bluuebunny/crossref_metadata_2025 huggingface dataset:
Studies on DNA-cleaving agents: computer modeling analysis of the mechanism of activation and cleavage of dynemicin-oligonucleotide complexes.
Authors: Wender P A , Kelly R C , Beckham S , Miller B L
Published: May 2006

Dynemicin A is a recently identified antitumor antibiotic. Upon activation, dynemicin is reported to cause double-stranded cleavage of DNA, putatively through the intermediacy of a diradical. Computer modeling of this activation and cleavage process is described herein as part of an effort to establish a structural hypothesis for this mechanistic sequence and for the design of simple analogues. Intercalation complexes of duplex dodecamers [d(CGCGAATTCGCG)]2 and [d(GC)6]2 with both enantiomers of dynemicin and of all related mechanistic intermediates are evaluated. Examination of these structures shows that cycloaromatization of dynemicin to a diradical intermediate results in the rotation of the diradical-forming subunit with respect to the intercalation plane that is of an opposite sense for the two dynemicin enantiomers. In addition, the activation of the (2S) enantiomer of dynemicin occurs by a less restricted approach trajectory than the corresponding (2R) enantiomer. In all complexes, the 5'-3' strand is at least 1 A closer than the 3'-5' strand to the diyl intermediate. As a result, complexes are produced in which the diyl moiety is aligned along [(2S)] or across [(2R)] the minor groove, leading to different predictions for the selectivity of radical-initiated, oxidative lesion of DNA. Molecular dynamics simulations are found to support these predictions, including the 3-base-pair offset cleavage reported for dynemicin.
Pertactin, an Arg-Gly-Asp-containing Bordetella pertussis surface protein that promotes adherence of mammalian cells.
Authors: Leininger E , Roberts M , Kenimer J G , Charles I G , Fairweather N , Novotny P , Brennan M J
Published: May 2006

A 69-kDa protein has been identified on the surface of the Gram-negative pathogen Bordetella pertussis that can elicit a protective immune response in animal models. This protein is associated with virulent strains of B. pertussis but its function has remained unclear. In this report we demonstrate that purified preparations of the 69-kDa outer membrane protein can promote the attachment of Chinese hamster ovary (CHO) cells. The interaction between the mammalian cells and this protein can be specifically inhibited by an Arg-Gly-Asp (RGD)-containing synthetic peptide that is homologous with a region found in the 69-kDa protein sequence. These studies indicate that a specific cell binding site containing an Arg-Gly-Asp sequence may be involved in the interaction of this bacterial protein with mammalian cell surfaces. To further investigate the role of this protein as a bacterial adhesin, a mutant of B. pertussis W28 that does not express the 69-kDa protein was constructed using the plasmid vector pRTP1. This mutant was 30-40% less efficient at adhering to CHO cells and to human HeLa cells than was the parent strain. These data support a role for this 69-kDa outer membrane protein in the attachment of B. pertussis to mammalian cells. We propose the name "pertactin" for this protein.
Quantitation of ColE1-encoded replication elements.
Authors: Brenner M , Tomizawa J
Published: May 2006

Replication of the Escherichia coli plasmid ColE1 initiates from an RNA primer. This primer is formed by a ColE1 RNA II molecule that remains hybridized to its DNA template in the origin region after transcription. Continued hybridization is inhibited by prior binding to RNA II of another ColE1 transcript, RNA I; and this interaction is regulated by the plasmid-encoded Rom protein. To understand the quantitative aspects of regulation of ColE1 synthesis, we have measured the levels of RNA I, RNA II, and Rom protein in vivo, as well as the half-lives of the RNAs. The intracellular concentrations of RNA I, RNA II, and Rom protein were found to be about 1 microM, 7 nM, and 1 microM, respectively; and the RNAs had half-lives of about 2 min. A simple model derived from these results indicates that the plasmid copy number is little affected by the rate of RNA II synthesis but is strongly dependent on that of RNA I.
A broad-spectrum human lung fibroblast-derived mitogen is a variant of hepatocyte growth factor.
Authors: Rubin J S , Chan A M , Bottaro D P , Burgess W H , Taylor W G , Cech A C , Hirschfield D W , Wong J , Miki T , Finch P W
Published: May 2006

A heparin-binding mitogen was isolated from conditioned medium of human embryonic lung fibroblasts. It exhibited broad target-cell specificity whose pattern was distinct from that of any known growth factor. It rapidly stimulated tyrosine phosphorylation of a 145-kDa protein in responsive cells, suggesting that its signaling pathways involved activation of a tyrosine kinase. Purification identified a major polypeptide with an apparent molecular mass of 87 kDa under reducing conditions. Partial amino acid sequence analysis and cDNA cloning revealed that it was a variant of hepatocyte growth factor, a mitogen thought to be specific for hepatic cells and structurally related to plasminogen. Recombinant expression of the cDNA in COS-1 cells established that it encoded the purified growth factor. Its site of synthesis and spectrum of targets imply that this growth factor may play an important role as a paracrine mediator of the proliferation of melanocytes and endothelial cells, as well as cells of epithelial origin.
Role of a carboxyl-terminal helix in the assembly, interchain interactions, and stability of aspartate transcarbamoylase.
Authors: Peterson C B , Schachman H K
Published: May 2006

