bluuebunny/crossref_metadata_2025_split huggingface dataset:
AtCOX17, an Arabidopsis Homolog of the Yeast Copper Chaperone COX17
Authors: Balandin Teresa , Castresana Carmen 
Published: October 2002

Abstract
We have identified a new plant gene, AtCOX17, encoding a protein that shares sequence similarity to COX17, a Cu-binding protein from yeast (Saccharomyces cerevisiae) and vertebrates that mediates the delivery of Cu to the mitochondria for the assembly of a functional cytochrome oxidase complex. The newly characterized Arabidopsis protein has six Cys residues at positions corresponding to those known to coordinate Cu binding in the yeast homolog. Moreover, we show that the Arabidopsis COX17cDNA complements a COX17 mutant of yeast restoring the respiratory deficiency associated with that mutation. These two lines of evidence indicate that the plant protein identified here is a functional equivalent of yeast COX17 and might serve as a Cu delivery protein for the plant mitochondria. COX17 was identified by investigating the hypersensitive response-like necrotic response provoked in tobacco (Nicotiana tabacum) leaves after harpin inoculation. AtCOX17 expression was activated by high concentrations of Cu, bacterial inoculation, salicylic acid treatment, and treatments that generated NO and hydrogen peroxide. All of the conditions inducing COX17 are known to inhibit mitochondrial respiration and to produce an increase of reactive oxygen species, suggesting that gene induction occurs in response to stress situations that interfere with mitochondrial function.
Steroleosin, a Sterol-Binding Dehydrogenase in Seed Oil Bodies
Authors: Lin Li-Jen , Tai Sorgan S.K. , Peng Chi-Chung , Tzen Jason T.C. 
Published: October 2002

Abstract
Besides abundant oleosin, three minor proteins, Sop 1, 2, and 3, are present in sesame (Sesamum indicum) oil bodies. The gene encoding Sop1, named caleosin for its calcium-binding capacity, has recently been cloned. In this study, Sop2 gene was obtained by immunoscreening, and it was subsequently confirmed by amino acid partial sequencing and immunological recognition of its overexpressed protein in Escherichia coli. Immunological cross recognition implies that Sop2 exists in seed oil bodies of diverse species. Along with oleosin and caleosin genes, Sop2 gene was transcribed in maturing seeds where oil bodies are actively assembled. Sequence analysis reveals that Sop2, tentatively named steroleosin, possesses a hydrophobic anchoring segment preceding a soluble domain homologous to sterol-binding dehydrogenases/reductases involved in signal transduction in diverse organisms. Three-dimensional structure of the soluble domain was predicted via homology modeling. The structure forms a seven-stranded parallel β-sheet with the active site, S-(12X)-Y-(3X)-K, between an NADPH and a sterol-binding subdomain. Sterol-coupling dehydrogenase activity was demonstrated in the overexpressed soluble domain of steroleosin as well as in purified oil bodies. Southern hybridization suggests that one steroleosin gene and certain homologous genes may be present in the sesame genome. Comparably, eight hypothetical steroleosin-like proteins are present in the Arabidopsis genome with a conserved NADPH-binding subdomain, but a divergent sterol-binding subdomain. It is indicated that steroleosin-like proteins may represent a class of dehydrogenases/reductases that are involved in plant signal transduction regulated by various sterols.
A T-DNA Insertion Knockout of the Bifunctional Lysine-Ketoglutarate Reductase/Saccharopine Dehydrogenase Gene Elevates Lysine Levels in Arabidopsis Seeds
Authors: Zhu Xiaohong , Tang Guiliang , Granier Fabienne , Bouchez David , Galili Gad 
Published: October 2002

Abstract
Plants possess both anabolic and catabolic pathways for the essential amino acid lysine (Lys). However, although the biosynthetic pathway was clearly shown to regulate Lys accumulation in plants, the functional significance of Lys catabolism has not been experimentally elucidated. To address this issue, we have isolated an Arabidopsis knockout mutant with a T-DNA inserted into exon 13 of the gene encoding Lys ketoglutarate reductase/saccharopine dehydrogenase. This bifunctional enzyme controls the first two steps of Lys catabolism. The phenotype of the LKR/SDH knockout was indistinguishable from wild-type plants under normal growth conditions, suggesting that Lys catabolism is not an essential pathway under standard growth conditions. However, mature seeds of the knockout mutant over-accumulated Lys compared with wild-type plants. This report provides the first direct evidence for the functional significance of Lys catabolism in regulating Lys accumulation in seeds. Such a knockout mutant may also provide new perspectives to improve the level of the essential amino acid Lys in plant seeds.
Whole-Plant Gas Exchange and Reductive Biosynthesis in White Lupin
Authors: Cen Yan-Ping , Turpin David H. , Layzell David B. 
Published: October 2002

