3 mutation does not prevent nuclear localization of phyB. These results suggest that either there is substantial redundancy in phyB and elf3 function, or the two genes regulate distinct signaling pathways.
A Germination-Specific Endo-β-Mannanase Gene Is Expressed in the Micropylar Endosperm Cap of Tomato Seeds
Authors: Nonogaki Hiroyuki , Gee Oliver H. , Bradford Kent J. 
Published: July 2002

AbstractEndo-β-mannanase (EC 3.2.1.78) is involved in hydrolysis of the mannan-rich cell walls of the tomato (Lycopersicon esculentum Mill.) endosperm during germination and post-germinative seedling growth. Different electrophoretic isoforms of endo-β-mannanase are expressed sequentially in different parts of the endosperm, initially in the micropylar endosperm cap covering the radicle tip and subsequently in the remaining lateral endosperm surrounding the rest of the embryo. We have isolated a cDNA from imbibed tomato seeds (LeMAN2) that shares 77% deduced amino acid sequence similarity with a post-germinative tomato mannanase (LeMAN1). When expressed in Escherichia coli, the protein encoded by LeMAN2 cDNA was recognized by anti-mannanase antibody and exhibited endo-β-mannanase activity, confirming the identity of the gene. LeMAN2was expressed exclusively in the endosperm cap tissue of tomato seeds prior to radicle emergence, whereas LeMAN1 was expressed only in the lateral endosperm after radicle emergence.LeMAN2 mRNA accumulation and mannanase activity were induced by gibberellin in gibberellin-deficient gib-1mutant seeds but were not inhibited by abscisic acid in wild-type seeds. Distinct mannanases are involved in germination and post-germinative growth, with LeMAN2 being associated with endosperm cap weakening prior to radicle emergence, whereasLeMAN1 mobilizes galactomannan reserves in the lateral endosperm.
A Comparative Analysis of the Plant Cellulose Synthase (CesA) Gene Family
Authors: Holland Neta , Holland Doron , Helentjaris Tim , Dhugga Kanwarpal S. , Xoconostle-Cazares Beatriz , Delmer Deborah P. 
Published: July 2002

Abstract
CesA genes are believed to encode the catalytic subunit of cellulose synthase. Identification of nine distinctCesA cDNAs from maize (Zea mays) has allowed us to initiate comparative studies with homologs from Arabidopsis and other plant species. Mapping studies show that closely related CesA genes are not clustered but are found at different chromosomal locations in both Arabidopsis and maize. Furthermore, sequence comparisons among the CesA-deduced proteins show that these cluster in groups wherein orthologs are often more similar than paralogs, indicating that different subclasses evolved prior to the divergence of the monocot and dicot lineages. Studies using reverse transcriptase polymerase chain reaction with gene-specific primers for six of the nine maize genes indicate that all genes are expressed to at least some level in all of the organs examined. However, when expression patterns for a few selected genes from maize and Arabidopsis were analyzed in more detail, they were found to be expressed in unique cell types engaged in either primary or secondary wall synthesis. These studies also indicate that amino acid sequence comparisons, at least in some cases, may have value for prediction of such patterns of gene expression. Such analyses begin to provide insights useful for future genetic engineering of cellulose deposition, in that identification of close orthologs across species may prove useful for prediction of patterns of gene expression and may also aid in prediction of mutant combinations that may be necessary to generate severe phenotypes.
Chitinase Genes Responsive to Cold Encode Antifreeze Proteins in Winter Cereals
Authors: Yeh Sansun , Moffatt Barbara A. , Griffith Marilyn , Xiong Fei , Yang Daniel S.C. , Wiseman Steven B. , Sarhan Fathey , Danyluk Jean , Xue Yi Qi , Hew Choy L. , Doherty-Kirby Amanda , Lajoie Gilles 
Published: July 2002