The six individual catalytic polypeptide chains within the two catalytic trimers of Escherichia coli aspartate transcarbamoylase (ATCase; EC 2.1.3.2) are folded into two discrete structural domains interconnected in part by helix 12, which comprises residues 285-305 and is located near the carboxyl terminus of the chain. The essential role of this helix in folding of the chains and their assembly into ATCase was demonstrated by introducing a stop codon at the position corresponding to amino acid 284, 291, or 299. Cells containing these mutations are pyrimidine auxotrophs lacking ATCase-like protein in cell extracts. In contrast, stable active enzyme is formed from chains truncated at position 306 or 307, showing that all 310 amino acids are not required for assembly. Replacements of Gln-288, Asn-291, Arg-296, and Ala-298 were introduced to assess the effect of alterations within helix 12 on protein stability. Stability of the trimers was measured both by differential scanning microcalorimetry and by the rate of exchange of chains at 4 degrees C when mutant trimers were incubated with succinylated wild-type trimers. Melting temperatures of the mutant trimers spanned a range of more than 20 degrees C, with a few higher and others lower than that of wild-type trimers. Large changes in interchain interaction energies were observed for the trimers, but there was no direct correlation between the ease of dissociation of the trimers and their thermal stability. Calorimetry on the mutant holoenzymes revealed alterations in the interactions between trimers and regulatory subunits within the intact enzymes. The striking changes in stability of both trimers and holoenzymes demonstrated that effects of relatively localized amino acid replacements in helix 12 are manifested by indirect global alterations propagated throughout the structure.
Evolution of the major histocompatibility complex: molecular cloning of major histocompatibility complex class I from the amphibian Xenopus.
Authors: Flajnik M F , Canel C , Kramer J , Kasahara M
Published: May 2006

Class I major histocompatibility complex (MHC) cDNA clones have been isolated from an expression library derived from mRNA of an MHC homozygous Xenopus laevis. The nucleotide and predicted amino acid sequences show definite similarity to MHC class I molecules of higher vertebrates. The immunoglobulin-like alpha-3 domain is more similar to the immunoglobulin-like domains of mammalian class II beta chains than to those of mammalian class I molecules, and a tree based on nucleotide sequences of representative MHC genes is presented.
Transmural distribution of extracellular purines in isolated guinea pig heart.
Authors: Zhu Q Y , Headrick J P , Berne R M
Published: May 2006

The purine adenosine appears to be involved in regulation of coronary vascular tone. Little is known concerning the levels and distribution of adenosine and related purines in the extracellular fluid of the heart. We have measured epicardial and endocardial levels of adenosine, inosine, hypoxanthine, AMP, and IMP in isolated constant flow perfused guinea pig hearts by using a recently developed technique with porous nylon sampling discs. Venous effluent purine levels were also measured. Concentrations of all purines measured, excluding IMP, were significantly higher in endocardial fluid samples than in epicardial fluid samples (P less than 0.05). Conversely, IMP levels were significantly lower in endocardial than in epicardial samples. The magnitude of the endocardial/epicardial ratios for adenosine, inosine, hypoxanthine, AMP, and IMP were approximately 12:1, 4:1, 5:1, 4:1, and 1:2, respectively. To assess cellular damage, lactate dehydrogenase activity was measured in all fluid samples and was not significantly different in endocardial and epicardial fluid. These data support the existence of significant transmural gradients for extracellular purine levels in crystalloid perfused guinea pig hearts. Transmural differences in vasoactive adenosine levels may be partially due to the greater endocardial oxygen consumption and metabolism and may be involved in maintaining relatively high subendocardial blood flows in the face of high intramyocardial pressures.
Multiple forms of mouse 3 beta-hydroxysteroid dehydrogenase/delta 5-delta 4 isomerase and differential expression in gonads, adrenal glands, liver, and kidneys of both sexes.
Authors: Bain P A , Yoo M , Clarke T , Hammond S H , Payne A H
Published: May 2006

Observations of patients deficient in the steroidogenic enzyme 3 beta-hydroxy-delta 5-steroid dehydrogenase/isomerase (3 beta HSD) have suggested the presence of distinct 3 beta HSD structural gene(s) that are expressed at peripheral sites, possibly the liver. We now report the isolation of cDNA clones representing three forms of 3 beta HSD from mouse Leydig cell and liver libraries. The three forms share significant identify but differ from each other by 5-10% within their coding regions. RNA that hybridizes to radiolabeled 3 beta HSD probes is present in the gonads, adrenal glands, liver, and kidneys of both sexes. Ribonuclease protection analysis using antisense probes derived from each of the three forms demonstrates that one form, 3 beta HSD I, is restricted to steroidogenic tissues. Two other forms, 3 beta HSD II and III, are expressed in liver and kidney but are not detected in steroidogenic tissues. A polyclonal antibody raised against the human placental form of 3 beta HSD recognizes a 42-kDa protein in gonadal and adrenal tissue and a 45-kDa protein in liver. The antibody recognizes a 42-kDa protein in kidney only weakly. 3 beta HSD enzyme activity is present in testicular, adrenal, hepatic, and renal tissue, with adrenal tissue possessing the highest specific activity. When expressed as total 3 beta HSD activity for whole organ mass, activity is greatest in the liver. The results demonstrate that the mouse liver is a significant site of 3 beta HSD activity and demonstrate the existence of multiple 3 beta HSD structural genes in the mouse.
Direct observation of vibrational coherence in bacterial reaction centers using femtosecond absorption spectroscopy.
Authors: Vos M H , Lambry J C , Robles S J , Youvan D C , Breton J , Martin J L
Published: May 2006

