bluuebunny/crossref_metadata_2025 huggingface dataset:
Transgenic indicator mice for studying activated retinoic acid receptors during development.
Authors: Balkan W , Colbert M , Bock C , Linney E
Published: May 2006

Retinoic acid (RA) receptors (RARs) are ligand-inducible transcription factors that bind to specific DNA sequences associated with the regulatory regions of RA-regulatable genes. Since RA has been implicated as an important factor both in normal development and in teratological studies, one would like to have a model system that detects the presence of activated receptors during development. We have constructed a recombinant reporter gene that has three copies of the RA response element (RARE) from the RAR beta-2 promoter 5' to the herpes simplex virus thymidine kinase promoter; this regulatory region is coupled to the bacterial beta-galactosidase reporter gene. This construct was RA inducible in transient transfection assays in F9 embryonal carcinoma cells. Transgenic embryos with this reporter gene construct exhibited restricted and reproducible patterns of beta-galactosidase activity during embryogenesis, beginning between gestational ages day 7.5 and 8.5. At day 8.5, beta-galactosidase activity was detected in the closed neurotube and somites. Day 8.5 embryos, from pregnant females fed RA 14 hr earlier, exhibited a greater intensity and distribution of beta-galactosidase activity. Similarly, at later stages of gestation, maternal RA exposure resulted in enhanced embryonic beta-galactosidase expression. This type of transgenic indicator mouse should be useful in detailing the role of activated RARs during embryonic development.
Dorsal-ventral patterning in Drosophila: DNA binding of snail protein to the single-minded gene.
Authors: Kasai Y , Nambu J R , Lieberman P M , Crews S T
Published: May 2006

The Drosophila snail gene is required for proper mesodermal development. Genetic studies suggest that it functions by repressing adjacent ectodermal gene expression including that of the single-minded (sim) gene. The snail gene encodes a protein with a zinc-finger motif, and here we report that the snail gene product is a sequence-specific DNA binding protein. The snail protein recognizes a 14-base-pair consensus sequence that is found nine times in a 2.8-kilobase sim regulatory region. These results provide evidence for the direct control of sim transcription by snail.
Evidence for immune selection of hepatitis C virus (HCV) putative envelope glycoprotein variants: potential role in chronic HCV infections.
Authors: Weiner A J , Geysen H M , Christopherson C , Hall J E , Mason T J , Saracco G , Bonino F , Crawford K , Marion C D , Crawford K A
Published: May 2006

E2/nonstructural protein 1, the putative envelope glycoprotein (gp72) of HCV, possesses an N-terminal hypervariable (E2 HV) domain from amino acids 384 to 414 of unknown significance. The high degree of amino acid sequence variation in the E2 HV domain appears to be comparable to that observed in the human immunodeficiency virus type 1 gp120 V3 domain. This observation and the observation that the HCV E2 HV domain lacks conserved secondary structure imply that, like the V3 loop of human immunodeficiency virus 1 gp120, the N-terminal E2 region may encode protective epitopes that are subject to immune selection. Antibody-epitope binding studies revealed five isolate-specific linear epitopes located in the E2 HV region. These results suggest that the E2 HV domain is a target for the human immune response and that, in addition to the three major groups of HCV, defined by nucleotide and amino acid sequence identity among HCV isolates, E2 HV-specific subgroups also exist. Analysis of the partial or complete E2 sequences of two individuals indicated that E2 HV variants can either coexist simultaneously in a single individual or that a particular variant may predominate during different episodes of disease. In the latter situation, we found one individual who developed antibodies to a subregion of the E2 HV domain (amino acids 396-407) specific to a variant that was predominant during one major episode of hepatitis but who lacked detectable antibodies to the corresponding region of a second variant that was predominant during a later episode of disease. The data suggest that the variability in the E2 HV domain may result from immune selection. The findings of this report could impact vaccine strategies and drug therapy programs designed to control and eliminate HCV.
Evidence for a programmed life span in a colonial protochordate.
Authors: Rinkevich B , Lauzon R J , Brown B W , Weissman I L
Published: May 2006

The variety of theories that have attempted to define the mechanisms of aging and life span can be broadly divided into two alternative but nonexclusive viewpoints. The first stipulates that random changes of cellular and molecular structures lead to death following progressive "wear and tear." The second argues that life span is, at least in part, genetically programmed, and therefore aging may also result from time-dependent intrinsic processes. Here we demonstrate that ramets (clonal replicates) experimentally separated from colonies of the acidian protochordate Botryllus schlosseri died months after their separation, almost simultaneously with their parent colony and sibling ramets. In addition, in experimentally joined chimeras between ramets of senescent and nonsenescent colonies, elements from different parent colonies displayed parent-colony-specific timing of mortality. Thus, the senescent phenotype was simultaneously expressed both in chimeras and in unfused ramets of the parent colony that was undergoing senescence, whereas control ramets from the other partner survived. These findings provide experimental evidence for a heritable basis underlying mortality in protochordates, unlinked to reproductive effort and other life history traits of this species.
Role and regulation of interleukin (IL)-2 receptor alpha and beta chains in IL-2-driven B-cell growth.
Authors: Nakanishi K , Hirose S , Yoshimoto T , Ishizashi H , Hiroishi K , Tanaka T , Kono T , Miyasaka M , Taniguchi T , Higashino K
Published: May 2006