Abstract
Antifreeze proteins similar to two different chitinases accumulate during cold acclimation in winter rye (Secale cereale). To determine whether these cold-responsive chitinases require post-translational modification to bind to ice, cDNAs coding for two different full-length chitinases were isolated from a cDNA library produced from cold-acclimated winter rye leaves. CHT9 is a 1,193-bp clone that encodes a 31.7-kD class I chitinase andCHT46 is a 998-bp clone that codes for a 24.8-kD class II chitinase. Chitinase-antifreeze proteins purified from the plant were similar in mass to the predicted mature products ofCHT9 and CHT46, thus indicating that there was little chemical modification of the amino acid sequences in planta. To confirm these results, the mature sequences ofCHT9 and CHT46 were expressed inEscherichia coli and the products of both cDNAs modified the growth of ice. Transcripts of both genes accumulated late in cold acclimation in winter rye. Southern analysis of winter rye genomic DNA indicated the presence of a small gene family homologous toCHT46. In hexaploid wheat, CHT46 homologs mapped to the homeologous group 1 chromosomes and were expressed in response to cold and drought. We conclude that two novel cold-responsive genes encoding chitinases with ice-binding activity may have arisen in winter rye and other cereals through gene duplication.
Pericycle Cell Proliferation and Lateral Root Initiation in Arabidopsis
Authors: Dubrovsky Joseph G. , Doerner Peter W. , Colón-Carmona Adán , Rost Thomas L. 
Published: July 2002

Abstract
In contrast with other cells generated by the root apical meristem in Arabidopsis, pericycle cells adjacent to the protoxylem poles of the vascular cylinder continue to cycle without interruption during passage through the elongation and differentiation zones. However, only some of the dividing pericycle cells are committed to the asymmetric, formative divisions that give rise to lateral root primordia (LRPs). This was demonstrated by direct observation and mapping of mitotic figures, cell-length measurements, and the histochemical analysis of a cyclin-GUS fusion protein in pericycle cells. The estimated duration of a pericycle cell cycle in the root apical meristem was similar to the interval between cell displacement from the meristem and the initiation of LRP formation. Developmentally controlled LRP initiation occurs early, 3 to 8 mm from the root tip. Thus the first growth control point in lateral root formation is defined by the initiation of primordia in stochastic patterns by cells passing through the elongation and young differentiation zones, up to where lateral roots begin to emerge from the primary root. Therefore, the first growth control point is not restricted to a narrow developmental window. We propose that late LRP initiation is developmentally unrelated to the root apical meristem and is operated by a second growth control point that can be activated by environmental cues. The observation that pericycle cells divide and lateral root primordia form without intervening mitotic quiescence suggests that lateral organ formation in roots and shoots might not be as fundamentally different as previously thought.
Transposon-Mediated Single-Copy Gene Delivery Leads to Increased Transgene Expression Stability in Barley
Authors: Koprek Thomas , Rangel Sergio , McElroy David , Louwerse Jeanine D. , Williams-Carrier Rosalind E. , Lemaux Peggy G. 
Published: July 2002

AbstractInstability of transgene expression in plants is often associated with complex multicopy patterns of transgene integration at the same locus, as well as position effects due to random integration. Based on maize transposable elements Activator(Ac) and Dissociation(Ds), we developed a method to generate large numbers of transgenic barley (Hordeum vulgare var Golden Promise) plants, each carrying a single transgene copy at different locations. Plants expressing Ac transposase (AcTPase) were crossed with plants containing one or more copies of bar, a selectable herbicide (Basta) resistance gene, located between inverted-repeatDs ends (Ds-bar). F1 plants were self-pollinated and the F2 generation was analyzed to identify plants segregating for transposed Ds-barelements. Of Ds-bar transpositions, 25% were in unlinked sites that segregated from vector sequences, otherDs-bar copies, and the AcTPase gene, resulting in numerous single-copy Ds-bar plants carrying the transgene at different locations. Transgene expression in F2 plants with transposed Ds-bar was 100% stable, whereas only 23% of F2 plants carryingDs-bar at the original site expressed the transgene product stably. In F3 and F4 populations, transgene expression in 81.5% of plants from progeny of F2plants with single-copy, transposed Ds-bar remained completely stable. Analysis of the integration site in single-copy plants showed that transposed Ds-bar inserted into single- or low-copy regions of the genome, whereas silencedDs-bar elements at their original location were inserted into redundant or highly repetitive genomic regions. Methylation of the non-transposed transgene and its promoter, as well as a higher condensation of the chromatin around the original integration site, was associated with plants exhibiting transgene silencing.
Expression of a Gibberellin 2-Oxidase Gene around the Shoot Apex Is Related to Phase Transition in Rice
Authors: Sakamoto Tomoaki , Kobayashi Masatomo , Itoh Hironori , Tagiri Akemi , Kayano Toshiaki , Tanaka Hiroshi , Iwahori Shuichi , Matsuoka Makoto 
Published: July 2002