It is shown that vibrational coherence modulates the femtosecond kinetics of stimulated emission and absorption of reaction centers of purple bacteria. In the DLL mutant of Rhodobacter capsulatus, which lacks the bacteriopheophytin electron acceptor, oscillations with periods of approximately 500 fs and possibly also of approximately 2 ps were observed, which are associated with formation of the excited state. The kinetics, which reflect primary processes in Rhodobacter sphaeroides R-26, were modulated by oscillations with a period of approximately 700 fs at 796 nm and approximately 2 ps at 930 nm. In the latter case, at 930 nm, where the stimulated emission of the excited state, P*, is probed, oscillations could only be resolved when a sufficiently narrow (10 nm) and concomitantly long pump pulse was used. This may indicate that the potential energy surface of the excited state is anharmonic or that low-frequency oscillations are masked when higher frequency modes are also coherently excited, or both. The possibility is discussed that the primary charge separation may be a coherent and adiabatic process coupled to low-frequency vibrational modes.
Human auditory evoked gamma-band magnetic fields.
Authors: Pantev C , Makeig S , Hoke M , Galambos R , Hampson S , Gallen C
Published: May 2006

We have discovered a ca. 40-Hz transient magnetic oscillatory response, evoked in the human brain by the onset of auditory stimuli, consisting of four or more cycles locked in phase to stimulus onset in approximately the 20- to 130-ms poststimulus interval. The response originates in the supratemporal auditory cortex, some millimeters deeper and anterior to the source of the larger-amplitude slow-wave M100 component of the evoked magnetic field and moves in a posterior arcing trajectory 1 cm or more in length. The oscillatory cortical activation elicited by auditory stimuli may be similar to the gamma-band cortical oscillations elicited by olfactory and visual stimuli and may represent an essential component of auditory perceptual processing.
The Bacillus subtilis sigL gene encodes an equivalent of sigma 54 from gram-negative bacteria.
Authors: Débarbouillé M , Martin-Verstraete I , Kunst F , Rapoport G
Published: May 2006

The levanase operon in Bacillus subtilis is expressed from a -12, -24 promoter and transcription is stimulated by the regulator LevR, which contains a domain homologous with the central domain of the NifA and NtrC family of regulators. We isolated mutants defective in the expression of the levanase operon. These strains contain mutations that define a gene, called sigL, located between cysB and sacB on the genetic map. The sigL gene was cloned and sequenced. It encodes a polypeptide containing 436 residues with a molecular weight of 49,644. The amino acid sequence of SigL is homologous with all sigma 54 factors from Gram-negative bacteria, including Rhizobium meliloti (32% identity) and Klebsiella pneumoniae (30% identity). B. subtilis sigL mutants have a pleiotropic phenotype: (i) the transcription of the levanase operon is strongly reduced and (ii) in minimal medium lacking ammonia, sigL mutants cannot grow when arginine, ornithine, isoleucine, or valine is the sole nitrogen source. These results indicate that the sigL gene encodes an equivalent of the sigma 54 factor in B. subtilis, to our knowledge, the first of this type to be identified in Gram-positive bacteria.
Photosynthetic electron transport in genetically altered photosystem II reaction centers of chloroplasts.
Authors: Roffey R A , Golbeck J H , Hille C R , Sayre R T
Published: May 2006

Using a cotransformation system to identify chloroplast transformants in Chlamydomonas reinhardtii, we converted histidine-195 of the photosystem II reaction center D1 protein to a tyrosine residue. The mutants were characterized by a reduced quantum efficiency for photosynthetic oxygen evolution, which varied in a pH-dependent manner, a reduced capacity to oxidize artificial donors to photosystem II, and P680+ reduction kinetics (microsecond) that were essentially similar to wild type. In addition, a dark-stable radical was detected by ESR in mutant photosystem II particles but not in wild-type particles. This radical was similar in g value and lineshape to chlorophyll or carotenoid cations but could have arisen from a tyrosine-195 cation. The ability of the photosystem II trap (P680+) to oxidize tyrosine residues suggests that the mutant tyrosine residue could be used as a redox-sensitive probe to investigate the environment around the photosystem II trap.
Preferential T-cell receptor beta-chain variable gene use in myelin basic protein-reactive T-cell clones from patients with multiple sclerosis.
Authors: Kotzin B L , Karuturi S , Chou Y K , Lafferty J , Forrester J M , Better M , Nedwin G E , Offner H , Vandenbark A A
Published: May 2006

Multiple sclerosis is an autoimmune disease in which T lymphocytes reactive to myelin basic protein (BP) could play a central role. T cells specific for BP were cloned from the blood of multiple sclerosis patients and normal individuals, and expression of T-cell receptor variable region genes was analyzed. A remarkable bias for use of beta-chain variable region (V beta) 5.2 and, to a lesser extent, V beta 6.1 was seen among BP-specific clones from patients but not from controls. The preferential use of V beta 5.2 for BP recognition did not reflect altered expression of this V beta in the peripheral repertoire. Interestingly, shared V beta 5.2 usage was apparent for clones specific for different BP determinants, even when derived from the same individual. The concurrent demonstration by others (J. R. Oksenberg, M. A. Panzara, A. B. Begovich, H. Erlich, R. Murray, M. Sherritt, S. Stuart, C. C. Bernard, and L. Steinman, personal communication) that T cells within demyelinating areas of multiple sclerosis brains preferentially express V beta 5.2 and V beta 6.1 suggests that the BP-specific clones derived from blood may be relevant to disease pathogenesis. These findings may have important implications for the treatment of multiple sclerosis.
Multiple human D5 dopamine receptor genes: a functional receptor and two pseudogenes.
Authors: Grandy D K , Zhang Y A , Bouvier C , Zhou Q Y , Johnson R A , Allen L , Buck K , Bunzow J R , Salon J , Civelli O
Published: May 2006