AbstractSimultaneous measurements of CO2 (CER) and O2 (OER) exchange in roots and shoots of vegetative white lupin (Lupinus albus) were used to calculate the flow of reducing power to the synthesis of biomass that was more reduced per unit of carbon than carbohydrate. On a whole-plant basis, the diverted reductant utilization rate (DRUR which is: 4 × [CER + OER]) of shoot tissue was consistently higher than that of roots, and values obtained in the light were greater than those in the dark. An analysis of the biomass being synthesized over a 24-h period provided an estimate of whole-plant DRUR (3.5 mmol e−plant−1 d−1), which was similar to that measured by gas exchange (3.2 mmol e− plant−1d−1). Given that nitrate reduction to ammonia makes up about 74% of whole-plant DRUR, root nitrate reduction in white lupin was estimated to account for less than 43% of whole-plant nitrate reduction. The approach developed here should offer a powerful tool for the noninvasive study of metabolic regulation in intact plants or plant organs.
Arabidopsis Transcriptome Profiling Indicates That Multiple Regulatory Pathways Are Activated during Cold Acclimation in Addition to the CBF Cold Response Pathway[W]
Authors: Fowler Sarah , Thomashow Michael F. 
Published: October 2002

Abstract
Many plants, including Arabidopsis, increase in freezing tolerance in response to low, nonfreezing temperatures, a phenomenon known as cold acclimation. Previous studies established that cold acclimation involves rapid expression of the CBF transcriptional activators (also known as DREB1 proteins) in response to low temperature followed by induction of the CBF regulon (CBF-targeted genes), which contributes to an increase in freezing tolerance. Here, we present the results of transcriptome-profiling experiments indicating the existence of multiple low-temperature regulatory pathways in addition to the CBF cold response pathway. The transcript levels of ∼8000 genes were determined at multiple times after plants were transferred from warm to cold temperature and in warm-grown plants that constitutively expressed CBF1, CBF2, or CBF3. A total of 306 genes were identified as being cold responsive, with transcripts for 218 genes increasing and those for 88 genes decreasing threefold or more at one or more time points during the 7-day experiment. These results indicate that extensive downregulation of gene expression occurs during cold acclimation. Of the cold-responsive genes, 48 encode known or putative transcription factors. Two of these, RAP2.1 and RAP2.6, were activated by CBF expression and thus presumably control subregulons of the CBF regulon. Transcriptome comparisons indicated that only 12% of the cold-responsive genes are certain members of the CBF regulon. Moreover, at least 28% of the cold-responsive genes were not regulated by the CBF transcription factors, including 15 encoding known or putative transcription factors, indicating that these cold-responsive genes are members of different low-temperature regulons. Significantly, CBF expression at warm temperatures repressed the expression of eight genes that also were downregulated by low temperature, indicating that in addition to gene induction, gene repression is likely to play an integral role in cold acclimation.
Hydrogen/deuterium exchange and mass spectrometric analysis of a protein containing multiple disulfide bonds: Solution structure of recombinant macrophage colony stimulating factor‐beta (rhM‐CSFβ)
Authors: Yan Xuguang , Zhang Heidi , Watson Jeffrey , Schimerlik Michael I. , Deinzer Max L. 
Published: October 2002

AbstractStudies with the homodimeric recombinant human macrophage colony‐stimulating factor beta (rhM‐CSFβ), show for the first time that a large number (9) of disulfide linkages can be reduced after amide hydrogen/deuterium (H/D) exchange, and the protein digested and analyzed successfully for the isotopic composition by electrospray mass spectrometry. Analysis of amide H/D after exchange‐in shows that in solution the conserved four‐helix bundle of (rhM‐CSFβ) has fast and moderately fast exchangeable sections of amide hydrogens in the αA helix, and mostly slow exchanging sections of amide hydrogens in the αB, αC, and αD helices. Most of the amide hydrogens in the loop between the β1 and β4 sheets exhibited fast or moderately fast exchange, whereas in the amino acid 63–67 loop, located at the interface of the two subunits, the exchange was slow. Solvent accessibility as measured by H/D exchange showed a better correlation with the average depth of amide residues calculated from reported X‐ray crystallographic data for rhM‐CSFα than with the average B‐factor. The rates of H/D exchange in rhM‐CSFβ appear to correlate well with the exposed surface calculated for each amino acid residue in the crystal structure except for the αD helix. Fast hydrogen isotope exchange throughout the segment amino acids 150–221 present in rhM‐CSFβ, but not rhM‐CSFα, provides evidence that the carboxy‐terminal region is unstructured. It is, therefore, proposed that the anomalous behavior of the αD helix is due to interaction of the carboxy‐terminal tail with this helical segment.
Two β‐rich structural domains in GABAA receptor α1 subunit with different physical properties: Evidence for multidomain nature of the receptor
Authors: Shi Haifeng , Tsang Shui Ying , Zheng Hui , Sturgis James N. , Xue Hong 
Published: October 2002