Abstract
A major catabolic pathway for gibberellin (GA) is initiated by 2β-hydroxylation, a reaction catalyzed by GA 2-oxidase. We have isolated and characterized a cDNA, designated Oryza sativa GA 2-oxidase 1 (OsGA2ox1) from rice (Oryza sativa L. cv Nipponbare) that encodes a GA 2-oxidase. The encoded protein, produced by heterologous expression inEscherichia coli, converted GA1, GA4, GA9, GA20, and GA44 to the corresponding 2β-hydroxylated products GA8, GA34, GA51, GA29, and GA98, respectively. Ectopic expression of theOsGA2ox1 cDNA in transgenic rice inhibited stem elongation and the development of reproductive organs. These transgenic plants were deficient in endogenous GA1. These results indicate that OsGA2ox1 encodes a GA 2-oxidase, which is functional not only in vitro but also in vivo. OsGA2ox1was expressed in shoot apex and roots but not in leaves and stems. In situ hybridization analysis revealed that OsGA2ox1 mRNA was localized in a ring at the basal region of leaf primordia and young leaves. This ring-shaped expression around the shoot apex was drastically decreased after the phase transition from vegetative to reproductive growth. It was absent in the floral meristem, but it was still present in the lateral meristem that remained in the vegetative phase. These observations suggest that OsGA2ox1 controls the level of bioactive GAs in the shoot apical meristem; therefore, reduction in its expression may contribute to the early development of the inflorescence meristem.
Expression of a Pseudomonas aeruginosa Citrate Synthase Gene in Tobacco Is Not Associated with Either Enhanced Citrate Accumulation or Efflux
Authors: Delhaize Emmanuel , Hebb Diane M. , Ryan Peter R. 
Published: July 2002

Abstract
Aluminum (Al) toxicity and poor phosphorus (P) availability are factors that limit plant growth on many agricultural soils. Previous work reported that expression of a Pseudomonas aeruginosa citrate synthase gene in tobacco (Nicotiana tabacum; CSb lines) resulted in improved Al tolerance (J.M. de la Fuente, V. Ramı́rez-Rodrı́guez, J.L. Cabrera-Ponce, L. Herrera-Estrella [1997] Science 276: 1566–1568) and an enhanced ability to acquire P from alkaline soils (J. López-Bucio, O. Martı́nez de la Vega, A. Guevara-Garcı́a, L. Herrera-Estrella [2000] Nat Biotechnol 18: 450–453). These effects were attributed to the P. aeruginosa citrate synthase increasing the biosynthesis and efflux of citrate from roots. To verify these findings we: (a) characterized citrate efflux from roots of wild-type tobacco; (b) generated tobacco lines expressing the citrate synthase gene from P. aeruginosa; and (c) analyzed selected CSb lines described above. Al stimulated citrate efflux from intact roots of wild-type tobacco and root apices were found to be responsible for most of the efflux. Despite generating transgenic tobacco lines that expressed the citrate synthase protein at up to a 100-fold greater level than the previously described CSb lines, these lines did not show increased accumulation of citrate in roots or increased Al-activated efflux of citrate from roots. Selected CSb lines, similarly, failed to show differences compared with controls in either citrate accumulation or efflux. We conclude that expression of the P. aeruginosa citrate synthase gene in plants is unlikely to be a robust and easily reproducible strategy for enhancing the Al tolerance and P-nutrition of crop and pasture species.
Crystallization and preliminary X-ray analysis of the formiminotransferase domain from the bifunctional enzyme formiminotransferase–cyclodeaminase
Authors: Kohls Darcy , Croteau Nathalie , Mejia Narciso , MacKenzie Robert E. , Vrielink Alice 
Published: July 2002