Substantial proportions of resting B cells constitutively express low levels of IL-2 receptor (IL-2R) alpha and/or beta chains. The expression of these chains is differentially regulated by anti-IgM and IL-2/IL-4. The anti-IgM induces IL-2R alpha chain expression, whereas each of the two cytokines induces IL-2R beta chain expression in a dose-dependent manner. Moreover, IL-2 induces the growth of B cells, when the cells were pretreated with IL-2 or IL-4 for 24 h. The magnitude of this IL-2-driven B-cell growth depends upon the level of IL-2R beta chain expression. Costimulation of the B cells with IL-2 and anti-IgM shifts the dose-response curve, and the cells proliferate at an IL-2 concentration as low as 40 pM. These results indicate that the levels of anti-IgM-induced IL-2R alpha chain and IL-2-induced IL-2R beta chain determine the sensitivity of the cells to IL-2.
Netropsin specifically enhances RNA polymerase II termination at terminator sites in vitro.
Authors: Ueno A , Baek K , Jeon C , Agarwal K
Published: May 2006

We describe an in vitro system that emulates the specific and efficient transcriptional termination associated with the human gastrin gene terminator in vivo. The system involves a dC-tailed DNA template containing the gastrin gene terminator sequence, purified RNA polymerase II, and purified elongation factor TFIIS. In this system, the basal level of termination by RNA polymerase II at the gastrin gene terminator is specifically enhanced by netropsin, an (A + T)-rich minor groove-binding peptide. This enhanced termination is maintained even with TFIIS, which normally suppresses termination at this site. In vitro termination is terminator sequence-specific. Mutant sequences that reduce or abolish termination in vivo show corresponding reductions in activity in the in vitro system. This in vitro emulation of in vivo activities of wild-type and mutant terminators strongly suggests that netropsin and a putative termination factor may share some aspects of their biochemical mechanisms. The general applicability of this system to the study of RNA polymerase II elongation and termination is suggested by the enhancement of termination seen at both the gastrin and human histone H3.3 gene terminators.
Long-term sensitization to the activation of cerebral delta-opioid receptors by the deltorphin Tyr-D-Ala-Phe-Glu-Val-Val-Gly-NH2 in rats exposed to morphine.
Authors: Melchiorri P , Maritati M , Negri L , Erspamer V
Published: May 2006

In experiments to evaluate responses to the activation of cerebral delta-opioid receptors, repeated daily injection of the selective delta-opioid agonist Tyr-D-Ala-Phe-Glu-Val-Val-Gly-NH2 ([D-Ala2]deltorphin II) into rat brain resulted in the development of tolerance, whereas repeated daily injection or continuous infusion of morphine resulted in sensitization to the behavioral activating effects of the delta-opioid agonist. Although the rats did not modify their spontaneous locomotor activity after morphine withdrawal, they became markedly hyperresponsive to the locomotor and stereotypy-producing effects of a challenge dose of the delta-opioid agonist. Sensitization to activation of delta-opioid receptors persisted for at least 60 days after discontinuing morphine treatment. These results show that the development of tolerance and long-term sensitization to opioids involves delta-opioid as well as mu-opioid receptors.
Transposon Tn5 excision in yeast: influence of DNA polymerases alpha, delta, and epsilon and repair genes.
Authors: Gordenin D A , Malkova A L , Peterzen A , Kulikov V N , Pavlov Y I , Perkins E , Resnick M A
Published: May 2006

Interaction between short repeats may be a source of genomic rearrangements and deletions. We investigated possible interactions between short (9 base pairs) direct repeats in yeast by using our previously described system for analyzing bacterial transposon Tn5 excision in yeast. Mutations of either POL3 or POL1, the proposed structural genes for polymerases delta and alpha, respectively, yield high levels of excision at semipermissive temperatures. pol2 (corresponding to polymerase epsilon) and pol2 pol3 double mutants do not exhibit enhanced excision. A majority of excision events involve direct repeats and are precise; the remaining imprecise excisions occur within or in the vicinity of the repeats. The three DNA repair pathways identified by rad1, rad6 and rad18, rad50 and rad52 mutations were examined for their possible role in Tn5 excision; no enhancement was observed in mutants. However, the pol3-stimulated Tn5 excision was reduced in rad52 and rad50 mutants. This suggests the potential for interaction between the systems for DNA double-strand break/recombinational repair and DNA synthesis. Based on the suggestion of Morrison et al. [Morrison, A., Araki, H., Clark, A. B., Hamatake, R. H. & Sugino, A. (1990) Cell 62, 1143-1151] that polymerases delta and alpha are responsible for lagging-strand synthesis and that polymerase epsilon is responsible for leading-strand synthesis, we suggest that Tn5 excision is stimulated under conditions of altered lagging-strand synthesis, possibly due to extended opportunities for single-strand interactions between the inverted insertion sequence I550 repeats of Tn5.
Anticodon-independent aminoacylation of an RNA minihelix with valine.
Authors: Frugier M , Florentz C , Giegé R
Published: May 2006

Minihelices mimicking the amino acid acceptor and anticodon branches of yeast tRNA(Val) have been synthesized by in vitro transcription of synthetic templates. It is shown that a minihelix corresponding to the amino acid acceptor branch and containing solely a valine-specific identity nucleotide can be aminoacylated by yeast valyl-tRNA synthetase. Its charging ability is lost after mutating this nucleotide. This ability is stimulated somewhat by the addition of a second hairpin helix that mimicks the anticodon arm, which suggests that information originating from the anticodon stem-loop can be transmitted to the active site of the enzyme by the core of the protein.
Genes encoding transcription factor IIIA and the RNA polymerase common subunit RPB6 are divergently transcribed in Saccharomyces cerevisiae.
Authors: Woychik N A , Young R A
Published: May 2006