AbstractThe type A γ‐aminobutyric acid (GABAA) receptor is a major inhibitory neurotransmitter‐gated ion channel. Previously, we identified a membrane‐proximal β‐rich (MPBR) domain in fragment C166‐L296 of GABAA receptor α1 subunit, forming nativelike pentamers. In the present study, another structural domain, the amino‐terminal domain, was shown to exist in the fragment Q28‐E165. The secondary structures of both fragments were β‐rich as measured using FTIR spectroscopy and estimated from the CD spectra to be 42% and 51% β‐strand for Q28‐E165 and C166‐L296, respectively. The CD spectrum of the combined fragment Q28‐L296 was additive of the spectra of the two fragments. In addition, denaturation curves of both fragments were characteristic of cooperative transitions, supporting their domainlike nature. C166‐L296 required 6.5 M of guanidine chloride for total denaturation, therefore it is extraordinarily stable, more so than Q28‐E165. Moreover, effects of detergent on the molecular masses of Q28‐E165 and C166‐L296, as monitored using laser‐scattering spectroscopy, indicated that intermolecular interactions were much more significant in C166‐L296 than in Q28‐E165. Effects of pH on their molecular masses suggested that ionic forces were involved in these interactions. Together the results show that the two adjacent fragments form independent folding units, MPBR and amino‐terminal domains, different in secondary structure content, denaturation profile, and polymerization status, and suggest that the former may play a more important role in receptor assembly and that the extraordinary stability may underlie its intrinsic tendency to form oligomers. More significantly, the present study has provided direct evidence for the long‐postulated multidomain nature of this family of receptors.
A structurally conserved water molecule in Rossmann dinucleotide‐binding domains
Authors: Bottoms Christopher A. , Smith Paul E. , Tanner John J. 
Published: October 2002

AbstractA computational comparison of 102 high‐resolution (≤1.90 Å) enzyme‐dinucleotide (NAD, NADP, FAD) complexes was performed to investigate the role of solvent in dinucleotide recognition by Rossmann fold domains. The typical binding site contains about 9–12 water molecules, and about 30% of the hydrogen bonds between the protein and the dinucleotide are water mediated. Detailed inspection of the structures reveals a structurally conserved water molecule bridging dinucleotides with the well‐known glycine‐rich phosphate‐binding loop. This water molecule displays a conserved hydrogen‐bonding pattern. It forms hydrogen bonds to the dinucleotide pyrophosphate, two of the three conserved glycine residues of the phosphate‐binding loop, and a residue at the C‐terminus of strand four of the Rossmann fold. The conserved water molecule is also present in high‐resolution structures of apo enzymes. However, the water molecule is not present in structures displaying significant deviations from the classic Rossmann fold motif, such as having nonstandard topology, containing a very short phosphate‐binding loop, or having α‐helix “A” oriented perpendicular to the β‐sheet. Thus, the conserved water molecule appears to be an inherent structural feature of the classic Rossmann dinucleotide‐binding domain.
GEM: A Gaussian evolutionary method for predicting protein side‐chain conformations
Authors: Yang Jinn‐Moon , Tsai Chi‐Hung , Hwang Ming‐Jing , Tsai Huai‐Kuang , Hwang Jenn‐Kang , Kao Cheng‐Yan 
Published: October 2002