Three genes closely related to the D1 dopamine receptor were identified in the human genome. One of the genes lacks introns and encodes a functional human dopamine receptor, D5, whose deduced amino acid sequence is 49% identical to that of the human D1 receptor. Compared with the human D1 dopamine receptor, the D5 receptor displayed a higher affinity for dopamine and was able to stimulate a biphasic rather than a monophasic intracellular accumulation of cAMP. Neither of the other two genes was able to direct the synthesis of a receptor. Nucleotide sequence analysis revealed that these two genes are 98% identical to each other and 95% identical to the D5 sequence. Relative to the D5 sequence, both contain insertions and deletions that result in several in-frame termination codons. Premature termination of translation is the most likely explanation for the failure of these genes to produce receptors in COS-7 and 293 cells even though their messages are transcribed. We conclude that the two are pseudogenes. Blot hybridization experiments performed on rat genomic DNA suggest that there is one D5 gene in this species and that the pseudogenes may be the result of a relatively recent evolutionary event.
Heterotropic interactions in aspartate transcarbamoylase: turning allosteric ATP activation into inhibition as a consequence of a single tyrosine to phenylalanine mutation.
Authors: Van Vliet F , Xi X G , De Staercke C , de Wannemaeker B , Jacobs A , Cherfils J , Ladjimi M M , Hervé G , Cunin R
Published: May 2006

Aspartate transcarbamoylase (EC 2.1.3.2) is extensively studied as a model for cooperativity and allostery. This enzyme shows cooperativity between the catalytic sites, and its activity is feedback inhibited by CTP and activated by ATP. These regulatory processes involve several interfaces between catalytic and regulatory chains as well as between domains within these two types of chains. As far as the regulatory chain is concerned, its two domains are in contact through a hydrophobic interface, in which a tyrosine residue is inserted in a pocket involving two leucine residues of the allosteric domain and a valine and a leucine residue of the zinc domain. To probe the possible implication of this hydrophobic core in the CTP and ATP regulatory effect, the tyrosine was replaced by a phenylalanine through oligonucleotide-directed mutagenesis. Interestingly, the resulting mutant shows a complete inversion of the ATP effect; it is now inhibited by ATP instead of being activated by this nucleotide triphosphate. This mutant remains normally sensitive to the feedback inhibitor CTP. This result shows that the hydrophobic interface between the two domains of the regulatory chain plays an important role in the discrimination between the regulatory signals promoted by the two allosteric effectors.
Drosophila 60A gene, another transforming growth factor beta family member, is closely related to human bone morphogenetic proteins.
Authors: Wharton K A , Thomsen G H , Gelbart W M
Published: May 2006

The 60A gene, a member of the transforming growth factor beta superfamily of signaling proteins, has been identified in Drosophila melanogaster. From its inferred protein sequence we predict the precursor is secreted and processed to release a growth factor-like molecule. The 60A gene is expressed throughout development with peaks of transcription during early embryogenesis, in pupae, and in adult males. The putative 60A protein shows greater sequence similarity to three vertebrate family members (human bone morphogenetic proteins 5, 6, and 7) than to its only Drosophila relative, the protein product of the decapentaplegic (dpp) gene. This observation suggests that the duplication event that gave rise to the two transforming growth factor beta-like proteins in Drosophila predates the divergence of chordates and arthropods.
Germ cell-specific expression of a gene encoding eukaryotic translation elongation factor 1 alpha (eEF-1 alpha) and generation of eEF-1 alpha retropseudogenes in Xenopus laevis.
Authors: Abdallah B , Hourdry J , Krieg P A , Denis H , Mazabraud A
Published: May 2006

We have studied by in situ hybridization the expression of the genes encoding the somatic form and the oocyte form of Xenopus laevis eEF-1 alpha. The somatic form of eEF-1 alpha (eEF-1 alpha S) mRNA is virtually undetectable in male and female germ cells of the adult gonad but is very abundant in embryonic cells after the neurula stage. In contrast, another form of eEF-1 alpha (eEF-1 alpha O) mRNA is highly concentrated in oogonia and in previtellogenic oocytes but is undetectable in eggs and embryos. eEF-1 alpha O mRNA is also present in spermatogonia and spermatocytes of adult testis. The latter finding identifies eEF-1 alpha O mRNA as a germ cell-specific gene product. Although germ cells contain very little eEF-1 alpha S mRNA, several eEF-1 alpha S retropseudogenes exist in X. laevis chromosomes. These genes are thought to arise in germ cells from reverse transcription of mRNA and subsequent integration of the cDNA copies into chromosomal DNA. We suggest that eEF-1 alpha S pseudogenes are generated in primordial germ cells of the embryo before they differentiate into oogonia or spermatogonia.
Monoclonal antibody-targeted superantigens: a different class of anti-tumor agents.
Authors: Dohlsten M , Hedlund G , Akerblom E , Lando P A , Kalland T
Published: May 2006