The gene encoding Saccharomyces cerevisiae transcription factor TFIIIA has been found adjacent to RPB6, a gene that specifies a subunit shared by nuclear RNA polymerases. Analysis of DNA upstream of the RPB6 gene revealed an open reading frame that predicts a protein, designated PZF1, with nine C2H2 zinc fingers. The presence of nine C2H2 zinc fingers in PZF1 protein, a hallmark of amphibian TFIIIA proteins, suggested that PZF1 might be a TFIIIA homologue. We found that purified recombinant PZF1 specifically binds the internal control region (ICR) of the 5S rRNA gene in S. cerevisiae. The presence of nine C2H2 zinc fingers, the specific binding to ICR DNA, and the similarity of the predicted molecular mass of PZF1 with that determined for purified yeast TFIIIA, together indicate that PZF1 is TFIIIA. The yeast and amphibian TFIIIA proteins share only a limited number of residues outside of those normally conserved in C2H2 zinc fingers; these conserved residues may provide clues to the sequence specificity of these proteins. The PZF1 gene was found to be single copy, transcribed into a 1.5-kilobase mRNA, and essential for yeast cell viability. Interestingly, the yeast RPB6 and TFIIIA coding sequences are divergently transcribed and are separated by only 233 base pairs, providing the potential for coregulated expression of components of RNA polymerases and the 5S rRNA component of ribosomes.
Integration of cytoplasmic calcium and membrane potential oscillations maintains calcium signaling in pituitary gonadotrophs.
Authors: Stojilković S S , Kukuljan M , Iida T , Rojas E , Catt K J
Published: May 2006

Pituitary gonadotrophs exhibit spontaneous low-amplitude fluctuations in cytoplasmic calcium concentration ([Ca2+]i) due to intermittent firing of nifedipine-sensitive action potentials. The hypothalamic neuropeptide, gonadotropin-releasing hormone, terminates such spontaneous [Ca2+]i transients and plasma-membrane electrical activity and initiates high-amplitude [Ca2+]i oscillations and concomitant oscillations in membrane potential (Vm). The onset of agonist-induced [Ca2+]i oscillations is not dependent on Vm or extracellular Ca2+ but is associated with plasma-membrane hyperpolarization interrupted by regular waves of depolarization with firing of action potentials at the peak of each wave. The Vm and Ca2+ oscillations are interdependent during continued gonadotropin-releasing hormone action (greater than 3-5 min), when sustained Ca2+ entry is necessary for the maintenance of [Ca2+]i spiking. The initial and sustained agonist-induced Ca2+ transients and Vm oscillations are abolished by blockade of endoplasmic reticulum Ca(2+)-ATPase, consistent with the role of Ca2+ re-uptake by internal stores in the oscillatory response during both phases. Such a pattern of synchronization of electrical activity and Ca2+ spiking in cells regulated by Ca(2+)-mobilizing receptors shows that the operation of the cytoplasmic oscillator can be integrated with a plasma-membrane oscillator to provide a long-lasting signal during sustained agonist stimulation.
Cyclophilin-dependent stimulation of transcription by cyclosporin A.
Authors: Larson T G , Nuss D L
Published: May 2006

Exposure to cyclosporin A (CspA) increased laccase (lac-1) transcript accumulation in the chestnut blight fungus Cryphonectria parasitica. This response was suppressed by compounds that interfere with calcium-dependent signal transduction and by the presence of a virulence-attenuating mycovirus. CspA stimulated the accumulation of mRNA from a nonhomologous reporter fused to the lac-1 promoter, indicating that the increased transcript levels resulted from an increase in promoter activity. Based on the current model for the regulation of lac-1 transcription, these results suggest that CspA interferes with a negative regulatory pathway that normally constrains lac-1 promoter activity. Significantly, CspA did not stimulate lac-1 transcription in mutant strains deficient in CspA binding activity, directly demonstrating a requirement for the interaction of CspA and cyclophilin in the modulation of lac-1 transcription. Our results establish that CspA treatment can stimulate gene transcription and that cyclophilin is the cellular receptor that mediates this activity.
Serotonin 1B receptors in the developing somatosensory and visual cortices are located on thalamocortical axons.
Authors: Bennett-Clarke C A , Leslie M J , Chiaia N L , Rhoades R W
Published: May 2006

Serotonin (5-HT)-immunoreactive axons are densely distributed in the primary visual and somatosensory cortices of rats, mice, and hamsters for the first 2 weeks of life, and a recent study from this laboratory has demonstrated that 5-HT1B receptors assume a pattern that exactly matches that of the serotoninergic axons. The differential distribution of these receptors is also transient. In the present study, we combined receptor binding autoradiography with neurochemical ablation of 5-HT axons or electrolytic lesions of the dorsal thalamus in an effort to determine the neural elements upon which the 5-HT1B receptors were located. Subcutaneous injections of the toxin 5,7-dihydroxytryptamine, made on the day of birth, totally eliminated the dense and patterned 5-HT innervation of the somatosensory and striate cortices of rats killed on postnatal day 8 but had no qualitative effect upon the distribution or density of 5-HT1B receptors in either of these cortical regions in animals killed at the same age. Conversely, electrolytic lesions of the dorsal thalamus made on postnatal day 6 resulted in a complete loss of the dense and patterned distribution of 5-HT1B receptors in rats killed on postnatal day 8. These results indicate that thalamocortical axons transiently express 5-HT1B receptors.
Cathepsin D gene is controlled by a mixed promoter, and estrogens stimulate only TATA-dependent transcription in breast cancer cells.
Authors: Cavaillès V , Augereau P , Rochefort H
Published: May 2006