AbstractWe have developed an evolutionary approach to predicting protein side‐chain conformations. This approach, referred to as the Gaussian Evolutionary Method (GEM), combines both discrete and continuous global search mechanisms. The former helps speed up convergence by reducing the size of rotamer space, whereas the latter, integrating decreasing‐based Gaussian mutations and self‐adaptive Gaussian mutations, continuously adapts dihedrals to optimal conformations. We tested our approach on 38 proteins ranging in size from 46 to 325 residues and showed that the results were comparable to those using other methods. The average accuracies of our predictions were 80% for χ1, 66% for χ1 + 2, and 1.36 Å for the root mean square deviation of side‐chain positions. We found that if our scoring function was perfect, the prediction accuracy was also essentially perfect. However, perfect prediction could not be achieved if only a discrete search mechanism was applied. These results suggest that GEM is robust and can be used to examine the factors limiting the accuracy of protein side‐chain prediction methods. Furthermore, it can be used to systematically evaluate and thus improve scoring functions.
Influence of the Lateral Ventricles and Irregular Skull Base on Brain
Kinematics due to Sagittal Plane Head Rotation
Authors: Ivarsson J. , Viano D. C. , Lövsund P. 
Published: October 2002

Abstract
Two-dimensional physical models of the human head were used to investigate how the lateral ventricles and irregular skull base influence kinematics in the medial brain during sagittal angular head dynamics. Silicone gel simulated the brain and was separated from the surrounding skull vessel by paraffin that provided a slip interface between the gel and vessel. A humanlike skull base model (HSB) included a surrogate skull base mimicking the irregular geometry of the human. An HSBV model added an elliptical inclusion filled with liquid paraffin simulating the lateral ventricles to the HSB model. A simplified skull base model (SSBV) included ventricle substitute but approximated the anterior and middle cranial fossae by a flat and slightly angled surface. The models were exposed to 7600 rad/s2 peak angular acceleration with 6 ms pulse duration and 5 deg forced rotation. After 90 deg free rotation, the models were decelerated during 30 ms. Rigid body displacement, shear strain and principal strains were determined from high-speed video recorded trajectories of grid markers in the surrogate brains. Peak values of inferior brain surface displacement and strains were up to 10.9X (times) and 3.3X higher in SSBV than in HSBV. Peak strain was up to 2.7X higher in HSB than in HSBV. The results indicate that the irregular skull base protects nerves and vessels passing through the cranial floor by reducing brain displacement and that the intraventricular cerebrospinal fluid relieves strain in regions inferior and superior to the ventricles. The ventricles and irregular skull base are necessary in modeling head impact and understanding brain injury mechanisms.
Identification and Analysis of Amino Acid Mutations in Porin IB That Mediate Intermediate-Level Resistance to Penicillin and Tetracycline in
Neisseria gonorrhoeae
Authors: Olesky Melanie , Hobbs Marcia , Nicholas Robert A. 
Published: October 2002

ABSTRACT

PenB
is the third resistance determinant in the stepwise acquisition of multiple resistance genes in chromosomally mediated resistant
Neisseria gonorrhoeae
(CMRNG). Alterations in

por
IB

, one of two alleles at the
por
locus that encodes the outer membrane protein porin IB (PIB), were recently reported to be responsible for the increased resistance to penicillin and tetracycline conferred by
penB
, but the specific mutations conferring antibiotic resistance were not identified experimentally. To determine which amino acids in PIB confer increased resistance, we transformed a recipient strain with chimeras of the

por
IB

genes from strains FA1090 and FA140 (
penB2
). These studies revealed that two amino acid changes, G120D and A121D, were both necessary and sufficient to confer increased resistance to penicillin and tetracycline. Site-saturation and site-directed mutagenesis of Gly-120 and Ala-121 revealed that both a single mutation, G120K, and the double mutations G120R A121H and G120P A121P also conferred antibiotic resistance to the recipient strain. The identical mutations in PIA increased penicillin and tetracycline resistance either moderately or not at all. Analysis of

por
IB

genes present in the GenBank database from 51 clinical isolates demonstrated that lysine and aspartate mutations at positions 120 and/or 121 also occur in nature. These studies demonstrate that charged amino acids at positions 120 and 121 in PIB are highly preferential for conferring resistance to penicillin and tetracycline in
N. gonorrhoeae
.
Immunomodulatory Effect of Zidovudine (ZDV) on Cytotoxic T Lymphocytes Previously Exposed to ZDV
Authors: Francke Sabine , Orosz Charles G. , Hsu Jason , Mathes Lawrence E. 
Published: October 2002