The bacterial superantigen staphylococcal enterotoxin (SE) A (SEA) directs cytotoxic T lymphocytes (CTLs) expressing particular sequences of the T-cell receptor (TCR) beta chain to lyse tumor cells expressing major histocompatibility complex (MHC) class II molecules, which serve as receptors for SEs. We now report that chemical conjugates of SEA and the colon carcinoma-reactive monoclonal antibodies (mAbs) C215 or C242 mediate T cell-dependent destruction of colon carcinoma cells lacking MHC class II molecules. SEA was covalently linked to the mAbs C215 and C242 via a PEG-based hydrophilic spacer. The C215-SEA conjugate targeted CD4+ as well as CD8+ CTLs to lyse a panel of colon carcinoma cells lacking MHC class II molecules. T-cell recognition of mAb-SEA conjugates was SEA specific, since SEB-selective T-cell lines with potent cytotoxic activity towards Raji cells coated with SEB did not respond to the C215-SEA conjugate. Unconjugated SEA did not induce T-cell lysis of MHC class II- colon carcinoma cells but efficiently directed CTLs against MHC class II+ Raji cells and certain interferon-treated MHC class II+ colon carcinoma cells. These results suggest that SEA-mAb conjugates retain the SEA-related selectivity for certain TCR beta-chain variable region (V beta) sequences but, in contrast to unconjugated SEA, mediate the TCR interaction in a MHC class II-independent manner. The cytotoxic activity mediated by C215-SEA and C242-SEA conjugates was blocked by excess of C215 mAb and C242 mAb, respectively, showing that the specificity in the targeting of mAb-SEA conjugates is defined by the antigen reactivity of the mAb. These results demonstrate that bacterial superantigens may be successfully conjugated to mAb with preserved T cell-activating capacity. The circumvention of MHC class II binding of SEs by conjugation to mAb suggests that such conjugates may find general application as antitumor agents, taking advantage of the extreme T cell-activating potency of superantigens.
Human immunodeficiency virus can infect the apical and basolateral surfaces of human colonic epithelial cells.
Authors: Fantini J , Yahi N , Chermann J C
Published: May 2006

The gastrointestinal tract is considered to be a major route of infection for the human immunodeficiency virus (HIV). To understand the interaction of HIV with epithelial cells of the intestinal mucosa, we have studied the infection of a human colon cancer cell clone HT-29-D4. The enterocyte-like differentiation of this clone can be modulated in vitro according to the concentration of glucose. We show that: (i) undifferentiated HT-29-D4 cells can be infected by HIV types 1 and 2 (HIV-1 and HIV-2) strains with no subsequent effect on cell growth; (ii) undifferentiated HT-29-D4 cells express a CD4-related antigen bearing epitopes of the immunoglobulin-like variable (V) region domains V1 and V2 of CD4 but lacking the epitope known to be involved in HIV envelope recognition; (iii) differentiated HT-29-D4 cells can be infected by HIV after an interaction with either the apical brush border membrane (luminal side) or the basolateral side (serosal side); (iv) the CD4-like molecule is restricted to the basolateral domain of differentiated cells; and (v) the infection is not inhibited by anti-CD4 monoclonal antibodies (mAbs) OKT4, OKT4A, Leu-3a, Bl4, 13-B-8-2, S-T4 or S-T40. We conclude that epithelial intestinal cells may represent a major site of entry for HIV. Infection of these epithelial cells may occur via the basolateral membrane by HIV-bearing lymphocytes or macrophages of the lamina propria and via the apical membrane by HIV present in the bowel lumen. This infection may remain silent for up to 9 months, and the virus can be rescued by cocultivation with lymphoid cells. These data may give an explanation for the long latent seronegative state that may occur in a HIV-infected individual.
Critical role of a hydrogen bond in the interaction of phospholipase A2 with transition-state and substrate analogues.
Authors: Yu L , Dennis E A
Published: May 2006

The inhibition of phospholipase A2 by an amide substrate analogue, 1-hexadecylthio-2-hexadecanoyl-amino-1,2-dideoxy-sn-glycero-3-phos phocholine, and a phosphonate transition-state analogue, 1-hexadecylthio-1-deoxy-2-hexadecylphosphono-sn-glycero-3-ph osphocholine, is dramatically influenced by pH. However, these two inhibitors show opposite pH dependencies. The amide analogue acts more potently under basic conditions, whereas the phosphonate acts more potently under acidic conditions. In both cases, ligand binding is perturbed by protonation of an enzyme functional group with an apparent pKa of 6.1, which corresponds to that of a histidine residue. Thus, His-48, which has previously been implicated in catalysis, appears to be critically involved in the hydrogen bond interactions between the enzyme and these two inhibitors. The amide analogue binds most effectively to the enzyme when His-48 is deprotonated. Upon protonation of the histidine residue, the amide cannot form a critical hydrogen bond and loses its ability to interact effectively with the enzyme. In contrast, the phosphonate analogue binds much tighter to the protonated form of the enzyme than to the deprotonated form. The phosphonate analogue needs a bridging hydrogen between the oxygen on its phosphorus atom and the N delta 1 of His-48 to form a strong hydrogen bond. At optimal pH values for inhibitor binding, both the amide and the phosphonate analogues are potent competitive inhibitors of cobra (Naja naja naja) venom phospholipase A2. The IC50 for the amide was 4.4 x 10(-4) mol fraction and for the phosphonate was 1.6 x 10(-5) mol fraction. Under the experimental conditions used, this corresponds to a bulk concentration of 2 microM and 70 nM, respectively.
The phenotype of lymphoid cells and thymic epithelium correlates with development of autoimmune insulitis in NOD in equilibrium with C57BL/6 allophenic chimeras.
Authors: Forsgren S , Dahl U , Söderström A , Holmberg D , Matsunaga T
Published: May 2006