The cathepsin D (cath-D) gene, coding for a ubiquitous lysosomal aspartyl protease, is overexpressed in aggressive human breast cancers, and its transcription is induced by estrogens in hormone-responsive breast cancer cells. We have determined the structure and function of the proximal 5' upstream region of the human cath-D gene from MCF7 cells. We show that the promoter has a compound structure with features of both housekeeping genes (high G+C content and potential transcription factor Sp1 sites) and regulated genes (TATAA sequence). By RNase protection assay, we show that transcription is initiated at five major transcription sites (TSSI to -V) spanning 52 base pairs. In hormone-responsive breast cancer cells, estradiol increased by 6- to 10-fold the level of RNAs initiated at TSSI, which is located about 28 base pairs downstream from the TATA box. The specific regulation by estradiol of transcription starting at site I exclusively was confirmed by primer extension. Moreover, the same estradiol effect was observed in the ZR75-1 cell line and in MDA-MB231 estrogen-resistant breast cancer cells stably transfected with the estrogen receptor. Site-directed mutagenesis indicated that the TATA box is essential for initiation of cath-D gene transcription at TSSI. In breast cancer biopsy samples, high levels of TATA-dependent transcription were correlated with overexpression of cath-D mRNA. We conclude that cath-D behaves, depending on the conditions, as a housekeeping gene with multiple start sites or as a hormone-regulated gene that can be controlled from its TATA box.
Quantitation of zidovudine-resistant human immunodeficiency virus type 1 in the blood of treated and untreated patients.
Authors: Mohri H , Singh M K , Ching W T , Ho D D
Published: May 2006

A nonselective ex vivo assay was used to directly detect and quantify zidovudine (AZT)-resistant human immunodeficiency virus type 1 (HIV-1) in the blood of treated and untreated patients. In contrast to previous reports, drug-resistant virus was detected in peripheral blood mononuclear cells of a few of the patients who had never received AZT. The AZT resistance of HIV-1 isolates from one untreated individual was confirmed by further susceptibility studies in vitro and by the finding of a characteristic mutation (Lys-->Arg at codon 70) in the reverse transcriptase. In patients who were clinically stable while on AZT, HIV-1 titers in plasma and mononuclear cells were generally low but resistant viruses already predominated. In those individuals who were deteriorating despite AZT administration, high levels of viremia were observed, and the resistance phenotype was nearly universal. These findings serve to emphasize the magnitude of the AZT-resistance problem in patients on drug treatment.
A proposal for a new approach to a preventive vaccine against human immunodeficiency virus type 1.
Authors: Temin H M
Published: May 2006

Human immunodeficiency virus type 1 (HIV-1) is a more complex retrovirus, coding for several accessory proteins in addition to the structural proteins (Gag, Pol, and Env) that are found in all retroviruses. More complex retroviruses have not been isolated from birds, and simpler retroviruses have not been isolated from humans. However, the proviruses of many endogenous simpler retroviruses are present in the human genome. These observations suggest that humans can mount a successful protective response against simpler retroviruses, whereas birds cannot. Thus, humans might be able to mount a successful protective response to infection with a simpler HIV-1. As a model, a simpler bovine leukemia virus which is capable of replicating has been constructed; a simpler HIV-1 could be constructed in a similar fashion. I suggest that such a simpler HIV-1 would be a safe and effective vaccine against HIV-1.
Isolation and expression of human 1,25-dihydroxyvitamin D3 24-hydroxylase cDNA.
Authors: Chen K S , Prahl J M , DeLuca H F
Published: May 2006

Human 1,25-dihydroxyvitamin D3 24-hydroxylase cDNA clones were isolated from an HL-60 cell cDNA library by using a reverse transcription/polymerase chain reaction-generated human cDNA probe. The 24-hydroxylase cDNA consists of a 1539-bp open reading frame encoding a 513-amino acid polypeptide. Protein sequence analysis shows that the human 24-hydroxylase is 90% homologous (82% identical) to that of the rat, with 100% homology in the 21-amino acid heme-binding region. Northern blot analysis showed that the 24-hydroxylase cDNA probe hybridized to a 3.4-kb mRNA species. Treatment of HL-60 cells with 0.1 microM 1,25-dihydroxyvitamin D3 for 24 hr produced a 30-fold increase in the 24-hydroxylase mRNA level. This result is consistent with previous studies in the same cell line, in which 24-hydroxylase activity was elevated to a maximum in 24 hr by a similar treatment with 1,25-dihydroxyvitamin D3. To verify the identity of these isolated cDNA clones, two polymerase chain reaction-amplified human 24-hydroxylase cDNA fragments containing the entire coding region were used to produce 24-hydroxylase enzyme activity in two genetic expression systems. Transient levels of 24-hydroxylase activity were measured in transfected mammalian COS-1 cells and in recombinant baculovirus-infected Spodoptera frugiperda (Sf21) insect cells.
In vitro and in vivo functional characterization of bovine vitamin K-dependent gamma-carboxylase expressed in Chinese hamster ovary cells.
Authors: Rehemtulla A , Roth D A , Wasley L C , Kuliopulos A , Walsh C T , Furie B , Furie B C , Kaufman R J
Published: May 2006