ABSTRACTIn a previous study, zidovudine (ZDV) was shown to cause a concentration-dependent inhibition of antigen-specific cytotoxic T-lymphocyte (CTL) clonal expansion (S. Francke, C. G. Orosz, K. A. Hayes, and L. E. Mathes, Antimicrob. Agents Chemother. 44:1900-1905, 2000). However, this suppressive effect was lost if exposure to ZDV was delayed for 24 to 48 h during the antigen sensitization period, suggesting that antigen-primed CTL may be less susceptible than naive T lymphocytes to the suppressive effects of ZDV. The present study was undertaken to determine if naive T lymphocytes were more sensitive to the suppressive effects of ZDV than T lymphocytes previously exposed to antigen. The 50% inhibitory concentration (IC50) values of ZDV were determined on naive and antigen-primed T-cell responses in an alloantigen system. Lymphocyte cultures with continuous antigen exposure (double prime) were more resistant to ZDV suppression (IC50= 316 μM) than were naive lymphocytes (IC50= 87.5 μM). Interestingly, lymphocytes that were antigen primed but deprived of antigen during the final 7 days of culture (prime/hold) were exquisitely sensitive to ZDV suppression (IC50= 29.3 μM). The addition of 80 μM ZDV during the initial priming of the single-prime (prime/hold) and double-prime cultures did not select for a more drug-resistant cell population. The differences in ZDV sensitivities are likely a reflection of the physiological properties of the lymphocytes related to their activation state.
Efficacy of Quinupristin-Dalfopristin in Preventing Vascular Graft Infection Due to
Staphylococcus epidermidis
with Intermediate Resistance to Glycopeptides
Authors: Giacometti Andrea , Cirioni Oscar , Ghiselli Roberto , Orlando Fiorenza , Mocchegiani Federico , Riva Alessandra , Del Prete Maria Simona , Saba Vittorio , Scalise Giorgio 
Published: October 2002

ABSTRACT

A rat model was used to investigate the efficacy of quinupristin-dalfopristin (Q-D) in the prevention of vascular prosthetic graft infection due to methicillin-resistant
Staphylococcus epidermidis
with intermediate resistance to glycopeptides. The in vitro activity of the compound was compared to that of vancomycin by MIC determination and time-kill study. Moreover, the efficacy of collagen-sealed Q-D-soaked Dacron was evaluated in a rat model of graft infection. Graft infections were established in the subcutaneous tissue of the backs of 120 adult male Wistar rats. The in vivo study included a control group, one contaminated group that did not receive any antibiotic prophylaxis, two contaminated groups that received grafts soaked with 10 and 100 μg of Q-D per ml, respectively, and two contaminated groups that received grafts soaked with 10 and 100 μg of vancomycin per ml, respectively. Rats that received Dacron grafts soaked with 100 μg of Q-D per ml showed no evidence of infection (<10 CFU/ml). In contrast, for rats that received Dacron grafts soaked with 10 μg of Q-D per ml and Dacron grafts soaked with 10 or 100 μg of vancomycin per ml, the quantitative graft cultures demonstrated 2.2 × 10
2
± 1.3 × 10
2
, 2.2 × 10
6
± 1.9 × 10
5
, and 5.6 × 10
2
± 0.3 × 10
2
CFU/ml, respectively. Taken together the results of the study demonstrate that the use of Dacron grafts soaked with Q-D can result in significant bacterial growth inhibition and show that this compound is potentially valuable for prevention of vascular prosthetic graft infection.
16S rRNA Mutation-Mediated Tetracycline Resistance in
Helicobacter pylori
Authors: Gerrits Monique M. , de Zoete Marcel R. , Arents Niek L. A. , Kuipers Ernst J. , Kusters Johannes G. 
Published: October 2002

ABSTRACT

Most
Helicobacter pylori
strains are susceptible to tetracycline, an antibiotic commonly used for the eradication of
H. pylori
. However, an increase in incidence of tetracycline resistance in
H. pylori
has recently been reported. Here the mechanism of tetracycline resistance of the first Dutch tetracycline-resistant (Tet
r
)
H. pylori
isolate (strain 181) is investigated. Twelve genes were selected from the genome sequences of
H. pylori
strains 26695 and J99 as potential candidate genes, based on their homology with tetracycline resistance genes in other bacteria. With the exception of the two 16S rRNA genes, none of the other putative tetracycline resistance genes was able to transfer tetracycline resistance. Genetic transformation of the Tet
s
strain 26695 with smaller overlapping PCR fragments of the 16S rRNA genes of strain 181, revealed that a 361-bp fragment that spanned nucleotides 711 to 1071 was sufficient to transfer resistance. Sequence analysis of the 16S rRNA genes of the Tet
r
strain 181, the Tet
s
strain 26695, and four Tet
r
26695 transformants showed that a single triple-base-pair substitution, AGA
926-928
→TTC, was present within this 361-bp fragment. This triple-base-pair substitution, present in both copies of the 16S rRNA gene of all our Tet
r
H. pylori
transformants, resulted in an increased MIC of tetracycline that was identical to that for the Tet
r
strain 181.