The mechanisms contributing to the development of autoimmune insulin-dependent diabetes mellitus have been analyzed in allophenic mouse chimeras of the NOD in equilibrium with C57BL/6 strain combination (where NOD is nonobese diabetic). Occurrence of lymphoid cell infiltration (insulitis) in pancreatic islets was observed in the majority of such chimeras. The development of insulitis was found to correlate with major histocompatibility complex chimerism in lymphoid cells and in thymus cortical regions. Chimeras with more than 50% of C57BL/6 lymphoid cells rarely developed insulitis. Our data suggest that the correlation with the thymic cortical region is absolute. Thus, all individuals displaying NOD or NOD/C57BL/6 thymic cortical regions developed insulitis, whereas we have not observed insulitis in chimeras with only C57BL/6 thymic cortical regions. Thus the positive selection of T cells appears to play a crucial role in the development of insulin-dependent diabetes mellitus.
A single amino acid change in a myelin basic protein peptide confers the capacity to prevent rather than induce experimental autoimmune encephalomyelitis.
Authors: Smilek D E , Wraith D C , Hodgkinson S , Dwivedy S , Steinman L , McDevitt H O
Published: May 2006

Experimental autoimmune encephalomyelitis (EAE) is an experimental demyelinating disease of rodents. In (PL/J x SJL) F1 mice, it is induced by immunization with the myelin basic protein peptide Ac1-11. Ac1-11 [4A], a myelin basic protein peptide analog with a single amino acid substitution, (i) binds to class II major histocompatibility complex molecules and stimulates encephalitogenic T cells in vitro better than Ac1-11, (ii) is nonimmunogenic and nonencephalitogenic in vivo in (PL/J x SJL)F1 mice, (iii) prevents EAE when administered before or at the time of immunization with Ac1-11, and (iv) prevents EAE when administered later, near the time of disease onset. Initial studies suggest that Ac1-11 [4A] does not prevent EAE by competitive inhibition or by activation of regulatory cells. Thus, substitution of a single amino acid in a myelin basic protein peptide confers the capacity to prevent rather than induce EAE, even after peptide-specific encephalitogenic T cells have been activated.
Characterization of a ceramide-activated protein kinase: stimulation by tumor necrosis factor alpha.
Authors: Mathias S , Dressler K A , Kolesnick R N
Published: May 2006

Recent investigations have identified a signal-transduction system involving sphingomyelin and derivatives. In this paradigm, sphingomyelin hydrolysis by a sphingomyelinase generates ceramide, which may be converted to the protein kinase C inhibitor sphingosine or to ceramide 1-phosphate. Ceramide may have second-messenger function because it induces epidermal growth factor receptor phosphorylation, presumably on Thr-669 in A-431 cells. The present studies describe a kinase that may mediate ceramide action. With a 19-amino acid epidermal growth factor receptor peptide containing Thr-669, a membrane-bound activity that phosphorylated the peptide was detected in A-431 cells. Activity was linearly related to ATP (0.3-300 microM) and peptide concentration (0.02-1 mg/ml), possessed a physiologic pH optimum (pH 7.0-7.4), and was Mg(2+)-dependent. Other cations--Ca2+, Mn2+, and Zn(2+)--were ineffective. Natural and synthetic ceramide induced time- and concentration-dependent enhancement of kinase activity. Ceramide (0.5 microM) increased kinase activity 2-fold by 30 s, and activity remained elevated for at least 15 min. As little as 0.001 microM ceramide was effective, and 1 microM ceramide induced maximal phosphorylation. Sphingosine was similarly effective. Because tumor necrosis factor (TNF) alpha rapidly induces sphingomyelin hydrolysis to ceramide during monocytic differentiation of HL-60 cells, its effects on kinase activity were assessed. Kinase activity was increased 1.5-fold at 5 min and 2-fold at 2 hr in membranes derived from TNF-stimulated cells. The effective concentration range was 3 pM-30 nM TNF. Exogenous ceramide induced a similar effect. In sum, these studies demonstrate the existence of an unusual Mg(2+)-dependent ceramide-activated protein kinase that may mediate some aspects of TNF-alpha function.
Directed mutagenesis of an iron-sulfur protein of the photosystem I complex in the filamentous cyanobacterium Anabaena variabilis ATCC 29413.
Authors: Mannan R M , Whitmarsh J , Nyman P , Pakrasi H B
Published: May 2006

In oxygenic photosynthetic organisms the PSI-C polypeptide, encoded by the psaC gene, provides the ligands for two [4Fe-4S] centers, FA and FB, the terminal electron acceptors in the photosystem I (PSI) complex. An insertion mutation introduced in the psaC locus of the filamentous cyanobacterium Anabaena variabilis ATCC 29413 resulted in the creation of a mutant strain, T398-1, that lacks the PSI-C polypeptide. In medium supplemented with 5 mM fructose, the mutant cells grew well in the dark. However, when grown in the same medium under light, the doubling rate of T398-1 cells was significantly decreased. In intact cells of T398-1, bicarbonate-dependent whole-chain electron transport (PSII and PSI) could not be detected, although partial electron transport reactions involving either one of the two photosystems could be measured at significant rates. The low-temperature EPR signals attributed to the [4Fe-4S] centers FA and FB were absent in the mutant cells. Chemical titration measurements indicated that the ratios of chlorophyll to the primary donor P700 were virtually identical in membranes from the wild-type and mutant cells. Moreover, room-temperature optical spectroscopic analysis of the thylakoid membranes isolated from T398-1 showed flash-induced P700 oxidation followed by dark rereduction, indicating primary photochemistry in PSI. Thus stable assembly of the reaction center of PSI can occur in the absence of the Fe-S cluster cofactors FA and FB. These studies demonstrate that Anabaena 29413 offers a useful genetic system for targeted mutagenesis of the PSI complex.
Immunochemical dissection of the Ultrabithorax homeoprotein family in Drosophila melanogaster.
Authors: Lopez A J , Hogness D S
Published: May 2006