Coagulation factor IX is a serine protease for which high-level expression of biologically active protein in heterologous cells is limited due to inefficient proteolytic removal of the propeptide as well as vitamin K-dependent carboxylation of multiple amino-terminal glutamic acid residues. We have overexpressed the vitamin K-dependent gamma-carboxylase cDNA and monitored its ability to improve factor IX processing in Chinese hamster ovary (CHO) cells. From amino acid sequence analysis of bovine liver vitamin K-dependent gamma-carboxylase, degenerate oligonucleotides were used to isolate a 3.5-kbp bovine cDNA that encoded a 758-residue open reading frame. Expression of the cDNA in COS-1 and CHO cells yielded 17- and 16-fold increases in the in vitro gamma-carboxylase activity of microsomal preparations, respectively. Anti-serum raised against a predicted peptide sequence reacted with a 94-kDa polypeptide in the partially purified bovine liver preparation as well as in stably transfected CHO cells. The amount of antibody reactivity correlated with the increased ability to carboxylate a peptide substrate in vitro. These results strongly support the conclusion that the cDNA encodes the vitamin K-dependent gamma-carboxylase. Transient transfection of the gamma-carboxylase expression vector into factor IX-expressing CHO cells did not improve the specific procoagulant activity of secreted factor IX. In contrast, transfection of an expression vector encoding the propeptide processing enzyme PACE (paired basic amino acid cleaving enzyme) did improve the specific activity of secreted factor IX by 3-fold. These results demonstrate that the ability of CHO cells to modify glutamic acid residues to gamma-carboxyglutamic acid in secreted factor IX is not limited by the expression of the vitamin K-dependent gamma-carboxylase alone.
Tissue-specific versus cell type-specific expression of the glial fibrillary acidic protein.
Authors: Kaneko R , Sueoka N
Published: May 2006

Expression of the glial cell-specific gene encoding glial fibrillary acidic protein (GFAP) is regulated in a tissue-specific (neural tissue versus other tissues) as well as a cell type-specific (glial cell versus neuron) manner. Using a family of rat neurotumor RT4 cell lines in which neuronal/glial differentiation occurs in vitro, along with cell lines of different tissue origins, we identified by transient- and permanent-transfection assays two negative regulatory regions, GFAP downstream regulators 1 and 2 (GDR1 and GDR2). Both regions lie 3' of the transcription start site; GDR1 is in a 2.7-kb region extending from the first intron through the fifth exon, and GDR2 is within 1.7 kb 3' of the polyadenylylation site. GDR1 alone is responsible for tissue-specific expression (suppression in nonneural tissues), while both GDR1 and GDR2 are necessary for cell type-specific expression (suppression in neuronal cells).
Colocalization of centromeric and replicative functions on autonomously replicating sequences isolated from the yeast Yarrowia lipolytica.
Authors: Fournier P , Abbas A , Chasles M , Kudla B , Ogrydziak D M , Yaver D , Xuan J W , Peito A , Ribet A M , Feynerol C
Published: May 2006

Two sequences (ARS18 and ARS68) displaying autonomous replication activity were previously cloned in the yeast Yarrowia lipolytica. The smallest fragment (1-1.3 kb) required for extrachromosomal replication of a plasmid is significantly larger in Y. lipolytica than in Saccharomyces cerevisiae. Neither autonomously replicating sequence (ARS) is homologous with known ARS or centromere (CEN) consensus sequences. They share short regions of sequence similarity with each other. These ARS fragments also contain Y. lipolytica centromeres: (i) integration of marker genes at the ARS loci results in a CEN-linked segregation of the markers, (ii) an ARS on a plasmid largely maintains sister chromatid attachment in meiosis I, and (iii) integration of these sequences at the LEU2 locus leads to chromosome breakage. Deletions performed on ARS18 show that CEN and ARS functions can be physically separated, but both are needed to establish a replicating plasmid.
Gene amplification in Rhizobium: identification and in vivo cloning of discrete amplifiable DNA regions (amplicons) from Rhizobium leguminosarum biovar phaseoli.
Authors: Flores M , Brom S , Stepkowski T , Girard M L , Dávila G , Romero D , Palacios R
Published: May 2006

A genetic element that allows the positive selection of different genomic rearrangements was used to analyze DNA amplification in Rhizobium leguminosarum biovar phaseoli. Discrete amplifiable DNA regions (amplicons) were detected in different regions of the genome of the model strain CFN42, including the chromosome and several large plasmids. Amplicons were mobilized into Escherichia coli using a genetic approach that involves the introduction of an origin of replication active in E. coli and an origin of conjugal transfer into the amplifiable DNA regions of the Rhizobium genome. The strategy can be a valuable tool for studies on genome organization and function. We propose that amplicons define a structural characteristic of the genome that may play an important biological role.
K+-conducting ion channel of the chloroplast inner envelope: functional reconstitution into liposomes.
Authors: Wang X , Berkowitz G A , Peters J S
Published: May 2006