Formiminotransferase–cyclodeaminase (E.C. 2.1.2.5–E.C. 4.3.1.4) is a bifunctional enzyme involved in the histidine-degradation pathway which exhibits specificity for polyglutamylated folate substrates. The first function of the enzyme transfers the formimino group of formiminoglutamate to the N
5 position of tetrahydrofolate, while the second function catalyses the cyclodeamination of the formimino group, yielding N
5,10-methenyl-tetrahydrofolate, with efficient channeling of the intermediate between these activities. Initial studies have shown that the enzyme consists of eight identical subunits of 62 kDa each, arranged as a circular tetramer of dimers. It is this formation which results in two different dimeric interfaces, which are necessary for the two different activities. The identical subunits have been shown to consist of two domains, each of which can be obtained as dimers. The formiminotransferase domain has been crystallized in the presence of the substrate analogue folinic acid. The crystals belong to space group P212121, with unit-cell dimensions a = 64.4, b = 103.7, c = 122.3 Å. Both a native data set and a mercurial derivative data set have been collected to 2.8 Å resolution.
Lactate dehydrogenase from the hyperthermophilic archaeon Methanococcus jannaschii: overexpression, crystallization and preliminary X-ray analysis
Authors: Lee Byung Il , Chang Changsoo , Cho Seung-Je , Han Gye Won , Yu Yeon Gyu , Eom Soo Hyun , Suh Se Won 
Published: July 2002

L(+)-Lactate dehydrogenase (LDH) is a key enzyme in anaerobic metabolism which converts pyruvate to lactate. LDH from the hyperthermophilic archaebacterium Methanococcus jannaschii has been overexpressed in Escherichia coli and crystallized in two crystal forms at 297 K using 2-methyl-2,4-pentanediol as precipitant. Type I crystals grew rapidly and diffracted to at least 2.8 Å Bragg spacing upon exposure to Cu Kα X-rays. X-ray diffraction data to 2.9 Å have been collected from a native crystal. The type I crystal is tetragonal, belonging to the space group P42212, with unit-cell parameters a = b = 99.74, c = 170.00 Å. The asymmetric unit contains two LDH subunits, with a corresponding crystal volume per protein mass (V

m
) of 3.05 Å3 Da−1 and a solvent content of 59.7%. Type II crystals, which grew more slowly, diffracted to at least 1.8 Å Bragg spacing upon exposure to Cu Kα X-rays. X-ray diffraction data to 1.9 Å have been collected from a native crystal. The type II crystal is orthorhombic, belonging to the space group P21212, with unit-cell parameters a = 47.65, b = 125.10, c = 58.08 Å. The asymmetric unit contains a single LDH subunit, with a corresponding crystal volume per protein mass (V

m
) of 2.50 Å3 Da−1 and a solvent content of 50.8%. Therefore, the type II crystal is more suitable for high-resolution structure determination than the type I crystal.
Scanning X-ray spectrometer for high-resolution Compton profile measurements at ESRF
Authors: Suortti P. , Buslaps T. , Fajardo P. , Honkimäki V. , Kretzschmer M. , Lienert U. , McCarthy J. E. , Renier M. , Shukla A. , Tschentscher Th. , Meinander T. 
Published: July 2002

A scanning-type crystal spectrometer for high-resolution Compton profile measurements has been constructed at the High Energy Inelastic Scattering Beamline (ID15B) of the ESRF. Radiation from a seven-period asymmetrical permanent-magnet wiggler or from a superconducting wavelength shifter is focused horizontally onto the sample by a bent-crystal monochromator. Typical energies are 30, 50 and 60 keV, the flux on the sample is 1012 photons s−1, and the relative energy bandwidth is 3 × 10−4. The spectrometer operates in the Rowland circle geometry, where the sample is fixed and the cylindrically bent analyser crystal and the detector move on the focusing circle by synchronized translations and rotations. The main detector is a large-diameter NaI scintillation counter, the incident beam is monitored by an Si diode, and scattering from the sample is detected using a Ge detector. The recorded spectrum is corrected for the energy-dependent response of the spectrometer, background and multiple scattering, and converted to the momentum scale. The resolution of the spectrometer is calculated from the geometrical factors and the reflectivity curve of the analyser crystal, and the result is checked against the widths of the elastically scattered line and fluorescent lines. So far, 0.1 a.u. resolution in electron momentum has been achieved. The typical average count rate over the Compton profile is about 1000 counts s−1 from a weakly absorbing sample.
Bis(N-cyclohexyl-N-ethyldithiocarbamato-S,S′)lead(II)
Authors: Baba Ibrahim , Farina Yang , Othman A. Hamid , Razak Ibrahim Abdul , Fun Hoong-Kun , Ng Seik Weng 
Published: July 2002