The homeotic gene Ultrabithorax (Ubx) specifies metameric identities in multiple tissues of the thorax and abdomen in Drosophila melanogaster. Alternatively spliced Ultrabithorax mRNAs encode five protein isoforms that differ in internal sequences immediately adjacent to a homeodomain DNA-binding motif. Each of these proteins is phosphorylated in vivo at multiple serine and threonine residues. An extensive panel of monoclonal antibodies was raised against the Ultrabithorax proteins, including antibodies specific for individual isoforms and antibodies that discriminated between different phosphorylation states. Characterization of these antibodies provided insights into shared and isoform-specific features of Ultrabithorax protein structure that may be functionally important. Immunohistochemical staining experiments demonstrated that each isoform is expressed in a different stage- and tissue-specific pattern and suggested that Ultrabithorax protein phosphorylation is also developmentally regulated. These results support the hypothesis that alternative splicing and phosphorylation modulate developmentally specific functions of the Ubx gene.
Zinc transfer from transcription factor IIIA fingers to thionein clusters.
Authors: Zeng J , Vallee B L , Kägi J H
Published: May 2006

The rapid induction of thionein (apometallothionein) by many endogenous stimuli such as steroid hormones, cytokines, and second messengers suggests that this cysteine-rich, metal binding protein participates in an as yet undefined role in cellular regulatory processes. This study demonstrates with DNA and RNA binding assays and in vitro transcription measurements that thionein suppresses the binding of the Xenopus laevis zinc finger transcription factor IIIA (TFIIIA) to 5S RNA and to the 5S RNA gene and abrogates the capacity of TFIIIA to initiate the RNA polymerase III-catalyzed synthesis of 5S RNA. The effect is reversed by the addition of zinc and is not observed in the TFIIIA-independent transcription of a tRNA gene by the same RNA polymerase. In view of the strong tendency of thionein to complex posttransition metals such as zinc, one effect of its enhanced synthesis in vivo could be to reduce the intracellular disposability of zinc and thus modulate the actions of zinc-dependent enzymes and proteins, most notably those of the zinc finger transcription factors.
HLA class I-restricted human cytotoxic T cells recognize endogenously synthesized hepatitis B virus nucleocapsid antigen.
Authors: Bertoletti A , Ferrari C , Fiaccadori F , Penna A , Margolskee R , Schlicht H J , Fowler P , Guilhot S , Chisari F V
Published: May 2006

Knowledge of the immune effector mechanisms responsible for clearance of hepatitis B virus (HBV)-infected cells has been severely limited by the absence of reproducible systems to selectively expand and to characterize HBV-specific cytotoxic T lymphocytes (CTLs) in the peripheral blood of patients with viral hepatitis. By using a strategy involving sequential stimulation with HBV nucleocapsid synthetic peptides followed by autologous, or HLA class I-matched, HBV nucleocapsid transfectants, we now report the existence of CTLs able to lyse target cells that express endogenously synthesized HBV nucleocapsid antigen in the peripheral blood of patients with acute viral hepatitis B. The CTL response is HLA-A2 restricted, mediated by CD8-positive T cells, and specific for a single epitope, located between amino acid residues 11 and 27 of HBV core protein; these residues are shared with the secretable precore-derived hepatitis B e antigen. Equivalent lysis of target cells that express each of these proteins suggests that their intracellular trafficking pathways may intersect. The current report provides definitive evidence that HLA class I-restricted, CD8-positive CTLs that recognize endogenously synthesized HBV nucleocapsid antigen are induced during acute HBV infection in humans and establishes a strategy that should permit a detailed analysis of the role played by HBV-specific CTLs in the immunopathogenesis of viral hepatitis.
A triplex DNA-binding protein from human cells: purification and characterization.
Authors: Kiyama R , Camerini-Otero R D
Published: May 2006

A protein that binds to an oligonucleotide triplex, (dT)34.(dA)34.(dT)34 (TAT triplex), was purified from HeLa cells by a combination of conventional column chromatography and triplex DNA affinity chromatography. The protein has an apparent molecular mass of 55 kDa on sodium dodecyl sulfate/polyacrylamide gels. Although the protein has an affinity for AT duplex and TAT triplex, a higher affinity for TAT triplex was demonstrated by comparing the elution profiles from an AT duplex and a TAT triplex affinity column. The protein has a moderate affinity for poly(dA-dG).poly(dT-dC) and a very low affinity for single-strand (dA)34 or (dT)34 and various sources of duplex DNA including poly(dA-dT).poly(dA-dT). The possible biological function of this triplex DNA-binding protein is discussed.
Masculinization of female isopods (Crustacea) correlated with non-Mendelian inheritance of cytoplasmic viruses.
Authors: Juchault P , Louis C , Martin G , Noulin G
Published: May 2006