Potassium flux between the chloroplast stroma and cytoplasm is known to be indirectly linked to H+ countertransport and, hence, stromal pH and photosynthetic capacity. The specific molecular mechanism that facilitates K+ flux across the chloroplast envelope is not known and has been a source of controversy for well over a decade. The objective of this study was to elucidate the nature of this envelope protein. To this end, solubilized protein in detergent extracts of purified chloroplast inner envelope vesicles was reconstituted into artificial liposomes, and cation fluxes into these proteoliposomes were measured. Results of inhibitor studies and counterflux experiments indicated that a K+-conducting ion channel was solubilized and functionally reconstituted into the proteoliposomes. This transport protein may be a nonspecific monovalent cation channel. This report represents a direct demonstration of ion channel activity associated with the limiting (inner) membrane of the chloroplast envelope.
Structural features that specify tyrosine kinase activity deduced from homology modeling of the epidermal growth factor receptor.
Authors: Knighton D R , Cadena D L , Zheng J , Ten Eyck L F , Taylor S S , Sowadski J M , Gill G N
Published: May 2006

To identify structural features that distinguish protein-tyrosine kinases from protein-serine kinases, a molecular model of the kinase domain of epidermal growth factor receptor was constructed by substituting its amino acid sequence for the amino acid sequence of the catalytic subunit of cAMP-dependent protein kinase in a 2.7-A refined crystallographic model. General folding was conserved as was the configuration of invariant residues at the active site. Two sequence motifs that distinguish the two families correspond to loops that converge at the active site of the enzyme. A conserved arginine in the catalytic loop is proposed to interact with the gamma phosphate of ATP. The second loop provides a binding surface that positions the tyrosine of the substrate. A positively charged surface provides additional sites for substrate recognition.
The E1 protein of bovine papilloma virus 1 is an ATP-dependent DNA helicase.
Authors: Yang L , Mohr I , Fouts E , Lim D A , Nohaile M , Botchan M
Published: May 2006

For efficient DNA replication of papillomaviruses, only two viral-encoded proteins, E1 and E2, are required. Other proteins and factors are provided by the host cell. E2 is an enhancer of both transcription and replication and is known to help E1 bind cooperatively to the origin of DNA replication. E1 is sufficient for replication in extracts prepared from permissive cells, but the activity is enhanced by E2. Here we show that purified E1 can act as an ATP-dependent DNA helicase. To measure this activity, we have used strand displacement, unwinding of topologically constrained DNA, denaturation of duplex fragments, and electron microscopy. The ability of E1 to unwind circular DNA is found to be independent of origin-specific viral DNA sequences under a variety of experimental conditions. In unfractionated cellular extracts, E1-dependent viral DNA replication is origin-dependent, but at elevated E1 concentrations, replication can occur on non-origin-containing DNA templates. This conversion from an origin-dependent replication system to a nonspecific initiator system is discussed in the context of the current understanding of the initiation of chromosomal DNA replication.
Positional specification of ventricular myosin light chain 2 expression in the primitive murine heart tube.
Authors: O'Brien T X , Lee K J , Chien K R
Published: May 2006

To study the process of ventricular specification during cardiogenesis, we examined the in situ expression of cardiac ventricular myosin light chain 2 (MLC-2v) mRNA during murine embryogenesis. As assessed by hybridization with a specific MLC-2v riboprobe, mRNA expression can be found in the ventricular region at day 8.0 postcoitum (pc). MLC-2v expression is high in the ventricular portion of the heart tube, with no detectable expression in the atrial or sinus venosus regions. The proximal outflow tract of the heart tube also expresses MLC-2v mRNA at minimally detectable levels at this time but then displays a temporally and spatially distinct pattern with expression well established in the proximal out-flow tract region adjacent to the ventricular segment by days 9-10 pc, eventually reaching levels comparable to the trabeculated ventricular myocardium. By day 11 pc, prior to the completion of septation, expression then becomes restricted to the ventricular region at and below the level of the atrioventricular cushion. Transgenic mice harboring a 250-base-pair MLC-2v promoter fragment fused to a luciferase reporter gene demonstrate reporter gene activity from at least day 9 pc. Ventricular region-restricted expression of the luciferase reporter in the embryonic heart, as assessed by immunofluorescence and direct assay of reporter activity in microdissected atrial and ventricular muscle specimens, was confirmed from at least day 15 pc on. Taken together, this provides evidence for early positional specification of MLC-2v gene expression in the primitive heart tube and indicates regional specification of part of the ventricular muscle gene program can precede ventricular septation during mammalian cardiogenesis. Since the 250-base-pair promoter fragment is active developmentally in transgenic mice, this establishes it as a molecular target for the process of ventricular specification in the developing heart tube.
5'-CGA sequence is a strong motif for homo base-paired parallel-stranded DNA duplex as revealed by NMR analysis.
Authors: Robinson H , Wang A H
Published: May 2006

The structure of the non-self-complementary DNA heptamer d(CGACGAC) at low pH has been determined by the quantitative NMR refinement procedure designated SPEDREF (SPEctral-Driven REFinement). Acid-base titration of the molecule indicated a prominent n = 2 pKa near 6.8. In the pH range up to 6.0, the heptamer forms a remarkably stable double helix, which was conclusively shown to be an unusual homobase-paired parallel-stranded double helix (termed II-DNA). In this II-DNA helix, the 5'-CGA trinucleotide is the structural motif that accounts for the stability, with the C+-C hemiprotonated base pair (in which C+ is N3-protonated cytosine) providing for the alignment site and the unusual interstrand G-A base stack in the GpA step furnishing the additional stabilizing forces. The exchangeable proton data from two-dimensional nuclear Overhauser effect spectroscopy are in total agreement with the refined structure. We conclude that the 5'-CGA or other related sequences (e.g., 5'-CCGA) are powerful motifs in promoting the II-DNA or II-RNA conformations that may play certain biological functions.
A protein complex of translational regulators of GCN4 mRNA is the guanine nucleotide-exchange factor for translation initiation factor 2 in yeast.
Authors: Cigan A M , Bushman J L , Boal T R , Hinnebusch A G
Published: May 2006