The Pb atom in the title compound, [Pb(C9H16NS2)2], is chelated in an anisobidentate manner by the dithiocarbamate group [Pb—S = 2.710 (2)/2.883(2) Å and 2.700 (2)/2.841(2) Å]. The four-coordinate geometry is raised to six through the involvement of the double-bonded S atoms of adjacent dithiocarbamato groups; the Pb...S interactions [Pb...S = 3.457 (2) and 3.508 (2) Å] result in a chain structure for the compound.
X‐ray crystallographic and kinetic correlation of a clinically observed human fumarase mutation
Authors: Estévez Marcel , Skarda Jeremy , Spencer Josh , Banaszak Leonard , Weaver Todd M. 
Published: July 2002

AbstractFumarase catalyzes the reversible conversion of fumarate to S‐ malate during the operation of the ubiquitous Kreb's cycle. Previous studies have shown that the active site includes side chains from three of the four subunits within the tetrameric enzyme. We used a clinically observed human mutation to narrow our search for potential catalytic groups within the fumarase active site. Offspring homozygous for the missense mutation, a G‐955–C transversion in the fumarase gene, results in the substitution of a glutamine at amino acid 319 for the normal glutamic acid. To more fully understand the implications of this mutation, a single‐step site‐directed mutagenesis method was used to generate the homologous substitution at position 315 within fumarase C from Escherichia coli. Subsequent kinetic and X‐ray crystal structure analyses show changes in the turnover number and the cocrystal structure with bound citrate.
A refined solution structure of hen lysozyme determined using residual dipolar coupling data
Authors: Schwalbe Harald , Grimshaw Shaun B. , Spencer Andrew , Buck Matthias , Boyd Jonathan , Dobson Christopher M. , Redfield Christina , Smith Lorna J. 
Published: July 2002

AbstractA high resolution NMR structure of hen lysozyme has been determined using 209 residual 1H–15N dipolar coupling restraints from measurements made in two different dilute liquid crystalline phases (bicelles) in conjunction with a data set of 1632 NOE distance restraints, 110 torsion angle restraints, and 60 hydrogen bond restraints. The ensemble of 50 low‐energy calculated structures has an average backbone RMSD of 0.50±0.13Å to the mean structure and of 1.49±0.10Å to the crystal structure of hen lysozyme. To assess the importance of the dipolar coupling data in the structure determination, the final structures are compared with an ensemble calculated using an identical protocol but excluding the dipolar coupling restraints. The comparison shows that structures calculated with the dipolar coupling data are more similar to the crystal structure than those calculated without, and have better stereochemical quality. The structures also show improved quality factors when compared with additional dipolar coupling data that were not included in the structure calculations, with orientation‐dependent 15N chemical shift changes measured in the bicelle solutions, and with T1/T2 values obtained from 15N relaxation measurements. Analysis of the ensemble of NMR structures and comparisons with crystal structures, 15N relaxation data, and molecular dynamics simulations of hen lysozyme provides a detailed description of the solution structure of this protein and insights into its dynamical behavior.
High–resolution crystal structure of deoxy hemoglobin complexed with a potent allosteric effector
Authors: Safo Martin K. , Moure Carmen M. , Burnett James C. , Joshi Gajanan S. , Abraham Donald J. 
Published: July 2002

AbstractThe crystal structure of human deoxy hemoglobin (Hb) complexed with a potent allosteric effector (2‐[4‐[[(3,5‐dimethylanilino)carbonyl]methyl]phenoxy]‐2‐methylpropionic acid) = RSR‐13) is reported at 1.85 Å resolution. Analysis of the hemoglobin:effector complex indicates that two of these molecules bind to the central water cavity of deoxy Hb in a symmetrical fashion, and that each constrains the protein by engaging in hydrogen bonding and hydrophobic interactions with three of its four subunits. Interestingly, we also find that water‐mediated interactions between the bound effectors and the protein make significant contributions to the overall binding. Physiologically, the interaction of RSR‐13 with Hb results in increased oxygen delivery to peripheral tissues. Thus, this compound has potential therapeutic application in the treatment of hypoxia, ischemia, and trauma‐related blood loss. Currently, RSR‐13 is in phase III clinical trials as a radiosensitizing agent in the treatment of brain tumors. A detailed structural analysis of this compound complexed with deoxy Hb has important implications for the rational design of future analogs.