When in genetic females external male characters differentiate, the phenomenon is called "male pseudohermaphroditism." This male differentiation occurs in terrestrial isopods (Crustacea, suborder Oniscoidea) and sometimes involves only some epithelial areas (gynandromorphous mosaics). It is not induced by male hormones or by abnormal ovary function. This intersexuality is transmitted maternally (by the intersex females) or paternally (by the brothers of intersex females) to between 30% and 60% of their offspring. Although it occurs at 20 degrees C, the male differentiation disappears when breeding takes place at 27 degrees C. Male characters differentiate in normal females--even in other Oniscoidea species (Porcellio dilatatus, Porcellio laevis, Armadillidium vulgare)--after injection of a 0.22-micron filtered tissue extract. Since an inhibitor of bacterial protein synthesis (gentamycin) does not inhibit this masculinizing effect, we infer that neither organelles nor bacteria are involved. Intersexuality is always correlated with the presence of cytoplasmic viral particles in both intersex-female and transmitter-male tissues. Striking similarities to the Drosophila S virus are noted. A reovirus-like Oniscoidea masculinizing virus, which probably acts only on the epithelial areas sensitive to the male hormones, is most likely the causative agent of this intersexuality. Here we report the conversion of secondary sexual characters putatively caused by a virus.
Functional analysis of an oxygen-regulated transcriptional enhancer lying 3' to the mouse erythropoietin gene.
Authors: Pugh C W , Tan C C , Jones R W , Ratcliffe P J
Published: May 2006

Erythropoietin, the major hormone controlling red-cell production, is regulated in part through oxygen-dependent changes in the rate of transcription of its gene. Using transient transfection in HepG2 cells, we have defined a DNA sequence, located 120 base pairs 3' to the poly(A)-addition site of the mouse erythropoietin gene, that confers oxygen-regulated expression on a variety of heterologous promoters. The sequence has the typical features of a eukaryotic enhancer. Approximately 70 base pairs are necessary for full activity, but reiteration restores activity to shorter inactive sequences. This enhancer operates in HepG2 and Hep3B cells, but not in Chinese hamster ovary cells or mouse erythroleukemia cells, and responds to cobalt but not to cyanide or 2-deoxyglucose, thus reflecting the physiological control of erythropoietin production accurately.
Immunoglobulin-like PapD chaperone caps and uncaps interactive surfaces of nascently translocated pilus subunits.
Authors: Kuehn M J , Normark S , Hultgren S J
Published: May 2006

Molecular chaperones are found in the cytoplasm of bacteria and in various cellular compartments in eukaryotes to maintain proteins in nonnative conformations that permit their secretion across membranes or assembly into oligomeric structures. Virtually nothing, however, has been reported about a similar requirement for molecular chaperones in the periplasm of Gram-negative bacteria. We used the well-characterized P pilus biogenesis system in Escherichia coli as a model to elucidate the mechanism of action of a periplasmic chaperone, PapD, which is specifically required for P pilus biogenesis. PapD probably associates with at least six P pilus subunits after their secretion across the cytoplasmic membrane, but PapD is not incorporated into the pilus. We used purified periplasmic complex that PapD forms with the PapG adhesin to investigate the function of interactions between the chaperone and its targets. We demonstrated that PapD binds to PapG to form a stable, discrete bimolecular complex and that, unlike cytoplasmic chaperones, the periplasmic PapD chaperone maintained PapG in a native-like conformation. Bound PapD in the complex was displaced by free PapD in vitro; however, the in vivo release of subunits to the nascent pilus is probably driven by an ATP-independent mechanism involving the outer membrane protein PapC. In addition, the binding of PapD to PapG in vitro prevented aggregation of PapG. We propose that the function of PapD and other periplasmic pilus chaperones is to partition newly translocated pilus subunits into assembly-competent complexes and thereby prevent nonproductive aggregation of the subunits in the periplasm. These data provide important information for understanding the mechanism of action of this general class of chaperones that function in the periplasmic space.
Activation of the erythropoietin receptor promoter by transcription factor GATA-1.
Authors: Zon L I , Youssoufian H , Mather C , Lodish H F , Orkin S H
Published: May 2006

Erythropoietin, a glycoprotein produced by the kidneys in response to anemia and hypoxia, is a major growth factor for cells of the erythroid lineage. Erythropoietin interacts with high-affinity cell surface receptors (EpoR) present on developing progenitors and is required for their survival. Previously we characterized the gene for EpoR and demonstrated that its promoter acts in a cell-specific manner. Here we show that the hematopoietic-specific transcription factor GATA-1 is necessary, and indeed is sufficient as the sole cell-restricted regulator, for activation of the EpoR promoter in fibroblast transfection assays. Hence, GATA-1, which participates in transcriptional control of the majority of erythroid-expressed genes, also acts on the promoter of an essential lineage-restricted receptor (EpoR). This central contribution of GATA-1 to EpoR promoter function provides a mechanism whereby a cell-restricted regulator may ensure the viability and subsequent maturation of progenitor cells during hematopoietic differentiation.
Functional analysis in yeast of cDNA coding for the mitochondrial Rieske iron-sulfur protein of higher plants.
Authors: Huang J T , Struck F , Matzinger D F , Levings C S
Published: May 2006

cDNA clones coding for the nuclear-encoded mitochondrial Rieske iron-sulfur protein (RISP) have been isolated from maize and tobacco. Complementation analysis of hybrid proteins consisting of different domains of plant and yeast RISPs showed that the carboxyl two-thirds of the plant protein is functionally equivalent to that of the yeast protein. The amino terminus of the RISP, however, seems to be species specific because this region is not interchangeable between plant and yeast proteins. Complementation analysis of hybrid proteins also identified a structurally conserved domain probably essential for the function of bc1 complex RISPs. A specific domain from the plant RISP was found to cause temperature-sensitive respiratory growth in yeast. We have demonstrated that yeast can serve as a model system to study the structural and functional relationships of plant gene products that are enzymatic components of the mitochondrial respiratory chain.