In Saccharomyces cerevisiae, phosphorylation of the alpha subunit of translation initiation factor 2 (eIF-2) by protein kinase GCN2 stimulates translation of GCN4 mRNA. In mammalian cells, phosphorylation of eIF-2 alpha inhibits the activity of eIF-2B, the GDP-GTP exchange factor for eIF-2. We present biochemical evidence that five translational regulators of GCN4 encoded by GCD1, GCD2, GCD6, GCD7, and GCN3 are components of a protein complex that stably interacts with eIF-2 and represents the yeast equivalent of eIF-2B. In vitro, this complex catalyzes guanine nucleotide exchange on eIF-2 and overcomes the inhibitory effect of GDP on formation of eIF-2.GTP.Met-initiator tRNA(Met) ternary complexes. This finding suggests that mutations in GCD-encoded subunits of the complex derepress GCN4 translation because they mimic eIF-2 alpha phosphorylation in decreasing eIF-2B activity. Our results indicate that translational control of GCN4 involves a reduction in eIF-2B function, a mechanism used in mammalian cells to regulate total protein synthesis in response to stress.
Identification of cell-specific and developmentally regulated nuclear factors that direct myeloid and lymphoid expression of the CD11a gene.
Authors: Shelley C S , Farokhzad O C , Arnaout M A
Published: May 2006

Human CD11a/CD18 is a noncovalently associated heterodimeric receptor expressed exclusively on the surface of lymphocytes and myeloid cells. To begin to understand the mechanisms that direct the expression of the genes encoding this receptor, we have cloned and characterized the promoter region of the CD11a gene and localized cis-acting elements involved in its expression in lymphoid and myeloid cells. One such element is the "LYM" box, which interacts with two sets of DNA-binding activities, one primarily expressed in lymphocytes and preerythroid cells and the other expressed predominantly in myeloid cells. A second element required for expression of the CD11a gene contains the "GAGA" sequence RRRGAGGAAG (R indicates a purine), which interacts with the DNA-binding activities MS-1 and MS-2. MS-1 is expressed exclusively in myeloid cells and probably represents a member of the Ets family of transcription activators. MS-2 is present in epithelial, preerythroid, and lymphoid cells but is only detected in myeloid cells after differentiation. MS-2 also binds to a second element within the CD11a promoter and homologous elements present in the promoter regions of the CD11b and CD43 genes. Since MS-2 interacts with a number of different gene promoters and is developmentally regulated in myeloid cells, it may play a major role in regulating myeloid gene expression.
Specific labeling and permanent activation of the retinal rod cGMP-activated channel by the photoaffinity analog 8-p-azidophenacylthio-cGMP.
Authors: Brown R L , Gerber W V , Karpen J W
Published: May 2006

Cyclic nucleotide-gated ion channels play a key role in visual excitation and a variety of other signaling pathways. The photoaffinity probe 8-p-azidophenacylthio-cGMP (APT-cGMP) has been developed for structural and functional studies of the cGMP-activated channel of retinal rod outer segments. Using this analog, we have demonstrated both specific labeling of the channel in a partially purified biochemical preparation from bovine rod outer segments and permanent activation of the channel current in excised membrane patches from salamander outer segments. After UV illumination, a 32P-labeled version of APT-cGMP was shown by SDS/PAGE and autoradiography to be covalently attached to the 63-kDa channel subunit. This incorporation was significantly reduced by 8-Br-cGMP but was not reduced by 5'-GMP. In patch-clamp experiments APT-cGMP was a potent activator of the channel; APT-cGMP typically opened half of the channels in a patch at a 10-fold lower concentration than cGMP. Exposure of membrane patches to UV light in the presence of APT-cGMP resulted in a persistent current observed in the absence of bath-applied nucleotide. This current increased with repeated exposure of the patch to both UV light and fresh APT-cGMP, approaching the maximum current originally evoked by saturating (500 microM) cGMP. At this point, addition of 500 microM cGMP caused a negligible increase in current. The persistent current had several other properties expected of current through cGMP-activated channels: it was outwardly rectifying; outward current was blocked > 90% by 2 mM internal Mg2+, whereas inward current was blocked much less efficiently; a low concentration of cGMP caused a larger increase in current atop a half-maximal persistent current than it did originally. We conclude that the persistent current was caused by the covalent tethering of cGMP moieties to channel binding sites, resulting in irreversible channel activation. APT-cGMP should prove useful for further studies of these and similar cGMP-binding sites and in the identification of unknown cGMP-binding proteins.
Yeast DNA-repair gene RAD14 encodes a zinc metalloprotein with affinity for ultraviolet-damaged DNA.
Authors: Guzder S N , Sung P , Prakash L , Prakash S
Published: May 2006

Xeroderma pigmentosum (XP) patients suffer from a high incidence of skin cancers due to a defect in excision repair of UV light-damaged DNA. Of the seven XP complementation groups, A-G, group A represents a severe and frequent form of the disease. The Saccharomyces cerevisiae RAD14 gene is a homolog of the XP-A correcting (XPAC) gene. Like XP-A cells, rad14-null mutants are defective in the incision step of excision repair of UV-damaged DNA. We have purified RAD14 protein to homogeneity from extract of a yeast strain genetically tailored to overexpress RAD14. As determined by atomic emission spectroscopy, RAD14 contains one zinc atom. We also show in vitro that RAD14 binds zinc but does not bind other divalent metal ions. In DNA mobility-shift assays, RAD14 binds specifically to UV-damaged DNA. Removal of cyclobutane pyrimidine dimers from damaged DNA by enzymatic photoreactivation has no effect on binding, strongly suggesting that RAD14 recognizes pyrimidine(6-4)pyrimidone photoproduct sites. These findings indicate that RAD14 functions in damage recognition during excision repair.
Conservation of genetic information: a code for site-specific DNA recognition.
Authors: Harris L F , Sullivan M R , Hickok D F
Published: May 2006

We present findings of genetic information conservation between the glucocorticoid response element (GRE) DNA and the cDNA encoding the glucocorticoid receptor (GR) DNA-binding domain (DBD). The regions of nucleotide sub-sequence similarity to the GRE in the GR DBD occur specifically at nucleotide sequences on the ends of exons 3,4, and 5 at their splice junction sites. These sequences encode the DNA recognition helix on exon 3, a beta-strand on exon 4, and a putative alpha-helix on exon 5, respectively. The nucleotide sequence of exon 5 that encodes the putative alpha-helix located on the carboxyl terminus of the GR DBD shares sequence similarity with the flanking nucleotide regions of the GRE. We generated a computer model of the GR DBD using atomic coordinates derived from nuclear magnetic resonance spectroscopy to which we attached the exon 5-encoded putative alpha-helix. We docked this GR DBD structure at the 39-base-pair nucleotide sequence containing the GRE binding site and flanking nucleotides, which contained conserved genetic information. We observed that amino acids of the DNA recognition helix, the beta-strand, and the putative alpha-helix are spatially aligned with trinucleotides identical to their cognate codons within the GRE and its flanking nucleotides.
A molecular phylogeny for marine turtles: trait mapping, rate assessment, and conservation relevance.
Authors: Bowen B W , Nelson W S , Avise J C
Published: May 2006

Nucleotide sequences from the cytochrome b gene of mitochondrial DNA were employed to resolve phylogenetic controversies and to assess molecular evolutionary rates in marine turtles (Chelonioidea). Findings of special relevance to conservation biology include discovery of a distant relationship between Natator and other cheloniid species, the paraphyly of Chelonia mydas with respect to Chelonia agassizi, and genetic distinctiveness of Lepidochelys kempi from Lepidochelys olivacea. A longstanding debate in evolutionary ecology was resolved by phylogenetic mapping of dietary habits, which indicates that the spongivore Eretmochelys imbricata evolved from a carnivorous rather than a herbivorous ancestor. Sequence divergences at intergeneric and interfamilial levels, when assessed against fossil-based separation times, support previous suggestions (from microevolutionary comparisons) that mitochondrial DNA in marine turtles evolves much more slowly than under the "conventional" vertebrate clock. This slow pace of nucleotide replacement is consistent with recent hypotheses linking substitution rate to generation length and metabolic pace.
Identification of the activating region of catabolite gene activator protein (CAP): isolation and characterization of mutants of CAP specifically defective in transcription activation.
Authors: Zhou Y , Zhang X , Ebright R H
Published: May 2006

We have isolated 21 mutants of catabolite gene activator protein (CAP) defective in transcription activation at the lac promoter but not defective in DNA binding. The amino acid substitutions in the mutants map to a single region of CAP: amino acids 156-162. As assessed in vitro, the substituted CAP variants are nearly completely unable to activate transcription at the lac promoter but bind to DNA with the same affinity and bend DNA to the same extent as wild-type CAP. Our results establish that amino acids 156-162 are critical for transcription activation at the lac promoter but not for DNA binding and DNA bending. In the structure of CAP, amino acids 156-162 are part of a surface loop. We propose that this surface loop makes a direct protein-protein contact with RNA polymerase at the lac promoter.
High-frequency germinal transposition of DsALS in Arabidopsis.
Authors: Honma M A , Baker B J , Waddell C S
Published: May 2006

We have established an efficient transposontagging system in Arabidopsis thaliana using the Activator/Dissociation (Ac/Ds) elements from maize. This system consists of two components, a stable trans-activator, Acst, that supplies transposase, and a cis-responsive Ds element. Ds and Acst were constructed with different selectable and screenable markers to facilitate monitoring of Ds excisions and insertions as well as segregation of Ds and Acst. Fusions of the 35S, rbcS, or CHS promoters to Ac transposase were used to trans-activate DsALS, a Ds element carrying an herbicide-resistance gene. The ALS gene encoding acetolactase synthase, which confers resistance to chlorsulfuron, functioned as a versatile marker for selection of plants grown in tissue culture as well as in soil. Thirty-five Acst lines were crossed to two DsALS lines, and the resulting progeny were assayed for germinal transposition of DsALS. Trans-activation of DsALS by Acst resulted in germinal excision frequencies of up to 64% when using 35S promoter-Ac transposase fusions, up to 67% when using rbcS-transposase fusions, and up to 1% when using CHS-transposase fusions. Amongst progeny bearing terminal excisions, Southern analysis revealed that 45% from 35S-Acst crosses and 29% from rbcS-Acst crosses carried reintegrated DsALS elements. The Ac/Ds system we have developed should prove to be an effective tool for stable gene tagging in Arabidopsis.